text:
What is the role of Homocysteine in cognitive function?
I'm looking at this link : Homocysteine and cognitive impairments and am looking for more information on specific cognitive impairments associated with elevated levels Homocysteine. That article is not very clear on that point. I've seen some research papers about the study of this in elderly people and cardiovascular studies. I'm interested in average adults.
I've been fascinated with the effect/lack of thereof of vitamin B6 on dreaming and Homocysteine is the first thing that I've stumbled upon in quite some time that is directly related to the B family of vitamins. Has there been any research about what Homocysteine gets metabolized to if exposed to B-Complex vitamins versus Vitamin B6 alone?
Thank you for your input!

I'm not sure if this answers your question, but I'll give it a try anyway. Here's a diagram of homocysteine metabolism. Vitamin B12 is a cofactor for homocysteine methyltransferase, and folic acid is required for tetrahydrofolate (THF). As both vitamins are involved in homocysteine metabolism, the symptoms of folate and vitamin B12 deficiency are similar. Vitamin B12 deficiency can result in neurological symptoms due to abnormal myelin, but folate deficiency does not. Vitamin B12 also metabolizes methylmalonyl-CoA to succinyl-CoA as seem here, so the methylmalonic acid level is often measured to test for vitamin B12 deficiency.
Hyperhomocysteinemia is the condition of high levels of homocysteine, but it is usually due to low vitamin B12 or folate.

Thank you for a very informative answer! The diagram of    homocysteine metabolism confirmed that there are two possible ways that the amino acid gets metabolized and I will investigate this more thoroughly.


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Is there a normal human melatonin concentration to light level curve?
I'm looking for a graph or a curve that would show the typical concentration of melatonin in blood or saliva for humans over 24 hours. It would be good to know the photoperiod for the same human as well.
I know that melatonin release is inhibited by blue light, perceived through the retina, with melanopsin being the photopigment that signals suprachiasmic nucleus to suppress melatonin release. This is why it would be great to see melatonin data alongside light exposure data.
Thank you for any hints on where I can find such information!

Found a few samples here: http://ars.els-cdn.com/content/image/1-s2.0-S0024320503008142-gr2.gif this shows the nocturnal melatonin peak, which is apparently very important for well being

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Is there an optimal illumination level for human habitats/workplaces?
I know of melanopsin, a photo pigment in mammal eye that helps regulate circadian rhythms. It responds most strongly to blue spectrum light. There have been experiments that demonstrated that intensity of light is proportional to the impact on circadian rhythm regulation/ melatonin suppression.
This is why I'm interested if there is some optimal illumination intensity that has been demonstrated to result in better health/cognition in humans. I heard anecdotal reports of full spectrum lighting improving attention in classrooms, but is there some chart or figure which says how much is "too much light".

It seems there has been some work done on too much light affecting human health, but in regards to lack of darkness at night, rather than too much during the day. Without the appropriate amount of darkness at key times melatonin production and the major clock regulator or SCN can be disrupted and lose sync with the peripheral clocks. See here [1] for a comprehensive article with loads of information and other links to studies done on this topic.
This part in particular illustrates some of the problems associated with too much light:
"Overexposure to sun-mimicking light is also believed to play a role in the increase of insulin resistance, type 2 diabetes and obesity in developed countries (where round-the-clock illumination is more prevalent). Some research also shows that too much sun-mimicking light ups our craving for carbohydrates.
Before humans started cultivating grains, carbohydrate energy was available only from spring to fall. In response, our bodies evolved to stock up on carbohydrates during the growing season to prepare for winter, when no carbohydrates were available. In turn, we didn’t crave carbohydrates in the winter. All that changed with the light bulb, write T. S. Wiley and Bent Formby, PhD, in Lights Out: Sleep, Sugar and Survival (Atria, 2001)"
This might be a bit off topic but check out http://www.lightingdeluxe.com/workplace-lighting-ergonomics.html and the HSE has some info on what the required lighting conditons in the workplace should be [2]. They only mention lighting conditions with reference to reducing levels of stress in the workplace though.
Also not directly related but pretty cool; an article in Science from 1998 found that light shining on the back of the knees may be able to regulate circadian rhythms [3].
[1] http://experiencelife.com/article/light-rhythms/
[2] (scroll to the lighting section) http://www.hse.gov.uk/humanfactors/topics/lighting.htm#lighting
[3] Wright, K.P. Jr. & C.A. Czeisler. Absence of circadian phase resetting in response to bright light behind the knees. Science 297, 571 (July 26, 2002).
or if you don't have access http://www.genomenewsnetwork.org/articles/08_02/bright_knees.shtml

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Is the water-splitting enzyme a component of photosystem II?
Can Somone answer a bit bizarre question which is that in light reaction . Photosystem uses enzyme to split the water up to hydrogen ions and electrons and oxygen.But is this water-splitting enzyme in or out of the photosystem 2(PS II)?
Great thanks

where have you looked for answers to this question? Can you give a bit more background?

I too have just been studying Photosynthesis :)
From what I understand the PSII is the enzyme that splits water. Water splitting occurs in PSII. In that case what you could further ask is where in this big enzyme does it take place?
Basically the PSII is composed of many protein-complexes and pigments. One of them known as the oxygen-evolving complex (you can read more here: https://www.google.co.in/?gfe_rd=cr&ei=3AgsWd2VMunn8AezuYqYAQ#q=oxygen+evolving+complex) is the site in PSII where the water splitting takes place.
You can also study about photosynthesis here (https://www.khanacademy.org/science/biology/photosynthesis-in-plants).
Hope it helped!


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Do mosquitoes allow for DNA transfer between unrelated species?
A mosquito can bite individuals of different species and eventually allow for some blood of one species to enter into the bloodstream of another species which I suppose may eventually cause DNA transfer, that is horizontal gene transfer
Do mosquitoes increase horizontal gene transfer among the species they parasitise? If yes, is it considerable or negligible?

The question is rather broad for the moment. Sure mosquitos carry diseases, they will clearly affect other species evolution (incl. the famous interplay between malaria resistance and sickle cell amenia). Is there any selection pressure or any co-evolutionary mechanism you are interested in?

@Remi.b, nothing in mind, just curious if the trace amounts of transfer is having an impact over the long term, and if so, was it large or negligible.  Simple curiousity, having effectively zero bio science expertise.

What do you call the trace amounts of transfer? Do you have in mind existence DNA transfer between individuals of the same species via blood transfer or something like that? Or are you wondering whether the cost of the blood loss via mosquito suction is important?

@Remi.b.  More dumbed down than that I guess.  Do we have 'bits of  antelope or elephant traits in us' because of mosquitoes.

Oooh ok, I think I get your question. I completely rephrased your post. If I misunderstood your point (or if you don't like the edit for any reason), feel free to roll back the edit.

@Remi.b.  Thanks.  Nice edit, although you probably made me sound smarter in this area than I'd confess to.  :-)

In general foreign materials may be transferred from one organism to another in a mosquito, as is obviously the case with malaria, but for DNA to make it from inside the cells of one organism to inside the cells of another organism is exceedingly rare. In general DNAses and RNAses are present anywhere around living cells so when DNA is released it is quickly chewed up into useless fragments. Most likely this happens readily inside the digestive tract of a mosqito (Evolutionarily this makes sense as it would be extremely bad if a mosquito started absorbing genes from any of the organisms it was feeding off of!). Furthermore, DNA is an enormous charged molecule and does not easily pass through a cellular membrane. In a laboratory setting, DNA may be transferred into organisms with the help of electroporation or "gene guns" but this requires large amounts of identical genes to be effectively forced into cells, and even then, efficiencies of gene transfer are low. In short, no, it would be effectively impossible for a gene to be transferred from one organism to another by a mosquito. However, if a virus gets transferred by the mosquito...

...not to mention that DNA would have to enter not just any cell but specifically cells in the germ line.

I would not use malaria as a general justification that foreign materials can be transferred by mosquitoes. Malarial sporozoites must actively migrate to the salivary glands of mosquitoes in order to be transmitted in their bite.


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How do prions cross the blood brain barrier?
How does the PrP scrapie protein maintain its confirmation while going through the GI tract? How does the PrP scrapie protein cross the blood brain barrier?
Wouldn't the host immune system recognize the prion as "not self" and attack it?

Googling your title question gets about 231,000 results. What specifically are you having difficulty with?

hmm idk how to be more specific but i guess I could say: "what structural part of the PrP scrappie protein provides it transport across the blood brain barrier ?"

The link you provided raises more questions than it answers.. I dont see why we cant vaccinate against prions (or maybe just parts of it) if they spend so much time in secondary lymphoid organs?

I am not sure if a perfect answer is possible owing to the fact that Prion diseases are still incompletely understood, and are actively under research. On a preliminary search, I found some papers which address the issue (cited at the end).

Since $PrP^C$ is normally found in the body, its role and its transport is also relevant to the issue. It seems to undergo bidirectional transport across the BBB using a saturable mechanism, mostly a specific transporter (1). It is taken up peripherally, and by several regions of the brain with the possibility that it is involved in various brain functions including modulating the BBB itself. Amyloid Beta-protein, with several kinetic and dynamic similarities with $PrP^C$, is shown to have BBB altering effects. (2) How far do the pathological prions follow this is seemingly unknown.
Autonomic nerves seem to play a role in their transport.(3) When challenged with prions, sympathectomy delays or even prevents the disease, whereas sympathetic hyperinnervation accelerates prion pathogenesis. There have been studies to elucidate the transport via the nerves, such as (4) and (5).

