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Why can't the human eye focus blue light?
I recently noticed that it is hard to focus on blue light sources, especially at night. When observing a blue light source, e.g. a neon sign, it looks somewhat blurry. A sign with a different colour right beside it looks sharp.
I already know about the three kinds of cone cells in the human eye (I'm not a biologist) with their spectral sensitivity peaks in in short (S, 420–440 nm), middle (M, 530–540 nm), and long (L, 560–580 nm) light wavelengths [1]. But does the spectral sensitivity correlate with focus? Or does our eye lens refract blue light in a different way?
When I screw up my eyes looking at a blue light, it becomes less blurry, but then all the other colours are blurred.
[1] http://en.wikipedia.org/wiki/Cone_cell#/media/File:Cones_SMJ2_E.svg

Interesting observation. In addition to aberration, which I suspect to play very little part, I'd hypothesis the role of neural network in visual pathway. What happens when only blue light detectors fires in this network?
Additionally, blue light detectors usually have 1/3 of sensitivity than other colors detectors. Also if a blue-detector is tightly connected with other blue-detectors (I don't know if this is true) then exciting one with also excite few others thereby giving a blurry image.

Shouldn't visual lateral inhibition reduce this effect and therefore sharpen the image?

It might, then the suggestion would be that we dont have strong lateral inhibition among blue detector neurons. just a hypothesis.

The same thing happens in photography when you see an image with colorful shadows of objects on it - this is called chromatic aberration. Check this wiki page if you're not familiar with. Now this happens because the lens in the objective has different refractive properties for different wavelengths or if go the other way around different wavelengths refract differently within the same material. This is why the famous triangular rainbow prism is capable of separating the sunlight to rainbow. So back to the question: in our eye there is the eye lens that is responsible for focusing. Let's assume that it is homogenous enough. So when light enters into our lens it refracts to separate colours and our lens is not complex enough to fully compensate for this. The second picture is a good approximation of the human eye lens in shape.
Edit: so when you focus one color perfectly the others will be blurry a bit since those will be out of focus due to different refraction.

taken from: http://commons.wikimedia.org/wiki/File:Prism-rainbow-black.svg

taken from:http://en.wikipedia.org/wiki/Chromatic_aberration#/media/File:Chromatic_aberration_lens_diagram.svg

This does not answer the question fully, as it only explains why blue is out of focus when the eye is focused on an object of lower-frequency (eg red). OP tried to focus on both.

umm well yes, but I thought that it's obvious that the logic goes vica-versa, yet this is an assumption that my logic works for everyone else.... :) Answer edit here we go!

Combination of factors:

Red and green (which are, from the evolutionary standpoint, the same frequency, as the red and green cones are recent variants of one another while the blue cones are distinct, they use a different photoreactive enzyme) are the dominant resolution source for human vision, while blue cones are much more important for expanding our ability to detect color (chrominance). It's why we have more red and green cones than blue ones (IIRC the ration is 10:1, though that may be way off).

Since focus is much more important to spatial resolution (details) rather than color resolution, the human "autofocus" is biased to favor the red-green band. Blue gets short shrift because of its relatively minimal importance to resolution. An experiment: if you mess around with the three color channels of an image in a photo program like Photoshop, messing up the blue channel affects the final color image the least, given the same amount of "messing" (like noise or deresolution).
Last but not least: as noted, chromatic aberration means that the different colors won't quite match up. It's not normally visible, likely because our brains auto-compensate when combining the different cone inputs into the final image (Canon digital cameras recently acquired a similar ability.) Not everyone is going to notice the effect: this is probably because blue focusses "shorter" in terms of lens focal length than red. So, you are much more likely to notice "blue fringing" if your unaided vision tends towards the nearsighted side (like mine does), given the focus center on red/green -- and you'll see it worst with distant blue sources than near ones. If you know someone who has worse nearsighted vision than yours and wears glasses (and neither of you have astigmatism) try using their glasses and see what happens.

Welcome to BiologySE... thanks for your contribution. Could you please add some references to back up your claims? We generally appreciate all answers and questions to reference outside sources (and not just personal knowledge). You can just edit your answer and add references either in the text or at the bottom. Thanks!

Light is scattered by gas molecules in air. The shorter the wavelength of light, the more it is scattered by the atmosphere. Because it has a shorter wavelength, blue light is scattered ten times more than red light. One reason is that
blue light has a frequency that is closer to the resonant frequency of atoms than e.g. red light (Exploratorum). Due to this scattering the eye has difficulty focussing as object edges get fuzzy.
The scattering of blue light degrades vision in normal day light, especially in foggy conditions when light scattering is at its worst due to the droplets of water in the air. Yellow filters (for example yellow sports sunglasses) improve visual acuity by filtering out the aberrant blue light (Laramy-K Optical).
Fun fact
The predominant scattering of blue light makes that the sun is clear in the sky as a yellowish circle, while the sky is blue due to the fact that it is the blue light predominantly being scattered away from the sunlight.

As well as natural shortsightedness to blue, due to chromatic aberration in the lens of the eye, there are also no S cones at the centre of the fovea. This means that focussing on a point source of blue is difficult and can be uncomfortable for some observers. Hope this helps.


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Why we have just 2 teeth cycles, primary and secondary not more?
After baby teeth go, secondary teeth grow, is there a scientific reason why they are just 2 sets not more?

I found this question http://biology.stackexchange.com/q/27547/15122 which answers the history section of my question

Which of Tinbergen's four why-questions are you asking? See e.g. http://www.sciencegamed.co.uk/science/2013/mar/nikolaas-tinbergen-four-questions.html.

This not a duplicate. The first part of the question is why humans usually only have two sets of teeth.

Humans are diphyodont animals, which means we are having two sets of teeth cycles, on contrast, the polyphyodont animals which are having multiple tooth cycles. The first deciduous teeth(milk teeth,baby teeth or primary teeth) then followed by the permanent teeth. Milk teeth develop from the embryonic stage and continue to develop for 6-7 years and gradually erupts forming the permanent teeth. The permanent teeth is developed and it pushes the milk teeth from the bottom which result in the shredding of milk teeth.
Most of these polyphyodont animals uses their teeth for more severe purposes like grabbing and slashing. Due to these massive work load, their tooth are considered as their main advantage for survival. Also their tooth are subjected to heavy flaws while they grab or slash, so having multiple tooth cycles help them ensure healthy teeth all over their life time. On the other hand considering the diphyodonts, their tooth have been using for chewing and grinding and they will having low flaws compared to the others. So from the evolutionary standpoint increasing the number of tooth cycles are not so economic for them.
Reference

there are plenty of polydont grinders and chewers. polydont is the default, mammals are weird for losing it.

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Measuring a plant's electric activity any instructions where to place electrodes?
I would like to measure a plant's electric activity / voltage, I've looked online to find out where to place the electrodes and what type of electrodes to use but they seem to very wildly.  Any ideas?
At the moment

I plan on wiring one end of a needle to the stalk and one end to the soil.
The connections from the plant would go to a laptop mic input to record the signal then I would normalize the signal.
I would then process the signal in MATLAB/Octave using FFT.

Any thoughts or videos on connecting the electrodes to the plants or trees?
I did find this Development of Bio-Machine Based on the Plant Response to External Stimuli

A quick glance on Google scholar only revealed plant-electrophysiological studies deploying single-cell recordings. You can't do single-unit recordings in an intact plant with your sound card connected to a needle. What potentials are you exactly planning on measuring? Without specification of your target potential this question cannot be easily answered (that is, not by me :-)

Further, I strongly doubt that the amplification of the AD converter is sufficient, and the amount of noise in the signal will probably sky rocket due to your setup being poorly isolated.

I vote to close as OP has not edited and clarified question after comments

I'm looking to measure voltage

And how would you use FFT to analyze it? You are expecting oscillating activities in single cells recorded with your sound card? It all doesn't line up...

Import the signal into matlab or octave and use their FFT function to analyze it (see #3 from question)

What they do in the linked paper is injecting current and recording it back. Is that what you want? FYI: The paper, and journal for that matter, sorry to say, is of exceptional low quality.

If you could add more detail as to what you wish to record that would be great. I'm happy to upvote this question once it is clear, and more than happy to attempt an answer once I know what you are exactly after.

I found this link that has a lot of good info and directions http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835954/

@AliceD thanks I'm going over some of the papers I found online at the moment to see which electrodes they use. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835954/

The roots of plants have been used more often than the actual stem of the plant e.g. http://pubs.acs.org/doi/abs/10.1021/es071938w

I would love to get more info about the roots and signal activity but the link you provided requires me to pay along with the title being about "Microbial Fuel Cells Generating Electricity from Rhizodeposits of Rice Plants"  and the abstract being very brief

Perhaps you will find what you are looking for in the closing report of the FP7 project that funded the article. http://cordis.europa.eu/result/rcn/140451_en.html

authors: امیرمهدی خدابخشی

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What gives diarrhoea caused by Cholera its milky colour?
The diarrhoea caused by the Cholera bacteria is a milky colour, also known as 'rice-water' like. Why is this? I have a fairly good understanding of how Cholera acts on the body.

The color of our feces is caused by the breakdown products of the hemoglobin, namely Bilirubin and Stercobilin, which depending on the concentration, cause a yellow to brown color. See here for details.
Since the amount of liquid lost by the cholera diarrhea with up to 250ml/kg bodyweight is really high, there is only very little to nothing of these breakdown products available in the feces. This causes an absence of color.


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What is the chemical composition / empirical formula of Herpes Simplex 1?
Viruses such as polio are so well documented that a search for "empirical formula polio" gives you something like
 C332,652
 H492,388
 N98,245
 O131,196
 P7,501
 S2,340

We know that the virus consists of 70% protein, 22% phospholipid, 6.5% DNA, 1.5% carbohydrate (from the book Herpes Simplex and Pseudorabies Viruses by Kaplan)
Is there any information on the actual chemical composition of HSV1 and varieties?
Thanks!

