text:
Species Distribution Modeling: Mammal river species
When working with mammal river species, what parameters would you use to study them  (I have max and min temperature, average rain, slope and obstacles in the river)
Something like type of riparian forest?
Is there any good example of species distribution modelling of mammal river species?
Thanks, Héctor.

I think it will depend on what aspect of the species you are looking at. For example, if you want to model distribution to study predator-prey interaction, you might want to get information related to predator presence, geographical aspects (e.g. for helping camouflage) etc. In contrast if you want to study distribution for the purpose of migratory behavior, you can consider reproductive age, time and other ecological aspects etc. Their weight will depend of your goal.

I just tried "species distribution model river otter" (picking the first river-dwelling mammal I could think of) on Google Scholar and got quite a few hits ...

Mainly the aim is to know which is the  most negative parameter that is affecting it. Problem is that it is really associated to the river,  much more than the otter, depending its diet on athropods... (No data of arthropods), ¿Anything abiotic that could affect?(snow didn't affect...)

can you tell us what species you're interested in? voles? manatees?  river dolphins ... ????

Yes,  it's Galemys Pyrenaicus ( Pyrenean desman)  related to  moles


text:
What are the pros & cons of site-directed mutagenesis? What are the alternatives?
For a lab course we have been assigned to "remove a stop codon, using mutagenesis, that is in the middle of a gene in order for the full gene to be expressed. This will then fluoresce."
To do this we are considering site directed mutagenesis, which can replace the stop codon, however is this a good method? Are there any alternatives to SDM using Quikchange that are better? What are the pros and cons of the SDM we are thinking of performing? To see if we succeeded we will then use DNA sequencing and gel electrophoresis.
Our overall plan looks like this:

Gathering plasmids from E. coli
Gel electrophoresis of the plasmid DNA
Perform the mutagenesis using Quikchange
Transformation by heat-shock
PCR
Use a lac promoter to produce the gene protein

One issue I could think of was, how do we make sure the primers carrying the mutation don't anneal to each other due to their complementarity?
Is overlap-extension a good alternative? Are there any advantages to using transposon-based or point-directed mutagenesis?
Thank you!

If it were my lab, we'd just order a synthetic gene…

Depends... is this about the process or the result?

SDM will be the perfect tool for this mission, unless the plasmid in question is very large (20+ kb).
When you have performed the SDM, digest the products with dpnI to remove the original plasmids, transform e.coli and use a selective media matching your plasmid. Only bacteria with the plasmid will then be able to survive and form colonies, pick several colonies and perform a miniprep for each and sequence the area of interest. You can use the rest of the miniprep with the correct plasmid for transformation and expression. So skip step 5.

Although, as you say SDM is the most suitable tool, are the other forms of mutagenesis: transposon-based and point directed also applicable for this lab if we wanted to? And can you think of any cons with using SDM in this case?

The 'Quickchange' method is probably what you want. If you are worried about self complementary (which you shouldn't be too much) you can actually stagger the primers so they are not fully complementary. only the 10bp need to overlap where the mutation is. I included a small diagram below where the X marks the base you want to change

One alternative, which I use more than the SDM is by using TypeIIS restriction enzymes. This way you can mutate as many bases as you want in one go!
See this article

source: Stack Exchange

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

sort: votes


text:
Restriction enzyme type II
Why can't a type II restriction enzyme cut a nucleic acid with the following base composition:

A: 28% C: 15% G: 35% T: 22%

I don't really get your question... First, a restriction enzyme cut at recognition site, I never heard about base content distribution (can you link a source?) Second, in any DNA sequence the percentage of A is equal to the percentage of T and the same is true for C and G. What king of DNA sequence can have 28%T and 22%T? So it must be RNA you are talking about. But then T is not correct, it should be U. Please add more details to your question.

Welcome to Biology.SE. To me, this seems like a homework question (those are off-topic here, see link) so I put a flag to it. Please show some effort to answering the question yourself, if you want to avoid the question being deleted/closed. What do you know about the enzyme? What dies the base composition tell you about the sequence in question? Basically, let us know that you are trying. Thanks!

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


text:
Where can I find a list of transcription factors that are used in somatic embryogenesis?
Where can I find a list of TFs that are used in somatic embryogenesis or zygotic embryogenesis?


text:
Why is lower case used in front of a capitalized acronym (e.g. rDNA)?
Examples: rDNA, mRNA, tRNA.
Why do we use small case for "r" in "rDNA", etc? Any particular reason?

I’m voting to close this question because it is about the history or philosophy of coining abbreviations/acronyms rather than a problem in biology.

It's just a stylistic approach because "DNA" or "RNA" is an abbreviation by itself that has become a whole noun. Those terms clearly separate the modifier from the overall DNA/RNA. It makes it easier to read. Terms like DNA and RNA are almost always known just by those acronyms, whereas something like mRNA is known both as "messenger RNA" and "'m' RNA" but almost never as "messenger ribonucleic acid."

These letters are used to indicate the different types of RNA and DNA. Especially RNA has lots of (functionally) different variants, so this helps discering between them.
Your exmaples in particular:
 - mRNA is short for messenger RNA
 - tRNA is short for transfer RNA
 - rDNA could be ribosomal or recombinant DNA (writing rDNA is very uncommon, mostly ssDNA or dsDNA are used)

"For DNA this way of writing is very uncommon." Nope. I often read ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA) or mtDNA (mitochondrial DNA) etc..

@adjan  Ah true I didn't think about that, I edited the answer. rDNA is still uncommon though ^^

I don't agree with that minimized claim, either! I see rDNA used all the time in scientific papers, textbooks, and even informal literature. While it's true that the abbreviation is problematic because of the ambiguity, it is usually pretty clear from context whether they mean "ribosomal" or "recombinant".

The poster didn't ask what the abbreviations meant, he asked why lower case.

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


text:
Does translation have a way of preventing mismatching between mRNA codons and tRNA anti-codons?
What happens in translation if a tRNA with an inappropriate (non-cognate) anti-codon binds to the A-site of the ribosome carrying mRNA?
For example, what would happen if an ile tRNA with the anti-codon 3'-UAG-5' occupied the A-site when juxtaposed to a met codon: 5'-AUG-3'? This would seem possible to some extent as two of the three  bases pair correctly.
Does something prevent this occuring or are incorrect amino acids removed or the protein degraded?

Welcome to Biology.SE! Although it is an interesting question, its answer can be found quite easily. What research have you done before asking it here?

Its really unclear what you are asking, only three tRNA are present in the ribosome at any one time. The wiki for translation may help you. https://en.wikipedia.org/wiki/Translation_(biology)

John Btw I have edited my question  but still i would like to ask whether right tRNA interacting with the right codon in the mRNA is just permutation stuff.Like what would happen if a tRNA with anticodon AAA occupies the site of the codon with its nucleotides say,GGG.

I have edited this question quite extensively so that it addresses a non-trivial point which I don't believe is off-topic. It may be more sophisticated than the OP intended, but it represents a means of rescuing the question, as one is asked to do.

After the edits I think it's a valuable question +1. Thanks @David for your efforts. If folks disagree with the re-opening feel free to start another round of closure or flag the question.

Summary
Non-cognate codon–anticodon interactions on the ribosome do occur, but do not normally result in misincorporation of amino acids into protein. This is because aminoacyl-tRNA binds the ribosomal A-site in an EF-1A–aminoacyl-tRNA–GTP complex, and hydrolysis of GTP must occur before the peptide bond can form. The non-cognate interaction appears to be unable to trigger this hydrolysis and dissociates from the ribosome.
More Detailed Explanation
The hydrogen bonding between the bases of the mRNA codon and the tRNA anticodon is the basis of the specificity of decoding. It is easy to see that a codon such as 5’-GGG-3’ would form nine hydrogen bonds with an anticodon 3’-CCC-5’, but none with an anticodon 3’-AAA-5’. However, as the question makes clear, the situation is not quite so simple if two of the codon bases form the correct hydrogen bonds. A more telling example is shown below (here with the same tRNA, but different codons), where the difference between a his-tRNA interacting with a His codon and a Gln codon is only the strength of a GU ‘wobble’ base pair, often reckoned to be that of a single hydrogen bond. Certainly there is a difference in energy of the two interactions, but not enough to prevent a significant extent of miscoding.

The answer to this conundrum turned out to be the solution to another long-standing puzzle — that of why GTP is required in the binding of aminoacyl-tRNA to the A-site of the ribosome, which is directed by EF-1A (originally known in bacteria as EF-Tu). The GTP is not required for peptide-bond formation — the energy for that is supplied by the ATP in the tRNA synthetase reaction. It transpires that the role of GTP is in maintaining the fidelity of translation. The hydrolysis of GTP only occurs when the correct tRNA is bound — presumably the conformation of the incorrect interaction does not allow this to occur — so the non-cognate tRNA will eventually dissociate from the ribosome.

It is interesting that the other elongation factor, EF-2 (EF-G), involved in translocation of the peptidyl-tRNA, binds to the same site on the ribosome in a complex with GTP, and that translocation and removal of the deacylated tRNA can only occur after hydrolysis of GTP. It is as if the requirement for GTP hydrolysis ensures that the system is in the correct conformation before the next step of the complex process proceeds.
References
Berg et al. provides a general account, freely available online. A more detailed structural consideration can be found in a review by Nilsson and Nissen, which requires library access.