There are several other studies on this issue, and following the cited references might help you find them.
Reference number 3 also has information on the immunological response to prions.
References:

Banks WA, Robinson SM, Diaz-Espinoza R, Urayama A, Soto C. Transport of prion protein across the blood–brain barrier. Experimental neurology. 2009 Jul 31;218(1):162-7.
Giri R, Shen Y, Stins M, Du Yan S, Schmidt AM, Stern D, Kim KS, Zlokovic B, Kalra VK: Am J Physiol Cell Physiol. 2000 Dec; 279(6):C1772-81.
Aguzzi A, Zhu C. Five questions on prion diseases. PLoS Pathog. 2012 May 3;8(5):e1002651.
McBride PA, Schulz-Schaeffer WJ, Donaldson M, Bruce M, Diringer H, Kretzschmar HA, Beekes M. Early spread of scrapie from the gastrointestinal tract to the central nervous system involves autonomic fibers of the splanchnic and vagus nerves. Journal of virology. 2001 Oct 1;75(19):9320-7.
Glatzel M, Heppner FL, Albers KM, Aguzzi A. Sympathetic innervation of lymphoreticular organs is rate limiting for prion neuroinvasion. Neuron. 2001 Jul 19;31(1):25-34.

Thanks for the answer satwik, it certainly provided me with a lot more of an understanding than before.

'bidirectional transport'?


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Why do stomata close in low intensity light?
Stomata close during high intensity light to prevent excessive transpiration but why did they close during low intensity of light? Please explain in easy- understand language because i'm  in just 10th standard.

Think closed state as default state, it is the light which opens the stomata, So in the absence of light stomata go backs default(closed or resting or inactive) state.

Do you have a source in support of your assertion that high light intensity causes stomata to close?

The primary function of open stomata is to promote gas exchange in leaf tissue: atmospheric carbon dioxide is a substrate for photosynthesis. A side effect of opening the stomata is an increase of water loss through transpiration. If light intensity is low then photosynthesis will be depressed: under these conditions it makes sense to close the stomata to conserve water.


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Is "reaction center" the same as "photosystem"?
I have a diagram which labelled a part of PSI (Photosystem I) as "reaction center". But I have read on several websites that the reaction centers are PSI (the whole complex, not just a part of it) and PSII.
So, which one is correct? And if the reaction center is only a part of these PSI and II complexes, what does it contain? And what does it do?


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What is the mechanism of regulation of PER /CRY genes?
I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate each other. Do these genes encode proteins that once created bind to the DNA and cover the transcription sites for other genes(like PER protein covering the binding site of CRY)?
A lot of diagrams and descriptions of the process are very complex, and I would appreciate a simple answer (if it exists).

Wikipedia gives a very good explanation of this, on the page for the suprachiasmatic nucleus.

For example, in the fruitfly Drosophila, the cellular circadian rhythm
  in neurons is controlled by two interlocked feedback loops.
In the first loop, the bHLH transcription factors clock (CLK) and
  cycle (CYC) drive the transcription of their own repressors period
  (PER) and timeless (TIM). PER and TIM proteins then accumulate in the
  cytoplasm, translocate into the nucleus at night, and turn off their
  own transcription, thereby setting up a 24-hour oscillation of
  transcription and translation. In the second loop, the transcription
  factors vrille (VRI) and Pdp1 are initiated by CLK/CYC. PDP1 acts
  positively on CLK transcription and negatively on VRI. These genes
  encode various transcription factors that trigger expression of other
  proteins. The products of clock and cycle, called CLK and CYC, belong
  to the PAS-containing subfamily of the basic helix-loop-helix (bHLH)
  family of transcription factors, and form a heterodimer. This
  heterodimer (CLK-CYC) initiates the transcription of PER and TIM,
  whose protein products dimerize and then inhibit their own expression
  by disrupting CLK-CYC-mediated transcription. This negative feedback
  mechanism gives a 24-hour rhythm in the expression of the clock genes.
  Many genes are suspected to be linked to circadian control by "E-box
  elements" in their promoters, as CLK-CYC and its homologs bind to
  these elements.
The 24-hr rhythm could be reset by light via the protein cryptochrome
  (CRY), which is involved in the circadian photoreception in
  Drosophila. CRY associates with TIM in a light-dependent manner that
  leads to the destruction of TIM. Without the presence of TIM for
  stabilization, PER is eventually destroyed during the day. As a
  result, the repression of CLK-CYC is reduced and the whole cycle
  reinitiates again. (http://en.wikipedia.org/wiki/Suprachiasmatic_nucleus#Fruitfly)

The suprachiasmatic nucleus (SCN) is a tiny part of our brain residing in the center. It maintains a biological clock through a gene expression cycle in the individual neurons. The mechanism for humans is very similar to the mechanism for fruit flies, as explained above, but to rehash a bit...
In the fruit fly model there are five players: CLK, CYC, PER, TIM, CRY.
CLK and CYC are transcription factors for PER and TIM, and bind to their promoters in order to activate the expression of PER and TIM.
When the expression level of PER and TIM gets very high, the PER and TIM proteins return to the nucleus, and inhibit their own transcription factors (CLK and CYC) through molecular interactions.
The CRY protein is light-sensitive, and so daylight (or artificial light) will cause CRY to destroy the TIM proteins. Without TIM, we no longer get the PER-TIM dimers that inhibit the CLK-CYC transcription factors.
In humans and other mammals it's the same concept, but with slightly different players (e.g., homologous genes).
What's important here is that we have a biological clock on the cellular level. We haven't gone into how this clock is used yet... But, it's my understanding that the SCN uses the information to tell the pineal gland when to produce melatonin.
The melatonin causes us to be drowsy, lowers our body temperatures, and causes us to fall asleep.
You can see another cycle at work here - our body temperature, which rises with wakefulness, and declines with sleep.
This gives a more general answer to how circadian rhythms are used to influence our sleep cycle. Your question was how the genes involved in circadian rhythms regulate each other. The answer is the transcription-translation negative feedback loop described above.
Hope this helps...

Great answer! I didn't know about "e-boxed" genes, that's something to take a look at !


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How many kg of seed can one expect from 230 kg of cotton fiber?
So I'm working with data from recent cotton harvest from a seed company. They're more interested in cotton seed than the fiber itself. I'm trying to come up with seed yield numbers for an array of cultivars but the data I was given came in kg of harvested fiber. Excluding any changes between cultivars due to genetics,
Does anyone have an idea of how many kg of cotton seed I can get from a given yield of cotton fiber?
Kind regards,

That would be a great question for Agriculture&Farming.SE (still suggested in Area51 and quite far from having its won site though).

According to this document (pdf) the rate is around 700 lb seed per 500 lb of fibre.
seed = 1·4 × fibre
230 kg fibre ≅ 320 kg seed
(Strangely, the rate has fallen over time.)

That is strange…

Curious, it has indeed. 230 kg of fiber in our case yielded 226 kg of seed.


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Why is there no toxic effect on the bulbuls feeding on Cascabella thevetia (oleander) nectar?
I have a huge Cascabella thevetia by my house and I know that its sap and fruits are extremely poisonous.However I have seen red vented bulbuls and wasps feed on its nectar.Also this confirms it but doesnt specify nectar infact it says plant parts...The same source says the poison affects vertebrates and the birds are definitely vertebrates.So why it doesnt affect them?

I realise that you are asking for an explanation, but note that the WP page that you link to specifically mentions that bulbuls aren't affected.

@Alan Boyd yes.they are'nt.why does it happen when it is so toxic to humans?what is that biological phenomenon that brings about this difference?That is exactly what I want to understand.

The toxicity of Cascabela thevetia is due to the presence of cardiac glycosides such as thevetins A and B. Although these compounds are highly toxic for humans and several domestic animals, other vertebrates are much less sensitive to them.
This review article discusses various aspects of oleander toxicity, and the authors draw attention to species-specific differences in toxicity.

In addition to dogs and cats, Szabuniewicz et al., (1972) also examined oleander toxicity in monkeys, goats, mice, rats and chickens. Dogs, cats, goats and monkeys were found to be very sensitive to the cardioactive glycosides extracted from dried oleander leaves. In contrast, the rodent and avian species were observed to be insensitive to oleander cardioactive glycosides.

They go on to suggest that differences in the toxin target molecule, the cardiac Na⁺,K⁺ ATPase, is the most likely explanation for this:

Akera et al., (1979) postulated that the low affinity between cardiac glycosides and rat cardiac Na⁺,K⁺ ATPases could be due to stearic constraints in substrate (glycoside) binding. In this scenario, quaternary conformation of the OL-subunit glycoside binding sites physically precludes the simultaneous binding of all three glycoside structural components. Species-specific quaternary conformation of Na⁺,K⁺ ATPases coupled with subtle differences in glycoside composition (e.g. various sugar moieties attached to the steroid backbone) could, thus, conceivably account for the observed species-specific responses to cardiac glycosides, including those found in oleander.

We have a tendency to assume that susceptibility to the toxic effects of plant materials is universal, but the toxicity of onions and chocolate for domestic animals are clear examples that this is wrong. The variation in sensitivity to the toxins in oleander is a good example coming from the other direction.
Shannon D. Langford & Paul J. Boor (1996). "Oleander toxicity: an examination of human and animal toxic exposures". Toxicology. 109 (1): 1–13. PMID 8619248. doi:10.1016/0300-483X(95)03296-R.


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Do lobsters possess a nervous system to feel pain?
I was reading an article, which it mentions that lobsters do not have a nervous system:

Lobsters have very poor eyesight and no nervous system. They walk slowly
  on the sea floor but are capable of swimming backwards by the curling
  and uncurling movement of their abdomen.

But in Wikipedia, I read that only 3 types of multi cellular animals do not posses a nervous system:

The only multicellular animals that have no nervous system at all are
  sponges, placozoans, and mesozoans, which have very simple body plans.

Which none of them seemed like a lobster to me. In this answer, it is claimed that every living organism feels pain somehow.
Now I would like to know the answers of these questions:

Is the article about the lobsters true? They have no nervous system which means they feel no pain even if killed?
Is the claim in the answer true? Literally one of the claims must be wrong, since they conflict with each other somehow.

As for the answer you linked to, it states: I believe every living organism (even single cell ones) experience pain somehow, which is hardly a scientific claim. Also: The scientific answer depends on how you define pain, which is an important caveat. If you were to define pain as the ability to sense damaging stimuli (which to me seems inappropriate), then every organisms indeed can feel pain.

