Chansensei

to Levi with an old friend

2011-03-08T04:21:00.003+08:00

It has been more than 10 years since we last sit down and have a deep conversation. And it was 4 years ago when we last met up for dinner.
When we finally met again in Rovaniemi on Friday, we realise that none of us has changed much (except for more white hair, less elastic skin and less energy for adventurous sports) and still had so much to talk about even though we had been apart for so long. HC realised that I am speaking in a foreign English but also noted how quickly I switched to local style after a night of chatting. totally cool lah! :)

I had always admired HC for his inner strength and resolution. I am not sure if I had ever written about him before on this blog but he was the one with only $2 in his pocket and had reach a stage in his financial status (while studying in university) to decide whether to eat lunch or not. He always worked hard for his goal and is a friend I can depend on. His health has suffered recently and he will be on long-term treatment. It sadden me that such fate befalls him but at the same time I admire his optimism over it even though I know he must have struggled with it through the initial stage. It must also be difficult not to be able to tell your parents about it... HC, my dear friend, take care until we meet again. Maybe in an Irish pub in London.

thanks G

2011-03-08T04:00:00.003+08:00

This long overdue post goes out to 3G who were threatened by Mr Ngan to write notes for me. :P. I received them the day before CNY's eve and it was with smiles and laughter when I read through them a few times. Thanks people! I have blue-tacked them on my wall and your video still continues to bring me much cheers :P.
Stalking is mutual yah? Those PE shots were excellent! Remember to send in your micelle pic if there is another bio wk!

We just started the Spring break but things continue to be busy. I am currently trying to sort out my Master thesis, seek out an internship as part of my course and plan for an exchange next Spring. All the administrative work...eeks!
But something really exciting for me will be the opportunity to teach in a Finnish secondary school next term. How will the kids be like? What am I going to teach? While I am still working on the latter, the idea of laughing in class is intoxicating!! Muahahaha! Can't wait!

Oh, and I caught the northern lights !!!!! hippee!!! not once but twice! :) Don't be too jealous :)

INFJ.ME

2011-02-18T19:58:00.003+08:00

INFJs are deeply concerned about their relations with individuals as well as the state of humanity at large. They are, in fact, sometimes mistaken for extroverts because they appear so outgoing and are so genuinely interested in people -- a product of the Feeling function they most readily show to the world. On the contrary, INFJs are true introverts, who can only be emotionally intimate and fulfilled with a chosen few from among their long-term friends, family, or obvious "soul mates." While instinctively courting the personal and organizational demands continually made upon them by others, at intervals INFJs will suddenly withdraw into themselves, sometimes shutting out even their intimates. This apparent paradox is a necessary escape valve for them, providing both time to rebuild their depleted resources and a filter to prevent the emotional overload to which they are so susceptible as inherent "givers." As a pattern of behavior, it is perhaps the most confusing aspect of the enigmatic INFJ character to outsiders, and hence the most often misunderstood.

This empathy can serve as a classic example of the two-edged nature of certain INFJ talents, as it can be strong enough to cause discomfort or pain in negative or stressful situations. More explicit inner conflicts are also not uncommon in INFJs; it is possible to speculate that the causes for some of these may lie in the specific combinations of preferences which define this complex type. For instance, there can sometimes be a "tug-of-war" between NF vision and idealism and the J practicality that urges compromise for the sake of achieving the highest priority goals. And the I and J combination, while perhaps enhancing self-awareness, may make it difficult for INFJs to articulate their deepest and most convoluted feelings.

New Year 2011

2011-01-14T13:47:00.002+08:00

Dex had declared the demise of this blog and perhaps he is not that wrong because sometimes it is just so convenient to drop a random note in fb in the midst of all the work. Yes, there is homework and examinations. :P
Despite the mega photo-uploads, work came in at a regular pace with multiple readings and for an exam, sometimes we have to read two books so that we can comment on them.
This week is the first week of school and I am already kind of stressed and tired despite still behaving like the energetic me, in trying to complete journal readings for reviews/summaries that might aid in my master's thesis. Testimony to that will be me writing this blog now upon waking up at 6am (slept at 1215am), even after submitting the work last night. Maybe my adrenaline and some other stress hormones were just running a tad too wildly for a while to calm down. I am doing basic shopping therapy later (grocery and necessities).

In the midst of all these, moments of reliefs were found in making chocolate rolls for my friends to welcome Day 1 of school, K's surprise party at 11pm when he returned from Turkey and also a sauna/dinner with him the next day while he tries to get his kitchen up and running again. K is like my brother in this little city of Oulu and I did miss his presence over the holidays.
The most wonderful thing I have experienced thus far is the warmth of the relationships I had established with people here. Edglo bears special meaning with a bunch of people who shares, supports, loves and cares for one another. Then there is my Sunday dinner gang who is like another family to me - K.A.T. and the fun we have every now and then when we gathered. i am already feeling the pang of loss for missing next sun's dinner but it is also important to meet A in Copenhagen. How often do you get to meet a friend who flew from US and being so close to you in a foreign neigbouring country? A was my constant in University and we had shared much over Spinelli and Science canteen food. Someone said that with current air travel, meeting someone is not difficult but it is. There are friends whom I missed and yet to see after 7 years. When work bogged you down, how does one even find sufficient time to travel? And because of this, even though I am enjoying my time here with new-found friends, every happy moment was mixed with a profound sense of sadness but also an unfounded sadness located somewhere in the future. This bittersweet feeling is rich maybe because of the experience in US even though I know this is different. I shall just enjoy the bittersweetness of it for it is actually like being in school when I know that every kid which passes me by will move on and to a better future ahead. There should be joy and happiness in having to share a special journey together. The future is unknown and perhaps we will meet again in the most amazing place or circumstances.

And now I am getting a little sleepy. Sighz.
As I settled down in this little city, it is perhaps also time to find things to fill my time instead of logging on to fb too often :P.
given my frequency of blogging, here is wishing everyone a Happy Chinese New Year ahead. :) Dong Dong Chiang!

2 months

2010-11-07T16:36:00.002+08:00

From 2 wks in Oulu to 2 months here and how things had changed.
It is snowing relatively heavy now because visibility has dropped a bit and the google forecast informed minus zero temperature for the entire week.
The daytime is shorter as well, from the sun setting at 9pm when I first came to now at around 4-5pm. The only good thing the early nightfall was that I can do more work since I concentrates better "at night". My room is also done up now with posters and lamps from ikea. Oh yea! I went to Helsinki and Stockholm last week when it was my autumn break. Ooooo....IKEA stuff from Sweden, totally authentic. I got H&M stuff there too which I realised was Sweden-export :). I would have gotten absolut vodka too except that I don't drink that stuff. mm not much anyway. :P I will prefer my sweet cider.

Thus far, I already had 2 examinations and a paper submission. The last exam was on Friday actually so I was really chiong-ing to read the assigned two books before the exams since I could not manage it during the break. But I think I will pass the exams. hopefully, if not I will have to take it another time which I sincerely hope not to. :P
Life as a student is really different but I think that is also because of a more mature outlook of life. Last night I invited frens over for dinner and to lounge in my sofa. That was just so nice and comfortable instead of the partying (which I had not been to one yet actually). On one hand I wished we could talk longer but on the other, work awaited as I seriously need to do some catching up after my trip - yes, i am definitely procrastinating with a blog entry now :P

I heard OP is around the corner - so good luck to all!! I will probably not do so well for OP here because they claimed that my singaporean accent is very strong. Accent? I was confused until I heard two Singaporeans in Stockholm ahhah. So ok, sometimes I tried to accommodate with clear pronunciation instead of letting my words tumble over my singaporean way. last night I was going to show my frens my travel trips videos when I stumbled upon the clip I made for 3L. The memories of a great time and I could not help it but watch it again before I head for bed. Then Deng also started to post 'My Dear Class' - I must say his camera is really pro hahha. 3G is really camwhorish but I really enjoyed the photos and others have such funny stuff like GL's hysterial rabbit talk and G's updates on hilarious stuff in class and his comic strips (I am not stalking!! serious!!)
As I wrote all these, I started to wonder, who read this blog now as it slowly sinks into oblivion like the titanic. But I will hold on to it a little longer as the name chansensei gets immortalize even in this little city oso I am holding on to this link.

Hugs to all, from the little oulu city. :)

2 weeks in Oulu

2010-09-12T17:00:00.003+08:00

It has been 2 official weeks and somewhat it still feel a bit surreal but also like it has been so for quite a while. Lessons have started this week and while they are still mainly introductory except for Survival Finnish, I am excited by them all and remains keen to share my thoughts and experiences. Yah, experiences are truly something that can come with age though one classmate of mine refuses to believe that I am older than her, maybe because of my camwhoring antics. But others sense my subtle behavioral manners that spoke otherwise I think because I am composed most of the time and I will get things organised or facilitate interactions between people. Somehow, I still find myself very much in the teacher mode, taking care of my fellow classmates like staying behind to make sure everyone is accounted for when we move as a bunch, taking their pictures at random moments and sometimes dispense advice to them.
@ wk 2, I am happy to have known some of my classmates better and I now hang out regularly with an international bunch of Japanese, Russians, Turks, Iranians, Taiwanese, Brazilian and Indians. Perhaps there will be more to come.
But what school goes into full steam for all of us, let's hope that we still get to meet up occasionally.
School-wise, I really think it is a bigger world out here. With so many international students and with the quality of teachers here, I really feel like part of a global population and I realised that I can, too, contribute to a wider, global community. Here, our dreams get a little bigger. Still, for those who are doing your degrees overseas, while it could be the same for you too but don't forget to keep the heart and motivation true and clear. Egos and dreams do not have to correlate. But still, I do miss classroom teaching.
Perhaps some highlights:
- went to a Finnish sauna!
- Got a bicycle after a week at a steal!! :): In Oulu, cycling is a basic mode of transport and is supported by a good extensive cycling tracks! And here, the vehicles do give way to pedestrians and cyclists at junctions! This will of cos save me 6Euro for a roundtrip to downtown and time to walk to visit my friends.
- I can walk to school in 10 mins!! (isn't that all familiar :P) and I am happy to have the city library branch opposite my block! =) - and yes, they have some English books! :P
- bought a study table and chair from the recycle center yesterday. In Finland/Oulu, with things being so expensive, it is common to buy things from 2ndhand stores (definitely true for the poor students!) and recycle center. Next thing I need to get is a bigger bed, after which I can stop renting the same things and save costs. Shopping has thus become quite a pasttime for me now, in such stores and also in supermarkets.
- it is really like building an identity and creating space for yourself, getting everything from scratch. I am glad that previous occupants have left plenty of stuff for me to utilise like frying pan, pots and plates etc. At least I don't have to buy them. But just like last week, I cleaned out the kitchen and bathrooms, and bought stuff to make them more...homely? My flatmate does not care that much about the common area but I think it is important. And I managed to make him smile twice ahah. He looks a bit too serious but I supposed he found it amusing that I am buying things for the kitchen and I made him potato salad specially too when I made some for a bbq the other day. That is one point to me! :P
- Last wk was Oulu Day over the weekend. It is a day when museums are opened for free and there are performances in various venues of the city. There are banners and the market place gets more crowded. (see pics!). I went on Sat but skipped the Sunday to do work. :P
- This Friday, there was a simple reception in the city hall where the mayor of the city came to give a speech and there was food and drinks (champagne included :P) to welcome the international students. So cool! But what was nice was for a bunch of us to head down to coffee house later on for a nice chit-chat session :).
- Yesterday, my turkish fren brought us to play mini-golf!

While everything seems like fun and play but there was adjustment made and is still being made.
- I need to plan for my meals, from preparation to eating. Sure you can survive by getting take-out all the time but I also saw coming here as an opportunity to do my own cooking since I can use the kitchen. you should see my share of the cupboard. There are many stuff in there! Perhaps I should stop going to the supermarkets otherwise I will keep thinking of new dishes that I can do (and so I bought the stuff) but don't have that much time to cook really haha. But this really also means adjusting how I use time. There will not be food waiting for me anymore.
- cold weather. I was feeling cold when I first got here. The skin got dry and I felt tired. But now I have gotten used to the weather. In fact, I wore less these days, even less than my classmates and most Finns.
- The sun sets at 9pm. It is so weird that my dinner time gets screwed up.
- Like I said before, feeling a spot for myself in this apartment.
- Being by myself like this. I think I am too used to having pple around me.
I suppose all this will only get better with time. Let's see how things go.

this post came late

2010-09-02T03:18:00.002+08:00

This post came late because there was the packing to do, the endless meet-up sessions with friends and to really try to be at home.
Then really, there were the ceaseless waves of affections from students that caught me off-guard and I was touched by them all - before I leave, on the day i leave and for Teachers' Day. They are all reminders of years meaningfully and well-spent in a vocation that I will surely missed. When a friend/colleague of mine bought me dinner and I started to relate how I saw on my own development as a teacher over past few years and how I enjoyed the lessons and lectures when I unexpectedly teared and had to pause for a break. How will this new change turn out? I have no idea as I tried to get used to the whole idea of studying again, adapt to a new environment and rewire my brain. One of my colleague said, because it is me, he was sure I can manage - well, I hope so. This morning I felt rather sad then I realised that I missed my own laughter = my usual dose of endorphin!! There is surely not many things I can laugh at or with here now. What are my students whom I can bully?! :P. The only thing I could do was smile and asked strangers what are all the stuff in finnish that I am buying. I must say that the people do look kind of serious here but they will drop that seriousness and smile with helpfulness. That is fun!!! :). I also make sure I smile first. No point having a sulky face yar? :) I still want to hahaha tho kekeke.

Mmm...I am deviating a little but I am really not too sure what to put down on this post because there was so many things.
First, I thank all of my students who taught me alot, who made me laugh (btw 3G - I watched the video many times hahahaha), who believed in me and who allowed me to linger in their memories longer.
There are also things I noted like how C will come up to me after every lesson to say thank you. It was an effort made to do so personally and I know. So I thank C. A couple of students said that they wanted to do well in biology to show their appreciation. But I value not your grades as much as you as a person with a heart of gold and resilience to take on new challenges. I saw and sensed that in many of you so I am already thankful. Don't belittle yourself for you have many strengths but you need to recognise them.

So on this TD, I also thank you for being part of my life.
now.. I can start blogging about Finland!! ;P

point to note

2010-08-21T16:35:00.003+08:00

in the last piece of work:
1) thanks to KT, it should be icosahedral head. it is ICO.

2)

3)know that virus can take its envelope from any fellow of the endomembrane system. It doesn't have to be plasma memb all the time!!
But when describing in general, for the syllabus, we will stick to plasma memb as the one best studied.

Eg. Herpes Virus - the nucleocapsid is assembled in the nucleus. The capsid buds off from the inner nuclear memb trasiently before fusing with the outer memb so that you get the nucleocapsid into the cytoplasm where it bud into golgi vesicles containing the viral proteins --> you get an enveloped virus (with membrane) enclosed by the membrane of the golgi vesicles. The virus is released by exocytosis/fusion with cell membrane.
It is pretty cool! If u are confused, you got to draw it out!

4) Hijack - what does it possibly entail? (this is not a comprehensive list)
a) destroy the host's genome --> no competition
b) modify host's RNA polymerase for its own use
c) produces its own viral polymerase and disable host polymerase
d) produce viral-related sigma factor and destroy host cell sigma factor (for phages) - linked to b) ; you are going to learn about sigma factor soon!

Ok!! That's all I have !!

Sorry folks but was away in Hongkong with my parents until Wed. Great trip but no need to do my travel blog since I fell sick on Day 1. But it was a great trip! :)

Cheers

Clearing Up

2010-08-07T23:55:00.003+08:00

Was told that I should update this blog more often.
I did not realise that pple do drop in because this blog has gone relatively quiet for about 2 years before the unexpected surge in traffic this year due to the pressing need for more time to discuss several topics.
Also, even since I started my lecture series, there was barely enough time to sleep, eat and mark so blogging has to take a back seat.=)
yesterday felt like the end of a marathon when I collapsed on Thurs night after NDP celebration and dinner with my class. I finally see more of the camwhoring side of them with the 1-8 poses :).
Even the next day on Friday when I slept in a little later, I felt a little wasted in the afternoon and a short nap just to get back into the rhythm again. It was too much for me lah - staying up until 3-4am for the entire wk and not including those usual late nights that accompanied lectures last wk.

But I was glad that lectures went well and most of the students seemed to be able to get the big idea. And with it, I felt my own development and growth as a lecturer over the past few years. The ability to draw connections and try to convey materials in its beautiful simplicity without assaulting the senses with too much details. well...at least two students from another class told me that they were able to understand and did not sleep in my lectures. It was actually always exciting to lecture just that the preparation could be really exhausting. Haha, I think I am just slow in that because I like to imagine and rehearse my lectures in my head as I prepared the powerpoint slides. But like my bro said, this flow of ideas and thoughts can be very important - just the way I would expect my student to be thinking as they process the information or write it down. The logic and beauty of life.
I think I am going to miss lectures for a while.

This wk was spent on clearing my backlog of marking and reorganising the virus material(and preparing bacterial answers and mcqs). I would get home in the evening, slept for an hour or slightly more just so that I could be awake later in the night and wee hours of the morning to clear the marking and to work out some notes/amendments I promised to provide. So much to work on so that I can leave in peace, knowing that I have wrapped up this challenging topic nicely so that students will have an easier time studying it and therefore appreciating it. Virus can be quite cool! Sighz...so much more I want to and can teach them. But then I know they will be in good hands :)

Got to stop here. too tired. hahah will write on the farewells another time. I still have a list of stuff to clear :) Eeks!

counting down

2010-07-23T22:33:00.002+08:00

even though I had totally no concept of time and date, I suddenly realised that my time with the classes and the staffrm will come to an end very soon.
With so many things still on the plate, the end is blocked by the piles in front of me.There is so much I want to teach, so much things I want to do in school, to be there for people, to bring some laughs to an intense environment that I felt a little guilty at leaving them all behind, the dreams and the hopes I held in the education system.

When I was (much) younger, I wanted to go away, leaving everything behind to explore a new world. I saw the excitement on my friends' faces when they left while I saddened by their departure, I thought to myself then that I do not want to be the one left behind. But now that the role has reversed, I realised there is a nagging hurt even for the one who leave. Maybe it is an age thing because when you are younger you have less baggage in life or maybe because I was simply contented where I was.
Still, while the heart was feeling a little overwhelmed, the lagging mind realised that the move is logical and for the better, and a rare opportunity not to be missed.
So the mind will drag the heart along like the plasma membrane dragging and separating the replicated bacterial chromosomes. But I guess eventually things will be set right. there is no right or wrong but just a change.

The Sensei has to forge ahead and do what he always advised the students. Be brave!

But I realised I did slow down in these few weeks so much so that I can feel the songs I listen to. No longer are they background music to accompany me while clearing work but suddenly, they touched me again like they once did in past. Sharing one that goes way back:

——————————————

Stayed up almost the entire night (except for 2 hours of sleep) to sort out the powerpoint. It was amazing that I managed to stay awake all the way for lessons and lectures until 6pm before I gave up, packed my work and went home. I think I am getting too old for such endurance test. Crashed at home for 2 hours and now am up and running again. One more to go.

aftet Hodge Lodge

2010-07-16T23:27:00.001+08:00

Was told that I have to know this WAKA WAKA!

raNdoM

2010-06-27T15:29:00.002+08:00

21st

Definitely not mine :) but attended another bday birthday last night and realised that this was the 3rd one this year with the same bunch of ex-students.
Over the course the years, these fellows have changed and I too wondered if I did.
When I started to shift back the stuff in school back home early this wk, I was also reading the cards and notes written by these kids to realise my own progression over the same period of time.
I paused and asked myself if there exists a need to leave because there are still so much I can learn, so much to give and so much more to do as a teacher and as a person. Then I remembered that this trip was started with an ideal bigger than myself for I knew deep down that this journey will bring more to others in time to come.
Be brave and find that adventurous side again!

The Model Student

J said A must be a model student with her positive attitude in learning and incessant questioning. I thought for quite a long time and started asking myself, what is a model student?
There is no definition of one because it is relative. There are some teachers who insisted on perfect silence while others preferred a bombardment of questions during lessons. There are others who loved the natural high achievers but there are also others who preferred those flapping in water but brimming with potential.
to me, I think we be who we are but know to be kind, respectful, sincere and generous with our friends, peers and teachers/seniors. And it is more than what you do in class but also outside class that speaks of you.

If J goes by that definition, I am definitely not a model student in sec sch or jc (but I am a friend of singa! ahha) but i would be one in uni yet still i know one of my lecturers does not like me for asking too much questions =P

changes/ new questions

2010-06-27T15:05:00.004+08:00

- Pls note the 1 correction in the Summary ; contributed by YF
- the following are good questions posed by students over the hols:

Could I just find out, is the human genome considered a segmented genome? Segmented genome = genes arranged on more than 1 strand of nucleic acid?

