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Which organism has the smallest genome length?
Which animal/plant/anything has smallest length genome?

Since you said plant/animal/anything, I offer the smallest genomes in various categories...
(Kb means Kilobases, Mb means Megabases. 1 Kb = 1000 base pairs, 1Mb = 1000Kb)

Smallest plant genome: Genlisea margaretae at 63Mb (Greilhuber et al., 2006)
Smallest animal genome: Pratylenchus coffeae (nematode worm) at 20Mb (Animal Genome Size DB)
Smallest vertebrate genome: Tetraodon nigroviridis (pufferfish) at 385Mb (Jailon et al., 2004)
Smallest eukaryote: Encephalitozoon cuniculi (microsporidian) at 2.9Mb (Vivarès & Méténier, 2004)
Smallest free-living bacterial genome: Nanoarchaeum eqitans at 491Kb (Waters et al., 2003)
Smallest bacterial genome: Carsonella ruddii (endosymbiont) at 160Kb (Nakabachi et al., 2006)
Smallest genome of anything: Circovirus at 1.8Kb (only 2 proteins!!) (Chen et al., 2003)

Refs...

Chen, C.-L., Chang, P.-C., Lee, M.-S., Shien, J.-H., Ou, S.-J. & Shieh, H.K. (2003) Nucleotide sequences of goose circovirus isolated in Taiwan. Avian Pathology: Journal of the W.V.P.A. 32 (2), 165–171.
Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S. & Barthlott, W. (2006) Smallest Angiosperm Genomes Found in Lentibulariaceae, with Chromosomes of Bacterial Size. Plant Biology. 8 (6), 770–777.
Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., Nicaud, S., Jaffe, D., Fisher, S., Lutfalla, G., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 431 (7011), 946–957.
Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H.E., Moran, N.A. & Hattori, M. (2006) The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella. Science. 314 (5797), 267–267.
Vivarès, C.P. & Méténier, G. (2004) Opportunistic Infections: Toxoplasma, Sarcocystis, and Microsporidia. In: World Class Parasites. Springer US. pp. 215–242.
Waters, E., Hohn, M.J., Ahel, I., Graham, D.E., Adams, M.D., Barnstead, M., Beeson, K.Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X., Mathur, E., Ni, J., et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proceedings of the National Academy of Sciences of the United States of America. 100 (22), 12984–12988.

The plant and bacterial ones I had floating around in my memory having read about them previously, so a bit of googling confirmed the names. The animal ones I got from the Animal Genome Size DB, and from Wikipedia. I guessed that viral genomes would be the smallest, so I also searched for the smallest viral genome. Then I went back to the literature (by searching Google Scholar for organism name + "genome size") to check all my facts and provide reliable references.

Nice answer Richard.

Smallest free-living bacterial genome: Nanoarchaeum eqitans at 491Kb (Waters et al., 2003)
I downloaded this paper it says that this is archaea and its obligate symbiont not a free living bacteria. Please read carefully and then upload it.

"Smallest genome of anything" is wrong. There are virus-like elements like viroids with as little as ~200 bp 'genomes'. Some viroids have as little as one RNA enzyme, others have not even this.

I want to say Mycoplasma genitalium with a genome size of 582,970 bp. Turns out the answer is Nanoarchaeum eqitans with a genome of 490,885 bp.
http://en.wikipedia.org/wiki/Nanoarchaeum
http://www.ncbi.nlm.nih.gov/pubmed/14566062

That's the smallest genome of a free-living organism. And until 2003 you would have been right about Mycoplasma, which were previously the smallest known in that category.

Both Mycoplasma genitalium and Nanoarchaeum equitans are obligate parasites / endosymbionts. This means that they depend heavily on their host to support their vital functions and they have lost many of their own genes.
A really free-living organism with an extremely small genome (~1309 kbp, 1354 genes) is the heterotrophic marine alpha-proteobacterium Pelagibacter ubique [1].
See a larger analysis here: https://alamot.github.io/smallest_genome/
[1]: https://www.ncbi.nlm.nih.gov/pubmed/16109880 Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005). «Genome streamlining in a cosmopolitan oceanic bacterium». Science 309: 1242–1245.


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How often does parthenogenesis in mammals happen?
Probably everyone knows that mammals can't produce viable offspring by parthenogenesis.
But there are reports of human chimeras (see: a human parthenogenetic chimaera) and it's known for mice to quite often develop parthenogenetic embryos that will not survive past the 10th day of gestation (see: birth of parthenogenetic mice that can develop to adulthood).
So, how often does parthenogenesis happen in mammals and how long do parthenogenetic embryos survive? I have heard an estimate that 0.01% of human blastocystes are parthenogenetic with gestations always ending in miscarriage before the 3rd month, but I couldn't find any source for this claim.

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What are cranial nerve nuclei?
I am having a really hard time trying to understand what cranial nerve nuclei are. I have been reading/watching videos and I keep hearing, "that is where the cranial nerves make connection with the brainstem." Also, I keep hearing that some cranial nerves may have multiple nuclei and some nuclei may have multiple nerve synapsing there; however, this information doesn't really help me understand what they are. Are they a processing center? If so, doesn't information get processed in the cortex?
So the main question is: What is a cranial nerve nucleus and what is it's function? What does it mean by "where nerves make connections"?
I am attaching the image which I've been studying. You may refer to that when answering this question.

Nerves (including cranial nerves) are constituted of neurons, and other supporting cells and structures (e.g. myelin sheath and extracellular protein matrix). Neurons are highly specialized cells that have a particular cellular anatomy:

As you can see, the cell body (or soma) contains the nucleus, and projects it's axon towards other structures in the body, sometimes more than a meter away! Cranial nerves (like other nerves) are a collection of the axons, not the cell bodies themselves. The cell bodies reside together, in the brainstem, forming what we call nuclei. So that's simply what they are.

That makes more sense now. I was overthinking a "nucleus". But the reason I was doing that was because of the picture I posted. How would interpret those colored columns and relate them back to this? I am thinking that those colored columns represent different types of nuclei? If so, how do you explain their size?

@JagmeetSingh The colored columns represent the nuclei themselves. The larger they are, the larger the number of cell bodies and the bigger the nerve they project. For example, the sensory part of the CN V (Trigeminal, in blue) innervates the skin of the whole face, whereas CN VI (Abducens, in yellow) innervates one single extra-ocular muscle (the lateral rectus). So you can imagine why the trigeminal sensory nucleus is much larger than the abducens nucleus.

A cranial nerve nucleus is not the nucleus of a nerve cell (neuron). As Wikipedia says, a cranial nerve nucleus is a collection of neurons in the brain stem.

@mgkrebbs That contradicts what Maljam said. Do you know where information (sensory or motor) goes after it synapses at the nuclei and via what medium? Am I even thinking in the right direction? If so, I am slowly starting to understand CN nuclei, even though the long colored columns still confuse me.

The neurons of a CNN connect cranial nerves to the brainstem.  Information flows both ways: sensory neurons within a CNN conduct info from the associated cranial nerve into the brainstem, and motor neurons in the same CNN conduct info in the reverse direction into the same cranial nerve.

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What is this spider found in day time?
.
South India
Arm to arm about 3 inch in length. Day time. was hiding inside a cardboard storage box.

It's definitely a species of Huntsman spider maybe of the genus "heteropoda" or "olios". Sorry I couldn't be more help.

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Is there a method to isolate half of the chromosomes of a cell?
Each cell has 2N number of chromosomes, I wonder if currently there is a technique allows isolation of N number of chromosomes out ?

Hi and welcome to Bio.SE! What problem are you having and what research have you done so far? Have you considered extracting DNA from gamete cells, likely sperm? That may suit your purpose.

does meiosis count?

Thanks for the reply , I am thinking some procedure or tech other than gamete cells, like extracting N number of chromosome from a somatic cells like epithelial cells? :)


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Amplification technique for proteins similar to PCR for DNA?
I know PCR can be used to amplify a tiny sample of DNA in order to perform experiments. Is there a similar technique to use on a protein sample? More specifically, I'm not interested in "cutting" up the protein but simply making more of the original sample.

You can't amplify proteins. You just have to express more and/or purify better.

You can use in-vitro translation kits but they require mRNA as a template and the amplification is not exponential as in PCR. There is no biological mechanism to synthesize proteins using themselves as a template. This is unlike the DNA and RNA.

PCR takes advantage of the polymerase mechanism, which can build more nucleic acid from a template of nucleic acid. There's no such mechanism by which protein can be produced from a read of protein, as it's really the ribosome which produces protein from a nucleic acid template, right? As canadianer notes, you can only hope to express more, and purify it nicely!

Pull down the gene, make a cDNA and clone it into a high copy inducible expression vector. Transform bacteria or yeast and grow a culture under selection. Let them grow to 10^10 or more, then induce expression. Purify lots and lots of protein. If you can't get the gene, then you could undertake the very difficult task of sequencing the entire protein. Then you make a synthetic cDNA from the sequence and use that in your expression vector. You cannot get around the Central Dogma; DNA<->RNA->Protein

There isn't any technique with one exception. PCR generates DNA from DNA so you can establish cycles. For protein synthesis, an mRNA is a template to produce proteins. Most likely proteins you are interested in would not synthesize mRNAs, so that you can not establish cycles.
The exception I said earlier is Protein Misfolding Cyclic Amplification (PMCA). Some disease associated misfold proteins can induce misfolding of the same polypeptide which is not misfolded. So you can establish cycles of misfolding reaction.
PS:
There are technique to synthesize proteins from DNAs or RNAs, but they are not chain reactions.
https://www.promega.com/products/protein-expression/eukaryotic-cell-free-protein-expression/
https://www.neb.com/products/e6800-purexpress-invitro-protein-synthesis-kit

It is impossible to amplify protein like PCR. DNA and RNA can undergo PCR because basepairs are complementary: A-T C-G A-U. But amino acids are not complementary; can you find an amino acid that matches glycine? Besides, proteins are not only a single polypeptide chain like DNA, proteins need to be folded after polypeptide chain are synthesized. Usually a protein molecule need more than one polypeptide chain to combine together to form a protein molecule. It can not happen that it works as PCR.