Welcome to Biology.SE. What do you mean with atomic arrangement?

Thanks!  I'm mostly curious about the chemical composition in elements like in the above.

Thanks! Arrangement sounded like you were interested in the spatial relationships between (all the) atoms

You should modify your question as people are giving misplaced answers.

I doubt that such a formula exists for HSV 1, and for good reason: It actually is one of the most massive viruses known

I'm voting to close this question as off-topic because the atomic composition of viruses has no relevance to contemporary biology.

The Herpes viruses have a unique four-layered structure: a core containing the large, double-stranded DNA genome is enclosed by an icosapentahedral capsid which is composed of capsomers. The capsid is surrounded by an amorphous protein coat called the tegument. It is encased in a glycoprotein-bearing lipid bilayer envelope 1.

You can watch an animation of infection and steps of replication here, and below the video, they say that

HSV is a nuclear replicating, icosahedral, enveloped DNA virus. The HSV envelope contains at least 8 glycoproteins. The matrix or tegument which contacts both the envelope and the capsid contains at least 15-20 proteins[2].

In this definition of the structure, they at least assigned some values to the makeup. Additionally, in wikipedia, the viral genome is listed which I would recommend you take a look at as well. It can be found here but here is the synopsis of the table
UL1 through UL56
US1 through US12
RS1, ICP0, LRP1, LRP2
RL1, LAT

Additional resources:

HSV Genome 2nd link
The use of microarrays to analyze gene expression
Structural properties of HSV promoters
Animation of the Construction of a HSV-1 DNA Microarray for Global Analysis of Transcript Abundance
Animation of the Time-dependant Changes in HSV-1 Transcript Abundance During Productive Infection
Some Genetic Functions Encoded by Herpes Simplex Virus type 1
Herpes Simplex Virus Oligonucleotide Probes used in the DNA-microarray


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Friendly Spider found at home, London
What kind of spider is this? It was very friendly and shy, we spotted it inside our house and we carefully took it to the forest. Hope it will be a nice environment for this kind of spider... One of my kids loves to play with spiders and I would like to be advised on what kind os species he can approach or not. Thanks in advance.

Thanks, Jason, for decoding the image! Why was it coded? Would like to know how to avoid it next time.

Just to be sure: is it London, UK you are located at?

London, UK yes.

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how to compare two different enzymes with same Km?
I have a test today I study at HUJI and I encountered this question which I can't figure out: if two different enzymes have the same kM and the same substrate what can I say about the two?

same Vmax
dosn't have the same Vmax
may or may not have the same Vmax
the proportion between kM to Vmax has to be 0.5


text:
Greek grasshopper?
What is this fearsome insect seen on a Greek Ionian island?

During which point in the day did you observe the cricket?

That is in the family Tettigoniidae. It is a male. Species is Eupholidoptera chabrieri https://wikivisually.com/wiki/Eupholidoptera_chabrieri


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With respect to which METRIC is my DNA 99% similar to any other person's DNA?
I clarified my question, by editing the title. Using the comments  and links below, I have answered it myself:
The answer to my question is: The similarity is between 98.4%-99.9%, depending on which type of differences you include. The numbers relate to writing my and the other person's DNA as a long string, and compare differences (change of letter, missing/inserted letter). The most important differences seem to be SNPs (=difference in a letter in a gene-coding sequence) and account for 0.1% of difference between our 2 DNA's:

http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=110248
http://book.bionumbers.org/how-genetically-similar-are-two-random-people/

I have striked out the original question text, because it includes some motivation and interpretation, which seems false.
edit: It was suggested that the question is a duplicate to "Same" DNA vs genes but this might seem not to be the case, as this question just concerns the used metric (compare answer below).

99.9% vs 88%:
2 person's DNA is 99.9% the same (which goes down to 99% in some sources), e.g. http://book.bionumbers.org/how-genetically-similar-are-two-random-people/
Does this number include differences in copy-number variations and maybe other ?
On the other hand https://www.nature.com/scitable/content/global-variation-in-copy-number-in-the-13571 says that there may be up to 12% of some other differences (I am not sure what those differences mean).
Question:
I have been pouring through the internet and books, but have not yet understood to which metric this 99.9% number refers to? (I am a pure mathematician)
My hypothesis what it means:
If we look at a 1000 base-pair long snippet of the DNA of person A, then we will find this same snippet somewhere also in person B's DNA, with just one difference in one of the 1000 base pairs.
Now, if the latter is true, then this means that my DNA may still be significantly different than my neighbours, e.g. by containing a different number of repetitions in the non-coding DNA.
Ultimately, my DNA could be only, say, 2% similar instead of 99.9% (depending on the number of different repetitions), if we used as a metric the number of single base changes (including single deletions/insertions), we need to do to go from the DNA of person A to the DNA of person B (assuming we wrote down each other's DNA in one long string). Question 2: In fact, I would be quite interested to know how much the DNA of two people is similar using this last metric?

Please quote the exact passage in the Nature paper which you think says that there may be 12% of other changes. I have looked at the paper, searched for "12%", and all I can find is the statement " A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations." If you think that this meanss that individuals differ by 12% you are mistaken and your question is based on a false premise and should therefore be withdrawn.

@David Thanks for the comment. My question is fully independent of the 12% number, so withdrawal may be a bit too much. I use the number in my motivation. You may be correct that I misunderstood, because the sentence you mention is the one I am referring to. Compare also the BBC-article http://news.bbc.co.uk/2/hi/science/nature/6174510.stm - my misunderstanding possibly reinforces the need for an answer to my question: Which metric are we talking about? If you have some explanations or links/books, that can give me a better understanding, I am happy to learn as I have little clue right now :)

The 99.9% metric is quite straightforward — a simple base for base comparison between two DNAs — and is dealt with in my answer to this question. If you want to analyse something different like gene duplications (as in the paper you cite) you need to understand the biology and devise your own metric. Any paper with such in it will have it defined (possibly in the supplementary material.


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Open database of whole slide digital pathology images
I am looking for sequential image sections (stacks) of biological structures (such as liver, kidneys etc.) that I can download and use. Most of the pathology images I have found are either one image or 3-4 sections. I am looking for >50 sections to test some code.
Is there a public repository for this kind of data?

you could try the new Google tool https://toolbox.google.com/datasetsearch - it's searching for open scientific data. You might also find something here: https://github.com/sfikas/medical-imaging-datasets

thank you. Unfortunately i could not find any stacks or sections in the sites you recommended. I am looking for series of images (stacks or sections), it seems that those are not widely available.


text:
Real Time PCR Test Chemistry
I am working on building a real time PCR machine. Is there any chemistry set that I can purchase online to:

Identify if PCR amplification was successfully done.
Test fluorescence dyes that could be used to validate if the fluorescence detector optics worked; i.e. something I could excite with a specific wavelength and monitor for fluorescence.

I am looking for something that is not dangerous and only serves the single purpose of validating the real time PCR machine.
Mods please advise if I need to move to Chemistry StackExchange

Are you asking for specific and proven techniques ? or information on something like a thermocycler? Other than that, I have no idea what a pcr "machine" is.

I am asking for two things 1) Something that will confirm that PCR occurred (ie color change after 30 cycles of PCR). 2) Something that will fluoresce at a specific frequency when excited by an excitation frequency.

What level of accuracy do you expect for the identification of the PCR product?

If you're looking for a simple fluorophore just to make sure your detector is working, Auto parts stores carry fluorescent dyes to track oil leaks. Probably won't be useful for measuring amount of DNA though.

I just remembered that I used to extract fluorescent dyes from highlighters by breaking them open and passing ethanol through the marker. That would be another easy source of dyes to test your detector.

There are two different ways to detect PCR product in real-time PCR: dyes which bind to DNA in general, such as SYBR Green I, or probes specific to your PCR product. There's a summary of the benefits of each here, with the following table:

You can buy either online; they'll be fairly expensive but I can't think of an obvious way to get them cheaper if you're interested in high-confidence validation.
[edit] forgot to mention that you will also need to normalise the reporter signal against a reference dye such as ROX (https://www.thermofisher.com/order/catalog/product/12223012).


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Why does renal artery stenosis lead to activation of Renin-Angiotensin system?
To my current understanding, stenosis or narrowing of the arteries would mean higher blood pressure, similar to atherosclerosis. So the Renin system should be suppressed to counter the high blood pressure. But..
I have read in a textbook that renal artery stenosis means lower blood flow in the kidney due to the narrowing of the artery. Thus the Renin system is activated to increase blood pressure.
So why does narrowing of the renal artery cause a decrease in blood pressure, and not increase?

Read your own question closely; the answer is right there. What purpose does the renin-angiotensin system serve normally? How is blood pressure determined at different places in the body? Why would a reduced blood pressure in the kidney elicit activation of renin-angiotensin system? How would that affect the rest of the body?

I understand how the renin-angiotensin system works. What I do not understand is why a stenosis in the renal artery leads to a decrease in blood pressure whereas atherosclerosis in other blood vessels leads to a increase in blood pressure. Aren't both narrowing of the blood vessels? So why the different outcomes?

So why does narrowing of the renal artery cause a decrease in blood pressure, and not increase?

It doesn't. It causes an increase.
If the blood flow to the kidney is decreased for any reason (for example, hemorrhage or dehydration), the kidney is one of the organs that will protect it's perfusion by causing an increase in BP through the renin-angiotensin-aldosterone system (RAAS).
Very briefly: decr. blood flow -> renin secretion by juxtaglomerular cells -> conversion of serum Angiotensinogen into Angiotensin I (+ ACE) -> Angiotensin II => elevated BP (by a host of mechanisms).
If there is renal artery stenosis, the kidney will try to compensate for this (locally) reduced blood flow by activating the RAAS. The kidney doesn't 'know' that the blood flow/pressure is only locally reduced. It will cause systemic hypertension as a way to increase it's blood flow.
Atherosclerosis is a whole different ball of wax.


text:
can you tell me what kind of animal this is?