I guess so if you used that definition alto i am not aware of the term being used for human genome. It is more likely to be a term used to differentiate the type of viral genome. Because virus, being so small and needed very few genes, it can also easily have all its genes on one strand of nucleic acid.
Diff fields in biology used terms differently.

What are the sources of the viral envelope? The notes mention nuclear, vacuolar and plasma membranes. Could it come from the other membraneous organelles like golgi or ER? Some websites mention that it could come from the golgi membrane too. Or are these three mentioned because there is greater tendency for viruses to find themselves surrounded by these membranes inside a cell but less likely (still possible?) to be surrounded by e.g. ER or a chloroplast?

Yes, in fact i am more towards having the viral envelope coming from nuclear membrane, ER or Golgi, plasma (and will ignore vacuolar).
And no chloroplast.
Where the envelope comes from deps on the types of virus but typically examples will refer to plasma membrane but let's not forget about the rest!!
I need to draw this out for you all to see how is this possible so we will leave it here first.

Does naked virus mean that it doesn't have an envelope or that it ONLY has a nucleocapsid and nothing else? So is a bacteriophage a naked virus? Since it doesn't have an envelope but it has other structures besides a nucleocapsid. Or is the tail fibre, base plate etc considered part of the capsid?

Naked virus is without envelope.
because you wouldnt have only naked DNA/RNA floating around so yes, the nucleic acid will be encloseed by capsid proteins.
tail fibres, base plates are not part of capsid but these are not impt in the classification. in other words, you can classify virus as naked or enveloped; with or without a membranous envelope.
So your phages are naked viruses despite having the tails and base plates.

For viruses, why do some bacteria undergo lytic cycle while some go lysogenic? wouldn't it make more sense to just lyse repeatedly and kill off as many cells as possible?

A temperature phage undergoes a lytic or lysogenic cycle depending on the environment its host is in. If the bacteria is in a environment with a lot of nutrients such that it is conducive for growth, the phage will see this as a great opportunity to undergo lytic cycle because it means that out there, there will be many bacteria to infect (since the bacteria are likely to be growing exponentially!) Joy to the phages which can infect many many more!. COnversely, if the bacteria is in a medium with little nutrients and are not actively dividing, the phage will do into the lysogenic cycle and wait for a better moment.
Another possible scenario is UV light. If there is irradiaton of bacteria by UV light, the phage will undergo lytic cycle. Reason being that to the phage, if the DNA of the bacteria is damaged, it may limit/impede cell division of the bacteria so it rather escape and find another host while it still can!!
PS: I don;t mean to make the virus sounds so lively cos we know that they are intermediate betw being a living and non-living things yah? They are pretty economical tho =)

The notes wrote that the SER catalyses the synthesis of carbohydrates, but er when i checked campbell reece it was stated that it metabolises carbohydrates and synthesises lipids): so which is it?

The notes also highlighted that the SER is also known to be involved in the synthesis of lipids. (impt!!)
As for carbohydrates, SER is known to metabolise it, rather than synthesise it.
Golgi Apparatus is where the bulk of carbo is synthesised tho.
But what other specific roles of SER do you know?

The classic example to study SER is liver cells where it is in abundance and have highly specific roles (which are what we study)

when they say that the RER is a membrane factory for the cell as it "adds membrane proteins and phospholipids to its own membrane".. what does it really mean? does it mean that the proteins produced by its ribosomes are directly incorporated into its membrane without going through modification by the golgi apparatus..? and i also read in campbell that the RER synthesises its own phospholipids [not in notes].. so are those the phospholipids that are incorporated into the membrane? >< (then what are the phospholipids produced by the SER for? D: ) does it matter anyway ><

It is inaccurate to talk about RER as membrane factory. we usually just refer to ER as the membrane factory. There is no need to make a distinction.
The basic idea is that phospholipids are synthesised at the ER where they are first incorporated. Through budding off and fusing, phospholipids may be added to any membrane-bound organelle involved in the endomembrane system (chloroplast and mitochondria are not included). For example if the plasma membrane needs to expand like after mitosis and the cell gets bigger in size to achieve optimal surface area: vol ratio, the additional PL are made at the ER and transported via Golgi A before fusing with exisiting plasma membrane.
Also, if the ER needs modified proteins, it can obtain them from vesicles budding off from the GA. the trafficking is two-way not just one-way. so that is not a problem.

in our notes, it was stated that a transport vesicle moves to the plasma membrane in the process of exocytosis. do we need to make the distinction between the type of vesicle it is here, and if so, shouldn't it be a secretory vesicle?

transport vesicle is very generic term. it can be a vesicle going to the plasma member or to other organelle like lysosomes or back to ER.
but as i mentioned in class, if you know the contents are going out of the cell via exocytosis, pls use secretory vesicles. that clearly defines its role and is awesome.

Polymerisation of HbS

2010-06-09T15:43:00.000+08:00

Before I forget. The polymerisation of HbS.

DNA review summary; corrected

2010-06-09T15:40:00.006+08:00

All of them are up as promised.
Am sorry that it took quite a while. All the worksheets have been placed in your class pigeonholes on Mon.
for any question, you can email me.

AS was kindly pointed out, pls note the following mistake:
Chain termination for translation:
it will stop when the stop codon is in the 'A; site not 'E' site
The release factors will end the 'A'site

DNA and genomics MCQs_with comments

2010-06-09T15:39:00.000+08:00

M&M comments

2010-06-09T15:37:00.002+08:00

I hope our laughter during the day was reassuring

2010-05-22T22:17:00.003+08:00

C said that this site was getting too depressing...is it? =P
All the laughters had been spent in school that's why. HAHAHAH.

So I decided to write something happy here to balance it out.
Today is PTM day and we had such a good time talking behind the students' backs!! Heh! =)
But the greatest takeaway was knowing that the class has come along nicely and that we are now one big family if not working towards. And to know that even in my absence, they will be there for one another

MCQ answers only

2010-05-22T22:14:00.002+08:00

I hope to be able to run through some of these questions in class.
But look through first k?!!!

thanks!

DNA & Genomics : Replication, Transcription, Translation

2010-05-21T23:15:00.015+08:00

Disclaimer: most videos do not cover all the things highlighted in notes so just get a feel of the processes.

Replication
Video 1
http://www2.le.ac.uk/Members/jlb34/research/replication%207v3-3.swf/view
Video 2
http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120076/micro04.swf::DNA%20Replication%20Fork
(however, this V2 lacks SS binding proteins!)

Question posed:
Why can't DNA polymerase (the other one) catalyse the formation of the phosphodiester bonds between the adjacent nucleotides of Okazaki fragments if it is able to elongate the Okazaki fragment after removing the RNA primer ? Why do we resort to DNA ligase?

Good Question!
We need to consider the nature of the 2: DNA polymerase and DNA ligase, both of which are enzymes.What is the important thing about enzymes? They have a substrate specific active site.
when DNA polymerase elongate the Okazaki fragments, the phosphodiester bond is formed between the free 3'OH end and a free nucleotide (nucleoside triphosphate). The reaction/formation of the bond also involve the removal of pyrophosphate (PPi) - the 2-phosphate group.

On the other hand, the substrate for DNA ligase is different. They are the free 3'OH end and a single 5' phosphate group extending from the adjacent fragment. The ligase only needs to join them up!

Thus although both involves the formation of phosphodiester bond, the different substrates involved demands the use of different enzymes.

Transcription

Video1:

Consider or note the following questions.
1) How are 2 DNA strands separated? (compare to transcription)
2) what happens to the 2 DNA strands as the RNA polymerase move along (and read) the template strand in the 3'-> 5' direction
3) what kind of nucleotides are involved? (compare to transcription)
4) where does transcription start? (compare to transcription)

Translation
Video 1:
http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__how_translation_works.html
Video 2:
http://www.vcell.ndsu.edu/animations/translation/movie-flash.htm

Consider or note the following questions in understanding the process.
1) the mRNA is being read in what direction? (compare to R and T above)
2) In what sequence does the following binds to mRNA: small ribosomal subunit, large ribosomal subunit, initiator aminoacyl-tRNA carrying methonine.
3) Which site will methionine reside in initially?
4) By how much does the ribosome move each time?
5) What does the stop codon encode for? Or does it encode for anything?

Out of Syllabus (OFS) Questions

2010-05-21T21:27:00.008+08:00

nO.1
R/S between tRNA, mRNA and rRNA in translation.
we had discussed extensively on the roles of tRNA and mRNA in translation but often skip rRNA. We only know rRNA as a component of ribosomes but what are they doing in ribosomes?

Let's appreciate the fact that different rRNAs are found in the 2 ribosomal subunits.

So what are their roles?
1) Peptidyl transferase is an enzyme found in the large ribosomal subunit that catalyse the formation of a peptide bond between the polypeptide chain (peptidyl-tRNA) in P site and the adjacent aa (aminoacyl-tRNA) in the A site of the ribosome. Now the elongated chain is now attached to the tRNA at the A site.
This peptidyl transferase is rRNA in action = it is a ribozyme, an RNA enzyme.

2) They are known to interact with
a) mRNA (rRNA in small subunit - translation step 1: small subunit binds to the mRNA..=)),
b) anti-codon regions and 3'CCA ends of the tRNAs at the P and A sites (rRNA in both subunits - no prize for guessing which for which).

3) also the subunit are able to interact because of interaction between the rRNAs in the 2 subunits!

COol yeah?!
Actually rRNA is not as well-studied so I will stop here.
_____________________________

nO.2
Proofreading mechanism of DNA polymerase in details

DNA polymerase has intrinsic 3'-> 5' proofreading exonuclease activity
(exo=outside; nuclease=enzyme that cleave nucleotides; exonuclease = enzyme that remove/cleave nucleotides from the terminal)

From Wiki:
When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading).

How does the DNA polymerase know when there has been a mistake?

anticodon and codon pairing is very impt btw the tRNA (AC) and mRNA (C).
Incorrect base pairing --> conformation is altered/distortion in shape of the regular double helix which is recognised as a mismatch of base pair to initiate the exonuclease activity.

NOTE: not all DNA polymerase have proofreading capability (there are many types of DNA polymerase but the one we are interested in for replication has such capability)

________________________

Amendments and Otherwise

2010-05-21T20:25:00.010+08:00

nO.1

Water Potential Notes
As pointed by D, on page 3, (c) pressure potential for plants only -
bullet number 3 - when a plant cell is in a solution with a higher (less negative) water potential, there is a net movement of water into the cell.

nO.2
Does nucleotide has one or three phosphate(s)?
It can be one, two or three, which also means that the term is non-specific.

To be specific, the raw material for DNA replication or transcription are deoxyribonucleoside triphosphates and ribonucleoside triphosphates.
Otherwise, we used the term free XXnucleotides very loosely.

You should know that nucleotide = nucleoside (pentose sugar + nitrogenous base) + phosphate grps

nO.3
Why are the dividing cells in tutorial so dark? Shouldn't there be only a dark spot known as nucleolus for cells in interphase?

Actually the diagram given wasn't so good. For cells in interphase, yes, you should be able to see the nucleolus quite well!:)

Cells in prophase are quite easily identified. I usually look for those in late prophase when you should be able to see individual chromosomes very well.
At interphase, you will not be able to see individual chromosomes.
One should note that mitosis is a continuous process so there are always intermediates stages.

PS: The chromosomes are usually stained so that one can see the them easily for the mitotic process.

http://www.vcbio.science.ru.nl/en/image-gallery/show/PL0096/labels/
http://www.microscopy-uk.org.uk/mag/artnov04macro/jronionroot.html
http://course1.winona.edu/sberg/IMAGES/anaphas.JPG
(for practice?)

Enzyme MCQs

2010-05-13T23:31:00.002+08:00

LT test 2
D asked about using rate in length change to determine the rate of digestion. he pointed out that the change in length would decrease as the circle gets bigger.
I agreed. The method provided is a rather crude one (qn asked to estimate)
A better option is to use Area. In fact, we do have scripts that used area and we accepted it as well. =)

The Cat Is Out of the Bag

2010-05-13T20:57:00.003+08:00

It finally jumped out, delivered in a mix-bag of sadness and relief.
Relief because it has been a weight on my mind for a while, unable to share and always trying to find the right moment. I wanted to let my R know during class camp but they were having such a good time that the moment never came. Then I realised perhaps there will never be a right moment.
Sadness because when it was out, it felt so real. I wasn't ready for it and wished I had more time instead of the short intermission to talk to R. But on hindsight, it was for the better before words get choked.
I am going to miss them more now after the class camp. Did they realise that they are a great bunch as one?

So the heart was a little squashed today.

Broke the news to all my classes. It is true. Saying farewell was not easy but at this age, I also know that it is not wise to leave your goodbye at the very end.
The only consolation is in knowing that even if I stay this year, I wouldn't be able to stay until the end of next year to witness their graduation.

Half-way through the day, I realised that being a teacher also means that even when you felt a little battered and wanted to sit down somewhere to contemplate, you still have to continue to ensure the smooth running of events for the students

---
I started the year tentatively,wary about getting too involved with the classes in case I do go off (after sending in my application in Jan) but it was difficult to keep that distance and not wanting to know them better. When the acceptance came as a surprise three wks ago, I wished that I could have done even more and better.
----
Coming to the end of the week.
Like any other time, we have to make the best out of what ever we have.

Cell Structure and membrane MCQs

2010-04-29T21:38:00.003+08:00

ROG - for test tmr, pls put down the mark you got from the last lecture test on the RH corner of your paper? I lost the data when I changed laptop. will remind again.

too Much

2010-04-26T20:36:00.003+08:00

I got frustrated in class today. In retrospect, a big part of the frustration came from within me, in realising that we spent so much time marking and having meetings - one after another - that I had difficulty finding time to craft up better answers, to revisit and think through the questions again and to make learning worthwhile for the students each time I stepped into the classroom. With changes in the scheme of work and the attempts (or over-attempts) to do more things, I felt myself lagging behind. I don't mind staying up until 4 am to complete my markings but I asked myself, surely we can do better?

There was less time to deliberate and discuss in class and it was rushing tutorials from one to another (esp in time for test) that I panicked, worrying that the students did not know what I was talking about and that a lesson went to waste. I don't mind having the buzz in my class but I worried that students did not get what I was trying to say.
Then again, maybe I worried too much.
How much can I worry about them, I realised. I can only try my best to deliver and hope that they had picked up as much from me as possible - the skills and the content. How can I possibly dictate their learning?
(I must have said this before. If I did, it is a reminder to myself that I need to be objective about this)

I sometimes change the answers not because the answers were not accurate or good but I wanted something more comprehensive and wholesome that really brings out the essence of the topic, to show that one truly understands the topic and is able to relate to it.I wanted to tell a story. Often, we list a series of points to help us mark the scripts but a list of facts say nothing about one's level of understanding and I wanted to raise the bar for them. Hopefully.

I had aired my concerns to my bosses and hopefully we will have quality time with the students.

Another day. Time to start marking again.

A whole new week

2010-04-17T21:09:00.002+08:00

Friday marks the end of my lectures for term2. For H2 that is. Hipee!! :)
It had been a week of lectures, references and marking. At least 3 days in a row, I stayed up til 3am to finish up the work.
Tues was the worst because I got so upset with my lousy lecture that I stayed up to redo my powerpoint with brand new animations. At least I am proud of my newly created animation :P.
Wed, I went home to nap from 8-11pm then started marking tutorials until 4am before another round of nap to take on the world.
Thurs, I stayed up to improve my slides and create new slides for the next half of lecture.
Friday, ended with a happy note. I was quite pleased with lecture except for the fact that LT1,once again,jinxed me again with no sound and a broken down projector (replaced with a portable one). I recalled that fateful day when I had to use transparencies in LT1 some years ago.
Whoosh! At least one big item is off the checklist and now for the rest. 6th more weeks and I crossed my fingers with all the looming deadlines.
_________

Two separate lecture grps and in each case, I caught someone taking pictures of my slides. Was it rude or was my slide that good? Should we condone such actions? What do we expect from them?

Fear of not doing well

2010-04-05T23:26:00.003+08:00

It is always 'been a while since I last blogged'. I think I have been playing fb games too often to distract myself from all the piling work which unfortunately will never decrease. Of course, there were times when I want to blog but was just too tired like 2 wks ago when I was running short on sleep again and I realised that as I grew older, the lack of sleep makes me more snappy. I remembered it wasn't this bad last time because my friend once asked me if I will be grouchy when I suffered from the lack of food or sleep and I replied none of the above - she wanted to make sure I don't snap at her when we went backpacking haha. But I guess now one of them has won the contest. [2 weeks ago I was on a super tight schedule to prepare lecture notes, a mini-lecture, marking tutorials & practicals and trying to get out of the holiday inertia which actually wasn't much of one since I doing marking 5 out of 7 days. I don't know why this year the marking felt so endless. geez.] Anyway I did snap a little when someone fooled around in lab that week. I think my brain wasn't functioning that well then so for the first time, I took off and left the lab. Standing outside the lab, I was trying to decide if I should blow my top or if the sense of irritation was due to the lack of sleep and so I shouldn't really scold the kid. Ok, in the end I didn't when I walked back in.

So why this entry anyway? Because I wrote a mail to my CT class recently and I think I would like to share the message with all my ex-students. Something for you to ponder over:

As many of us prepare for interview, be it for next wk's medicine, for some scholarship or a post down the line in the future, it is very easy to get carried away with the fear of not doing well and so our faces crunch up during interview as we tried to think of the most intelligent or even witty answers.

RELAX

Truth is, no matter how good you think your answers may be or even how good you are, there is no reason to worry to hit the bull-eye, philosophically-speaking.

Each batch of interview or each year, the assessors may look for something different in a cohort. For medicine, there are years when they want sportsman to spice up the faculty or they want people heavily involved in community etc because they want diversity to jazz up this community that is getting homogenous. Then another year, they may feel that there are too many sportsman so they go back to choosing academically strong students and it goes on. Thus to a certain extent, some choices were pre-determined. And this scenario is applicable to all communities and faculties as the world progresses these days.
So why worry?

An interview is a face-on assessment, to see in real life the person who did the writing and to determine (hopefully) if the material written has been blown out of proportion. But the key thing, esp for medicine, is still the smile and sincerity. In those minutes, you will be like seeing a patient, so be compassionate. It is the first impression of a patient as seen from the eyes of the interviewers. Anyway, please pity them :) cos they are sitting in the whole day or days dealing with young fellows like you , sometimes irritating sometimes CMI and most of all, some of them were made to go down to conduct the interviews when they prefer to stay in their offices...mmmm... maybe playing farmville? Or one of current fav of Zooworld!! :)
So don't worry! :) I guess during the intermission period when interviewees come in and out, they may just whip out their iphones and start playing these games and feed their animals hahah.

In a recent book I read by a renowed education fellow, he noted that it was wrong to assess one based on an interview whereby the candidates are supposed to come up with a super witty or good model answer spontaneously or within a given time-frame (some interviews are like that)- and that was the impression given to us by tv programms.
why is it wrong is because all of us come with differently personalities (Myers-Briggs yah?) . Some of us preferred style is to consider the scenario carefully while others tend to be more impulsive and dive in. Of cos there are others who are really superb. this kind of tests does no justice to people who like to contemplate and look at things from all perspectives who are equally important in an organisation.
Anyway, there is no need to be pressured to come up with a super-fast response for I have learnt too (or rather because I am not quick-minded haha) , to take my time to consider my responses and be sincere and truthfully about it.

So what I am saying is that an interview is no indication of your ability and the many wonderful qualities you have as a person.
There are many times when we simply could not figure out why some people pass an interview and others dun so the selection is really dependent on the candidates in the year, projected future based on current global progress and even wimps and fancies of the interviewers. So many variables which we cannot control. so why worry hahah.

To prepare yourself, I ask you to take some time to consider again why you want the interview, the scholarship, the post.
this is very impt: only when you look deeply into what you want and why you do certain things, can you convince others of your dreams and purposes.
only when you believe in yourself can you convince others to believe in you.

And if it helps, think of zooworld when you go for interviews

dun be disappointed ok?

2010-03-06T23:49:00.002+08:00

The night before the results were out, my CT rep asked me not to give her the disappointed look when I passed her the results.
I was surprised at her comments because there was the exact thing I cannot do because I remembered the look on my form teacher's face when she handed me my O levels results. It wasn't that I did very badly, although I was naturally disappointed at not being able to replicate or emulate my results for the prelims, but somewhat I felt rejected and from that moment, for a young boy, things fell apart.

The recovery was slow but meaningful.

Many years down the road as I sat on the other side of the table, I asked who am I to judge each set of results? So it was with no expectation when I gave them out because at the end of the day, all of us need to deal with our own disappointments and that is more than enough for one to handle. I can offer them a shoulder or a word of wisdom but I will never be disappointed in them because I know they have given your best shot and there are things beyond any of our control. So as long as it takes them to the next level, I will be happy for them and will be proud of them because knowing all my kids, I know they have much to offer to this world, to the people around them and to blossom in their own capacity in time.

Adios, classes of 2009. Continue to move on with dreams because the best has yet to come. N Thank you for everything.

