Monday, December 31, 2007

tumb tumb...

So much to write home about. Not really up for it though after a new year's bash ;)
Anticipation is all time high and the scale of happenings is going to go up exponentially with each day that passes.
Nervousness, anxiety, adventure, excitement and sheer joy. A mocktail of a different kind to give one the high of highs.

Sunday, November 18, 2007

Differentiated

Behavioural Neuroscience it is.
Making fruit fly larvae race and flies jump is gonna be the way of life. Of course with a little bit of genetics and electrophysiology and imaging and biochemistry. And perhaps some gene construct designing and transgenics :D *high, delirious*

Dunno if its gonna be Mumbai or Bengaluru though.

Saturday, October 06, 2007

The Chain of Chains

An E. coli cell divides. That the DNA is passed on to every "new born cell" post-division is no big deal. But along with DNA the daughter cell must also receive at least a bare minimum non-DNA things to make use of this genetic information. Which is why a cell division involves distribution of cytoplasmic goodies between daughter cells than just budding off of a replica of the original DNA molecule.
This means that every cell, each and every one of them that we are made up of and those we see around us in other beings have at least once shared a single cell membrane at some time point since the first membranated organism in the primordial soup upto this moment. And this truth will remain so as long as there continue to be cells. The mother of all chains - this cytoplasmic connection.

Tuesday, September 25, 2007

Fly Custards and Fly Jelly

Fly Custard
The corn medium has smell. I wonder how much influence that smell is having on the larval olfactory circuit which I intend to put to "adaptation/recovery" tests. The smell is a cocktail. And my worms have ploughed through it endlessly before they were abducted for a larval plate test.

Can the smell be fixed? So lets think of something else. Wish there was a Matrix like "pod" for the larva. A larva living its life oblivious to "reality". Life would be so easy for the fly worker. el yo el

Excuse me on my lack of information as basic as this. I guess the fly cannot be grown on just glucose. The vitamins et al things must be imported into the worm body as it develops and the yolk resources get exhausted. But m gonna test this one.

Fly Jelly
Lets get a fly couple to mate on an agarose gel block soaked in glucose solution. A sort of fly date on the beach el yo el. Then see if the eggs hatch and observe how far a larva goes through its development. This way there would be little smell that the larva would have seen in its "past life" and would be an olfactory virgin when I show it the aromatics during my plate tests.

P.S.: A genetic way of doing it (one of the ways (at least in principle) ) would be making a line which is conditional mutant for olfactory receptor expression and induce the receptor expression just before your plate test. But I suppose it could also have its caveats and may be plain un-doable.

P.P.S.: The P.S. was put there to save face just in case the glucose-gel-beach way was found to be just too ultra low tech by some. :D

Sunday, September 16, 2007

On Evolution

A gene may get duplicated. This may be followed by mutation in one of the copies. Functionally if this "mutated" version is very different from its counterpart then one will call it a new gene rather than simply an allele of the "original" gene. Thus a species gets a new gene. But it may also simply acquire a gene "horizontally". The rates of both these phenomenon taking place would be expected to be determined by the species under consideration. Still one may ask, generally how do they compare in their contribution to creation of new genes?
Furthermore, once a gene has been acquired by a species its maintenance would be contingent upon its contribution to the species fitness. It would be conserved if it is useful else lost if redundant (or found to be deleterious). What are the rates of this "gene dumping" phenomenon? Wondering if these "rates" could be quantitated. Then it would be interesting to compare the rate of acquiring a gene and the rate of losing a gene. Dont remember why I thought of these questions but still it would be fun to know their answers if possible.

Friday, September 07, 2007

Wiring - An Interlude : The 2nd Rotation


The promised wiring blog posts are still to arrive. Maybe I am still ruminating the ideas expressed in the last two neuro lectures (its been 2 weeks already). One was on olfactory and the other on optical path-finding. Who knows, these posts may not even happen.

Newayz.

The olfaction lecture + couple of posters on olfaction + AWS + fly seems like such a cool system + other things = too difficult to resist rotating in the olfaction lab.

So here I am. Begins officially this Monday. Already been assigned to a "project" and given a dozen papers to read. The latter in preparation of a sort of a mega-journal club this Tuesday.

If you smell what the rock... :D

P.S.: Picture - C155-Chops larval pre-exposure to excitatory light just before the the "Larval Plate Test".

