Last Game of The Season

The 22nd gold.

Mr R said that today is my final assignment with the team and I nodded absent-mindedly as I reflected on the days passed since I took on the sport as my cca. It has been quite a ride and the boys have been most incredible. At this point when things are really out of my control, I shall look back fondly on those days and know that things couldnt have been better. =)

Good job guys!

Virus Test

This week we will be having a test on Virus.
However, the entire test will be split into 2 parts: 1) Essay + 2) MCQs + structured.

3S: Tues - Essay
Fri - MCqs & Structured

3Q: Wed: MCqs & Structured
Thurs: Essay

3L: Fri: Essay

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Next wk: Bacteria.

Differences btw Monocot and Dicot

http://www.ucmp.berkeley.edu/glossary/gloss8/monocotdicot.html

Most of the differences we often discussed between monocot and dicots are morphological in nature. The biochemical/molecular differences are currently still being explored.

Common Errors for Photosynthesis Prac

If the light is at a fixed distance away from the extract, the light intensity is actually the same for all tubes.
Why is it that the tube that is subjected to white light turns green the fastest? Because it is exposed to all wavelengths of the visible spectrum, not because it is subjected to maximum light intensity.

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Plants reflect the green light (thus it appear green) which explains why it takes longer for DCPIP to be reduced with the green filter-------------------X (buzz out).

PLants still do absorb the green wavelength but to a lesser extent compared to all the other wavelengths!!! Most are reflected.

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Semi-Retirement + Syllabus

A random conversation with some students in the canteen revealed how little our students know what to expect for the A levels so here is the examination format:

And so you can see, MCQs is important and we have already completed 20% for SPA.








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Semi-retirement

Today saw the commencement of the NUS Softball Open and I went down to toss a few balls. I felt better today because I can see the results of my workout for the past two weeks when balls actually comfortably sailed through the air with a smaller projectile although the speed still deemed improvement. At least the accuracy was there. I am not bragging but I was known for speed and accuracy in my time. Still that did not stop me from breaking the news to the team that I would be entering seclusion mode after this game as I decided to concentrate my efforts in preparing my kiddos for their prelims & ultimately A's.
Perhaps it was a sign when someone took a look at my glove and commented that I could display the battered, old thing already.

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Get a life, Sir.

someone said after I have run through my weekly schedule with him.
It took me a while before I realised that I am actually living my life and it does not have to be translated into partying or walking down the streets of Orchard because when you are doing things you are passionate about and care about, you are living.

The Complicated Matter of Ti Plasmid

It took me several hours to seek out relevant information and piece things together in a coherent fashion because online information can be rather vague at times or inappropriate so read with patience.

Background

Let's look at the Ti plasmid in its natural form:

As mentioned in class, it has two main regions - the T-DNA (transfer DNA) and non T-DNA region.

T-DNA

T-DNA consists of 3 parts you should at least take note of:

1) left and right borders (about 25 bp)

These would be where the products of the vir genes (see later) will nick to splice out the T-DNA

2) opine synthesis genes

Opines when expressed in the transformed plant cell are nutrients for the bacteria Ag. tumefaciens

3) tumor producing genes

In this category you will find many reference to genes that encodes enzymes which control the synthesis of auxins and cytokinins. Some sites will simply refer to the genes for auxin or cytokinin production.

(3L: I was right after all! For a moment I was torn between their true nature: do the genes encode for enzymes or for the protein)
Non T-DNA region

Here is where you find the OriR and Vir genes. Vir or virulence genes serve to aid the transfer of T-DNA to the plant cell.

Alright if you insist.... on the diagram above, you also see opine catabolism gene yah? Because the opines produced will be metabolised by the bacteria for enerfy and are of no use to the plant.

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Recombinant form of Ti Plasmid.

In this diagram, we can see that the tumor-causing genes and opines synthesizing genes are removed and replaced by your gene of interest e.g. gene for Bt toxin and plant selectable marker e.g. kanamycin resistence gene.


Note to point: The plant selectable marker and gene of interest are coupled!

(This is what I have to confirm because there are too many possible combinations/methodologies in the market right so the the simplest one (I think) is to treat the two as coupled to each other. In other words, if a transformed cell exhibited kanamycin resistance, we can safety say that the gene of interest is also present in the cell. Okie?
This would resolve the issue Slagoon has on having a plant cell that may exhibit kanamycin resistance but does not have gene of interest.)

You will realise the presence of a BACTERIAL selectable marker e.g. antibiotic resistance as well, outside the T-DNA region. That one is like your selectable first marker we used to talk about. When the plasmid is induced to enter the bacteria, this marker will allow one to know if the bacteria has been transformed.