Tomorrow is just another day

2010-03-04T22:11:00.002+08:00

Writing this blog because once my Swoosh-kid said he dropped during exam time because he couldn't get to sleep. So I wondered if tonight insomnia will hit some of my kids.

Some declared tmr as Judgement Day but I beg to differ. Tmr is, however, the day a new journey will start. No matter how the results go, remember that the judgment was by others and only represent a part of you. Whether good or bad, it is important not to let the judgment of others on a part of you fully determine who you are. A new journey awaits ahead for you to explore your potential in many other areas.
Life after JC can be more exciting and some of my kids simply blossoms after that. We all find our own defining moments.

Regards, all the best kiddos! javascript:void(0)

Everything New

2010-02-20T20:35:00.002+08:00

This is the 2nd time I fell sick this term and for the same thing - sore throat and its accompanying ailments.
One more time and I shall conclude that the condition is reproducible with my niece and nephew as the causes.
But was on MC yesterday but went to school still to conduct the practical because I meant it to be a follow-up from the lesson the day before and I promised the kids I would close it with all the questions I left hanging.
I was glad that lesson was in the morning because by noon, my head felt like it was stuffed with cotton wool and I validated my mc and went home to sleep off the daze (after informing the h3 class that I cmi and would have to push the lesson to next wk).
A lot of sleep and water did the trick and I felt immensely better today altho the head is still in a drugged state.

Went for lesson just now and today we got a new teacher and she spoke so fast that I could not string my thoughts together. Blamed it on the mist-filled mind but I knew better that for a strong visual but weak audio learner, it will never be easy. I saw words dance erratically in the air and images collide as she went into high gear and verbosity reigned. Does anyone else experience the same thing? I will have to work harder to rewire my neurons so that I can be a more adequate audio learner. sighz..my classmates are so much better at it.

--------
Feb is almost over and I felt a sense of loss with my class(es). I barely knew them and I floundered with my decisions. Perhaps I was a little impatient with them because it was a great year last year, with everything so familiar and comfortable that I forgot the initial tentativeness and worry. Or maybe my expectations have grown which I should never have because every class will never be the same. still, I missed the happiness of every morning and my very own laughter. Perhaps it is the one-intake syndrome and it will pass and I will find my CG again, especially with so many changes occurring in school.

With the amended testimonial on my desk it is one more time and a final signature to seal the memories.

Before they come in...

2010-01-31T20:30:00.004+08:00

Orientation will end next week and the whole cycle will start again. Just like that, a click of the finger and we are back at ground zero to do battle for another two years.
What will my new year's resolutions for my classes this year?... Will have to think about that.

You know age is catching up when you picked up a bat and do some swings, only to have an aching back for the next 3 days that almost incapacitated you, made you walk with a funny gait and applied yoko yoko for the first time ever. The only good thing that came out of it was a firmer trunk with less volume at the love handles. I probably imagined the latter but I really have to take care of this back of mine and start stretching before I become too brittle.

The last time I stopped at the softball trip to Chiang Mai. It was a nice trip - restful I dared say because I was finally able to sleep through the night since the start of the holidays. Perhaps there was just too much tension at the start, be it to meet the looming deadline of testimonials or to prepare my own Uni apps or to prepare the trip itself. So the trip was a good one and I enjoyed making the side trip for CIP recce, away from the kids and away from routine. The first day was spent surveying the potential new site, visiting the village where we constructed a water filtration system under CIP and to buy a computer and printer for my translator, Chala with the money collected.
It was at the village when I felt the impact of progress. Instead of straw houses, some houses are now made of concrete. There are now two churches and the village head had his own provision store too. Surveying the whole area from the top of the hill, I realised that our work had brought benefits. At the same time, as more and more help arrived and more and more villagers willing to buy concrete buildings from Habitat for the Humanity, the rustic charm of the 'village' which I once lived in will disappear.
2nd day was a 8-hour journey to Chala's orphanage to bring them the books and electronics. We traveled from 9am to 4pm, one-way because the driver decided to take a 'short-cut' that turned up to be a longer way because we had to go up and down a mountain. I could feel my stomach swimming with discomfort at the end of the ride down the mountain and was glad to stop for lunch to rest out the swirling motion.
The ride back was faster and I got back at 9pm. It was an entire day of traveling but it ended on a high note as I lied down on the bed and watched the fireworks went off outside my windows as the Thais celebrated the New Year with fanfare. It was a beautiful sight.
The next few days were a blur because we played games every day and it was a routine. But mango sticky rice saved the day! :)

-------

Speech in English had never been my forte because I had difficulty catching with the nuances of words and I believed that my hearing was awful --> so pardon my expression. After so many years, I realised why - because it was just so different from Chinese where a single word can hold a profound meaning on its own. But in English, you need to string words to express yourself. Why is it that I never see it that way? As a simple tool for communication.
For the same reason, I struggled when I took elementary French, trying to seek out non-existent depth in each word.
So I decided to work hard on my listening capacity and change the neuronal circuitry in my head. I started my Spanish lessons. I may not be good at this but I am definitely going to make an effort in it. I had already seen how readily my younger counterparts picked up the new language and their verbal verbosity in English. But I will get there.

__________

moral stand.
feathers were ruffled recently with the clashes of the titans in the world. I applauded at the showdown.
There are people who liked to bully their way through things, eliciting demands and not ready to compromise.
We all need the moral courage to now stand up and say 'no more!' - not with stubborn defiance but with compassion. Be courageous to earn less but be responsible for your fellow man in this world. Be courageous to have less so that you can give more.
We say we want to earn as much as possible. But what can we take away when we leave this world? We say we want to leave something for our descendant but don't they care? A father went to seek financial help to keep his 5-rm flat during the financial meltdown when he could be financially comfortable with a smaller flat. Why? Because he wanted to leave the flat to his kids. But how many kids live with their parents these days with some many ready to make their own nests?
There was a philanthropist cum businessman who told his children right from the start that he was not going to leave any inheritance to them. They had to earn their footing in this world. But what he did provide was good education, opportunities to learn and a good environment. All his children did well on their own merits and when he died, all his money went to the charities.

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And for the last entry today...
someone write a note to me recently and halfway through it, my eyes were already moist.
Sometimes it took us a long time to realise what we enjoy or what we are capable of. I am glad she found out the she did enjoy Biology at the end of her JC journey. What I was glad about was how she chose to pick herself up towards the end and persevered all the way instead of throwing in the towel.
Life is a journey and through it, we learnt more about ourselves and our abilities. No one can define it for us.

Off to Chiangmai

2009-12-29T00:14:00.003+08:00

Before the year ends, it is to the airport again - soon that is - to Chiangmai , making this the 6th trip to the same place for work in 3 years.
This time however I will be there mainly for the softball trip even though I will be taking two days off to recce for a suitable CIP expedition. I am looking forward to meeting Chala again (my translator) and also hopefully the drivers, johnny and yut who were with us the last few rounds. I kind of missed them even though we couldnt converse much in English.
This trip I will be bringing this huge box of books for Chala's orphans (which was collected by JH and I packed them today) and I am preparing for my Santa Claus' role of buying a computer for them, buying mattresses for them so that they don;t have to sleep on cold floor, buying food for the new year and some additional cash to tide them for a year hopefully. The money for this venture was kindly contributed by myself and 2 students+teacher from the last Chiang Mai trip. It will be a good way to start a new year after all.
_______

Soft Shell Crabs

2009-12-26T22:47:00.002+08:00

Sometimes, we just eat whatever we know without thinking.

Went to Swensen the other day on my own to have a meal. They have the Disney menu! Haa just when I though I would like to stay in Disneyland resort for a day. =)
Anyway I had a chili crab soup with soft shell crabs. Something like that.
While biting into one of the crabs, it struck me: if it has a soft shell, how is it going to defend itself against predators? What is it defense mechanism?
The ignorant me found the answer here : http://en.wikipedia.org/wiki/Soft-shell_crab
soft-shell crab are crabs in the process of molting.

Tidbits for the month. Feel free to share!

As we come to the end of the year

2009-12-26T21:05:00.003+08:00

Bunny said that I don't update my blog very often or was it how come I don't update my blog?
It was intentional but I was busy working on other sites and because this round, I tried to disseminate the info I had gathered to the whole school population through R.Discovery. Plus I was a bit lazy to log on. haha This is supposed to be a biology but it had served as my own ramblings at times I realised. Thoughtful ramblings I hoped =)

It was almost the end of the year already and just when I finally was able to feel rested, I realised I am going to start school all over again. I think I was quite tensed past few weeks (so I bought an oto eye massager=P).
1) writing testimonials. It was a fight against datelines, trying to find time to type after/before invigilation periods. Each piece was a work that I kind of relished in, masochistically speaking. Poring over written thoughts of others (which brought me some laughs), their own very reflections and my own insights, I assembled each piece with a better understanding of my student. I would like to say that every one is done with sincerity and hope for a new future, and every one is really for each single individual. At least until the amendments come in :).
Typing of testimonials ceased on 1 Dec and in between that and prom night, I churned out my own personal statement (after uploading everything else for UCAS and Naviance) for my own overseas application. For 3000 characters, they wanted several inclusions and because even this personal statement is graded on a scale of 1-6, it was quite daunting. It got worse when I realised that there are only openings for 20 students worldwide.
Then it was prom night. I cannot remember how mine went, probably as camwhoring as 5 sept even though there was no digital camera then. It was my first official time wearing my ever first pair of contact lenses then and like many others, I wore a suit. fast forward many years ahead, things don't really change much =) (the girls always looked very different that fateful night) except I felt older because I am and I had less friends ahah
Then all of a sudden, I was on my way to Bali with my friend on a short trip on Mon afternoon (I had to go back to school to settle paperwork for softball trip..arrgh). I remembered dumping my clothes and electronics into my backpack and left for the airport because my friend paid for an extra 20kg for checkin with jetstar so there was no reason to strategise my packing since I knew that I would never hit 20 kg.
Bali was not bad but I thought I suffer from the incessant working for the past one month to be able to reach a a peaceful mental state. In other words, my mind was still rather fidgety. But a break was still a break. It was still good to be able to not think of any work even if it was only for 5 days. =)
Back to Singapore, I had to do up part two of my application. This was the stressful part and took me a week to formulate a research theme when I had not done any for so long, totally unfamiliar with social research, no in tune with current educational landscape but had so many ideas, some practical to do while others are idealistic. I would pace up and down the house to find my muse until I decided not to worry too much but just write what I believed in, thought was feasible and put them down in black and white. I trusted in my scientific basis of judgement and because I only knew so much (I don't have time to do enough research). A neat piece of work (at least my fren told me) and so I hoped the people reading it will be as excited as my friend was. Like my students, I took a day to get my certificates endorsed (NIE and NUS), weighed my envelope and finally sent the envelope out to meet the dateline. And that was only this week. hahaha
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BREAK BREAK!
Christmas Eve. I went out to run some errands (like cutting my locks and rejuvenated with short hair) and had a starbuck coffee at the cityhall link. I liked sitting down with a drink and listening to cheesy xmasy songs (at the appropriate year only pls). It always bring a smile to my face with its festivity. I always think about Love Actually! http://www.youtube.com/watch?v=5m2T5yfgsZ0

I read this newspaper article and it picked out pple wearing supposedly nice stuff and interviewed them. Other than the fact that I thought the clothes were not that outstanding by themselves (shirt and tie - isnt it norm? but perhaps they are less common among young pple in orchard) but to print about a 19 yr old wearing more than a $1000 on himself, arent we sending out a wrong msg? for one thing, it is NOT normal bcos a typical 19 yr old cannot afford it and it is also not true that only branded stuff are tasteful or value for money. These days, the branded goods are more inferior in quality so it takes a discerning shopper to get the best deals actually. Anyway , I just hoped that the young generation were not misled ...mmm i shall keep an eye out for that column next time.

Watched AVATAR (3D) today with my friends. J's treat because he passed his IPPT with me with a silver as his PTI for the past 2 weeks! AVATAR was awesome and my friend thought I fell asleep because I did not move at all. Nope. I was running through the forest! :)
James Cameron had really brought it home with this alien species although typical themes were explored. Still I enjoyed. I loved the bio stuff! - Signal transduction! nervous-like system in the roots! the part where the Na'vi plunged into the animals? I thought it was a simile to how pple plug into comp/virtual reality in sci fic actually but they changed the perspectives. There were parts that reminded me of Hayao Miyazaki's earlier works (the raccoon guy) like the floating mountains - Castle in the Sky and feeler-like sensor - Nausicaä of the Valley of the Wind.
But more importantly, I hope pple are not just blown away by the concepts or animations but think about how it really mirror real life. In our determination to get resources for our own needs, for our personal interest we often disregard others. Species went extinct, indigenous tribes slowly phased out (the only untouched ones are in papau new guinea i think) - and thus their knowledge of nature, and isn't that the reason why japan started WWII? We also see it in deforestation, pollution and how the bigger companies/some countries are operating in their drives to maximise economic returns. without a care, without a heart - and that is actually the thing we should work on and is working on - care and respect for others because life is not all about us.
I envy the Na'Vi and their connection with nature because they understood symbiosis, mutualism and the interdependancy of all living things.
The good thing is many pple are starting to appreciate nature again, to feel the live pulsating from underneath and start to care for Mother Earth.
------------
RANDOM

my students who do not know that these songs came from somewhere: :)

FaV

2009-11-22T11:11:00.003+08:00

2 years later, out of the blue, I got a call from Melvin which brought a smile to my face.
A dinner at pepperoni and one of them drove to pick me up. It was like a role reversal but was nice :)
I am definitely not the best conversationalist in the world but I enjoyed basking in the atmosphere, hearing them moved on to a new phase in life, chartering new grounds, like we all once did. And to know that they are doing fine. In fact, I finally hear from Yam boy which I thought of a few pages ago and that was great.
my heart smiled and chuckled throughout the night, even when I din say much.
Isaac recalled my chronic sleep deficiency while teaching them and I recalled the those days in classrooms when the afternoon sun will shine in and all those funny antics they have. I remembered the day when they received their A's results and those times we spent before A's to consolidate their content.
(Besides them, others included) there were those late nights in the canteen, library and at random times, sometimes until the school closed. I remembered going home late all the time but yet still enjoying those moments when I walked past the canteen because I would always meet some students from my classes and others as well who liked to test me on content :). This year there wasn't so much of it though.

These are a bunch of great kids. They fooled around, played paper soccer in classroom, keep talking incessantly in class in the first row, drew on each other's faces, dozed off at times. How did I survive through all these? =P Then you looked beyond that to see the great hearts they have and to remind myself that in education, it is not all about the grades and how meek the students are that define them (as some deemed). They too need the freedom to explore about themselves and learn. For some, they are already at that stage of their needs but for others, this came later in life or they are in the midst of it all while in jc. So we give them the space to think for themselves, and take ownership of their choices. These kids also have much to offer with their creativity, their sincerity, their determination (even when it came toward the ends) and their generosity - these will take them far in life and I think they are doing great! yup! I still remembered their cheekiness in doing a row of flowers at the start of lectures.- wished i have taken a pic :)

[In case I am being accused of favourtism, there were of cos many 07students whom I have met here and there and who also brought back great memories. But during this part of the year, reflections are the norm (with more time at hand) and there are things I want to pen down to remind myself and also to others after the string of conversations last night. =) ]

Tmr on your mark get set GO!

2009-11-09T22:56:00.000+08:00

GOOD LUCK TO ALL!! =)

Stress Reliever - kick off those shoes!!

2009-10-25T23:06:00.002+08:00

Unabashedly, i had been grooving to this!

For Samuel

2009-10-25T23:02:00.002+08:00

I think we have seen this in notes:
Waht I want to remind you is that:

If non-disjunction occurred at Meiosis II, two gamates are normal and two others have n+1 and n-1
If non-disjunction occurred at Meiosis I, all the gamates are affected, being either n+1 or n-1

It's about Giving

2009-10-14T21:53:00.003+08:00

Went to school today and one of my friends asked how much effort should we put into farewell assembly? "Even if I do a lot, I don't think they will appreciate." He pointed out about the time I stayed up til 3am+ to work on some pet project of mine.
I guess I never will really know if pple appreciate but then I thought, it is not about receiving but the giving that make one happy.And I guess teaching is not a profession that you may want to talk about instant appreciation or gratification despite a Teachers' Day. I think the relationship goes beyond sch time. For now, I want to be able to look back and say that I have given the best possible for my students, for them to have a good start in mind and heart for the future.

If you never open your heart in the first place, you cannot expect others to open theirs first.

Updates on Questions Given

2009-10-10T14:58:00.005+08:00

Explanation for 08 HCI MCQs as highlighted by Alicia
-------
Pls also note that MCQs answers to 0708 H1 and H2 are up on Discovery in the folder with all the Explanations.
3B will want to take a look at H10708 answers after you have done the questions. A copy of the questions has been passed to the model student to zap for the class. (pls pass word around).
Again I want to stress that doing TYS is to give you a good feel of the questions that cambridge set. At this stage, you should be able to look at the questions and ask yourself if you can answer the questions. If you can't then look for me and you probably need to refine your content (PS: 08 P2 is quite tough).
Also while doing other schools' Prelims questions, if you find that certain answers are not well-elaborated or that you are able to think of better answers - that's credit to you. Sometimes answers are more vague to give ourselves leeway in marking. Alternatively you can check in with me.
--------

I still love this video after two years! For you all!

Nobel Prize in Medicine or Physiology 09

2009-10-07T17:32:00.001+08:00

And this year it goes to researchers who worked on Telomeres!! :)
http://www.scientificamerican.com/article.cfm?id=nobel-prize-medicine-2009-genetics&sc=WR_20091006

Tough at 30

2009-09-23T17:52:00.002+08:00

IP-PT and shooting today for reservist.
As usual, i am pretty pathetic at shooting because I have never been very stable. But then it was my first failure since i passed out and after getting a marksman the last round 4 years ago. Yet I cannot expect much if my skills fluctuate as much as my bullets every time :P
But ha! I showed the youngsters that I can still make it at 30 for IPPT :P
I was actually surprised at my own performance but then again, I had been working out for the whole year.
39 sit-up, 9 pull-ups, 8.9 shuttle run, 255 standing broad jump and 10.58 2.4km. not bad at all *pat on the back* and 29 points.

nonetheless, the best part was still getting to know the pple who turned up. The comadarie and support we had shown one another, the chit-chat and the strong spirit! Yea! I am looking forward to tomorrow already!

LOst

2009-08-29T16:32:00.002+08:00

Last night I left the school with a heavier heart than expected.
KTV singing continued in the lounge as some of us rejoiced at a well-deserved break with songs of the last century.
It's great to see friends winding down but I am not sure if it is just me, tiredness, anxiety or sadness that prohibited me to immerse into those moments. Maybe it was a mixture of all.
Tired because of accumulative sleep deficiency that comes from crafting test answers and revision materials til late into the night for consecutive days.
Anxiety swelled when I realised it was the last tutorial for the two years. There was so much more I want to teach these kids and so much more things to relate and maybe a little more silly examples to give. My heart palpitated a beat more and my tear glands swelled a little as I wrapped up the lessons because I have always been terrible if not awful with spoken words. At a loss of what to say, I let the feelings swept over me and lingered. So we took pictures, laughed and cheered to mark our time spent together in a tutorial class before the sprint to the A's.
With an unsettled heart, I would like to think that I have done the best I possibly could in this two-year term. From the ultraman-ness, games, cheers,the sabo-ing of pple and those times in the canteen. And now I can leave the stage and let the kids take the limelight.
And to these kids, I would like to thank them for the wonderful times, their tolerance and participation to my wild ideas, their slightly deafen ears and their trust.
M very grateful on TD to have such a bunch.
----------
Feeling a little lost this wkend, without the usual rush and craziness even though there are datelines to work on. I think I will just rest for now.

Hang in there!

2009-07-25T15:10:00.003+08:00

I couldn't believe how tired I was this week.
Sorting out the revision work,checking the answers, preparing two sets of summaries, writing CT comments (i never replicate hor! or so I think...) and also starting my external volunteer work. And after 3 consecutive late nights or should I say early morning at 2am? I finally crashed on Thurs for a well-deserving sleep that rejuvenated me for another day of school and pumped me up to stay awake for the Transformer movie last night which my fren treated because he had going-to-expired GV vouchers! Lucky me! =)
And because I was too tired to run this week, I was glad to do my pilates in school yesterday to redeem myself for the lack of proper exercises this week! =)

And we all in the staff room know, the time has finally arrived when the J2 teacher's world gets a little chaotic and swarmed with madness as we pushed along, grabbing at any threads of sanity and haunted fellows. Such exciting time! Swoosh! Jia You ba - to all! Staff and students alike!

-----------
Last Friday I saw a student in the evening. Even though I knew he had stayed back to study, I asked nonetheless. When he walked away, I saw that determination set on his shoulders and also of fear as he tried to take on the last lap.
Moments like this, you are reminded that this is also no time to pause for too long because there are those who need the support.

Then I thought of yam-boy. Where is he? It is almost two years already...

Questions Everywhere

2009-07-24T14:21:00.013+08:00

The questions amassed over the few weeks....

