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Genetic carrier Pedigree of Recessive Traits
A human male and female couple with normal colored ears discover that, in both of their families, their fathers (who have normal ears) each had siblings with red ears.  Red ears is a rare autosomal recessive disorder.  None of their grandparents had red ears.  Assume that the red ears in both families were caused by mutations in the same gene, that there were no new mutations within the pedigrees, and that the mothers of the couple were not carriers of the disease gene.
A) based on the information, what is the probability that the male in the couple is a carrier of the red ear disease gene?
B) if the couple had 1 child, what would be the probability that child would have red ears?
I was discussing this problem over with a friend and we got different answers.
A)I think the answer is 25%.  I multiplied 1/2 and 1/2.
B)6.25%.  I multiplied 1/4 and 1/4.

Is red turning to green a copy error or is it another distinct phenotype?

@RoryM i mixed up the colors.  the question is edited

@leonardo updated question


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What is the mechanism that directs myosin walking?
Myosin, dynein and kinase all "walk" towards specific ends of the microtubule or actin filament they are on. I'm most familiar with the walking mechanism for myosin, where ATP fuels conformal changes in the binding region, but I don't understand how it chooses to go one direction over another. Actin fibers' positive and negative ends are fueled by the addition of G-actin via ATP and its subsequent reduction to ADP, so I suspect that this process is somehow involved in determining the direction of myosin's movement.
As just a secondary thought, are there differences in the mechanisms of the movement between the three walking molecules listed above?

Good question that got me waist-deep in PubMed. It appears that the directionality of myosin motors is due to the angle at which the actin-binding catalytic domain is attached to the neck region. This review by Vale and Milligan, 2000, sums up the "unzippering" of the neck region that contributes the force for the movement (a video from the review adapted for Alberts' textbook is also informative).
Most myosins move towards the plus end of actin, but myosin VI moves towards the minus end. The neck region of myosin VI attaches to the head region at a different angle than conventional myosins and this is the apparent reason for the change in direction preference (see Figure 1 in review by Rodriguez and Cheney, 2000; also Volkmann and Hanein, 2000; Masuda, 2008).
And for your entertainment, an awesome movie of myosin V walking by Kodera et al, 2010 on YouTube.

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Cine-MRI versus MRI
Could someone explain the difference between Cine-MRI and MRI?  I am reading conflicting things online, such as Cine-MRI uses ECG-gating, or that Cine-MRI takes many images of the same position of the heart before stitching together the final result, and it is confusing me.

I'm not familiar with the technique, it is as I'm sure you already know very specialised and I've found it fairly difficult to find resources specific to cine-MRI.  At a glance at the wikipedia entry, however, there are a few differences that I can point out to you.
A normal MRI will take a snapshot image of a section of the body in time, therefore can not be used to show motion of internal structures.  By contrast, cine-mri takes several snapshots at different times and stitches them together into an animation, allowing the physician to see movement.  For example, the technique is useful for imaging the beating heart and has also been used to examine the flow of cerebro-spinal fluid.
ECG gating refers to how the images are collected when the scan is of the heart.  The timing of the scans matches up with the electrical activity in the heart measured with a surface ECG.  As a undoubtedly hugely oversimplified example, the scanner might take an image at P,Q,R,S and T on the ECG waveform before then stitching them together into an animation:

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What's the name of this bird?
This morning I saw a bird that I have never seen before. Since it was quite big, I'm very interested in knowing its name.
The bird was quite big, at least 2-3 times of a common blackbird. The wings were completely black but the whole back strip was quite yellow. Also the tail was yellow. The tail widens towards the end.
The bird flew very strange... it trundled towards the ground and then flew back up some meters before trundling down again. I observed the bird in Zurich, Switzerland at the outer border of the city. A big forest is quite near and there are some huge trees very close to the bird.
Then one last thing to add: I'm not really sure about that, but it could be that the bird had a nest on top of a big tree.
Any ideas which bird that could be?

When you say "yellow" do you mean bright yellow or brownish/cream?

It's rather bright yellow.

It's behavior and size makes it sound like a bird of prey... but its colors are definitely not those of a bird of prey.

Could it be a red kite? it is quite common in your area and there is no proof of vulture or eagle seen that period of time around Zurich (I guess it would be reported if it was); the form of the tail could be useful, the kites are the only one with a forked tail if not forked, it is another bird of prey (if you can confirm this point as well)

Following your answer to my comment, I deduced the “yellow” color to be more brownish as there is not big bird with really bright yellow color (like the golden oriole).
 With these parameters I search as well in the ornitho.ch database (all observations given by ornithologist professionals and amateurs) : there was no observation of vulture or eagle in that area (could be possible sometime when they migrate).
Then the more possible answer was a red kite which is quite common summer time in this area (mainly on the north part of Switzerland).