@canadianer Well yes, when a living organism can heal itself, it means it can feel the damage. I was actually wondering about the same pain that most of the animals (including humans) feel; the unbearable feeling.

"I was reading an article, which it mentions that lobsters do not have a nervous system:" - Neuroscientist chiming in here... this is a really good cue you should stop reading the article if you are looking for science.

@JackJohansson "...when a living organism can heal itself, it means it can feel the damage"- How so? Unless you're extending "feel" past a conventional meaning, then there countless organisms that this is isn't remotely true for.

@HarrisWeinstein - would love to know how you determine whether or not another organism can feel.

@AlwaysConfused I didn't write the article.

@AlwaysConfused That's why i asked it here. But the comments seem like its a crime to ask.

@youcantryreachingme Possessing a nervous system is a good start.

I do not have a link to this but I read that lobsters will fight over territory or mates or whatever and the loser of such a fight will avoid the winner for some time afterward. So whatever the lobster uses for a nervous system allows it to both remember and recognize other lobsters. (Yellow jacket wasps will fight for "pecking order" and remember whom they have fought before and feed peacefully next to each other once hierarchy position is established.)

Yes they feel pain, at least in certain areas of their body without a doubt. Research has been done to test whether they feel pain consciously (a signal to the brain that is perceived allows for learned response) or if it is just a reflex response (Nociception), and there is good evidence they actually perceive it especially in the antenna.
source
Source 2

Now that's something i liked to know, despite the other comments that aren't any constructive. Thanks!

Can you please provide a source?

There already is one but I'll add another.

To answer if lobsters have a nervous system:
YES

References:
Mapping of serotonin-like immunoreactivity in the lobster nervous system
BS Beltz, EA Kravitz
Journal of Neuroscience 1 March 1983, 3 (3) 585-602
http://umaine.edu/lobsterinstitute/education/life-of-the-american-lobster/anatomy-biology/

Bonus picture:


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Fastest G protein coupled reactions
As per few references, fastest G protein coupled reaction known is Drosophila melanogaster phototransduction which produces quantum bumps with average latency of 45 ms (and peak response around 200 ms). Another reaction is chemotaxis which is also in that order. I was wondering are there any known examples which are as fast as these responses?
P.S: Many ion channels are GPCR which triggers very fast but most of them takes long time (in order of seconds) to give peak ion concentration
P.S.S: By fastest I mean, minimum time required to give peak response after activation of receptor(s).
Update:
In abstract case, Let's say you got signal from outside at time t = 0. Now this will leads to reaction cascade which will take time 't1'. Assume output of this is opening of channel which will increase concentration of ion X. Now X will reach it's peak concentration at time t = t1 + t2. So I am looking for such reaction cascades with minimum time 't' (t1+t2).

That is not the property of the receptor. There are many other factors that dictate the response time (the time required to achieve steady state).

Yes. I am asking for smallest reaction times which involves GPCRs. And it need not be steady state. Peak time is not steady state.

Even peak time is a function of a lot of different parameters. Btw peak can be observed only in case of certain network architectures. A single reaction doesn't peak; you need a feedback (or some other kinds of motifs). Anyways, what do you exactly mean by reaction time? What is the reaction here. There can be several downstream effects some of which can be early while others are delayed.

Why do you want to know this? A little context might make the question more answerable.

@WYSIWYG , I think you didn't get my question (or I didn't explained properly). Let's say you got signal from outside at time t = 0. Now this will leads to reaction cascade which will take time 't1'. Assume output of this is opening of channel which will increase concentration of ion X. Now X will reach it's peak concentration at time t = t1 + t2. So I am looking for such reaction cascades with minimum time 't' (t1+t2).

@GoodGravy , I just wanted to know smallest time delay between signal and response in GPCR.

@Dexter but there can be several steps in a cascade and some of them might take more time than the others to reach the peak. What I am saying is that the response is not just dependent on the receptor but also on the other molecules interacting with it. Not only that; initial conditions, the magnitude of the signal etc also matter.

@WYSIWYG, exactly. There will be many steps which will ideally create time delay for output of particular signalling cascade. I am looking for such time period. Assuming all other interactions are also involved in setting up this delay, I was curious to know how fast these reactions can be.

So does this question boils down to "What is the shortest GPCR reaction, i.e. with the receptor and effector being separated by a minimum number of steps?"

I wouldn't say minimum number of steps. Time required to execute all these steps should be minimum.

@Dexter I don't really understand what is the purpose of the question. Curiosity or you are looking for parameters for your mathematical model? In any case nobody has checked all the GPCR pathways. The number of downstream steps and also the architecture of the network determine the response time. An example of long term effects of GPCR signalling would be growth, which might take many hours to reach steady state. That would be the maximum limit. Olfactory/visual stimulus should be the fastest because these are quickly converted to electrical signals.

It's my curiosity. I had heated discussion with my friends on same topic. So I wanted to know scientifically what is reality.

Mammalian rod cells, the most numerous photoreceptor cells in the retina, reach a max depolarization after a single photon stimulus at 100-120 ms, implying a time constant (1/k) of about 25 ms (see Chen et al., Nature 404:557).  This is on the same order of speed as the fly eye, maybe a tad faster.  Non-photoreceptor GPCRs are probably slower, but few folks have tried to measure these effects. The m1 muscarinic acetylcholine receptor catalyzes Gq activation with a time constant of about 500 ms (Mukhopadhyay and Ross PNAS 96:9539), but there may be faster ones.

Drosophila photoreceptors are way faster than rod cells. Check out reference I provided in question.


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Did modern alligators and caimans come from prehistoric crocodiles?
I know that crocodilians have been here since the time of the dinosaurs. I also know that crocodiles came first. But alligators have been here for a good 37 million years. Did alligators come from crocodiles when the crocs swam into freshwater areas?
And since the alligators and caimans are 2 groups in alligatoridae did they have a common ancestor?
And also if alligators came from crocodiles (which might or might not be true), why isn't it more like this:
Crocodylidae $\rightarrow$ Alligatoridae $\rightarrow$ Alligatorinae $\rightarrow$  Alligator
for alligators and
Crocodylidae $\rightarrow$ Crocodylus
for crocodiles?

The tree of crocodilomorpha is here on wiki.

This is the phylogeny of the Crocodilia, as best as we currently know it:
The order Crocodilia is a monophyletic group including all living crocodile and alligator species. That means that all of these species share a common ancestor and all descendants of that ancestor are part of Crocodilia.
Within the Brevirostres, three superfamilies exist - the now extinct Borealosuchus, the Gavialoidea, within only two species not already extinct, and the Brevirostres.
The Brevirostres are the monophyletic group containing the crocodiles and alligators (that includes the caimans).

Did alligators come from crocodiles when the crocs swam into freshwater areas?

That very much depends on what you mean with "crocodile". If it's Crocodylidae, then no, these are sister groups. If it's only the true crocodiles (Crocodylids), no, those evolved after the split with alligators. If it's Crocodilia, then yes, alligators evolved from crocodiles.

And since the alligators and caimans are 2 groups in alligatoridae did they have a common ancestor?

Yes. However, saying that is rather boring - all life has a common ancestor. If you mean whether they have a common ancestor and all descendants of that ancestor are either alligators or caiman, then yes.
Additional source: Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae


text:
Does inorganic particles have pattern recognition receptor?
Does silica or carbon particles (inorganic substances causing silicosis and anthracosis) have Pattern Recognition Receptor (PRR) on macrophages/dendritic cells? Because phagocytic activity depends on PRR. If it doesn't have how it engulfs it?

Pinocytosis....

I think that I have posted this link for you before NIH Bookshelf: Janeway's Immunobiology. You are continually asking questions on this site about immunology that would be answered if you simply read this book (even though this edition is slightly out of date). It is a free resource and it will explain everything you are looking to find out, and then some, about the basics of immunology. The only annoyance is that in order to read you need to enter a search term, you cannot read cover to cover like a normal book.


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Does a DNA sequence has its own derivation tree or pattern?
I am new to bioinformatics and natural language processing. In linguistics, they have Treebank - derivation/parse tree for each sentence. For example, a sentence "Sara sleeps" can be visualized by a tree: Sentence -> Subject Verb, Subject -> Sara, Verb -> sleeps.
I've heard about Genbank, a database for nucleotide sequences. Does a DNA has its own derivation tree, or is any pattern in a DNA sequence already known with current technology? I only heard about repeats.

Hello kate, I don't understand your question. The "derivation tree" you are describing is a structure which is specific to linguistics. How could a DNA have such a thing? It does not represent human language.

Thank you for the comment. I think DNA has its own "language" which is probably unknown yet. My question is,(1) is the "language" of DNA already known? (2) is there any hint already known for understanding the "language" of DNA? Hint might be anything, such as patterns.. because I don't really understand much about bioinformatics.

DNA does not have its own language, it's a simple storage medium. It encodes information, but not in any way similar to a human language. Maybe this encoding fulfils the definition of a formal language, but if you have never gone into that branch of maths, any comparison will be more confusing than enlightening.

So better to think it as a storage medium.. Thank you very much!

The Gene Ontology Consortium might be of interest to you.

Thank you for the valuable information. So to understand the "language" of DNA, or at least to understand how DNA sequences are derived, simply parsing the nucleotides/DNA sequences is not enough because they are mere storage? To cover protein etc is too big for me for now, but it is interesting.

@kate I still don't understand your question. What are DNA sequences supposed to be derived from?

By "derive" I mean as in "derivation" or "derivation tree" in formal languages field.

I think protein (not DNA) domains might be something close to what you are looking for https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-domains

Thank you very much for your all warm and informative comments. I thought that studying DNA sequences only is enough but it seems that's not the case; it's much more complex than the languages that human made by themselves. Hope I can catch up on proteins and gene ontology, at least grasp the basic understanding. Thank you very much for your help.