I would say impossible is a stretch. An inventive biochemist could create molecules that are "complimentary" to each amino acid similar to a Dna polymerase. Then a protein would be needed to both detect and translate this similarity into protein elongation. Unlikely, hell yes, impossible, no.

-1. There is literally no known mechanism through which this can be carried out. Designing functional proteins de novo is way out of reach of modern biochemistry.

Even if you succeed in that process, the protein is still linear or worse.

there multiple mechanisms for testing this methodology. Why would anyone initiate this process de novo? Evolution both in nature and the lab starts from a pre existing template. And all proteins are linear to begin with.


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Why is cognitive maturity related to organism lifespan in larger animals and mammals?
I am not a student of biology, so I should provide some context to me asking this rudimentary question. While doing a graduate-level course on Reinforcement Learning, the instructors focused on how we as mammals have such amazing intellectual potential and how we tend to learn by examples of outcome based on our actions. This set me thinking about the high disparity between different species of multicellular organisms in how we mature.
I would state a couple of examples to back my point, I am unsure if this list is conclusive or not.
Elephants(Average Lifespan: 60-70 years): Elephant babies tend to stick to their families until they generally mature.
Humans(Average Lifespan: 70-80 years): Human babies are generally dependent on their parents for at least 8-12 years before they start demonstrating some intellectual maturity, which is a good 10-15 percent of their average lifespan)
Birds(Average lifespan is species-dependent, but assuming a 10-year span): Bird offsprings are extremely fast learners and tend to veer off independently within months of their birth.
Fishes (Medium to short lifespan): Not an extremely well-publicized parenting method for their offspring. Fishes learn to swim and hunt for food at extremely young ages, which is a sign of cognitive maturity.
Insects (Short Lifespan): Generally parenting is related to feeding offsprings for a short while before they become entirely independent.
As can be observed, the general span for the attainment of cognitive maturity in such organisms seems to be an inverse function of the average lifespan of the parent, and I wonder, what could be the reason for it?
I absolutely apologize for any inaccuracies I might have cited because what I state is purely from a layman's observational perspective. I would be delighted to know what the bright folks here have to say on this matter.

This answer might not completely answer your question, since this just explains the case in humans, but I think you can give this a read while waiting for a more accurate one. I would recommend you to read this amazing paper.
Generally, across animal species, the longer it takes an organism to reach maturity, the longer it lives. How the timing of onset of maturity relates to longevity in humans, is still a matter of debate. In this regard, it is of special interest whether the onset of intellectual maturity is associated with longevity, as the brain and associated parts of the central nervous system comprise an organ system that is widely thought to have played a vital role in humans’ evolutionary success.
First, they talk about defining cognitive maturity:

It would seem intuitive to define intellectual development as that part of the lifespan in which ability increases and intellectual maturity as that part in which ability plateaus or decreases. In such a model, an inflection point or peak in ability would mark the onset of intellectual maturity. It is unlikely, however, that the multidimensional abilities of composing and writing reach their peaks when a composer's or writer's work is made public for the first time. Rather, we regard maturity as a state that is attained when a certain relevant threshold is crossed, regardless of whether ability increases after that point.

Looking into the case of humans, it may be either a genetic mechanism or plasticity that couples rate of development and maintenance and repair. In the former scenario, genes that alter the rate of development such that maturity is reached earlier, would have as a concomitant effect the downregulation of maintenance and repair, leading to a shorter lifespan. (This is a shortened version- please go through the paper for more detail)
They conclude stating that the onset of intellectual maturity is associated with longevity. So, you are right about cognitive maturity of an organism being related to its age, and it points out to a really interesting result- blooming composers and writers live longer than child prodigies- as pointed out in a paper in ResearchGate.
What could be the reason for it? American psychologist Jerome Bruner proposed the purpose of the period of immaturity as being a time for experimental play without serious consequences, where a young animal can spend a great deal of time observing the actions of skilled others in coordination with oversight by and activity with its mother. So, there is the obvious need for a period of immaturity and this varies amongst different mammals. (source)

This was indeed insightful!

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What triggers creative thought in humans?
Creativity, innovation and ideation. Is there something in the brain that makes the brain think that way, as opposed to "normal baseline". What triggers creative thought in humans?

Define idea, please. I have no idea what you mean with the term.

I mean the positive effect on cognition that allows a person to be innovative, think of new things, and in general be more creative.

I'm quite sure that, if there is such a system, evolution will select against it. Most people live quite well without being innovative or running after any new idea they come up with. I really think you're overly optimistic about the idea. Einstein also said genius is 5% inspiration and 95% transpiration.

Being overly optimistic about the idea supports my point :) This is exactly what I'm interested in - what are the systems involved in this and how long does it take for the system to reach homeostasis, where a person is no longer excited about the idea.

But don't you see? Being overly (!) optimistic about anything is a source of illusion that can, in the extreme, get you killed and certainly shortens your lifespan if applied constantly. That's why I said, evolution will select against it.

@rwst, I guess you a re a plant guy :). In animals, it is perspiration and not transpiration.

So you mean creativity?

Cretivity, innovation or ideation. What makes the brain think creative thoughts?

@rwst, innovative people would have been more likely to live longer than those who couldn't invent things.  Tribes that could invent tools and weapons would surely outlive tribes that could only use their bare hands to catch food.


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Can parts of a human brain be asleep independently of each other, or vary in the times required for them to fall asleep?
I know that some birds and marine animals can continue complicated activity (swimming, flying?) while one hemisphere of their brain is asleep.
I'm interested if human brain has some parts of it that can be asleep while others are awake? In other words, can a human brain be only partially asleep while experiencing insomnia or similar sleep disturbances?
If human brain can have different parts "sleeping" independently of each other, is it possible that the times to "fall asleep" vary between these different parts of the brain?
I would appreciate research articles on the topic or just the names of brain regions that may exhibit behavior described above.
Update: I've taken a look at R&K "principles and practice of sleep medicine"' and it mentions the following parts as involved in sleep:
Medulla, preoptic area, hypothalamus, thalamus, entire neocortex involved in NREM.
Neurotransmitter systems: histaminergic, orexinergic, serotonergic, noradrinergic
Sleep factors: adenosine, interleukin-1 and other cytokines, prostaglandin D2, growth hormone releasing hormone, nitric oxide, all promote sleep in or around preoptic area.
This makes me hypothesize that drugs that modify the effects of these systems (ex- caffeine affecting adenosine) could result in sleep- related disturbances in these systems, potentially causing them to fall asleep later that usual. But I'm looking for more info to fihre out if this is true

Related CogSci question: http://cogsci.stackexchange.com/questions/3602/what-is-the-mechanism-behind-unihemispheric-sleep-in-animals

Reading K&R "Principles and practice of sleep medicine" 4th edition, on page 15, under sleep onset I've noticed the following paragraph:

Is "falling asleep" a unitary event? Our observations suggest that it
  is not. Different functions, such as sensory awareness, memory,
  self-consciousness, continuity of logical thought, latency of response
  to a stimulus and alterations in the pattern of brain potentials all
  go in parallel in a general way, but there are exceptions to every
  rule.

The book continues to mention that it is possible to drift in and out of sleep for a few seconds.
I've became aware of experiments on split brain patients (severed corpus colossum) which revealed that two brain hemispheres have their own conscious awareness. Some experiments even paralyzed one hemisphere to see how the other one responds. As such, it appears that a human can function with only one hemisphere active at a time.

Have you ever tried to read a complicated book after several hours of hard work that required a high concentration? Imagine that you have forced a particular area of your brain. After a hard work, the areas of the brain that we used to finish a work seem don't respond to any stimulation and make us feeling tired and as we can't understand what we are doing anymore. This happens because we have forced that particular area of the brain and it needs to reinforce the connections it made and to do this, it has to sleep, such as we do during the conscious (you know you are going to sleep) sleeping. Eventually we can say that some particular areas of our brain must sleep if forced to a hard work and they do it when you feel like you can't get something which you know you can. A recent study has demonstrated this by understanding physiological functions of sleeping.
Nature article of Vyazovsky V. et al. Vol. 472, pages 443-447, April 2011 (I am not copying the link anyway, have to search it by yourself). Or to Science of Bushey D. et al. Vol. 332, pages 1576-1581, June 2011. And on Nature Review Neuroscience of Diekelmann S. And Born J. Vol 11 number 2, pages 114-126, February 2010.

Can you add some evidence to your answer, backing this assertion up, such as the "recent study" you refer to?


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Are there special constants in biology that define organism's morphology?
In math, there are special numbers, like Pi (3.14159...) and e (2.71828...). In chemistry, there's numbers like avogadro's number (6.0221413e+23). For example a circle can be defined in terms of 2 * Pi.
Are there any significant constant numbers in biology that define the shape of an organism (ex: mammal)? I'm talking about stuff like shoulder to hip ratio or length of an organism, etc?
Here's an example that came to mind - different fetuses developing into different organisms. Is there any constant that is the same for these at some stage of development? Like the ratio of head to tail?

A fundamental idea of biology is individual variation. Though I don't know, I expect that there would be few, if any, constants shared between members of a group (outside of the molecular level).

The golden ratio turns up in a lot of places, if that's what you mean

To give context to the question: I'm interested if there are some numerical patterns to gene expression during organism's development.

I don't know if this is what you mean, but take a look at BioNumbers.
Also, mathematical constants like pi are different from physical constants. Mathematical constants are true in a mathematical (logic) sense, and do not need to be related to any physical quantity. They are derived by logic. Physical constants, on the other hand, typically describe an observed relation between two types of quantities. They are derived by measurement.