__________CT________________________
1) virus MCQ 19 for CT
Comment: A RNA virus does not have to be a retrovirus e.g. influenze but a retrovirus definitely will have RNA as its genetic material.
Why not C? I think C is a poor choice. Because it is talking about bacteriophage (lysogenic) when the question is making reference to an animal virus i.e. herpes(latent) so it doesn't tell me anything about the herpes virus because it is irrelevant. Also, the teaches argued that when given a choice, an omission is always a poorer option.

___________Cloning________
2) http://www.dnalc.org/ddnalc/resources/pcr.html
If you have trouble visualising how PCR can lead to the amplification of a specific DNA segment, this is a good site.

3)Commercially, the insulin chains are produced separately but are fused with the beta-galactosidase. Cyanogen bromide is needed to first cleave the beta-galactosidase so that you can get pure chain A and chain B before The two chains are subjected to oxidation for the formation of disulphide bonds between them.

________Plant Cloning_________

b) Why is sulphur needed for nucleic acid synthesis? Or just simply plant growth?
There are many minerals needed for good plant growth but we do not know exactly the roles they play.
It is intuitive to think of the importance of nitrogen and phosphorous but what about potassium and sulphur in notes? Here is something for you:

Sulphur

Both the yield and quality of crops grown on sulphur-deficient soils are reduced unless sulphur is included in the fertilizer treatment. Sulphur fertilizer can increase crop yields and quality and result in significant economic returns to producers. Sulphur fertilization also improves overall fertilizer efficiency.
(http://www.sulphurinstitute.org/learnmore/faq.cfm#plants)

Potassium

Potassium is the only essential plant nutrient that is not a constituent of any
plant part. Potassium is a key nutrient in the plants tolerance to stresses such as cold/hot
temperatures, drought, wear and pest problems. Potassium acts as catalysts for many of
the enzymatic processes in the plant that are necessary for plant growth to take place.
Another key role of potassium is the regulation of water use in the plant
(osmoregulation). This osmoregulation process affects water transport in the xylem,
maintains high daily cell turgor pressure which affects wear tolerance, affects cell
elongation for growth and most importantly it regulates the opening and closing of the
stomates which affect transpirational cooling and carbon dioxide uptake for
photosynthesis.

c) what is autoclave? (verb and noun)
is a device to sterilize equipment and supplies by subjecting them to high pressure steam at 121° C or more.

d)If all plant cells are totipotent, what is the advantage of using a meristems?

It is virus-free!! =)

e)when we say "low in auxin" in plant cloning, this is relative to the auxin itself and not in comparison wtih cytokinins. Pls see diagram.

(a) other questions
http://chansensei.blogspot.com/2007/08/how-does-plant-virus-infect-plant.html
http://chansensei.blogspot.com/2007/07/complicated-matter-of-ti-plasmid.html
http://chansensei.blogspot.com/2007/07/callus-and-tumor.html

_____________ stem cell____________-

1) SCNT: read more:

(WIKI)
In SCNT the nucleus, which contains the organism's DNA, of a somatic cell (a body cell other than a sperm or egg cell) is removed and the rest of the cell discarded. At the same time, the nucleus of an egg cell is removed. The nucleus of the somatic cell is then inserted into the enucleated egg cell. After being inserted into the egg, the somatic cell nucleus is reprogrammed by the host cell. The egg, now containing the nucleus of a somatic cell, is stimulated with a shock and will begin to divide. After many mitotic divisions in culture, this single cell forms a blastocyst (an early stage embryo with about 100 cells) with almost identical DNA to the original organism.

Some researchers use SCNT in stem cell research. The aim of carrying out this procedure is to obtain stem cells that are genetically matched to the donor organism. Presently, no human stem cell lines have been derived from SCNT research.
In 2005, a South Korean research team led by Professor Hwang Woo-suk, published claims to have derived stem cell lines via SCNT,[6] but supported those claims with fabricated data.[7] Recent evidence has proved that he in fact created a stem cell line from a parthenote.[8][9]

The impetus for SCNT-based stem cell research has been decreased by the development and improvement of alternative methods of generating stem cells. Methods to reprogram normal body cells into pluripotent stem cells were developed in humans in 2007. The following year, this method achieved a key goal of SCNT-based stem cell research: the derivation of pluripotent stem cell lines that have all genes linked to various diseases.[10] Some scientists working on SCNT-based stem cell research have recently moved to the new methods of induced pluripotent stem cells.

Stresses placed on both the egg cell and the introduced nucleus are enormous, leading to a high loss in resulting cells. For example, Dolly the sheep was born after 277 eggs were used for SCNT, which created 29 viable embryos. Only three of these embryos survived until birth, and only one survived to adulthood.[11] As the procedure currently cannot be automated, but has to be performed manually under a microscope, SCNT is very resource intensive. The biochemistry involved in reprogramming the differentiated somatic cell nucleus and activating the recipient egg is also far from understood.

In SCNT, not all of the donor cell's genetic information is transferred, as the donor cell's mitochondria that contain their own mitochondrial DNA are left behind. The resulting hybrid cells retain those mitochondrial structures which originally belonged to the egg. As a consequence, clones such as Dolly that are born from SCNT are not perfect copies of the donor of the nucleus.

Concerns
One concern is that blastula creation in SCNT-based human stem cell research will lead to the reproductive cloning of humans. Both processes use the same first step: the creation of a nuclear transferred embryo, most likely via SCNT. Those who hold this concern often advocate for strong regulation of SCNT to preclude implantation of any derived products for the intention of human reproduction. [17], or its prohibition.[14]

A second important concern is the appropriate source of the eggs that are needed. SCNT requires human eggs, which can only be obtained from women. The most common source of these eggs today are eggs that are produced and in excess of the clinical need during IVF treatment. This is a minimally invasive procedure, but it does carry some health risks, such as ovarian hyperstimulation syndrome, and in very rare instances even death

2) where can you find adult stem cells?
(definition given in test is okay -
ESC is based on origin: inner cell mass of blastocyst
ASC: undifferentiated cells found among differentiated cells in a tissue or organ
found in the body after embryonic devt, in growing

(http://stemcells.nih.gov/info/basics/basics4.asp)

(WIKI)
When to use the term ASC?
The term adult stem cell refers to any cell which is found in a developed organism

Also note:
Fetal stem cells are primitive cell types found in the organs of fetuses. The classification of fetal stem cells remains unclear and this type of stem cell is currently often grouped into an adult stem cell. However, a more clear distinction between the two cell types appears necessary.

___________others_________

Why is AP always generated at the muscles ?
Kindly ignore my reference on RMP in muscles with reference to the above.
AP is always generated because typically more than enuff ACh is released.
In fact the RMP os skeletal muscle fibre is about -70 to -90mV (similar to neurons) not -40mV. While that of smooth muscles (e.g. found in the heart) was the one that is around -55mV, very close to threshold potential!

Mmmm...that's all? :)

Oops!

2009-07-19T22:57:00.001+08:00

Sorry! The updates are not ready! I left the stuff in school!

cloning II McQs

2009-05-31T22:07:00.001+08:00

my parting gift in case it wasnt in the answers....
tata pple!!

a blog site for this trip.

2009-05-31T14:17:00.002+08:00

http://www.travelpod.com/members/chansensei

I think I am so going to be dead!

Odd Stuff

2009-05-31T14:14:00.003+08:00

One is a limpet and the other barnacle. Which is which?

From Evol 2 again

Qn23: clarification. It is onto not ortho-logy.
Ontology is developmental biology:
The theory of recapitulation, also called the biogenetic law or embryological parallelism, and often expressed as "ontogeny recapitulates phylogeny.
But is of course refuted on many fronts (so is not important)
The recapitulation theory claims that each successive stage in the development of an individual represents one of the adult forms that appeared in its evolutionary history.
(This idea is too extreme! If this is true, we will have real gills which close up later during embryo devt!)
Modern observation
Species which have an evolutionary relationship typically share the early stages of embryonal development and differ in later stages. Examples include:
• The backbone, the common structure among all vertebrates such as fish, reptiles and mammals, appears as one of the earliest structures laid out in all vertebrate embryos.
If a structure vanished in an evolutionary sequence, then one can often observe a corresponding structure appearing at one stage during embryonic development, only to disappear or become modified in a later stage. Examples include:
• Whales, which have evolved from land mammals, don't have legs, but tiny remnant leg bones lie buried deep in their bodies. During embryonal development, leg extremities first occur, then recede. Similarly, whale embryos have hair at one stage (like all mammalian embryos), but lose most of it later.
• The common ancestor of humans and monkeys had a tail, and human embryos also have a tail at one point; it later recedes to form the coccyx.
In other words: there is embryological devt does not show us the actual evol history.

Qn7: The simplest organism is found at the end of a tree. Which end?(hint: How does a real tree look like?) – towards the pointed end of a V-shape

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Jane was asking about some questions on the cloning and gene therapy MCQs. I will post it up once i have time. Seemed like I have to do it while overseas cos i am really rushed for time here :P

H3 bio also......

Let me pack first k? I havent even settle lodging yet so.....shucks!!!!!

A few good question from 3B and random voices from the grapevines

2009-05-26T12:41:00.003+08:00

1) (molecular clock) How can we reconcile the generation time and mutation rate of a particular gene. If a common gene is found in bacteria and an eukaryote, given the relative fast reproduction rate of bacteria, shouldn't the gene accumulate more mutations over the same time span and if so, how does that allow us to decide the point of divergence?

Ans: the generation time and rate of mutation is normalised for a valid comparison to be made btw different organisms!! =)

2) (not impt) why is there two origin of replication in pBluescript?

Ans: Pls ignore f1 origin. pBluescript is what we called a phagemid: a hybrid betw phage and plasmid.
- WIKI: http://en.wikipedia.org/wiki/Phagemid
A phagemid or phasmid is a type of cloning vector developed as a hybrid of the filamentous phage M13 and plasmids to produce a vector that can grow as a plasmid, and also be packaged as single stranded DNA in viral particles. Phagemids contain an origin of replication (ori) for double stranded replication, as well as an f1 ori to enable single stranded replication and packaging into phage particles

3) Co-evolution
Each party in a coevolutionary relationship exerts selective pressures on the other, thereby affecting each others' evolution. e.g parasite or mutualism relationship

4) why is the size of the cloning vector important? (sensei)
together with the gene of interest, it is advisable not to have the recombinant plasmid at too biga size because small means higher copy number, greater stability and greater transformation efficiency.

5) why is it that HIV RT is a 3-in-1 model while the RT in cloning we still need to remove RNA (from RNA:DNA hybrid) with RNase H and later use DNA polymerase?

The RT in cloning is a different version and we choose not to use it because if the enzyme has multiple functions, its efficiency (less cDNA) can be compromised when it choose to degrade the RNA of the PolyA tail:OligerT DNA primer instead of elongating the DNA chain.

6) Using terminal transferase: how is the length of CCC or GGGGG ensured (if it is)

ANS: It isn't. They may not be heavenly made matches in terms of length but the gaps at the ends of the 5' strands can be filled in with nucleotides under the catalytic action of DNA polymerase and the nicks in the strands were sealed by DNA ligase.

evol mcQs

2009-05-13T22:29:00.000+08:00

Comments for the week

2009-05-10T23:18:00.004+08:00

A few things to run through for the week on mock and evol:

Mock:
(esp to Jane)
Absorbency is not the equivalent of wavelength. It is more related to intensity.

But let's us examine what is intensity first -a greater intensity of light means having more photons (increased conc) to strike a surface.
Compare this with wavelength - the wavelength of light will determine the amount of energy the photons will carry.
Therefore, having a higher intensity of light at a particular wavelength means having more photons of a particular energy.
How is this related to absorbancy?

The maximum absorbance of a plant is determined by the photosynthetic pigments it contains. If you shine blue light at it, how much of the energy can it absorb? If you start at low intensity, the plant can probably photosynthesize more if you increase intensity until other limiting factor comes into play.
you may ask: but didnt we fix the intensity of the light?
Yup you did but a plant will have difficult capacity to absorb different colored light (diff wavelength). For green color , you may need x photons to reach max, but for blue you may need 10x photons to hit its max so while the intensity of the light has been fixed, the effect on the rate of photosynthesis due to diff colored light will differ and each of them has it own max absorbance before other limiting factor comes to play. So if intensity is not high enough, you may give same rate of photosynthesis for different colored light because one may have reached its max while the other has not.

-----------------

Evol

The story of marsupial. It was once thought (and perhaps still so) that marsupials are the ancestors of placental mammals but evidence is emerging to suggest that these two groups branch off at about the same time.
But they are still deliberating on why Marsupial are found in high conc in Australia: the drift? different selection pressure? or both?

http://www.ucmp.berkeley.edu/mammal/marsupial/marsupial.html

http://en.wikipedia.org/wiki/Marsupial

http://bcb705.blogspot.com/2006/05/continental-drift-marsupials-and.html

---------------

a few highlights we have learnt from Evol - just to clarify:

1) there is something called the species-area relationship: in short, when you looked a group of islands, you have to consider the size of it and the distance it is from the main island to predict variety of species

2) For neutral mutations, the key is really having no effect on fitness
For a mutation that leads to no change in phenotype, it is definitely neutral since there would not be a change in fitness either.
But mutations that do affect phenotype in measurable ways but do not affect the organism's fitness should also be considered as neutral.
It is definitely reasonable to do so because that will account for variants we see in our population due to spontaneous mutation. But we will consider it as a minor for now.

We often work with "no change in phenotype' as in the notes because that was what Kimura first proposed and most probable since it is considerably rare to have a change in phenotype without affecting fitness - although not impossible.

---------

Reiterate:
Evo MCQs Part 2.

32: (A) - bcos the question compared "btw" population. each population will see an increased in genetic variation but btw population, there is less distinction since they each now shared certain common alleles/genes.

--------

A question came to mind by alicia some time back:

How does membrane-bound AChE hydrolyse ACh? How can persistent signaling be achieved?
If they are membrane-bound, how do they hydrolyse ACh? If all ligand-receptor interaction is transient, how can there be persistent signaling?

The binding of ligand and receptor is indeed transient. What AChE offer to do is to hydrolyse free ACh so that the concentration of ACh in synaptic cleft increases for an increased probability of binding of the ligand to receptor and thus an observed substained signaling (the reversible reaction is less likely to go backward yah?) Persistence in signal does not refer to a tighter binding but increased probability/prolonged of so.

Such a Crappy Week

2009-05-10T22:43:00.002+08:00

i think it all started with the loss of the game. The weight of it all loads up on the chest and it was a difficult period (together with other stuff) and I still feel it even though I am slowly dissolving it into another learning point, another thing to ponder over. maybe retail therapy tmr will help.
it is not about the winning or the losing. It was the lack of spirit from the players and my own haplessness. As I sit in the chair under the sun, squinting to watch the games, there are moments when I thought: should I stand up and shout at them,should I rally them up for an inspirational moment? M I just going to sit here and do nothing. In the end that is all i did - sit there but i figured I am really not an inspiring person because I am not really articulate enough. And I really can't scold them because I don't know how to even though I am mad at them for not living it up to themselves and their abilities. The scolding? I left that to coach.
I was seething because I wanted these kids to win, to bring it home for themselves and not for me. 6 years of games and I hoped this year will be the year that they can finally find themselves in a final to play the greatest game in their 6 years. There is such a good chance this year after working on getting in the DSA, the arrangement for Sat trainings and all the favours I pulled . But they blew it - at least for now - because they din have the heart to make it work.

I felt a little betrayed but more than ever, sad - for them for the defeat that should not have been. I asked: can I do better? what should I have done? Did I miss something out? Maybe I did. Maybe I didn't.

A student told me I was hard on myself. And it is difficult not to maybe because I recalled the difficulties I once had and dont want others to experience that misery I had.

Then come the lessons. you just know it when you are out of sorts. It has been a while since I felt that but it came back and the lessons were horrible I thought. I don' think anyone was listening or convinced for neither am I. So I looked at my classes and go with the theme of the week: can I do better? what is going wrong? is it inexperience and the lack of sound methodology? too emo?
Then I saw my colleagues coming up with this and that for their classes and suddenly I felt that I shouldnt be taking my classes because they deserve better.

Towards the end of this entry, I suddenly recall what I have been reading (again) recently: that the most important person to give your compassion to is to yourself. Because too very often, we are too harsh on ourselves.
So let's take a break. treat ourselves a little/more better.

Questions on Cloning notes

2009-05-06T21:55:00.002+08:00

Someone asked:
we have used lac and trp operon in synthesizing human growth factor/ insulin and anti-thrombin. Does it matter which operon is used?

Ans: Nope. Don't worry about it because the examples are given because that was just what people had worked with in making those protein. By now, I am sure things have moved on and they may be using other operons. =)

Can we use a RNA primer?
Does it matter if we have a RNA:DNA hybrid if we just want to check the sequence?

Ans:It doesnt really matter just that there is no reason to have such a hybrid. Why use RNA when DNA primers can also be readily synthesized?

Also, will we have end-replication problem if we use RNA primers?

Ans: No, because there will not be any DNA polymerase coming along behind the primer to remove it and fill the space with DNA. so The primers will flank the sequence/gene of interest.

Pls Stand Up.

2009-04-29T20:50:00.003+08:00

Had civics today. Something that I don't think I do very often on the Wed's half period.
Why the urgency? i am glad that the school is looking into the attitude and discipline issues that appeared to be deteriorating . it is definitely something on my mind for quite a long time already although I havent channel much energy into it.
We asked ourselves: who is the R'sian, pls stand up.
In a global society where individuality is celebrated, how much leeway can we afford to give our students? Do they understand the proper decorum? do they possess basic courtesy and empathy? If we do not look into this, can they survive out there? because if they dun, they will lose the respect of people they work with and what kind of legacy are they going to leave behind?
Pride - such a strong word, but is something we can identify with. when you tell pple where you are from, you will be surprised with the respect they give you...but can you continue to earn it? Is it just good grades when there are tons of pple who are potentially just as capable? It is the attitude, the heart and the passion that is going to bring that best out of an individual. The school does offer an environment for exploration but did you just abuse it?
I must admit that because to me, it is the intangible that speaks so much, I often neglect the presentation of a student because I used to work with pple with all sort of appearances. But when i think about it, we cannot neglect how we present ourselves because there are expectations placed on us. We are part of a legacy.

A non-thru-train student once told me that he wasn't sure if he is capable enough to be consider a R'sian and that puzzled me for a while. Is that what being a R'sian is all about? A R'sian goes beyong his/her grades and if he has doubts about himself, he should discard because he has so much more to offer compared to many others who has been in the system.

R'sian. Pls stand up.

Nervous MCQ explained

2009-04-22T15:53:00.001+08:00

Nervous System:

Qn6: This is akin to question 19. If the sodium-potassium pump is not working, the new RMP will go towards zero/near zero – a value achieved when sodium and potassium ions are allowed to diffuse down its electrochemical gradient to reach its own equilibrium potential.

The initial RMP is already at -70mV. So to get to 0mV, it is largely determined by the influx of sodium channels and the speed at which the RMP gets to zero is impeded by the relatively low permeability of membrane to sodium ions (less leak channels).

Qn: I thought sodium-potassium pump does not contribute to the establishment of RMP?

Alternatively we mean: why is RMP at a particular value?

And that is primarily due to the differential permeability of the membrane to different ions which can readily influence the RMP values.
The pump may not contribute to the establishment of the RMP but it plays a role in the maintenance of it so that each ion cannot reach its own equilibrium potential by maintaining the relative concentration of each ion across the membrane.

Qn 19, no ATP -> sodium-potassium pump will not work. The new RMP is achieved mainly due to the influx of Na+ (since K+ is already pretty near to its equilibrium potential) and so the outside is now less positive.

Qn 20: acetylcholine: non-proteineous; an ester (of acetic acid and choline) – it is not a steroid and choline is an amine.

we have our ups and & downs

2009-04-21T18:14:00.002+08:00

It was draining and disorientation, returning from a course on Mon. Despite the great ideas that I took away, it does not guarantee a better today when I did tutorial and suddenly felt so unprepared. I thought I had everything sorted out only to realise that nothing is sorted out. It is the same as Friday remedial when I was stumbled at my own inadequacy and I have to start to think: what is happening to me? Am I not coping or am I trying too hard?

The thing with marking tutorial is that the weaknesses of your students get too glaring. When you decided to personalise the correction measures, it gets too demanding and frustrating because too many pple too many different styles. It eats me to know that I cant do it but perhaps, we are not meant to do that but do the best for the masses and hope that the rest catches along.

A colleague msg me out of the blue to talk about the disillusion that was felt as marking goes on and on. It is endless. But yet, does the kids appreciate it? Some complained that we are forcing them to copy and hand up work. But isn't tutorial suppose to be done anyway? Others lamented about the parts not marked.
It gets very irritating because we are not obligated to mark for that is not how JC works but we did anyway. Yet the kids put out their hands and demand because we have been taking care of them too well. We shouldnt even give answers.
We write the same comments, we poured over the words.
If a script takes 15 min, one hour will see 4 scripts done. assuming 28 in a class, it is 7 hours. that is one whole day. 2 classes - 2 days. and we mark tutorial and practicals. where has the time gone to?
we hope to prepare more things for them - summaries and discussions but the red pen is still leaking ink. Perhaps we are really trying too hard because how many really bother with what we do with their tutorial?
---- this is not a complaint as well as a review on whether we can be more efficient and value-add.