From your example I guess that by "deriving" you mean something like decomposing into elements with diverse functions. Maybe we could apply this concept to DNA sequences: Some parts code proteins, which are decomposed into triplets, each of which codes an amino-acid. Other parts have regulatory functions: They can be motifs not coding a protein, but instead allowing a protein or something else to bind and modify the expression of nearby protein-coding parts. Other parts may contribute to the physical structure of the chromosome, or may have no function at all.

Yes, this is what I mean. Thank you very much for your answer! Do all these - e.g. where is the part in a DNA sequence that involve in  function x - already known?

There are regulatory motif databases, and prediction algorithms for functions in a sequence, but all this is not fully known. Indeed, things are rarely fully regular in biology, so every bioinformatics predictions ideally should be completed with experimental confirmation. Also, the same sequence can sometimes be parsed in various way: a single DNA sequence may encode several proteins, depending on which portions are actually translated into amino-acids.
Some keywords you may be interested in: start codon, stop codon, open reading frame, 3'UTR, 5'UTR, binding box.


text:
Why is chromatin not condensed during interphase but is in prophase
Cell cycle goes through three processes:

Interphase
Mitosis
Cytokinesis

Why are chromatins not condensed during interphase but instead condensed at prophase of mitosis? What makes them condense at prophase?

What resolution answer are you looking for here? Chromatin is complicated. If it was condensed during interphase, how would it be used? It would be folded up and inaccessible.

but then why is it condensed in prophase? and I still don't understand why are they condensed at prophase?

So that it can be partitioned neatly into daughter cells. If I understand correctly, your question boils down to "why is chromatin condensed at all?" ?

exactly. Also what makes them not condensed at Interphase?

This question is far too broad. From What types of questions should I avoid asking? in the [help]: "If you can imagine an entire book that answers your question, you’re asking too much." I suggest reading the Wikipedia article on chromatin and the linked articles on, for example, the structure of DNA.

is there a brief explanation of the causes that lead to this process?

Here's an image that explains the cell cycle:

And here's one that explains Mitosis as a subcategory of the cell cycle:

Chromosomes condense on the metaphase plate before they are pulled apart by kinetochore microtubules in a Tug-of-war. Chromosome condensation is not yet fully understood, but nucleosome structure is hypothesized to play a role. This is a very good question and is definitely not too broad.


text:
kinetics question
An enzyme has a $V_{max}$ of 50 $\mu$mol product formed $(min * \text{mg protein})^{-1}$  and a $K_m$ of 10 $\mu$M for the substrate. When a reaction mixture contains the enzyme and a 5$\mu$M substrate, which of the following percentages of $V_{max}$ will be closest to the initial reaction rate ($V_o$)
a) 5%
b) 15%
c) 33%
d) 50%
e) 66%
Can someone explain this to me; I know michaelis-menton but I don't understand the solution to this or how to find it.

You literally just have to plug in the numbers in the Michaelis Menten equation.

I don't think you understand MM kinetics.
In your case the $V_{max}$ value depends on the amount of the protein. If we assume 1mg protein, then $V_{max} = 50\frac{\mu{M}}{min}$.
According to MM kinetics:
$V = V_{max}.\frac{S}{K_M+S}$
so
$V_0 = V_{max}.\frac{S_0}{K_M+S_0} = V_{max}.\frac{5\mu{M}}{10\mu{M}+5\mu{M}} = V_{max}.\frac{1}{3}$
or in other terms
$\frac{V_0}{V_{max}} = \frac{1}{3} = 33.3\%$

@ChrisCook If you consider that inf3rno answered your question, then you should check it to indicate future users that you received an answer that helped you. It also reward the one who answered with 15 points of reputation and therefore encourage users to answer your future posts.

sorry, new to the site; I checked the check under his answer, I assume this is what you meant?  thanks


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How to convince suspension cells to adhere more tightly?
I'm developing a cell-based assay in 96-well plates that requires adherent cells, as they need to be washed at least twice during the protocol. I'm using in-house strains of HT1080 cells (some overexpressing a certain protein of interest) that unfortunately have been selected for suspension growth in chemically-defined media (50/50 CD-CHO/CD-293). I can convince them to adhere by culturing in DMEM with 10% FBS and growing them in CELLBind flasks, but they still tend to pull away if there is very much shearing force, such as during the wash steps, or when they're in PBS during the assay wash and incubation steps (maybe 2 hours total for now, I'm still optimizing that).
Unfortunately, the parameters of my experiments don't allow me to keep the cells in serum-containing media during the assay, as it would interfere with the uptake of my drug. Like I've said, when in PBS they start detaching, and I would assume the same in HBSS, which I don't really want to use anyway due to its low buffering capacity in CO2 incubators.
Might DMEM alone (without FBS) provide a little more impetus to stay attached during the assay? What would the effect be of increasing the amount of FBS to say 15 or 20% during culturing - would that promote stronger attachment? I'm a little hesitant to coat the wells with poly-D-lysine, as my readout is on a fluorescent imager, and I'm worried it would substantially increase background. I don't really have enough time to re-select the cells for adherent growth (although if I'd known about these issues from my predecessor 3 or 4 months ago I would have started right away...), so are there any other tricks I can try in the meantime? Are there any media supplements I could use to promote adherin expression or something like that? Any tips or advice at all would be appreciated.

I'd suggest splitting out your edit into a new question, it looks like it would be a fine question on it's own.

@MadScientist - that's true, I hadn't thought of that. Coming right up!

I don't remeber this anymore exactly, but weren't there cell culture plates available which had a membrane bottom which allowed you removing liquids by centrifugation while the cells stayed on the membrane?

Have you looked into trying the DropArray microplates? They're a new technology where you don't need to centrifuge your cells to wash them...an old colleague of mine works for the company and they're pretty cool about demoing the products/instruments for you. It's http://www.curiox.com/.
I think most people that use the system are using suspension cells- because of the challenges you listed above, so may be worth a look!
Good luck!

Interesting. I'll have to check them out a little more. I'm not developing the assay anymore (I posted the question a year ago), but I ended up switching platforms to flow cytometry, and just used round-bottom/v-bottom plates.


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Why doesn't local anesthesia affect muscles?
While having a dental surgery, I've got this question that why I can still talk, open/close my mouth, move my lips and so on while I can't feel anything at all in my mouth?
If the local anesthesia interrupts the alert that goes through brain, how is the muscle still functional? Is it some sort of one-way interruption which only disables the alert that go "from" the nerve "to" the brain? Or are there different nerves for this task?

Why isn't anyone just saying that local anesthetics block sensory neural pathways, not motor neurons? There are two differing neurons, motor and sensory. Is not that the bottom line? This is what I assumed, but ended up confused after reading the answers provided.

@michelleb this is because local anesthetics block both sensory neurons and motor neurons. They block a specific receptor site inside $Na^+$ channels found in all axons, preventing propagation of an action potential. All neurons need this channel in order to send signals, so it's not a matter of a difference in the physiology of a sensory vs. motor neuron, it's about the anatomy of the specific nerves involved.

@Nicolai's answer is not entirely correct.
Background
The most common local anesthetics are all the "-caine" drugs - like novocaine, lidocaine, - and even cocaine has some of the same pharmacology, as well as other effects (in movies this is why cops might rub some white powder on their lips - if it's cocaine, it will make their lips tingle; this is not standard training for non-movie police; also not advised for drug sellers or purchasers, because for exactly this reason cocaine is often cut with other -caines or other compounds that give a tingly feeling).
What all of these drugs do is to block voltage-gated sodium channels. These are the channels that propagate action potentials through axons and excitable dendrites. Other local anesthetics that aren't used in the clinic, like tetrodotoxin from pufferfish, block the same types of channels. At sufficient concentrations, local anesthetics block all nervous activity: unlike @Nicolai's answer, they do shut down nerves (as a brief note for terminology: nerves are bundles of axons containing many many individual fibers).
So back to your original question: how come the muscle isn't impaired during dental surgery?
Geometry of innervation of the face
Take a look at this picture of the nerves innervating the facial muscles and the muscles themselves: https://bmc.med.utoronto.ca/cranialnerves/wp-content/images/c_07/Facial-vii12_labelled768.jpg (note: I wasn't able to find a good image that has a license allowing me to reproduce it here; if someone finds one and wants to edit it in, please do - thanks!)
They mostly come in from the sides of the face, and so they are further away from the site of local anesthetic injection. The muscles themselves also extend further away. It may be that the muscle is partly anesthetized, but you don't realize it.
Limited diffusion and location of injections
Diffusion of local anesthetics is limited because they actually act inside cells, and only the unionized form can diffuse across cell membranes. Once inside the cell, the tend to be ionized and therefore get "stuck". Therefore, they don't typically diffuse nearly as far as other compounds of similar size, especially lipophilic compounds.
The nerve endings that sense pain, on the other hand, have to be at the surface of the skin/mucous membranes. That is, they are exactly where the local anesthetic is being injected. The objective of local anesthesia is often to inject enough to affect only those surface tissues, trying to spare the deeper tissues.
Effects on nerves
However, it isn't too uncommon to overdo it and to paralyze the underlying muscles or nerves. Even nerves far away can be affected, for example see this paper discussing cases where the local anesthetic travels near the eyes and impairs eye movement. There are also other non-dental procedures where block of a particular nerve is the intended result: this can be seen as an alternative to general anesthesia. One example is the use of an epidural (essentially into the space around the spinal cord) injection during childbirth or surgery. The extent of paralysis depends on the dose, however, and usually the intent is to avoid major paralysis and use other drugs like opiates to assist in preventing pain.

Sorry to say, but this isn't exactly correct either. In dental procedures, nerve bundles are usually the target of the anesthetic block. Similar to digital blocks in laceration repair. We block either side of the base of the finger, yet the finger can still move quite easily.