At this point in time you might ask(or I rather) : can we use any antibiotic resistance marker in both cases?!
NO!! Try not to at least.
Kanamycin (or neomycin) resistance gene is highly popular as a Plant selectable marker because it is rather toxic to the plant cell, coupled with the fact that it is not used in medical treatment (thus lower the risk of cultivating kanamycin resistant bacteria in our gut when we eat the transgenic plant, and the fact that the gene might subsequently spread through horizontal transfer).

For bacterial selectable marker, we can still go back to ampicililn and tetracycline (these are not usually used for plant because they are less toxic to plant and also the fact that they are very common in medical treatment)

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And so the plasmid get transferred.
Note that only the T-DNA get transferred and not the entire plasmid. The T-DNA is spliced out and chaperoned to the plant nucleus by enzymes and proteins (respectively) which are encoded by the vir genes.

Then TaDA! you get a transformed plant cell that will survive on an agar plate full of kanamycin and has the gene of interest!

I will leave the growth of this plant cell to you. ..



Nites! It is Friday night!Zzz.........

Several Questions That Went Round & Round

Micro-organism and Microbe (interchangeable)

A microorganism or microbe is an organism that is so small that it is microscopic (invisible to the naked eye). Microorganisms are often illustrated using single-celled, or unicellular, organisms; however, there are exceptions because some unicellular protists are visible to the naked eye, and some multicellular species are microscopic. The study of microorganisms is called microbiology. Microorganisms can be bacteria, fungi, archaea or protists, but not viruses and prions, which are generally classified as non-living.

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What is a Hybrid? - This is a tough one

In biology, hybrid has two meanings.

The first meaning is the result of interbreeding between two animals or plants of different taxa. Hybrids between different species within the same genus are sometimes known as interspecific hybrids or crosses.

The second type of "hybrid" are crosses between populations, breeds or cultivars within a single species; between different sub-species within a species → intra-specific hybrids. This second meaning is often used in plant and animal breeding. In plant and animal breeding, hybrids are commonly produced and selected because they have desirable characteristics not found or inconsistently present in the parent individuals or populations. This rearranging of the genetic material between populations or races is often called hybridization.
(note though that hybrid plants/animals can still be inter-specific)

My own words:
Most of the time when we referred to hybrids, we are talking about interspecific hybrids. Intraspecific hybrids refer to the offspring of subspecies which is the equivalent of races.

An interesting thought by JH: Does that mean that when a Chinese mates with a Causasian, their child is a hybrid? This is rather debatable because the ‘race’ we often quoted for humans in different geographical locations is regarded as a social construct by some and with that all human beings can be taken as a species (the human race). Pls do NOT go around calling pple hybrids.

To find out more and to confuse further, check out these sites:
en.wikipedia.org/wiki/Hybrid
http://en.wikipedia.org/wiki/Subspecies
http://www.answers.com/topic/race-1?cat=biz-fin

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Does DNA have to be integrated into host genome to get a transformed cell?

Nope. If I may refer you to your bacterial transformation, the entry (and subsequent expression) of plasmid in a bacteria cell will give you a transformed bacteria cell. Nonetheless, you should note that for transgenic plant, the DNA must be integrated into the plant genome to get a transformed cell that will give rise to it.

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In GMO notes:
Chinook Salmon versus Altantic Salmon

Why do we have Chinook Salmon GH inserted into Atlantic Salmon genome?
Because Chinook Salmon are generally much larger in size but are found in Pacific.

Why do we fuse the Chinnok Salmon GH with the Ocean Pout Promoter (of its anti-freeze gene)?

There is no particular reason why the promoter for the anti-freeze gene of an Ocean Pout is used except that it works well. Below are excerpts taken from its patent:

"To be acceptable in aquaculture, the promoter(s) and gene(s) used in transgenic fish should be derived preferably from fish protein genes without posing any potential health hazards.

Functional analysis of other antifreeze promoters, including wolffish (WO), sea raven (SR) and winter flounder (WF), shows that they can be used in a similar fashion . Here only the Ocean pout antifreeze protein promoter is used as a teaching example in producing transgenic fish.

Unlike the type 1, alanine-rich AFP from the winter flounder which is synthesized only in the winter, the Ocean pout AFP is present all year around, albeit at a higher concentration during the winter months (Fletcher et al. 1989). The following data demonstrate that the OP-AFP promoter is a very effective promoter for inducing GH gene or other desired compatible gene expression in fish, such as Atlantic salmon. Although there is no antifreeze gene in salmonids, it is likely that the transcriptional factors controlling the OP-AFP gene expression exist in salmon"

Callus And Tumor

Callus and Tumor

(in notes) – plants form callus in response to injury

TRUE – this is a protective mechanism, forming a layer to cover the injury and to prevent water loss.

But this is different from tumor formation involving agrobacterium tumefacien. In tumor formation, the cells are being hijacked to undergo uncontrolled cell division and secretes opines. Although this is another lump of cells, because of its nature, we don’t refer it as callus at all.