Next time you see a bird of prey, try to take notice of the tail form (forked or flat or round) that can help more for determining the bird.

Hmmmm... the only one I can think of fitting at least in part your description would be the golden oriole (Oriolus oriolus).
I say partly because it definitely is not 2-3 times a blackbird, could be slightly bigger, but on average it is the same size. Also it sounds extremely unlikely that you have spotted it in early March in Zurich, as they should be in Southern Africa right now.
Image, from Wikipedia:

I could not find anything else fitting your description in my field guide (Mullarney & Svensson - Birds of Europe)

It was definitively way bigger. More like a eagle or vulture. And the black part is way bigger. The yellow part is only a small strip over the back and the tail.

hmmm... I cannot find anything like that. We'll have to wait for some ornitologist :) I'll leave the golden oriole photo as it is a very nice bird!

From what I understand of the flight description you give, and given the size and habitat, I would suggest to have a look at woodpeckers. Dryocopus martius is large and black.
Another idea (my favourite, actually): a bird of the genus Tetrao: they can be black and large, live in the forest, and the tail widens towards the end.
Other suggestions, but I really doubt it's relevant:
- cormoran (Phalacrocorax for the size, dark color, and I've seen some perched in trees, and ther's a lake in Zürich);
- Accipiter (for the flight and habitat):
- Milvus (for the size, the tail, and the dark colour):
- cuckoo (Cuculus canorus);
- magpie (Pica pica, black, makes nests on top of high trees, but I suppose you would have recognised it without hesitation).
The yellow stripe on the back matches none of the above suggestions.

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Reverse transcription PCR optimization
What is the ideal amount of RNA to use for the RT? and how much cDNA to use then for the PCR?
I did RT with a solution of RNA of 0.36 ug/ul. Then for my PCR I used 1 ul of the cDNA obtained and used 25 cycles because I was hoping to see a difference between an endogenous level and an overexpression. However, I detected no band at the expected height of 500 bp but a diffuse band at 100 bp. What can this 100 bp represent? primer dimer? I switched to 35 cycles and I used either the same amount of cDNA or add 3 times more cDNA. In both cases I got bands at the expected height (but stronger when I put more cDNA) and still big bands at 100 bp.

RT PCR refers to reverse transcription I assume? Not to real time PCR?

@Alexander Galkin Why did you remove the PCR tag? I think the question is really about RT PCR, and not RT in particular.

@GerganaVandova Do you think that we need a special tag for RT PCR? Isn't it too confined area? I wasn't sure whether to correct it "PCR" or to "reverse transcription" and chose the last one. If you feel it is wrong, feel free to retag the question, it is more than welcome in the community.

@Alexander Galkin Yes, I believe the question is more about PCR rather than RT. You are probably right that RT-PCR tag is too specific. The PCR tag is good enough.

I agree with Gergana, this is a PCR question. I also believe that a PCR tag should be enough for all its variations (RT-, Q-, nested, etc)

I see big fuzzy bands around 100bp as well. They're most likely RNA contamination. To get rid of them, digest your RT-PCR products with RNAse-H. But if you just need to visualize your band of interest, and the fuzzy bands aren't getting in the way, it shouldn't be a problem.
I usually input anywhere from 1-2 ug of RNA into my RT-PCR reaction using the Invitrogen Superscript III kit for a total volume of 20 ul. After the reaction, I use 1/10 the volume of that (2 ul) for downstream (PCR) applications. This usually gives me nice results.
To optimize RT-PCR for detection of a specific target, consider using gene specific primers (make sure to use only anti-sense primers) in your RT-PCR instead of oligo-dT or random hexamers. This enriches your target when you use them for downstream applications. When you use GSPs though, make sure to run a parallel reaction with control (i.e. beta actin) primers to prove that your RT-PCR reaction is working.

There is no single "ideal amount" of RNA. I would suggest you to do a titration curve to determine the best amount for your specific assay. The band at 100 bp could be a non-specific amplification. You could try to increase slightly the annealing temp to see if that removes (or reduces) the lower band. Alternatively, you can consider a different primer set or even a nested PCR.
Also, it is still possible that you may look at a splicing alternative in that band. Do your primers span more than one exon?


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Where is the line between Anaerobic and Aerobic?
I am well aware of traditional anaerobic respiration (lactic acid or alcohol produced - no Krebs cycle) and traditional aerobic respiration (O2 is used at the end of the Citric acid cycle).
I am wondering how to classify respiration that uses the Citric acid cycle, but consumes a nitrite/ate or sulfite/ate instead of O2. Is that anaerobic or aerobic?