Wednesday, September 05, 2007

Wiring : An Interlude - DBS TIFR AWS On Adult Neurogenesis

Epigenetic mechanisms speculated in neurological stress response in maternal separation paradigm of mice neurobiology model.

This one hit me like a bullet. Shaken.

Sunday, August 26, 2007

Wiring : An Interlude

The answers are coming.

-Morpheus to Neo, The Matrix.

Friday, August 24, 2007

On Biological Evolution

Neo-darwinism is a thing of beauty. These days it hardly happens that one does not suspect it to be behind a given biological phenomenon. But it mostly comes as an after-thought. I wonder if it has any predictive use at all.

Monday, August 13, 2007

Wiring 1

Was feeling a little under the weather. I hope a dengue bearing mosquito is not to blame. Damn! I could feel I was not at my analytical best. But it was a neuro lecture, so a hightened sense of understanding was my default state. Could have been much better.

So the questions...

The lecture moved on. I was getting kind of desperate as it seemed the answers weren't on the menu. The lecture began with a recap session which seemed unusually long. Then the flow of the discussion kept getting led astray mostly due to certain over-enthusiatic individuals who seemed to get ahead of themselves. A pack I think I once certainly belonged to and one which I think I am transiting. Let the prof talk, you might lose out on some vital insight in your attempt to push/validate your ideas amidst the discourse. This is some sort of a policy that I have (unknowingly?) adopted these days. Wait and watch and pounce when you just have to, an almost compulsive act.

All in all kind of less than my expectations (greed?). But...

At the end along came an idea. A classification of memories was touched upon slightly. Motor memory and declarative memory. My face might have lit up. Yeah, just when I was gonna conclude a wasted lecture. "Functional memories". I felt reassured. I have not been reading useless stuff after all; amidst short naps on the D-block library couch.

I am glad I saw a thread. At the end of the lecture. So be it. Have been promised a talk on the developmental problem of the sense of smell in the next lecture by a seasoned and a highly motivated student. Also have been urged to do some home-work on how the smell problem was such a special problem before it was cracked by a certain Linda Buck. Will fit in the home-work thing tomm since kinda jobless these few days. At least until 21st when I get my time on the NMR machine again...

The sense-of-smell talk is going to be interesting in every way.

Friday, August 10, 2007

Reality Check

After attending a neuro causerie.
I wonder whether when I myself master the jargon and fluorescent imagery my past scriblings will seem even to me as nothing more than idle doodling. (Not that they don't at all seem so now :P)

Thursday, August 09, 2007

The Wait


In the coming couple of weeks my neurobiology course will conclude. It will end with how-the-brain-gets-wired themed lectures. I guess two of these plus a lecture focused on a special kind of wiring - the wiring of the optical pathway. Nothing less than a feast.

Following are the typical questions whose answers I will be fishing for in these lectures.
  • The basis of instincts. Especially the behavior of just born calves. Where does this information come from?
  • Nature of data structures. Is the location and form of a given memory identical (or at least similar) in two different humans? For e.g. say the neuronal data structure corresponding to a given memory - say the English numeral 1 (i.e. basically a shape).
  • Imagination. Imagination is a brain activity unlike other brain activities such that you have neuronal activity in absence of an external input. How does one imagine?
  • Perception. Making an image of the world around you is a biological challenge in itself. A 100% biological lens followed by a bunch of 100% biological cables and ultimately a 100% biological "processing center". Marvelous. Still, beyond that how does an individual perceive an object. For e.g. when I see a square I feel a square. I wonder if some kind of reflection phenomenon - reflection of neural impulse encoded information within the brain would be necessary for perception. Say back and forth between the two cerebral hemispheres. This question is perhaps intricately related to the puzzle of imagination stated before.
Yeah, pretty much it. I hope to get at least a start towards solving these puzzles from these lectures. A reasonable expectation I suppose.

Wednesday, August 08, 2007

BioSphere


Biology is like a sphere. Every worker thinks the field he is researching is central to biology.

Monday, August 06, 2007

On Biological Evolution

Following two general ideas about biological evolution are the result of an informal discussion with a fellow colleague.