Celebrate or Not

2009-04-09T22:44:00.002+08:00

when students made an improvement, you like to celebrate and give a pat on the back saying well done.
when students made the efforts but still failed to make it past her/his expectations, you like to say dun give up and keep going because this journey has not reached the end for the tortoise still have the distance to go.
And I failed utterly in both while in class. Torn by the polarizing needs, I went into a blabber of words.

I stood in front of one student and felt a familiar wave of emotions swept over me: of my own struggles as a student,of the hardships I had to face because of my own decisions. And how sometimes things somehow doesnt seem to work out no matter how hard I tried.
I wondered how often will this feeling return to haunt me. Maybe forever in my capacity as a teacher but then it also reminded me that I was stronger because of it. If there is a positive trait my brother can see in me is perseverance. How I sometimes struggled on, torn and frustrated in the face of adversary, but refusing to give in until I have tried my best to the very end. I guess some pple called it stubbornness which is most probably true as well. =P

I hope all my students can also learn to pick themselves up after every fall because life, we realise, is not a smooth journey. But you can decide how you want to manage your ups and downs. And if Ups and Downs are part of this journey we are taking, there is no need to linger too long at one spot because life goes on.

Judging from the results, I realised with disappointment that there is so many things I should/could have done with students this term.
Maybe I had done it all wrong. Maybe it was the series of lectures (H1/2/3) that I had to handle. Maybe I have to think harder.

But right now, I have not given up and there is a journey to continue. Banbette!

If I wasnt doing cancer....

2009-04-03T21:39:00.002+08:00

I would have done bees among the many insects I was curious about:

From Scientific American:

1) WHO TO TAKE THE PLACE OF DECLINING HONEYBEES POPULATION?

Honeybees have been dying in record numbers in the U.S. for at least the past two years. Experts attribute the mass deaths to a catchall condition known as colony collapse disorder (CCD), although both a cure and the culprit remain elusive. Despite as much as a 35 percent loss of bees per year, we remain almost entirely dependent on what until recently was a self-renewing annual population of billions of honeybees to pollinate over 130 kinds of fruit and nut crops.

"We can't rely on the honeybee forever," says Blair Sampson, an entomologist with the U.S. Department of Agriculture (USDA). That's a problem, given that entomologists have yet to come up with a viable alternative. But researchers report that another bee known as the blue orchard, or Osmia lignaria, holds out promise of filling in the void.

The blue orchard bee, also known as the orchard mason bee, is one of 3,000 bee species native to the U.S. and is currently the subject of intensive study by the USDA's Pollinating Insect Biology, Management and Systematics Research Unit at Utah State University in Logan.

James Cane, an entomologist at the Logan bee lab, has been working for 10 years to increase the availability of these bees and he says there are now a million blue orchards pollinating crops in California.

The reason these bees are considered the best potential honeybee stand-ins, Cane says, is that unlike some specialist native species, blue orchard bees, like honeybees, can pollinate a variety of crops—including almonds, peaches, plums, cherries, apples and others.

In just about every other respect, however, these bees are totally unlike their European brethren. For one, they tend to live alone. In the wild, rather than hives, they inhabit boreholes drilled by beetles into the trunks and branches of dead trees. When cultivated, they will happily occupy holes drilled into lumber or even Styrofoam blocks.

The blue orchard bees also do not produce honey, rarely sting and, owing to their solitary nature, do not swarm. They are incredibly efficient pollinators of many tree fruit crops—on a typical acre, 2,000 blue orchard bees can do the work of more than 100,000 honeybees. Their biggest drawback is that beekeepers can only increase their populations by a factor of three to eight each year. (Honey bees can grow from a small colony consisting of a queen and a few dozen workers to a population of 20,000 foragers in a few months.)

"We're still in the development stage of applying all the research that has been done" by USDA's Agricultural Research Service, says David Moreland, CEO of AgPollen, the world’s leading producer of blue orchard bees for the California almond industry.

Of the nearly 700,000 acres (285,000 hectares) of almonds cultivated in California this growing season, as many as 300 acres (120 hectares) were pollinated by blue orchards, according to Moreland. Growers' inspiration for trying the new pollinator is simple economics—last season they were paying up to $300 to rent a single hive of honeybees, 10 times what they paid a decade ago. This trend has made blue orchard bees cost-competitive with honeybees, but only barely.

"It's not clear we can [raise blue orchard bees on a commercial scale] in a cost-effective way," says Karen Strickler, an entomologist at the University of Idaho from 1993-2000 who has worked with solitary bees and who currently distributes them to beekeepers and hobbyists through the bee dealership PollinatorParadise.com, located in New Mexico.

Another solitary bee, known as the leaf-cutter, is the success story on which scientists and beekeepers hope to model the trajectory of the blue orchard bee.

"Ninety percent of all alfalfa seed in the U.S. is grown using the alfalfa leaf-cutter bee for pollination," Moreland says. "That's huge—that's an industry that over the past 25 years went from zero to the preferred bee. So there's a model there that says: 'This has happened before, it can happen again.'"

Cane, described by his peers as one of the world experts on orchard bees, cautions that these bees currently can only supplement—and not supplant—honeybees.

"The sheer number of bees you would need—at least 500 per acre (0.4 hectare)—it will never replace honeybees," says Cane. "That's an outrageous number if you think about it."

AgPollen's Moreland is more optimistic. "If we got to the point that we could not maintain populations [of honeybees]," he says, "this is one way to ensure that the largest dollar specialty crop in California for export—the almond—doesn't lose its pollinator."

2) STINGLESS BEES MUMMIFIED THE NASTY TRESPASSERS

Bees are under attack around the world. One of their nastiest foes: small hive beetles (Aethina tumida). Native to sub-Saharan Africa, these invaders can completely destroy the hives of common honeybees, which they have been pushing around throughout the U.S. and Australia.

"When [small hive beetles] invade a colony, their larval feeding and the spoilage that ensues converts the comb and honey into this lavalike substance. They make an incredible mess out of the comb and [bee] brood and everything else," says James Cane, an entomologist at the U.S. Department of Agriculture's (USDA) Pollinating Insect Biology, Management and Systematics Research Unit at Utah State University in Logan.

For a time, scientists were concerned that the parasite might also threaten Australia's native stingless bees (Trigona carbonaria), but it turns out these critters are made of tougher stuff than their European honeybee cousins.

Researchers recently discovered that although they lack stingers, these bees are pros at immobilizing interlopers. Mark Greco and Peter Neumann, entomologists at the Swiss Bee Research Center in Bern, discovered that as soon as the beetles enter a hive, worker bees in the colony surround them and force them to immediately pull their legs under their carapaces, adopting what is known as the "turtle" protective posture. This stance employs the beetles' hard shells to shield them from attack, but it also prevents them from moving. Worker bees take advantage of this, gluing the immobile beetles to the walls of the hive with resin collected from plants; they then "mummify" their captives with a substance called batumen, a mix of plant resins, wax and mud.

View photos of Mummifying Bees

Greco says he and Neumann call the process mummification because "the beetles remain incapable of moving, and therefore die."

Honeybees exhibit a similar behavior, called social isolation, but it is significantly less effective against the small hive beetle. To isolate the invaders, honeybees construct small chambers around the beetles, but do not seal them off completely. Instead worker bees guard the entrances of these chambers, which often allows the beetles enough time to mate and produce their hive-trashing larvae. In contrast, the stingless bees' mummification process takes a total of 10 minutes from start to finish, at which point the beetle is completely immobilized and starves to death without any further attention from the members of the hive.

The researchers discovered this rapid mummification behavior by taking high-resolution digital x-rays of entire hives with medical computed tomography (CT) scanners, a new twist on an old procedure known as radioentomology.

"It is really kind of a novel approach," says Jeff Pettis, research leader at the USDA's Bee Research Laboratory in Beltsville, Md. "You can get at some biological questions that you can't get at otherwise."

Greco and Neumann report in Nature Precedings that they were able to witness the entire battle between the bees and beetles play out in high-resolution 3-D by using a "micro CT" scanner that took snapshots of a stingless bee hive every five minutes for an hour and a half.

Even though the study was published on a prepress service, which means it has yet to be peer-reviewed, other experts in the field praised the authors' methodology and findings.

"It's a really clever way to keep track of what's in the colony without having to take apart the colony," says Christina Grozinger, an associate professor of entomology at Pennsylvania Sate University in University Park.

Ultimately, this research may help Australian growers reduce their dependence on the relatively vulnerable European honeybee. It turns out that stingless bees are better than honeybees at pollinating peppers, a commercially important crop in Australia.

"We place manufactured beehives containing colonies of these bees in the greenhouses," Greco says, "and the bees pollinate the vegetables without stinging the workers."

3) BEE FLIGHT SOLVED

In the 1930s French scientists determined that bees could not fly. They knew, of course, that the insects could and did. But according to their calculations, this feat was aerodynamically impossible. They based that conclusion on the fact that wings as small as a bee's could not possibly produce enough lift to allow the bee to get airborne. The problem was, they presumed that the bee's wings were stable, like an airplane's, when in fact honeybees flap and rotate their wings 240 times a second. This flapping, along with the supple nature of the wings themselves, allows a bee--or any flying insect, for that matter--to create a vortex that lifts it into the air. But the specific aerodynamic mechanics of that process as it pertains to the honeybee, with its stubby wings, has remained a mystery until now.

New research from Michael Dickinson of the California Institute of Technology and his colleagues finally explains how Apis mellifera flies. Unlike other flying insects, honeybees use short wing strokes of less than 90 degrees and a high number of flaps every second to stay aloft. The researchers found that when challenged to fly in difficult conditions, such as a mixture of oxygen and helium that mimicked air density at more than five miles up in the atmosphere, the bees resorted to wider strokes but maintained the same high flapping frequency.

This means that honeybees are using a wing stroke pattern that is less efficient than the broader strokes and slower flapping of fruit flies and other insects, despite their constant foraging for food and other necessities. But it also means that a bee can generate more lift when it needs to--when it must carry a heavy load, for example. The researchers speculate that this odd set of strokes may have arisen from precisely this need, as the social creatures sometimes must fly while burdened with nectar or larvae. A report detailing the new findings is being published online this week by the Proceedings of the National Academy of Sciences.

Running Thoughts Running Away

2009-03-19T23:54:00.002+08:00

School holidays and I am sure it is as hectic for me as it is for the students although I am sure all of us are grateful for that extra sleep-in periods - at least I am although sleep does not come as easily because it always takes a while to adjust and I am quite tensed up with work - all the backlog due to lectures (H1,H2 and H3 all in 3 weeks)..yet before you know it, hols is over :P

So I did the Nervous System this year..... I remembered the frustration my last batch of kids felt when faced with this topic so I decided to volunteer myself for this topic this year and really try to work it out, simplifying yet retaining the beauty of it. It has always been one of my fav topics and it was a challenge. But I hope that I have done this topic justice and that I had delivered the punchlines during lectures. Part of me also felt a bit stressed because I heard one of us was pretty good and funny at delivering this lecture series but I looked at myself and decided that I am just not that funny. I guessed as a matter of personal preference I like power-packed information bytes. mm... At least my boss thought the last lecture was decent =P and hopefully the students too.
Just cleared the tutorials. Whoosh.

------

Some of the Bs have shown improvements and an attitude to back them up. I am actually quite glad for them.
Let's hope that we can go from strength to strength and make it all worthwhile.

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There is something wrong with me.
I am having problems with my eyes-hand-thought coordination - tying wrong stuff or unable to type coherently - so i have to do a double check.
There are also issues with my speech recently. Seemed like I am starting to have trouble verbalising my thoughts as well as i used to. Not that it was that great in the first place but now it is a bit awkward. Maybe it is all those kiddy talk I uses with my niece.
Or maybe i am suffering from some slow-acting disease...

Answers

2009-03-16T09:14:00.005+08:00

Chi-Square

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For Bemedial students:
MCQs:M&M (just in case i did not give the answers/ esp for late hand-in-er)

MCQs:Bacteria

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And all the time we talked about the complex signaling in eu. Perhaps this is a good one for cell proliferation and I used to study components of it. .

MCQs update

2009-02-25T12:00:00.002+08:00

So I was right even tho my frame of mind is not.

From notes:
1) It is not telomeric DNA per se, but rather the association of an ensemble of proteins with telomeric DNA, that is essential for the formation of a protective cap structure. In human cells, a central component of the end-capping structure is the telomeric double-stranded DNA binding protein TRF2.

TRF2 is actually an important protein for this capping structure alto we did not talk much about it

2) Does Satelite DNA have high incidence of AT sequences?
There must be something unique about satelite DNA to make it stand out (a separate band from the rest of the genome).
Satelite DNA can have AT-rich sequences or GC-rich sequences, depending on the basic unit of a tandem repeat.

they just dun get it

2009-02-22T22:56:00.003+08:00

Sometimes or many times, we dun get what we want.
I know because I used to fight for my rights and my vindication, and defeats came crashing by.
I remembered it as a difficult taste to swallow each time when you tried and tried yet there are things that you cannot overcome.
But in retrospect, it is all part of growing up. it reminded us not to give up and keep on trying becos there is always hope for the opportunity. I guess that will be the lesson I want my kids to learn when i refused to buckle and give them the extra credits even tho i sympathised, to be fair to others . they are probably cursing and swearing behind my back because i dun think they see the way i do
so me too, am learning that some lessons are just harder to deliver for I felt the strain on the relationship.

I think I am just trying too hard sometimes. trying to deliver opportunities to them, offering them choices, for things that I never get to do in my time Perhaps I will just let it be. For it will be easier.

hospice

2009-02-18T20:27:00.002+08:00

Visited my fren's mum this afternoon after hearing news that she has taken a turn for the worse last night.
battling colon cancer for 3 years, she has almost reached the end of the road as my fren and his sister stay vigilant by her side.
But what caught me off-guard was how different auntie looked.
she looked nothing like the lady I once knew when I visited my fren in the past (since sec sch)
She now looks like any other patients, bedridden, sunken and shriveled - a lost page in my memory.

Bringing tea for my friend and her sister, I eventually bade farewell to auntie,
Lost to the world in that morphine-induced bliss.

AFter tutorial clarifications

2009-02-04T21:06:00.003+08:00

Just to recap and consolidate:

Hayflick limit : cell division limit =
critical length of the telomeres we have been talking about.

This is in response to GY's question: when you reach the critical length of telomeres and enter a state of cell senescence, do you also undergo apoptosis? (good one!)

When telomeres of cells reach Hayflick limit/critical lengths, it enters cellular/replicative senescence (an inability to divide) or apoptosis.

Senescence and Apoptosis are different situations and either case will take place depending on cellular conditions.

Questions of the Week

2009-02-01T15:20:00.001+08:00

Contributed by ST:

> 1) are enhancers and silencers found within or between genes?

Both are be found anywhere- in non-coding regions (betw genes) or within genes (in the introns) But we recognise that enhancers are distal elements (pretty far away from the promoter). Little is said about silencers so we gather that they do not have to be distal.

> 2) when saying that the transposable elements are repetitive DNA, does it mean that they are a long string of repeated nucleotides, e.g. CAGCAGCAGCAG or is it because there are multiple copies of transposons scattered throughout the genome (due to the copy and paste mechanism of retrotransposons) ?

Thanks for clarifying this! I noticed this while checking the notes and wanted to point this out!
Transposons does not have tandem repeat. Its basic characteristic is in its ability to jump! The notes could be clearer: the "repetitive" part is really about the many copies that can exist due to the copy and paste mechanisms of retrotransposons which so very common in us. So you are right!

> 3) "Telomeres do not exist as a free end, but as a loop - formed when the 3' single-stranded ends DISPLACES the same sequence in an upstream region of the telomere, causing a single-stranded region to form." I don't really get the bolded parts.

The 3'OH overhang will displace an identical sequences upstream (of ssDNA 1) to form complementary base-pairing with the other DNA strand (ssDNA2). The displaced single-stranded DNA (ssDNA) which of the same sequences as the 3'OH overhang is now left hanging like a hump-like structure you see in your notes because it has no one to base-pair with.

> 4) what is the relationship/difference between gene amplification and gene duplication?

gene amplification usually imply multiple copies (more than 2).
gene duplication is only 2 copies.

But that being said, this is however not necessarily true in the case of cancer study where gene duplication is already considered as gene amplification since an extra copy of the gene is usually sufficient to wreak havoc in your cells.

So check the context although it is usually not an issue

> 5) How does the development of tumours support natural selection? Why do cancer cells have better growth advantage?

the growth advantage comes with mutations (that can benefit of cos!).
With accumulated mutations (that can only exist because the cells do not die readily as seen in tumor cells), some of these cells have been altered such that they are better at surviving e.g. use less resources to survive and are able to outcompete others and dominate.
This is natural selection at the molecular scale!

PSL

2009-01-31T19:48:00.003+08:00

I promised a student that I would throw with him today to sharpen his skills so I went down to school for training even though it wasnt my day of duty.
But the greatest take-away today was seeing the ex-sec1 students whom I used to mentor as a PSL in sec4. They have returned for their 10-year anniversary in RI. It was an incredible reunion for me and to see that they have grown so much even tho after a certain age, it really doesn't matter anymore..

Just couldnt resist taking a photo together :)

Polling!!

2009-01-31T14:02:00.002+08:00

I have set up a poll in preparation for my next set of lecture notes.
Not that I can promise that I will change since time is short but it will be helpful.
Typically, I plan the notes in a sequential manner of events to build a story. But then the story is in my head so it may not translate well onto paper because the reader forms his/her own story.
We are all trying to make concise notes without the overload so it is good to hear from the readers =P

How does homologous recombination work?

2009-01-30T22:48:00.002+08:00

Today in class, we have talked alot about crossing over at homologous regions.
so what is really happening during crossing over at the molecular level?

It will be easier if you can look at these :)
It involves nicking, crossing over to form a heteroduplex and subsequently the cleaving at the Holliday junction

(quite cute)

Just a can of abalone

2009-01-25T22:47:00.002+08:00

There is an ongoing drama series on Channel 8 about reunion dinner. In one of the scene, the old man brought out several cans of abalone, each depicting a year of non-attendance by his children, while his dead wife sit in front of the TV.
That scene brought tears to my eyes. Not because of the dead wife but the cans of abalone.

I wondered how many of my ex-students remembered the story about my Uni friend who came from a poor family in Negri Sembilan. He was here on a scholarship but the scholarship barely covered his Uni fees and when he first came here, he had to find alternative sources of income to see him through daily needs.
Then there came a point in time when he was left with only $2 in his pocket and he had to make the choice of saving it or having a meal. In the end he was so hungry, he bought the food.

After graduation from Uni, there was one night on the eve CNY when I received a surprise call from him. He was calling from the train and he told me in his excited tone that on his lap was a can of abalone that he bought with his salary and he was bringing it to celebrate CNY with his family.
A can of abalone.
Some of us never thought more of a can of abalone.

PS: suddenly I realised that I may have mentioned this before. But nevertheless, I am reminded every CNY when there is abalone on TV

Low Frequency

2009-01-25T13:37:00.002+08:00

Happy CNY everyone!!!

Rabbit said that I don't update this site very often.
How very true. I hope this new template will encourage me because the previous one was a little intense for me. But also because I don't hear that many questions in class these days. Is that a good sign?
Otherwise it is because I am too lazy to type my thoughts out because it will usually takes me hours. How do pple find time to do so? Amazing. Maybe my typo speed is just too horrendously slow compare to the youngster. Arthritis, ouch ouch. =P

Resolution
A new year resolution will be to have a clean bill of health and get rid of the accumulated fats from the sedentary lifestyle & stress I endured in the past years as I approached a new decade this year. For that I really need to better manage my time and I have done so quite well thus far because I decided that there is nothing to gain by worrying and have started to focus more and work with greater efficiency with my decision to procrastinate less and not getting distracted by the internet.
I have also started to sleep earlier and wake up earlier so that my organs would have more rest and of course the exercising! I am proud that I have persevered in my efforts to keep up with my running regimen although I have little love for it in the first place. Now running has become a little addictive and easier. Except that I probably have to watch my left knee.
- I think all this come with the realisation that my metabolism has dropped and a change of lifestyle is needed in order to keep fit and healthy in this occupation and may be some readjustment in my priorities in life so that I can hopefully do more for others. Oh and yes, I can fit into my clothes better =).

But...when will work overwhelm me? Hopefully not.