Thank you so much for taking your time to answer my question!!!


text:
What is the effect of flash pasteurisation on Maillard reactions or production of AGEs in milk?
Does flash UHTP homogenision and pasteurisation change significantly the extent of maillard reaction in milk compared with traditional batch pasteurisation? If this is significant does this effect the nutritional value of the milk?
Initial research; i have found via my wikisearch  http://www.food-info.net/uk/colour/maillard.htm and on pub med an abstract: J Nutr Sci Vitaminol (Tokyo). 1990;36 Suppl 1:S57-69.Influence of processing on protein quality.
Mauron J.
Source University of Fribourg, Switzerland.  i dont have full access to pubmed papers.
background to question.I have developed a sensitivity or intolerance to UHT and typical homogenised and pasteurised milk in the supermarket and any products with milk solids. I can consume non homogenised batch pasteurised milk from the specialty organic store, thus the curious chemist in me was alert. Either my body doesn't produce sufficient of the necessary enzymes ,ruled out by the latter scenario,  or the composition of the milk has changed in modern high throughput pasteurisation.
In Flash pasturisation we have P.T and V all being varied to increase proximity and likelyhood of collisions of reactants as well as temporary emulsification.
There is another term AGE see http://agefoundation.com

I think this is better off on [biology.se]

This is only an partial answer, as I do not have the time now to look for other references.
In the chapter about milk, Harold McGee's beautiful book "On Food & Cooking" says (pg. 21 of the 2004 edition, bold is mine):

Flavors from cooking
  Low-temperature pasteurization slightly modifies milk flavor by driving off some of the more delicate aromas, but stabilizes it by inactivating enzymes and bacteria, and adds slightly sulfury and green-leaf notes (dimethyl sulfide, hexanal). High-temperature pasteurization or brief cooking - heating milk above 170°F/76°C - generates traces of many flavorful substances, including those characteristic of vanilla, almonds and cultured butter, as well as hydrogen sulfide. Prolonged boiling encourages browning or Maillard reactions between lactose and milk proteins, and generates molecules that combine to give the flavor of butterscotch.

He continues by speaking about the different types of pasteurization, and says (pg.22-23)

The third method of pasteurizing milk is the ultra-high temperature (UHT) method which involves heating milk at 265-300°F/130-150°C either instantaneously or for 1 to 3 seconds, and produces milk that, if packaged under strictly sterile conditions can be stored for months without refrigeration. The longer UHT treatment imparts a cooked flavor and slightly brown color to milk; cream contains less lactose and protein, so its color and flavor are less affected.
  Sterilized milk has been heated at 230-250°F/110-121°C for 8 to 30 minutes; it is even darker and stronger in flavor, and keeps indefinitely at room temperature.

So, it appears as if indeed there may be some Maillard reaction going on in UHT, although it is probably minor (otherwise the milk would be much darker in color, as it is the case for sterilized milk).
The book also speaks about homogenization, but it does not mention anything specific about Maillard reaction there (homogenization is not carried on at high temperatures, so it does makes sense not to have it).
To answer your question:

Does this effect the nutritional value of the milk?

Well, according to this presentation (but, be warned, it does not cite any reference!) it seems that it does, although I don't think the Maillard reaction is specially involved.
http://www.slideshare.net/Aslal_saja/effect-of-uht-treatment
Specifically it says that the irreversible changes that occur are:

Whey protein denaturation (35 to 100% of denaturation of $\beta$-lactoglobulin)
Slight increase in the size of casein micelles
Whey protein-casein micelle interaction
Maillard reactions
Fat globule composition changes (although no changes in nutritional value of milk fat)
Vitamin content changes (20-30% loss in vitamin B1 and B12. Markedly reduced content in vitamin C and folic acid if high level of oxygen were present during the treatment, no changes in vitamins A, D, E and beta-carotene).

It also says that:

Biological value and net protein utilization of UHT milk were lower for stored milk than directly used milk. Lysine loss during UHT is high but not significant to affect milk nutritional values.

I don't know whether the fact that you have problems when drinking UHT milk has anything to do with Maillard reaction or any of the other modifications brought by UHT treatment, and I will not venture in there, as I am not an MD and prefer not to give any sort of medical advice.

Thanks I have my digestion problems are sort by minimizing processed dairy intake and pressed flavours like HVP.

Try:
Food: The Chemistry of its Components (RSC Paperbacks) [Paperback]
Tom P. Coultate (Author)  and What Einstien told his Cook by R.L.Wolke


text:
Could sex alone drive complexity?
Imagine that complexity is measured by a positive number $f_n$.
If one has no prior knowledge about the positive number $f_n$ then from Bayesian theory one can assign $\log f_n$ an "improper" uniform prior over the range $-\infty$ to $\infty$.
A random mutation might increase or decrease the complexity of the offspring $f_{n+1}$. If we assume the offspring's complexity is likely to be close to the parent then we could simply model the random change in complexity by:
$$log f_{n+1} = log f_n + \Delta\ \ \ \ \  \hbox{with probability 0.5}$$
and
$$log f_{n+1} = log f_n - \Delta\ \ \ \ \  \hbox{with probability 0.5}$$
where $\Delta$ is some small number.
Such a random evolution will lead to the log of the complexity performing a random walk.
But now add sex.
Assume the complexity of a sexual organism is the average of the complexities of its parents.
$$f_{child} = \frac{f_{male} + f_{female}}{2}.$$
If one evolves the simple model now one finds that the complexity of the population grows exponentially.
Is this idea interesting or not? :)

What is complexity? I think you need to very explicitly define what this concept is, with regards to your model.

True - I could have modeled simplicity instead but that seemed a bit perverse!

Is it interesting?  Perhaps, but "complexity" is a vague notion.  If you want to simplify and just say "variation" then sure, sex increases variation.  But so does that random mutation you brought in.  Really, all you need for increased variability is some difference between generations and genetic Drift will take care of the rest.  Mutation is enough, which is clear from asexual organisms.  Sexual reproduction tends to increase diversity, but that has nothing to do with "complexity."  The environment, in particular interaction with other organisms, drives complexity more than anything.

A concrete theoretical version of my model could be a population of random computer programs or Turing machines. I would define the complexity of a computer program as its run time not the size of its code.
Mutating programs will have varying run times whose logs just perform a random walk.
But if you allow pairs of those programs to occasionally combine in such a way that they generate a child program with a run time that is the average of their own then the run times of the population will grow.


text:
Are original x-ray diffraction data available
Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these data may be downloaded?

In many cases they are available.  One of the establishing principles of the Protein Data Bank (PDB) was to store not only the models (atomic positions and identities) of macromolecules and proteins, but also the originating X-ray data, more recently in structure factors.
If the question is 'why are they giving only the structure factors and not the original data they took' - such a task would require a lot of curation effort for very little scientific benefit.   Scaling the individual sets of data from the detector used to be a bear of a task.  The original myoglobin structure would entail scanned films in an ancient format from the 50s.  Nobody would be able to use that now without hacking the image format, if it wasn't on paper tape or cards.  In fact in that case the structure factors are not available.  Scaling many or several data collections together was often done with custom tweaks into the 70s and then in the 90s data collection became more routine, but several generations of x-ray detectors became popular and then faded from the market.  Each had its own eccentricities and requirements for combining data sets from multiple reads.
The purpose of having structure factors available is to allow anyone to reconstruct the electron density and evaluate the interpretive act which is tracing a peptide through electron density.  Since that format is mainly independent of the detector and has been fairly consistent over the years, it delivers a significant amount of scientific bang for the buck.
If you want raw image data or detector-proprietary data before multiple data sets from different crystals before they were combined you will have to contact the authors, who would probably have to sift through a sea of DVDs to get to it.  In older cases it might be tapes.
So as far as Structure factors, which are essentially the square root value of the combined and scaled Intensity data, they are available and a part of every submission to the pdb:
Look on any X-ray Structure Page at RCSB.  For example this one.
There is a box called "Experimental Details" and you can download the structure factors there by clicking a link.
If you are looking for more than one at a time, there are bulk downloads available through their download page.  Check the "Structure Factors" box.  Raw intensity data should be available if you look around for it as well.
Further Suggestion:  I was thinking that if you look at the scaling software that comes with the X-ray detectors you might find some tutorials with unscaled raw data.  I found one example at Marresearch - hen egg white lysozyme.

let me misuse this comment to bring your attention to crystallography.SE proposal. We don't know if it will gather enough people to make it worth its own site, although such site could be helpful. Now some relevant questions are asked on biology, chemistry, physics, earth science and math, but most of people in this field prefer dedicated mailing lists or forums such as ccp4bb, rietveld, xrayforum.

sounds good @marcin - i'll do what i can to support it!  it would be great to have it all in once place.


text:
By what mechanism does an obstructed bile duct cause excess fat in the stool?
By what mechanism does an obstructed bile duct (for example gallstones) cause steatorrhoea (excess fat in the stool)?

The function of bile produced by the liver and concentrated in the gall bladder is to aid in fat digestion.  Bile acts as an emulsifier to allow the fat to be packaged into small droplets, micelles.  The breakdown of fats into small micelles greatly increases the surface area for lipases produced by the pancreas have to act on.  These are then absorbed across the intestinal wall.

Bile breaking down large fats into small micelles
If this first step of bile production and transport is lacking (due to liver dysfunction or obstruction anywhere in the biliary tree), the fats are not packaged into micelles and are consequently very hard to digest.  They pass through the entire alimentary canal virtually undigested causing steatorrhoea, fatty, bulky and foul smelling stool.

The Biliary Tree

Gallstones 'block' the plumbing system (i.e. the biliary tree) that drains bile produced in the liver from flowing into the duodenum through the ampulla of Vater. Since bile is a dietary detergent for fats (cholesterol, triglycerides, free fatty acids), the blockage of bile impairs fat absorption in the small intestine and the fat passes into the large intestine and then into the stool. There is always a small amount of fat that passes into the feces (typically very low though), but if bile is not present to aid fat absorption then you get "fatty stool" aka steatorrhea.

Thanks also here for your answer. This seems like common reasoning, but some references of, e.g., supporting websites are still helpful. +1. I added one web link as an example. You use plenty of jargon, which is OK, but linking some terms may greatly improve readability.

AliceD - what 'grade level' are you supposed to answer on? Do you personalize that to the language being used in the question? Thanks for your advice!