I found this skull over 2 years ago and i have been unable to find another like it or even come across someone who knows what it is. i live in south mississippi and the animal it came from looked like a deer, or even a dog, it was almost completely decomposed. I have been curious for 2 years now and have posted this before on other sites with no luck. someone help please .

Looks rather like a boar skull, which would make sense in Mississippi (especially Southern Mississippi), where their population has been growing for decades.


text:
How to measure metabolic rates of microscopically small animals?
I want to measure metabolism rates in Tardigrades

Metabolic rates will be assessed immediately following their exit from cryptobiosis (an animal dormant state).
I know that oxygen levels is the usual way to measure metabolism, but tardigrades are extremely small and hence oxygen level differences will be minute. Is there any other way to characterize metabolic rates, or is there a way to make the oxygen method viable?

I edited your question for clarity. Could you add a size (x microns) of these critters?

PS welcome to Stack Exchange and thanks for your question :) Perhaps add a pic of these amazing critters as well.

Hi, thanks! Usually, tardigrades are about 0.5 mm (0.020 in) long when they are fully grown (I took this from wikipedia). A picture is as follows:

I couldn't hel[p myself and added a pic of these marvelous creatures... I slightly modified the text as cryptobiosis kind of masked the real question (it's redundant info basically).

Metabolism in other small organisms, such as bacteria, are measured by taking the metabolism of a very large population of organisms, and then dividing that by the count of organisms in order to obtain the metabolic rate of a given individual.
In this paper on the metabolism of E. coli, they looked at the various input and output chemicals. Glucose, biomass, oxygen, and carbon dioxide were all observed. Observation of multiple variables also helps in the reduction of errors by using the stoichiometric balance to make sure that no errors have occurred in the measurements.
The methodology section of the paper had the following techniques:

Continuous cultivations were performed at 28 °C, at a stirring speed
  of 800 r.p.m., and the pH was controlled at pH 6·6 with 2·5 mol NaOH
  l−1. The 2-l bioreactor (model SGI 7F-Set2; Setric) was equipped with
  standard measuring and control units (temperature, pH, dissolved
  oxygen, stirrer speed). A constant aeration rate of 1·33 v.v.m. was
  achieved by a mass flow controller (Brooks). Continuous cultivation
  was performed for at least eight residence times at a given dilution
  rate; steady-state conditions were verified by constant optical
  density and oxygen and carbon dioxide transfer rates. Except for
  glucose, all other substrates were in excess. The concentration of
  dissolved oxygen was always maintained above 20 % of air saturation.
  Analytical techniques.
Culture liquid was withdrawn from the bioreactor into an ice-cooled
  beaker. Cell dry mass was determined gravimetrically after
  centrifugation of a known sample volume. The pellet was washed twice
  with 0·9 % w/v NaCl and dried at 40 °C under vacuum for 48 h.
  Elemental biomass composition was analysed with a PE 2400 II elemental
  analyser (Perkin Elmer). Glucose was measured enzymically by a YSI
  glucose analyser (model 2700; Yellow Springs Instrument Co.). Organic
  acids, i.e. acetic acid, formic acid, lactic acid and pyruvic acid,
  were analysed by HPLC using an HPX-87H Aminex ion-exclusion column
  (Bio-Rad). The column, connected to a UV detector (λ=210 nm) and RI
  detector, was eluted at 50 °C with 5 mmol H2SO4 l−1 at a flow rate of
  0·5 ml min−1.

If the tardigrades are grown in solution, an identical methodology can be used to measure respiration rate.


text:
Are there neuron mediated reactions faster than reflexes?
I'm interested in how fast the human body can respond to a stimulus.  I know the fastest reflex, the blink reflex, operates around 100ms from stimulus to reaction.  I also know that the blink reflex is known as the fastest reflex in the human body.  My interest is in the fastest responses to stimuli I can find in the body.
Are there any faster responses to stimuli within the human body which use neurons but are not categorized as a reflex (due to some technicality), meaning they could be faster than the fastest reflex?  To the best of my understanding a reflex is defined by the use of neurons to convey the information, I'm just wondering if there are any grey areas which don't qualify as a reflex but may be faster.  I don't want to potentially write off an entire class of neurological behavior in my research simply because I stopped at the blink reflex.

I think the vestibulo-ocular reflex is the fastest. It typically operates in 7-15 milliseconds.

A reflex as fast as the blink in a neural circuit:
I would consider suppression of outer hair cells in the cochlea to be a reflex; the faster component of this reflex is about the same as the blink reflex, around 100 ms. The hair cells themselves aren't considered neurons, but the pathway that suppresses their motility certainly is.
A much much faster non-neuronal "reflex":
That said, the outer hair cells themselves also dance along quite fast in response to sensory input, even faster than the typical hearing range for humans, faster than 20kHz! In some ways, this is a reflex because you are taking sensory (specifically, auditory) information and turning it into a motor response, but all the "action" is taking place within one cell, and it isn't a neuron.
A more classical reflex that is substantially faster than 100 ms
Reflexes in the periphery can be much faster than 100 ms. The myotatic reflex, or stretch reflex, can be as fast as 30 ms in the knee - this is the reflex that is tested when a physician smacks you on the knee with a hammer (used as a test of spinal and peripheral nerve function, not as a punishment). It's likely there are other stretch reflexes that are faster just because distances to the spinal cord are shorter, but these might be more difficult to test (in this paper they report latencies as fast as 20 ms).
Eyeblink reflexes can also be faster than 100 ms!
For example, see this paper: strong auditory stimuli evoked blinks within about 20ms!
tl;dr: I'd check your source that 100 ms is the fastest reflex! I stuck with mostly human examples here (some of the hair cell work is in other mammals), but you will find even faster reflexes if you look at smaller organisms, such as insects.

I was thinking of human reflexes when I wrote the question, so your examples are spot on!  I've edited the question to add "human" to the wording, but that shouldn't invalidate anything in your answer.  Thanks for the answer!

@CortAmmon No worries, you did indeed have "human" elsewhere in the body of your question, but I certainly prefer it from biological, evolutionary, and philosophical perspectives when people refer to "the human body" rather than "the body" - as if all bodies are human or that the human is the archetype or exemplar animal, so thank you for the edit!

In a paper studying Rhesus macaques, Huterer and Cullen showed that latency of the vestibulo-ocular reflex (measured from head movement to eye muscle contraction) can be as little as 5 milliseconds1.
Reference:
1: Huterer, M., & Cullen, K. E. (2002). Vestibuloocular reflex dynamics during high-frequency and high-acceleration rotations of the head on body in rhesus monkey. Journal of neurophysiology, 88(1), 13-28.


text:
What is the minimum caloric intake for a truly starving adult
What is the minimum caloric intake for an adult?  I'm not talking about a healthy diet.  There's plenty of advice on that.  I'm wondering what the absolute limits of H. sapiens are.  When there's a multi-year famine, and the body is willing to shut down as much of its capacity as possible without actually failing to function for years at a time, how much energy is it consuming?
I know the Basal Metabolic Rate is a key factor to this, but the numbers I have seen for it are all "healthy" BMRs.  I'm interested in the unhealthy numbers.  For example, I'd consider maintenance of temperature optional for these circumstances (assume we have a temperate enough climate), and I presume heart rate and breathing will go down, decreasing those loads.  Obviously there's limits as to how many environmental constraints can be addressed (if I knew what environments this was studied in, I'd likely know which studies to look for!).  And obviously not everyone is the same, but that's an issue in every human study ever completed.

Threr's no single answer to this question, just generalizations. It depends on the person, their state of health when starvation starts, and what you mean by "truly starving". To me, truly starving means no food whatsoever. If you want an answer, there's only one place to get it, and it's not here. Hint: these experiments were done in the 40's.

http://jn.nutrition.org/content/135/6/1347.full

How much water does it take for a plant to keep some leaves? how long is a piece of string?

@anongoodnurse The existence of variation does not make the question less amenable to scientific analysis. The confounding factors you mention, along with many other relevant factors, I'm sure, as well as the problem of defining the outcome variable can all be in principle addressed empirically. Although doing experiments on the subject is unethical, naturally occurring events of famine or voluntary starvation can be also studied. Surely we all agree that qualified generalisations and statistical analysis are the bedrock of biological research.

@anongoodnurse The challenge of defining starving is why I started with my first paragraph defining the term as I use it.  I specifically wanted to step away from the anorexia/bulimia related content because the focus there is how to make those people healthy, not just continue functioning.

you need to define the mass, age, and activity level of the individual to get a reasonable answer. You also need to better define your ending conditions does the person to recover completely or can they suffer permanent damage from the starvation.

A better example is the stories of tibetan monks who wrote accounts of their experience to survive for months or years on faith alone, and watch their hair and nails fall out in the search for wisdom. they could tell you how fast a coma arrives from eating just 300 calories per day.
There isn't a minimum amount though, because it's all subjective for time until, temperature, survival chores, time until coma, time until difficulty moving... you can probably keep someone in an emaciated coma with intravenous injections, or someone could stay awake with high exposure risk to illness, hair loss, nail loss. The question is vague, and there are 100 scientific studies about calorie restriction, so you are hoping someone will read 10-20 pages until they find some information for you.
It also depends how many watts the human needs to use in that situation to stay alive.
In 30'C you probably need 30 watts to stay warm, and 20 degrees about 60 watts, so the value can double based on temperature, you must change your question a bit.
60 watts basal metabolic rate body temperature would use 70 calories per hour, about a slice of bread, so 1400 calories per day without bedcovers. It depends a lot on ambient temperature and exercise, for example 1 mile of walking uses 100 calories. At less than 1000 calories per day, exercise becomes difficult and the person gets thin. Jogging uses about 250 watts. Extreme athletes and triathletes peak at about 650 watts for sprinting.
There are 100ds of citations on caloric defficiency and restriction, with values around 350 - 700 per day, which change metabolism considerably:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014770/
https://www.ncbi.nlm.nih.gov/pubmed/2718912

I don't think it answers the question.

