text:
Functionality of vitamin A, Bx, C, D, E, K as used in cosmetics for the skin?
I was wondering if someone can compare the functionality of vitamin A, Bx (x means numbers, such as 1, 2, 3, ...), C, D, E, K in the skin?  They are used in cosmetics but what is their actual effect?
If there is some source that compares between them in particular, I think it will help me understand some important basics.
Some products:
GNC Vitamin C Moisturizing Cream
GNC Vitamins E, A & D Moisturizing Cream
Reviva™ Labs Alpha Lipoic Acid Vitamin C Ester & DMAE Cream
Reviva™ Labs Vitamin K Cream

I added a section to your question to ask for the effect the vitamins have on skin in general separating it out from their presence in cosmetics.  Feel free to re-edit if I've missed your point.

Bx and C are water-soluble so unless there are special uptake systems that I'm not aware of, they should have 0 effect if you rub them on the skin...

@Armatus: Perhaps I was not accurate enough. There are cosmetic products with ingredients of Bx and C derivatives.

Yes, my guess was that using those vitamins would probably be purely for marketing purposes, not for any actual effect :) Except for hair products maybe, but your question is about skin.

@Armatus (1) Why different for hair and skin? (2) How about their various derivatives, some of which may be more stable, soluble in water or oil, and therefore used for skin products? Such as L-Ascorbic Acid (a derivative of VC) has been used as antioxidant, VB3 and VB5 have been used for anti-aging.

@Tim (1) Skin is a protective tissue with the special purpose of keeping things out. Hydrophilic substances have no way of getting past it other than wounds, but lipophilic substances can dissolve through the cell membranes. Hair is a collection of dead cells and protein as far as I know and vitamins may have effects on them in some way. (2) As I said, there might be uptake systems of the skin that I don't know about which could be exploited by modifying the vitamins. Anti-aging is a disputed concept as far as I know.

Vitamin A: One study conducted in the 60's claims that vitamin A acid prevents formation of comedones in Acne Vulgaris [1]. Another one conducted in the 70's found no significant improvement of plantar warts when vitamin A acid was applied topically [2].
Vitamin D: Agents like calcipotriene associated with topical steroids are effective against psoriazis [3]. They inhibit keratinocyte proliferation, normalize differentiation and modulate the activity of immune cells [4]. Active form of vitamin D is also effective against vitiligo [5].
Vitamin E: It reduces skin damage induced by UV [6, 8], but it shouldn't be applied on scars [7].
Vitamin K: It prevents bruising after laser treatment and reduces the severity of eventual bruising [9, 10].
Vitamin B12: It is an effective treatment for atopic dermatitis [11] and children with eczema [12]. It could also potentially improve olfactory function when associated with corticosteroids [13].
Vitamin B1: It doesn't protect you from mosquitoes [14].
Vitamin B3: It improves fine lines/wrinkles, hyperpigmentation spots, texture, red blotchiness and sallowness [15, 16].
Vitamin C: It improves wrinkling by new collagen formation [17]. It is useful in sun-induced skin ageing [18, 19] where it increases density of dermal papillae [20].
And here are the results of a study [21] which assessed multiple vitamins:

Vitamins A, C, E, and B3 have been shown to have potent antioxidant and anti-inflammatory properties, but to achieve optimal effectiveness, products must be delivered in appropriate formulations. Products containing alpha-tocopherol (vitamin E), L-ascorbic acid (vitamin C), retinol (vitamin A), and niacinamide (vitamin B3), are effective for the treatment of photoaging. These compounds have also shown effectiveness in the treatment of inflammatory dermatoses, acne, and pigmentation disorders and wound healing.

The same study [21] also concludes that combinations are better:

There is emerging evidence that combinations of vitamins have additive effects that provide enhanced efficacy compared with individual compounds.

References:

Kligman AM, Fulton JE, Jr., Plewig G. Topical Vitamin A Acid in Acne Vulgaris. Arch Dermatol. 1969;99(4):469-476. doi:10.1001/archderm.1969.01610220097017.
de Bersaques J. Vitamin A acid in the topic treament of plantar warts. Dermatologica. 1976;150(6):369-71. PubMed PMID: 1201813.
Devaux S, Castela A, Archier E, Gallini A, Joly P, Misery L, Aractingi S, Aubin F, Bachelez H, Cribier B, Jullien D, Le Maître M, Richard MA, Ortonne JP, Paul C. Topical vitamin D analogues alone or in association with topical steroids for psoriasis: a systematic review. J Eur Acad Dermatol Venereol. 2012 May;26 Suppl 3:52-60. doi: 10.1111/j.1468-3083.2012.04524.x. PubMed PMID: 22512681.
Tanghetti EA. The role of topical vitamin D modulators in psoriasis therapy. J Drugs Dermatol. 2009 Aug;8(8 Suppl):s4-8. PubMed PMID: 19702030.
Gorman S, Judge MA, Hart PH. Immune-modifying properties of topical vitamin D: Focus on dendritic cells and T cells. J. Steroid Biochem. Mol. Biol. 2010 Jul;121(1-2):247-9. doi: 10.1016/j.jsbmb.2010.02.034. PubMed PMID: 20211255.
Burke KE, Clive J, Combs GF, Commisso J, Keen CL, Nakamura RM. Effects of topical and oral vitamin E on pigmentation and skin cancer induced by ultraviolet irradiation in Skh:2 hairless mice. Nutr Cancer. 2001;38(1):87-97. doi: 10.1207/S15327914NC381_13. PubMed PMID: 11341050.
Baumann LS, Spencer J. The effects of topical vitamin E on the cosmetic appearance of scars. Dermatol Surg. 1999 Apr;25(4):311-5. PubMed PMID: 10417589.
Krol ES, Kramer-Stickland KA, Liebler DC. Photoprotective actions of topically applied vitamin E. Drug Metab. Rev. 2001;32(3-4):413-20. doi: 10.1081/DMR-100102343. PubMed PMID: 11139138.
Shah NS, Lazarus MC, Bugdodel R, Hsia SL, He J, Duncan R, Baumann L. The effects of topical vitamin K on bruising after laser treatment. J. Am. Acad. Dermatol. 2002 Aug;47(2):241-4. PubMed PMID: 12140470.
Cohen JL, Bhatia AC. The role of topical vitamin K oxide gel in the resolution of postprocedural purpura. J Drugs Dermatol. 2009 Nov;8(11):1020-4. PubMed PMID: 19894369.
Stücker M, Pieck C, Stoerb C, Niedner R, Hartung J, Altmeyer P. Topical vitamin B12--a new therapeutic approach in atopic dermatitis-evaluation of efficacy and tolerability in a randomized placebo-controlled multicentre clinical trial. Br. J. Dermatol. 2004 May;150(5):977-83. doi: 10.1111/j.1365-2133.2004.05866.x. PubMed PMID: 15149512.
Januchowski R. Evaluation of topical vitamin B(12) for the treatment of childhood eczema. J Altern Complement Med. 2009 Apr;15(4):387-9. doi: 10.1089/acm.2008.0497. PubMed PMID: 19368512.
Heilmann S, Just T, Göktas O, Hauswald B, Hüttenbrink KB, Hummel T. [Effects of systemic or topical administration of corticosteroids and vitamin B in patients with olfactory loss]. Laryngorhinootologie. 2004 Nov;83(11):729-34. doi: 10.1055/s-2004-825676. PubMed PMID: 15538662.
Holzer RB. [Protection against biting mosquitoes]. Ther Umsch. 2001 Jun;58(6):341-6. PubMed PMID: 11441693.
Bissett DL, Miyamoto K, Sun P, Li J, Berge CA. Topical niacinamide reduces yellowing, wrinkling, red blotchiness, and hyperpigmented spots in aging facial skin. Int J Cosmet Sci. 2004 Oct;26(5):231-8. doi: 10.1111/j.1467-2494.2004.00228.x. PubMed PMID: 18492135.
Bissett DL, Oblong JE, Berge CA. Niacinamide: A B vitamin that improves aging facial skin appearance. Dermatol Surg. 2005 Jul;31(7 Pt 2):860-5; discussion 865. PubMed PMID: 16029679.
Fitzpatrick RE, Rostan EF. Double-blind, half-face study comparing topical vitamin C and vehicle for rejuvenation of photodamage. Dermatol Surg. 2002 Mar;28(3):231-6. PubMed PMID: 11896774.
Humbert PG, Haftek M, Creidi P, Lapière C, Nusgens B, Richard A, Schmitt D, Rougier A, Zahouani H. Topical ascorbic acid on photoaged skin. Clinical, topographical and ultrastructural evaluation: double-blind study vs. placebo. Exp. Dermatol. 2003 Jun;12(3):237-44. PubMed PMID: 12823436.
Farris PK. Topical vitamin C: a useful agent for treating photoaging and other dermatologic conditions. Dermatol Surg. 2005 Jul;31(7 Pt 2):814-7; discussion 818. PubMed PMID: 16029672.
Sauermann K, Jaspers S, Koop U, Wenck H. Topically applied vitamin C increases the density of dermal papillae in aged human skin. BMC Dermatol. 2004 Sep 29;4(1):13. doi: 10.1186/1471-5945-4-13. PubMed PMID: 15456516.
Burgess C. Topical vitamins. J Drugs Dermatol. 2008 Jul;7(7 Suppl):s2-6. PubMed PMID: 18681152.


text:
What would cause red-haired people to become fewer?
There is this misconception that red-haired people are going to die out. This person on the Internet ("howstuffworks") also connected it to a marketing campaign of a hair dyer company. But I'm interested in a specific citation that he gives in that text, because it's cited on Wikipedia (so I want to check it):

While redheads may decline, the potential for red isn't going away. ["Red Alert." National Geographic. September 2007. Page 14.]

I don't have that National Geographic magazine, but I wonder: Why should the population of redheads decline? If it doesn't have a selection disadvantage, the frequency of the alleles causing red hair (which are recessive) should stay equal and if further assuming random mating in the human population, also the frequency of people with red hair, should stay equal, shouldn't it? So is the howstuffworks author wrong?

I don't think random mating is a realistic assumption...