Now that is a truly great question. We have a meta site http://meta.biology.stackexchange.com/ and I really encourage you to post this (I can do it for you if you wish). In general, personally, I scan the question and if the level of OP is obviously rock bottom I adapt my language accordingly. In general, this site is targeted for MSc students and grad students. But younger folks tend to be attracted for sure, as well as older ones like me :) Btw - this post is really accessible.


text:
What is the cannabinoid autoreceptor?
"Is there a cannabinoid autoreceptor? And if so what is the cannabinoid autoreceptor?"
(i.e. is the cannabinoid autoreceptor CB1, CB2 or is it one of the G protein coupled receptors, GPR18, GPR55 or GPR119?)
Where:

An autoreceptor is a receptor located presynaptically that sends back negative feedback that inhibits the synthesis of the neurotransmitter to which the autoreceptor belongs and this negative feedback also inhibits the release of the neurotransmitter from storage vesicles into the synaptic cleft.
The CB1 and CB2 receptors are respectively called the first and second cannabinoid receptors and are a pair of G protein coupled receptors.
GPR18, GPR55 and GPR119 are G protein coupled receptors that are also activated by some lipid messengers including a few of the endocannabinoids and their related compounds.

CB1 and CB2 are indeed particular genes which are present in neurons, but also liver and other tissues.  The HGNC website is a good resource for questions like this - HGNC is the international organization that tries to unify and track gene names.
The official gene names are CNR1 and CNR2 respectively.  Gene names are a bit of a mess, since many genes have been found by different experiments and so have many names.
CNR1 has other aliases, I see:
CANN6, CB-R, CB1, CB1A, and CB1K5.
CNR2 has only the one alias: CB2.
I also searched the HGNC website for those alternate gene symbols and they appear to be different genes, although CB1 and CB2 are GPCR class receptors, humans have hundreds of these genes.  Most cell scientists would not be surprised if cannabinols bound other receptors - the fact is probably only that CB1 and CB2 bind strongest and were found first.  Often weak binding is important to specific pharma/neuro responses.
That is to say there shouldn't be any single Cannabinoid receptor in the animal repetoire.  CB1 and CB2 almost certainly have a primary function other than cannibinol binding.  Primates evolved in the old world and cannabis is thought to have originated in the Himalayan regions.  From an evolutionary standpoint, the activity of cannabinoids is as much coincidence as anything, so you would expect that a single receptor gene is unlikely.


text:
What makes DNA helical?
Why isn't DNA like RNA; why isn't RNA like DNA, that is, helical? Why are RNA chains straight?

The helix shape of DNA molecule is a consequence of its secondary structure. This refers to the bases contained in the molecule which pair, thus determining tertiary structure [1].
Basepairing also occurs in RNA, so it can form a double helix. In fact, RNA is composed of short helices packed together [2]. Base pairs maintain DNA's helical structure no matter the nucleotide sequence [3].
A nucleic acid strand is composed of nucleotides joined together by covalent bonds between the sugar of one nucleotide and the phosphate of the next. Adenine pairs with thymine and cytosine pairs with guanine by hydrogen bonds and form the double-stranded structure [3]. Because covalent bonds are stronger than hydrogen bonds, the double helical structure of DNA is easily broken by heat [4], but the nucleotides remain bonded together.
Here is the tRNA molecule (you can see it has short helices):
"TRNA-Phe yeast 1ehz" by Yikrazuul - Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons.
Here is the DNA structure:
(source: wikimedia.org)"ADN animation" by brian0918™ - Own work. Licensed under Public domain via Wikimedia Commons.

References:

Wikipedia contributors, "Nucleic acid double helix," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Nucleic_acid_double_helix&oldid=609435163 (accessed June 26, 2014).

Wikipedia contributors, "RNA," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=RNA&oldid=612056511 (accessed June 26, 2014).

Wikipedia contributors, "DNA," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=DNA&oldid=611891356 (accessed June 26, 2014).

Wikipedia contributors, "Nucleic acid thermodynamics," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Nucleic_acid_thermodynamics&oldid=606379256 (accessed June 26, 2014).

RNA (single or double stranded) actually can and does form a helix in the absence of certain complex 3D structures. The RNA helix is typically A-form, as opposed to B-form for typical DNA. The A-form helix is right-handed like the B-form but is more compact (2.6 Å rise versus 3.4 Å) and wider (26 Å diameter vs 20 Å). The differing helices arise from the 2'-OH present in RNA which sterically hinders the formation of a B-form helix (by constricting the ribose to C-3' endo pucker).

[From Wikipedia. Double stranded DNA helices. A-form is on the left, B-form in the middle and Z-form on the right. There are other forms not illustrated here.]

[From Wikipedia. A hairpin loop (the result of intrastrand base pairing in a single RNA molecule) that has adopted an A-form helix.]

[Just emphasizing that a single strand nucleic acid, even without secondary structure, also forms helices.]

The helices of both DNA and RNA form in aqueous solution because of the hydrophobic and aromatic (which also implies planar) nature of the bases themselves. By forming a helix, the bases within one strand come closer together which is thermodynamically more favourable because of stacking interactions between the conjugated ring systems as well as the exclusion of water from their hydrophobic surfaces (which thus increases entropy).


text:
Can someone who is color blind recover color vision by surgical means?
I am currently studying color blindness, and there is no medicine that can help it. Is it possible nonetheless for someone who is color blind to have their eyes restored to normal color vision by replacing the patient's eyes with donor eyes? Please explain any answer. Thanks!

No this is not currently possible as eye replacement surgery is not possible.
Colour blindness is either congenital genetic, such as your X linked forms, or due to a degenerative condition such as retinitis pigmentosa. It can also be acquired through retinal damage or brain injury such as stroke effecting specific areas of the visual cortex.
One of the major problems in restoring colour vision would be that the brain itself may not have the required structure to interpret the signals. The visual cortex is 'patterned' as we develop beginning inside the womb and continuing as a baby. During this process neurological connections in the visual cortex are stimulated so that we develop the necessary networks to interpret the signals from our eyes. If we lack the input of our eyes the brain conducts something called neural pruning where the unused neural connections are destroyed never to be regrown. Therefore if you lack visual stimulus for colour you prune these connections. If we were to somehow replace this colour stimulus later our brains would not be able to interpret it. In a somewhat similar circumstance to this it has been found with individuals who are born with congenital cataracts. If they have their cataracts fixed later in life having spent their childhood blind, despite being able to 'see' they cannot interpret the images they receive.
In individuals who loose there colour due to degenration of the retina, if we were able to repair the retina, through stem cell or transplant therapy then perhaps colour vision would return.
An individual who lost colour vision due to brain injury cannot have their colour vision returned as we cannot repair such injuries.

I agree with this answer but I'm not so sure people whose vision was restored would not be able to use the some of the information. Such a hypothetical treatment would be very similar to deaf people getting cochlear implants. The chance of success with these decreases with every increase in year but it's not zero at any age: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518393/

@mimat I guess it depends a lot on the time in which sensory loss happened. If it happened during early development, neural pruning would be more advanced than if it happened during adulthood.

Most forms of color blindness are caused by defects in the eyes, not the brain.  Usually the receptors in they eye that are supposed to be sensitive to one fraction of the visible spectrum don't work properly.  So yes, replacing the whole eye (I don't know if that's possible now) would in theory fix those forms of color blindness, thought it's likely that the brain would be confused getting a new kind of signal that it had never received before.


text:
What is the normal duration of human sexual intercourse?
Wikipedia is saying:

Men's typical ejaculatory latency is approximately 4–8 minutes

How the researchers measured this? How did they know if the test subjects weren't suffering from premature ejaculation?
And is this measured from the start of erection or from the start of penetration?

First, "premature ejaculation" is a matter of definition. Here is an authoritative source. From the American Urological Association's news site, a 2008 notice:
'The ISSM [Int'l Soc. for Sexual Med.] has defined premature ejaculation as “a male sexual dysfunction characterized by ejaculation which always or nearly always occurs prior to or within about one minute of vaginal penetration; and, inability to delay ejaculation on all or nearly all vaginal penetrations; and, negative personal consequences, such as distress, bother, frustration and/or the avoidance of sexual intimacy.”'
The main author of the ISSM paper was Sharlip. Sharlip ID, Hellstrom WJG, Broderick GA: The ISSM definition of premature ejaculation: a contemporary, evidence-based definition. J Urol, suppl., 2008; 179: 340, abstract 988.
If this is the threshold for PE then it is not a stretch to say that almost anything else is within normal limits. If "typical latency is 4-8 minutes" then 1.5 minutes would be near the low extreme of normal.
I think the issue of stress is at least as important as duration. If something isn't bothersome it never becomes a medical issue.
A nice study involving 491 men is reviewed here. The mean IELT (intravaginal ejaculatory latency time) is 5.4 minutes. As you can see from the graph on the site, most of the results are contained in the first few minutes with a tail of longer times to the right.
The original source for that information is MC Waldinger et al. A multinational population survey on intravaginal ejaculation latency time. Journal of Sexual Medicine 2005 2: 492-497. This also addresses your question about the timing of measurement--it's post-entry.
An expert in this area could update my information but it's a recent average so I don't think things have changed much.


text:
Diffusion of Hypotonic solution into solution with glucose and starch
Cell walls are selectively permeable to ions and organic molecules. Sometimes the selectivity is passive and a reflection of the physical laws governing diffusion. We can do simple experiments that strengthen intuition about transport across biological membranes. The following homework question concerns a situation which tests understanding of the basic ideas of osmosis and diffusion generally.

A bag made of a flexible semipermeable membrane is filled with a 10% glucose and 5% starch solution. This bag is permeable to water and glucose but NOT to starch. The bag is suspended in a a beaker containing a 10% glucose solution. In 30 minutes the bag can be expected to

(A) swell
(B) shrink slightly
(C) collapse entirely
(D) become impermeable to glucose
(E) remain the same

Since the bag is impermeable to starch, I know that the solution in the bag isn't going to diffuse outside so it won't shrink, but would water from outside flood into the bag to try to dilute the starch concentration to the point that it's isotonic? Or am I not understanding some fundamental principle of diffusion?