I'm not reading through 20 pages of rambling science articles to find out that there isn't an answer! There isn't an absolute minimum, same as there isn't a minimum amount of water for a plant to survive, and people don't starve for years.


text:
How does nitrogen gas partial pressure change when ascending during scuba dive?
Scuba divers suffer decompression illness in which during sudden ascension, gas bubbles form in blood vessels and do not get reabsorbed quickly, leading to various problems including a stroke.
The mechanism is as follows. At high pressure, more nitrogen gas in the air can be dissolved in the blood. This is due to Henry's law, which states that with greater partial gas pressure exerted onto the liquid, more gas is dissolved. When the partial pressure of nitrogen gas returns to normal, solubility of the blood decreases, leading to the formation of gas.
From above, it seems that the air that blood is exposed to (the lung's alveoli in most cases) changes in the partial pressure of nitrogen gas. Another study isolated the effect of partial pressure by conducting an experiment in which the subject's breathed air was changed from heliox (combination of helium and oxygen) to nitrox (combination of nitrogen and oxygen) without change in total pressure and this led to bubble formation.
However, it is hard to imagine that the pressure of the air breathed in by a scuba diver would change, due to the fact that air is brought from an oxygen tank that seems to be independent of outside pressure. Thus I ask the question: if the air breathed in by the diver does not change with depth, how does nitrogen partial pressure exerted on the blood change?

What has your research told you?

I do not understand your reason for asking that question. Could you specify because I stated what I know and the assumptions made? I do not have resource on which I can test my assumptions.

The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Since this is a pretty common textbook-style topic, there is a lot of information available about depressurization from scuba diving in particular.

I have not found any online (as shown by edits), but I would love any specific reference that I could look at.

please delete this question. I will re-ask it. I do not like the fact that I asked the question under the premise that blood pressure does change when even that is not certain to me when reading various sources anymore.

You can simply edit the question, including the title if you so choose. The only time to avoid doing that is once you've already gotten answers if the changes would make the answers invalid. Thanks for doing some more work on your own!

The change has been made. Please feel free to answer (dear community)!

'However, it is hard to imagine that the pressure of the air breathed in by a scuba diver would change, due to the fact that air is brought from an oxygen tank that seems to be independent of outside pressure' You are misinformed about both points. SCUBA tanks usually use ordinary compressed air, and are equipped with a regulator valve that matches the pressure of the gas supplied to the diver to the ambient pressure. The regulator is essential Too much pressure would burst the divers lungs, and too little would keep the lungs from inflating.

Thank you I did not know about the existence of regulator valves. In that scenario, it makes sense because the pressure of air going to the lung is dependent on water pressure. The question can be closed now.


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GPCRs: Gi and Gs
GPCR = G-protein coupled receptor
Gi = G inhibitory alpha subunit
Gs = G stimulatory alpha subunit
Are there structural differences between Gi and Gs subunits (secondary structure)? Or is it just categorization by effect on cAMP level? (Gi inhibits cAMP production, while Gs stimulates cAMP production)

Adding some more background is recommended. A good start is to remove any unnecessary acronyms and supplying some background to what the physiological function of both these peptides is. And what effort, if any, you have put in looking up the structure of both subunits (crystallography etc).

@AliceD. This is perfectly clear if you know GPCRs.

@cagliari2005, I know what G-prot couples Rs are, I am just trying to prevent question closure. Otherwise it'll be tagged as homework.

Jenny, both subunits differ in amino acid sequence - so differences in primary structure are inherent. Can you elaborate what you are after exactly? Secondary and/or tertiary structure perhaps?

This is question of how the subunits are categorized. So is it the structure of subunits or effect on cAMP? Or is there a very high correlation between the structure and effect on cAMP that they are essentially the same method of categorization?

Also, I didn't know that there was the difference in the amino acid sequence. That helped me grasp the difference between the two subunits somewhat.

Gi and Gs have a structurally different sub unit in their alpha chain.

The receptors for PGE1 and adenosine interact with inhibitory Gi,
  which contains the same β and γ subunits as stimulatory Gs but a
  different α subunit (Giα). In response to binding of an inhibitory
  ligand to its receptor, the associated Gi protein releases its bound
  GDP and binds GTP; the active Giα · GTP complex then dissociates from
  Gβγ and inhibits (rather than stimulates) adenylyl cyclase.

Both β1- and β2-adrenergic receptors are coupled to G proteins (Gs), which activate adenylyl cyclase. In contrast, α1 and α2 receptors are coupled to two other G proteins, Gq and Gi, respectively. Gi inhibits adenylyl cyclase, and Gq stimulates phospholipase C to generate IP3 and DAG as second messengers.

Also this,

A comparison of chimeric receptor 1, which interacts with Gs, and
  chimeric receptor 3, which interacts with Gi, shows that the G protein
  specificity is determined primarily by the source of the
  cytosol-facing loop between α helices 5 and 6. A comparison of
  chimeras 1 and 2 indicates that α helix 7 plays a role in determining
  the ligand-binding . B. Kobilka et al., 1988, Science 240:1310; W. A.
  Catterall, 1989, Science 243:236.

I'd recommend reading through this:
http://www.ncbi.nlm.nih.gov/books/NBK21718/

So in summary, structure between 5th and 6th helix is different between Gs and Gi, and this leads to binding to adenylyl cyclase at different sites, one being stimulatory and one being inhibitory. And this means a very high correlation between structure and function. Thank you for your answer!


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Why do animals use glycogen for their polysaccharide storage whereas plants use starch?
The polysaccharide storage form of glucose in animals is glycogen, whereas in plants it is starch. Both of these are polymers of α-glucose with α-l,4 glycosidic linkages and α-l,6 glycosidic branch points (Wikipedia article on polysaccharides). The only difference that most sources mention (e.g. Berg et al.) is that glycogen contains more branches than starch.
It is not clear to me from this information what effect the different branching would have on the structures of the polysaccharides, nor why one rather than the other would be preferred in animals and plants.

It is surprisingly difficult to find a proper answer to this question on the internet — my own answer was only found after consulting specialized reviews. I therefore think this is an important question and have therefore edited it, tightening up the wording, avoiding the implication that polysaccharides are the only storage form, and spelling out the chemistry. If the original poster is still active on the list I hope he will accept these changes.

What about fungi? Do they even have storage polysaccharides and if so, what kind?

Summary
The key difference between glycogen and amylopectin (the main constituent of starch) is not the number of α l,6-glycosidic branches, but their arrangement.
In glycogen branches are successively subdivided, producing a relatively small globular structure that is unable to grow further. It is soluble in an aqueous environment and, with its numerous exposed ends, can be metabolized rapidly — appropriate for animal cells in which energy reserves must be mobilized in response to immediate demands, e.g. for muscle contraction.
In amylopectin there is a long central polysaccharide chain from which branches of limited size extend at intervals. This produces much larger semi-crystalline particles (starch grains), a form especially suited to long-term bulk storage in seeds and tubers.
The Chemistry

This is the common feature of glycogen and the amylopectin portion of starch. (The amylose portion is unbranched.) In glycogen there is approx. one branch point per 10 glucose units, whereas in amylopectin the figure is 1 per 24–30 (source: Wikipedia).
The Topography
The contrasting branching topography of the two polysaccharides, mentioned above,  is illustrated diagrammatically below:

This is a two-dimensional representation. In three dimensions the glycogen spreads out in all directions from a central point — actually the primer enzyme, glycogenin. In three-dimensions the amylopectin strands mainly lay side by side.
The Macro-structure
The illustration below, modified from Bell et al., shows the different shapes and sizes of the macromolecular structures. It should be mentioned that semi-crystalline nature of amylopectin is aided by the helical conformation of the chains.

Rather than providing a précis of the review of Bell et al. (Journal of Experimental Botany, Vol. 62, pp. 1775–1801, 2011) I shall quote from them directly (omitting their citations).
As regards glycogen they write:

Each chain, with the exception of the outer unbranched chains,
  supports two branches. This branching pattern allows for spherical
  growth of the particle generating tiers (a tier corresponds to the
  spherical space separating two consecutive branches from all chains
  located at similar distance from the center of the particle). This
  type of growth leads to an increase in the density of chains in each
  tier leading to a progressively more crowded structure towards the
  periphery.
Mathematical modelling predicts a maximal value for the particle size
  above which further growth is impossible as there would not be
  sufficient space for interaction of the chains with the catalytic
  sites of glycogen metabolism enzymes. This generates a particle
  consisting of 12 tiers corresponding to a 42 nm maximal diameter
  including 55,000 glucose residues. 36% of this total number rests in
  the outer (unbranched) shell and is thus readily accessible to
  glycogen catabolism without debranching. In
  vivo, glycogen particles are thus present in the form of these limit
  size granules (macroglycogen) and also smaller granules representing
  intermediate states of glycogen biosynthesis and degradation
  (proglycogen). Glycogen particles are entirely hydrosoluble and,
  therefore, define a state where the glucose is rendered less active
  osmotically yet readily accessible to rapid mobilization through the
  enzymes of glycogen catabolism as if it were in the soluble phase.