The howstuffworks article notes that National Geographic did not endorse or provide any evidence for a claim that "redheads may decline". To me, that wording just means they don't know one way or another (may [or may not]).  All these sorts of silly claims may be related to the eugenics movement of a hundred years ago, which thought that "undesirable" recessive genes could be eliminated from populations by preventing homozygotes from breeding. Of course, they didn't realize that the majority of recessive alleles in a population are typically in asymptomatic heterozygotes.

Let's consider a possible scenario, with a simplified assumption that red hair is a simple Mendelian recessive trait.
Let's say we have a population that is 10% red hair. Everyone with red hair lives on one island, and they only breed among each other. They all have red hair, so we can infer they are all homozygous recessive (rr) for that trait. Everyone without red hair lives on the other island. Red hair never appears in this population, so we can infer they are all homozygous dominant for the non-red hair trait (RR).
Now, we develop inter-island transportation, and breeding becomes randomly assorted among the whole population. The allele frequencies stay the same: 10% r and 90% R. There is no selection based on the red hair trait. However, from Hardy-Weinberg we would calculate that only q^2 = 0.1^2 = 1% are homozygous recessive. 2 * p * q = 2 * 0.9 * 0.1 = 18% are heterozygous carriers for red hair, but they don't express the phenotype.
Just by changing the mating scheme, you can go from 10% with red hair to 1% without any change in allele frequencies.
It seems reasonable to infer that something like this is happening in the real world. People with red hair are much more common in certain places in the world. When people tend to mate only with people in their local communities, the likelihood of homozygous recessive individuals is higher than when people immigrate and mate with partners around the world. That doesn't mean there is any selection for the red hair allele, just a consequence of the mating scheme. That's the takeaway from the National Geographic quote you found on Wikipedia:

"while redheads may decline, the potential for red isn't going away"

In this statement, "redheads" are the homozygous recessive folks that express the red hair phenotype. "Potential for red" is a colloquial way of referring to the allele frequency, "r".
Of course you could also get actual changes in allele frequency for reasons that have nothing to do with fitness of the red hair phenotype. If you think about population growth on a regional basis, if there is more population growth in countries with lower frequency of a red hair allele, then the frequency of red hair in the human population as a whole would decrease. It seems likely this is occurring today since regions with higher frequency of red hair (northern Europe/UK/Ireland, also the US) have lower population growth than those with lower frequency (Asia, Africa, South America). There's no hint that this would result in a disappearance of the trait, though.

In the end a clear "yes/no" answer is kinda missing, I read the piece and the conclusion is not really clear to me.

@PascalVKooten I read and answered the biology question in the title and explained the National Geographic quote. If by yes/no you're meaning the question about whether the "howstuffworks author" is right or wrong, I don't really have any interest in addressing that especially because it's a long piece with a lot of different statements, most of them not about biology.

@PascalVKooten - "While redheads may decline, the potential for red isn't going away." According to this answer, that's a correct statement. And in the future there will be no redheads is almost undoubtedly false.

Thanks Bryan for this extensive answer. I will search for evidence for the changed mating patterns that you mention in the coming days and include it in this answer.

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How does it make thermodynamic sense for photosynthesizers to turn CO₂ into O₂?
My understanding is that animal metabolism consists of exothermic reactions like
$$\ce{C6H12O6 + 6 O2  ->6 CO2 + 6 H2O + energy}$$
This makes thermodynamic sense to me. Animals need an exothermic reaction to produce the energy we need to move around, etc. However, the other half of the picture, plants and other photosynthesizers producing oxygen, has never made complete sense to me. Are plants consuming $\ce{CO2}$, a "low energy" (I think) substance, and producing higher energy $\ce{O2}$ as a waste product? Is there so much energy available for photosynthesis that plants can afford to waste some of it producing $\ce{O2}$ simply to have enough carbon atoms to store energy via sugars?

The purpose of photosynthesis is to convert a non storable source of energy into a usable and storable form of energy.  If looked at from this perspective, it makes thermodynamic sense to produce higher potential energy substances in photosynthesis.

I've posted a related question to get a few clarifications so I can understand the answers below.

@kuzzooroo What do you not understand in the answers? If you need clarification you should request for it using comments. Also, please accept the answers if they have provided the right answer to your posted question.

OK, thanks for the guidance, @WYSIWYG. I think maybe the clarification I should have asked for is, is it even reasonable to via photosynthesis (in its totality) as $$\ce{6 CO_2 + 6H_2O + light -> C_6 H_{12} O_6 (sugar) + 6 O_2}$$ and is it reasonable to consider the resulting oxygen as a waste product?

@kuzzooroo That reaction is not correct representation of photosynthesis. Oxygen is a byproduct but as mentioned in the answers the light reactions and production of oxygen is not directly coupled to sugar synthesis from $\ce{CO_2}$.

Oxygen in photosynthesis does not come from carbon dioxide. It comes from water and this is the step that actually requires light: Photolysis of water.
The proton produced in this process is used to synthesize ATP and NADPH by a chemiosmotic process similar to what happens in mitochondria.
These biochemical pathways are also referred to as Light reactions.
Carbon fixation (or Calvin-Benson Cycle) requires energy (in the from of NADPH) and is therefore dependent on light reactions. The light has no direct role in carbon fixation. Oxygen production also, is not directly coupled to carbon dioxide consumption.

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text:
Introductory books about evolution
This days I read some debates on evolution. That made me more interested to read something reliable on topic - I mean books.
I'm christian - although I think it doesn't matter on that topic - and I would like to read a book that presents all weaknesses and strengths (as much as possible) of evolution. I want that not to be presented as a debate on creationism, but to be a book on evolution theory explanation and presentation.
I also would appreciate if you know to give some details about the author that wrote the recommended book. I mean if he/she is atheist or a christian or a skeptic.

You won't find a good book that presents the 'weaknesses' of the theory of evolution, and for good reason. There has to date been no convincing challenge to the theory, whilst it has been supported by experimental and circumstantial evidence as well as clear logic over and over and over again, as well as actually being observed taking place numerous times. The closest to what looking for is a book which presents our best understanding of how evolution works, or which discusses competing ideas about how evolution works - there's no question about whether it works.
The Selfish Gene by Richard Dawkins, whilst it contains some errors, has some very clear thinking about evolution in it, and in particular explains why group selection is a misguided idea.
The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene Koonin is a more up-to-date coverage of our current understanding of evolution, in particular with insights from modern genomics.
There are plenty of terrible books about the weaknesses of evolution, but they are deeply flawed. Pick one and I'll be happy to debunk it for you.

I really liked "Almost Like a Whale" by Steve Jones. He revisits the Origin of Species with 150 years of molecular biology - Darwin's logic all fits with the findings, and makes for an excellent read (far easier to get your teeth into that the original). Apparently the title refers to Darwin's observation that a bear, swimming in a lake and catching insects in its mouth, might conceivably evolve over time into a creature "almost like a whale".

Hi @Richard, I would only have a question. During my research, I found one claimed weakness of evolution theory from which it is deduced evolution more like a kind of belief, not like a scientific proved fact. This would be the fact that there are no transitional fossils. I also, in some poor research that I made, I found out that absolute dating is note quite reliable, and also it creates possibility of many more interpretations. Any suggestions on those two topics? (Especially scientific works that would treat this topic.)

N.B. I don't want to challenge you, although maybe that's an implication of my question. I'm mainly in search of some material on this issue that makes approaches from a scientific point of view as much as possible. Thanks. :).

@artaxerxe A little late, but I felt compelled in case others visit here. It's worth noting first that fossils are not the strongest evidence for evolution; rather, they provide pleasant corroboration for other fields and are easier to explain to non-scientists. That being said, the number of transitional fossils is still quite large. E.g. see [1], [2], [3].

Its not a book but the stated clearly series, http://statedclearly.com/videos/what-is-evolution/ it probably the best short clear summation of evolution I have ever seen, the berkeley understanding evolution site which is based in their book is more in-depth and also amazing. https://evolution.berkeley.edu/evolibrary/home.php

Almost anything by Richard Dawkins would be excellent value. I especially like his Climbing Mount Improbable as a short but gripping account of why evolution can achieve such astoundingly complex results.
Richard Dawkins (from my link above)

Richard Dawkins taught zoology at the University of California at Berkeley and at Oxford University and is now the Charles Simonyi Professor of the Public Understanding of Science at Oxford.

He is definitely an atheist.

Two recommendations:
1 - The Origin of Species by Charles Darwin.  This is a very accessible book, filled with clear explanations and examples, and conveys the wealth of evidence that Darwin collected as he developed his theory.  It includes a chapter on issues that people might see as "weaknesses", and convincing explanations as to why they are not.
Darwin began life as a Unitarian, and considered a career as a minister.  By the end of his life he had no belief in God.
2 - The Blind Watchmaker by Richard Dawkins, mentioned several times above.

+1 for The Blind Watchmaker. As for The Origin of Species, I haven't read it myself, but I suspect something more modern, such as the Selfish Gene, is better suited for an introduction.

I found The Origin of Species quite readable, but our understanding has developed somewhat since the 1850s.

The Voyage of the Beagle I would also add.

Another book by Dawkins which I find quite excellent is The Greatest Show on Earth. Unfortunately, you might find it a bit preachy in episodes since Dawkins gets – rightfully! – exasperated with some vocal, stupid critics.
Nevertheless, it’s a very compelling and interesting read, especially since it tackles some very complementary avenues of evidence for evolution. A similar outline is followed by Sean B. Carroll in The Making of the Fittest although he clearly focuses on the most compelling evidence for evolution: DNA – hence the subtitle: “DNA and the Ultimate Forensic Record of Evolution”.
I have no idea whether Carroll is religious or atheist – but shouldn’t that be strictly irrelevant?

+1, like your taste in books. @artaxerxe, I would also recommend Endless Forms Most Beautiful by Sean B Carroll for a great molecular introduction to evolution. http://en.wikipedia.org/wiki/Evolutionary_developmental_biology

Evolution is only fun when it is used to try to explain something. So to depart from the theme of Dawkins-books, consider:

Your Inner Fish by Neil Shubin

Shub is a Professor of Organismal Biology and Anatomy, Associate Dean of Organismal Biology and Anatomy and Professor on the Committee of Evolutionary Biology at the University of Chicago. He is famous for disocovering the Tiktaalik roseae or 'fish-with-hands'. The reason the book is fun is that it not only explains the basics of evolution, it uses it to show you something: why the human body is the way it is.