So when Ag. Tumefacien infect the plant cell through an open wound, will/can a callus be formed?

Yes it will for the above reason. But only those cells infected by the bacteria will become cancerous in nature

http://www.apsnet.org/education/lessonsPlantPath/CrownGall/pathbio.htm

Does the tumor have averse effects on the plant?

Crown Gall Disease

Both loss of yield and stunting of growth may occur when seedlings or young cuttings are infected in the early stages of plant growth. The lack of vigor, reduction in foliage, and water stress are associated with chronically diseased root systems. When more mature tree crops become infected, secondary growths will appear from the root systems near the trunk and the productivity of the plant is reduced since nutrients is siphoned away.

• gall tissue contains abnormally high amounts of auxin and cytokinin and have the machinery to synthesize those hormones
• this machinery is gained by the stable transfer of genes from Agrobacterium to the infected plant cells
• bacteria does not have to be present for the progession of the disease

Caring Attitude n I M Tired + Heartbroken (no More)

When you get plunge those emotions into your work to keep that passion alive, there is a lot more at stake because you are potentially subjected to burns and hemorrhage. And today, I felt so burnt.

How Much Care Can I Give?

When someone do well, I recognised their achievements and gave them a little pat on the back. When someone improved after putting in those hours of hard work, even when it is only a simple grade improvement I gave them a little pat too in recognition of their perservance. When someone fail to do well even after all those hard work, I sympathize because it break my heart to see their dismayed face - afterall, I have been through that stage myself before too.

But when someone did not do well and when I know that they have not been putting those efforts during term time, what do I say? Give a smile and say 'you can do better?'. Ridiculous. Some knew their lacklustre effort, candidly accepted the consequences of their actions and ready to put in those hours again - for these pple, I am more than willing to work hard along with them. But there are others who are in denial.

If I did not console does that mean that I do not care? The efforts during term time, the hints I dropped... who was there to listen and who decided that it is not important and turn a deaf ear to all the nagging? who then, is the not so clever one? Some of them run away when they see me, fleeing from the guilty conscious that eat at them. Am I to chase after them? Are they so egocentric that they only see themselves and not realizing that there are many others out there for whom I have to drop those running shoes and stay with to guide. Do you not realise that the responsibility is yours to seek help from the tutors? The tutors will not turn away you away and often, it is the student who choose to walk away.

Neither is care about giving words of encouragement and consoling others. Sometimes we have to be cruel and harsh to remind others what is important. Those that truly don't care, will not even be bothered, afterall, it is others' future, not ours. But do we do that? It is a choice we all make.

While the students tried so hard but did not reap the rewards (they believed they deserve) doesn't the same apply to the teachers as well? When we tried so hard but yet the students did not produce the results, are we not allowed to feel the disappointment? We also have our emotional turmoil to deal with.

Maybe I need to move on.

Why is glass transparent? Or even some plastics?

Why is Glass Transparent?

This progression from ordered to random organization is the primary reason that light can pass through liquids and gases. Just like bricks stacked neatly on top of one another, the ordered molecules of most solids are virtually impenetrable to light waves. Depending on the substance, the light waves will be reflected, scattered, absorbed or, more likely, some combination of the three. But as the substance changes to liquid or gas and the molecules are not stacked neatly anymore, gaps and holes occur that allow portions of the light waves to pass through. The greater the randomness of the molecular organization of the substance, the easier it is for the light to pass through.

Glass is generally a manmade substance. Here is the basic way to make glass:
1. Take the most common glass material, silica, which is just plain old sand like you would find on the beach.
2. Heat it to an extreme temperature until it becomes liquid, then cool it.

The resulting substance has a molecular structure that is very random like a liquid yet that retains the strong bond and rigidity of a solid.

To find out more: http://science.howstuffworks.com/question404.htm


How is Glass Colored?
Glass is colored by

(1) impurities in the batch ingredients, or
(2) by one of three processes:

a. using a dissolved metallic oxide to impart a color throughout
b. forming a dispersion of some substance in a colloidal state, and
c. suspending particles of pigments to form opaque colors.

http://www.cmog.org/index.asp?pageId=759


Picture Viewing Through a Red Filter
http://www.pa.uky.edu/sciworks/physicspettingzoo/Red%20View%20Blue%20View.htm

It just struck me in an out of the blue fashion - we see the green filter because while green light is allow to pass through, it is also reflected off the white surface and transmitted into our eye through the same filter. Imagine having a black surface behind a filter, you would not see the color of the filter very well because when the green light hits the black surface, it will most likely absorbed.
Soundz sensible? =)

CT 2 Qn 21: The Amazing Graph Question

Why I am not buying the other options...