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Does artificial heat (shower/tea) affect diurnal rhythms in humans?
I've been reading that over the course of the day, human body temperature follows diurnal rhythm with the lowest body temperature observed some time close to the middle of the sleep episode, while the peak body temperature is observed some time close to sunset.
Circadian rhythm on Wikipedia
I'm interested if humans have internal organ systems or brain "sensors" that "read" the body temperature as a part of synchronizing their own internal circadian clock to the master clock of the human body.
If there are indeed such sensors, then I'm interested if they can be thrown "off track" by artificial heat sources, like hot food, drinks or showers.

Well if temperature follows optical input, then it's not the other way round, is it? With warming up your body, you may get all sorts of psychological effects that obscure the rhythm but you can't simply exchange cause and effect of the diurnal cycle.

I've clarified the question to address your comment. Could temperature be a part of how circadian oscillators are synchronized?

Yes, the human body has thermoreceptors that "sense" the current temperature, but these merely help with regulation--you know, shivering to raise internal body temperature and sweating to cool via evaporation. The hypothalamus is primarily responsible for making sure that the circadian rhythm itinerary is adhered to reasonably well. So no, if the thermoreceptors detect that the body temperature is 97 deg F but it's 5 pm, the body will not "get confused" and decide that it is actually 4 am because a human body is about 97 deg F at 4 am.


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Are these Gram stain substitutions acceptable?
In the context of a Gram stain on a blood smear:
Are the following acceptable substitutions and/or what differences could arise by substituting them?

Using methylene blue instead of crystal violet
Using carbol fuchsin instead of safranine

I've seen text implying they are OK substitutes, but didn't find anything saying the if, why, or problems associated with replacement.

I'm not a biologist.
From a chemist's point of view, these molecules should have similar polarity. Their structure is very similar, actually.
Considering your replacement rule is correct, I would say there wouldn't be much effect other than observing different colors. What is also plausible is that you'd have to reverse the interpretation of your results, e.g. methylene blue stains X, but crystal violet stains Y whereas carbol fuchsin stains Y and safranine stains X.
Was that clear?


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Does an annealing temp higher than primer's Tm contribute to primer dimer?
I am attempting to reproduce results from a number of journal articles all referring to the same SNP. In doing this I'm using the same primer set outlined in the articles. When I attempted a run the other day I experienced what I can only assume was primer dimer (~40bp product, bands not visible at expected bps.) While the primers and restriction enzyme were the same among numerous articles, the annealing temperatures in the reaction varied a fair amount (52-59C). All were above the individual Tms of the primers which struck me as odd.
Calculating the Tm via primer blast here are the numbers:
Forward Tm: 50.14  [5'-GCTCTACTTCCTGAAGACCT-3']
Reverse Tm: 51.67  [5'-AGTCTCACTCACCTTTGCAG-3']
Other sites gave slightly higher numbers (54-55) but they are still below the 57C that I used in my reaction. I do not have access to a gradient thermocycler otherwise I would have tried a range myself.
If an annealing temperature is chosen above the individual Tms how do the oligos have a chance to anneal with the template and eventually extend? I remember hearing the Tm calculation is more involved and includes finding where the melting curve changes direction. But on the surfance I would think the primers would never have a chance to anneal at such high temperature? What is wrong about my interpretation?

What kind of polymerase are you using?

Using a Maxime PreMix which includes Intron's i-Taq

I don't think primer dimers are your primary concern here. Usually in my experiences, I get primer dimers all the time, even if the reaction works and I get my bands of interest.
Maybe you ought to troubleshoot other aspects of your PCR that might account for why your reaction isn't working. Have you tried using a positive control with your primers? You may try varying the parameters of your PCR as well. Remember, standard Tms are calculated according to a 50mM salt concentration: is that what you're using?
Generally, if the annealing temperature is above the predicted Tms of your primers, this represents a more restrictive and selective amplification of your target. You usually use a high annealing temperature if you're seeing lots of non-specific products. Since you're seeing no products at all, consider lowering the Tm to that of your primers (50º).
If you start seeing non-specific products at that Tm, I'd do what we call a "Touchdown" PCR -- that is, you start the reaction at a higher annealing temperature, and as each cycle progresses, it "touches down" to a lower annealing temperature. The principle behind this is that it starts it off at a restrictive temperature -- so your yield is very low initially, but then by gradually decreasing the "restrictiveness" of the reaction, your yield will improve. This will still prevent non-specific amplification b/c the less restrictive amplification will be on the fragments already amplified from the restrictive condition. Remember, biology is not exact science. Just because something says the Tm is such and such does not mean it's absolute and doesn't give you some margin of error. For example, we exploit that margin of error to optimize our experiments in the example I outlined above.
Anyways, (might have went on a tangent a little bit) you also have to consider how you designed your primers. Primers wil high self-complementarity will self-anneal at higher Tms.

"biology is not an exact science" made me chuckle - just don't tell the chemists and physicists or they'll never let us live it down!

@RichardSmith They way I learned it: Me: So, where can I find a volumetric flask? Post-doc: scoffs Who do you think we are? Chemists? :)

Ironically this is one of the few times were I didn't design the primers and used what was mentioned in numerous papers.

@bobtheowl2 Hm.. This may be a last resort thing (and may take a million years) but you can always send an e-mail to the authors of those papers and see if they can help you optimize your reactions or share with you how exactly they did it.

Primer Tm calculations can vary significantly based on the method used. What I can tell you, is that the Tm really depend on the polymerase you are using for the PCR reaction and for each polymerase there is a set of PCR conditions you have to follow.  As I use Phusion® Hot Start High-Fidelity DNA Polymerase from Finnzymes, I will give you an example with it:
First of all, it is suggested to use the Finzymes Tm calculator to determine the Tms of your primers. Usually the Tms are higher than the ones calculated by IDT. Then, according to the length of your primers, different annealing temperature should be set:

for primers > 20nt, anneal for 10 – 30 seconds at a Tm +3°C of the lower Tm primer
for primers ≤ 20nt, use an annealing temperature equal to the Tm of the lower Tm primer

When calculating the Tm of your primers with the calculator:
Fwd primer Tm is 57.27
Rev primer Tm is 60.21
As they are 20bases long, your annealing temperature should be 57 degrees.
You are right that the annealing temperature shouldn't be higher than the Tm of the primers. I think the problem is that different polymerases and different Tm calculators are used in the papers you are referring to. I can discuss other PCR optimizations but let me know first whether the problem is not just the anneaning temperature.

I like your example and calculation. I guess I didn't think Tm was so polymerase specific before. Coincidentally it ends up at the same annealing temperature that I tried though.  Unfortunately the taq I am using gives very little information (and not an online calculator) in regards to choosing temperatures. I am close to ordering a new mastermix anyway, so I will likely try a different brand then. But as for my current problem there are enough variables that I plan to try the same annealing temperature again and if that fails completely then I may look at what @jp89 suggested also.

You can also contact the authors of some the papers you are trying to reproduce and ask them about the specific conditions they used. You shouldn't spend much time troubleshooting this by yourself.

Hey what happened with your experiment?


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Where does Taq polymerase migrate during electrophoresis?
Assuming a 1% Agarose gel with TAE.
Follow up questions:

Is there a way to stain for it?
Could the polymerase be captured and reused?

Unlike in an SDS-PAGE, where the SDS adds negative charges to all proteins, in a standard agarose gel for nucleic acids all proteins should move according to their own charge.
You can get a rough idea in which direction Taq would move by getting the amino acid sequence and calculating the isoelectric point at the pH you are running your get at. It might be that the protein isn't even negatively charged at this pH, then it would move in the opposite direction of the DNA out of the gel.
An exact prediction is rather hard, as it depends on the shape and size of the protein, the pore size in the agarose gel and the exact charge. It is not as simple as for DNA. You would have to just try it out to get an accurate value.
You can use any common method of staining proteins like Coomassie.
I think reusing the Taq is very unrealistic. It is still pretty stable at higher temperatures, so it will probably survive the temperatures the gel is running at. I would guess that you lose so much during PCR, gel and purification that it would not be worth the effort. And you would need to purify it extremely well, unless you want to amplify the same DNA in all your future PCR reactions. Any DNA contamination left from your gel might interfere with your later reactions.
If you require a very large amount of Taq and want to cut costs, I'd rather try and produce and purify the enzyme yourself. That should save you a lot of money if you really use a lot of it, but it is likely not worth it on a small scale.

A very good question and a better answer, these were.

The calculated isoelectric point of Taq polymerase is 6.03, and the pH of TAE buffer is 8.0, so Taq is below its pI and is therefore negatively charged, like the DNA.
Taq polymerase is indeed very easy to prepare. There is a protocol here but this requires you to find a suitable strain carrying an expression plasmid. Perhaps another SE.Biol question?


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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?

Related: http://biology.stackexchange.com/questions/973/how-long-can-i-store-extracted-rna

My rule of thumb for DNA samples (in TE or water) - if I have plans to use it that week, I store at 4C. If I plan on using it within a month, I store at -20C. If I'm not sure when I will use it, I keep multiple aliquots at -80C. DNA can degrade by acid hydrolysis in water, because of contaminating nucleases in the sample, and by multiple freeze/thaw cycles.

Is there any long term storage option at room temperature? http://biology.stackexchange.com/questions/2231/how-to-diy-preserve-pet-dna-today-so-that-it-can-be-used-in-20-years
-Thanks!

DNA has a half-life of over 500 years under perfect circumstances. However, DNA degrades over time, and when kept in solution, it is difficult for there to be exactly 0 microbes, DNases or chemicals present which can hydrolyze the helix. It degrades over time and old DNA samples kept even at -20C very frequently show poorer results, especially when it is thawed repeatedly. Primers can also degrade gradually at room temperature, etc.