I also recommend Jerry Coyne's book, "Why Evolution is True."
As an introductory text book, I recommend "Evolution" by Douglas J. Futuyma. This is a very good introductory book covers almost everything about evolution. It aims to give you an overview not the detail.

The Ancestor's Tale .
This is an utterly, utterly fascinating book.

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What are the allowed evolution operators (on protein encoding sequences)?
What are the evolution operators, meaning allowed actions on the DNA sequence that encodes a protein.
I assume all evolution of genes is a result of duplication errors. So an answer could look somewhat like this: duplication of gene into two identical ones, omitting of nucleotide, addition of nucleotide and so on.
And some followup questions:

Does this mean that originally there were very few genes and they were very short?
If so - how few? How short?

It is incorrect to assume that all evolution of proteins is a result of duplication errors. Sequences can be changed in situ as well.

Also, evolution does not really act on proteins but on genes.

@terdon and all other base sequences that have any biological function like regulatory elements. I'm not sure how this question could be answered as it seems to be based on some false premises.

@MadScientist yes, I mean that evolution acts at the nucleotide rather than the amino acid level but felt it would be better understood by the OP if I said "genes".

The question is simply what kind of errors does the DNA replication machine do (or other mechanism  with which evolution occurs). I called it protein sequences, but of course I mean the DNA that encodes a certain protein. I rephrased for clarity.

Your follow up questions are vague.

I think what @AP means is that this question doesn't have the clean answers you are looking for.

An old microbial geneticists' adage is: anything that can happen will happen, and you just need to find a way to select for what you are seeking.
A look at the Wikipedia page on mutation might be instructive.

Looks like this is what I've been looking for.

The most frequent mechanisms are

Intragenic mutations: when existing genes mutate modifying gene function.
Gene duplication: leads to related genes in a single cell. A gene duplicates and then as two copies are available, one is free to change
Segment shuffling: leads to hybridisation of different DNA segments.
Horizontal transfer is transfer of DNA from one cell to another
Transduction: infection of cells by viruses or other intracellular pathogens where their DNA can integrate into the genome

You are incorrect to say all evolution occurs due to duplication. Your follow up questions are too vague. Genes can become larger or smaller, but yes as they increase so does their diversity.

Can you please clarify the following:
What exactly are intragenic mutations? What exactly is their mechanism?
What is the mechanism for complete gene duplication and segment shuffling?
Why didn't you mention single nucleotide errors by the replication process?


text:
How can I clean phenol extracted RNA?
I extracted RNA from skin and quantified it in an Nanodrop machine. The 260/230 ratio was very low and two peaks appeared in the absorbance curve, but the RNA is ressuspended in RNAse free water. How can I clean it?

wash it with chloroform..

Phenol absorbs at 230 nm, this is the most likely contamination in your case. You should try to avoid pipetting from the phenol phase, or use a phase lock gel to make this easier. I assume you washed it a few times with pure chloroform after the phenol/chloroform mixture, that should help to get rid of the phenol.
I only precipitate my RNA with 1-1.5 volumes of isopropanol after the chloroform/phenol extraction, that should be sufficient for most uses. Just add the isopropanol, keep it at -20°C for 30 minutes and then centrifugate it at 9000 g for 20 minutes, redissolve the pellet in water.


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Displaying nucleotide at a single position from RNA-seq reads in a BAM file
How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am interested in. This seems like you should be able to do it but I can't figure out how.
To be clear I have a BAM file of a bunch of reads. I'm looking to do something like samtools magic reads.bam chr3:10000 where I get back something like:
T T T T T T T T T T T T T T T T T T T A A A A A A A A A A A A A.

I just want to sanity check the output of bcftools by actually looking at the base calls.

Your best option is to create a tab delimited position list file:
chr3    1000

You can then use the samtools mpileup -l pos.txt option
-l FILE      list of positions (chr pos) or regions (BED)

This file can also be in bed format if you are interested in specific regions


text:
Effect of histidine on the binding affinity of HisP
I was asked the following question by my teacher:

A gene regulatory protein called HisP regulates the enzymes for
  histidine biosynthesis in the bacterium E. Coli.  HisP is a protein
  whoes activity is modulated by histidine.  Upon binding histidine,
  HisP alters its conformation, dramatically changing its affinity for
  the regulatory sequences in the promoters of the genes for the
  histidine biosynthetic enzymes.
If HisP function sas a transcriptional repressor, would you expect
  that HisP would bind more tightly or less tightly to regulatory
  sequences when histidine is abundant? Why?

My own attempt at a solution:
Less tightly.  If histidine is abundant, HisP's job is to stop the histadine pathway as a "repressor."  If HisP binds less tightly to promotors, the pathway should not produce as much histadine.

Still if you change your question as (If histidine is abundant, HisP's job is to stop the histidine pathway as a "repressor." If HisP binds less tightly to promotors, the pathway should not produce as much histidine.)
Then it should be under another assumption that what is the effect of HisP binding promoter of enzyme's gene. Is it suppressing the transcription or amplifying the transcription.
If it suppresses transcription then answer is more tightly, if it amplifies the transcription then answer is less tightly. I suggest you put this clearly in your answer, as the question is not quest accurate.

I guess your answer might be wrong.
The question should be under another assumption that how does this protein HisP regulate histidine biosynthesis. positiver or negative feedback regulation.
Generally, amino acids synthesis is regulated by negative feedback loops so that cells could control the amount of amino acids they want. In this case, the answer should be more tightly. As it functions as a repressor then it should bind promoter more tightly so that to repress the transcription more which then generate less histidine synthesis enzyme. (I believe this is what your teacher want you to answer)
In the other case, biosystems sometimes have the positive feedback regulation so that they can amplify the sensitivity to the environment noise or generate bistability (phenotypic switching). In that case, the protein bind promoter less tightly in order to generate more histidine.


text:
How many human proteins have a solved 3D structure?
I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.

I think you are going to have a lot of issues with redundancy, especially if you want to know the number of unique proteins.

@GWW I guess that writing a small script can get rid of the redundancy.

You may have better luck asking this question on biostar.

Notice that “solved” is very subjective. Not all of the structures are of high quality, and some of them are just plain incorrect due to experimental errors.

many of these proteins only have a domain or two solved as structures. animal proteins are hard that way.  that's where this question becomes a little difficult imho.

6405 proteins mapping to 5220 genes, according to Ensembl.
In Ensembl's BioMart, you can select the PDB ID as external reference. Export the results and count the unique proteins/genes that have a PDB ID.

PDB is a good resource for answering such questions, since it will let you filter results by many additional parameters. To count and extract 3D structures of human proteins:

Open Advanced search tab of the PDB website.
Select Biology -> Source organism from the menu.
Type Homo sapiens (human).
You can reduce redundancy by checking Remove Similar Sequences at n% identity below.
Submit query.

To add further filters, click Refine Query with Advanced Search. There you can extract structures by deposition date, quality (eg. resolution or R-factors for structures solved by X-ray diffraction), ligands, enzyme classification, etc. (by checking Add Search Criteria)
Search for human proteins with removal of homologues with 90% identity cutoff fetches 7117 structures. The number of good quality X-ray protein structures (resolution < 2.5A) is currently 3964  (with the same identity cutoff).
You can then download the fetched list or create custom reports (menus below).
A good tool (also used by PDB) for generating non-redundant protein datasets is cd-hit.

From your comments it doesn't seem like you are adverse to writing some custom scripts so one option would be to take advantage of the NCBI Structure database.  You can filter it by organism and then download the results as a text file / XML.  If you need access to the raw PDB data you could then download the PDB archive and examine the ones in your filtered list.

PDBe's new search system is designed to answer just such questions
http://www.ebi.ac.uk/pdbe/entry/search/index?organism_synonyms:HUMAN&view=macromolecules
shows there are 6964 unique human macromolecules with structure data in the PDB.
Of course, many will be fragments of proteins rather than the whole molecule.


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How can a monocot get so massive?
Some monocots (such as palms) are impressively thick and massive, yet botanists maintain that they don't have secondary growth. Why do botanists say this?  How can it get so big without secondary growth?

The vascular system is different in monocots and dicots. In dicots the vascular tissues are arranged in concentric circles; one of these rings is meristematic cells (undifferentiated cells that can differentiate into any cell type). This ring of meristem tissue is called the vascular cambium and is where secondary growth occurs - xylem grows inwards and phloem grows outwards.
Whereas:

Monocots have a distinctive arrangement of vascular tissue known as an
  atactostele in which the vascular tissue is scattered rather than
  arranged in concentric rings. Many monocots are herbaceous and do not
  have the ability to increase the width of a stem (secondary growth)
  via the same kind of vascular cambium found in non-monocot woody
  plants. However, some monocots do have secondary growth, and because
  it does not arise from a single vascular cambium producing xylem
  inwards and phloem outwards, it is termed "anomalous secondary
  growth". (Wikipedia)

For palms specifically:

Palm trees increase their trunk diameter due to division and
  enlargement of parenchyma cells, which is termed diffuse secondary
  growth. (Wikipedia)

Parenchyma cells are type of cells found in plant ground tissue, which makes up the bulk of plant mass.

We tend to call dicots eudicots these days.

@poshpaws who is "we"? I work in the Ag industry and I hear "dicot" thrown around more often in conversation. Maybe it matters less when you're not trying to write academic papers. :)

Sorry, yes I should have said "the preferred academic term". In the real world people still call them dicots!

@poshpaws thanks for the comment though - it gave me reason to read up on all the plant taxonomy I'd forgotten and renewed my fondness for magnolias!