Regarding amylopectin they write:

Amylopectin defines one of, if not the largest, biological polymer
  known and contains from 105–106 glucose residues. There is no
  theoretical upper limit to the size reached by individual amylopectin
  molecules. This is not due to the slightly lesser degree of overall
  branching of the molecule when compared to glycogen. Rather it is due
  to the way the branches distribute within the structure. The branches
  are concentrated in sections of the amylopectin molecule leading to
  clusters of chains that allow for indefinite growth of the polysaccharide.
  Another major feature of the amylopectin cluster structure
  consists of the dense packing of chains generated at the root of the
  clusters where the density of branches locally reaches or exceeds that
  of glycogen. This dense packing of branches generates tightly packed
  glucan chains that are close enough to align and form parallel double
  helical structures. The helices within a single cluster and
  neighbouring clusters align and form sections of crystalline
  structures separated by sections of amorphous material (containing the
  branches) thereby generating the semi-crystalline nature of
  amylopectin and of the ensuing starch granule. Indeed the crystallized
  chains become insoluble and typically collapse into a macrogranular
  solid. This osmotically inert starch granule allows for the storage of
  unlimited amounts of glucose that become metabolically unavailable.
  Indeed the enzymes of starch synthesis and mobilization are unable to
  interact directly with the solid structure with the noticeable
  exception of granule-bound starch synthase the sole enzyme required
  for amylose synthesis.

Coda
The paucity of information on plant starch metabolism would seem to reflect  a combination  of their being less is known about plant biochemistry, and less general interest because of a general focus on medical and animal biochemistry. Although an animal biochemist myself (and, thus, previously ignorant of the information in this answer) I feel that it is time to redress this imbalance.

Your labels for the alpha 1>4 and alpha 1>6 linkages in the first diagram are the wrong way around.

well glycogen can be broken down into sugars a lot faster, many more branches means many more ends to clip individual sugars off of, that's how you mobilize the sugar for use, it is clipped of the end of a strand. With many more branches glycogen can mobilize more sugar more quickly.  This is not important in plants but in animals that need to be able mobilize lots of energy in a hurry, glycogen works better. Additionally glycogen is a smaller molecule and easier to make, not surprising since glycogen is the ancestral condition for plants and animals.
As for why plants switched to starch, or more precisely gained it through symbiosis, starches folded crystalline structure makes it a higher density energy store but also slows its release, it is however more stable, which is important if you are going to be storing it for a long time. Animals would likely switch to starch too if they did not have to break it down to digest it, just because they take in so much of it. But since they have to break it down there is no real incentive the build it back into starch when glycogen has some advantages and quite frankly since the pathway is already there and evolution has a lot of "eh good enough".

Any references for either of the claims?

Added, and good thing to my old notes were wrong about ancestral condition.

Some interesting ideas, but seems speculative. (1) It's true that glycogen can generally be mobilized faster than starch, but I'm not sure it's due to higher branching -- I would rather think it's due to the soluble nature of glycogen granules vs. the crystalline form of starch, which you mention later.  (2) What exactly do you mean by glycogen being "easier to make"? (3)  You seem to contradict yourself in saying that for animals "glycogen works better", and then that animals "would switch to starch too" if they could?

Sorry, (1) I meant  evolutionarily speaking animals probably would just use starch as it is if they did not have to take it apart then rebuild it to get it inside, since the advantage of glycogen is nominal. (2) Glucose is a simpler molecule with a shorter synthesis pathway. One step in starch synthesis involves producing amylopectin a molecule very similar to glucose. (1)the branching and the solubility are related and both definitely contribute, but starch is also a more complex molecules which requires multiple enzymes and must be unwound to be broken down into glucose.

There would seem no reason that animals could not have evolved to synthesize starch as a variety of bacteria do just that and the chemical bonds in starch and glycogen are identical. There is every reason that they did not evolve to synthesise starch, given its unsuitability for rapid release. Energy storage in animals is divided into two functionally distinct molecules: a limited amount of glycogen for rapid release and provision of glucose, and a larger supply of fat for slower release and which cannot provide glucose (except from the glycerol component).

@David  please read the full exchange you are basically restating what I already said. The reason  they never evolved it is they gain nothing by rebuilding glucose into starch instead of glycogen, the bonds are identical but the finished molecule and there properties are not.

I think you may not quite appreciate how SE is supposed to work. What matters is the questions and the answers. The comments are primarily to allow users to ask for clarification or query the content of these, after which, if appropriate, the question or answer can be modified, thus improving it. So the content of your exchange with Roland is not what is important; it is the fact that your answer still contains the unsupportable speculation “Animals would likely switch to starch too if they had the ability totsynthesise it.” Your answer would be improved by deleting this.

@david,  I thought you were referring to my comments, that's a good catch I will fix that.

What is your basis for saying glycogen is a "simpler molecule" and "easier to make"? Also, your mention of storage of starch in plants "for a long time" is fine for seeds and tubers, but more problematical for starch in leaves, which is apparently formed during the day and broken down at night.

@David the fact it is a simpler molecules and easier to make. I included links to justify each, glycogen can be large but  starch can be much larger molecule glycogen is self limiting in size due to its branching pattern. its production pathway is also shorter. I will clear that up a bit. for the second part some starch is broken down at night, not all, plants have slower metabolisms which makes stability more of an issue, now there is a bit of chicken and egg quality to this.

I don't see that one molecule is simpler than the other. Both include the same chemical bonds. Starch granules are larger on average, but size is not complexity. The differences I can see are (1) initiation — it is known how this works for glycogen with glycogenin, is it known how this operates in starch? Is the plastid membrane involved? (2) control of topology of branching — is anything known about either process? (3) packaging of starch in seeds etc. — is there some surface layer? Is this the same in leaf starch? Interesting questions, but I don't think they have simple or easy answers.

by looking at mutant plants we can tell a lot of the sugar produced is never converted into starch in the first place. this source from my answer actually answers a lot of your questions, https://www.ethz.ch/content/dam/ethz/special-interest/biol/plant-sciences/plantbiochemistry-dam/pdf_Dokumente/Publi_nr_37.pdf


text:
Is a sequential double transformation acceptable?
Standard protocol states having two compatible vectors being transformed simultaneously during the same procedure. I've come across a situation in which transforming one vector, obtaining results, and then transforming the other is preferable. Is there any reason to think that this wouldn't work? Do I risk losing my first vector upon transformation of the second?

I'd assume that you use different antibiotic resistances for selection, that way you should be able to ensure that both plasmid are taken up successfully.

you do, but some will maintain both plasmids, so the two antiobitics on the plate still should give you want you want.

If the plasmids you wish to transform are very big (more than 20kb), the co-transformation might not be very efficient (you might not get any colonies). Electroporation should work though, as electrocompetent cells are more efficient than chemically competent cells. Alternatively, as you have read, you could transform your first plasmid and select for it, and then make these cell that harbor it competent and transform the second plasmid. As long as you select for the plasmids (with kan/carb/etc resistance marker), the cells that grow on the selective media will keep both of them. If I were you, I would try the co-transformation and then if it doesn't work I would do the sequential transformation.


text:
Does ethanol destroy RNase?
I've gotten conflicting advice on this: some people believe one can remove RNase contamination simply by spraying the bench, pipettes, gloves, etc. with ethanol. Others think ethanol does not destroy RNase and special reagents are needed to prevent RNase contamination.
So does ethanol remove RNase contamination? If not, what reagent does?

See the answer from shigeta below - "inhibition" isn't really the right way to think about this, since that may imply a specific interaction when talking about an enzyme.

Good point, I changed the wording of the question to convey the need for permanent denaturation.

I think the protocols to clean glassware take no chances and just care about RNA degradation rather than targeting one class of enzymes.
EtOH is supposed to denature RNAse and any other proteins on the surface.
Other chemicals such as Diethylpyrocarbonate  (DEPC) used to wash glassware kill all biochemical activity by reacting with nucleophilic moieties in the protein (-OH, -SH -NH(2/3) ).   (See comments below for more.)
These treatments are followed by heating at 300-450 F for 2-4 hours.  This is not a specific RNAse decontamination - all biological activity is killed.
RNAse activity is not assessed by specific detection of a particular enzyme, but rather judged by the degradation of an RNA sample in the lab environment.  So specific inhibition isn't worthwhile - any protein that might interact with and degrade RNA is called an RNAse in these protocols.

The heat treatment is called depyrogenation and not only completely removes all biological activity, it also destroys pyrogens (fever inducers) such as LPS or endotoxin.

Thanks for adding to this guys.  I think you can see how the reagents really clean up the glass. I'm familiar with the protocols, but I've not worked with RNA myself.

You don't want to only inhibit or temporarily denature RNAses, if you work with RNA you have to permanently inactivate the RNAses. I work with RNA, and I haven't seen anyone use ethanol to remove RNAses, I would not trust it to work reliably. RNAses are really stable enzymes, they even survive autoclaving to some part, so I would not be suprised if they can refold after ethanol exposure.
The usual methods to remove RNAses are

Treatment with 0.1% DEPC (heat up to at least 60 °C, or autoclave if possible to remove residual DEPC later). Cannot be used with e.g. Tris buffer or anything else that reacts with it. DEPC is carcinogenic, so you should follow the proper safety procedures.
Anything made of metal or glass, heat up to 250 °C for around 2 hours
1M NaOH for at least 30 minutes (you need to wash thoroughly to remove the NaOH)

You should be aware that anything that destroys RNAses will likely do the same to your RNA.
Autoclaving does not protect completely against RNAses, but it still reduces RNAse activity significantly. So while you should not rely on autoclaving to get rid of RNAses, in my experience it is sufficient if you start from a source that is unlikely to contain a lot of RNAses. Pipette tips (not loose tips out of a bag, to minimize handling) and millipore-filtered water are pretty safe after they are autoclaved.
There are also commercial RNAse inhibitors, but I've only used them in cases where I had to mix RNA and protein, and the protein wasn't completely RNAse-free.


text:
Can I use PCR buffer instead of cDNA synthesis buffer?
I am using Fermentase First strand cDNA synthesis kit but its buffer is over. I need to work today but I have not access to any sorce currently. I have PCR buffer in the lab. Can I use PCR buffer instead of cDNA synthesis buffer? What are your other suggestions? Thank you

This page has the recipe for 10X M-MuLV RT buffer:

500 mM Tris-HCl
750 mM KCl
30 mM MgCl2
100 mM DTT
pH 8.3

If you have the basic reagents, I suggest making that.


text:
Physiological indicators of happiness and well being
If I understand it correctly, levels of serotonin in the brain can indicate if a person is happy. What other physiological measures indicate happiness or well being for a humans?
I am looking for indicators which can be measured quantitatively but don't be very strictly correlated with 'happiness'. And on the flip-side is there physiological  indicators that a person is/not depressed?