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How can promoter binding sites be determined?
I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it to be the housekeeping $\sigma^A$. However I have found out from the Bacillus subtilis transcription factor database, that $\sigma^A$ binding sites have been found in the promoters of $\beta$ (rpoB) and $\delta$ (rpoE) subunits, and a whole bunch of alternative $\sigma$ factors, but it says nothing about $\alpha$ or $\beta ^{\prime}$.
So I want to know if there is a way for me to find out, without entering a wet lab!
Firstly; how do we know that something is a transcription/sigma factor binding site? What is it about the region? And how do we know which TF/SF it is a binding site for? Could the same transcription/sigma factor have multiple different binding site motifs?
Secondly; Since the genome for B. subtilis is available, would I be able to find out binding site motifs for all the sigma factors, and then determine which is/are contained within the promoter for the $\alpha$ subunit? I.e. if I know the TF/SF sequence, is there a way of finding out which promoters it can bind to?
Finally; the main purpose of this question is to find out how rpoA is transcribed, and I know that in general sigma factors are required in bacteria for specific transcription initiation, but could it be that rpoA transcription is non-specific, and that the sigma factor is just not involved in its transcription?
Please let me know if there is anything I can do to improve my question, I can provide references if it would be a good idea. Thanks!

its hard - most of the techniques that don't involve having the protein for the transcription factor are unreliable and unspecific.

I don't have a definitive answer, but I can perhaps offer some insight. Given the necessary function of rpoA, I would be willing to bet that SigA is the factor responsible for its transcription, so I will focus my discussion there.
Predicting promoters without experimentation can be very challenging given their immense variability. The idealized core promoter consists of a -10 region, a spacer and a -35 region. Recognition of the promoter by a sigma factor is done at the -10 and -35 regions: each sigma factor recognizes a different consensus sequence. Bacillus subtilis SigA recognizes the consensus sequences TTGACA (-35) and TATAAT (-10). They key word there is consensus however, as it is rare that a promoter will actually contain these exact sequences. In reality, 3/6 nucleotides matching could be considered reasonable. Between the -10 and -35 regions is a spacer with conserved length. In the absence of transcription activators, SigA requires a 17 +/- 1 nucleotide spacer. This is due to thermodynamic constraints. Very briefly, promoter melting (at -10) is dependent the angle between the -10 and -35 regions. Given the helical nature of DNA, this angle is in turn dependent on the distance between the -10 and -35 regions. If the angle is just right, the untwisting of the DNA to align the promoter elements and thus allow sigma binding provides the energy to melt the promoter. If the angle is too large, the regions can never align. If the angle is to small, alignment will not provide enough energy for melting. Complicating this are non-standard core promoters and various flanking sequences that all play a role in transcription initiation. As a direct answer to one of your question, a single sigma factor can bind to many different DNA sequences with some conserved regions.
Fortunately, the B. subtilis genome has been sequenced. Your search for the promoter might involve looking for the -10 and -35 regions 5' to the rpoA gene. This however doesn't take into account that rpoA might be part of a polycistronic operon and thus under the control of a promoter further upstream. Suh et al. (1986) did basically this and reported:

Our DNA sequence analysis suggests further experiments to study regulation within the rpoA region. Because inhibition of polycistronic message translation by free protein S4 is one of the chief controls of alpha operon expression in E. coli (16, 23), the apparent absence of S4 from the B. subtilis alpha region suggests different regulation. Although the close coupling of the rpsM and rpsK genes in our sequence (Fig. 3) supports the notion of a translational coupling similar to E. coli, the putative rpoA promoters in the relatively large intercistronic distance following rpsK are also different (28, 29). However, the apparent absence of a rho-independent terminator in this region could indicate that significant transcription occurs from additional upstream promoters in B. subtilis as well as in E. coli (28).

Albeit this is an old paper, but I was unable to find more recent studies in my quick research. Basically they compared the B. subtilis rpoA gene to that of Escherichia coli, where it is located in an operon with ribosomal proteins rpsM, rpsK, rpsD and rplQ (under the control of a single promoter). They found both similarities and differences. They were able to find two possible SigA core promoters in the region between rpoA and rpsK (the next gene 5' to rpoA in B subtilis). There was also a relatively large distance between the two genes, suggesting that they are not part of the same operon. Furthermore, they were able to find a ribosome binding site (Shine-Dalgarno sequence) between the hypothetical promoters and the translation start site. On the other hand there is no transcription terminator between rpsK and rpoA which suggested that a promoter further upstream regulated rpoA expression. After their sequence analysis, they suggested that further experimentation was required.
In conclusion, it's hard to find promoters just by looking at the sequence. Even if you do find a possible promoter, it's impossible to say whether or not it is utilized without experimentation. That said, given that the alpha subunit is necessary for cell function, that the rpoA gene appears to be transcriptionally tied to ribosomal proteins (which are also necessary for cell function) and that SigA is the predominant factor in log phase B. subtilis, I feel that it is very likely that SigA is ultimately the factor responsible for rpoA expression
I also thought I'd mention that there are various online bioinformatics tools that attempt to predict promoters, but I will not comment more on them because I have not used them.


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Homologies to insect wings
All winged vertebrates have wings which are homologous to each other and to the forelimbs of the non-winged vertebrates. But what about insect wings? Are all insect wings homologous, and are there any homologies between insect wings and any vertebrate limbs?

Insects and vertebrates are extremely distantly related: they're on opposite sides of the oldest split among bilaterally symmetric animals.  Their most recent common ancestor lived in the pre-cambrian and was almost certainly worm-shaped with no limbs at all.  There's no way that insect wings are homologous to any body parts of vertebrates.
The evolution of insect wings is a somewhat difficult topic, because it happened 350 million years ago in animals that do not fossilize well.  Wikipedia discusses several possible theories for what parts of non-winged insects are homologs of insect wings.  Currently the situation does not seem to be resolved.

Insect wings (and legs) and tetrapod limbs are analogous structures. Insects are protostomes, whereas vertebrates are deuterostomes; both lineages separated in the Precambrian from something resembling a worm (some Ediacaran organisms, such as Kimberella, have been proposed to be protostomes, whereas some others, such as Burykhia, are tentative tunicates, which are the closest living relatives of vertebrates). The arthropod ancestors of insects evolved legs in the Cambrian, whereas tetrapod limbs evolved from fins (among tetrapodomorphs, via a Tiktaalik-like stage) in the late Devonian, which themselves evolved from folds (the pectoral fins first evolved within ostracoderms in the late Cambrian or Ordovician, whereas the pelvic fins arose in jawed fish in the Silurian). The origin of insect wings is still largely unknown, but the point is that they aren't homologous with vertebrate limbs/fins.

It would be great if you could add some references.


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At what stage of meiosis does "first meiotic arrest of oogenesis" occur?
An exam question asked what stage of meiosis corresponds with "first meiotic arrest of oogenesis". I can't work out the answer from the wiki page - can anyone explain which step this refers to?

Prophase of first division. Check Wikipedia.

Well, the answer in one line is....... Diplotene of meiosis 1......or simply prophase 1

@JasjeetSingh I think Jasjeet's answer is very good because it is answering exactly what I am asking for. I do not agree with the decision to move his answer to a comment here. - - You should at least offer him a reason why you did the change. He is new here, and the more important, it is. - - Again, I really like his answer with open perspective indicated by ... in the topic because it is open.

When females are in their mother's womb all their Oogonium (plural Oogonia) are being made, they they undergo mitotic divisions to become a primary oocyte. Then, the primary oocytes start to undergo meiosis I -  but meiosis I is arrested. This is the first meiotic arrest. Meiosis I continues when a female hits puberty, every month one or more primary oocytes undergo meiosis I and create secondary oocytes. These secondary oocytes will then  start the second meiotic division, but this second meiotic division is arrested as well. It is arrested for about 24 hours, waiting for a sperm to fertilise it in the Fallopian tubes. The only time an egg (or in medical terms - secondary oocyte) will complete meiosis II is if a sperm penetrates the egg, and then it is called an ovum, which develops into a zygote and a then foetus.
Therefore, the answer to your question will be - the first meiotic arrest in oogenesis will occur from the time the primary oocytes are created in the womb, until a female reaches  puberty. starting puberty until menopause every month one or more primary oocytes will mature and complete the first meiotic division.

Could you recommend a book that explains oogenesis in human beings in details?

Meiosis consists of two divisions. Both are somehow similar to "ordinary" type of cell division - mitosis, but there is no DNA replication between them. As mitosis, each of two meiosis divisions might be divided into 5 stages:

Profaze (condensation of chromosomes, formation of microtubular spindle apparatus between two centrosomes)
Prometaphase (the nuclear membrane desintegrate and chromosomes and microtubules attach to kinetochores of chromosomes)
Metaphase (The chromosomes align at the metaphase plate)
Anaphase (segregation of chromosomes)
Telophase (restoration of nuclear membrane, cytokinesis)

The first division is crucial for reducing number of chromosomes. The prophase is subdivided to following stages:

Leptotene (condensation of chromosomes)
Zygotene (homologous chromosomes form tetrads )
Pachytene (crossing over)
Diplotene (chromosomes separate a little, sister chromosomes remain bounded in chiasmata)
Diakinesis (futher condensation of chromosomes, the nuclear membrane desintegrates)

In animals the function of meiosis is producing gametes. In case of oogenesis (in human) this process starts during prenatal development. Between 12-th and 25-th week of female fetus development cells called oogonia become primary oocytes and enter meiosis, but become arrested in stage of dictyotene, which is prolonged diplotene of prophase of first division. Then they wait 12 up to 50 years (too long waiting increase risk of chromosomal disjunction disorders such as Down syndrome in children of old mothers), covered by a layer of cells - primordial follicle. At the beginning of each menstruation cycle one or a few of the follicles become growing (the follicle cells divide, but oocyte is still waiting). At the stage of Graafian follicle the follicle is about 75 times bigger and there is a cavity full of liquid between oocyte and surrounding cells. The hormone signal - LH from pituitary gland - brakes the meiosis block, the primary oocyte divide into secondary oocyte and small first polar body (which quickly degenerates). At this time the follicle breaks - its ovulation. The oocyte starts second division, but stops at the metaphase. This second arrest ends when sperm cell penetrates into oocyte. The second, small polar cell is released and haploid nuclei of ovum and spermatozoon fuse together.
more:
http://www.ncbi.nlm.nih.gov/books/NBK10008/

very well written, I was confused by the subphase of prophase. Need to study them to undertand wiki better. Thank you!