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If a receptor is inhibited throughout embryogenesis, could there be observable phenotypic differences in the adult?
So I read a journal article entitled "Maternal hypoxia and caffeine exposure depress fetal CV function during primary organogenesis" (Momoi, et al., 2012) and in essence the article speaks of the period of time in embryological development when the cardiovascular system is developing as being the time when the fetus is most susceptible to epigenetic events, and how adenosine and its A2 receptor have a role in dilating coronary arteries in hypoxic conditions. It later goes on to say that since caffeine is an adenosine A2 receptor antagonist, mothers who consume caffeine regularly create a suboptimal environment for the fetus - this is referred to in the article as IUGR (intrauterine growth restriction).
My question is: Are there any effects (or do you believe there could be effects) of this inhibition occurring during development that affect the fetus later in life? As in, do you think there would be adult phenotypic changes of any kind due to the regular inhibition of a receptor during development?
I thought about this for a while and all that was apparent to me is that if the mother was both consuming caffeine and hypoxic, then the fetus could experience myocardial damage because its coronary arteries wouldn't be receiving the signal to dilate and the heart might be "starved" of the proper oxygenation. But even so, the receptor would still be present in the adult. Do you think there could be a decrease in transcription of a receptor that is continuously blocked (you don't need to address this in your answer -- notice that I'm asking for an opinion, which you can choose to give or withhold)?
FYI: I'm writing a review on how maternal prenatal health contributes to the epigenetic profile of offspring and I'm actually focusing more on the epigenetic contributions to the adult hypertensive phenotype. I stumbled upon the CV/adenosine article and was curious about whether there could be any long-term changes, so I asked all you wise folk. It has been observed that mothers fed a low-protein diet give birth to children with reduced nephron count and glomerular hypertrophy -- my goal is to understand what the current state of knowledge of this mechanism is. So if you have any ideas about anything here, or you've got an awesome resource related to this material, I'd really appreciate hearing about it.


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Birds placing sticks on train tracks?
I live in a semi-rural area in Germany, close to a park which trains go through every 20 minutes.
Today, I saw something that left me perplexed.
There is a large population of birds that look like crows or ravens, yet fatter. They seem to be quite social and move around in large groups. Today, I spotted one carefully laying sticks from a nearby tree on the train track while the others seemed to spectate.
What exactly was that bird doing? Is this common? Did it have a purpose, or was it just coincidental?

Some corvids do use tools, and are fast learners. Could these be using the train and tracks as tools to cut sticks up smaller?

There is a book, In the Company of Crows and Ravens that details human-corvid interactions. That might provide insights for you. The link is: http://yalepress.yale.edu/yupbooks/book.asp?isbn=0300100760

@EnergyNumbers - I want to believe :)

If the birds are doing in this in a place where you can watch them repeatedly, why not set up camera to watch them?  I recommend a pocket camcorder with a big SD card (which is nice to have in general).  I don't think anyone will be able to tell you for sure without footage of what they do after putting them on the tracks. They could have just chosen a really bad place for a nest, or it could even be courtship behavior.

If the sticks were somewhat large, they may have been putting them on the tracks so that the trains would break the sticks into smaller pieces (which would probably be easier to build nests with).

There is a large population of birds that look like crows or ravens,
  yet fatter. They seem to be quite social and move around in large
  groups.

First of all, this seems like a crow. Crows are very social birds, they live in flocks or murder.

Theory: It may be a Mating Ritual?

No! The have a very spectacular mating ritual!.

Theory: It's Making a nest

Obviously No! Crows nests are always way hidden at 18-60 feet above ground(mostly) in the tree trunk.
My Theory
Crows are very curious birds. What you saw, might be a new play the young crows found. It's common that crows will do unusual thing when spectated by the elders and siblings.

Crows have been known to use human actions in order to accomplish their own purposes: read this story about them using cars and waiting for the lights to change at a crossroads. Then of course, the question is whether they have a specific purpose in your case with these sticks, or whether it's just... for the fun of it?


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Why does vision go blurry after microscope use, and how to prevent it?
After using a binocular microscope recently for about 20 minutes, my vision went blurry and for an hour or so it was much harder to read small text. This occurs to a (far) lesser extent whenever I use it for a shorter time.

Why does this occur?
Which is the optimal microscope light intensity so this does not happen?
What other variables should I beware of?

Wow, I use microscopes daily and I never had this problem. What type of microscope / light source are we speaking about?

@nico It's an 'apex researcher' microscope. For lighting it's a small lamp mounted underneath the slide hole and lens. I don't know what's the standard for microscopes so I can't really comment if it's anything out of the ordinary.

Could it be because you are focusing at a fixed distance for a long time? I would try changing my focus every 5 mins by looking someplace far away.

@Alyosha: OK, that is a fairly standard brightfield microscope. The only thing I can think of is that your problem may be due to the fact that the lenses of the microscope are not top quality and may give some optical aberrations that your eyes got used to during the 20 minutes.

I'll try Memming's idea in the future.
Thanks all.

@Alyosha If you have gotten reliable answers to the problem you faced and you no longer have the same issue, I would request you to close the question.


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Chicken Genome what are the LGE 'chromosomes'?
The chicken genome identifies two "LGE" sequences in the chicken genome.  Are these distinct chromosomes or some highly variable sequence from the genome that is put in a separate sequence? I'm thinking they are not really separate chromosomes.... It would be great to know a little bit about their biology.  the papers didn't seem to help me.

LG stands for "linkage group". It seems the Chicken Genome Sequence group (Hillier et al., 2004) allocated several linkage groups (alleles or genes which tend to be inherited together) to the microchromosomes (tiny chromosomes typical of birds and reptiles), in this case called "linkage group E64" and "linkage group E22....". There are a load more microchromosomes which are the ones numbered 28-31 and 33-38 which haven't yet had their sequences resolved (Burt, 2007).
References:

Burt, D.W. (2007) Emergence of the Chicken as a Model Organism: Implications for Agriculture and Biology. Poultry Science. 86 (7), 1460 –1471. Available from:  [Accessed: 8 February 2012].
Hillier, L.D.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A.M. & Delany, M.E. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432 (7018), 695–716.

So this makes them a little bit like the 'random' chromosomes in the human builds i guess.


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What kind of spider?
I’d much appreciate help figuring out what kind of spider this is. I’m in Western Washington, in the northern suburbs of Seattle. Its outside, on the eaves of the house. Particularly wondering if a yellow sac spider.

Interesting!  The size, shape and posture, as well as the visible patterning on the body, are all reminiscent of Dolomedes tenebrosus, the common terrestrial fishing spider here in the east.  However, there are a couple of odd things here:
1.  Dolomedes is a genus only found (as far as I know) in the eastern half of the US,
2.  The abdominal color pattern is a bit off from what I would expect (dark flank marks at the front of the abdomen, especially), and
3.  That looks like an egg sac the spider is sitting on top of, as if it was guarding, but fishing spiders (as far as I know) do not make egg sacs like that - they make ball-shaped egg sacs which they carry around with them using their fangs to hold them.
The thing is, nothing else rings a bell with me - the only other large wandering hunter that would be anything like that in the Pacific NW, that I know of, is the Giant Crab Spider Olios giganteus, which doesn't look much like that, although it does make a silken retreat/egg sac protection.
I confess that I am stumped, although I can confidently say that it is not a Yellow Sac Spider.
However, I can suggest two good options for identification:
the Burke Museum: https://www.burkemuseum.org/collections-and-research/biology/arachnology-and-entomology/contact-form
and Bug Guide: https://bugguide.net/node/view/6/bgimage
both of which can often do identifications from photos alone (although with spiders, this can sometimes be tricky).
Good luck!

This is not a Cheiracanthium (a yellow sac spider) as those are fairly homogenously-colored with no discernable markings or speckles.
This is a Running Crab Spider of genus Philodromus. Here is a picture of Philodromus Spectabilis from Washington state:

(Source: https://inaturalist.org/observations/140737985 identified by two arachnologists )
The crab-like stance places this in the crab and running-crab superfamily Thomisoidea and the fact that the second legs are its longest legs separates this from the normal crab spiders, placing this is the Philodromidae (running crab spiders) as regular crab spiders have their front-most legs longest.
There are no Giant Crab spider (Olios sp) this far north in the US.
There are other genera of running crab spiders in Washington, but they are distinguished by a darker cardiac mark and/or significantly different leg proportions.
It is not always possible to identify spiders to species level with photos, but P. Spectabilis is a close match. There are over a dozen species of Philodromus found in Washington state.


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Can mitochondria be regenerated by the cell?
In the cell, division of mitochondria takes place on a regular basis, but what if there are no mitochondria present in cell (suppose all of them died), then can the cell make new mitochondria on its own?

No. Cell will die due to shortage of ATP. Also, making an organelle requires much more than just proteins.

Additionally: Dying mitochondria release (besides other substances) a lot of Calcium ions and Cytochrom C which triggers apoptotic cell death.

If we were to suppose, as in the question, that all the mitochondria in a cell 'died' ('were irreparably damaged' would be better, as they are not independently alive) without any other consequences the cell would have no way of regenerating them. Even if the cell had another source of ATP (see @another 'Homo sapien' comment) such as anaerobic glycolysis, one very clear reason is that the mitochondrial DNA could not be replaced (there are no copies of it in the nucleus). If the mitochondrial DNA were not replaced, then there would be no way of making the mitochondrial proteins it encodes.
The cell would die for a more immediate reason than suggested in the comment, and one that should be of interest in relation to a less well-known function of mitochondria. Mitochondria play a key role in the process of programmed cell death — apoptosis. In this process signals cause the mitochondrial membrane to become permeable and allow the efflux of cytochrome c, which is a signal for activating the apoptopic pathway. Presumably if mitochondria were damaged by other means the leaching out of cytochrome c would have the same effect, causing the death of the cell.
If you think of the overall economy of an organism, it's often easier to make new cells rather than trying to repair ones that are beyond redemption.
Further Information

Mitochondrial DNA: http://www.ncbi.nlm.nih.gov/books/NBK26924/
Apoptosis and mitochondria: https://en.wikipedia.org/wiki/Apoptosis#Activation_mechanisms


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What is this Japanese study of the Pfizer vaccine measuring?
https://www.pmda.go.jp/drugs/2021/P20210212001/672212000_30300AMX00231_I100_1.pdf
If you put it into google translate, the abstract contains the following:

"In the biodistribution test, luciferase RNA-encapsulated LNP was intramuscularly administered to BALB / c mice. theAs a result, the expression of luciferase was observed at the administration site, and the expression level was lower than that in the liver.Was also recognized. Expression at the administration site of luciferase was observed from 6 hours after administration, and 9 days after administration.Disappeared. Expression in the liver was also observed 6 hours after administration and disappeared by 48 hours after administration. Also,Intramuscular administration of radiolabeled LNP encapsulating luciferase RNA to rats to quantify biodistributionUpon evaluation, the radioactivity concentration was the highest at the administration site. Liver is highest except at the administration siteIt was good (up to 18% of the dose)."