So to be clear, the neuron itself is not paralyzed? One quick question, If we do a LA on inner ear, is it still able to send crucial feedbacks to the brain? By the way, thanks for the long and nice answer :)

@anongoodnurse Thanks! Today I learned... Feel free to edit my answer or add your own. Is that always how things are done for dental procedures? Presumably those nerves are separate from the ones that control the muscles. Or is it just because the different fibers have different thresholds? My experience is in rodent surgeries, where we just inject under the skin. I thought the nerve endings were particularly vulnerable. For the finger, isn't part of that because the actual muscles that move the finger aren't in the finger itself?

For dental procedures, yes. Topical (mucosal) anesthesia is just to pierce the mucosa and get to the deeper nerve bundle. And yes, (that was a stupid example, sorry) the muscles that control finger movement are in the forearm, but other sensations can still be felt (e.g. pressure.) I think it's the type of nerve fiber. IV lidocaine can decrease pain (or, e.g., the cough reflex during a crash intubation) but doesn't cause paralysis because of differing nerve types. Interesting, too, is the effect on cardiac muscle. Btw, been reading about tinnitus; very interesting. Thanks for that.

@anongoodnurse Started reading some papers where people studied dose-dependent effects of lidocaine so I can improve my answer. Ran into some authors I know personally...oops.

@BryanKrause - Ahhaha! I've done that too. Luckily, we can't be experts in everything.

@Bryan's answer isn't totally correct.
Short Answer: There are different nerves. Motor neurons and sensory neurons are not identical and anesthesia affects them differently.
When dentist inject novacaine they are targeting the V3 or V2 nerve trunks, where both sensory and motor neuron bundles are in close proximity. Take a look at this illustration for clarification
https://operativeneurosurgery.com/lib/exe/fetch.php?w=400&tok=5831b0&media=trigeminal_nerve.jpg The injection site is usually near the jaw at the side of the face, this allows the whole side of either zone be sufficiently numb. So it must be a difference in the physical makeup of the neurons.
Some of the differences between motor and sensory neurons are: Motor neurons are long, multipolar, and contain efferent fiber, sensory neurons are short, unipolar, and contain afferent fibers. Myelin is a protective sheath of proteins and lipids that protect and insulate the nerve fibers. Myelination is the process in which myelin is formed over  the nerve fibers. But afferent and efferent fibers undergo different types of myelination. Progression of anesthesia is related to the diameter of affected never fibers, conduction velocity, and myelination. The difference in myelination between the two types of fibers is the main reason anesthetics mostly affect sensory neurons.

Welcome to Biology.SE! This looks like a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion and leaves non-experts with no way to follow up on your answer. ——— This is a good example of how to format references. ——— You may also want to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site.

The answer to this question boils down to 'because local anesthesia does not interrupt the nerves themselves'.
From the wiki article on local anesthetics (LA):

All LAs are membrane-stabilizing drugs; they reversibly decrease the rate of depolarization and repolarization of excitable membranes (like nociceptors). Though many other drugs also have membrane-stabilizing properties, not all are used as LAs (propranolol, for example). LA drugs act mainly by inhibiting sodium influx through sodium-specific ion channels in the neuronal cell membrane, in particular the so-called voltage-gated sodium channels. When the influx of sodium is interrupted, an action potential cannot arise and signal conduction is inhibited.

This means that the LAs don't actually shut down nerves. What they shut down is the ability of nerves to sense mechanical movement. Because mechanical movement on the cellular level is a bit different from what we usually associate with it, this means that in an area affected by LAs the nerves can not report feelings of pain, touch or temperature [actually also spicy taste] to the brain. All other nerve functions (including muscle control) are not affected

Thanks for the answer. It's also interesting that how we can talk under LA effects just like normal situation. Was wondering if we can walk normally if our feet or head is under LA effect too?

@JackJohansson You should still be able to walk in theory, but it will feel very 'wierd' and you will have higher chance of stumbling, because all sensory feedback from your moving legs is missing. E.g. you will not feel the moment your foot hits the floor, so you're brain may not automatically adapt the position of your foot to 'roll' it over the floor.

This is also why people under LA do more damage when they bite their tongue, they can't feel it and can't feel the position of the tongue well.

This answer is incorrect for the most part.

the quoted text and your assessment of it are incompatible, voltage-gated sodium channels are not for sensing mechanical movement.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Why does regular bread yeast fail to thrive in pond water?
I thought I'd try adding regular yeast to water taken from my 75 gallon pond, with the idea that the yeast would be a good "bottom of the food chain" kick start to feed the little beasties, along with warmth and light, to allow the creatures to multiply faster than they would in the pond, to be added back the pond as feed. But to my surprise, the yeast won't grow in the pond water, at least, not like when you make bread with it. I've tried adding sugar, molasses, and "proofing" the yeast, but each time, the yeast does not thrive. Is something eating it as soon as it starts to grow, or is something using a nutrient it needs, or what?
The pond is established, with lots of plants, only a few fish, and ammonia levels are 0 ppm. It is an (apparently) thriving ecosystem. My question is, why won't yeast grow and froth up in that water?

How much sugar are you adding to the 'growth medium'?

I'm adding about a teaspoon of table sugar to a half gallon of water, same amount for molasses. With tap water, the water/sugar/yeast mixture foams and froths within minutes. Using pond water, it does not.  I even got a mixture of tap water, one cup water, one teaspoon sugar and a tablespoon of yeast. After ten minutes, this mixture was foaming and frothing, when added to the pond water, yeast activity stops, as near as I can tell.

For any microbiologists reading this, the supplementation is approximately 0.1% sugar.

What exactly is 'yeast' in your experiment?

I'm using regular bread yeast.

Is it fresh yeast or dried yeast?

I'm using regular bread yeast.

The yeast is packaged dry yeast. It is definitely good yeast, since after the first try I made sure the yeast was good by "proofing" it.

I am not a specialist of fish, but yeast infection is a thing. For the sake of your thriving ecosystem, I would advise you to ask on pets.SE or somewhere similar if having yeast in a pond is a good idea at all.

A few random thoughts.
I think that one problem here is that by using dried yeast you aren't really measuring growth or survival. Over a short time period much of the fermentation that you see probably has very little to do with viable cells. Dead cells in dried yeast act as permeable packages of enzymes and can promote fermentation.
Following on from that, it may be that components of the pond water can poison the fermentation carried out by the dead cells.
Thirdly, if you are using frothing as a measure of CO₂ production it is possible that there are components of the pond water that collapse that foam by removing stabilisers (probably protein).
Next, Saccharomyces isn't an obvious choice for use as an aquatic micro-organism since it is adapted/selected for growth in high sugar concentrations.
If I was trying to do this I think I would try to culture from the dried yeast under conditions where you do see activity, add lots more sugar (as if you were brewing), and look for actual production of yeast cells. Yeast settles out of suspension very easily so you might be able to pour off most of the liquid and add the cells to your pond. But I have no idea how well such cells will do in a pond.

Thank you for your thoughts. I think my question is actually related to your second paragraph,  "it may be that components of the pond water can poison the fermentation carried out by the dead cells". I'm trying to understand what that would be.

It was never my intention that the yeast survive in the pond. I was using yeast to feed the "little beasties", to promote their growth, which could then be added to the pond. I just find it interesting that with the substitution of pond water for tap water the yeast does not become active. I WAS using frothing as an indication of carbon dioxide production. I put the lid on the bottle and no (or very little) carbon dioxide production. I got the idea because yeast is used to feed brine shimp and daphnia.

Now I think the simplest explanation would be that something is eating up the sugar before the yeast has time to rehydrate and become active.


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What is the relationship between DNA molecules and the chromosomes?
Regarding the human genome, if the DNA molecule is two continuous strands, with each gene occupying a segment in it, and there are 46 chromosomes each with some genes, where is the physical boundary of each gene?
My understanding of a molecule is a collection of atoms bound together by covalent bonds thus giving the substance its properties.
My reading so far gives me the understanding that the nucleus of a cell contains DNA, whose molecule is that famous double helix. At the same time, I read that the genes are packed into 46 chromosomes. This got me confused. How is the DNA molecule split into 46 parts?

I don't really understand what you're asking.

Ehh! Can you make it clear what you are asking.

Isn't DNA one molecule?

What research have you done to try to answer this question from available sources on the internet or in books? If you had completed the introductory guided tour you would be aware that you need to demonstrate such prior effort. This question is standard introductory material that can be found in numerous places on the internet.

Yeah, DNA is one molecule, but its nearly impossible to pack one such long molecule into chromosome. So, its split into 23 parts, and each part has a duplicate with it. I suggest you should keep studying...

To cite @canadianer, I don't really understand what you're asking but the following may help you.
Genome composition
First of, in the genome of most eukaryote (incl. all plants, fungi and animals), in general, genes constitute only a small part of the genome. Typically, in humans genes occupy 26% of the genome (24.5 for introns and only 1.5 for exons).
What does a genome look like?
Introduction
You say

Isn't DNA one molecule?

I think this question shows an important misunderstand you have. Note that I will only talk about the nuclei of eukaryotes below.
DNA is a type of molecule, which is constituted of two anti-parallel strands. In the human genome, we have 46 chromosomes, that is 46 independent DNA molecules. Now, these exact numbers vary depending on the moment in the cell cycle you want to consider but this is a story for another time.
A little more advanced
Below is a karyotype of a human allowing you to visualize the chromosomes. The 46 chromosomes we have go by pairs (pair of homologuous chromosomes) and on the image, they are numbered by pairs, the last pair being the sex chromosomes. By the way, can you identify the sex?

Note now that, depending on the moment in the cell cycle you want to consider, each homologuous chromosome may be constituted one 1 or 2 DNA molecule, each of them being called a chromatid. Chromatids are physically attached by the centromere. Two physically attached chromatids are called sister chromatids.
More information
For the moment, I threw some vocabulary at you but it was probably a bit hard to follow. You can get more information at the posts

Chromosome and chromatid numbers during cell cycle phases
The human has 46 double chromosomes or simple chromosomes?

or simply an intro course to genetics such as the following three courses by Khan Academy

Classical and molecular genetics
DNA as the genetic material
Central dogma (DNA to RNA to protein)

Thanks, so it's 46 different DNA molecules and not just one DNA molecule in the cell nucleus.