Lol, I just noticed that Graafian follicle is also arrested in stage of dictyotene that is subphase of prohpase II. So the stage of meiosis of Graafian follicle is prohpase II. - It seems that similar analogy works in different arrested stages: always being in the accumulating stage i.e. prophase.

@Masi, Graafian follicle is just next stage of development of primordial follicle.

You jump a bit. After primordial follicle comes Primary follicle, then secondary follicle and finally Graafian follicle. So the next stage of development of primordial follicle is Primary follicle in my opinion.


text:
Can parents' learned traits be transmitted genetically?
I am wondering whether a behavioral trait (e.g. fear or stress experienced in the lifetime of the parent) can be transmitted genetically to its offspring?
I understand that a behavioral tendency for stress acquired through evolutionary time can be transmitted from parent to child, but I'm wondering whether a trait not present before can be transmitted between 2 generations.
For example many studies claim that offsprings of holocaust survivors inherit psychopathological disorders. I'm wondering how this inheritance could occur genetically given such a short time period?

You may want to have a look at: http://biology.stackexchange.com/questions/2875/can-rats-pass-on-memories-of-a-maze-to-their-offspring and http://en.wikipedia.org/wiki/Epigenetics

I think this is a duplicate of the question @nico mentions. In particular, the answer there completely solves this question.

This is a perfectly good question, but my answer linked above is relevant. The short version: it's not genetic; stress is transmitted hormonally from mother to child.

“many studies claim” – do you have any reference for that? This sounds very dodgy. Some naive epigenetics studies claim similar results for mice but their interpretations are simply not backed by the data.

@KonradRudolph he's right that many studies claim increased stress-related disorders in Holocaust survivors' offspring. I'll write up a full answer and include some. The key point is that none of those studies claim it's a genetic effect; that was an assumption of the asker.

Vote to reopen - whilst the other question is similar, there are specific features related to the human case which warrant a separate answer (which I was just about to post when the Q was closed!)

Strictly speaking no. There are ideas about cultural inheritance though that seem relevant here: see http://www.ncbi.nlm.nih.gov/pubmed/11425279.  Cultural inheritance theory uses the plasticity of the human brain as the evidence for the underlying genetics of culture.  I.e. we aren't born with the ability to speak English because our parents learned it but we have an the underlying brain structure that is controlled by genetics to learn cultural traits.  It seems far more likely that the phenomenon you describe with holocaust survivors is more related to some environmental effects (from their parents) than anything genetic.  In the comments stress hormones in pregnant mothers were mentioned.  Any impact these have on the offspring are not truly "genetic", they're termed "maternal effects" in the evolution literature.  In fact most selection studies go to great lengths to control for them or eliminate them.  They aren't truly genetic because these traits would never get passed down to the grandoffspring of the original mother.

I am just repeating @emhart answer but wanted to highlight the semantic.
There are several ways an individual can inherit from its parents.

Genetics

Through transmission of DNA. An acquired trait cannot affect DNA sequence directly and therefore cannot be inherited genetically by the offspring (this sentence is the answer to your question). Note however, that the environment in which an individual is found and the amount of stress an individual is experiencing may affect its mutation rate. But this has nothing to do with transmission of an acquired trait.

Non-genetics (or "environmental in the broad sense")

Environmental in a very narrow sense. For example, a dam that a beaver transmits to its offspring, a good habitat that the parents had to fight for. Note in the broad sense, any non-genetic inheritence should be considered as being part of the environment. Environmental change that an individual has caused (niche construction) of fighted for can potentially be inherited by the offspring
Cultural. For example a language, a method to hunt seals or a method to clean potatoes. Cultural modifications acquired by an individual can potentially transmitted to the offspring
Epigenetics. It includes any modification over the DNA and histones and any content of the egg. Something an individual has lived can affect the types of epigenetic modifications that a parent can transmit to its offspring.

Genetic and epigenetic characteristics can be exclusively transmitted from parent to offspring (setting aside horizontal gene transfer and transduction), while environmental characteristics and cultural characteristics can potentially inherited between any two individuals. In the field of population genetics, the ratio of the phenotypic variance that is due to (additive) genetic variance over the total phenotypic variance in a population is called heritability (in the narrow sense).
There are plenty of important keywords in my (and @emhart's) answer. You might want to have a look at the wikipedia entries for all these concepts. You might also want to have a look at this answer.


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Does consuming sodium benzoate (preservative E211) cause problems during pregnancy?
There seems to be strong evidence to support the claim that sodium benzoate (E211) causes hyperactivity in young children, e.g. Bateman et al. (2004) and McCann et al. (2007).  This leads me to consider whether or not E211 is harmful during pregnancy.
A study by Mowafy et al. (2001) found a slight decrease in survival rates for pups of pregnant rats given sodium benzoate; they also found a more significant drop in mean weight of their pups.
Question: Could the consumption of sodium benzoate by the mother be harmful during human pregnancy? How would this be the case?
References:

Bateman, B., Warner, J.O., Hutchinson, E., Dean, T., Rowlandson, P., Gant, C., Grundy, J., Fitzgerald, C. & Stevenson, J. (2004) The effects of a double blind, placebo controlled, artificial food colourings and benzoate preservative challenge on hyperactivity in a general population sample of preschool children. Archives of Disease in Childhood. [Online] 89 (6), 506 –511.
McCann, D., Barrett, A., Cooper, A., Crumpler, D., Dalen, L., Grimshaw, K., Kitchin, E., Lok, K., Porteous, L., Prince, E., Sonuga-Barke, E., Warner, J.O. & Stevenson, J. (2007) Food additives and hyperactive behaviour in 3-year-old and 8/9-year-old children in the community: a randomised, double-blinded, placebo-controlled trial. The Lancet. [Online] 370 (9598), 1560–1567.
Mowafy, A.R., Darwish, A.M., El-Kholy, S.A. & Abdel-Mohsen, S.H. (2001) Effect of food preservatives on mother rats and survival of their offspring. The Journal of the Egyptian Public Health Association. 76 (3-4), 281–295.

This is really a medical question, which are off-topic here.

I think if you reformulate this scientifically in terms of teratology it might be a great question.  Right now, in addition to being on the medical advice side, as Mad Scientist has pointed out, it's framed in a bit of an alarmist fashion.

Alright, so here's an edited version of it; nothing about my personal reasons for asking the question.  (I'm not really sure how to add in "teratology").  As per the general rules of these sites, if you think you can improve the question (and not change the overall meaning) feel free to edit.

@DouglasS.Stones It's a good edit.  I'm personally unsure of the scientific correlation between an agent that might cause hyperactivity and one that might cause harm to a fetus, but it provides a lead-in for your question, so I think you did the right thing.

There is some evidence to support the idea that sodium benzoate may be detrimental to the development of the foetus:

TERATOGENIC EFFECTS: Classified POSSIBLE for human.
DEVELOPMENTAL TOXICITY: Classified Reproductive system/toxin/female, Reproductive system/ toxin/male [SUSPECTED].

MSDS for Sodium Benzoate
This has been shown experimentally in rats by Minor & Becker in 1971.  They introduced high doses of up to 1000 mgkg-1 intraperitoneally and recorded reduction in foetal weight and "gross anomalies".  Whilst I struggled to find a copy of their original paper, it is referenced in the Catalog of Teratogenic Agents1 (Thomas H. Shepard).
There is some evidence to refute this, however.  The Acceptable Daily Intake limits on sodium benzoate is a maximum of 5mgkg-1, at this dose there is no noticeable effect of exposure. (2,3)  The latter paper by EC food safety standards goes further:

There appear to be sufficient studies to conclude absence of teratogenic potential, with an overall NOAEL* for developmental toxicity of 500 mg/kg bw/day, based on effects on fetal weight.

*(No observed adverse effect level)
So the consensus from the food safety bodies suggests that E211 should not pose harm to an unborn child in the quantities allowed to be present as an additive.

1 Emire, Ronald J. "306: Benzoate, Sodium." Catalog of Teratogenic Agents. By Thomas H. Shepherd. JHU, 2004. 44-45. Google Books. Google. Web. 10 Feb. 2012.
2 Nair, B. "Final Report on the Safety Assessment of Benzyl Alcohol, Benzoic Acid, and Sodium Benzoate." International Journal of Toxicology 20.3 (2001). International Journal of Toxicology. Web. 10 Feb. 2012.
3 Scientific Committee on Food. Opinion of the Scientific Committee on Food on Benzoic acid and its salts. Rep. 24 Sept. 2002. EUROPEAN COMMISSION HEALTH & CONSUMER PROTECTION DIRECTORATE-GENERAL. 10 Feb. 2012


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Antibody-antigen database
Is there a database where I can find an affinity estimate if I provide a given antibody and a given antigen sequence ?
Input : antibody + antigen sequence
Output : quantitative binding/affinity estimate
Many thanks.

great question.. I am also looking for something similar.. actually looking for "Input : quantitative binding/affinity estimate  + antigen sequence Output : antibody"

The binding constant of an antibody-antigen complex remains an empirical measurement.
There have been many efforts to solve this problem quantitatively and qualitatively over the years since the original crystal structures of an lysozyme-Fab complex there are over 400 structures at the www.rcsb.org in a search for antibody antigen complexes.
At this point the general methodology is to model the structure of the antibody-antigen complex.  Then from the complex a free energy of binding is estimated, or more reliably, variants which might bind more tightly can be modelled.
There are tools available to do this work, but they are still far from perfect.  This 2012 paper compares a new antibody-antigen crystal structure against the results of several modeling suites.  In Table 4 the authors show that the invariant parts of the structure as well as some of the hypervariable loops are really precisely modelled, but hypervariable region 3 was way off in this case (rms error of about 2 Angstroms).  Which is not precise enough to calculate actual free energy of binding.
Currently while free energies of binding and therefore estimates of binding constants are not reliably calculated from protein complex structures.  Such software is in practice used to rather compute the relative binding strength of two models (see this 2012 example).
This 2010 paper which describes SnugDock, a newer suite of software, outlines a state of the art antibody-antigen design process (emphasis added).