1)
- If division is by meiosis, the DNA content will keep on dropping and it is hard to determine that from the (edge of the) graph.
- If you are making reference to the graph we used in meiosis, n-2n-4n, do note that in those graph, the drop is sharp for a discrete difference and not a gradual one.
- Even if the cells at the tip have n amount of DNA, it should divide by mitosis.

2) no question about it. Wrong.

3)
- We cannot really determine that from the graph. It only can serve as a possibility in the remote sense since we do not know what happen beyond the edge on the right - will there be cell divisions?
- does not account for the horizontal part of DNA per cell

CCA reallocation

When the news came on Tues, it took my breath away for hours.
There was no foretelling signal to warn me of the adjustments I had to make although rumors had floated around for a while. Perhaps I was an escapist then, fearing the inevitable and wishing that it will never happen but it did. So it is official, I am leaving cricket and going to softball.

Why am I sad if I am going to softball which is probably my comfort zone, someone asked.

It is not about the game and why do pple have to assume that I will want to stay in my comfort zone when I have always challenge myself over the years to break free? I am back in teaching not to find my former glories on the field and I guess the passion for the game is different ever since I left it 10 years back to pursue other dreams in life that have mattered more to me 'til now.

It is about relationships built over the past few months. It is just a bit difficult to have it end almost abruptly like a kite with its string cut and I needed the time and space to adjust. I think some of us will have that feeling before the year is out. I mulled over it. That evening, after cricket training, I found myself shuffling my feet with deliberate slow steps on my way home as I contemplated the change. While I felt the dip in my happy-o-meter and the heaviness of the heart, I also realized the good times and the important lessons imparted in the past few months. It was definitely not a wasted trip and hopefully the boys think so too.

I know I will definitely missed my cricket boys for their idiosyncrasies and all their bullshit. And the better news is, I will be closing the season with them after all. Three more games to go.

12-hours

A colleague of mine went to attend a course on leadership for civil servants.
It was highlighted by others that if a member of their service has worked for 2 12-hour shift, they should be entitled to a 2 days off because to be on task for that long a session in 2 consecutive days is very draining.
Then my colleague blurted out "but teachers do 12-h shift all the time" and garnered a look of shock from others.

People often have the misconception that teachers start early in the morning but get to leave school in the early afternoon. While that is potentially possible, it is often unlikely. We start our day at 7-8am, often working til 5pm-6pm just like everyone else (10-11hr) then perhaps we will go home for dinner and spent the rest of the night preparing lesson, setting questions or just clearing admin work like testimonials, cca reports, updating own work reviews etc.

Certain jobs, although have a 12-h shift, the work stays while on duty and is abandoned after shift but not for us. I guess to a certain extent, it may be a personal choice of how much more miles you are willing to go for the students you are teaching although sometimes it is not. If it is, the teachers are quite lucky. I realised that students who have teachers as parents are generally more sympathetic although the parents are often the ones who are more demanding.

That probably explains why teachers will crash to bed on Friday nights and really value their holidays when throughout the term, they are kept on their feet with really no option to slack unlike the students who will choose to hand up their work late with a lame excuse sometimes, helps to delay the admin work and creates amazingly complicated troubles.

But I think the great thing about the job is that it is purposeful and meaningful. And those who choose to stay in the service, take it upon themselves to pass on invaluable lessons, not only in the academic side but also in life. Yet the fire can only burn with sufficient support, if not the fire will be dowsed with fatigue and sadness. It reminded me of another occupation with high attrition rate: social workers. Working with them, you see the sacrifices they often have to make for the kiddos, whether is it staying really late for night activities after school or burned their wkends. But it is also this very giving nature of theirs that makes it a pleasure to work with them - and the volunteers too who are all there not for themselves.

To digress, while out yesterday morning to distribute flyers as part of our fund-raising efforts for the end-of-year CIP trip, L told me about his less glamorous past after I spotted a suspicious bruise on his eyebrows and was concerned if he has gotten into a fight. It was his willingness to confide and ability to ditch shadows of his past that deserved a clap although I could still feel the remnants of the past holding him hostage, judging from the bruise. I guess there will always be things that are harder to walk away from.
I was informed of a kid-swap too and I will be taking O who has more piercings on his face than I thought possible and throw in a mohawk, you get a lethal combination. Old-fashioned and unworldly-wise, all these piercing disturbed me and I need to suppress the teacher-ness with regard to them. I think it is a youth thing. The blood, the hormones, the belief of invincibility. When I took the opporunity to work with O, he is actually quite funny and slipped readily into the role I gave him. And the teacher-ness still did manifest but only when I guided and gotten him to do his mental sums on counting the letterboxes. I think he was quite happy with it because before I left for cricket day camp in the afternoon, he told the social worker that he got to do quick multiplication, with a smile.