I could only find this image on Google image search catch but it said it was from http://lecturer.ukdw.ac.id/dhira/Metabolism/RespAnaer.html

http://toxics.usgs.gov/definitions/aerobic_biodegradation.html

Your question is based on a bit of confusion about electron acceptors that is very common and that drives microbiologists crazy. Energy (as ATP) is generated when electrons are moved from an electron donor to an electron acceptor. In respiration, the electron acceptor is inorganic -- oxygen for aerobic respiration or an inorganic molecule such as sulfate or nitrate for anaerobic respiration. Use of an organic molecule such as pyruvate as an electron acceptor is properly called fermentation. Both anaerobic respiration and fermentation are termed anaerobic because they don't use oxygen. Any introductory microbiology textbook will cover these concepts in detail, because they are important to understanding the metabolic diversity of bacteria. Brock Biology of Microorganisms is a good text.

A friend of mine checked 8 different introductory biology textbooks: 6 of them described respiration as using oxygen. However 2 of them did not specifically state oxygen as the terminal electron acceptor, which I am convinced is technically correct. Nitrogen as a terminal electron acceptor is an exception and not the rule, which is why it is so often overlooked in textbooks.

Anaerobic respiration is a respiration where the final electron acceptor is different than oxygen. The final acceptor can be a less oxidizing than oxygen, like sulfate (SO42-), nitrate (NO3-), or sulfur (S). For example bacteria that use sulfate are obligate anaerobs.
The Krebs cycle cannot take place in the absence of oxygen, although oxygen is not directly involved in the cycle. The oxygen is required for the electron transport chain, which oxidized NADH and FADH2 back to NAD+ and FAD+, which are involved in the four reduction reactions of the cycle.
Thus, aerobic respiration includes both Krebs cycle and final electron acceptor of oxygen, whereas anaerobic respiration does not.

I thought that NADH and FADH2 could be recycled using Nitrites - I edited in a diagram.

I still don't think that denitrifying bacteria will utilize Krebs cycle. Why would they do it anyways if no energy whatsoever comes from it?

One GTP (ATP) still comes out of one turn of the Krebs cycle. Although inefficient, there is still some sort of gain.

@jp89 All energy produced in the Krebs cycles comes from the electron transport chain, i. e. energy cannot be produced without oxygen.

"Most microbes respire (use an electron transport chain), although oxygen is not the only terminal electron acceptor that may be used. " - http://en.wikipedia.org/wiki/Microbial_metabolism , see also; http://nitrificationnetwork.org/Introduction.php (Ctrl+F, electron transport chain)

@JoeHobbit It might be that denitrifying bacteria have Krebs cycle, but I think that this still classifies them as anaerobs. I will do more research and will let you know.

The Kreb cycle can indeed take place. You speak of the final electron acceptor being different than oxygen, but for what process? Surely you are referring to the electron transport chain? That would power the regeneration of NAD+ and FAD+. Thus anaerobic respiration includes the Kreb and the ETC.

@GerganaVandova Good One! I would suggest you to format it (just a little bit) by highlighting the bottom-line

Agree that anaerobic respiration involves the electron transport chain and alternative terminal electron acceptors such as nitrate. However, respiring cells (whether respiring aerobically or anaerobically) can run the Krebs cycle. As long as there is a terminal electron acceptor, the NADH/FADH2 generated by the Krebs cycle can be oxidized back to NAD+ or FAD.

Welcome to biology.SE. Your answer, while interesting, does not address the question asked: "I am wondering how to classify respiration that uses the Citric acid cycle, but consumes a nitrite/ate or sulfite/ate instead of O2. Is that anaerobic or aerobic?"

The status of this question and its answers is completely messed up. This post has the correct answer - use of anything other than oxygen as a terminal electron acceptor is anerobic respiration. Cells using anerobic respiration will (normally) have a Krebs cycle. The answer from @Gergana Vandova is incorrect, despite its upvote score.