One could envision a complete computational antibody engineering pipeline starting from the antibody sequence and ending with accurate predictions for optimized antibody-antigen interactions. In this paper we have been successful in reaching the second step by computational docking using computational models of the monomer antibody. The next stages may be additionally challenging. High-resolution complex structures might next be used for computational alanine scanning, computational affinity maturation or alteration of binding specificity. For antibody therapeutics, structures will help define drug mechanisms for regulatory approval, enable epitope mapping and humanize constructs. These applications require varying amounts of resolution and further testing will reveal the full utility of the SnugDock predictions.

As you can see, the method recommended is to create a series of models to try to create tighter relative binding.

Thanks a lot! Do you know any database displaying the empirical measurements you mention at the beginning of you answer ?

Good question - this reference might be a good one for you http://nar.oxfordjournals.org/content/40/D1/D1230.short. Not sure if its still around.


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Do vitamins help our memory?
It is commonly believed that vitamins can help our memory.
Is this really true? What is the biological basis of this?
Is there any specific research paper on the subject?

Welcome to Biology.SE. You should try your question on skeptics.SE where you can provide any NOTABLE claim and they will tell you whether your claim is supported by scientific evidences or not.

Why the close votes? The question was a bit "bare", sure, so I edited it a little. In any case I think it fits this site very well.

There seems to be no effect of vitamins. This paper ("Preventing cognitive decline in healthy older adults." found no evidence for herbal supplements, vitamins or fatty acids improve cognitive functions.
There seems to be some evidence ("Preventing Alzheimer's disease-related gray matter atrophy by B-vitamin treatment.") that a cocktail of hig dosed vitamins including folic acid, Vitamin B6 and Vitamin B12 can slow Alzheimer's disease. But: The benefits were only seen in participants which had high blood levels of homocysteine. This amino acid is linked to a higher risk of heart disease for which the B vitamins are postive for the outcome. So this might only be helpful for people with too high homocysteine levels.
And its questionable if high doses of antioxidants (like vitamin A or E) are not only not helpful, but can cause actual damage. This is due to the fact that they catch up reactive oxygen species, which might otherwise trigger the cell to go into apoptosis and prevent it from becoming a cancer cell. Here is the paper: "Antioxidants accelerate lung cancer progression in mice.".


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Deep diving in mammals
Mammals like seals often dive and can remain under water for more than 70 minutes.
How do seals know when is it the time to come up?

I imagine that their breathing is controlled in the same way as ours. During a dive, oxygen will be used up and carbon dioxide will be produced, dissolving in the blood as bicarbonate and tending to decrease the pH of the blood.
Peripheral chemoreceptors in the circulatory system detect all of these changes and signal the need to breathe. This would tell the seal that it is time to head for the surface.
Diving mammals have various adaptations for prolonged diving, most importantly large reservoirs of blood containing haemoglobin which is oxygenated before a dive, as well as high concentrations of myoglobin in muscle which can also act as an oxygen reservoir.

Check this article in the today's issue of science. Was going through the TOC just before I looked at this question. It is about how myoglobin is more efficient in deep divers. Reinforcing the fact in the last statement of Alan's answer.


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What is the concentration of ATP in an average cell?
Can someone give me some references showing the average concentration of ATP in a cell?

The concentration of ATP depends strongly upon cell type, its current activity (for muscle, neuronal and secretorial cells). Besides, the local concentration of ATP in certain cell areas (mitochondria, near myosine heads, near membrane, in synaptic vesicles) might be orders of magnitude higher than that in other parts of cytozole.

Do you have a reference to an estimate of the ATP concentration in mitochondria?

Answer
This article covers the energy charge and ATP concentrations of an array of muscle cells from many different organisms. Since many factors come into play (amount of glucose available, rate and regulation of glycolysis and cellular respiration, use of energy in metabolism, etc.) it is expected for the ATP concentration within the cell to vary significantly. The ATP concentrations reported span from approximately 1 to 10 mM.

References
 - Beis, I, and E A Newsholme. “The Contents of Adenine Nucleotides, Phosphagens and Some Glycolytic Intermediates in Resting Muscles from Vertebrates and Invertebrates.” Biochemical Journal 152, no. 1 (October 1975): 23–32.

Muscle cells generally need much more ATP than any other cell in order to to relax. The concentration in other cells (for example neurons) can differ significantly from these values.

Alternatively: http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=atp+concentration&org=
As LanceLafontain answered, most of the numbers fall within the range of .5-10 mM

Both answers have 10 mM as upper limit, but why is there a discrepancy in the lower range? 1 or 5? That's quite a big difference IMO.


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How to know if a woman is fertile without actually making her pregnant?
How to know if a human female is fertile (can give birth to child in future) without making her pregnant? Any signs, tests?

Menstruation would be an obvious one

If you are talking potential for fertility. There are a few...

Having regular periods
Healthy weight. Extremely thin women tend to stop ovulating. Obesity also impairs fertility by altering hormone levels.
Whether she has been using birth control (i.e., "the pill") in the recent past. It takes a while for the body to get back to normal.
Smoking impairs fertility
stress

Source
If you are talking about immediate fertility...
While I would not rely on them for the purposes of birth control there are several observable physiological changes that correlate with ovulation and fertility. These include

body temperature. There are patterns of elevated body temp associated with ovulation.
cervical mucous. The mucous gets "slippery and stretchy".
the cervix itself becomes less firm and slightly open during ovulation.

Source
If we are talking about anatomical cues that are proxy's for fertility, there are clues based on the concept of sexual selection.

Ample breasts. Indication of potential mammary tissue and ability to suckle child.
Wider hips. Indication of ability to deliver child with minimal complications.

Note that these cues can be deceptive. Fat tissue may be deposited in both locations to imitate the fertility cues. Source

Of course. There's several fertility tests available to determine the quality and quantity of egg reserve, and whether or not the there are abnormalities in the uterus.
However, some of them are invasive procedures, and all of them should be performed by a professional. I doubt the layperson would know what they're looking at on an Ovarian Ultrasound.
If you're asking whether there's an "easy" way that doesn't involve a trip to a doctor - then I would say 'no.' Casual inspection would only reveal any abnormalities in the vagina and the opening of the cervix, and hormone tests are only partial indicators.
Then again, if a woman has reached physical adulthood and is under the age of 38 then the chances of being infertile (or have difficulty conceiving) are quite low - about 3% to 10%. Infertility is usually much more of a concern to women who wait until after the age of 35 to have children, as there is a definite biological window (the number of eggs the woman was born with) to consider that starts to close as a woman nears her 40's.
It's also important to note that trouble conceiving can stem from either partner, and there's about a 40%-50% chance in a couple trying to conceive the male has an 'issue' and the woman is perfectly healthy.


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Recommended applications for commercial antibodies
Commercial suppliers of primary antibodies for given protein targets typically list recommended applications, for which the antibody has presumably been shown to work. I am usually looking to use them for immunofluorescence, and my impression (which admittedly may be based on an unrepresentative sample) is that most antibodies are recommended only for use with Western Blotting.
Why is this? Is WB the most common application? The most general? Is it easier to test for than IF?
And, perhaps more to the point, how seriously should one take these recommendations? If an antibody is not recommended for IF, does that mean that it probably won't work? Or that it may well but no-one's bothered to check? Or that it almost certainly will?

Maybe WB is easier for them to test?
In general, however, my recommendation is to check if they provide refs to paper using those antibodies and look at the images on the paper.
Be careful putting your trust in the supplier's pictures, I have seen obviously photoshopped images on commercial websites.
Also always double-check the referenced papers, as sometimes they don't really use the same product that is sold...
Other than that, in my experience, the recommended application is just that: recommended. The antibody may as well work for other application.
That said, note that there is a rationale for an antibody working for WB and not IHC, for instance: perfusion with fixators such as PFA will change the 3D structure of the target protein and may mask (or reveal) certain epitops, so the antibody may be more or less efficient depending what form of the protein you're dealing with (native, fixed in PFA, fixed in glutaraldehyde, SDS-denaturated etc.)

Antibodies for WB and for IF have fundamentally different requirements for the epitope structure. Antibodies for WB recognize denatured structures extended by SDS treatment. Antibodies for IF often will need to recognize a native-like structure.
Depending on the supplier, some will have lots of antibodies for IF. I suggest looking around some more.


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number of chromatids seen in karyotype
The karyotype is performed on a cell whose cycle has been stopped in metaphase or pro metaphase, using colchicine or by other means. In the textbooks I read that during the S phase each of the 46 chromosomes is duplicated, giving, again, 46 chromosomes, but, and here I am deducing, 92 chromatids. When we perform the karyotype, we only see 23 pairs of chromosomes (46, that is), and, it looks like to me, the same number of chromatids (46 as well). What am I missing? Why can't we see 92 chromatids in the karyotype?
Thanks a lot for your attention.

Possible duplicate of Karyotypes Appearance

See this question. Karyotypes do not show the entire structure. It's a good question, though, and shows you've been putting some thought into this.