Check out Wikipedia Article on serotonin. There are multiple serotonin receptors in the human brain, and mutations of those receptors are related to depression and suicide. As such, serotonin levels aren't really a metric of happiness. I would look at long term behavior as an indicator of happiness or depression

There are beahvioral, physiological, and psychological indicators of happiness, and on the flipside of depression, all of which are quantitative.
Levels of the neurotransmitters serotonin and dopamine in the brain are a physiological indicator of depression. Higher levels of serotonin are correlated with increased happiness and decreased anxiety. Dopamine also contributes to good mood, and in addition causes an increase in activity and willpower. Both serotonin and dopamine show decreased levels in depression. However, it is important not just to look at general levels of the neurotransmitter, but to also consider which parts of the brain show decreased neurotransmitter levels. Depression correlates with decreased serotonin and dopamine levels in the amygdala, thalamus, and hyppocampus. (http://www.health.harvard.edu/newsweek/what-causes-depression.htm)
Behavioral tests of depression are used on laboratory animals. The most common tests are the forced swim test (in which scientists measure how long a mouse persists swimming in a water container before it gives up) and the tail suspension test (in which scientists measure how long a mouse struggles to free itself when suspended by its tail). (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270071/)
In addition, self report questionnaires are designed to quantify depression in people. Some popular ones are the Beck Depression Inventory (BDI-II) (http://en.wikipedia.org/wiki/Beck_Depression_Inventory) and the Beck Hopelessness scale (BHS) (http://en.wikipedia.org/wiki/Beck_Hopelessness_Scale).

Hi, thanks this was a useful post. As a secondary question: do you know if any of these indicators (or others) could be tested for after a person has died? And even when the body has degraded to a skeleton?

I don't know of any indicators that can be used after death. Depressed people tend to have less gray matter in certain parts of the brain (http://www.ncbi.nlm.nih.gov/pubmed/18838632, http://www.ncbi.nlm.nih.gov/pubmed/18669941), but that could be a sign of many other mental diaseases, and wouldn't help in studying skeletons.

Facial Microexpressions can indicate happiness.  Not sure about depression, but sadness and other correlates might be useful there:

Microexpressions express the seven universal emotions: disgust, anger, fear, sadness, happiness, surprise, and contempt. Nevertheless, in the 1990s, Paul Ekman expanded his list of basic emotions, including a range of positive and negative emotions not all of which are encoded in facial muscles. These emotions are amusement, contempt, embarrassment, excitement, guilt, pride, relief, satisfaction, pleasure, and shame.

MRI seems to have some happiness metrics - though its not the easiest or cheapest method.


text:
Does boiling or frying fish make Omega3 be denatured?
I read some articles about omega-3, and I found there are two different opinions about how sensitive omega-3 is to heat. one is Applying heat to omega-3 make omega-3 become trans-isomer which is very bad for the body. and the other is Applying heat to omega-3 doesn't make omega-3 become any bad compound. I want to know which is true. I think maybe Applying heat to omega-3 make trans-fatty acid, but I want to know exact temperature. and what about boilling or frying fish? Wiil applying heat to fish make trans-fatty acid too?


text:
does the amount of blood circulate in a body is same before and after amputation?
if a person loose his hand in an accident do the blood flows through his body is equal to the volume of blood before accident? how human body manage with that blood which is deserved by the missed body part? if human body have such a mechanism. does it effect other body parts? or is there any change in the proportion of blood flows through different arteries?

The kidney regulates the amount of blood being produced and removed from/recycled in the body. Even if somehow the body lost no blood when it lost the limb, the kidneys would remove the excess blood as it filters.
I think the misconception in asking this question is that the body knows how much blood to produce for the body. Yet, that isn’t the case, it just regulates the amount based on different signals it gets from the blood.
More info: https://www.ncbi.nlm.nih.gov/m/pubmed/17630596/

Still doubt remaining. does it affect the volume of blood received by other body parts?

If you are talking about due to the arteries being severed, the blood vessels remodel themselves to make sure the body still gets enough blood. If you aren’t talking about it, the kidneys remove the excess blood until the other parts of the body receive the same amount.

okay. do you have any reference papers associated with these kind of remodeling of  arteries. if so please share the link

@DJoseph I guess I don’t specifically have an article on amputation, but here is just a general one about wound healing https://www.sciencedirect.com/science/article/pii/S0022202X15528571 and using general knowledge that it amputees do regain circulation.


text:
totaling OTU from 2 or more observations and assign to new observation in OTU table from qiime
I am new to microbiome processing pipeline but I want to ask, How do I combine two observations and assign it to a new single observation in the OTU table resulted from QIIME.
Here is the situation. I am doing river microbiome analysis. I have water sample named A-P, P for particle-attached sample and A for its and A-F for free-living sample for the same site. They are just different in the filter size being used.
I extracted the DNA, sequenced, and processed the raw reads separately using QIIME for all the 110 samples. But now, I am doing analysis on "R" and i need to combine A-F and A-P as one observation, namely only A. It seems simple to do on "R" for only one observation. But, I have 110 observations needed to be merged to 55. Are there any simple ways doing that without doing it one by one either in "R" or QIIME
Thanks,
Bob Adyari

There is no word "wanna" in English. I have changed it to "want to" in your question.

Which is the output you are working on from QIIME? is it biom-format?

sorry for the long missing. I figured it out already in a bit complicated way. So, I ran collapse_samples.py in qiime to merge two samples to one new. Thanks anyway


text:
Why did a lot of common insects evolve such a thin waist?
Something that doesn't quite make sense to me is why lots of insects like ants, bees and wasps have a such a small petiole when it connects many major organs to the rest of their body from a suddenly much wider abdomen.
Normally from an engineering standpoint, you don't increase the width of a cantilever from a joint because the torque applied to a joint already increases with the length of an overhanging segment, so increasing the width would only multiply the torque that joint or opposing segment needs to balance.
It could have something to do with ants being so small that large  torque isn't an issue in proportion to their body size, but if it wasn't, then why do their legs also get thinner as they measure further in length from their body?

Human limbs also get thinner the further they go from the body, and it's not because they'd buckle under their own weight otherwise.

But it would be even harder for those limbs to move due to the extra torque that needs to be counteracted to move a specific direction. Joints are especially thicker than the shaft of a bone because they face more strain during locomotion and impact, and it makes sense bones would get thinner because if they were thicker, they would be that much harder to move at the same distance.

The normal engineering of cantilevers at the human scale can be relaxed at insect scales.  At the small sizes of ants and wasps, gravity is a very minor factor because of the gravitational force affecting small masses as compared to the electromagnetic forces within and between materials.  Not only does this mean insects can easily walk up walls and across ceilings, but also the extra weight of a wider, heavier cantilever (the abdomen) can be supported and moved by the material of a narrow supporting joint.(the petiole).  Similar consideration occurs for the inertial force due to mass.

This thin waist is called petiole (aka.  wasp‐waist).
How many times did the petiole evolve?

Why did a lot of common insects evolve such a thin waist?

Reading this question make it feel that you are assuming that several lineages evolved this petiole independently. It would be wrong. The petiole evolved once only and all the species that are having a petiole today (ants, bees, wasps, ...) are descendent of this lineage that evolved this petiole.
The taxon of all these species having a petiole is called Apocrita, which is a suborder of hymenoptera. You can learn much more about the phylogeny of these taxons in Rasnttsyn and Haichun (2010).
Why did it evolve?
The early lineage who evolved this trait where parasites (or even parasitoids at that time, I am not sure). This lineage was laying their eggs in tree trunk (or maybe already in other insects larvea if they were already parasitoids). The constriction that is the petiole allowed these individuals to have greater maneuverability for depositing their eggs accurately (Peters et al., 2017; Wilhelmsen et al., 2010).
The evolution of this petiole greatly affected the future evolution and diversification of Apocrita as things like stings and even maybe eusociality. From Peters et al., (2017)

The evolution of the wasp waist, a constriction between the first and the second abdominal segment greatly improving the maneuverability of the abdomen’s rear section, including the ovipositor, was a major innovation in the evolution of Hymenoptera that undoubtedly contributed to the rapid diversification of Apocrita

So if it was thicker, they wouldn't be able to maneuver their abdomen as well to use as a stinger or to lay eggs? But if their petiole was thicker, wouldn't there also be more muscle tissue that could move in a desired direction?

@VaneVoe Well, more muscles does not necessarily give you more flexibility. You need some room to make the movement. Just like if you take a cardboard cylinder and creat a "petiole" in the middle, the movement will be greatly increased. I am no good physiologist but it feels pretty intuitive to me that this thinner waist increase movement amplitude. Watch a video of a wasp using its sting and you'll see how much flexibility they have at their petiole compared to other, thicker, body parts.