Another decade. I think I am only one among my friends who is happy about it hahaha but really, is there a reason to be sad since the passing of time is always inevitable? Anyway I am planning a retreat for my batchmates this year and hopefully it takes the edge off from others :P

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Revisiting Bacteria Again

2009-01-25T10:22:00.004+08:00

1) Do you always leave a portion of the phage genome behind in specialised transduction?
The answer is YES.
It is pretty inevitable because for specialised transduction to take place, there is incorrect excision (such an event is actually quite rare!) and we called the subsequent resultant a "defective phage" because it does not contain all its viral genetic material anymore.
The part of viral genome left behind (and hence part of the bacterial genome removed) can be from either ends of the prophage.

[The next question that comes to mind will be "is it possible to have an incorrect excision such that the viral capsid and sheath does not form because their genes are not excised out?" Theoretically possible but what is the point if there is no transducing phage form? Since there won't be any genetic transfer, it is therefore of no interest to us - similarly if there isn't any intact bacterial gene. What scientists want to determine is really if there is genetic transfer to bring about variation in a particular species of bacteria. This is all about evolution.]

I realised that I have answered some of these questions before so I am refering you to:
http://chansensei.blogspot.com/2006/09/how-plasmidvirus-integrate-into.html

I would like to point out a couple of interesting notes in the last picture to you, showing integration and correct/incorrect excision of plasmid:
1) integration is a single crossing over event at the att site (att-attachment)
- result: you should appreciate where the genetic markers (a,b,c) are before and after integration

2) bonus question: does only recombination occur for specialised transduction?
- answer: NO but recombination is the most common. the other possible is shown in the diagram and explain below: (not impt though)

[Question: Does the truncated viral DNA injected by the defective phage into the host bacteria behave like a typical phage DNA? The behaviour of that piece of DNA really depends on the viral genes that have been removed upon incorrect excision e.g. if the gene for proteins needed for integration is removed, the DNA will not be integrated into the bacterial chromosome OR (from bonus question) if the defective phage infects a bacteria that has been earlier infected by a normal phage (now serves as a helper phage) and the truncated viral DNA integrates into the bacteria chromosome (you get a double lysogen!) - any missing genes can be expressed by the intact DNA of the normal phage.]
http://books.google.com/books?id=3E_0H6dEvfQC&pg=PA386&lpg=PA386&dq=phage+helper+specialized+transduction&source=bl&ots=tpe0i6OXar&sig=tQFGjX3FUvMX0TfNWJHFCi4jHlQ&hl=en&sa=X&oi=book_result&resnum=6&ct=result

So we shall end our discussion here, leaving it to you, if you are interested, to find out about specific example. Lambda phage is the most common example.
But the DNA should circularize as per normal and we do expect the phenotype of the bacteria to change due to the genetic transfer.

2) Why some plasmid integrated into the bacterial chromosome to form Hfr?

There is no particular reason except for the fact that these plasmid contain a IS (insertion sequence) element and there is a homologous copy on the bacterial chromosome. Different Hfr strains have the plasmid inserted at different locations and at either orientation.

IS sequences, like transposons, are mobile elements so there is no fixed location where it can be found on the bacterical chromosomes. They may even be found in transposons.
http://en.wikipedia.org/wiki/Insertion_sequence

The plasmid can actually exist independently or be integrated so it can be referred to as an episome.
The integrated plasmid is only about 2% of the bacterial chromosome.

Diagram showing that the sex pilus is a separate entity from the mating bridge

Taking a break

2008-12-16T20:53:00.004+08:00

I thought I should update this blog since I have already sent out the instructions for the hols homework and finished marking all the submitted tutorials =)....

The unexpected political instability in Thailand brought waves of concerns and headaches in the management of airtickets, lodging and transport for the softball competition in Chiang Mai at the end of the year. Although, like my teams, I was keen to head down to the northern territory to visit friends from my YEP project last year, I felt the relief when the school decided to cancel the trip for safety reasons because there were too many uncertainties and I was troubled daily in trying to monitor the development and to make appropriate arrangement.

But still I did have a great holiday with my friends in Bali just last week, coming back with a good tan and glow, although the cloudy weather in Singapore promised it to be a short-lived phenomenon. =)
I brought my parents out in the last 2 hols but this time, I was glad to be able to enjoy the company of my friends again because there are something that you just wouldnt do with your parents - we went whitewater rafting on day 1, negotiating the bends and passing through waterfalls for more than an hour. A level 4 experience and it was great fun and a great drop towards the end! =)
The very next day was survived on minimum sleep as we woke up at 2am to travel and climb a volcano in the dark for more than an hour in order to see the sunrise. It was quite an exercise, firming the butts and challenging our balancing skills and I must concur that wearing sandals was definitely not the way to go. But still we made it in time to be rewarded with a glorious sunrise and monkeys who tried to snatch my breakfast! At the top, we could see the devastation made by the last eruption and how the lava cut through the land mass. Lying dormant now, the land is still hot enough to cook eggs buried within.And for the rest of the day, we were just wiped out. =P
One more day in Bali and two of us chose to take on the waves and learn how to surf. It was a dream fulfilled for me because it was a sports I had always wanted to do after reading the "The Three Investigators" when I was young because the protagonists live by a beach in California and will surf occasionally.=) 2.5 hours of surfing and it was a tiring affair! - not the actual wave-catching but to go against the waves after each attempt in order to get to the spot where the waves usually break. My tummy muscles and deltoids were sore for 3 days...But it was fun! And I was not too bad because I got the hang of it after about an hour to manage 3 consecutive nice maneuvers for a beginner. =)
But I also managed to bruise a rib while scrambling up the board in order to catch a good wave, making it painful to continue with my exercise regimen in the holidays now. =P - the perfect excuse :)
And for the last three days, we spent them in Lombok, an island close to Bali where we just unwound and devoured the books we brought in an idyllic setting. A peaceful retreat from the outside world....especially good for some cheem read.

Back to school again for CCA...feeling fresh and fit for now :)

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Now playing: Track 17
via FoxyTunes

When Weddings Become a Great Reunion

2008-11-27T10:53:00.002+08:00

H-3 lectures finished last week and I can finally checked that off my list of to-dos and try to clear work for the year so that I may have a peace of mind when I go for hols
The tense situation in Bangkok brought new worries for the Softball Chiang Mai trip which I already have much trouble with - I have been to Changi Ap 4 times to sort out ticketing issues, trying to get EduS $ from the secondary schools, trying to get hold of my personal contacts in Chiang Mai so that the kids will pay less. Sometimes I think I work too hard on this - I should have throw it to the agency to settle everything for me but then the idealist me rather choose to take the alternative route so that 1) kids will pay less and 2) give work and money to the Thai locals who are having difficulties themselves. I have worked with a Thai translator during my YEP trip last year and the last time when we communicated, the orphanage he was managing was facing a shortage of food and children falling sick. So I was hoping to use this trip to do some purchases for him and orphans.
I guess everything will hinge on the political climate in Thailand.

Anyway that aside, it was ringing wedding bells all over town.
On Saturday & Sunday, it was the wedding of my primary school classmate (she had it over 2 days). With the bride and all those around my table, it was 20 years of friendship and for some of us, even longer.
This group of friends are very special to me, even though I would usually be pretty reticent among them (it is difficult when they start to talk about marriages and diapers). But I appreciated their presence for that shared history and also, they always bring with them a very different perspective of life with their struggles which are often very different from my sec/jc classmates. Life has never been a bed of roses for some of them and very often they remind me how fortunate I am and also that the environment we are so comfortable in school is only a mere fraction of the world out there. I think that is why I want my students to go out there and touch the world beyond their immediate surroundings. As a school who supposedly produces leaders, how do you even lead when you do not know the nature of the majority of your population. If you decide that everyone in school is different enough, think again. Which brought us the question of the Community work we are doing - how much do we know about the client we are serving? Do we know their stories?
Bearing this thought, I am also concerned with the young leaders of these days whether they are lacking the 'person' touch while they run plans with great efficiency as one of my frens divulged after working in the gr-roots for a few years.
Don't keep your feets grounded but your heart as well.

The bride and I lived a few blocks apart and when I told my mum that I will be attending her wedding, she exclaimed 'oh, the one whom you always go to the bookshop with to buy things!'. So many years already and the funny things pple remember. And that's right, both of us used to pool our pocket money together to buy comics like doraemon, dragonball and professor IQ. But she got the better half of the deal because the dragonball books are with her hahah.

And on the funny things pple remember, another cupid had his arrow on my softball mate on Mon and I was seated with his secondary 2 classmates. It was particularly amusing when I realised that I know everyone around the table even though they were from a different class. There was TL, the guy you see on TV for Chinese cri**watch and we used to act in a Chinese drama together, there were JS and T who became my JC classmates, AM - a bigshot these days (apparently) and my JC OG mate, KG whom I have been working with recently and N who, for some reason, I can still remember his name. A lively bunch of pple and all of them single haahah.
But what was equally amusing was when KG remembered funny little facts about me like how I also used to be a 400m runner. No one remembered which race I preferred but in those days to do a full round under a min was pretty rare. Actually, come to think about it, I think I am more notorious than I chose to believe. hahah. Perhaps.
Then again, you realised the different profiles this group of frens held compared to the dinner the day before.

I must admit that after next year, I will be the only single among this group of friends

REthink ReExamine

2008-11-02T00:40:00.002+08:00

I went through a series of tests on Friday, staying awake and alert for 6 hours and that is no easy feat. In fact I should rest soon because my vision has been a bit blurred lately - an indication that my eyeballs are really weary enough. But rest will have to wait while I cleared the impending things on my checklist.

Anyway, I just want to say that - Give a smile and tell your tale because you WANT pple to understand and hear your side of the story. That is presentation. I think some of us see the TV newscaster with firm face and the stiffness that comes with the imagined freshly pressed jacket as the ideal model but presentation style can be driven by personality. I like to keep my hands free for gesturing because i find that by gesturing, I am less nervous and I don't have to keep a conscious effort to place my hands in a fixed position since I am usually quite excitable. There is no fixed way to tell a tale but all of us always love someone who is comfortable (think oprah) and hear that WANT in his voice.
I think I used to be super conscious with how I say things or my body language etc becos I hated to stand in front of everyone and make some noises. To a certain extent, I still do but it usually goes away when I WANT to make point or tell a tale.
Just like a sales person. you cannot sell if you dont know your product. When you know your product and want to share about it, talking about it is not the problem anymore.

Yet, sometimes we get complacent because we think everything is in the instruction manual of the product. But who is reading that thick manual? What the sales person say, he/she has to justify and be able to anticipate questions. The best sales persons is prepared for all possible questions and still convinced you.
To me, presentation and the thesis I handed up are two separate things. I always made a deliberate effort to make my slides coherent and be able to justify or comment on the points I have in my slides so that I can defend my thesis. I think a lot of pple forget that and got a little complacent. It may not be able whether you know it or not but whether you have prepared it or not.

Be that sales person who knows your own product which you have designed and toiled over. For those efforts, you want to tell a tale so be confident and speak with that passion. Dun wear that jacket if it does not suit you.

You have a story to tell so do tell.

Wrapping The Year

2008-11-01T23:46:00.002+08:00

The academic year has more or less closed.
The sadness & the joys were passing clouds that once marked our days.
There were many times when I wished I was better at talking to give reassurances or better advices. But I learned.
There were times when I wished a lecture or tutorial could be better conducted. But I learned - and I think this year's pro and eu is much better than the 1st series which I also lectured and prepared the notes for. More coherence and beauty.
There were times when I felt happy at a job well-done or friends made. I cherished those moments but they were gone too.

It has been an interesting year and I am thankful to my classes B & L for the learning journeys as well as my colleagues who supported me in many ways and once again tolerated my sonic laughter which threatened to bring the whole staff room down.

For the L's, I guessed I did not know I was in the company of two cows, paper, penguin, duckie, tape recorder, mirrors, sea cucumber, cat and seedless grapes to name a few. But whatever we are, we all can eat pizza haha. And I saw the posing power of the girls.

For B's, they were a great bunch too but next year I won't be having some of them in my classes anymore. For that Chang-Er who is flying away, all the best. For the those who needs the extra year, stay focused and keep working, and I hope that you had learnt something from me in this one year and found your footing in life. For the rest, dun drift away. There is still time but you need to focus and learn from mistakes. Haiz... din manage to take a pic with all on the last day.

FOr both classes: the most intriguing part of life and the lesson we really want to impart is not taking on the smoothest paths but to have the readiness to pick up after each fall and to learn from each experience.
And I recalled a comment made in class some time back about making ourselves stand out among the crowd and do something worthy....I went back and thought about it and realised what I really want to say is, I hoped you will challenge yourself to do and experience new things or things you think you want to try or do. Because experiences will allow you to discover yourself and maybe even a passion that you can identify with in life. I don't need my students to stand out but I want them to stand tall.

Ok.. it is back to H3 preparation.

Who & What R U?

2008-10-18T21:13:00.002+08:00

It has been many years since my last MBTI test and there has been changes since then. I supposed it is just part of growing up but what's good this time is having facilitators to explain each component of the letter so now I know that I am a justified I even though my boss looked at me in disbelief. If I have elaborate on my hibernating mode, it would be detaching myself from this highly-connected world. They said that internet, handphones and air flight brought all of us closer together and because it is true, I used to switch off my handphone, stay off the internet and live life as it has once been for 2 wks to a month. Sometimes I gave in to temptation and check my emails and smses in case of any emergency...mmmm that was before I started teaching. Now opportunities are limited. So sometimes, all I am asking for is a chance to recharge.
It made me realise why I was so super grumpy during the retreat the other day because I was working super hard the days before, reviewing the scripts of my students so that I may hopefully pull any on the borderline up, clearing my lecture notes so that it can be printed on time while sitting through indecisive and frustrating meetings. Not forgetting that I was struggling to mark in the week before. SO all i wanted during the retreat, when things supposed to wind down, is a good rest and nothing else. So I think I struggled through the activities and when it was finally over, I bought myself a iced cafe mocha from Starbucks and sit on the steps of marina square alone to chill. mmm..before the test, it never did occur to me that I NEED such time and that it was a way some of us recharge.
I think the test also reminded me how people around me works and why certain things are the way they are and why certain issues take forever to be resolved. Sometimes, we have to let go of ourselves more readily.

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I walked past a restaurant just now with it being one of the many along a stretch of road. It was dinner time and the only difference was that there was not a single customer in sight.
老板用手掩着脸面，独自在萧索的餐厅里秉承犀利的沉静。伫立在门外的我彷佛听到他无声的呐喊。说实在的，这餐厅当年还真蛮不错的。但不知从何时开始食物就每日况下，吃了一次你就没有理由再回返了。是惋惜还是无奈促使我停下步伐呢？
当我回头再度经过时，就有一位顾客坐了下来。。是可悲还是可喜呢？

Postcard from G

2008-10-04T21:34:00.003+08:00

It has been such a while since I left my footprint on this page. So many things have happened and so many thoughts have went by. But then it was a bit difficult when served with a last-minute notice to prepare for a series of upcoming lectures so I had to hide in this little corner in btw bio and chinese, isolated from the possibly distracting activities in the staff, to really work out this new set of notes because the topic is just so new. The information was really overwhelming but I guess that was always the challenge - how to simplify things such that it is readable but still retains its essence. I haven't perfected it but I have read and understand enough to give it my own point of view - so in that sense it is better than I first did it. =) But the verdict is still out there waiting to be passed.
Then it was the marking which I started real late like after everyone else has more or less finished (because of the notes)- but it was the plan. I wanted to do it while everyone is marking so that when they are done, I can take over readily and they can vet my notes for clarity and feel. But still, I got a little frustrated with my progress and thus stressed until I told myself - hey I should not aim to finish it in one shot but spread it out so that I can have time for other things like catching up with some impt frens, settled my j2 cca records, go for gathering. Isn't that I used to manage things? Sometimes we just forget how we are used to be like.
With that, I was also inspired by a student who exclaimed that running was totally endorphins-inducing and so I finally picked up my shoes and started running again- something which I have forgotten to do for a very long time. And it was devastating because then I realised how truly in denial I am in for my own fitness level and also how much I have grown into for the past 2 years. I can only say that the run to MacRitchie was purging - of all that cholestrol that is choking up my arteries so that I may get back my breathing rhythm back and figure how just how much of my muscles has dystrophied so that I can make realistic adjustment. Yup - no longer am I the 'flash' as I once was but a messy mass which seriously need to get back in shape. But I must say that run to macRitchie was beautiful with the evening sun reflecting off the water and the feel of nature - amid my endless gaspings of course. I do feel good afterall. I did a run in school in the morning today when I went to return some scripts -i felt better this time for I think I am accustomising to the routine pacing. I decided that I would get back in shape before my next birthday. maybe even clock a decent timing for sprints. mmm...perhaps for the 2nd thought =P.

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Finished marking today. My heart always raced when I marked my own classes (and I meant it) because I think it is not only an assessment for the students but for the teacher as well. from the scripts I think - did they understand what I meant in class, did they catch those pitfalls I always emphasizes. And it showed.
I am not sure if students realised but these days I never really go through the tutorials or at least it is never entirely about the tutorials and their answers - there isn't much of a point if I have marked the scripts and answers will be given yah? with experience and me being so rather anal about things, tutorial is the time I will spend on emphasizing the pitfalls that students tend to find themselves in, the types of questions a topic can come up with but we did not have the chances to delve into. I think it paid off - if the students have listened - because almost everyone in one class managed to secure certain marks but quite a number from another class which is more easily distracted had difficulty with, but then so did many others in the cohort. Still I felt sad for the latter because I know that they were working so hard for all their subjects during the last stretch and it is easy to see why they falter at the end...Funnily, it was my other class that confirmed the results because it was those who did not turn up for the last few lessons suffered from my red slashing while those who came dutifully put down the appropriate phrasing which is really standard.

I suddenly recalled a remark made by a student of mine: Sir, I have really studied but I just don't what to write during the exams... (to the effect). then I got to know that one of my kids gave up on the essay. These are the times when you feel very sad and vindictive: why why why?! then you melt because sometimes when we want something so badly we do blank out as an insurmountable sense of fear set in. I have been through it before and it takes huge amount of courage to find it in yourself to let go of the expectation you decided to place on yourself but just go and give it your best shot...fight, and fight it with some arrogance and belief.

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Frens

2postcards from Greece arrived in my mailbox the other day. so coincidental but very heartwarming.
One was from my niece who has quitted her job and is now lounging around, taking a well-deserved break. she noted that this is, for a while already, a trip without me. mmm... she has forgotten that she went to germany and austria without me some time ago! But at least she sent me a postcard =P, writing to me from Mykonos which is an island I did not have the leisure of time to go when I was there in Greece on my first ever backpacking trip 5 years back. For me it was the most amazing trip because it alternates so often between bliss and despair.

But the most heartwarming postcard is from CP who was on his honeymoon. CP and I go a long way back from sec school and being frens for so long, you just know the temperament of the person. Like I know exactly how he would respond to situations and how he would not bother to get his hair professionally cut for his wedding and how he could not be bother with the details of the banquet which in the end I settled for him so that it ran without a glitch . But I guess he also knows me well enough to arrow me to be the coordinator.
I guess friendship is something you built upon over the years gradually, bit by bit with sincerity and love. 1 -2 years down the road when I got busy with work and he with love, the bond remains and when the news of his wedding came a month before the actual event, I was pleasantly surprised but readily agreed to help him out.
I remembered his current wife (the then-gf )got a little jealous of us while we were on a japan backpacking trip because,as we havent met up for quite a while before the trip, we took time to catch up on the train to kyoto...and mm...he neglected her for a while. =P
Anyway, I thought it was awesome to be remembered to warrant a postcard while he is on honeymoon. =)

2008-09-21T21:02:00.000+08:00

As U race to the starting line.... Good Luck!!

A Few Updates B4 the Dash

2008-09-17T18:36:00.006+08:00

PHOTOSYNTHESIS/RESPIRATION

1) Chemiosmosis VS Photophosphorylation

The meaning of the two terms can be derived from the words themselves.

Chemiosmosis refers simply to the movement of H+ ions i.e. pump across the membrane when electrons move along the ETC to release energy for activity. The electrons then diffuse back across the membrane through the hydrophilic pore of the ATPase with a release of energy that is coupled to the synthesis of ATP.

(where H+ moves from and to depends on the topic)

Photophosphorylation: how light energy is used to phosphorylate ADP to make ATP or how light energy is converted to chemical energy.

This would cover the many events from PSII to PS I and how ATP is eventually synthesized. Thus, chemiosmosis plays a part in photophorylation but here we are concerned with the process of synthesis of ATP. Chemiosmosis is just about H+ movement -reference to ATP is minor but usually we include it in brief.

2) ATPase? ATP synthetase? ATP synthase?

It is ATPase or ATP synthase.

In DNA genomics we have aminoacyl-tRNA synthetase!

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M & M

3. In tutorial, there was a given answer (by me) comparing anaI and anaII: each chromosome in anaI is bound by spindle fibers from one pole while in anaII, each chromosomes is bound by spindle fibers from both poles

Amendment: This should be a difference in Metaphase not Anaphase. In anaphaseII, the 2 sister chromatids would have been separated so each chromosome is actually attached to spindle fibers from each poles...