Another translation (via DeepL) of the first part of the same paragraph:

In the biodistribution study, luciferase RNA-encapsulated LNP was administered intramuscularly to BALB/c mice, and the expression of luciferase was observed at the site of administration, and also in the liver, although at a lower level.
The expression of luciferase at the site of administration was observed from 6 hours post-dose and disappeared by 9 days post-dose.
The luciferase was also observed in the liver at 6 hours post-dose and disappeared by 48 hours post-dose.

Does this mean that they tracked the actual distribution of the vaccine in the body of the rats, or was it just a study of the lipid byproducts?

Since they are using luciferase, which emits light I would guess direct observation.

Would this study be a reliable measure of the distribution of the spike protein throughout the body? Or no?

Note the DeepL translation says expression was lower in liver while GoogTrans says the opposite.  The length of expression, though, they agree was shorter in the liver.

There are at least three types of studies being described.  In a paragraph before the quoted one, they talk about testing for the PEGylated lipids ALC-0315 and ALC-0159 in plasma, liver, urine, and feces. The lipids rapidly moved from the blood to the liver, and were found in the feces; none were detected in the urine.
The other two kinds of studies are described in the quoted paragraph.  One studied the protein product produced by the animal's cells from the administered mRNA coding for luciferase.  The cell product is detected by the light it emits.  The luciferase was detected both at the site of injection and in the liver, and continued being detected at the injection site for much longer.
The last study was of the same kind of mRNA nanoparticles, except that these were radioactively labeled.  The radioactivity from them was detected at the injection site and in the liver.  This indicates there were nanoparticles (or the radioactive components of them) present in both places.
So they tracked the lipids, and either the whole vaccine nanoparticles or some other component of them, but also, and most significantly, they tracked the animal's cellular product of the vaccine's mRNA (luciferase, standing in for the true vaccine's spike protein).

Thanks. When we see the data from Radiolabeled [Cholesteryl-1,2-3H(N)]-Cholesteryl Hexadecyl Ether, are we tracking just the nano-particles, and the luciferase is tracking where the spike protein would have expressed? Are the two correlated or not? This is a major sticking point as to what was being measured.

Since it's a lipid envelope component that was radiolabeled, that test tracks that part of the envelope, whether or not the nanoparticle remains intact. The luciferase measures a quite a different thing, a protein constructed by the animal following instructions of the mRNA. They would be correlated only in that both lipid and mRNA entered as parts of the nanoparticles.  They go their separate ways.

It looks like they're using the luciferase RNA as a substitute for the actual mRNA used in the vaccine because, since luciferase emits light when exposed to its substrate, it's easy to measure the expression and it's commonly used as a reporter for gene expression in many contexts. As far as I can tell, they seem to be using the same LNP formulation as the real vaccine, the only difference is the luciferase RNA substituted for the spike one. Unless there's a difference in how luciferase protein is expressed compared with spike (this seems unlikely to me), this experiment probably accurately reflects where spike is expressed after vaccination.
[disclaimer: I do not speak Japanese, and am answering with a great deal of assistance from Google Translate]

I have people telling me with absolute conviction that this study is only a study of where the lipid byproducts end up -- you're saying it is NOT that and is a genuine bio-distribution study of where the vaccine is delivered?

@sakurashinken As far as I can tell there is only luciferase RNA included, no luciferase protein. So, the only way they'd get luciferase activity would be if the thing they are injecting is getting RNA into cells that are then translating it into protein. So it's a measure of "if we deliver mRNA this way, where are the cells that end up translating that mRNA". It's a different mRNA than that which produces the viral spikes, but the presumption they make is that the delivery vehicle is what matters for distribution, not the identity of the transcript.

Thank you for the clarification.


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What is it about the housekeeping genes that makes them almost immune to gene regulation?
When it comes to eukaryotes, including ourselves, we have all different kinds of specialized cells and tissues that are so different, yet originally all came from the same single cell. And apparently the reason for that is differential gene expression, where different genes get to be expressed in different cells. But there are, however, a set of genes that gets to be expressed in almost all of the cells.
My question is not why, but what is it about these genes that in a way makes them above the laws of regulation? Is it in their sequence? Or are they located on a single chromosome or perhaps regions that are somehow non-regulatable?

Housekeeping genes aren't clustered on a single chromosome. It is perhaps not that 'housekeeping' genes - broadly expressed genes - are 'above the laws of regulation'; rather that their regulation is merely more straight-forward than that of specialised genes.
I can think of 2 factors that could be relevant:

Abundance of methylation sites (CpG sites)
Promoter sequences and hence the transcription factors regulating expression of housekeeping genes are distinct from those controlling specialisation

I think the second (promoter sequences) is the better explanation, since housekeeping genes are abundant in CpG islands; but I'll explain a bit about both.
tl;dr: Housekeeping genes have simpler promoter and enhancer regions that are not bound by particular complexes which act to inactivate regions of the genome in a hierarchical manner during differentiation (according to the transcriptional program). http://genomebiology.com/2007/8/7/R140
Preamble
In forming tissues during development, cells must differentiate from embryonic stem cells, which have very wide potential to express many genes and give rise to all cell types; to partially specialised stem cells e.g. hematopoietic stem cells (HSCs) which are limited to give rise to all blood cells but not, say, neurons or pancreas or skin. Completely differentiated cells have a much more restricted domain of possible expression, and are more-or-less condemned to their fate.
Waddington's developmental landscape is a nice metaphor for how cells specialise:

DNA Methylation
A major mechanism behind this one-way narrowing of potential is methylation of DNA, which suppresses transcription. As the ball rolls down the landscape it acquires new stretches of methylation on its DNA, rendering it inactive which (for our purposes) is permanent and irreversible.
DNA methylation consolidates its chromatin inactivating function by acting as a signal for proteins which chemically modify histones (around which DNA is wrapped in chromatin) with further signals to condense chromatin, which occludes the transcriptional machinery from doing what it does best. (There are also activating histone modifications, and we imagine chromatin being, roughly, in OPEN and CLOSED states regarding the possibility of RNA polymerase gaining access to the DNA.) Since histones are ubiquitous & regularly spaced over the genome, there aren't "non-regulatable" regions - chromatin is opened or closed by the interactions of various DNA binding proteins, some reading and writing signals on to the chromatin.
So one plausible hypothesis is that housekeeping genes are relatively devoid of CpG sites (where methylation occurs). However I think this is not true. Many human genes have regions abundant in CpG (called 'islands') around their promoters, and in particular virtually all housekeeping genes. When genes are active, these CpG islands are unmethylated - hence in most tissues housekeeping genes have unmethylated CpG islands, something else is keeping them unmethylated.
Specialised cells, through a hierarchical transcriptional program of 'master regulators', successively close unneeded regions of their chromatin during differentiation, and keep open regions containing housekeeping genes, and the 'specialised genes' that relate to its specialism - these regulators are transcription factors which recognise the regions they act upon by binding promotor or enhancer sequences.
Housekeeping promoters and transcription factors
Transcription factors bind to enhancer or promoter sequences and open or close the chromatin for RNA polymerase, usually as part of a co-operative complex of many factors, including proteins that modify the histones or methylate DNA.
A good hypothesis is that the promoter/enhancer regions of housekeeping genes differ from those of specialised genes which are inactivated in many tissues. The transcriptional programs in differentiation must call forth factors that bind and inactivate specialised genes but keep active things like actin, ribosomal genes, etc.
This paper finds that upstream regions of housekeeping genes are less conserved, and a particular set of promoter motifs are over-represented. This suggests that housekeeping genes have relatively simple regulation by a few transcription factors; they lack binding sites for those transcription factors with important specialised roles in development.
To summarise, I think the following is likely: Housekeeping genes' promoter and enhancer regions exempt them from the complex transcriptional programs of hierarchical inactivation responsible for cell differentiation that many other genes are subject to. Housekeeping genes simply lack the relevant binding sites for these specialised transcription factors; they have instead more simple 'core' promoter elements. All the DNA methylation and opening/closing of the chromatin is a consequence of the transcriptional program.

http://en.wikipedia.org/wiki/CpG_site
http://en.wikipedia.org/wiki/Embryonic_stem_cell
http://en.wikipedia.org/wiki/Hematopoietic_stem_cell
http://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070
http://en.wikipedia.org/wiki/Histone
http://genesdev.cshlp.org/content/25/10/1010.full
http://genomebiology.com/2007/8/7/R140   < most relevant thing to read, and the basis of my own conclusion

The problem with housekeeping genes is that they are often not stable and their expression depends on the cell types as well as the conditions. They can be stable under one condition, but are not under another. So this needs to be tested every time you have to choose a housekeeping gene - always use GAPDH or beta-Actin simply doesn't work or skews the results.
The reasons why the housekeeping genes are chosen is because they are thought to be independently expressed (more or less) in the cells and that the actual experiment has in influence on them. This is also the reason why genes involved in the energy metabolism or the structural integrity of the cell (like GAPDH or beta-Actin) are chosen. This idea is not wrong, but needs to be tested, since transcription regulation networks are complicated and often bear interesting, surprisinf (and unknown) relations.
The following articles should be interesting in this context:

Reference Gene Validation Software for Improved Normalization
Selection of suitable housekeeping genes for expression analysis in
glioblastoma using quantitative RT-PCR
Reference genes in real-time PCR

What also gives quite a lot of information including a large number of references on this topic is the website from Gene Quantification (which sell products in this field).