Specialized mechanical anchors join up arthropod exoskeletons to muscles and tendon cells. There's a complex network of interconnected matrix constituents, junctions and associated cytoskeletal elements. F-actin based fibres used as tendons fuse onto to myosin based structures which are used for muscle contraction.
The tendons can go through relatively thin areas of the insect with massive leverage. We think about robots and humans as using bones and metal joints with pivots and motors, when arthropods muscles move the exoskeleton rather than interior bones.
The exoskeleton constriction at the abdomen-thorax joint of arachnids and ants demonstrates the relative strength of insect exoskeletons, the exoskeleton material is so light and powerful relative to the size to permit the small form while conserving enough resistance.
The abdomen-thorax joints, which can be multiple segments, are bit it stronger than the legs. They are less likely to get damage there than on their legs. The abdomen and thorax are containers for all the internal organs, which is different than a mechanical limb, so they are bigger.
The slender waist allows for a lot of arthropod behaviour like weaving, stinging, burrowing, preening, symbioses, it's a complex field.
If humans can change the magnet based rotary muscles and use tendon based mechanics they can probably develop very cool machines for the future. here is the human designed comparison for arthropod locomtion:
https://www.youtube.com/watch?v=Vi1hwdWUHvU
https://www.youtube.com/watch?v=eYFYSYmv4v4
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2555930/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335404/

Apocrita insects (i.e. the clade containing bee, wasps and ants) are supposed to have evolved a thin waist because it gives them more flexibility to manoeuvre their abdomen. Most Apocrita are parasitoids and they need this flexibility to parasitize theirs hosts. The others have evolved a stinger: the petiole can serve them as a lever to better defend themselves against their natural enemies.
So while it's true that this thin waist brings physiological constraits (e.g. for food transit or the torque needed to move the abdomen), these disavantages are very likely over-rode by the adaptive advantage brought by the increased maneveurability of the metasoma (which carries the ovipositor/the stinger).
You can find more information about the petiole's evolution here and here.


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How much does calcium reduce iron absorption?
Generally calcium inhibits the absorption of iron, but to what extent? One atom of calcium will not block 100% of iron absorption, that clearly isn't feasible. On the other hand, if someone ate 10 pounds of calcium, they wouldn't absorb any iron. How can we quantitatively determine the inhibition of iron absorption for a given calcium intake?

In short: Calcium can inhibit absorption of iron, but this does not necessary have any significant effect on the long-term iron status in the human body.
Iron (Linus Pauling Institute):

The presence of calcium decreases iron absorption from both nonheme
  (i.e., most supplements and food sources other than meat, poultry, and
  seafood) and heme sources (meat). However, calcium
  supplementation up to 12 weeks has not been found to change iron
  nutritional status, probably due to a compensatory increase in iron
  absorption. Individuals taking iron supplements should take them two
  hours apart from calcium-rich food or supplements to maximize iron
  absorption.

In various studies, calcium from food or supplements in usual amounts decreased iron absorption by about 50%, but the calcium dose/iron absorption relationship cannot be simply quantified, because it is affected by several factors, for example:

Phytates in food inhibit the absorption of both calcium and iron (BiomedCentral).
Calcium may inhibit the absorption of nonheme iron from plant foods less than heme iron from meat (academic.oup.com).
Different calcium supplements may differently affect the absorption of different iron supplements.

The inhibitory effect of calcium on iron absorption is not linear and one may not be able to express it as a simple formula. Below are some examples from studies.

A review of studies, American Journal of Clinical Nutrition, 2010

The reported dose-effect relation between the amount of calcium given
  and the degree of inhibition of iron absorption differs from other
  factors influencing iron absorption.
  This dose-effect pitfall is illustrated by 2 studies...[Read more in the linked article ].

A review of studies, PubMed, 2010

The quantitative effect, although dose dependent, was modified by the
  form in which Ca was administered and by other dietary constituents
  (such as phosphate, phytate and ascorbic acid) known to affect Fe
  bioavailability. The results of most multiple-meal human studies
  suggest that Ca supplementation will have only a small effect on Fe
  absorption unless habitual Ca consumption is very low.

A study, PubMed, 1991

When taken without food, calcium carbonate did not inhibit the
  absorption of ferrous sulphate with doses of either 300 mg Ca and 37
  mg Fe or 600 mg Ca and 18 mg Fe. However, at the latter levels,
  calcium citrate and calcium phosphate reduced iron absorption
  significantly by 49% and 62%, respectively. All calcium supplements
  inhibited absorption of the iron supplement when taken with food. The
  absorption of dietary nonheme iron was also inhibited by all three
  supplements. This inhibition was less pronounced from a meal of high
  iron availability and low calcium content (28%) than from a breakfast
  meal of low iron availability and high calcium content (55%).

A study, American Journal of Clinical Nutrition, 2005

Calcium supplementation reduced heme and total iron without
  significantly affecting nonheme-iron absorption, regardless of meal
  bioavailability.

This doesn't really answer anything because it says nothing about the timing or ratio. Obviously if you don't take calcium supplements at the same time as you ingest iron, there is no problem, but when taken together calcium definitely inhibits the absorption of iron, you will be hard-pressed to find a certified nutritionist who says otherwise. That is why the article still recommends taking them two hours apart. The question still remains: by what percent does a given mass of calcium decrease iron absorption by? This can only happen if you ingest them within two hours of each other.

@VaneVoe, if you are asking how calcium supplements inhibit the absorption of iron supplements, please make this clear in your question. Food can affect iron absorption in so many ways that it makes your question unanswerable. Even with supplements alone, it may not be possible to answer with a certain "percent." They are individual differences in iron absorption, current iron stores in the body and different Ca and Fe supplement forms that affect absorption

You're the one who chose the focus on supplements, I am asking about per-weight inhibition, you chose to ignore that.


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Please help me to identify this creature, is it harmful and possible solution of how to get rid of these in my house
Please help me to identify this creature, is it harmful and possible solution of how to get rid of these in my house.
Please forgive me for bad image quality, some of these have white dot at the back(I guess male/female identification mark).
I am from north India, Punjab region
Please help me to get rid of these.
min size found: 3mm
max size found: 6-7mm

These look like mealybugs (Hemiptera: Sternorrhyncha: Coccoidea: Pseudococcidae); if so, then you have an infested houseplant (you're implying they're indoors).  Step one is to identify the houseplant that is harboring the animals; after that, I don't have much to tell you (I'm not an economic entomologist).

they are both indoor and outdoor, first these were out of my house, then I found these inside too. I don't have plants inside house but I do have flowering plants in my gallary, inside house but outside our living areas. I am not sure if they are really mealybugs, as they don't look much like them and I could not find any plant with these. these are mostly on wall and floor


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Where can I upload non-human Genotype data?
I have genotype data from few chicken population and I want to (need to) upload them somewhere online with free access. I have searched the web but I haven't found any place for non-human genotype data!
Does anyone have an idea where I can upload it, which is publicly available and user friendly?
bests

Does this Website help?

Thanks @Chris I checked the link. As long as I understood all those links are for "new variants discovered" or "data for GWAS study". I just have genotypes.

Isn't here any repository for this animals?

I did not find any site like that. You can upload the file in your university/lab website.

I don't think there is an answer for this question, as such a repository for chicken data does not exist.

@Chris: isn't that a suitable answer then?

@ChrisStronks This is basically is link answer, which obviously doesn't help. Or do I see this wrong?

I don't think that it is necessary to upload to a specialist or targeted repository if none are obvious. For some data types there is an obvious repository such as dbSNP. It does not sound like such exists.
Probably things have changed since the question was posted, but nonetheless I think that this is a useful question to have answered.
There are a variety of data repositories to which you can upload unstructured data that do not require you to host it yourself:

Open Science Foundation: free, non-profit dedicated to ensuring data access and scientific reproducibility.
FigShare: has free accounts, for-profit company.
Dryad: free, non-profit.
Zenodo: non-profit.


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Proinsulin is an 84 residue polypeptide with six cysteines. How many different disulfide combinations are possible?
Generally cysteine residues form disulfide linkages - so how many combinations are possible out of (say) six residues. Also can cysteine form bonds with all the residues?

I suggested some minor changes to the text of the question, but did not want to alter the second sentence : do you mean something like "can all these disulphide links be created"?

The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Unresearched questions may be subject to down-voting and closure.

yes, actually i wanted to ask can all disulfide links be created?

The short answer is that you need to use the binomial coefficient ("n choose k")
$$ \binom{n}{k} = \frac{n!}{k!(n-k)!} = \frac{6!}{2!(6 - 2)!} = 15$$

This is a mathematical problem rather than biological.
see this
the refined question would be this :
we have 6 items and we want to pack them in 3 groups of 2.(We assume that all six cysteines do form a disulfide bond with each other and none of them are ungrouped or left out.Let me know if you have the question about the latter situation.) How many different sorting are possible?
Disclaimer: I am terrible at these types of mathematics . but I believe I have found the right answer.
Method A :
Write all of them!
six items are called A,B,C,D,E,F respectively
Fix A.
AB/CD/EF
AB/CE/DF
AB/CF/DE
AC/BD/EF
AC/BE/DF
AC/BF/DE
AD/BC/EF
AD/BE/CF
AD/BF/CE
AE/BC/DF
AE/BD/CF
AE/DC/BF
AF/BC/DE
AF/BE/DC
AF/BD/CE
THE ANSWER IS 15
Method B:
you could also use C(n,r) function for better understanding but I'm going with this:
we have 6 items. Split them into 3 groups of 2. Group 1 ,group 2 , group 3.
calculate number of different combinations.
group 1 : 6 * 5 /2 = 15
(you can reverse the order of the first 2 objects and the group would still remain the same)
group 2 : 4 * 3 /2 =6
(you can reverse the order of the first 2 objects and the group would still remain the same)
(Two of the items are used in the previous group)
group 3 : 2 * 1 /2 =1
(you can reverse the order of the first 2 objects and the group would still remain the same)
(Four of the items are used in the previous groups)
You have to multiply these numbers . But do not forget that combination between group 1,2,3 does not matter(you can call any of them 1 , any of them 2 ,etc and the result would NOT change. It is just naming.)
3!=6
we have 6 repetitious/same groups counted in each unique combination . Therefore devide the whole amount by 6
15 * 6 * 1 / 6 = 15
About the second question the answer is no. Cysteine form disulfide bonds only with itself as far as I know

If the question is mathematical it is probably off-topic as it bears no relationship to the reality of biology. Even assuming a random chain finding different combinations, rather than the chain folding in a manner governed by the amino acid sequence) the possibility of a second disulphide bond forming after one has formed would depend on their relative location. In fact the protein probably forms first and then oxidation occurs. So the answer is 1.

the nascent protein translocates into the ER then it is oxidized to form S-S bonds. Suppose our protein has 6 cysteines. A biochemical procedure occurs by Ero1 and DPI which oxidizes the sulfurs exactly one after another ( i.e. cys1 is bound to cys2 and cys 3 to cys4 and cys 5 to cys 6) . This intermediate might be thermodynamically-instable . So here comes PDI again to REARRANGE the incorrect disulfide bonds , Literally testing each combination of S-S until it gets the most stable combination/conformation.  So in theory there might be all different combinations of disulfide bonds......