2nd mark is: whether centromere has divided or not
3rd mark is: the sister chromatids are pulled together towards each pole in anaI but the sister chromatids are separated and pulled towards opp poles in anaII

4. Crossing over = physical exchange of equivalent portions of genetic material. It is NOT when one non-sister chromatid is on top of the other/overlap.

5. Chiasma must form first before crossing over can take place. (amendment to notes)

6.What is the middle lamella (cytokinesis/Plant)

Cell walls consist of 3 types of layers:

Middle lamella:This is the first layer formed during cell division. The middle part of cell wall that is made up of pectic compounds and protein and cements the cell walls of two adjoining cells together. Plants need this to give them stability and so that they can form plasmodesmata between the cells. It is the first layer which is deposited at the time of cytokinesis.

Primary wall: This is formed after the middle lamella and consists of a rigid skeleton of cellulose microfibrils embedded in a gel-like matrix composed of pectic compounds, hemicellulose, and glycoproteins.

Secondary wall: formed after cell enlargement is completed. The secondary wall is extremely rigid and provides compression strength. It is made of cellulose, hemicellulose and lignin. The secondary wall is often layered.

6a. Mitosis, mitotic cycle, cytokinesis? (Inspiration from Qn 25 of mcQs.)

1) the cell cycle is also known as the mitotic cycle. Thus it will include the Interphase as well as the M phase (M for mitotic/mitosis PHASE).

2) the mitosis PHASE, comprises of Mitosis (pro-meta-ana-telo-phase)+ Cytokinesis

so mitotic cycle, mitotic/mitosis phase and mitosis are different ideas.

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VIRUS

7. Can many prophages exist in a bacteria? (I forgot whether I have addressed this) - (ADDITIONAL)

Depends on the context.
Once a lambda phage enter a lysogenic cycle as prophage, there is superinfection http://en.wikipedia.org/wiki/Superinfection where the DNA of other lambda phages is rendered useless

However, if the bacteria get infected by another type of virus, it is possible to have different type of prophages in the cell because the immune mechanism/inihibitory mechanism of lambda phage may not work on other types of virus. =)

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Bacteria

MCQ test

Lecture Notes

8. what is an effector molecule?
(note that we are talking about effector MOLECULE. Effector in physio is different)

An effector is a molecule (originally referring to small molecules but now encompassing any regulatory molecule, includes proteins) that binds to a protein and thereby alters the activity of that protein. A modulator molecule binds to a regulatory site during allosteric modulation and allosterically modulates the shape of the protein.
(http://en.wikipedia.org/wiki/Effector_(biology))

Thus tryptophan and lactose are effectors because they binds to repressors(a protein) to alter its function/activity - Trp activates it while Lac inhibit it. cAMP is also an effector molecule.
(it is just that effectors may have specific names or reference like co-repressor. 'Effector molecule' is an umbrella term.)

9. What is a metabolite?

Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules.
(http://en.wikipedia.org/wiki/Metabolite)
Very general. Not to worry over.

Do We Have a Role to Play?

2008-09-06T21:41:00.002+08:00

Can heave a sigh of relief now.
I finally got out of the house to catch "the dark knight' on Wed. The last one was so good with the directing and acting that I wouldn't want to miss this before the curtains fall in the next few weeks. Crossing the road to buy a cup of cafe mocha from Starbucks, I met a schoolmate from R-I who is now a pilot and looking good still - a good thing really since we are all theoretically reaching the prime of our life..although some are less fortunate in the 'ageing gracefully' department. We made small talk and we agreed that half the world has seen the show. A simple conversation and it made me realise that watching movies has stopped becoming a priority in our lives. In the past the movie theatres were exciting destinations for us and for me, it was an intense 2-hr session of plot, wit and drama. Talking during show or eating popcorn was a no-no and for that 2-hr you just lose yourself to another exciting world. I started watching movies on my own when I was P5. After school on Friday which was early dismissal day, I would head down to TP library to devour books or watch a movie at either of the two theatres there. In the past, the ticket stubs comes in either pink/blue or yellow and there are even circle seats. using a waxy pencil, the ticket lady would write your seat number on the stub after crossing out the same number on her seating plan. you take the stub and hand it over to one of the old uncles at the doors very much like those in Lido.
you dun get carpeted floor or plush seat but theatres in those day are huge (imagine the existence of circle seat on another level), seats are wrapped with synthetic leather and creaked with resistance. once, I saw a cockroach scurrying away.those were the days....

As we grow older, our priorities in life do change and in the last decade, with the emergence of internet and interconnectivity of the world, there is a perceptible change in landscape and the playground. How much do we need the theatres when there are so many online streaming venues?
Yesterday I went for a course and we talked about the loads of information that can be found at one's fingertips. If information is so readily accessible (last time we can only rely on books) online, is there a place for the teachers? What are our roles? If knowledge is no longer as powerful as it once was, what is?
one of my friends struggled with the notion but I told him that there still so much to do other that the answers that we give to the kids. If we want to secure the grades, we can just push and demand. But as the speakers from yesterday said, classroom is a place where we impart not only knowledge but also skills. Skills that empower our kids to cope with life and to reality. Our education has merely provided us with a simple, direct path that we can walk upon but there are other smaller foot paths that we can also take only if we choose to stop to smell the roses and then to discover them.
If you ask me, it is not about the greatness they attained in their future but I hope that they will have a life well-lived with integrity and love.

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I was troubled for a long time now until a friend I met up recently reminded me that the world has changed much since we left school and we have grown older as well. With
that, it is natural and perfectly fine to lose that simple innocence in things around us. It doesn't have to make you a worse person than before but simply wiser/more knowledgable. But keep that innocence in relationship I said because it is that essence that makes the world a better place to live in.

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Will not write anymore for now. Was so stressed up with marking in the middle of the week that I couldn't sleep well for a few nights. There was a night I slept at 2am but only to wake up at 6am to continue marking because I was so worried that I couldnt finish marking before hols ends and there are so many other things to do. My parents got a bit worried because I wasn't in a good state. But I eventually completed yesterday so I shall cherish these moments of bliss and rest early. And perhaps contemplate about the many questions that came up.

All the best pple!

Question that could not be found in your tutorial

2008-09-01T22:27:00.001+08:00

Happy T Day

2008-09-01T21:06:00.004+08:00

The year went by so fast and we were already celebrating T-Day while I am still basking in last year's. It has been a while and I hope I am wiser and more capable in my delivery.

The celebration in hall was awesome in the ambiance although hiccups in the AV dept was unfortunately plentiful. As least the street dance went ahead nicely and I managed to record it as my CT rep did the groovy thing. muahaha.
But there was a poignant moment which brought tears that linger in the orbits for a while - when they showed a powerpoint on quotes about this profession. I do not know what others thought: typical or cheesy but the Emo-disturbance wasn't because I think I have done well for I still have so much more to learn but because I was reminded of the 2 teachers who put me on this path. Perhaps more than some others, I can truly appreciate the quotes. As usual for the past decade, I bought and put their fav Royce into their pigeonholes before heading to school on Fri morning. One of them msged me during our concert and her words reverberates in my heart for a long time because I know she was having issues with management within these few years: 'Happy T-day to you too! you are one of the reasons I can go on teaching.....'. We asked ourselves why we do what we do. I want to tell her that she is also one of the reasons I choose teaching.

There were many well-wishes. Quite a number came as a surprise like students from REACH and RC-LF because our interaction had been somewhat limited. And of cos, my SQL08 whose msgs brought back such wonderful memories. =)

And I must say I was really impressed with the surprises from L. Such creativity, thoughtfulness and good taste in music (someone has been watching too much korean drama?!). I saw the effort in coordinating, choreographing and writing notes when you could be doing tutorials :P. I am also very grateful to have all of you for the rest of your 2-yr journey.

PS: The video is quite addictive and I have to stop clicking on it :P. Definitely something I can show off to hahah.

B too. I know it was probably difficult to get everyone to write something down since there is a lack of consistency in class size and I appreciates the effort. And I know often we go beyond words. =)

D and the softballers. The latter's R-rated card really kept the bio dept entertained =P. The former tell me that I am doing something right for them since taking over them during this interim period.

Mmm...gotta stop or it will be difficult to end and I have to start marking =P.
Thank all who cross my paths and keep me going.

Have a good hols!

the critical and old heart

2008-08-27T21:45:00.003+08:00

A student msged me recently to seek advice on his career choice and he made two statements that surprised me:

Why did you ask me for advice on such matter?
1.Because sir, you looks young but have a old heart.

An awkward expression. I told this to my fellow teacher-mentor and she said, this boy do know you.

2. Sir, you are too harsh on yourself
And realised that it is true. he said after spending two weeks together in chiangmai for the overseas expedition, there are something that you just know.

Of Course I M Upset

2008-08-20T21:14:00.002+08:00

B was really distracted today and little pockets of conversation carried on regardless of whether it was tutorial or the so-called catching up. Few listened. The jet lag did not help and I have trouble sorting out the emotional mayhem within. Some said I looked upset and how can I not?

Just a few hours before lesson, I met a member of the SB team who asked if I have bought goodies for the team and it was then when it struck me that I have not. A little embarrassed but it also made me realise that it was because the team has never/yet to make me feel part of it. Often, I don't feel appreciated and I felt like I am just playing an administrative role, so the relationship becomes very stale. Ironically, I got along better with other CCAs --- it was disturbing that I would say hi to many kiddos in other CCAs (who greeted me) as I walked towards the field but only to meet with silence in my own CCA as some conveniently ignore me. Yet it wasn't like that 2 years back with my cricket and softball teams which I have really bonded well with. I do wonder if it is because I demand too much from them this time?
I always tell the C-CAL under me during C-CAL cmp that the teacher-mentor has to be part of the team otherwise why would he/she want to work for the team and admittedly, I felt the inertia at various stages.

On the other hand, my classes were on my mind during my trip. So after hauling the load of goodies across the continents and entering a class which seemingly ignored you and whose members were only interested in their own conversations, I had to wonder about if there is something wrong with myself this year...and I was upset with myself. Sighz... in the end, I still gave out the goodies despite the brooding gloom because deep down I know I still really want to give it to them and without questioning. (the many thank-you softened the blow but it doesn't take away my worry for their studies).

------------------------

During my absence from school, a number of ex-students came by to say hi but instead have to drop a note. It was nice to 'hear' from them again but such is the way of fate. Sometimes, the 'goodbye, see you next time' never materialize. One came back from the States and visited the school on the day I left for Camb (when he had returned days before my departure date). So I didn't trust T when he said we will meet up during the x'mas period and I stayed at the airport yesterday upon landing so that I can send him off. And today, I met up with A in the late afternoon before she flew back to US tml morning even though she said it is alright if I am too tired from the jet lag.
In saying so, I am also glad to have met up with Rick in London after what seemed like an impossible mission. I must admit that I was really a bad conversationalist and I realised then that I really don't know much about him even though we have spent time working together in a US camp 4 years ago. so what brought us together? I think it was the sincerity we extended out to pple around us.

Bacteria/Plasmid

2008-08-16T07:42:00.002+08:00

I gave a lecture on bacteria the other day here in Camb and there were also additional materials which I dispensed for a wholesome learning experience. Anyway here is some tibits for the mind.

1) F factor = F plasmid

When you talk about F factor you are referring to the F plasmid itself. F factor is not a gene on the plasmid but represent the entire plasmid with the various genes that contribute to the particular characteristic i.e. having sex pilus.

2) F+ bacterium do not mate with F+ bacterium i.e. no mating bridge is formed between them.

Under normal circumstances, F+ bacterium with its pilus will bind to F- bacterium to draw them nearer to each other. This binding requires recognition of specific proteins on the F- bacterium which are missing in F+ bacterium. So once a F- bacterium receives a F plasmid, there will be changes in its surface proteins such that the above does not take place.

3) Additional: There are many other types of plasmids as well. There are some which confer tolerance to salinity, others produce toxins etc. However, there is one which I would like to talk about and there is the R factor.
R = antibiotic resistance
As the term implies, when a bacterium receives a R factor, it will become resistant to (specific) antibiotic. This is of course important in many of the laboratory work these days as well as the emergence of superbugs in hospitals.
There can be several types of plasmid in a bacterium. And some of these plasmids can make use of the mating bridge formed by the F factor to sneak into the receipient bacterium.

Counting Down

2008-08-14T07:27:00.008+08:00

Also thought of sharing some of the bits in Cambridge with you... =) - and now I can finally do it since I have finished my official homework brought from Singapore =( =P. It is amazing how time flies. after getting over the jetlag and clearing some work here and there, I am already heading home....

Some highlights thus far:

Punting Down The River Cam. It was really some exercise :P

Up the London Eye which we have replicated with our own Flyer

The Big Ben & Parliament (While on Cruise)

Although it looked absolutely non-descript unlike all the other bridges, this is the one and only "London Bridge"...is falling down....

One day, I went to attend an Econ Lecture but couldnt take it so I took the time to write lovenotes in a courtyard =)

I took the Biotech kids down to Eagles Pub where Watson & Crick came up with the structure of the DNA molecule. And there is no question about cam-whoring.

This is today's. I went with the literature grp to The GLobe which is a replicate of an open-air theatre built during Shakespearan time for plays. The construction of the Globe was actually initiated by an American in 1949. I watched a 3-hr King Lear play standing up, braving the sudden showers and totally enjoying it even though I couldn't catch everything. The acting was just superb!

Walking on the Millenium Bridge towards St Paul's. I like the bridge a lot. Modern and it felt 'open' , getting it a relaxed feel...

Mmmm... I am glad to have worked hard last week so that I may ease down this week for a more relaxed pace =)

Virus Updates

2008-08-14T06:45:00.002+08:00

Feeling a bit guilty here because I have yet to put up the updates on virus as promised and I could not find the correction sheet which I have typed out earlier *groan :(. But no worry, my retentive memory is somewhat still working :) - though I wish to be back in my classrooms talking about this interesting topic ....oh well.. at least I substituted it with a lecture here in Cambridge on bacteria to our Bio students here :P

Anyway here goes:

1) matrix proteins - what are they? Are they important?

From Wiki: In virology, matrix proteins are structural proteins linking the viral envelope with the virus core.

This protein is noted in both influenza and HIV but their implications are different. In influenza, the matrix protein M1 as seen in the given diagram IS also the capsid protein so there is only one level of protein layer enclosing the nucleoprotein. On the other handd, for HIV, the capsid protein and matrix protein genome. The matrix protein is really there to hold the gp41 to the membrane but that doesnt really matter. What you should note is that for HIV, therefore, there are two layers of protein enclosing the genome.

2) Is polypeptide = polyprotein?

They are two different things.
Polypeptide will fold to form one protein.
A polyprotein refer to polypeptide that can be cut into several pieces, each of which can be folded into various structural or enzymatic proteins. In the case of HIV for example, the gag gene encodes for the capsid and matrix protein while the pol gene encodes for the viral protease, RT and integrase. what do you think env gene encodes?

2a) what is this splicing business?
Due to alternative splicing, sometimes you get mRNA of either gag, gag-pol or just env.

3)If you have not made this change in your notes already, pls do. Page 19. Bullet 5/6. a double-stranded DNA is not a provirus. a provirus only exists when it is integrated into the host's genome. Just as we called the integrate phage genome in a lysogenic cycle a prophage.

4) Qn: How do you get a double-stranded DNA in HIV? Who is involved?

5) Your covering tutor should have covered with you on: influenza is a -ve sense RNA virus (-ve sense RNA implies that the genome cannot be used as mRNA directly and has to be converted to the +ve sense (mRNA) before translation can take place) thus the template used to make the new genome and proteins should be the +ve sense mRNA that is transcribed from the -ve sense genome... If not, I will talk about it again next time.

That's all I have I believe =)
Have fun!

Cambridge

2008-08-09T06:04:00.002+08:00

Finally a day when I am not so tired at night to pen my thoughts. I guess the jetlag has wore off substantially after a 50-min power nap in the afternoon...=)
How are my classes doing? I wondered but I know that they are in good hands and today I have finally finished and sent the updates I had wanted to prepare before I left to the respective covering tutors. They are so going to kill me even though they were already ready to do so when they realised that my classes are going to start on viruses, slightly ahead of others. =P
But clearing of work was really crazy before I left when I survived on 3 hours of sleep over 2 days - right up to an hour before I left for the airport - to mark the mock SPA, tutorials (structured only- cant make it for essay) for my 3 classes and also the MCQs before I flew off.
And thanks for all the well-wishes from 3L that morning via smses and the booklets and to T whoh had painstakingly collected the bklets so that I may read and write during my time in UK. I have already started on 3 =)

Before I came to Cambridge, I told a good fren/colleague of mine that I was baffled by my role in this trip which seemed to be so different from ISLE. Am I to let go and relax as advised to or do I be the disciplinarian that I expect myself to be? It would be so easy to take the backseat but I find it really hard to do so. Then she pointed out that that's because I would always make it a point to try and seize every moment as a teachable moment to instil values and social awareness. And I supposed that is the choice I have made so that my students can flourish as a person of good character in all sense.
Just as I have made the choice to spend time and mark all questions done in tutorials (except for this virus one) when we do not have to, hoping that each and every student will become aware of the error he/she tends to make and learn from it. Just as my students have to decide the amount of effort they are going to put in for this last stretch for their promos.

Choices choices. The choices we teacher have in our approach to this profession, as sent by a friend who is comtemplating to enter this profession after working in the private sector for 4 years http://www.asiaone.com/News/Education/Story/A1Story20080619-71705.html

late already. I am going to snooze...

Why have Thymine and not Uracil in DNA?

2008-07-13T16:04:00.003+08:00

JL asked this interesting question =)

Here is the answer as promised:

Thymine is actually methylated-Uracil.
The methylation will make DNA unrecognizable by nucleases and thus ensuring the integrity of the DNA genome for replication.
Also cytosine can spontaneously deaminate to become uracil (C--> U mutation is quite common). However, DNA repair proteins will be able to recognise/differentiate and fix it since this uracil is not methylated.

News in Science

2008-07-13T15:40:00.003+08:00

From Scientific American:

1)
Rutgers University researchers have found brain cells responsible for helping people overcome fear of things they once found scary. The finding, published in Nature, could pave the way for these so-called intercalated cells in the amygdala, a brain region that processes fear, to become drug targets for treating phobias (such as fear of heights and closed spaces) as well as post-traumatic stress disorder in soldiers and others. Scientists trained two rat populations--one with these cells intact and the other with them disabled--to fear a certain sound by giving them a mild shock every time it was played. After awhile, the animals would freeze in their tracks when they heard the noise, bracing for pain. The team then played the tone sans the shock. When they sounded the note again a week later, rats with healthy intercalated cells weren't bothered, whereas the others froze. The scientists believe that intercalated cells form "extinction memories," which associate something previously feared (such as an air raid siren or a car backfiring) with a harmless outcome.

Kind of interesting 'cos I used to do some readings on memory and learning

2)
Believe it or not, the world is becoming a happier place, at least according to the University of Michigan Institute for Social Research's 2005 to 2007 World Values Survey. The cheeriest country?: Denmark. The gloomiest: Zimbabwe—no surprise given the political unrest there. The U.S. ranks 16th on the list, just after New Zealand. According to the research, published in the journal Perspectives on Psychological Science, people are happiest in countries with the most tolerant social norms and most democratic political systems: Iceland, Switzerland, the Netherlands and Canada all rank among the top 10 happiest countries in the world. Researchers have surveyed more than 350,000 people on how happy they have been for the past 26 years based on their responses to the same two questions: "Taking all things together, would you say you are very happy, rather happy, not very happy, not at all happy?" As well as, "All things considered, how satisfied are you with your life as a whole these days?" Democratization and rising social tolerance have even more of an impact than economic growth on happiness, although all are important contributors. The citizens of India, Ireland, Mexico, Puerto Rico and South Korea all indicate that they're becoming happier. Alas, those in Austria, Belgium, the U.K. and Germany say their joie de vivre is waning.

food 4 thought: I read an article last year in ZaoBao last year. the reason for Danish Happiness is because most of them venture out/travel to find out what they want to do with their live after graduation. When they return and decide to become a cobbler or painter, it is accepted with blessings.