  • The period just before advent of cell membranes is what I shall refer to as the late primordial soup times. Assuming that during this period organic compounds which would be sources of carbon skeleton and free energy would be available in plenty and hence would not be a limiting factor for the survival of contemporary biologicals; it would be a free lunch. One would therefore expect the evolutionary pressures to be relaxed. However, after membranes were invented these diffuse biologicals would get a sense of individuality. Evolution would now have a well defined target for it to act upon.
  • When faced with a challenge only those cells who have invented a biochemical pathway to solve it will survive. But it probably was when the cell found a way to document this information in the form of genetic information that evolution got a firm substrate to work upon. With it also came the concept of "next generation of cells" who would re-use their ancestral biochemical logic than re-invent it. But the beauty is that the system still allowed for new experiments, in essence allowing the ancestral logic to be overriden.

The events following post-genetic material times probably are just biology trying to solve its own engineering problems.

Saturday, July 28, 2007

Functional Networks

Was reading a book in the D-block library today. Some brain-memory book, will tell you the name next time I edit this blog.
A pretty fantastic idea was expressed in it or so I believe. That it would be wrong to think of brain memory on the lines of computer based memory. Computer based memory has an "address" element attached to it. But a brain "memory" is functional.
By functional I mean that say in response to an external stimulus an individual has say two different reactions and the reactions are such that they require the usage of motor neurons. Each reaction will have a motor neuron firing pattern. The decision as to which of these two motor neuron bunches is fired will rest upon input from common node or a branch point. The memory read operation is thus integrated with its actual implementation or the final outcome.
The decision as to which bunch gets fired at a given time is clearly determined by the strength of the connection to this node. Beauty is this strength of connection is experience modifiable.
But hey, it was just a model...experiments might show an extremely strange picture. Plus this is a Saturday evening blog post :D
You never know.

Wednesday, July 18, 2007

Sab maya hai ?

virtually real ?...maybe. *shrugs*

Saturday, July 14, 2007

Fixity



...that one always has a choice.

Wednesday, July 04, 2007

3 . c 0 L 1 1%

>gi49175990refNC_000913.2 Escherichia coli K12, complete genome *


. . .

I guess I didnt have anything else to post. Sometime back I downloaded the E.coli genome sequence and placed the fasta file on my desktop for my amusement. Whenever I looked at that file I could not help but smile in my mind and nod slightly at the screen. Here is an organism - a bacterium frozen in a text document. Life cannot get more digital...



*only 1% sequence was posted, posting the whole genome would freeze the browser.

Monday, May 28, 2007

...phew !

but this is only the beginning...

a sense of belonging...what one does now is no longer going to be just personal curiosity...a concerted, directed effort backed by dedicated personnel and resources.

no trivial pursuits...not that they were ever so to oneself...but the way the world sees it...

one has now been absolved of the guilty pangs accompanying post-Lewin et al sessions...

i had coffee twice today. one frappe at the bangalore airport. one hot coffee aboard the Mumbai bound flight...

ones cAMP must be on overdrive now...caffeine can drive one crazy...phew !

Wednesday, May 16, 2007

Something On Genome Wide Repeats


Was readin up on chromosome organisation in Watson. Something came to my mind. Two things actually.

Transposon Dating: How rare are human transposition events? Can those sequences, which are relics of transposition events found in the genome-wide-repeat subset of the intergenetic DNA, be used for phylogenetic analysis ?

Gene Pool Hypothesis: DNA sequences in the genome wide repeat subset of the intergenetic zone are thought to be relics of transposition events. They play no functional role in the species with respect to lending their DNA as an expression template. Can one expect the evolutionary pressures to be relaxed on these zones relative to actual protein coding/regulatory genetic zones? If so, then could this rich pool of variable DNA sequences serve as a birth place of novel genes. A genetic nebula. Such novel genes, if they exist at all and are discovered would be expected to bear little homology to other pre-existing genes.

If a tree based on sequence homology for all the 27000 human genes is constructed what would it look like?
1.What is the kind of homology amongst these 27000 genes?

2.Out of them how many would have a true common single ancestral gene and how many would have formed independently of this ancestral root? Or how many roots can account for the entire human gene repertoire?

3.Would these independently formed nodes in this tree be good places to look for genes which makes humans more so than say other primates?

4.Have any of the above independently formed genes been derived from mutation in the transposition-events relics found in the genome-wide-repeat zones in the intergenetic DNA (discussed previously) ?

5.Can the above mentioned zones give rise to sequences coding for trans-regulatory-RNA apart from or if not full-fledged genes?

If any of the above 2 mechanisms are real then some of the complexity of humans can be ascribed to the above gene forming pools of the junk DNA component of the human genome.