The question is clever but I think you are right. It's the osmotic concentration that drives the movement. The 10% glucose has no net effect. The added starch means the osmotic conc. in the bag is higher and so water from the outside would enter the bag.

@daniel Note that starch will not form a true solution and cannot contribute to osmotic pressure. Colloidal dynamics are a little more complicated.

@WYSIWYG: I'm confident colloidal dynamics were not what the question contemplated, so if you are correct the question was badly written.

yes.. I understand that @daniel but if not looked at as a homework question, there are some interesting aspects to it.

This question appears to be off-topic because it doesn't have fit with the topics listed in the help center. Great question, though. Maybe better suited to Physics or Chemistry?

@jmusser: Every basic 1-year biology course with lab covers osmosis. There are currently 14 questions dealing directly or indirectly with osmosis on this site. The help center says questions have to be about biology, which this is. A basic grasp of osmosis is crucial to understanding membranes in a biological context.

Link to Meta discussion

The answer by @Allan Boyd is correct and well stated, you should accept it.

The bag will swell.
Diffusion results in molecules moving down their concentration gradient.
In the set-up described only glucose and water are able to diffuse. Glucose is at the same concentration inside and out so there will be no changes in glucose concentration. Water will move into the bag because it is effectively at a lower concentration (more correctly  - chemical potential) inside due to the presence of the starch. As water moves into the bag, increasing the volume, glucose will also move so that the glucose concentration remains equal on both sides. Thus there will be net movement of water and glucose into the bag.
@WYSIWYG has raised the spectre of colloids in the comments. I don't understand colloids so cannot comment, but I think that in the context of problems like this we are usually dealing with "soluble" starch. Here is an example of a calculation in which starch is treated as an osmolyte.

It should depend on the chemical nature of the suspended macromolecule (in this case starch and it will form a colloidal mixture). If the macromolecule is inert then it will just reduce the effective volume inside the bag.

@WYSIWYG are you saying that my answer is incorrect and the correct answer is E?

I think A) swelling is right answer. The water is at lower concentration in the bag than outside the bag so it will diffuse passively into the bag. Glucose concentration drops in the bag, but at the same time, glucose is diffused passively from outside into the bag so keeping the potential stable between glucose. Water will mostly diffuse, and some water.

@AlanBoyd.. I am not sure.. that is why I commented. Considering that starch has polar groups it can interact with water and may reduce the bulk water - in that case your answer will hold correct. I cannot conclusively say if it can give rise to oncotic pressure. I am not an expert in this area but this is what I understand. If we are really interested in that aspect we can migrate this question (with appropriate edits) to ChemistrySE/PhysicsSE

glucose will equilibriate.. that's what Alan Boyd said in his answer

@daniel can you explain what 'force' would prevent glucose from diffusing to equilibrium (= same concentration in both compartments)?

But, by definition, if the glucose concentration is higher on the outside then the rate of movement inwards will be greater than the rate of movement outwards. In my view the presence of the non-diffusible solute inside the bag will cause a net movement of water into the bag until this is exactly counteracted by the pressure created. The glucose is simply a passive observer and will equilibrate (equal concentration inside and outside). As I say, this is my view, and I am happy for someone to explain why this is incorrect.

DIY Diffusion Experiment
This procedure was done to see what happens qualitatively when semipermeable (dialysis) tubing containing a solution of  glucose and protein is immersed in a solution of glucose alone. Given that water would diffuse into the bag, the question to be answered was whether there would be an equilibrium increase of sugar concentration outside the bag.
Equipment: one-inch dialysis tubing, bovine serum albumin (BSA), dextrose, an inexpensive commercial glucose meter, test strips for the meter.
General procedure:  A control dextrose solution was divided between a sac made of dialysis tubing and a drinking glass.  A small mass of powdered BSA was added to the sac. The sac was suspended in the sugar-only solution and the solution outside the bag checked at 13 times during a 33-hour period. At about 8 hours protein was added to the bag since neither diffusion nor osmosis was being observed. After this the bag began to swell. Due to concern that BSA would affect the reading the measurements were compared with the control solution and not the inside of the bag$^1$.
Results: Results are given in the table below. Addition of protein is indicated by the arrow in the graph.
Discussion: This procedure was suggested in this answer at the Chemistry SE. The meter requires some practice to use. Protein was added to the bag in roughly 200mg increments until an influx of water occurred. The solutions had probably reached equilibrium within a few hours of adding the extra protein but fluctuation in temperature made this difficult to determine. The gross trends correspond to air-conditioner use.
Conclusion: This procedure was done twice with similar results. The results are qualitative and suggest that sugar diffuses out through the membrane. This result is consistent with the answer at PhysicsSE and also this website (Figure 4.1) which indicates that diffusion and osmosis (diffusion of water) both occur. At equilibrium the concentration of sugar is slightly higher outside the bag.
Problems/issues :  (1) The meter is very sensitive to temperature $^2.$ (2) Perhaps because the dextrose was incompletely dissolved the measurement of control solutions took about an hour to stabilize. That is why the measurements begin at 110 minutes. (3) The meter gave errors outside a range of 30-500 mg/dl and after checking the standard deviation for a few concentrations of dextrose a concentration of 90 mg/dl was chosen. (4) It was not assumed that the meter functioned properly in the presence of BSA. Except for the last measurements, the glucose was measured outside the bag only.
$^1$ Four measurements were taken with the meter within 2 minutes of the last measurement to check variability of the meter. The numbers [mg/dl] were: 90, 94, 93, 89, $\mu = 91.5, \sigma = 2.38.$ At the last measurement the glucose concentration inside the bag was checked twice and the meter gave: 72, 80.
$^2$ Concentration should remain the same after equilibrium [Fick equation] and should not be affected by temperature. Manufacture information for the meter omitted for this reason. Caveat emptor.
Table 1. Min.= minutes, contr. = control [mg/dl], dextr. = dextrose [mg/dl].
$$\begin{array}{c | c | c | c | c | c |c | c | c | c | c | c | c | c | } min. & 110 & 145 & 296 &  356 & 686 & 776 & 802 & 832 & 862 & 1352 & 1393 & 2053 & 2069 \\ \hline
dextr. & 90 &  80 & 88 & 83 & 90 & 91& 88 & 88 & 89 & 84 & 93 & 86 & 90 \\ \hline
contr.& 91 & 83 & 83 & 86 & 82 & 87 & 83 & 85 & 80 & 77 & 89 & 82 & 82   \\ \hline\end{array}$$
A graph (mg/dl v. minutes) was made from this table. The arrow indicates addition of protein to the bag.


text:
How does formaldehyde cause protein-DNA crosslinking?
How does formaldehyde cause protein-DNA crosslinking?  I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less polar solvent causes the DNA and protein to pull more tightly on each other than their pull on the solvent, but I haven't been able to find an answer online.

aldehydes actually react with amines in protein and DNA to covalently attach the protein to the DNA in such experiments.  check out slides 3+ http://synapses.clm.utexas.edu/lab/howto/cross-linking%20fixatives.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866014/
In this work they find that formaldehyde crosslinking happens by formation of a methylol adduct (due to nucleophilic attack by N or S in case of proteins) in protein which then attacks the DNA or vice-versa.
The final crosslink is by a methylene bridge
Formaldehyde can react to amino groups in nucleotides and proteins and form a schiff's base, but i dont have a clue how this is involved in crosslinking


text:
Any species returning to the land twice throughout their evolution?
Here's a question from my son I've found interesting enough to ask here. There are plenty examples of species returning back to the water environment, like dolphins, sea lions, walruses, some snakes, crocodiles etc.
The question is - are there any evidences that in evolution of certain species there was return to the land twice, that is, they've came from sea, then evolve as land species, then, again, evolved to somewhat marine or fresh-water and, finally, turn into land species again?
UPD Chordate are the most interesting but any example, even plants, would be nice.

What you describe in the last sentence is "returning to the water", not "returning to the land twice". What you mean is "water -> land -> water -> land", right?

Related: Has any flying creature evolved into a sea creature?

Are you interested exclusively in animals? Note that the absence of a clear definition of what is a "water species" and a "land species" might make it hard to answer.

I am sure that there are no animals that have gone from land to water, and then back to land. I am not sure about plants though. The transition to land is a very difficult one.  By the way, I would not say "returning to land twice", because they would only be "returning" once.

@KarlKjer Are you that sure. How about woodlice? Outside of animals, there are probably plenty of examples, esp. if we include prokaryotes but then again the question what it is to be a "land species" and a "water species" will matter

Yes, I am sure. Crustacians and Chelicerates evolved in water. I know that woodlice are both terrestrial and aquatic, but that does not necessarily mean the the aquatic species did not move onto land.

Crustaceans are paraphyletic, with insects nested inside them. The sister taxon to Hexapods is likely Remipedia, which are crustaceans that live in freshwater caves. So proto-hexapods evolved entirely on land. Not sure where myriapods evolved, but I would presume in water, because they are deeper on the tree than Hexapods.

Echidna is a good example, they came from platypus type ancestors aprox. 14-20 million years ago.

You list crocodilians as an example of animals returned to the water.  If so, there are extinct crocodilians such as Krabisuchus and Trilophosuchus that may have been more terrestrial, and would nominally be valid answers.  That said, crocodilians are too amphibious to find much satisfaction from answering this way.

Woodlouse
Life emerged in the water. Ancestors of insects, spiders, myriapods and crustaceans were probably terrestrial (please correct me if that is wrong) but then, crustaceans evolved to living in the water again. Finally, woodlice went back onto land!

Following your link in Wikipedia (and other) I wouldn't say that crustaceans appeared on land.

I did not say "crustaceans appeared on land" but "Ancestors of insects, spiders, myriapods and crustaceans [in other words, ancestor of all arthropods] were probably terrestrial". Again, I might be wrong. Can you please give me a reference stating that this ancestor was not terrestrial? From wikipedia > arthropoda, I could not find anything definitive but only that among the oldest fossils of arthropoda are marine and others terrestrial.

To hopefully resolve the question, I opened the post Were there any terrestrial species in the ancestry of all crustaceans?