As you noted, karyotypes are prepared from cells halted in metaphase or prometaphase.  In either of these phases, the chromosomes will have two chromatids bound together at the centromere with the chromatid arms lying parallel to each other.
The difficulty in seeing the chromatids in most karyotypes is due to the way they are prepared. Most karyotypes are prepared using Giemsa staining which causes contrasting bands to appear on the arms.  These bands have patterns characteristic for each chromosome type and thus allow the chromosome images to be identified and sorted into pairs.  Between the stain, lighting and exposure used to show the banding, the images don't show the separate forms of the chromatids well.
With alternative staining and lighting, the chromatids can stand out (all images from commons.wikimedia.org):

Still, in typical karotype photographs of sufficient resolution you can at times make out the separate forms of chromotid arms, or perhaps the "pinched waist" shape where the centromere draws the chromotid arms together:

So, yes, a normal human karyotype has 92 chromatids present; they just tend not to be apparent due to the preparation done to show banding.

Chromosomes and chromatides are referring to the same physical objects, although a chromatid is mostly referring to the DNA strand, and chromosome to the "colored object" (chromo=color, some=body) that people first saw under a microscope. So, yeah, don't get confused by that, it is just that biologists like to coin terms for specific contexts.
You can see a detailed explanation here.
Cheers,
Pedro

I'm familiar with the difference between chromosomes and chromatids, what I don't get is why we see 46 objects in metaphase, and not 92 (and by objects I mean independent molecules and also molecules linked at the center, so that two sister chromatids count as two objects, even though they are linked, by this definition)? If the chromosomes duplicate in the S phase, my reasoning goes, even though the copies may be 'linked' to the original in some way, shouldn't we still be able to distinguish them clearly (and thus distinguish 92 molecules, however they may be connected to each other)?


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Can someone identify this odd looking spider?
I found this spider crawling on my tile floor. We live in rural central Virginia.  I’ve found spider species with similar looks but nothing exactly like this. Its size was less than 1 inch. Can anyone identify it?

Some sort of jumping spider (Family: Salticidae)

Could be Thiodina sylvana... But I'm not sure. Thiodina occurs in Virginia. Take a look at this picture: https://www.flickr.com/photos/52450054@N04/6304831786 but be careful, it shows a male. Females tend to be more brownish

I agree with JulPal's comment from August.  It looks very much like a male Thiodina (now renamed Colonus) sylvanus.  As with many Salticids, the females look rather different, and it turns out that there is apparently a similar species of Colonus in the area, which can be distinguished in the field by the fact that the white mark on the carapace is not a block so much as a thick longitudinal line.
I attach an image from Tree of Life, with the link below:

http://www.tolweb.org/Thiodina_sylvana/5911

It is Tarantula which comprise a group of large and often hairy arachnids belonging to the Theraphosidae family of spiders

It would be good to explain how you know it is a tarantula. Maybe based on on the position of the chelicerae? I am surprised that there are tarantula as far North as Virginia.

It doesn’t look at all like a Tarantula to me. It’s size was less than 1 inch.

@Penni You should be mentioning that in the question. From this zoom, I would have guessed that it was much bigger.

Yes, I should have.. my bad. This is my first post, ever, so I’m a newbie. Thanks for your help, @TheLastWord.

It is not a Mygalomorph - the eyes are in the front of the head,  with two large ones right on the forward 'face', like a Jumping Spider, rather than clustered in a turret atop the round, flat carapace; the abdomen is long and teardrop-shaped, like a Jumping Spider, rather than large and bulky, with two obvious 'exhaust-pipe' spinnerets at the back; and the legs are short and stocky, like a Jumping Spider, rather than long and thick and very hairy.

It's pretty obvious that it's a jumping spider. Tarantulas look nothing even remotely close to that.


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What are the criteria for determining the influence of epigenetic factors?
Isolating a gene or sets of genes in diseases sometimes isn't enough to determine penetrance - epigenetic factors can have a significant effect. What are the criteria in determining whether epigenetic factors are significant?

First of all, the nature of penetrance is almost entirely unknown.  Likely it's a combination of epistasis and gene interactions, induced gene regulatory pathways, developmental noise, and other factors.  Epigenetics (imprinting, etc) may have little to do with penetrance, while chromatin structure may be a consequence of other things (most now regard histone modifications, etc, as consequence of transcription rather than heritable regulatory mechanism).  Currently, the field of epigenetics is undergoing a (long-overdue) reassessment.  Until that happens, anyone who wants to make claims of "epigenetics" is free to, so spurious claims are rampant.

Do you know any relevant papers/reviews on the issue?

Sorry, reviews on which?  Penetrance, epigenetics, or chromatin structure?

Sorry, my comment was not clear. I was wondering if there were reviews on the current view of epigenetics. You are saying that the field needs a reassessment, I was wondering if someone had analysed this issue in detail (why it need it, what are the things to better define etc)

A few years ago Youngson and Whitelaw wrote a review that started to separate epigenetics from inducible gene expression (http://chd.ucsd.edu/_files/winter2009/Youngson.TransgenerEpigenEffects.08.pdf), but it didn't go far enough.  There have been studies lately that show that histone modifications are probably consequence of gene expression, rather than carrying memory.  Similarly there are studies that show that DNA methylation does not "shut off" expression, and there is still not a single case showing that methylation changes alter endogenous gene expression.

Thanks, that is a good start. So, correct me if I am wrong, you are saying that it has been been shown that the methylation status can change depending on gene transcription, but not that methylation modulates transcription?

I don't know how kosher it is to redirect within the stack, but here is this: http://biology.stackexchange.com/questions/391/how-do-cpg-islands-remain-unmethylated/392#392

Yep, I read your other reply :) Thanks a lot.


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Are there dextral/sinistral higher animals?
For example, almost every dog I've met in my life (more than 20 subjects) uses their right paw touching one while asking for attention. Can it be used as a criterion for calling them dextral? If not, what?
However, I realize that even those dogs who live in the street might get influenced by dextral people:

There is no domestic animal which has so radically altered its whole
  way of living, indeed its whole sphere of interests, that has become
  domestic in so true a sense as the dog (Konrad Lorenz)

Is there any research about it?

Related: Do animals exhibits handedness (paw-ness?) preference?

Handedness has been studied in several different species of toads. As basal tetrapods, the authors argue that these taxa are unlikely to be influenced by human hand dominance and are thus a better model for studying the evolution of handedness.
Bisazza et al. (1997) studied "pawedness" in Bufo bufo, B. viridis, and B. marinus in wild-caught animals by determining which forelimb was used to remove a piece of paper from the animals' snout or a balloon placed over its head.
The results were mixed. B. bufo preferred the right forelimb in both tests, but B. viridis and B. marinus did not. B. marinus did preferentially turn its head left in another experiment, using the right forelimb for support.
A subsequent study by Malashichev and Nikitina (2002) showed that Bombina viridis is "lefthanded," while Bombina bombina is "ambidextrous."
So based on these studies, lateralization appears to have a long evolutionary history.


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How many people's DNA were involved in the compilation of the reference human genome?
I know that the reference human genome is complied from DNA portions from different people, most of whom were European. Do you know how many of them were involved? Do you know which ones were involved? Perhaps scientists like James Watson and George Church's DNA were in the reference genome. Also, I would assume that the NIH funded Human Genome Project's reference genome must be slightly different from the privately funded one.

tl;dr: In the Human Genome Project, they used the DNA of four people (though one male provided >70% of DNA. The Celera genome was compiled from five people.

In the [...] Human Genome Project (HGP), [...] scientists used white
  blood cells from the blood of two male and two female donors (randomly
  selected from 20 of each) -- each donor yielding a separate DNA
  library. One of these libraries (RP11 [anonymous donor from Buffalo,
  NY]) was used considerably more than others, due to quality
  considerations.
[...]
In the Celera Genomics private-sector project, DNA from five different
  individuals were used for sequencing. The lead scientist of Celera
  Genomics at that time, Craig Venter, later acknowledged (in a public
  letter to the journal Science) that his DNA was one of 21 samples in
  the pool, five of which were selected for use.
On September 4, 2007, a team led by Craig Venter published his
  complete DNA sequence,[21] unveiling the six-billion-nucleotide genome
  of a single individual for the first time.)

Source: Wikipedia

Can you please give me a link to the source of this text?

@GerganaVandova: Please follow the Wikipedia link. If you want original references, have a look at References 17-21.

Wow, I read so many papers regarding this matter, but never wikipedia. Thanks. But do you think it is really unknown exactly from which source the DNA came?

@GerganaVandova: If the HGP can track down RP11, or any other of the chosen donors, then they did a poor job at anonymizing the donors and might be sued for that. With Celera, who knows who might know? I'd almost bet that Venter was one of the five; I guess it may be possible to try and find out by aligning the Celera genome to the Venter genome.

Haha, is Venter's genome public?

@GerganaVandova: Yes, it is

I don't understand the point of this thread. The question was asked, and the accepted answer is just lifted from wikipedia. Why not just look in wikipedia in the first place? Is this the purpose of SE?

@Poshpaws: You may want to bring that up on Meta.

@Jonas Will do :)


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Quantum mechanics in biology
There is a growing interest in the applications of non-equilibrium quantum dynamics to describe biological processes (I'm not talking here about Penrose's old theories, but new stuff -- quantum coherence in light harvesting, magnetoreception etc.). What is the biologists' take on this? Is this just a whim of physicists looking for grants, or a serious part of biological research?

Absolutely a serious part of research - quantum mechanics defines chemical structure and reactivity. Whenever you see a headline like 'Scientists find quantum effects important in protein activity, weird huh?', read it as 'Scientists find pragmatic classical approximations inadequate in describing protein activity'.
In protein structure, for example, classical molecular dynamics/mechanics are important in generating computationally tractable problems, however they represent a tacit and streamlined parameterisation of underlying quantum mechanics. QM protein structures are usually too gnarly to compute (at least historically speaking), except in regions of interest like an active site, where a model fine-tuned for sequences of amino acids will probably fail badly anyway. As a concrete example, the group that I'm in is in part interested in computationally modelling the active site of plant photosystem II, which contains a cluster of spin-coupled manganese atoms. To glean any useful understanding of how this cluster functions via a computational model, an explicit quantum mechanical level of theory that takes into account electron exchange and correlation must be used. This requirement can probably be extended to any metalloenzyme.
And this isn't touching upon the resonance hole transfer that oxidises the active site, the Davydov solitons that manifest in protein alpha helices, or indeed the quantum electrodynamical origins of the Van der Waals interaction that causes everything to tend to stick to everything else.
Hope this is interesting :D
(note: I am not involved with PetaChem, I just think it's freaking awesome.)