Indeed, there 46 double-stranded DNA molecule in a human cell nucleus (although this number may be doubled depending on the moment in the cell cycle).

Actually, each double-helix is two DNA molecules, if you define molecule as atoms held by covalent bonds (as is typical). Each strand of the double helix is a separate molecule, but the two strands fit together so well that the (non-covalent) hydrogen bonding holds the two very long strands tightly together.

There are actually even more strands in the cell as a whole since mitochondria have their own strands. these strands are small short loops that do not contain many genes (~40 genes by many estimates)

@mkgrebbs. Sure, this is why I said double-stranded DNA molecule assuming hydrogen bounds are sufficient to consider the two strands together a single molecule. I avoided this discussion to avoid further complication given how introductory was the OP's question.

@John Indeed, this is why, I said in a human cell nucleus. The OP might be aware that there is DNA in the mitochondria as he says  in the cell nucleus himself. Again, I wanted to avoid further complications here (even more so that DNA is not organized into chromosomes in the mitochondria).


text:
Why isn't the DNA in bacteria always split up and replicating?
Isn't helicase always free floating in bacterial cells, and the DNA without a nuclear membrane and uncoiled and freefloating and so why doesn't the helicase keep breaking the double helix of DNA? Also, since other DNA synthesizing enzymes like polymerase and RNA primer and other replication enzymes also free floating, so why doesn't the DNA in bacterial cells keep replicating at all times?

Bacterial DNA replication is initiated at the oriC by DnaA in E. coli. Think about ways in which DnaA binding or activity can be regulated in a way that inhibits or permits DNA replication. In recently replicated bacterial DNA, the DNA is hemimethylated (parental strand has a methyl group, daughter strand doesn't): An inhibiting protein binds to hemimethylated DNA, that can block DnaA activity at the oriC. A DAM methylase adds methyl groups after a while to the newly synthesized DNA, in which case DnaA may bind. Due to the lag between replication and methylation, DNA replication can't be continuously initiated! This is one of many examples (for example, DnaA must bind ATP for it's mechanism of action), but the take home point is DNA replication must be initiated and if it can't be, then it doesn't take place!
THE INITIATION OF BACTERIAL DNA REPLICATION
Breaking that down: (note, this is in E. coli)

DnaA is a protein with DNA-binding activity. When many DnaA bind at the oriC, it causes the DNA to bend open and loop. At this point, DnaB would have access to the DNA, and this is the helicase that unwinds everything for replication (you'll also see that DnaB must be loaded onto the DNA by DnaC, a helicase loader). So blunty enough, oriC is an origin of replication, everything starts here. There are repeats of AT rich regions denoted 13mer and 9mer in the oriC (number of bases in the region if you will). We know that this is beneficial because AT rich regions are easiest to pull apart due to the number of hydrogen bonds between A and T.
In the example I provided, the assumption is that the DNA of E. coli is methylated on adenines on both strands. When replication occurs, the new DNA doesn't have this methyl group on it's adenines like the parental strand. A protein that recognizes and binds so-called hemimethylated (half methylated) DNA, SeqA, binds where it can, including in the oriC. It blocks DnaA subsequently for a short time, and falls off the DNA on its own. The DAM methylase adds the methyl groups when it can, and once it does the SeqA can no longer bind, but the replication-initiation complex thus can.
There are other modulators of DNA replication, and the concentration of the DnaA itself is a big factor because you need many units of DnaA to bind to facilitate initiation. So then you have to consider is DnaA being expressed strongly enough? And this has it's own pathway outside the scope of this question.

Ok, I get some of it. Could you explain it at a little lower level (keeping in mind that I am still a highschool student but I have done extended research so you can use some jargon). What is DnaA? and oriC? So when the DNA is methylated, it can replicate? then what does the inhibiting protein does (what does blocking DnaA activity do?)? So according to the lag point, the DNA, methylation activates replication? I get the core point though :P

@SarthakGarg I made some edits that explain it a little more detailed. Always keep note that this is in E. coli and other families may adopt different strategies, but the take-home point is there (you need the initiation complex).


text:
Where do the 2 electrons and H⁺ go when NADPH is turned into NADP⁺ during the Calvin Cycle?
I was wondering where the 2 electrons and H+ go when NADPH is turned into NADP+ during the Calvin Cycle? I know that during the light dependent reaction, 2 electrons (from water) and H+ combine with NADP+ (from the Calvin Cycle) to form NADPH, but after NADPH is used and is turned into NADP+, where do those electrons and H+ go?

where have you looked for this answer?

@VanceLAlbaugh my biology textbook. It does not have any information on it.

A reasonable source of information about the Calvin Cycle is Berg et al., but for this reaction the full structures are not shown. I therefore show them below in a diagram of my own:

I have coloured the hydrogen atoms to show where they go in reducing the phosphoglycerate (acid) to an aldehyde. You can think of the two electrons being used to form the additional covalent bond.
(The hydrogen phosphate is actually in equilibrium with other phosphate species, but this is not relevant to your question and so is not shown.)


text:
How many possible codons?
Consider a codon of the form NNK (where N = Adenine, Cytosine, Guanine or Uracil & K = Uracil or Guanine).  How many codons are now available? I know if all were available there would be 4^3 = 64 codons. How many are possible now? When I have tried combinations manually I got it to be 32, is this correct?

Yes, 32 is correct.
Technically, I have nothing to add what Gerardo Furtado and a tiger haven't already mentioned but a graphical representation of all permutations might help to understand this a bit better.
For the first 2 positions in the codon we have 4 bases to choose from (adenine, guanine, uracil and cytosine). So this can mathematically be represented as 4 x 4 = 16 or visually as:

Now, for the next position (the position of interest) we only have two bases to choose from (uracil and guanine). Leaving us with 4 x 4 x 2 = 32 different permutations, or visually:

You are welcome. I am glad it helped.

Yes, it is.
Gerardo Furtado has already provided a short answer in the comments, but allow me to explain why.
The 4^3 = 64 if all bases can be chosen freely comes down to 4*4*4=64, because you can choose from 4 options for each of the 3 bases.
If you restrict the possibilities of one of the bases, e.g. there are only 2 options for the third base (as in your example), the formula changes to 4*4*2=32, as you can choose from 4 options each for the first 2 bases and from 2 options for the 3rd base.
Edit:
If the 2 'N's from 'NNK' have to be the same, you can choose the first base freely (4 options), the second base is already defined (it has to be the same as the first base, 1 option) and there are 2 options for the 3rd base as described above. Thus, we get 4*1*2=8 possible codons
I hope I could clear this up.

Good explanation. For completeness, it would be extremely unusual if NNK denoted that the first two bases had to be identical: first off, it’s not the convention; IUPAC ambiguity codes are character wildcards, not variables in the common mathematical sense. And secondly, there’s little biological reason to consider codons where the first two bases are identical.

I absolutely agree.


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Chemosynthesis in Bacteria
The light reactions, if seen as a whole, are basically the oxidation of water to provide energy (ATP) to fuel the Calvin Cycle. The photons provide the activation energy for the same.
How then can we say that during chemo-synthesis bacteria get ATP in the first step by oxidizing inorganic substances like $H_2S$ or $CH_4$ because ultimately, it is similar to the light reactions and will require some activation energy?
Where does this energy come from?

These chemo-synthetic bacteria gets energy from oxidation of inorganic compounds. Following table from Biology of Prokaryotes shows main reactions used by different species,

This oxidation happens only if electron acceptor is available. These all reactions have negative Gibbs Free Energy, hence they are favorable reactions and happens spontaneously. Generally oxygen is preferred electron acceptor but in case of lack of oxygen nitrate, sulfate, $HCO^{3-}$ etc are used.

Could you please list the Gibbs free energy for a normal photosynthetic light reaction?

Check this. It has all numbers and calculations you need.


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What happens to H+ when Glycerate 3-Phosphate is converted to Triose Phosphate?
The conversion from Glycerate 3-Phosphate to Triose Phosphate requires:
$ATP \rightarrow ADP + P_i$
$NADPH \rightarrow NADP + H^+$
So what happens to the $H^+$?
Is it in-effect "recycled" back to the Light Dependent reaction.

The H+ is used for the photophosphorylation part, in which the H+ is pumped.. so yes, you are correct...

First off, I believe you have the production/consumption of the proton off, at least for the reaction with NADPH. Most reactions with NAD(P)H go like NADPH + H+ + (oxidized compound) --> NAD(P)+ + (reduced compound). In fact, in most reaction mechanisms the hydrogen that's actually on the NADPH is ends up covalently bonded to the reduced compound.
That said, acid-base reactions are some of the fastest reactions that can occur in the cell. The cellular environment is pH buffered, so any excess H+ ions would be rapidly taken up by the excess of buffering agents which are floating around in the cell. Likewise, when a hydrogen ion is needed in a reaction, it's pulled from the general pool of free hydrogen ions, and it is rapidly replaced from that same pool of buffering agents. As a consequence of this, it normally doesn't make much sense to talk about where hydrogen ions flow in the cell - there's just a general hydrogen ion pool which supplies and takes up any hydrogen ions that are needed/produced by the reactions in the cell.
The big exception to this is where hydrogen ion movement is restricted by things like membranes. The TCA cycle and the light-dependent reactions of photosynthesis being major examples of this. In those situations hydrogen ions are pumped across the membrane during the reaction, and there is a distinction between hydrogen ions "inside" and "outside" the membrane. But there isn't any distinction between any of the hydrogens on one particular side of the membrane.
The light independent reactions of the Calvin cycle, though, happen within the chloroplast stroma and don't pump hydrogen ions across the membrane. So the hydrogen ions generated/consumed by these reactions go into/come from the general stromal pool of hydrogen ions. Here they can be used by any reaction that requires/generates hydrogen ions - a major one of these would be the light-dependent reactions, which take hydrogen ions from the stroma and pump them to the lumen (and then release them back to capture the energy for phosphorylation). But the hydrogen atoms from the Calvin cycle enzymes aren't in any way "earmarked" for the light dependent reactions.