3) (For ZL who has been working hard @ pathlight)
Autism Genes That Control Early Learning

A new genetic analysis of large, inbred Middle Eastern families found that genes linked to a heightened risk of autism are crucial to a child's ability to learn.
A group of scientists, led by a team at Children's Hospital Boston, has pinpointed six new genes that may contribute to autism, a disorder characterized by asocial behavior, difficulty communicating and repetitive actions that affects an estimated one in 150 children born in the U.S. each year. They report in Science that all of the linked genes are involved in forming new and stronger connections, called synapses, between nerve cellsin the brain, which is the biological basis of learning and memory formation.  "We're showing, on the one hand, that autism seems to have a large genetic component," says study co-author Christopher Walsh, chief of genetics at Children's Hospital. "But, the genes that are involved are actually those that are involved in responding to the environment and learning."  The findings, Walsh says, reinforces the importance of early diagnosis of autism and intervention, particularly behavioral therapy and learning in enriched environments through repeated activities. Performing these sorts of tasks may help strengthen cellular connections, compensating for the malfunctioning genes.  The researchers studied 88 families in which one or more children had been diagnosed with autism, and the parents of each autistic child were cousins. Marrying second and third—and even first cousins—is not uncommon in the Middle East, and by studying such families scientists were able to track recessive genetic traits (caused by mutations that only affect individuals with two copies of the flawed genes). Such traits occur far more frequently in inbred families than in others.  The team found a total of six mutations affecting genes that had previously not been linked to autism. The mutations came in the form of deletions, where part or all of both copies of the genes were missing in a child with the disorder. All of the genes are known to be involved in parts of the same process: creating and strengthening synapses.  Normally, when nerve cells (neurons) activate in response to an environmental factor (such as processing a new face or a new sound), synapses between two active cells change to provide stronger connections so the cells can pass on information more efficiently. As the brain develops, new connections are continuously formed among nerve cells, reinforced and, in some instances, broken as the brain starts to mature and divvy up its different functions to specific groups of neurons.  According to the findings, "All of the relevant mutations could disrupt the formation of vital neural connections during a critical period when experience is shaping the brain," says Thomas Insel, director of the National Institute for Mental Health (NIMH) in Bethesda, Md. To wit, most children are diagnosed with autism between the ages of one and three years of age.  Walsh says the team believes these deletions—which in most cases found here only remove some, but not all, of the DNA that makes up a gene—may mean that the genes can regain some of their normal function. In fact, some of these genes may just be switched off. "This presents the possibility that in some kids we could get the gene going again without necessarily having to put it back in the brain," he says.  Jim Sutcliffe, a molecular physiologist at Vanderbilt University in Nashville, Tenn., in a Science editorial notes that the majority of autism research is geared toward prenatal development, even though the brain continues to develop well after a child is born. "Experience and environmental input play an important role in subsequent development," he says. He calls the notion that learning in early life is disrupted by these autism genes "an intriguing proposal," but says that further research is needed to validate it.  Dan Geschwind, a neurologist at the University of California, Los Angeles, says that to test the hypothesis that autism genes affect synaptic strength, it would be important to examine the 20 to 30 other genes that have been implicated in autism and see which ones also play a role in strengthening neuronal connections. "If its a significant proportion," he says, "that would provide support for the hypothesis being put forward."  Walsh notes that many children diagnosed with autism tend to show vast improvement when they are placed in environments that allow them to practice learning repetitively. He says that these activities essentially train the neurons to make up for their lost function.  "Our work reinforces the importance of early intervention and behavioral therapy," he says. "The more we understand about genetics the more we understand how important the environment is."

Achieving Ur Dreams

2008-07-13T12:09:00.002+08:00

Just last week during Civics, I showed my class part of "The Last Lecture' by Randy Pausch. The clip was introduced to me by my brother 2 months ago but I only got the time to review it recently and found it interesting possibly useful for my students.

Who is he? Below is a short excerpt from TIME:
http://www.time.com/time/specials/2007/article/0,28804,1733748_1733756_1736194,00.html

From his talk, I am sure the takeaways from each individual will be different because all of us have different experiences - some of us have already been there and done it, been there but forgotten about it or never been there. But regardless, there is something for everyone to think about.

1. Brick walls are there for a reason: they let us prove how badly we want things.
2. If someone criticize you that is good because it showed that the person cares. If one day no one bothers, then you worry because they have given up on you.
3. Make time for what matters -- Time is all you have. And you may find one day that you have less than you think.
4. Experience is what you get when you didn’t get what you wanted.
5. If we do something which is pioneering, we will get arrows in the back. But at the end of the day, a whole lot of people will have a whole lot of fun.
6. Be good at something; it makes you valuable.

If I may add my own:
Be Patient. Dreams need you to take the first step and slowly advance. So be prepared but don't lose faith in your choices because you never know when the right moment comes for you to take the plunge. Even should all fail, check out 4. =)

For my ex-students who are starting to venture out into the real world:
(http://www.businessweek.com/smallbiz/content/may2008/sb20080516_673343.htm)

Like millions of people, I watched the video of Randy Pausch giving his "last lecture" at Carnegie Mellon. Pausch, who is dying of cancer, created a lecture that offered life lessons (BusinessWeek.com, 11/21/07) as a guide for his children when they grow older. I developed an even greater appreciation for Pausch's wisdom after reading his book, The Last Lecture, and realizing many of the lessons can be applied to business leaders, entrepreneurs, small business owners, and managers in how they interact with customers and employees.

Encourage creativity. Pausch recalled how he liked to paint things on the wall of his bedroom. His parents were dismayed at first but soon relented after they saw how excited he became when he was painting. Pausch said he's lucky to have had parents who encouraged creativity and allowed him to express himself in unconventional ways. This reminds me of a recent article I came across about Google's (GOOG) Zurich offices. The office space is intended to inspire creativity with slides, aquariums, cable car shells that serve as conference rooms, even igloo-shaped work spaces. Google understands that to be creative, you can't always be sitting in a cubicle. Encourage creativity in your company's workplace.

Learn from Captain Kirk. Pausch was a fan of the Star Trek series growing up. He found a role model in Enterprise Captain James T. Kirk, who, according to Pausch, had the essence of a dynamic manager: He knew how to delegate, had the passion to inspire, and looked good in what he wore to work. "He never professed to have skills greater than his subordinates…but he established the vision, the tone."

Celebrate brick walls. "Brick walls are there for a reason," writes Pausch. "They give us a chance to show how badly we want something." Entrepreneurs and small business owners are faced with hurdles every day, some seemingly insurmountable. But if you're passionate about what you do, those brick walls are easier to scale and you have more fun on the climb.

Dream big. Pausch was attending camp in the summer of 1969 when men first walked on the moon. He remembers his camp counselors sending everyone back to their tents before the big event because it was getting late. Pausch thought to himself, "My species has gotten off of our planet and landed in a new world for the first time, and you people think bedtime matters?" When you put people on the moon, argues Pausch, you're inspiring everyone to achieve to their maximum potential. "Give yourself permission to dream. Fuel your kids' dreams, too. Once in a while, that might even mean letting them stay up past their bedtimes."

The same goes for your employees. People want more than a paycheck. They want to know their work is adding up to something meaningful. No, you may not be working on a project as exciting as sending a man to the moon, but in some small way, you are making the world a better place. Help your employees see the big picture and, more important, fuel their dreams of career and personal success.

Be the first penguin. Create a culture that celebrates risk. Pausch writes: "[I] encouraged students to attempt hard things and not to worry about failing…failure is not just acceptable, it's often essential." To encourage this way of thinking, Pausch would reward the group of students who took the biggest gamble with a stuffed animal—a penguin. The idea came to him when he realized that when penguins jump into the water where there are predators, one has to go first. According to Pausch, "Experience is what you get when you didn't get what you wanted."

Rediscover the lost art of thank-you notes. In business I have received just a couple of handwritten thank-you notes. But because they are so unusual, and so personal, I was left with a strong impression of the individuals who sent them. So it didn't surprise me that one chapter in The Last Lecture is dedicated to "the simplest yet most powerful things humans can do for each other…showing gratitude." Pausch shows that magical things happen when you send old fashioned thank-you notes. "If you are a B+ student, your handwritten thank-you note will raise you at least a half-grade in the eyes of a future boss or admissions officer. You'll become an 'A' to them."

Have fun. Pausch's colleagues say they will remember him as a person who had fun. Pausch writes: "I don't know how not to have fun. I'm dying and I'm having fun. And I'm going to keep having fun every day I have left. Because there's no other way to play it."

Buzz Around

2008-07-05T23:14:00.003+08:00

So I tried working around this new template I found for the blog, throwing in some elements here and there to make it look a little cooler and also not forgetting the tagboard which I have been incessantly reminded to put up, be it this batch or last batch. On recommendation, I have changed the tagboard provider so hopefully this will serve me well by not expiring because of inactivity. =)

There are many reasons why this blog suffers periods of constipation - due to the piles of work, lack of questions and inspiration. Hopefuly we get more questions this term to share!

Here are some:
1) CT MCQ question 5: which got me really stumped for the longest time in class - I apologised; when you are rushing the marking day and night, your brain do get a little bit more than fried. I think my eyes nearly popped out last night as I struggled to clear that last pile.
Anyway it took me a while to realise why I have never considered this question a problem until I tried too hard to break sentence up:
if you read statement C as it is meant to be, it is trying to tell you that melting point of FA increase with (increasing) chain length and decreases with (increasing) degree of unsaturation. The (increasing) component is implicit in the sentence structure - a linguistic issue. Just like: the food will go bad with time...

2) what is myoglobin?
Myoglobin is a single-chain globular protein of 153 amino acids, containing a heme (iron-containing porphyrin) prosthetic group in the center around which the remaining apoprotein folds. It is the primary oxygen-carrying pigment of muscle tissues.

(http://en.wikipedia.org/wiki/Myoglobin)

I remembered talking to some of you about red meat versus white meat. And yup. myoglobin contributes to why some animals are considered red meat and others white meat and also why some of us are the ideal machine to run 2.4km under 10 min while some of us struggle to do so but score in sprint =).

--------------------

A comment made by students during the week: Sir, you have friends all over the world...I pondered for a while and realised that it matters not if you have friends or not all over the world but to be remembered or remembered because you or that someone made an impact in each other's life. that is really what makes the memories so wonderful. maybe if there is chance, I will share why some of these pple are important to me.

Recuperating

2008-06-10T16:05:00.005+08:00

I just came back from a swim and it felt great! Exercising is like a ritual detoxing session for me especially in the holidays when you can idle some time away =P.

CCAL Camp 08

As the teacher-mentor of c6, I am really proud of the kids in my team. I can't say that I am a good facilitator but I definitely hope that they had learnt something from me and one another because to me, the camp was a great opportunity to mentor, not only to have fun. I remembered being quite stern with them on the first day we met but they lived up to expectations and kept the spirits up throughout the 4-day journey when we took good care of one another.
For some of these kids, you can really see that they have matured since the last time I saw them in RI and it gladden me to see them so.

They may not get the best sub-grp prize but how many can boast missing their kids only hours after leaving them? They had made the camp this year memorable for me and I do relish the fond moments with them. N they made me feel much loved with the big grp hug at the end before I left. To C6:

-------Right after the CCAL camp was the Sci Camp

Ahoy the pirates!
3 days of work and fun as we launched trebuchet, solved mystery, made new friends, indulged in some stimulating intellectual workshops and fought some wars!
IT was a crazy time for the students and the teachers I am sure. But the responses were rewarding, to know that the camp had made a difference in understanding and tackling science as a subject, and had enriched the lives of the participants with new found friends from other schools. The teachers as well. It made me realised the distance I can go and what do I want out of this whole education business.

Respire Expired

2008-06-09T22:31:00.003+08:00

So many things have happened in the past two weeks (and beyond) that I did not have time to sit down and think. But the memories brought a smile to my face this afternoon when I walked home today... Let's leave it at that for now to fulfil the promise I made.

Today I finally finished marking the Resp tutorials. Hipee! It was actuallly quite tough trying to overcome the inertia of starting to mark right after the completion of Science Camp because once again, I was suffering from another round of sleep deficiency starting from CCAL camp on the plate. But I did anyway despite languishing in serious dream-state on Thursday (the first day after the finale) so that I may make it today to ensure enough buffer time for students to review. Now I can finally sleep/rest with ease. =)

Resp tutorial: general debrief

Overall, there appears to be good understanding of the topic. Putting concepts down in words hopefully helps to distinguish it from photosynthesis.

1) should always try to relate 'oxidative phosphorylation' to the 'formation of ATP'; to say that electrons move down ETC so that oxidative phosphorylation can take place is correct but somewhat lacking.

2) For anaerobic R, some are unclear in their description. you need to realise that while pyruvate/ethanal is the final electron acceptor but being that does not guarantee a regeneration of NAD+. It is the reduction of pyruvate/ethanal in the subsequent step that regenerates NAD+.

3)why do we adopt anaerobic R? It is not to generate more ATP. If it is, I rather generate more with oxidative phosphorylation. Anaerobic Resp is really a backup plan to ensure that we still have a small but sufficient supply of ATP to sustain muscle contraction even when we are out of oxygen. Imagine running away from a bear. Yup, you need it.

4) Quite a handful did not mention the formation of proton gradient in order to generate ATP.

5) students needs to relate answers to the diagram/visual aids given e.g. Question 2; make reference to the molecules given e.g. phosphorylation of glucose!
Question 4d) students only needs to talk about how ATP can affect the enzyme although it was well-written. This is partly an enzyme question so need to mention: end-pdt inhibition/ binding to allosteric site / altering the 3-D conformation at active site; there is no need to talk about AMP/ADP and citrate.

6) Question 7 as well. Pls note that there is no competitive inhibition even though PKF reaches max activity at substrate concentration. The shape is wrong.
You also know it as an allosteric enzyme.
The management of PKF is actually very complex so I will leave it out here for now.

I will go through the answers properly when school reopens. Conceptually, things are fine so I will just round up the points you need to take note of.

For DNA genomics, there will be no answers given to be fair to all classes. However, I would recommend you to do MCQs to test your understanding of the topic itself.

To top it off:
Respiration MCQs

Cheers!! Happy Mugging!

Slowly all will be revealed

2008-06-01T00:05:00.003+08:00

Sorry 3L, I can only mark your tutorial after sci camp.
But I promise to sort it out asap so that you can review your work.

I think I still own
1) respiration review
2) MCqs answers for respiration

Hope I din miss out anything.

It's the mostly the same for 3B yah?
I am free for consultation on Thurs and Fri k?

Cheers!!

Questions of the Weeks Round Up

2008-05-17T22:31:00.006+08:00

1) For the photolysis of water, we talked about the highly oxidising nature of p680+. But isn't there a Mn complex involved?

Yes it is true. The Mn Complex will interact directly with water to extract the e- to be passed to p680+. But it is not required of you to know. =)

2) SER: tubular and RER: flattened?

A pic speaks a thousand words and better than the one I drew in class

3) How polypeptides can get into the lumen of RER?

The diagram shows that a partially formed polypeptide chain is directed to the RER by the peptide signal sequence where the rest of the polypeptide chain will then continue to be formed and entered the lumen.

4)
Cell Membrane

1 D 6 C 11 D
2 C 7 B 12 D
3 B 8 A 13 B
4 A 9 D 14 B
5 A 10 A 15 C

Common Mistakes/Correction to note:

4) the width is within 10nanometers!
7) you should know the nature of the core of bilayer; having a fluid mosaic is a consequence not a reason.
9) aerobic = there is production of large amounts of ATP; from the table we can deduce that the first two rows undergo passive diffusion and active transport but active transport is halted under anerobic conditions.
11) if you choice include any of the proteins, you are not listening in class when I mentioned that the presence of proteins to affect fluidity is only a minor point and definitely not their main purposes.
14) same above in 11.
15) similar to 9 whereby air bubbled implied oxygen introduced into culture → aerobic respiration.

Cell Structure

1 D 6 C 11 B 16 D
2 E 7 A 12 C 17 B
3 D 8 E 13 D 18 D
4 C 9 C 14 A 19 A
5 C 10 D 15 B 20 C

Common Mistakes/Corrections to note:

2) sucrose: used to maintain osmotic difference of the mitochondria with its external environment so that one can view it in its native shape under microscope.
5) at the slowest speed, the most dense organelles will be spun down and that will be the nuclei/dna.
6) you should know this!
7) B is wrong. It is pointing to the RER/ribosomes where rRNA/mRNA and maybe even tRNA are present.
9) hydrolytic enzymes are found in lysosomes!
10) expected to know. It is also the site for carbohydrate synthesis and detoxification
11) B is correct; bacteria do have cell wall.
13) D: NADP is found in chloroplasts; NAD is found in mitochondria; membrane- bound enzymes refers to enzymes that are bound to the membrane e.g. ETC which is made up of a series of enzymes (although we did not go into the details) like oxidase, reductase. Try Wiki.
17) refer to 9
19) (In metabolism some substances are broken down to yield energy for vital processes while other substances, necessary for life, are synthesized) so all we need to recognise is that products can be exported out of cell via exocytosis or budded off to another site within cell where the products are needed.
20) another major featuer of prokaryotic cell; remember your essay comparing chloroplast and mitochorion?

Gen XYZ

2008-05-11T10:34:00.003+08:00

Yesterday there was an article on Gen Y which left me thinking, which generation am I in? Found in the dead center of a crossroad of changes, my conclusion is a hybrid of X & Y.
The generation Y saw the rapid technological changes that manifested themselves in handphones, broadband computers, blogging and facebook to name a few. There is also a greater sense of individuality that prompted one to make reference to more self-confidence and possibility creativity which sometimes is really an illusion because sometimes there is a lack of maturity to handle those qualities and perhaps that is why we are seeing many more cases of youths falling into their own insecurities and turning to petty defiances. There are more venues of connections between people with facebook, friendster, myspace and maybe other virtual worlds that I am really ignorant about. For some, the gulf of human interactions did not close up because of these avenues but instead widen because relationship becomes superficial with 1000 names in your messenger but only 10 you can really turn to when you are in need - yet with 1000 names, do you make reach out to the 10 to let them know they matters? For others (like me) such avenue is a blessing as I seek out long-lost friends that dated back to primary school, overseas encounters which made a difference in my life and even just my current friends whom I cherished but went away.
If I may say, Gen Y is an exciting time when the tides may swing for each individual. It proposes a sense of purpose to create, to explore and to make a difference.

On a comparative note, Gen X is more subtle, resilient and empathetic. There wasn't so much encouraging notions and demands from the adults to the youths. We worked hard, failed with much heartbreak and moved on again. Through the failures, we gained a little bit of wisdom that we took with us through life. Without the virtual worlds, we chitchat around a real coffee table with our friends to learn not about the world issues that seemed so foreign and far away but more about things closest to us like relationships, difficulties in life and simply about life itself. There were many reflective moments that let us make connections not only with people but with life in general. These days empathy is often lacking because there are so many distractions and the fast pace at which things run, we often fail to sit down and ponder a little more about ourselves and issues around us, and that we all have social responsibility. I confess that these days I myself is losing my touch and I get a little upset about it once in a while and perform my own little rebellion against the senseless charging of life. But really, it doesn't take much to pause. Yesterday I went Toa Payoh library and I saw Ice-cream Uncle. I am not sure how many of us is a frequent patron of TP but uncle has been there for years. Years before other ice-cream men came to claim a piece of the earnings in a 10 metre radius. Uncle may not have a fancy vehicle with colorful display of various ice-cream or even look clean by other standards, but I will always buy from uncle, sometimes even when I am not sure if I want an ice-cream. I did not think uncle remember me to offer me a big cone but I will buy from him because he is getting old and I think he does not get as much business as the newcomers so if I can reach out, why not?
But I think gen x pple are a bit slow in learning not because we are less able but because we are so much more cautious with the moves we choose to take.

gen x or y?
I learnt how to type when I was 20 while in NS. I got my first hp after my first Uni exams, I am unclear about the notion of LAN but started on my first proper blog because of my students 2 years ago. I suppose I am catching up to a certain extent and learning but the cautious me will take a step back each time to remind me not to get overwhelmed and to get back to basics.

caught at a crossroad, life is not necessarily bad. I want to teach my kids the good and bad things of both generations. There are values that we should not forget lest the fabrics of the world collapse. Already I am seeing it.
I want to remind them that they are entering into the world of gen x when they come out of their studies...only to remind myself that I too will become obselete in 20 years' time.

Sad or Angry

2008-05-05T21:21:00.002+08:00

I reprimanded my class today. Mmm.. maybe reprimanding is the wrong word because I am real lousy at that. I was speaking from my heart would be more accurate. I told my friends that I am always weary after such a session. Then he reminded me that my tiredness did not come from an outburst/anger but from sadness. Sadness he said, is more tiring than anger. After all the effort, all the reminders and all the giving, it was sadness not anger.

I looked at these kids and thought, regardless how they did in their previous schools, here in the college it is a fresh new start. I was sad because I worried that they belittle themselves when they can be so much more. I have seen some bright sparks but their fires always dimmed before they have a chance to burn. I do not think they realise it themselves. And if we have a weaker foundation, it just means that we have to work harder to catch up, to be more responsible with ourselves and our goals at the end of the day. Slowly but surely together as a class we will make it there unless we choose not to work at it.
A friend said that I worried too much and perhaps I do but only because they meant something to me even when they waddle through the lessons with playfulness and some cheekiness. A time to play and a time to pay attention, we all need to work on that.

The day passes and while the sadness loses its core after seeing these silly kids with their grins at their ccas in the evening, I have to continue making some worksheets that I decided to create after much contemplation since last week.

*It is not my first heartbreak but perhaps there is more because of greater expectations of myself this year. When I first came in to teach a class of 07, they told me that they have learnt nothing from the relief teacher for a whole semester except that she loves char siew bun. And it was reflected in their fundamental in biological molecules and earlier topics which somehow, some never ever recovered from. I thought I will work hard this time to make sure that that doesn't happen to my kids. but I can only hope so.