While aerobic organisms during respiration use oxygen as a terminal electron acceptor, anaerobic organisms use other electron acceptors. These inorganic compounds have a lower reduction potential than oxygen, meaning that respiration is less efficient in these organisms and leads to slower growth rates than aerobes. Many facultative anaerobes can use either oxygen or alternative terminal electron acceptors for respiration depending on the environmental conditions.
Most respiring anaerobes are heterotrophs, although some do live autotrophically. All of the processes described below are dissimilative, meaning that they are used during energy production and not to provide nutrients for the cell (assimilative). Assimilative pathways for many forms of anaerobic respiration are also known:http://en.m.wikipedia.org/wiki/Sulfur_oxidizing_bacteria


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What are the function(s) of Alu elements in the cell?
My 2008 biology book (1) states that some 10% of the human genome consists of relatively short (~300 nucleotides long) Alu elements which do not code for proteins but many of which are transcribed into RNA. Do these Alu elements have any function in the cell?
(1) Biology, 8th ed., Campbell & Reece, 2008

Alu elements are a type of transposable element. They possess the means for their own duplication and movement.  Alu is a SINE-like element that is transcribed by RNA Pol III, and so a single DNA copy can make multiple RNA copies, each capable of inserting into DNA, so it's no wonder they have a very high copy number.  Here is a picture of one means of insertion http://www.nature.com/nrg/journal/v3/n5/box/nrg798_BX1.html, although there are likely others.
They do not have "a function" per se, in that they are not selected for, they are just rarely selected against and there are so many of them.  They do not add functionality, but rather are one half of the "war" between transposable elements and viruses versus the genome's evolution to mitigate the damage they cause.  They are, of course, commonly used as sources of new DNA for sequence evolution, or can be used to create transpositions or other chromosome rearrangements, but mostly they just fail to cause too much damage and so tend to accumulate in the genome.

Because of the retrotransposon ability of Alu and other interspersed elements, insertion into parts of the genome can contribute to genetic diversity among the population. This can be analogous to random point mutations accumulated throughout a lifetime.
Some of these mutations can be beneficial and increase the overall fitness of the organism. However, many of these mutations and random insertions are harmful especially when elements insert themselves into essential genes or tumor suppressor genes (which leads to cancer).

I've really not studied this, however wikipedia does a good job talking about some of the functions, particularly the associated diseases that result from changed in those sequences.  Of particular interest is this sentence:

The discovery of Alu subfamilies led to the hypothesis of master/source genes, and provided the definitive link between transposable elements (active elements) and interspersed repetitive DNA (mutated copies of active elements).

The article goes on to discuss the effects of Alu changes:

Alu elements are a common source of mutation in humans, but such mutations are often confined to non-coding regions where they have little discernible impact on the bearer[citation needed]. However, the variation generated can be used in studies of the movement and ancestry of human populations[citation needed], and the mutagenic effect of Alu[9] and retrotransposons in general[10] has played a major role in the recent evolution of the human genome. There are also a number of cases where Alu insertions or deletions are associated with specific effects in humans:
Associations with human disease
Alu insertions are sometimes disruptive and can result in inherited disorders. However, most Alu variation acts as markers that segregate with the disease so the presence of a particular Alu allele does not mean that the carrier will definitely get the disease. The first report of Alu-mediated recombination causing a prevalent inherited predisposition to cancer was a 1995 report about hereditary nonpolyposis colorectal cancer.
The following human diseases have been linked with Alu insertions:
Breast cancer
Ewing's sarcoma
Familial hypercholesterolemia
Hemophilia
Neurofibromatosis
Diabetes mellitus type II
And the following diseases have been associated with single-nucleotide DNA variations in Alu elements impacting transcription levels:
Alzheimer's disease
Lung cancer
Gastric cancer
Other alu-associated human mutations
The ACE gene, encoding Angiotensin-converting_enzyme, has 2 common variants, one with an Alu insertion (ACE-I) and one with the Alu deleted (ACE-D). This variation has been linked to changes in sporting ability: the presence of the Alu element is associated with better performance in endurance-oriented events (e.g. triathlons), whereas its absence is associated with strength- and power-oriented performance
The opsin gene duplication which resulted in the re-gaining of trichromacy in Old World primates (including humans) is flanked by an Alu element, implicating the role of Alu in the evolution of three colour vision.

Of course, there is still a great deal to study on this.  For instance, the University of Iowa has a team studying this "junk" DNA.

Part of the answer to how and why primates differ from other mammals, and humans differ from other primates, may lie in the repetitive stretches of the genome that were once considered "junk."
A new study by researchers at the University of Iowa Carver College of Medicine finds that when a particular type of repetitive DNA segment, known as a Alu element, is inserted into existing genes, it can alter the rate at which proteins are produced -- a mechanism that could contribute to the evolution of different biological characteristics in different species. The study was published in the Feb. 15 issue of the journal Proceedings of the National Academy of Sciences (PNAS).
"Repetitive elements of the genome can provide a playground for the creation of new evolutionary characteristics," said senior study author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the UI Carver College of Medicine and the UI College of Engineering. "By understanding how these elements function, we can learn more about genetic mechanisms that might contribute to uniquely human traits."
Alu elements are a specific class of repetitive DNA that first appeared about 60 to 70 million years ago during primate evolution. They do not exist in genomes of other mammals. Alu elements are the most common form of mobile DNA in the human genome, and are able to transpose, or jump, to different positions in the genome sequence. When they jump into regions of the genome containing existing genes, these elements can become new exons -- pieces of messenger RNAs that carry the genetic information.