Echidna come from platypus like ancestors about 14-20 mil years ago. so they count if platypus count as returning to water although not 100% of there like cycle.


text:
How is the human oxygen absorption dependent on the concentration of oxygen in respiratory air?
I just wanted to calculate the theoretical time span in which I could survive (conscious) in my apartment without letting the air on the inside exchange oxygen/carbon dioxide with fresh air. During my calculations I came to the point where I was unsure, if the oxygen amount already consumed, influences the future O2 absorption and consequently the CO2 production.
In this hypotetical scenario, I assume that the air in my apartment is homogeneous and ideally mixed, thus measuring the same level of oxygen anywhere on the inside. Furhter I assume that all of my rooms are completely empty, hence having volume of the living space * room height * oxygen concentration as my initially available oxygen amount. (I tried to be independent of the air pressure by using standard values for consumption depending on concentration and calculate how long it would take for the oxygen level to drop below/carbon dioxide to rise above a specific threshol (depending on what gets lethal first) ).
I asked this particular question and not "How long can one survive in a closed room...", because I have not found a useful answer yet considering the oxygen/carbon dioxide concentration, but the absolute amount of these gases in it.
In case it would be helpful/necessary: I am not familiar with biochemical, metabolic reactions and have not studied in this field before.
Thanks in advance.
PS: If you think, another stackexchange community would be more appropiate, please comment.

If you read about the effects of high altitude you should be able to map this on to your question in relation to oxygen requirements. However, in a closed room you would also have to consider the toxicity of accumulated carbon dioxide

As @AlanBoyd suggests, carbon dioxide will be a problem before lack of oxygen is. Read up on the Apollo 13 mission.

Related: https://biology.stackexchange.com/questions/53107/sitting-in-a-closed-room-filled-with-regular-air-for-how-long-will-the-air-las

@Alan Boyd: Would the effects of high altitude be the same?  There you have a 80/20 N2/O2 mix, but at lower absolute pressure.  In a closed room (assuming a good CO2 scrubber system) you would maintain a higher pressure, but decrease the percentage of O2.

@jamesqf I admit that the physics of gases was never one of my strengths. At high altitude the partial pressure of oxygen is lower because of the reduced overall pressure. In the closed room the partial pressure of oxygen falls because oxygen is consumed. Isn't it possible to use the fatal partial pressure derived from knowledge of altitude effects to deduce the fatal partial pressure in the closed room since it is the partial pressure of oxygen that determines the loading of haemoglobin in the lungs?

Please include your precise question in your question text. A title is quite separate. In your case your long "question" does not actually include your question and I am unclear what you have tried to calculate or wish to know.

@Alan Boyd: Well, that's what I'm wondering about.  Is it simply the partial pressure that matters, so that breathing a 100% oxygen atmosphere at 20% of sea level pressure would be the same as normal air at sea level?  Or are there effects from absolute pressure, the way there are effects from increased pressure when scuba diving?


text:
Do lizards expand in the summer and contract in the winter?

We all know that objects expand on heating and contract on cooling.

Lizards are cold-blooded animals, i.e. they become hotter and cooler depending on their outside temperature. Warm blooded animals like us however maintain a constant body temperature.
This must mean that lizards are cooler in the winters and hotter in the summers, which should mean that they expand in the summers and contract in the winters, although by a very unnoticeable amount.
Does this really happen? How does the lizard or other cold blooded animals accommodate this expansion and contraction?

if expansion or contraction is unnoticeably small then why need for some special mechanism for accommodation?

I think you might be over-extrapolating your knowledge a bit. Animals are mostly made of water, and water only changes density by about 1% between 0C and 37C, so you are overestimating the effects of expansion/contraction due to temperature (and most organisms don't experience such a wide range of core temperatures, outside of special circumstances).
Because water is such an important component of organisms, size would also change with variation in hydration levels (you can easily observe this in plants because many plants use water pressure to support themselves). I would expect this variation to be as great or greater than any expansion/contraction with temperature.
Also note that just because animals are cold-blooded doesn't mean they don't regulate their temperature. Cold-blooded animals move between sun and shade, water and land, etc to regulate their temperature externally.


text:
How extensive was interbreeding among human species?
I have read this article about non-Africans interbreeding with Neanderthals, Neanderthals interbreeding with Denisovans, and Asians interbreeding with Denisovans as well.
Now, I'm wondering what that even entailed.
Were populations of these species cohabitating a piece of land and completely mixing up? Would the humans of that time and place be 50/50?
Or would that just be a single act of interbreeding where an adventurous person had children with another species and those children became a part of the sapiens population?
Do the genetics suggest how much interbreeding happened or can they only say that some interbreeding happened?
Bonus, unrelated question. Does natural selection in any way suggest that mixed species offspring was better adapted to the environment and thus spread so far or can it just be a random event with little effect one way or the other that just spread regardless.

I suggest you remove the "bonus, unrelated question" and ask it separately.

Interbreeding between H. sapiens and neandertalis was quite limited.

Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability.

--Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans

... the interbreeding success rate between humans and Neanderthals was found to be below 2% (Fig. 2, Table 1, Fig. S1, and Table S1). Under demographic scenario A (Table 1), which is based on the most realistic demographic parameters, we estimate this interbreeding success to be even well below 1% (0.51%, mode of black curve in Fig. 2; 95% confidence interval: 0.33–0.89%). ...  If we assume that both species interacted for 10,000 y during the range expansion of modern humans (11), successful admixtures between Neanderthals and humans would have occurred, on average, only once every 23–50 y over the whole hybrid zone to produce introgression levels of 1–3%, which shows that they were extremely rare events.

--Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression
Note that this technically doesn't touch on "interbreeding" but rather addresses successful interbreeding; sterile individuals won't be detected in this approach, and even sub-fertile individuals (whose lineages died out) will be underrepresented.
We have strong evidence that male progeny of sapiens/neandertalis crosses were either sterile or extremely sub-fertile:

These results suggest that part of the reduction in Neandertal ancestry near genes is due to Neandertal alleles that reduced fertility in males when moved to a modern human genetic background.

--The landscape of Neandertal ancestry in present-day humans
And even apart from that, there's good evidence that hybrids were less "fit" (in evolutionary terms) than either parent:

After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. ...  We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids.

--The Strength of Selection against Neanderthal Introgression
So it's very likely that the rate of interbreeding, per se, must have been higher than the roughly once-per-generation rate that can be inferred from genome analysis, but most of the hybrids were sterile, or poorly adapted.  Of course, this is exactly what you'd expect from interspecies hybridization; the number of successful sapiens/neandertal hybrids through the millennia of their interactions was probably lower than the number of fertile mules in the past few hundred years.


text:
How does adjuvant enhance the immunogenicity of antigen?
My question is, How does adjuvant enhance immunogenicity of antigen?
I just want to know deeply about it , Any suggestions will be helpful!

A couple of points as this is your first post. A title is independent of a question, so even if your title is your question you should repeat it in the body of the question. If I am reading this on a phone I might not be able to see the title. And if your title is deemed poor, it might be edited. The second is that this is a quite broad and basic area. I find it difficult to understand why you couldn't find anything on the internet as a search for "adjuvant and immunogenicity mechanism" brought up several promising articles.

Well, it was a miscommunication between myself and the actual person who had this question and for the title concern, I'll fix it!

It depends on the adjuvant. I think this is too broad.

This is a quick answer to a very broad question since the mechanisms of adjuvants are very different. I'll try to summarize just a few. For a deeper understanding please start reading this paper and its references.
1) Aluminum salts (aluminum phosphate or hydroxide)

Studies suggest alum salts work by causing the formation of an antigen
  depot at the inoculation site from where the antigen is released slowly.
  The trapping of soluble antigen in the alum gel may also increase the
  duration of antigen interaction with the immune system. Other
  mechanisms of action involve complement, eosinophil, and macrophage,
  activation and increased efficiency of antigen uptake by antigen
  presenting cells seen with particulate matter with a size under 10
  micron.

2) Calcium salts
They work pretty much like aluminum salts but they are much better tolerated by the organism.
3) Bacteria-derived (peptidoglycan or lipopolysaccharide)
They are naturally recognized by the immune system and for this reason, they are used to simply boost the immune response.
4) Emulsions
They form a depot at the injection site, enabling the slow release of antigen. The immune system has more time to recognize the antigen and react.
5) Liposomes
They help to extend the half-life of antigens in the blood leading to a higher antigen exposure to antigen presenting cells after vaccination. A Very similar effect is achieved using microbeads made of artificial polymers.

Unfortunately the reference cited is relatively old (2004; a decade is a long time in this rapidly-moving field) and so the answer is dated as well.  The depot effect has never been shown to be real. Aluminum salts and liposomes have both been linked to NLRP3 inflammasome and uric acid modes of immune activation; and so on. More recent references include here and here, but there are literally hundreds of recent papers on the subject.

@iayork thanks for the extra references. My answer is far from complete, it's a very basic overview. The reader should consult further the literature, of course.

I voted to close the question as it's far too broad to answer properly in this format and shows no evidence of basic research.

@alec_djinn's  Sorry I didn't knew much about immunology or vaccination, I just had the basic knowledge and have just started studying the the subject, I appreciate your efforts and will from now do my research beforehand.

@iayork your link to the nature article is broken.


text:
What does a female mosquito need from blood?
I have come across many articles stating that female mosquitoes suck blood from vertebrate hosts to develop their eggs. Some also state that they need proteins, carbohydrates, iron etc., from human blood. But none of them (as far as I know) have stated what components exactly are needed from blood for their egg development. If proteins, what kind of proteins?

According to the Introduction to this paper:

Attractiveness to biting insects is important in medical contexts, mostly in the dynamics of transmission of pathogens by mosquitoes that cause diseases such as dengue and malaria. Blood feeding is an essential part of the lifecycle for most mosquito species as it provides females with the proteins necessary for egg production.