Great answer - common misconception that "house keeping genes" are consistent in expression when used as reference genes. It is common practise to include several reference genes in many experiments and to confirm empirically that they do not vary between your samples.

Either this - or (what I have also done) is to test a number of genes and then choose the stable ones.


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How can I get started in molecular biology?
I have a background in computer science and math and am interested in learning molecular / synthetic biology - what resources do people recommend?

Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. In particular, opinion-based questions like this are not appropriate for this site. Thanks!

I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

@AlwaysConfused We have a tag wiki that addresses what we expect for "book recommendation"-style questions. https://biology.stackexchange.com/tags/book-recommendation/info This one does not seem to follow those guidelines, and I'd probably vote to close it as a regular user. I will defer using my diamond power, though, unless I see it gets 4 votes to close from others.

@tyersome: Also, if you prefer physical books and have a state university or community college conveniently nearby, many of them have "community borrower" options for their libraries.


text:
Why does spraying water on plants help them survive in case of frost?
I've heard that spraying water on plants will help them survive the frost. Why is that?
Some say that you should do it in the morning right before the sun rises, and others spray water the whole time of low temperatures.
What is the explanation for why this spraying techniques works?

The question has already been asked in Physics.
According to the information there and here the sprinkling must continue throughout the period when temperatures are below freezing, and is only effective for temperatures down to around -5 °C.
Explanations invoke three interrelated effects: when water freezes heat is released so there is a warming effect; the temperature of an ice-water mixture is 0 °C; and an ice layer will insulate the leaf. As long as the temperature of the leaf stays above freezing there will be no frost damage.

Thanks, this sounds logical. But take a look at this answer: https://gardening.stackexchange.com/questions/33070/to-water-or-not-to-water-a-plant-right-before-near-frost-temps-in-mid-spring#answer-33075. It appears that fast thawing also plays some role here


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How can we calculate the constants of the SIR model?
I am not a biologist by profession, but I am attempting to implement a simple SIR model from the following paper. The paper assumes the following constants are known:
rc    = growth rate of susceptible group S
k     = carrying capacity of susceptible group in absence of infection
alpha = max value of per capita reduction rate of S due to I
a     = half saturation constant
gamma = natural recovery rate from infection
delta = death rate of recovered population
I found some coronavirus data from the following source, and I plotted the Italy data in particular:

Can I calculate the constants above from this type of data?
Is it a good assumptions for these "variables" to be constant?

Here is my attempt of the model with the constants given in the paper

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. In particular, this question seems like it might be a better fit for [Bioinformatics.SE].  Thanks!

@tyersome Are you an administrator- can you migrate it please? Thank you

Sorry, I'm not and so don't have that level of access. Is there some reason you can't copy this and post on that site (and then delete from this site)?

I'm voting to close this question as off-topic because it appears to be a question about mathematical modeling rather than biology.


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Why pouring salt in the wounds is painful?
Pouring salt in the wounds is so painful. I am sure you all experienced this. whats happend there?

De salt particles are alien bodies and can damage the tissue by mechanical means (This would also happen if you pour sand into an open wound). Also, the exposed tissue is vulnerable to dehydration, wich happens faster if the osmotic pressure is higher. Finally, nerve tissue is particulary sensible to changes in the ion composition of its sorroundings, so the added sodium may affect the action potential of the nociceptors.


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Time from stimulus to gene expression
My understanding is that gene expression, in response to some stimulus, generally occurs on the order of minutes. I'm curious about the extremes...the quickest and the slowest cases.
What is(are) the fastest time(s) recorded for genes being expressed in response to a stimulus? What are the slowest times?

The fastest I know of is the heat shock locus in Drosophila.  The transcription factor (HSF) accumulates within about 30 seconds, and RNA Polymerase can be seen to start accumulating within 3 minutes.
Katie L. Zobeck, Martin S. Buckley, Warren R. Zipfel, John T. Lis.  2010. Recruitment Timing and Dynamics of Transcription Factors at the Hsp70 Loci in Living Cells.  Molecular Cell 40(6): 965-975


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Transcription and translation of prokaryotic operons
I'm taking a molecular genetics course, and we're currently discussing prokaryotic operons. The lacZ operon came up frequently for me as an undergraduate as an example for teaching regulatory control of transcription, and the focus was always on determining whether the operon was transcribed under certain conditions (mutations, nutrients, etc). I don't remember much discussion about what happens after transcription. Today, however, I noticed something I had never seen before: three of the genes in the lacZ operon are transcribed simultaneously on the same transcript--I don't know how I missed this before!
My question is what happens post-transcription. Obviously there are 3 protein products. How are these products derived from the transcript? Is the transcript broken into 3 pieces, or does a single ribosome translate all 3 proteins from a single transcript substrate, or do ribosomes translate a single protein from a single transcript substrate at a time? Where could I find the relevant literature that elucidated the translation process?

As you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another.
The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), giving rise to three individual proteins.

How from one mRNA three protein products are translated? The polycistronic DNA consists of a promotor (Plac), which ensures that transcription will be initiated, and three open reading frames (ORFs) for for lacZ, lacY, and lacA. Upstream of each of the ORFs, ribosome binding sites (RBSs) are located. Translation is initiated by the binding of the ribosome with both the RBS and the start codon. Thus, multiple ribosomes can bind upstream of the three ORFs and thus resulting into three proteins.
There is not very thorough literature on the translation of polycistronic RNA in prokaryotes, mainly because the condition which is necessary for translation is the RBS and there is nothing specific for polycistronic translation. A brief overview on the subject can be found in several places, as I recommend the following:

Ralston, A. (2008) Operons and prokaryotic gene regulation. Nature Education
From Genes to Genomes: Concepts and Applications of DNA Technology
Molecular cell biology
Analysis of Genes and Genomes


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Mouse meta-globin mRNA problem

This is an mRNA strand of mouse meta-globin:
5'-ccccagauacggaauucgaau-3'
A) Which small RNA (below) is most likely to regulate expression of
  meta-globin?

5'-auucgaauuuucuaucugggg-3'
5'-ggggucuaucuuuuaagcuua-3'
5'-ccccagauacggaauucgaau-3'
5'-uaagcuuaaggcauagacccc-3'

B) This RNA most likely?

acts as an siRNA
inhibit meta-globin translation
increase meta-globin translation
help transport meta-globin mRNA back into the nucleus

My attempt:
I think A is 2 because the strand is complementary and will bind nicely to the mRNA strand.  For B, I'm between 2 and 3, but cant decide.

I'm going with 1) for A since you need the strand to be the reverse complement.

A) Is this a take-home exam question? 1) Yes, then I can't answer your questions for you. 2) No, well, I'll see if I have time tomorrow to get to it.

@Larry_Parnell this is a problem I found in an MCAT book.  (I'm studying for the mcat)

There are always exceptions but you can consider some general rules.
A is 1 i.e the sequence that is perfectly complementary (2 is complementary but direction is parallel — cannot base-pair), then B would be 1 (siRNA). Reasons (some are just based on general rules of siRNA design):

siRNAs have to be perfectly complementary
The size is also perfect for a siRNA (21nt)
U/A (2-3 residues) at the 5' of the siRNA
U at 10th position
GC content 43% (ideal 30-50%)

See here for guidelines for siRNA design.


text:
Predicting progeny of recessive mutations using recombination
I was asked this question on a test and got it wrong, but I'd like to know how to do it.  The answers are shown in the blanks below:

You are studying two recessive mutations in the fruit fly D.
  melanogaster. The red_ mutation causes flies to have red bristles
  (wild-type flies have black bristles) and the shiny- mutation causes
  flies to have shiny eyes (wild-type flies have eyes that are pebbly).
  You mate females from a true-breeding strain with red bristles and
  pebbly (wild-type) eyes to males from a true-breeding strain with
  black (wild-type) bristles and shiny eyes. F1 females are then mated
  to males that have red bristles and shiny eyes to produce F2 progeny.
If you analyzed 1000 male progeny in the F2 generation, how many flies
  of each possible phenotypic class would you expect, if:
The two traits are determined by two autosomal genes that are 15 cM
  apart:
Red bristles, pebbly eyes:_____ 425_______
Red bristles, shiny eyes: ______75____
Black bristles, pebbly eyes:____ 75_____
Black bristles, shiny eyes:____ 425______

My attempt:
So I know the 15cm=recombinants/parentals * 100 but I don't see how that formula can help.

First, the recombination equation is:
cM = recombinants/(recombinants AND parentals) * 100

Let's assign the following genotypes for clarity's sake:
RR = black bristles
Rr = black bristles
rr = red bristles
SS = pebbly eyes
Ss = pebbly eyes
ss = shiny eyes

F1 cross: rrSS x RRss = RrSs (all progeny)
F2 cross: RrSs (F1) x rrss = ?

You would have the following gametes:
Parent 1, RrSs = RS, Rs, rS, rs
Parent 2, rrss = rs, rs, rs, rs

Draw your punnet square and you get the following genotypes of the offspring.
So your GENOTYPES of your F2 cross will be RrSs, Rrss, rrSs, rrss
Let's translate those to phenotypes.
RrSs: black pebbly (parental)
Rrss: black shiny (recombinant)
rrSs: red pebbly (recombinant)
rrss: red shiny (parental)

Now let's look at recombination frequency.
15cM = (recombinants/(recombinants+parentals)*100
recombinants/(parentals+recombinants) = 15/100

This tells you for every 15 recombinants, you have 85 parentals. If you scale this up to 1000, that's 150 recombinants for every 850 parentals.
Your 150 recombinants comes from 75 black/shiny and 75 red/pebbly.
Your 850 parentals ceoms from 425 black/pebbly and 425 red/shiny.
Anyways that was my attempt which appears to be directly opposite to what your answer key says. Did you copy it down correctly?


text:
How do biologists infer correct ORF of a DNA sequence?
Each DNA (RNA) sequence has 6 possible Open Reading Frames(ORF). My question is: What are the theoretical bases of in vitro or in silico tries to find correct reading frame of a sequence?
Is it just distance between Start and Stop codons, or are there some other factors with more important impacts in this subject?