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What is the difference between SOLiD, 454, and Illumina next-gen sequencing?
I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in terms of sample/library preparation and chemistry. How difficult is it for a protein veteran but next-gen newbie to get high-quality useful reads? I'm mainly going to be looking at antibody diversity, but consider this in general terms for any next-gen project.
I understand the basic theory of fluorescent chain-termination sequencing, but it's been a number of years since I last did it, and my career is now taking me back into the DNA realm.

I think this question is a bit broad and perhaps you should read through the manuals / data sheets for the respective products.

I'll narrow it a bit.

Here is a short summary of the sequencing technologies you listed. Illumina is the most frequently used one.
Roche/454 FLX Pyrosequencer technology is based on pyrosequencing method, which utilizes the use of the enzymes ATP sulfurylase and luciferase. After the incorporation of each nucleotide by DNA polymerase, a pyrophosphate is released, which further takes part in downstream light-producing reactions. The amount of light is proportional to the incorporated number of nucleotides. The DNA is fragmented and adapters are ligated at both ends. The fragments are mixed with agarose beads, which carry adapters complementary to the library adapters, and thus each bead is associated with a unique DNA fragment. The beads and DNA fragments are isolated in individual micelles, where emulsion PCR takes place and million copies of the single fragments are amplified  onto the surface of each bead. Each bead is placed in a well of picotiter plate (PTP), as the wells have dimensions such that only one bead can fit per well. Enzymes are added to the beads and pure nucleotide solutions are added with an immediate imaging step. On one side of the array a CCD (charge-optic device) camera records the light emitted from each bead. The first four nucleotides (TCGA) are the same as the start of the adapter, which allows for the emitted light to be calibrated according to the type of nucleotide added. The major disadvantage of this method is the misinterpretation of homopolymers (consecutive nucleotides, e.g. AAA or CCC). Such areas are prone to insertions or deletions, as the length of the stretch can be inferred only by the intensity of the light emitted. On the other hand, substitution errors are very unlikely. The 454 FLX instrument generates ~400 000 reads per instrument-run, as the reads are 200-400bp. The greatest advantage of this platform is the read length, which is the longest of all second generation technologies. Although sequencing on 454 platform is more expensive than sequencing on Illumina platform (40USD per Mega base versus 2USD per Mega base), it could still be the best choice for de novo assembly or metagenomics applications. (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).
Illumina is the most frequently used one. The DNA to be sequenced is fragmented into about 200 base strands. Adapters are ligated onto the ends of the fragments and one of these adapters is hybridized on a flow cell. Illumina essentially utilizes a unique "bridged" amplification reaction that occurs on the surface of the flow cell. Localized PCR reaction is performed, and each of the hybridized pieces of DNA will get locally amplified to generate clusters which will have the exact same molecule. Subsequently, the DNA sequence is determined by adding a primer on one of the ends of the molecule. A mixture of modified nucleotides is added. Each one of them carries a base-specific fluorescent label attached to it. Also, each one has the 3' OH group blocked which ensures the incorporation of one nucleotide at a time.  The flow cell is placed under a microscope and when light is shined on its fluorescence, the emission light shows which base was incorporated on each one of those clusters. The Illumina read length is approximately 35 bases, but over billion reads are generated at a time. The major error type is substitution, rather than deletion or insertion (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).
The SOLiD platform utilizes the use of DNA fragmented library, which is flanked by ligated adapters. The fragments are attached to small paramagnetic beads and emulsion PCR is performed to amplify the fragments. In contrast to the other sequencing platforms, sequencing by synthesis is performed by utilizing DNA ligase, rather than polymerase. Each cycle of sequencing involves the ligation of a degenerate population of fluorescently labeled universal octamer primers. A specific position of the octamer (e.g., base 5) carries a fluorescent label. After ligation, images are acquired in four channels, followed by cleavage of the octamer between positions 5 and 6, removing the fluorescent label. After several rounds of octamer ligation, which enable sequencing of every 5th base (e.g., bases 5, 10, 15, and 20), the extended primer is denatured. Different primers can be used to examine the previous or next positions (e.g., base 3 or 6).  The platform can use primers which carry two adjacent correlated with label bases. This approach involves the examination of the bases twice in a cycle, which decreases the error rates. SOLiD read lengths are 25-35 bp, and each sequencing run yields 2–4 Gb of DNA sequence data (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).
References:

Mardis, E., Next generation DNA sequencing methods. Ann. Rev. Genomics Hum. Genet, 9: 387-402 (2008). DOI 10.1146/annurev.genom.9.081307.164359
Shendure, J. and Ji, H., Next-generation DNA sequencing. Nat. Biotechnol., 26: 1135-1145 (2008). DOI 10.1038/nbt1486

Do you have links to the papers and figures you cited? This kind of looks like it was cut and pasted from somewhere...

@MattDMo Yeah, it was pasted from an essay/review which I wrote for next generation sequencing. I will add  the references.

@MattDMo Thanks for your edit (I'm sure a second person will approve it soon), but if you're adding links, consider adding a DOI link as well, that way if PubMed changes their IDs or something, people can still find it.

@jonsca I use this link format according to the recommendations by PubMed. As far as I know, PMIDs are immutable. Also, this link format provides an abstract, and sometimes several choices for retrieving the full text - PubMed Central, journal homepage, Springer and its equivalents, etc.
Has there been any discussion on meta about which link format is best? If not, I can start one...

@MattDMo Definitely feel free to leave the PubMed link.  I was saying add the DOI link as well.  The DOI is a permanent identifier that follows the publication around nearly forever.  The link is http://dx.doi.org/<identifier here>.  If you'd like to start a Meta question about it, feel free.  I'm not trying to pick on anyone here, I just figure if you're already taking your valuable time to edit in the PMID, it's just one step further to get the DOI.

@jonsca Got it. Links have been added for your pleasure :)

@MattDMo One too many "feel free"s, I hope you felt free :) Thanks for doing so!  I may start a Meta question about it anyway, as I think it's great prevention against link rot.

It's not easy to write down a comprehensive answer to your question, I would suggest you read this paper Field guide to next-generation DNA sequencers, which provide very good comparison of the NGS platforms

Can you summarize that paper?

It's also not open-access, so I can't read it...

Which is why a summary would be nice...


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Why do farts stink, but perfume does not?
Why is it that natural things like farts, poop, halitosis etc., from which we are always surrounded smell "bad"; whereas manufactured products, such as perfume or glue smell "good" to most of us?
In my understanding, things smell "bad", because they are not good for us. But how are farts not good? And shouldn't artificial things like perfume or glue, which are relatively new to us, smell "bad"?

There are loads of "natural" things that smell good: flowers, food, your lover, your offspring, babies in general (at least to some people anyway), wood...

feels Good to know that m not the only with a 10 year old's sensibility ( on farty stuff ;)

Why is it that natural things like farts, poop, halitosis etc., from
  which we are always surrounded smell "bad"; whereas manufactured
  products, such as perfume or glue smell "good" to most of us?
In my understanding, things smell "bad", because they are not good for
  us. But how are farts not good? And shouldn't artificial things like
  perfume or glue, which are relatively new to us, smell "bad"?

Kind of a strange question but here is a quick and rough answer... There are at least three things to think of here.
Firstly, yes often natural things that are good for you have evolved to smell attractive, but not all natural things are good for you. Therefore a fart should not smell good just because it is natural. And it is likely that breathing farts non stop is not good for you.
Secondly, perfumes etc. have been chemically manipulated or designed to smell nice by human manufacturers - the preference for such smells existed before the specific perfume, the manufacturer simply designed a fragrance that was attractive.
And Finally... Not everything exists because of selection. Farts probably smell as a by-product of process of digestion rather than selection for avoiding them. Gas is produced during the digestion processes, the amount and odor (determined by the constituents of the gas) of gas will likely depend the efficiency of digestion and what is being digested. The dominant selection force affecting the odor is then probably related to digestive efficacy and selection against odor would only be (relatively) very weak.
It's better to digest food and fart a bit than it is to not digest but smell nice, digestion is quite important!

Flowers smell good to us. Is there any evolutionary advantage to us or to the flower ?

Generally speaking flowers smell good to pollinators - there are a limited number of possible scent chemicals and/or common arrays of "good" smell receptor in the world so I would suggest that there is likely to be some crossover - but that is pure guess work

Some comments from me: Most substances that smell bad contain some kind of sulphur components - and we are really sensitive to them. If I open a bottle with beta-Mercaptoethanol in a lab (and not in the fume hood) it will only take seconds until someone else starts protesting and opening up windows. Some of these chemicals are highly toxic (for example hydrogensulfide), so it makes sense that we are aware of them. Regarding the flowers: There are some flowers, that smell really awful, have you ever been close to a Ginkgo tree that is blossoming? Not very nice I can tell you...


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How is sweetness measured?
Some time ago, I read in a newspaper--though I can't recall the details--a list of (mostly artificial) sweeteners and a list comparing how many times sweeter each was than sugar. How is relative sweetness quantified? Is there a standard method?

Response of the gustatory receptor neurons can be measured using standard electrophysiological techniques, under different conditions(exposure to substances). For example see this article.
However, it is difficult to say if a person feels sweetness or not or how the substance produces complex taste perceptions in some people.

What I had read was the they had even measured the sweetness of something which was toxic (see the question's edit history). How could they have done that? Making a human have toxic material?

Please mention the source of this information. Toxic can also mean potentially toxic over continued use. They could have tested this in mice. To say anything we need to investigate the real source. Relying on newspapers for scientific facts is sometimes like playing chinese whispers. The reporters hear something, understand half. Add some of their interpretation and end up reporting erroneous information.

Hard to tell the source of it. Just remember reading and being amazed by the fact.