I imagine that the blood protein is simply a rich source of amino acids. This is supported by the finding that an artificial meal consisting of bovine serum albumin can support egg production in Aedes albopictus.
Update following answer from Greg Thatcher
Clearly there is evidence that iron from a blood meal reaches ovaries and eggs, although the paper doesn't provide direct evidence that this iron is essential. However this made me think more deeply about the paper that I cite above about feeding bovine serum albumin as an blood substitute. Could this have also supplied a significant amount of iron? The artificial meal was BSA dissolved in a phosphate-buffered saline. The authors don't specifically address the problem of iron contamination. The main component of PBS is NaCl. If they used AR-grade NaCl then the iron content will have been very low (0.0002% in one example that I found online). However BSA itself can bind metal cations (see here for example) so the protein may have contributed some iron. The authors do quote the source of the BSA that they used but I haven't been able to access a data sheet that might shed light on the level of iron contamination.
Of course it is entirely possible that blood is an essential source of both protein and iron.

What does a female mosquito need from blood?

This paper seems to indicate that iron is the most important ingredient.
To quote from the paper,

Among many nutrients in the blood meal, iron is required for optimal
  egg development and viable offspring

I would imagine that mosquitoes could get plenty of of proteins by feeding on other parts of the body or plants, but the blood of their chosen victims contains much iron, as hemoglobin requires iron to carry oxygen safely throughout the body.

+1 good find, but I'm not convinced by your suggestion for other sources of protein – aren't mosquitoes nectar feeders?

Certainly, mosquitoes get most of their protein from other sources, but the females need iron to produce eggs, and blood is a rich source of iron.  According to the virologists and  parasitologist I listen to on TWIV (http://www.microbe.tv/twiv/tag/mosquito/), it is the occasional female that bites two victims for her iron meal who then can spread various diseases.

Mosquitoes generally feed on plant nectar and fruit juice. Male mosquitoes do not take blood, so when you feel a mosquito plunge into your skin and start siphoning your blood, you can bet it is a female, every time.
female mosquitoes need nectar for nourishment, they also need protein to develop their eggs. That protein comes from your blood. Once they've gotten blood, the mosquitoes fly away to a warm, damp place to rest and wait for their eggs to develop. That takes up to five days. The females lay their eggs, and then move on to the next blood meal to feed the next batch of eggs.
Female mosquitoes can lay a set of up to 100 eggs about every third night after mating only once. They typically lay as many as three sets before dying.
Those eggs eventually hatch, and the whole mosquito life cycle starts over again.
This is what I got from :
tap here

Thanks for the reply. I agree that female mosquitoes suck blood for their  egg development. And, they need some proteins from blood. I'm just curious to know what kind of proteins are needed for egg development.


text:
Why don't animals produce alcohol
As I understand during anaerobic respiration, the electrons received from the decomposition of glucose are transferred to nicotinamide adenine dinucleotide and flavin adenine dinucleotide. As there is no oxygen the electrons are then transferred to something else, either Lactic Acid or Ethanol (in the case of yeast).
So why do animals produce Lactic Acid and not Ethanol?
Also, (I know this is silly, but) what would happen if they did?

exact answer: https://in.answers.yahoo.com/question/index?qid=20110227125518AAh0WrC

@DevashishDas. I dont think that link answers the question. Also, I am not sure what OP intends to ask- a. How is it that alcohol is not produced in animals b. Why (or for what greater reason) is it not produced. Answer to a. is trivial: animals don't have that enzyme.

@WYSIWYG: It was the first result on google to similar to the question.

Consider this from the point of view of integrating whole body metabolism.
The body operates on a fuel economy built around glucose. Active muscle produces lactate (C3) which is exported to the liver through the bloodstream. Liver converts lactate to glucose (C6) which is then exported to the tissues.
What if muscle produced ethanol (C2)? Liver metabolises this to acetate. This could be converted to acetyl CoA and so on to fatty acids, but there is no way to achieve net synthesis of glucose from acetate. Muscle can of course use fatty acids, so you could conceive of an alternative system based upon this. It may be that this is less efficent from the point of view of energy useage - I haven't checked this because there is a more compelling argument against using ethanol.
According to this paper, lactate levels in the bloodstream can reach 15 - 25 mM during exercise. If muscle exported ethanol instead of lactate then blood alcohol content (BAC) would reach the same levels.
The middle of that range, 20 mM ethanol, is equivalent to a BAC of 0.076% which is just below the legal limit for driving in the USA and the UK, and above the legal limit in many European countries. This BAC is associated with effects upon reasoning, depth perception and peripheral vision. So, from an evolutionary position it really wouldn't make sense to have a metabolic system based around sending this much ethanol through the blood.

Our metabolic system would be different if this would be our way...

yeah I agree with Chris totally

But the question wasn't about a hypothetical alternative metabolic system, it was about the existing one using lactate and not ethanol as an end product of fermentation. So yes, if our metabolic sytem was constructed differently it would be ... different.


text:
What is most simple eukaryotic genome?
Expressed in number of Base Pairs or Bytes, about how large is the simplest eukaryotic genome?
How much of this is 'junk-DNA' (non-coding)?

what do you mean by "most simple DNA molecule"?

you can synthesize DNA of any length, from 1 bp on up, so this question is kind of meaningless...

True.. but I implied that I wanted to know about the shortest naturally occurring DNA in eukaryotic cells.

Information content in mathematical sense?

I have to agree with @MattDMo, this question is meaningless in its current state (which is why I downvoted it and voted to close it). The problem would be much better if you were to clarify a few things. For example, what do you mean by "most simple DNA molecule"? Are you using the term "information" in the vernacular sense or in the theoretical sense? And if by "exists today" you really meant, "naturally occurring in eukaryotic cells", then it's better to say what you really mean. Addressing these concerns will help us as a community address your question meaningfully.

In case you were unaware, you can (and are encouraged!) go back and edit the text of your original question. We're not trying to condemn you for the way you asked the question, just providing suggestions for how you can clarify and improve the question, for your benefit and ours.

Hey @AndreasHartmann I've edited your question - hope this helps - feel free to change it again... thought this might help.  Most biologists don't think in terms of information content, which is not well defined beyond the 'one base = 2 bits' chestnut.

When you say genome, what exactly do you mean? All of the chromosomes? Biggest chromosome? Does mitochondrial or plastid DNA count? Do plasmids count?

How do you define simplicity? Because of what was discovered by the field of epigenetics, it is very difficult to figure out the exact entropy of a genome. @shigeta 's "times 2" model is only relevant for storage of sequence in a computer, not actual organisms.

You should edit your question to ask for the smallest eukaryotic genome, and maybe also ask for how compactness (% of coding sequence - junk DNA is a very obsolete term) varies with length. Everything else should be a separate question (which you can formulate after pondering your answers).

You asked about eukaryotes. The genome of the yeast Saccharomyces cerevisiae is 12.2 Mb.
The genome of the smallest free-living eukaryote, Ostreococcus tauri (a unicellular green alga) is 12.6 Mb
There are smaller eukaryotic genomes, but these are not free-living organisms they are intracellular parasites.

I'd be interested in some detail about why Saccharomyces is not 'free-living' and maybe a reference for what the smaller genomes are?

@Shigeta the question was ambiguous, and my answer didn't help. O. tauri is physically (i.e. cell size) the smallest free-living eukaryote. See http://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes for some genomes of obligate intracellular parasites such as Cryptosporidium.

According to this:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html
The shortest DNA of a individually living cell is that of Mycoplasma genitalium at about 580000 base pairs. -But it's not eucariotic!

...but M. genitalium is not a eukaryote!


text:
Are neurodegenerative diseases such as dementia inevitable?
For the sake of this question, let's imagine a person who lives to 200, would it be at all possible for them not to get dementia? Is it an inevitable disease as we get older or can it be avoided?

I won't think it becomes "inevitable" at 200...but yes, chances do increase, just like cancer

I think this is a great question but at this point it isn't really answerable without being substantially opinion-based.

To my knowledge the oldest verified human age is below 123 years (https://en.m.wikipedia.org/wiki/Oldest_people). To reach 200, revolutionary achievements are necessary. There is no telling, how these might change the probability of dementia occurring. I am afraid, any answer  is bound to be highly speculative.

While the chances do increase, the majority of people who make it past 100 don't suffer from dementia.

@jamesqf - There's a huge difference between 100 and 200. Also, the 'majority' is small, and gets smaller every half-decade. Rates (of dementia) increased exponentially with age from 12.7% per year in the 90–94-year age group, to 21.2% per year in the 95–99-year age group, to 40.7% per year in the 100+-year age group.. However, the answer is unknown and POB.

One of the best questions I have seen in a long time. It is very central in gerontolical research. I would argue that dementia would occur at somepoint, simply because more and more cells would be approaching the hayflick limit, leading to the inevitable loss of neurons at some stage.


text:
Do all parts of a plant contain the same type of cell?
I have only learned about the plant cell which is shown below. But plant stems alone are made up of different parts like xylem, phloem, parenchymatous cells, sclerenchymatous cells etc.
Are all the parts of a plant made up of cells like the one in this diagram or is the cell diagram changed for different parts of a plant?

The diagram shows an exemplary plant cell . Except for the raphide/druse crystals, which I do not know, all of these components are definitely present in every plant cell. Do note that this diagram is only an example and while it describes the basic components present in the cells, details can vary, since plants can have highly specialised vacuoles or plastids (like chloroplasts) in special cell types.
As @AlanBoyd pointed out, there are some specialised cases like the Sieve Tube cells, that do not have a nucleus. But in your average cell, you should find all of the components described in the diagram.
The differences between cell types are typically caused by the expression of different genes, that change the behaviour of each cell, and not directly by a change of how the cell is build up.

Do root hair cells contain chloroplasts?