I have edited your question a bit. Please feel free to roll back if this does not suit you

Homology, ESTs, codon usage, length of ORF

The start and stop codons depend on the ORF selected. If one of the six ORFs has nicely paired start and stop codons and the other five do not, then that is a pretty good hint. There are other ways to tell (shine-dalgarno sequences in prokaryotes, Kozak consensus sequences in eukaryotes, etc).

canadianer please explain more

TransDecoder is a commonly used program for extracting likely coding regions from transcriptome assemblies, which does the following to make a call:

TransDecoder identifies likely coding sequences based on the following
  criteria:

a minimum length open reading frame (ORF) is found in a transcript
  sequence
a log-likelihood score similar to what is computed by the GeneID
  software is > 0.
the above coding score is greatest when the ORF is scored in the 1st
  reading frame as compared to scores in the other 5 reading frames.
if a candidate ORF is found fully encapsulated by the coordinates of
  another candidate ORF, the longer one is reported. However, a single
  transcript can report multiple ORFs (allowing for operons, chimeras,
  etc).
optional the putative peptide has a match to a Pfam domain above the
  noise cutoff score.

So in essence, look for the longest ORF, and then use some secondary metric (hidden Markov model, position weight array, database query, etc) to refine your prediction.


text:
Why do neurons die so fast without oxygen and nutrients?
Some human tissue can survive without oxygen a couple of minutes, even hours.
Why are the neurons are so "weak" and depends so much on oxygen and other nutrients and cannot live without them for more than a few seconds or 1 or 2 minutes?
Are they missing some parts of their cells which can store nutrients for worse times in favor of their function or what is the case?

Maybe because as soon as the hardware stops, the "software" is no more? (half-joking answer)

This has been addressed on quora: http://www.quora.com/Neuroscience-1/Why-do-neurons-die-so-quickly-when-deprived-of-oxygen

So, it is not the lack of stored stuff(oxygen, nutrients) in neurons? Does that mean that they could in fact survive if they want to, but actually the way how they respond to the lack of oxygen makes them die so quicky? So, ste structure/organelas in them could in fact support them for a longer time, but the "dead" signals they are receiving (chemically) turn them off and they die?

Well, it's not really a "dead" signal - excitation is part of normal neuronal activity. Excitotoxicity is when there is too much excitation and it kills the neuron: http://en.wikipedia.org/wiki/Excitotoxicity

Neurons use lot of energy to maintain their polarized state, this is not required to other cells [1,2].
When O2 or blood flow (which is carrying the nutrients) is reduced, the neuronal ATP levels breaks down very fast, with 90% ATP depleted in less than 5 minutes. Without ATP, the neuron can not maintain the correct ion flux, so depolarization occurs causing glutamate excitotoxicity, cell swelling and finally cell death.
1] http://www.acnp.org/g4/gn401000064/ch064.html
2] http://www.scientificamerican.com/article.cfm?id=why-does-the-brain-need-s

There are many factors contributing to neurons dying much faster than other cell types.
This website does not provide original references (for this question, it does for the rest of the article) but sounds trustworthy: http://neuropathology-web.org/chapter2/chapter2aHIE.html
Some factors extracted from here are:

Aside from small amounts in astrocytes, there is no glycogen storage in the brain.
Fatty acids cannot cross the blood-brain barrier.
Lack of a backup energy sources such as creatine phosphate in muscle cells.

Which leave the brain crucially dependent on oxydative phosphorylation, i.e. glucose and oxygen. Additionally of course, neurons are metabolically highly active and use up the small amounts of stored nutrients available at a faster rate than most cells. This is because they need to maintain strong ion gradients across their entire membrane, which spans a larger area than most other cell types due to extensive axonic and dendritic trees; not to mention constantly exocytosing neurotransmitters from the axon's numerous terminals.
Coupled with excitotoxicity as the actual mechanism inducing cell death as explained in the Quora answer linked above (http://www.quora.com/Neuroscience-1/Why-do-neurons-die-so-quickly-when-deprived-of-oxygen), this seems to be a sufficient explanation.

The short answer is: neurons do NOT always die quickly when deprived of nutrients.  The longer answer is the following:
I am a professional researcher in brain ischemia (ischemia = no blood flow), which is the topic of the question. Armatus' answer was correct insofar as neurons have very limited energy reserves and therefore loose ATP very quickly. Gianpaolo R gave the correct time course for ATP loss.  However, Gianpaolo R's explanation of cell death applies only if the ischemia lasts for about 20-30 minutes.  In this case, the cells swell and lyse by a process called necrosis.
However, if the duration without blood flow (which is the duration with no oxygen and nutrients) is less than 20 - 30 minutes, then the cells do not die by necrosis.  It is less well-known to lay people, but well-known to neurologists that the neurons will die days or weeks after the ischemia in a process called "delayed neuronal death".
What is also less known to lay people is that if the duration of ischemia is less than about 7 minutes (this depends on the species, e.g. human, rat mouse, etc), no neurons die, and in fact, they are protected for a short while from a similar insult.  This is a phenomenon known as "ischemic preconditioning".
The explanation of necrosis is uncontroversial.  However, no one knows what causes delayed neuronal death or preconditioning responses.  The excitotoxicity mentioned by Armatus is a popular theory in the field, that has been largely discredited for a variety of reasons I will not go into here.  It is also popular to believe the delayed neuronal death is due to a process called apoptosis, but this also has fallen out of favor in recent years.
Hence, right now, there are many competing ideas as to why the neurons die in a delayed fashion, and the simple fact is, no one knows for sure why they die in this way.
As you may imagine, being a worker in this field, I have a theory that I think is the most feasible of all.  But it is a mathematical theory that applies to any injured cell, not just neurons deprived of blood flow.  The theory is very simple conceptually.  It says that when a cell is injured it gets damaged (call it D), but also activates genetic responses to protect itself (call this S).  If the genetic protective responses are greater than the damage, that is, if S > D, then the cell recovers and lives.  If the damage is greater than the stress responses (D > S), the cell dies.  The rate at which the cell recovers or dies is inversely proportional to |D - S| after D and S have run their course interacting with each other.
This last statement precisely answers your questions. Neurons will die quickly when |D-S| is a large number.  They will die slowly when |D-S| is a small number.
Now, this is just a qualitative description. The theory actually consists of mathematical equations that predict many things. You will note it is a true theory and does not rely on the biological specifics of the system under study. I am currently measuring the theory in my lab.  I am confident it will be a very useful theory not only for explaining brain ischemia, but many other forms of cell injury.
The original article detailing this theory can be obtained at this link.

AFAIK permanent brain damage occurs after ~7 minutes of ischemia.  So what is going on between the ~7 minutes during which "no neurons die," and the up to ~30 minutes during which "the cells do not die by necrosis?"


text:
Gel Electrophoresis - loading dye and more
I'm a student new to molecular biology coming in from an eco-evo background looking for tips from you molecular pros! It seems that I'm running quite a few gels. The loading dye I'm using is Gel Loading Dye, blue (6X). The supporting document calls for 5uL:25uL reaction and 10uL dye:50uL reaction. Here's the problem: I'm trying to get my PCR to work and so I'm doing a lot of 'just checking' trials where I only load 2uL of reaction to each well from different 20uL PCR reactions. What volume of Gel Loading Dye, blue (6X) should I use when running only 2uL of PCR product
My goal now is to learn to do a DIG in situ hybridization to localize the distribution of mRNA of a gene I'm interested in so any tricks and tips would be greatly appreciated!

The loading buffer you add to your samples for gel electrophoresis has a few different purposes, but the exact amount does not really matter. The purpose of the loading buffer is

to make the sample heavier so it is easy to get into the pocket and stays there
to visualize how far the gel has run
to denature the sample (only for denaturing gels)

Sample buffers for agarose gels usually use something heavier than water like glycerol or sucrose together with a tiny amount of a dye like bromophenol blue.
So in general there is no issue with using too much dye, but using not enough could lead to the sample being not heavy enough and problematic to pipet, or the sample not being properly denatured. I'd either use 1 ul of the sample buffer (smaller amounts can be annoying to pipett) for your sample, or dilute the sample to 5-10 ul and use the regular amount.

When using small sample volumes, it is advisable to use water to increase the volume and make handling and mixing with loading dye easier. For example, you may mix 2 uL of your sample with 1 uL 6X loading dye and 3 uL water for a final volume of 6 uL.


text:
Why is Paracetamol so great?
Every time I get ill (cold, flu etc) I take a couple of these wonderful tablets for up to 4 times a day and I, eventually, get better.  What exactly is paracetamol?  Why is it so effective and is it really not harmful as my doctor would have me believe?

If your doctor seriously tells you that taking paracetamol (or any other drug) liberally is not harmful you should really think of changing doctor...

Sachin didn't say the doctor said taking the drug liberally is not harmful.  I think the doctor would have said taking the drug when Sachin has a cold, flu etc. is not harmful.  Would it be ok if a doctor said drinking water isn't harmful?  Of course.  But if you drink too much water you'll die.  Remember the reason people go to physicians is for individual advice, not general advice.  That's why anyone asking for individual advice is encouraged to seek a physician.  Therefore I don't think you can judge the doctor, since you don't know the individual circumstances.

Paracetamol is a pain killer, it does not treat the cause of your illness, it only alleviates the symptoms. From its wikipedia page:

Paracetamol [...], chemically named
N-acetyl-p-aminophenol, is a widely used over-the-counter analgesic
(pain reliever) and antipyretic (fever reducer).

So, paracetamol does not make you better. Your immune system makes you better. Paracetamol just makes you feel better while you are waiting for your immune system to get an infection under control.
You should be aware that it is only safe in small doses and a toxic dose is not that much more than the recommended one (source):

Risk of severe liver damage (ie a peak ALT more than 1000 IU/L)
Based on the dose of paracetamol ingested (mg/kg body weight):
Less than 150 mg/kg - unlikely
More than 250 mg/kg - likely
More than 12 g total - potentially fatal

Again from wikipedia:

While generally safe for use at recommended doses (1,000 mg per single
dose and up to 4,000 mg per day for adults),[6] acute overdoses of
paracetamol can cause potentially fatal liver damage and, in rare
individuals, a normal dose can do the same; the risk may be heightened
by chronic alcohol abuse, though it is lessened by contemporary
alcohol consumption. Paracetamol toxicity is the foremost cause of
acute liver failure in the Western world, and accounts for most drug
overdoses in the United States, the United Kingdom, Australia and New
Zealand.

