Sunday 27 July 2008

human biology - What causes fingerprints to form and why is the pattern formed unique?

I would say genetic diversity is the primary reason which results in other reasons that you are looking for. At the lowest level, random crossing over at prophase I, random separation of homologous chromosomes at anaphase I, random separation of sister chromatids at anaphase II, and random fertilization: one sperm fertilizes one egg randomly.



The skin is developed from ectoderm so need to look at the formation of embryonic disc and specifically to the genesis of germ layers: ectoderm.



However, I would stick to the primary reasons, since it is extremely difficult to visualize the given formation - actually we do not have resources for it at the moment.




Very good question the last part. I have an intuition that skin develops randomly because of the above reasons. You would also need a lot of memory to make identical skins for twins! It has not been useful to have identical fingerprints between two people so evolution has not resulted into it.



Feeling surfaces and gripping are movements - not much space taken things, in contrast to the memory needed in storing the exact surfaces of skin from one generation to another. - Learning is a way to save resources here and it is a lot more efficient and than storing static information to species from one generation to another.

Sunday 20 July 2008

genetics - How many gigabytes of DNA are there on earth?

If you simply take one order of insects, Coleoptera, there are just under 400,000 described species with estimates from 850,000 to 4,000,000 species total in just this order. The number of primates is under 1,000. If your assumption of say 10MB for all other primates would be accurate, just adding in the low end estimate of 850,000 at 10MB per 1000 we are quickly at 8,500GB which seems to be a factorial out of the GB range.



So, we have a broad estimate of non-bacterial of plants, animals etc. at say 8,700,000.



Jason Gans found in a 1 gram of soil survey approximatly 1,000,000 bacterial species.



SO the total accounting for species number is totally impossible to estimate for anything at this time, let alone the genome.



Even for something as "common" as a giraffe, there are up to 9 sub-species with genome differences within each subspecies.



So, once we get them all decribed, we can then work on the genome sequence for each and get you some answers!

Friday 18 July 2008

Cell proliferation limit and senescence of embryonic stem cells and fibroblasts

Telomeres (caps on the ends of chromosomes that are gradually shortened during each cell division) determine the maximum number of times a cell can divide, known as the 'Hayflick limit'. Cells that are able to express telomerase, an enzyme capable of extending the telomeres, can divide indefinitely.



There are various types of stem cell in a body which replenish the 'pool' of cells in the tissue once they reach the end of their useful lifespan. Each stem cell expresses telomerase to lengthen the telomeres after a round of cell division. The inhibition of telomerase in somatic (normal) cells is a major 'challenge' for cancerous cells - in order to achieve uninhibited proliferation, they must express telomerase. Thus, there are many molecular similarities between stem cells and cancerous cells (well, with regards to telomerase, anyway!) [ref].



Fibroblasts are somatic cells - they are the 'normal' cells that make up the vast majority of organsisms. The only cells not known as somatic are gametes/germ cells and stem cells. They thus do not express telomerase, and have a replicative lifespan, also known as a Hayflick limit.



With regard to your question about engineering organs, there are many resident stem cells in tissues (and thus organs) that 'top-up' the somatic cells when required. As organisms age, this pool of stem cells becomes depleted [ref]. Artificially engineering an organ such as the heart (I assume this is what you mean) would be inherently difficult, as many vascular cells are not replaced, but can last a whole lifetime - this is also true for many neuronal cells. So replicative lifespan is not necessarily related to lifespan!

Saturday 12 July 2008

Does extracted DNA degrade after a certain time period?

For direct use as template in PCR runs. Chelex 100 5-10% w/v extraction. Without listing the whole protocol, in the end the supernate is decanted off and then stored at 4°C. I was under the impression that this could be stored and later used almost indefinately but two of four samples extracted several months back failed to produce a product (when it was known they should have).



Assuming no mistakes were made and the reactions were the same, is there a technical reason the template would degrade to an unusable point?