Sieve tube elements (phloem) are anucleate https://en.wikipedia.org/wiki/Sieve_tube_element?wprov=sfsi1

@AlanBoyd True, must cells in the roots will not have Chloroplasts. They will, however, have Leukoplasts instead, which are very similar and so the diagram as 'base plant cell' still holds.
The Sieve tube's I didn't know about before (see edit)


text:
Why does crossing over take place at all?
I already know that crossing over causes genetic variation. My question is that since DNA is a stable molecule, why would it undergo process like crossing over during which it becomes so unstable and develop a chance of mutation?

Cross over often result in mutation, this is true. But of course, not all mutations are caused by cross-over. Note that cross overs do not lead to higher genetic variance (or only as an indirect effect of causing mutations). I am unclear whether your question is "Is there selection for increased mutation rate?" or "Is there selection for increased recombination rate?"

Of course it leads to higher genetic variation: Without crossover, genes must mutate for the chromosomes used to vary at all. Splitting up previously-coupled genes creates potentially new chromosomes out of existing genes. That is increased variation in the population: it provides sexual reproduction a new pattern of genes to mix things up with. If the permutation isn't new, a specific case might not, but that process certainly increases diversity in the population.

It exists for the same reason sex exists at all -- for recombination of alleles of genes.

@TheNate It really is not the point of the question but recombination actually reduces genetic variance (unless some funny type of epistasis) both 1) by allowing selection to be more effective and 2) by reducing genetic differences between haplotype lineages. The idea that recombination increases genetic variance is a common misconception (hence the two upvotes you received). You can typically look at the work from Barton and and/or Otto. You might also want to have a look at this presentation by S. Otto starting at 5'30''

@AKV I am voting to close as unclear until you have addressed my comment from yesterday.

Crossing over is believed to be beneficial for evolution. It does not cause only mutations, it allows for the switching and mixing of genetic information. Thanks to crossing over entire protein families evolved, like the hemoglobins. Indeed it is one of the mechanisms that shaped the chromosomes.
Some in-silico simulation proved that, in general, adaptation take place faster if crossing over is applied.
Here some extra references for further readings.
https://www.ncbi.nlm.nih.gov/pubmed/28565671
https://www.ncbi.nlm.nih.gov/pubmed/28564047
https://www.ncbi.nlm.nih.gov/pubmed/28563027
https://www.ncbi.nlm.nih.gov/pubmed/28557225
https://www.ncbi.nlm.nih.gov/pubmed/28555659

The evolution of recombination rate is a complex subject (and is typically closely linked to the evolution of sex). You might want to go further in your answer.


text:
Does carbon dioxide from carbonated drinks enter the bloodstream?
When drinking soda or any other carbonated beverage, does some of the CO₂ find itself in the bloodstream? And if so, how long does it take until the carbon dioxide levels in the blood return to normal?

Is there enough CO2 to matter?
A can of soda contains about 2.2 grams of carbon dioxide (see this question from Chemistry.SE).
A human outputs about 1 kg of CO2 daily from respiration, though the rate can be much higher during physical activity. So, even if all of the CO2 content of a can of soda was absorbed into your blood, that's only 0.2% of your ~resting daily CO2 output.
A normal range for [partial pressure of CO in blood] is about 38-42 mmHg.
Gas exchange
The surface area of the lungs is something like 50-75 m2.
The surface area of the stomach is much smaller, closer to 1 m2.
Therefore, gas exchange is going to be much more efficient in the lungs than at the stomach.
Result
Any CO2 is going to be fairly efficiently cleared from expiration if it gets into the blood from the stomach. It's unlikely that you could detect any appreciable change in CO2 levels beyond what happens naturally as blood travels through the circulation and picks up CO2 from the periphery, and it's even less likely this difference would be greater than the difference between rest and exercise. That isn't even accounting for the buffering capability of the blood and diffusion into other tissues (both would smooth out any rise of CO2 over time) as well as not all of the CO2 will even make it to the stomach, and the gases that make it there can also leave via the esophagus.
As a sidenote, the Mythbusters partly addressed this issue in their episode on Mentos+coke. One of the factors they discussed is that much of the CO2 doesn't even make it to the stomach because it is released in the process of drinking, though they didn't quantify it. Therefore, CO2 is likely to have even less of an effect than described above.

As shown on MythBusters, most of the CO2 does not make it to the stomach.

@BrockAdams I assumed as much but couldn't find a decent citation to demonstrate it or estimate the quantity (and, once it was clear to me that even the full amount in the stomach would matter very little, I didn't look too hard). I'd be happy to add one if you find it.

IIRC, it was this episode (or similar): https://www.discovery.com/tv-shows/mythbusters/videos/exploding-stomach-minimyth.  PS:  who just drinks a lousy can of soda?  Double Big Gulp™ FTW!


text:
Possible Genotypes of 4 Alleles of Adh
There are four alleles of Adh which are Adh-1, Adh-2, Adh-3 and Adh-4.  Their respective frequencies are 0.11, 0.84, 0.01 and 0.04.  What are the Hardy-Weinberg frequencies of the possible 10 genotypes?
My Attempt:  First I thought that there were more than 10 genotypes (4*3*2*1) = 24.  I've never done HWE with 4 genotypes so im not sure how to use $p+q=1$ or $p^2+2pq+q^2=1$.

I may be wrong but to get the number of possible genotypes isnt it 4+3+2+1=10?. You can have A1A1,A1A2,A1A3,A1A4,A2A2,A2A3,A2A4 and so on. When you multiply you are counting some genotypes twice (for example A1A2 and A2A1. They are the same)

Those Hardy-Weinberg equations are the general case, used for only two alleles.  This question is basically answered here, for three alleles; you've got a situation of four alleles.  That means you need to have:
$(p+q+r+s)^2=1$
Where $p$, $q$, $r$, and $s$ are the frequencies of your respective alleles.  This expands out to the rather unwieldy:
$p^2+2pq+2pr+2ps+q^2+2qr+2qs+r^2+2rs+s^2=1$
Now it becomes a plug 'n chug assignment; simply assign the frequencies and calculate.

 Assuming $p$ is Adh-1, $q$ is Adh-2, etc., $p^2=0.0121$, $2pq=0.1848$, and so on.


text:
How Much Longer For The Gene For Blue Eyes?
In the year 1900 roughly 50% of the people in the United States were homozygous for the gene for blue eyes. By 1950 the number had dropped down to 30%. Just now, (2013) barely 12% of the people living in America are homozygous for the blue eye gene.
Given the current rates of third world immigration into the United States. When will the last blue eyed man and the last blue eyed woman conceive a child with blue eyes? Should people with blue eyes bring reverse discrimination suits?
Reference:http://www.boston.com/news/globe/living/articles/2006/10/17/dont_it_make_my_blue_eyes_brown/ By Douglas Belkin

Do you have any reference for this 50% value? I highly doubt it, since blue is a recessive allel.

Agree with @Chris,you should give a reference for every data that you have put !

@user10739 could you paste the quote - the link is behind a paywall

If you come through the first link via Google, you can read it: https://www.google.de/#q=%22Don%27t+it+make+my+blue+eyes+brown%22+boston+globe

You added something to the question about reverse discrimination suits, but I don't see any other reference to discrimination. What is the alleged discrimination being inflicted upon blue-eyed people?

The 'alleged discrimination being inflicted upon blue-eyed people' is a collection of social policies in the United States leading to their extermination.

Never.
Even if the country arrives at the unlikely day when there is no one alive in the United States with the blue eye phenotype, there are still plenty of people with the unexpressed recessive gene, and if two of them get together, those genes can combine to produce another blue-eyed child. If this happens twice, with one boy and one girl, and they happen to meet when they are in college and say "Hey cool, you have the same inexplicably rare kind of eyes as me. I think I want to marry you." then any children they have will also be blue eyed.
So even if the day came when you couldn't find a soul in the world with blue eyes, you will still never know if you've seen the end of them.


text:
If the brain has no pain receptors, how come you can get a headache?
I've read many years ago in books, that the brain has no nerves on it, and if someone was touching your brain, you couldn't feel a thing.
Just two days before now, I had a very bad migraine, due to a cold. It's become better now, but when I had it I felt my head was going to literally split in half, as the pain was literally coming from my brain.
So it lead me to the question: How come people can get headaches if the brain has no nerves?

The brain does not. However, the skull, muscles, and skin surrounding it to. :) Pressure differentials (your sinus cavities expand  beyond your nose!) and sore muscles (especially neck muscles) can cause or contribute to headaches.

The brain "has" nerves, depending on how you define it: http://en.wikipedia.org/wiki/Cranial_nerve more accurately as January notes it lacks nociceptors.

Brain, indeed, cannot feel pain, as it lacks pain receptors (nociceptors). However, what you feel when you have a headache is not your brain hurting -- there are plenty of other areas in your head and neck that do have nociceptors which can perceive pain, and they literally cause the headaches.
In especially, many types of headaches are generally thought to have a neurovascular background, and the responsible pain receptors are associated with blood vessels. However, the pathophysiology of migraines and headaches is still poorly understood.

So if I tear my head apart leaving brain miraculously intact I'll never get headache again? What part of my skull gets pain from stress? And which one is hurt by not sleeping? I think most headaches are not explained by skull being hurt.

"...with blood vessels" - would like to how vessels being contracted or dilated relates to pain.

You are correct in that the neurons themselves do not sense pain. However, the brain contains layers of coverings, blood vessels, the scalp and some muscles. All of these other structures have pain receptors. The coverings of the brain are called meninges and consist of the dura, arachnoid and pia. The dura in particular has a lot of pain receptors and may be responsible for many headaches. As a neurosurgeon I have seen this first hand during awake brain surgery when we open the dura. The patient usually doesn't report any pain when you drill a hole in their skull. However, they start to report dull pain or headache when you stimulate or touch the dura.

@ area51 - "The patient usually doesn't report any pain when you drill a hole in their skull" ?

They're probably under a local anesthetic, but it would be less shocking if that was noted explicitly.

The local anesthetic only numbs the scalp not the bone. Generally patients don't experience bone bain when drilling the bone. The next layer encountered is the dura. We generally don't number the dura and patients may report a dull pain or headache when manipulating or cutting the dura.