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Does biotin affect downstream experiments, such as RT-qPCR?
I have two biotins--one of which is binding my RNA with cleavable bonds, and the other with irreversible bonds. Does biotin have an effect if it keeps its bonds with RNA? If it does, why is this the case?

Having looked into this question, I came across this paper, where they mixed biotin labelled EGFR-mutant-specific oligonucleotide and isolated the target using streptavidin beads followed by real-time TaqMan PCR allowing a 40 fold increase in detection sensitivity of the mutant allele, suggesting that biotin does not effect nucleotides in PCR based experiments.
The life technologies webpage claims that Streptavidin-Coupled Dynabeads M-270 can be used in a PCR reaction as stated below although certain streptavidin-coupled beads can have an effect on the PCR reaction. Hence I do not think biotin itself would be a problem for an amplification reaction.

beads can be used directly in PCR, as they do not inhibit enzymatic reaction. Slight PCR-inhibition has been seen when 75–100 µg of Dynabeads® M-280 Streptavidin was used in 50 µL PCR reaction, and a concentration over 100 µg per 50 µL reaction seems to inhibit PCR completely. Dynabeads® M-270 Streptavidin do not show any inhibitory effect on PCR at these concentrations.

In fact you can buy kits such as this where you can generate/incorporate biotin into your RNA of interest for any purpose. The use of biotin and its incorporation into nucleotides seems prevalent in the literature and there are even kits for this purpose hence you should be on the safe side with your biotin labelled RNA experiments. I think the biggest challenge in RNA work is to keep it from degradation, which as far as I know is achieved through maintenance at -80 oC.


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How best to count bees entering and leaving a hive to measure hive activity?
This is my first question here, so I apologize for all mistakes I could have possibly made.
I'm a high school student in East-Central Europe and I need to complete some research for a biology contest (asking for advice is accepted, so I'm not cheating). My task is to analyze the influence of certain environmental factors (temperature etc., it's not that important for my question) on the activity of bees. The method is pretty simple: once a week I record the entrance to the bee hive (I do it on four hives), play it in slow-mo (It's impossible to count them properly without doing so) and simply count the number of bees entering or leaving.
Problem is, I don't know how long the observation should take. I play it in like X1/8, you need to play it twice (entering/leaving), so it takes a lot of time to gather one piece of information for a certain day. Till now I've been doing it for one minute - and there seems to be some kind of pattern to their activity analyzed that way. Yet, I'm not sure if it's actually eligible. I can't do the observation for hours - I still need to learn and have other duties.
So, what should I do? Could anyone give me some advice? Is one minute (several, like 6 times a day per hive) legitimate enough?
Thank you in advance.

I know of a person who used to do these experiments. They mentioned that they also used to mark each bee to track exactly.

One minute a day sounds far too short. Several one minute measurements throughout the day would be one way, or measuring a day in full, and then using a representative time-point would also be neat. I think it depends on the question you're answering. "hot bees are more productive" and "Hot bees hives have more bees" could look like the same result in your setup. @WYSIWYG I heard a similar story - painting moving bees sounds a bit precarious to me!

I'm no expert at this but these are some of the things that I would consider thinking about. How practical is it for you to count the total number of bees in the hive, based on lets say hive weight or the number of bees on one rack in the hive (then multiply by the total number of racks to give you an estimate of the total bee numbers in a hive) before you start collecting video data? This will at least put your influx/outflow number into some sort of prospective if you are counting in different times of days or if there are different wheather conditions in different days. This is easily achieved if you divide your influx and outflow numbers by the total (estimated) number of bees. This gets you two numbers (ratios) which you plot on the Y-axis. On the x-axis you can plot the passage of time and even colour code different days based on average (lets say) temperature to see if temperature had an obvious effects on your observations. But obviously all your instances of recording and time intervals between recordings needs to be constant!
So in many fly behavioural or locomotion function assays, scientists record fly movements at certain fps and analyse the videos. Now most of this video data analysis  is done using scripting in Matlab which is (I know to be) the tool choice for motion analysis. Now since you say you are at high school, this would probably be quite a challenge since the program is costly and scripting is not that easy (at least for me), so see if you can utilise the help of someone to get over this barrier. Once you do then you can analyse much longer videos at much higher frequencies, which will give you a better resolution on your data. If you could't then consider looking through web sites using search engines such as google for Matlab codes for motion tracking analysis scripts. I did this some time ago and there are wealth of information out there and once you do that you can get the communities help in websites such as stack overflow to help you refine your codes or any problems you may have with it, so long as you show evidence of your work. This is a great option since you can add variety of data (or different data aspects) to your project such as what is the average speed/velocity which your bees travel at in different times when entering/exiting the hive, is there a pattern to their travelling (e.g. straight line, zig-zag etc) and much more. I'm aware that this is beginning to sound like a PhD project and not a high school project but these are some things to consider. If programming is totally out of the question then you can look on internet to see what free programs are out there to aid you with your data collection. I briefly looked and saw this (http://www.youtube.com/watch?v=jWD8CHW06Ks) and this (http://www.researchgate.net/post/Does_anyone_know_of_FREE_software_for_motion_capture) just by simply typing into google "video motion tracking software" so look around and see if you can find anything which you can tailor for your own need.
Now regarding video length time, as correctly mentioned in Armatus response (if I'm not wrong and correct me if I am) it shouldn't matter for how long or how frequent you are recording so long as you keep the variables (i.e. time of recording, frequency of recording etc) to the minimum (i.e. not change them), or in other words keep your observation methodology constant through time, and try to come up with a practical schedule and if you explain your thought rational (experimental design) in your report, even a professor (i dare to say) wouldn't be able to argue with it but you always have to talk about the limitations of your study and that is key and that's where peoples project falls apart when an expert reviews it and finds holes and criticises claims made, which can not be backed up by the data/types of analysis gathered/performed!!
EDIT: Just to address some statistics issues, I would make your recordings from minimum of three hives per recording time-interval/point since in science n (number of observations) should be >= 3.
Anyways I hope my ramblings have been somewhat useful.

One thing that's certain is that the activity of bees varies according to time of day, so more important than how long you record for is probably at what time you record. If you always record at the same time of day, this should allow a reasonable comparison between results of different days. For example, recording from time 14:30 to 14:35 every day could be fine. You could then record conditions at this time each day (temperature, weather, etc.) along with this.
As for the exact length of your recordings: Of course, the longer they are, the better. More samples usually increases reliability and representativeness of your results. However, more importantly you want a practically useful time as well. This really depends on the actual number of bees entering into the hive within different time frames, as well as the baseline variability between days irrespective of the conditions you are investigating. I don't know anything about either of these :)
You want the number of entrances in your recording to be at a level where you will notice if there is a meaningful difference between days, and the only way of going about this is usually to start with a guess and then change if you notice that you can't really make sense of your results.

To further reduce the time it takes you, you could start out counting both entrances and exits from the hive - but then check if you get the same results if you only consider entrances. As a measure of bee activity, I would expect entrances and exits to be equivalent and thus it shouldn't matter whether you count either one or both.

Ideally, you would gather preliminary statistics to design the experiment. If you have a high variability, and your observation window is short, then small effects will be swamped by the variability. However, if what you are looking for has a big effect in the number of bees, then counting for a shorter time is going to be fine.
A rule of thumb would be to try recording 5 to 10 segments of 1 minute analysis and see what the variability is. If the standard deviation is small compared to the effects you are seeing, then 1 minute is fine.
If you want a more theoretical justification, Poisson distribution could be used as a first order approximation of the distribution. I don't know much about statistics specific for this kind of insect behaviors though.


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Why do chlorotic leaves have green veins?
If chlorotic leaves are chlorophyll deficient, why should the veins be green? shouldn't all the available chlorophyll be directed to the leaf lamina?


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What is the difference between cell, membrane and animal based assay?
I am reading a review about MRP1, discussing it's ability to extrude different compounds from cell interior. When describing the different experiments conducted to observe the MRP1's reaction to different modulators, the writers refer to cell based, membrane based an animal based assays.
What is the difference between these three assays? What would be the purpose of choosing each of them for a specific test?
Thanks alot,
Yaron.

Can you perhaps link the review you are reading?

Sure,
http://www.annualreviews.org/doi/abs/10.1146/annurev-pharmtox-011613-135959


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Common genes and enzymes involved in pathogen entry into host
Many microbes like Salmonella, E.coli, Legionella pneumophila etc. enter host cells via cystoskeleton remodeling of the host cell. Do all microbes follow the same path or there are any other ways for the microbe to enter the host cell. What are the most prominent and significant enzymes involved in these and what are the genes involved in the same. It's a general question as I am looking for the common genes and enzymes that most microbes employ the mechanism of cytoskeleton remodeling.

Passing through plasma membrane by remodeling host cell seems reasonable choice but actually most of pathogen use cell's normal functions like endocytosis, phagocytosis, pinocytosis etc to enter (well, indirectly you need actin remodeling for this also but pathogen is not doing it actively. ). Check this review for some 'simple' mechanism pathogen use to enter cell. As far as your question about enzymes, there are lot of common enzymes (specially manipulating kinases) which are important in these pathways.Pathogens use lot of other factors to exploit host. Cytoskeleton remodeling is indirect output of many of these signaling events. Just to put into perspective, recently hiked on social media, Ebola virus use micropinocytosis like mechanism to enter into host cell. Some other representative examples in following figure (Source :Gruenberg and Goot 2006 )


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Why don't the minus ends of microtubules shrink?
Is this because $\alpha$-tubulin is always in the GTP state? Or is it because $\gamma$-TuRC stabilizes the minus end?

Depolymerization of microtubules does occur at both ends, it is only that the kinetics are different at the plus-end than at the minus-end. Due to dynamic instability, depolymerization occurs about 100 times faster at the GDP end than the GTP end, but both will depolymerize, just at different rates.


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DNA from sweat on the hat band?
My father died in 1987.  I have an old cowboy hat of his.  Can I use a FamilyTreeDNA test kit to recover any DNA?

Related: Does sweat contain DNA information?

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