Extremely interesting! Can you provide some links to papers about the Mn clusters?

@quant_dev - unfortunately there's very little that isn't behind a paywall, but if you don't have an institutional subscription and are happy reading abstracts, this is a decent start. IIRC the authors looked at the active site and proximate protein environment of PSII using a QM simulation (spin-unrestricted density functional theory) embedded in a molecular mechanics simulation. This paper indicates that elements of PSII WOC kinetics are affected by the Jahn-Teller activity of Mn sites.

Do you know about some out-of-equilibrium stuff as well?

@quant_dev - please elaborate on what you mean

I mean the cases when quantum mechanics is used to describe non-equlibrium dynamics, not the groundstate or some other stationary state of the system. For example, energy or charge transport.

@quant_dev - That link from petachem shows the time evolution of a protein at an ab initio level of theory. I'm not well acquainted with the state of the art, but Car-Parinello molecular dynamics is a type of density functional theory that can handle potentially large molecules.

Don't forget about deuteriating drugs!


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Hearing and neurons- do ears have a sampling period?
From what I have read, outer hair cells in the human ear amplify incoming signals and inner hair cells "pick-up" the signals and generate action potential. However, neurons have refractory periods during which they cannot fire again. Does this mean that the human ear has a "sampling period" within which it cannot "pick-up" sounds?

Inner hair cells (IHC) do not fire action potentials themselves. It's the auditory-nerve that synapses with IHC that generates action potentials. The firing rate of the auditory nerve can be as high as few hundred Hz with a refractory period as short as 1 ms or so (depends on the animal).
However, it is important to note that the signal is not sampled at this rate. As you may know, the auditory signal is first transformed to the "frequency" domain through the physical structure of cochlea. Each inner hair cell therefore is roughly only encoding the relative strength of a frequency band. There are presumably inner hair cells in the human cochlea that correspond to a range centered around 18 kHz for example, but neither the neurotransmitters of the corresponding IHC nor the auditory nerve can fire at 18 kHz. Nevertheless, the amplitude modulation at this high frequency is what is transmitted.
Also, thinking of neural firing as a "sampling period" is not always a good analogy. There are debates about this, but it could be that precise timing of action potential carries large amount of information about the stimulus (perhaps not so much so in early auditory system.)
If you want to see some computational modeling work for inner ear, IHC, and auditory nerve, I recommend the Meddis IHC model:

C. J. Sumner, E. A. Lopez-Poveda, L. P. O'Mard, R. Meddis. A revised model of the inner-hair cell and auditory-nerve complex, J. Acoust. Soc. Am. 111 (5) 2002

I agree with your explanation. I think cochlea can be modeled as a bank of band-pass filters giving a spectrogram-like analysis of the audio. Lets consider the 18KHz IHC for example. If the auditory nerve connected to this IHC fires(sensing a strong 18KHz band), it cannot fire for another 1ms. Does this mean that I can hear the 18KHz signal only after 1ms again?

@user1155386 No. Signal is ENCODED by the train of action potentials. The information is there and can be DECODED if needed. This is more so because the amplitude envelope of the 18kHz signal will not change very fast. The brain is capable of interpolating through time, and it has many mechanisms for short-term memory. Things do not have to be represented instantaneously.

It probably bears mentioning that there is an extensive feedback stream from the auditory cortex to the thalamus that serves as a sifting mechanism for the incoming signal.


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Would exposure to a strong magnetic field have deleterious effect on the human?
This article states of a 25T magnet, ".. If are ever caught in one of these devices, let’s just say you probably won’t live to tell the tale."
Is the above statement in order? What effect would exposure to such a high magnetic field have on the exposed human?

That article contains some blatanly wrong statements, I woulnd't consider it trustworthy at all. 25 Tesla is not the strongest magnet in existence (see e.g. a 45 Tesla hybrid magnet built in 1999). Those high-field magnets usually have a very small bore, so you can't put a human into the maximal magnetic field of the magnet, as there's just not enough space inside.

@MadScientist: Thanks, the question is updated to be more to-the-point now

I don't think you need to remove that part, I just wanted to point out the errors in the linked article

First thing comes to my mind is the Hall effect. Any directional ion or electron flow will experience a force (depending on the orientation with respect to the magnetic field). So if the magnet is very strong, I think some of the ion channels for action potential generation and propagation would malfunction. (11 mT stopped action potentials for a while but recovered in mouse as reported here.)
However, according to these papers static magnetic fields has little biological effect, and it seems to be reversible. But, this reports genotoxicity in 4.5T (in vitro), and developmental disorders in 1.5T (in vivo, mouse). Contradictory reports indicate we do not know the full answer yet as usual.

"Strong" is en entirely relative term, but given the number of MRI's performed, its pretty clear that fields several orders of magnitude larger than the Earth's background 0.5 gauss are at least "mostly harmless" with an exposure of limited duration.
From an FDA publication regarding MRI scanners:

There are no known harmful side-effects associated with temporary exposure to the strong magnetic field used by MRI scanners. However, there are important safety concerns to consider before performing or undergoing an MRI scan.

This article describes human brain imaging with a 9.4T instrument, although this is about 10x larger than the strength of most MRIs. Note that "no detrimental effects" does not mean zero effects, but this is starting to get into the range of the 25T described above. There are 20T+ MRI machines avaialble, but I could not find an article describing use on live organisms. There is just this one on dead mice parts.


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Why do Bee stings cause swelling?
Why is it that when a bee stings, a little area around it gets swelled?
I think it is some sort of defense mechanism of the body.  But how does it help?

Bee, or other insect stings/bites, will cause a reaction to occur due to chemicals being released from your immune system.  This can result in anywhere from a small bump to anaphylaxis, which can be life-threatening if not treated right away.

From Southern Cross Medical Library:

An anaphylactic reaction occurs when the body's antibodies respond to the insect venom by releasing chemicals such as histamine and serotonin that trigger the allergic reaction.

Whatever the reaction, it is correct to say that the reaction to an insect sting/bite is a defense mechanism of the body.  An interesting study done by Stanford University School of Medicine was done and discusses these immune mechanisms:

Innate immune responses occur in subjects exposed to a foreign substance, such as a pathogen or a toxic material like venom, for the first time. [...] Immune cells called mast cells, which reside in most of the body’s tissues, are poised to unleash signals that turn on defense responses when a pathogen or toxin intrudes.  Prior immunization is not required for these types of innate immune responses, nor is the development of specific antibodies. In contrast, during an adaptive immune response, the immune system creates antibodies that can recognize the toxin or pathogen that is invading the animal’s system. Adaptive immunity is typically a faster, more specified and more effective form of defense than innate immunity, the research team explained.

More explanation of the non-specific immune response:

If a bee stings you, the presence of the bee venom triggers a nonspecific immune response. White blood cells arrive first on the scene to rid the body of bee venom antigens. As war wages between antigens and white blood cells, battle signs may appear on the affected skin. Inflammation (redness, swelling, heat, and pain) results as the body wards off invaders.

If the body detects an antigen that it previously met, a specific immune response occurs. In this response, the body has been trained to recognize and neutralize a familiar specific antigen; its immune system "remembers" the antigen. Such systemic (not restricted to the initial infection site) immunity enables a faster, longer lasting immune response than does a nonspecific response.

Therefore, these reactions to bee stings and other foreign toxins help us to better develop our immune system to protect against potential future encounters with these insects.

is the swelling only characteristic of the non-specific immune response? Does the immune system react differently to second and subsequent bee stings?

There is some information at this site http://bindaree.com.au/hints/bee-stings/ that states: In a non-allergic person, many stings can be sustained without threat to life, and repeated stings produce a tolerance or immunity resulting in a gradual decrease in reaction severity. This is due to the body’s production of appropriate antibody which neutralises the toxin subsequently injected.


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Why does squinting allow you to see objects more clearly?
How does squinting alllow one to see clearer pictures? What are the harmful effects?

This is an optical pinhole effect.  If the amount of light passed through the lens decreases, the sharper the image is at the focal point.  For a camera this is accomplished by increasing the f stop (f22 is a smaller aperture size than f6 — f-stop is an inverse number).  For the eye the iris will dilate (get larger) or contract to be smaller.  In very bright light, you can cut down on large amounts of light coming in by squinting, which creates a slit in front of the eye lens.
In photography this increases the "depth of field". Which is to say that more objects are in focus and sharp.  It works the same for our eyes of course.

In this image you can see as the aperture is smaller, any given point on the focal plane (right hand line) receives light from a smaller angle (i.e. from less of the image field).
I am not a physicist, but that's a first order explanation
@Luke reminds me that there was a question about whether squinting is harmful.  There is another reason that we squint.  If we are nearsighted or if we are getting older, we have a tendency to squint not because there is too much light coming into our eyes, but because our lenses are not focusing very well.  Is it harmful to strain our eyes?  Maybe, but it won't kill you.  Reading glasses won't either.

I can't think of any harmful effects, can you? Maybe constantly squinting would actually alter the shape of your eye/retina slightly, thus meaning you'd always need to squint (or get glasses)?

@Luke i added some thoughts to the answer.  I think eye strain that results from squinting when your eyes are not really seeing things well might tend to hurt your eyes.  squinting because the light is too bright is probably a good thing and might be as good or better than sunglasses.

squinting may be harmful b/c it reduces number of blinks?  affects the production of tears?

its probably better to be in a not too brightly lit temperate environment