That the brain doesn't have pain receptors has somewhat drifted into the corpus of general knowledge, perpetuated by pamphlets, books and documentaries.
Your question caused me to look up wikipedia. Citing:

A headache or cephalalgia is pain anywhere in the region of the head
  or neck. It can be a symptom of a number of different conditions of
  the head and neck. The brain tissue itself is not sensitive to pain
  because it lacks pain receptors. Rather, the pain is caused by
  disturbance of the pain-sensitive structures around the brain. Nine
  areas of the head and neck have these pain-sensitive structures, which
  are the cranium (the periosteum of the skull), muscles, nerves,
  arteries and veins, subcutaneous tissues, eyes, ears, sinuses and
  mucous membranes.


text:
What type of biome is this?
There is a region that gets about 812mm of precipitation and is mildly hot all year long.
I believe this region is a tropical savanna, but I'm not 100% sure.  Is this correct?

I'm not familiar with the definitions of a tropical savanna I'm afraid. Is this a homework question?

Well, first of all 812mm is a pretty precise value to be preceded by the word "about". "Mildly hot", on the other hand, is too vague a term for your question to be answerable. If you update your question with better parameters, you may get more helpful answers.
In any case, according to this page, a tropical savanna has mean monthly temperatures at or above 64°F (~18°C), which may or may not qualify as "mildly hot" by your standards, and annual precipitation averages between 30 and 50 inches which means between 762mm and 1270mm.
So, I what you are describing could be a tropical savanna, but as I said before, I can't tell unless you update your question with more information. Have a look at this site, it may be of help.

i made a typo.  i updated my question

Well, in that case @user832680, it may well be a tropical savanna :).


text:
Clustal Omega - convert from distance into # of substitutions
I have a set of nucleotide sequences for which I have aligned using Clustal Omega. In particular, I performed a full alignment, and obtained a full distance matrix.
The distance matrix scores range between 0 and 1. I am looking to use this score to back-compute the number of different positions present in the alignment. Is this possible? If possible, I'm looking to avoid using code (my own or otherwise) to re-compute the number of positions differing between each pair of segments, and instead compute it directly from the distance score.
Here is a toy example of what I am receiving from ClustalOmega:
Sequence    1    2    3    4
1           0    0.1  0.06 0.1
2                0    0.4  0.23
3                     0    0.05
4                          0

The numbers are the "distances" as calculated by ClustalOmega. According to the README file, they are computed by the k-tuple measure. I tried parsing the original paper (published in 1983 in PNAS), but I could not figure out how k-tuple distances are computed, and I could not figure out how the distance metric (as reported like above) is computed from k-tuple distances.
I would like to convert those numbers into the number of positions that differ between each pair of sequences when the two are aligned. This includes substitutions, insertions, deletions. I am currently doing this for 520 sets of virus sequences. Is this possible?

What exactly do you mean by "positions" in your alignment? How many sequences are we talking about? Can you show an example of the matrix and your desired result?

Sure, let me update the original question.

It uses a gonet matrix to compare each of these two sequences. Since you you could have insertions and extensions as well as substitutions, it becomes a 3 parameter problem. 1open + 6penalty + substituion_penalty = X. X can be solved by a linear combination of subsituion_penalties, extensions, and insertions. So I think this will be really really hard.

with that being said. Clustal spits out the multiple sequence alightment. Why don't you just look at sequence 1 and sequence 2 and see what the insertions and subtitutions are!

Haha, it looks like I will have to do that in the end. I was trying to see if I could take the lazy route and not write a few lines of code. Thank you for all of your input nonetheless!

@jwillis0720 if you are still around then can you post this as an answer.

It uses a gonet matrix to compare each of these two sequences. Since you you could have insertions and extensions as well as substitutions, it becomes a 3 parameter problem. 1*open + 6*penalty + substitution_penalty = X. X can be solved by a linear combination of substitution_penalties, extensions, and insertions. So I think this will be really really hard
with that being said. Clustal outputs the multiple sequence alignment. Why don't you just look at sequence 1 and sequence 2 and see what the insertions and substitutions are!


text:
What are the main mechanisms of interaction between the nervous and immune systems?
We know from pop science that our psychological states have an effect on our immune systems ("worrying ourselves sick", etc.), but what are the actual mechanisms through which our nervous systems pass information to the immune system?
Cell mediators come to mind, but where in the body would a nerve cell release an interleukin or other factor? (Put another way, are neurons releasing these factors as a part of their normal cell metabolism and the side effect is a communicative effect with the immune system?)

It is not only the immune system that prevents us from getting ill. Worrying much in my opinion won't make you catch a cold; rather, you can get problems with your cardiovascular system (arrhythmias, hypertension, angina pectoris) or limbic system (panic attacks, sweating attacks etc.).
The connections are many; here are some possible ones:

There are many glands in our body that are either densely innervated (like the thyroid gland) or are a part of nervous system (like pituitary gland, epiphysis). They can release hormones directly to our blood and make our hormone profile unstable, hence also impacting the immune system.
Sympathetic/parasympathetic nervous system is under direct control of the CNS (N.vagus, carotide sinus sinus etc.) and can dramatically change the peripheral resistance of our vascular system by constricting (=> angina pectoris, hypertension) or dilating (swellings, bowel movements problems -> constipations etc.) the small vessel. This alone can start so many different mechanisms resulting not only in being ill, but also being dead.

Speaking about connection between the nervous and immune system we must consider that:

Many neuromediators, like adrenaline, for example, have clear effects on immune cells.
The mediators and humoral factors released by nerve endings can easily diffuse outside of the synaptic cleft and act locally, attenuating immune response.

Here's pretty much the first thing that popped up on pubmed:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144148/
 So clearly there are direct neurotransmitter receptors on immune cells themselves. Pick a favorite neurotransmitters and search "xyz and the immune system".
However, I can't tell you how relevant that is in terms of actually affecting large scale shifts in immune function. I think the previous poster Alexander Galkin had it right in that the nervous system affects hormones which have the ability to coordinate large scale, complex immune system shifts. It's like the president calling the generals to organize some troop movement and how many troops to deploy, what their targets are, etc.
I just wanted to add that tidbit that our "soldiers" do in fact carry cell phones. If the president wanted to, he could call the troops personally.

Yeah, I definitely realize there's quite a bit of info out there about it. :)   This question was from the early days of the site when we were trying to get a variety of content out there.  Great addition to the other answer!


text:
Are there any known consequences of the right-handedness of the DNA double helix?
In this article it is suggested (without evidence) that the right-handedness of DNA may be the cause that "kick[s] off asymmetry in the early embryo [of snails]".
On the one hand we know that symmetry breaking in an organism's development happens at multiple levels, from molecular to larger structural levels (see this). On the other hand we also know that right-handed DNA double helix does have many notably distinct properties from their left-handed cousins (see this). Are there any visible macroscopic asymmetries in some organisms that are known to be ultimately traceable back to DNA's handedness? More generally, what could be some consequences of the right-handedness of DNA double helix?

The short answer is no, there currently aren't any visible macroscopic asymmetries in some organisms traceable to DNA's handedness.
The long answer is still no, but I want to clarify that this "no" is more of a "not really". This is because there can be potentially drastic consequences when left-handed DNA is present in a cell in addition to the traditional right-handed DNA.
Let me explain. First, left-handed DNA is officially called Z-DNA. Right-handed DNA, which is the normal DNA configuration, is named B-DNA. There's a third type of DNA, which is also right-handed, that is called A-DNA. A-DNA is essentially super-coiled B-DNA.
Z-DNA isn't that unusual, and it is regularly found in human cells in addition to B-DNA. One study, done in yeast, found that Z-DNA can act as a nucleosome boundary element. Another study, by Kwon and Rich, found that the consequences of Z-DNA weren't as benign. The vaccinia virus requires Z-DNA to bind to a key protein that has anti-apoptosis activity. When Z-DNA does this, apoptosis is effectively blocked.
Furthermore, Z-DNA has been found in patients suffering with Alzheimer's Disease. Suram, et al., found that the hippocampus of severely affected AD patients used Z-DNA instead of B-DNA. This change in the DNA coil has potentially drastic consequences with regards to gene expression.
Finally, the presence of Z-DNA antibodies were found in patients that suffered from Systemic Lupus Erythematosus (SLE). Lafer, et al., describes how non-SLE patients do not have these antibodies, which suggests that Z-DNA is involved in the clinical manifestation of SLE.
So, with those thoughts in mind, yes, there can be visible asymmetries traceable to DNA handedness. In fact, some tumors depend on genes that have Z-DNA domains (one study by Alan Herbert found that it was about 40% of tumors on their panel). While this isn't really what I think you're asking, it's technically true as tumors do qualify as visible asymmetrical phenotypes traceable to DNA handedness. Diseases associated with Z-DNA could also technically qualify as since they're diagnosable, they're visible in that manner.
Regardless, there is currently no proof that the handedness of our DNA actually causes any real macroscopic phenotypic effect in the developmental stages of life. The reason why left-right asymmetry happens in organisms is due to asymmetric gene expression, not the direction of the DNA coil. This review by Michael Levin talks explicitly about how the left-right borders are established in embryonic development, and there is nothing regarding the direction of DNA's double helix.
Nonetheless, DNA handedness is still a rapidly developing field. I anticipate that more research on these subjects will quickly become available. But as of now, no. Snails shells are not right-handed because of the right-handedness of their DNA.

The review link by M Levin is corrupted. Can you fix it?

Just fixed the review link. It should be working now.

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


text:
Why do the vines change their spinning direction?

Look at the vines holding onto the lattice. The "vine springs" change their spinning direction in the middle. Why? And how do they achieve this?
(By the way, what's the name for this plant? Is is correct to call these "springs" vines?)
Edit: I notice that some vines fail to get in touch with the lattice, in such case they still change direction.

I believe what you are referring to are tendrils, the positively thigmotactic curly things that help some vines attach and climb. That sure looks like a cucumber to me, certainly a cucurbit anyway.