I am sure someone else can explain the pharmacokinetics and details of action of paracetamol. I just wanted to point out that paracetamol can be dangerous and should be treated with respect.

Over-the-counter paracetamol pills are usually 500mg. Therefore, the 150 mg/kg figure you listed for acute liver damage in a 60kg adult would be 60*150/500 = 18 pills in the span of a day or so. Cumulative damage can occur at lower doses but I think this is only seen in people who take it to control chronic pain.

The mechanism lies within the production of the messenger molecule Prostaglandin and COX-2 inhibitor. (Graham & Scott 2005, Mechanism of Action of Paracetamol, wikipedia: COX-2_inhibitor & Prostaglandin). Thinking back to my school days, these are involved in the transmission of signals in neurones related to pain. Paracetamol reduces how much is produced making reducing signalling activity. I am by no means an expert on this and hope someone can expand on this further, hopefully this will prompt people! Also, please don't try to work out how many you can "safely" take, tolerances vary greatly

Paracetamol, also known as acetominophen and Tylenol is a Non Steroidal Anti Inflammatory Drug (NSAID).  Other NSAIDs include aspirin and ibuprofen (Advil).
NSAIDs all help with inflammation, reduce fever, but each has its own effect. Aspirin tends to thin the blood more than Paracetomol.  Paracetomol also has less effect on inflammation, but acts to reduce fever (antipyretic) and reduce pain (analgesic).  Your doctor has probably chosen this prescription because your needs fit better to this drug's properties.
Ibuprofen for instance probably causes more problems more frequently when it's used frequently, one of the most common being ulcers because ibuprofen inhibits generation of stomach acid, but cancer and a slew of other problems can crop up.
While it is true that Paracetamol is the leading cause of pharmaceutical liver damage in North America, its toxicity as a drug is fairly moderate and the high number of cases is due to the fact that it is sold as an over the counter drug (with no prescription required) and is taken millions of times a day. The FDA has recently lowered the dose of Paracetamol to four 300 mg doses a day - but that's still 1.2 g a day.
Its important to watch to see if you are one of those people who have an adverse reaction or if your liver is under stress.  You should not use this drug beyond its expiration date - it really does matter in this case.
Still, all told, you probably could just take a handful of aspirin and feel just as good, but this prescription should get you feeling a little better a little faster, especially if you have pain or fever.
It's true what @terdon says that acetominophen is not curing you, but drugs really mostly balance the body - healing never comes from pharmaceuticals, they often just let the body heal with fewer obstacles or discomfort.  I know I feel that when my fever comes down that I'm on the  mend - though thats not necessarily the case.

I thought that paracetamol was not traditionally classified as an NSAID, because it is not an anti inflammatory drug? Its effect on fever appears to be related to a central influence on temperature regulation via prostaglandines. Additionaly, it is to my knowledge not known for any influence on coagulation processes, while NSAIDS  do have that characteristic.


text:
How long can I store autoclaved disposables and reagents?
I want to stock up on autoclaved disposables, such as Eppendorf tubes, pasteur pipettes etc., and some buffers.
If I don't open the container after autoclaving, how long can I store autoclaved materials and consider them still sterile? Does it make a difference if the material is dry or if it is a liquid?

This is a non-answer, but may be worth checking out for other reasons: http://ohp.nasa.gov/policies/pdf/WFF_Autoclave_Recommendations.pdf

This page for surgical instruments says it's 2  months, or 6-12 months: http://www.research.drexel.edu/forms/compliance/iacuc/pol_autoclaving.pdf.  I imagine that disposables might be less...

@dd3: why would it be less?

@nico: To be honest, I was mostly thinking of degradation of plastics. That's probably not the issue here, though.

Not really an answer I know, but too long for the comments...
This is still too broad a question.  a well sealed, sterile plastic usually has a use by date, but can probably be used more than a year after you receive it.  But these cases are not usually the issue.
Its sterile medium and chemicals, each of which needs to have their own due date.  LB can be used months after autoclaving, but antibiotics break down chemically in weeks (ampicillin 1000x stocks lose their potency in a month).  Even in the refrigerator Agar plates show colonies after a couple of months and dry out quickly.
So more details would be necessary and the case by case policy is the rule.
added in response to comments
Its really a matter of how well they are sealed. An autoclaved bottle will stay sterile forever, until something gets into the bottle - it depends on how well you have sealed things up and the storage conditions.  For stuff sterilized in lab I would tend to use it within a couple of months. For eppendorfs we'd tend to sterilize a few hundred in a beaker and not worry about them...
Our experiments were working with purified protein were only medium sensitive to bio-contamination; they would be done in a few hours and then sterile filtered again.  If you were purifying RNA for instance you would be much more paranoid I'm sure.
If you start to see contamination I would lower the use date and or improve your protocol.
Plastics that come sterilized and sealed by the manufacturer in 3-5 mil plastic bags have really long use by dates and I've used them for up to a year after we received them.

Thanks, I was asking specifically for plastics and buffers, such as PBS. No medium or antibiotics.

I wouldn't use sterilized buffers more than a week after I made them - sterile filtering is easy to do just before you use them.  but that's me.

Great, so from what I gather: sealed autoclaved plastics can be used even after a year of storage. It is safe to presume buffers are good for a week. That pretty much answers my question. I think it outlined clearly in the answer for future reference.

i see - i've added to the response.  this is getting into subjective territory, but I put in some more detail there... there are bound to be those who disagree :) if you are starting to work with animal cells or bacteria it will really vary.  This answer might be enough to get you started...

can you even safely autoclave ampicillin? I would have thought it would degrade in solution at that temperature.

i don't think so.  the general protocol is to make a 1000x concentrated solution, sterile filter it then add after autoclaving. ampicillin goes in solution so freeze the stock solution at -20C and use the plates within a month or so...

http://openwetware.org/wiki/Ampicillin#Stock_Solution describes this fully.

If you work in a lab, there must be a SOP(Standard Operating Procedure) and you can (You should...) follow that. Each lab will have different standard so providing a single definitive answer here may not be beneficial.

Thanks, but I posted this because it's up to me to establish the SOP in this case :)

I expect there to be different established practices. I just need a ballpark of the amount of time I can store autoclaved products - that should be an objective measure.

The question is quite clear: how long autoclaved plasticware stays sterile? Sterility does not in any way depend on SOP. Either something is sterile or it is not.


text:
What are the long-term negative effects of going without water/food for a period of time
There are no good answers anywhere. so asking: this is not about days of survival without water. This is about long-term negative effects induced from not drinking water for at least the mentioned days.
Please link the most reliable link (has to be heavily-reviewed, meticulously-designed studies) that answers this question so I can look into it futher. Multiple studies are needed for it to be reliable.
A related question is the same question for going without food, but with water (I'll ask this in a seperate question if the answer isn't already in the answer you provide).
This is for modern human beings as it applies to the majority of people. Also you can comment with the most reliable resources on the topic so we can read into it.
Important: NO comments without reliable scientific sources are relevant or reliable (has to be heavily-reviewed, meticulously-designed studies) so we can look into it further by ourselves. Please don't comment/answer without one.

This is the second time this EXACT question has been asked. Complete with bolded sections and all. Like the last time it was asked, you will not get any answers. You are asking for studies that do not exist, and as far as I'm aware there simply aren't any known long-term affects from temporary starvation or dehydration.

Please read the FAQ section on etiquette when posting: "Treat others with the same respect you’d want them to treat you".  I don't believe that this requirement has been met with your tone in this question.  Regarding @MCM's comment, don't vandalise content you have previously posted to the community.  I realise that the cross posting issue has been resolved Skeptics side, however a more constructive course of action would have been to flag your original question for reopening.

Besides its confrontational style, the way this question was asked suggests the author hasn't really looked into this or at least isn't clear on what questions they should be asking.  It is true that, in modern scientific culture, you cannot get approval to lock a bunch of college kids in a room for a week without food or water so you can check in with them years later and look for long term health effects.
But there are a LOT of indirect ways to study this, either by studying populations that have suffered starvation (through famine or war) or brought it upon themselves (anorexia). Or you can look at animal studies, which might not give precise consequences for humans, but can be far better controlled (you can lock them up for a week and keep them around for a year). And they will have strong implications for humans, even if the results are numerically different.
Back at human population studies, you also don't need full starvation studies (X days without any food) to find that there are long term consequences, simple caloric restriction (CR) is well established as having long term negative consequences. I don't think it's a big stretch to assume that full starvation would (at the least) exacerbate these effects. On the other hand, there's a lot of recent age-related research showing controlled CR can extend lifespan from yeast up through mice. Though it's also well established that it can (for instance) reduce fertility at the same levels.
I'll just give a couple links on population studies on starvation. Starvation is much easier to research because (as I recall) people can live for about a month without food or sleep, but a week without water and you're just dead. Population studies seem like the best way to get at the question you're asking (consequences of chronic starvation).  But as I said, these aren't controlled studies, you have to go out and find a relevant population and get what data you can. You're not going to just run across a dozen people who all went for exactly one week without food in 1943 and then went back to their normal lives. These are single study papers, but they each cite at least a dozen related papers (including reviews) and should be more than sufficient to nucleate further literature searches.
Severe caloric restriction in young women during World War II and subsequent breast cancer risk
http://onlinelibrary.wiley.com/doi/10.1111/j.1742-1241.2012.02966.x/full
Comparison of metabolic profiles of acutely ill and short-term weight recovered patients with anorexia nervosa reveals alterations of 33 out of 163 metabolites
http://www.sciencedirect.com/science/article/pii/S0022395612002488
If these don't address what you're after, then please be more clear about what you actually need (and WHY this isn't it).  And, you know, this is a public forum that runs simply by the good graces of interested and knowledgable scientists. So please try and be a little nicer in how you phrase your questions.