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
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!
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
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
--------
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: :)
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
--------
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
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. =) ]
For Samuel
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
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.
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
Explanation for 08 HCI MCQs as highlighted by Alicia
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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.
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I still love this video after two years! For you all!
Nobel Prize in Medicine or Physiology 09
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
http://www.scientificamerican.com/article.cfm?id=nobel-prize-medicine-2009-genetics&sc=WR_20091006
Tough at 30
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!
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
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.
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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!
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...
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
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? :)
__________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? :)
a blog site for this trip.
http://www.travelpod.com/members/chansensei
I think I am so going to be dead!
I think I am so going to be dead!
Odd Stuff
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
-------
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
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.
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.
Comments for the week
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.
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
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.
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
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.
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.
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.
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
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.
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
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.
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
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!
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....
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
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.
-------
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...
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.
-------
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
Chi-Square
------------------------
For Bemedial students:
MCQs:M&M (just in case i did not give the answers/ esp for late hand-in-er)
MCQs:Bacteria
-------------------------
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. .
------------------------
For Bemedial students:
MCQs:M&M (just in case i did not give the answers/ esp for late hand-in-er)
MCQs:Bacteria
-------------------------
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
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.
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
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.
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
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.
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
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.
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
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!
> 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
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 :)
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!!
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
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?
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)
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
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
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
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
-------------
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
-------------
Revisiting Bacteria Again
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
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
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