Is there a rule of thumb about how long it can reasonably be expected to last?

neuroscience - Brain + ethanol experiment suggestions needed

The main problem with what you are asking is that you want to show effects on vigilance and memory in vitro. That is just not possible: if you want vigilance and memory you need a live animal, there is no way around it.



Next point: you have an audience of non scientists, so you can lose them very quickly if you start speaking about NMDA, LTP or similar things without a clear explanation, so start with that: get a nice review (Pubmed is a good start, as always), and give a simple theoretical explanation of one of the mechanisms involved. It is then important to clearly explain the experiment you will perform, and what you are expecting to see in case there is an effect.



Unfortunately the best way to see effects on NMDA receptors would be electrophysiology. This is not trivial and, if you have never done it, I would not suggest going that way. However, if you have access to an electrophysiology setup you will most likely have access to someone who uses it, and that could make the experiment for you.



I am not an expert on this topic, but a quick research on Pubmed seems to indicate that alcohol can, for instance, reduce LTP in hippocampal neuron.
Maybe what you could do is having someone patch hippocampal neurons and show how an LTP protocol is used. You don't necessary have to show them the whole thing (I doubt anyone in a right state of mind would bare to stay until the whole experiment is performed in control condition first, and alcohol later...).



Also, the results of these experiments are often non obvious to analyse, so you should have some data prepared and analysed earlier and quickly show how analysis is performed, before showing the final results.



Calcium imaging experiments could also be used and would probably give results that are easier to understand for a laymen audience.



See for instance Fig. 1 or Fig. 5 of this paper (just the first one I found, there surely are other):
Ethanol alters calcium signaling in axonal growth cones.

Friday 11 July 2008

homework - What is the structure and function of chromosomes during interphase?


So the DNA in some chromosomes must have the pieces of information about how to do the DNA replication. - I am not sure about thing.




Genomes contain what is called the "origin of replication" - specific sequences in the DNA that tell DNA polymerase where to bind and to initiate replication.



As for your main question, I'm a little confused as to what you're asking. In a general sense, chromosomes function as carriers of genetic information. In eukaryotes, nuclear DNA is organized in the nucleus on linear chromosomes which carry most of the genetic information an organism needs to survive. In bacteria, the chromosome is a circular piece of DNA. In eukaryotes, the chromosome is also bound by histone proteins, which serves to regulate expression of certain genes and to help anchor the chromosomes to the inner nuclear membrane.

genetics - What exactly is meant by the expression "differentially expressed"?

Although each cell of your body essentially contains the same DNA and the same genes, cells in different tissues express (turn on) different genes under different conditions. Measuring differential gene expression involves looking at the amount of expression for a gene (or set of genes) in two contrasting scenarios. The contrast could be across different times, different tissues, different conditions, different related species, etc.



When, you say a gene is "differentially expressed", this is very context-specific. The phrase means nothing by itself, and it is only useful in terms of the applicable contrast. For example, the statement "gene A is differentially expressed" is uninformative, while the statement "gene A is differentially expressed in liver and muscle tissue" is descriptive--it tells you that liver tissues and muscle tissues have a significantly different level of gene A products. Often the terms "up-regulated" and "down-regulated" are also used to provide additional detail. In the context of the previous example, the statement "gene A is up-regulated in muscle tissues" tells you that the level of gene A products is higher in muscle tissues than in liver tissues.

Wednesday 2 July 2008

biochemistry - Can elements of one's environment act directly as hormones?

A hormone is defined as "a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism" (I'm just taking Wikipedia definition).



Hormones work by binding to specific receptors present on their target cells so, if there is something in the environment that mimics the hormone, by binding to the same receptor they can act as hormones: these substances are called xenohormones and can often act as endocrine disruptors compounds (EDC), by acting on various organs in the body.



Probably the most known xenohormones are xenoestrogens that are been studied as possibly harmful for human health (e.g. linked to breast cancer), and as an environmental hazards, as they can, for instance, cause reproductive problems in fish.



Xenohormones are not necessarily bad, though. Some analogs of human hormones are used in therapy, having being synthesised specifically, for instance, to have higher potency then their natural counterparts.