The less stable combinations are later degraded . Here's the references: Molecular Cell Biology Lodish et al 8th ed chapter 13  figure 13-19 . Also take a look at  M. M. Lyles and H. F. Gilbert, 1991, Biochemistry 30:619.


text:
Terrestrial locomotion of bats and pterosaurs
Bats and pterosaurs have skin attached to their forelimbs that aid them in flying and when they are on land, they use all four of their limbs to walk in a quadrupedal posture. Can these organisms be considered as true quadrupeds? Is there a different term used for this type of locomotion?


text:
Length of upstream and downstream of tss important for gene regulation o
I want to find SNPs in the upstream and downstream regions of transcription start sites of some 42 genes implicated in a disease (on which I am working).
Are there any suggestions on what length should be covered both upstream and downstream? Is there a database which can give the transcription factor binding region of both upstream and downstream regions as a batch query? Or a paper to which I can refer for the search length for looking for SNPs?


text:
Classifying Polypeptides (and/or Proteins)
Since polypeptides are a linear chain of twenty amino acids, each having a single letter abbreviation (e.g. Alanine = A). So can a polypeptide be represented as just the sequence (say: ADN for an Alanine, Aspartic acid, Asparagine polypeptide)?
This method of classifying polypeptides would lead to a possible 8000 (20**3) variations just for 3-amino-acid-polypetides (3200000 for 5-amino-acid-polypeptides, etc.) and that there would be many variations; and for longer polypeptides - that is, proteins - there would be even more variations.
Or are only the important polypeptides and proteins named, since not every variation of polypeptides and proteins are found in the body? I would've thought that many proteins (and enzymes, etc.) are incredibly specific and so they could be classified in some methodological way, as opposed to just 'lipase' or 'carbohydrase' which provides no structural information (though it would have a long methodological name).

You can certainly refer to short peptides by their sequence. I don't know of any exact boundaries, but I've seen tripeptides referred to by either their three letter codes (Ala-Asp-Asn) or even the chemical name (alanylaspartylasparagine) although obviously that gets ridiculous pretty quickly.

As the largest known protein, titin also has the longest IUPAC name of
  a protein. The full chemical name of the human canonical form of
  titin, which starts methionyl... and ends ...isoleucine, contains
  189,819 letters and is sometimes stated to be the longest word in the
  English language, or any language. However, lexicographers regard generic names of chemical compounds as verbal formulae rather than English words

For more than around 5 amino acids, just the sequence makes more sense. It would be interesting to analyse scientific paper abstracts to see how many have the sequence as the 'name', but anyway.
When we get to proteins, it would be unhelpful to refer to them by their sequence. They usually have names - enzymes are often named by what they act on (like 'alcohol') and how they act on them (like 'dehydrogenase'). In addition, there are structured names called E.C. numbers - sarcosine dehydrogenase is 1.5.8.2, for example.
As you point out, there are a very large number of sequences that do not correspond to proteins found in an organism. To name one of these is tricky, and if someone synthesises one then they would have to come up with some naming scheme to refer to it.

Not to mention that referring to a full protein by sequence alone starts to become redundant because the primary structure becomes slightly less interesting when compared with 2/3/4-ary structure. While a peptide is still short (say less than 10 AA) it probably doesn't have much structure, so its sequence becomes responsible for its chemical activity primarily, and referring to it like that still makes sense.

Thank you, that all makes sense, but if single letters for the abbreviations of amino acids are only used not name polypeptides of length <5 amino acids, then what's the point in abbreviation it. Surely a 'ALRDNNA' polypeptide would have similar chemical properties (and/or functions) to a 'ALRDNL' polypeptide. If that's not what would categorise families of polypeptides, then how else?

I think you may need to clarify what you mean by polypeptide 'family'. The only polypeptides that are generally assigned names beyond just their sequence are ones which demonstrate particular functions or where someone has contracted the name for convenience. For example, I did some work on poly-glutamine and polyproline. They were stretches of 10,20,30,40,50 amino acids, but we're all proline or glutamine. It wouldn't make sense to refer to them as PPPPPPPPPPPPPPPPPPP when polyP(20) is easier.


text:
Does protein structure depend on phylogeny?
Proteins have two basic secondary structure forms - beta strand and alpha helix. Do these depend on the organism or do the two forms exist for every protein?
For tertiary and quaternary structure: do such motifs depend on the position or does each organism have a specific form of protein structure?

Welcome to Biology SE. However I am afraid your question is too general and at a very basic level. You can learn about proteins by carefully reading information available on the internet, for example sections such as this in Berg et al. or the entry in Wikipedia. If, after studying the examples there you are still confused, come back with a well-formed question.

The OP asks what is the relation between levels of protein folding and phylogeny. It's a good question, I think it could be rephrased with the aid of a native speaker.

I agree with @David - this question is exceedingly basic and should be understandable by reading textbooks, websites, etc - it is not a very well-formed question.

@Rodrigo Although I tend to agree with David on this, and I think you re being generous in assuming it's about folding and phylogeny, it is possible the question is good.

@Muna Ar : What do you mean by 'depend on the position'?

@gilleain I mean in the those structural motifs may vary when we change the position we are in the protein for example , the beginng of the chain or at the end ...

@MunaAr I see  - the position along the chain. I think that the answer is : no, there is no strong dependence of secondary structure on chain position.

@gilleain so if a protein folds into a tertiary structure having a zinc finger motif  for exemple , that would be all along the chain right  ?Sorry I'm newbie in the domain

@MunaAr I assume so - but I haven't actually checked. That could actually be a good question just by itself : "Are there any motifs whose frequency depends on position along the chain?" or something like that.

Beta sheets and alpha helix are secondary structures that are simply very common to proteins. Their formation depends on the Amino acids that make up particular stretch in the primary sequence. For example alanines in a row will naturally tend to twist up into a alpha helix in water (medium matters). There are no hard and set rules to determine Tert. Structure or quart (aside from modeling but you have to validate in the end so its not entire end case)

So the tertiary and the quarternary  depend on the protein , it could have a tertiary or quart as it could not right ?

Tert depends on primary sequence and environnment. Quart depends on some level of symmetry in tert structure that allows for optimal contact between subunits


text:
Are there proteins with multiple motifs?
Does each protein adopt a single specific structural motif (zinc finger for example) or are there any proteins with multiple motifs along the chain?

Your question is very unclear. Please [edit] your post to add context and explain exactly what you're asking.

@MattDMo I think some of the confusion is my fault. I suggested some of the wording, here : http://biology.stackexchange.com/questions/49168/does-protein-structure-depend-on-phylogeny but didn't quite get what the real question was. I'll make an edit, and Muna Ar can revert if it's not right

You are right @gilleain still waiting for answers though :D

Most large proteins contain multiple motifs; if you search online for pictures of protein structures, this should be immediately evident. Here's an example from something I was working on the other day: the WD40 repeat motif. It appears in many proteins, but those proteins are certainly much more than a bunch of WD40 units. If you investigate some of the proteins listed at the bottom of that Wikipedia page, you should be able to confirm that they are complex and made of many different sorts of domains, shapes, and parts.
You also mention zinc fingers; those are a DNA-binding motif that show up in many, many different DNA-binding proteins. Those different DNA-binding proteins have many different functions, and their specificity is handled by a vast array of different sorts of motifs and domains that sit on top of/outside of the zinc finger itself. The Wikipedia article on zinc fingers shows many different structures in which zinc fingers can be embedded, and even those structures are only small parts of the actual functional proteins that perform work in a cell.


text:
How do environmental conditions differ between nitrogen fixing bacteria and denitrification bacteria?
I am currently experimenting with aquaponics and need to better understand nitrifying and denitrifying bacteria.
From my research it seems that both varieties are anaerobic. From an engineering perspective, how would I control the environment such that nitrifying bacteria would dominate a water medium or vice versa? I'm thinking some combination of the following should provide some level of control; pH, temperature, surface area, tds, nitrogen partial pressure, concentrations of fixed nitrogen and types, etc.


text:
Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes
I'm in BIO 203 (for reference to my skill level), and I noticed the textbook makes a whole section out of transcriptional activator proteins, their function and applications in eukaryotes, but in prokaryotes the term "activator protein" is used only once when mentioning the lac operon.
Are they the same type of activator proteins? Do they employ the same mechanisms?

In general transcription activators are transcription factors. These are very different in eukaryotes although some families share similar domains (e.g. two component signalization). I recommend you read through these two chapters to get a more complete overview on the differences.
https://www.ncbi.nlm.nih.gov/books/NBK21683/
https://www.ncbi.nlm.nih.gov/books/NBK21572/

As it stands your answer does not explain how these are different, and the two separate chapters you cite do not make such a comparison. For your answer to be useful you need to explain brielfy in what way they are different.