There is a paper by Srikanta et al entitled An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair (PDF).
Hope that helps.


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Nucleotide frequencies in Kimura's two-parameter model
Here's an excerpt about Kimura's two-parameter model from Felsenstein's Inferring Phylogenies:

"The model is symmetrical, and one can immediately see that, after
  enough time has elapsed, it will be equally likely for the base to be
  a purine or a pyrimidine."

I think I understand the assumptions of the model but it's not obvious to me why the equilibrium frequencies are equal. Why is that so?

If sufficient time has elapsed, there will be a large number of transversions present between the original base and the final state. The initial state will therefore not matter.
Say, you flip (turn over, not toss) a coin at random intervals. For short time and few flips, the initial state will matter. But if you go on flipping it for millenia, the final state will be essentially random -- you will not be able to tell what was there in the beginning.

Good answer. In the case of the model, am I right to think that equilibrium frequencies are equal because there is an equal chance of a base being a pyrimidine or purine in both the initial and final states? With enough time the base will mutate multiple times and can also mutate back to it's original state, therefore, the initial state does not matter. ... Imaginary sequence of events for a single nucleotide: A>G>C>A>G is just as likely A>G>A>C>T and in this example there is one transition and one transversion. Am I correct in my thinking?


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How is the number of mitochondria in a cell regulated?
How does the cell regulate the number of mitochondria in a cell? What happens when there are too many or too few?

The concept you refer is recognized as mitochondrial biogenesis and it is regulated by AMPK which senses the cellular energy demand. If you have few mitochondria in the cell, the electron transport chain works suboptminally generating less ATP. When the AMP/ATP ratio is high (low ATP) AMPK is activated, and turns on the catabolic pathways required to produce more ATP, included mitochondrial biogenesis.


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Good source that explains the evolution of single-celled organisms "from scratch"
Are there any books or sites that detail, step-by-step, the evolution of the first single-celled organisms (bacteria, archaea) from a Miller-Urey-like beginning? That is, assumes only amino acids, then from there to self-replicating proteins, until culminating in the formation of a basic cell?

Origin of Life: Chemical Approach is an edited volume by Piet Herdewijn and M. Volkan Kisakürek.
here is the book's description from the webpage:

Dedicated to the fond memory of two great pioneers of this science, Leslie E. Orgel and Stanley L. Miller, this compilation of reviews and original manuscripts provides an overview of the current state of the art, written by some of the eminent "players" in this creative domain of "explorative chemistry".
  Since we are still far from finding a definitive answer to the most fundamental of questions in science, "chemistry" here is defined in its broadest sense. It is against this background that the contributions cover such a wide range of theories, including chemistry and selection, evolution of the pioneer organism, chemical aspects of synthetic biology, ribozyme catalysis of metabolism in the RNA world, intractable mixtures and the
  origin of life, the chemical etiology of nucleic acids, interstellar amino acids, and even the chemistry that preceded life's origin.

Pricy, but it's on order. Will let you know if it fits the bill.

Cool. I have the luxury of being at university with a pretty good library but I definitely found it useful for teaching origin of life concepts in a fairly robust manner.

@C.LawrenceWenham Did it fit the bill?

I quite like the account given in Early evolution without a tree of life, where alkaline hydrothermal vents (like "Lost City") are theorized to have formed pre-biotic compartments with a proton gradient (i.e. an energy source) from which cells could have evolved.

From a more geology-oriented perspective:
Robert M Hazen (2007) - Genesis: The Scientific Quest for Life's Origins
Noam Lahav (1999)- Biogenesis: Theories of Life's Origin
J William Schopf (2001) - Cradle of Life
I have watched Hazen's nice "Origins of Life" DVD/Video Course. There he says that the Miller-Urey stuff has gotten less popular. Their atmosphere contains too much Nitrogen, Hydrogen  and focuses on the water surface and the open water body.
More recent research points to a more CO2-rich atmosphere, and that life evolved deeper in hot water at the bottom of the ocean.

+1 - Hazen's course is an excellent introduction.


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Is there an equivalent to "Fields Virology" for Bacteria?
I've gotten a staggering amount of use out of my copy of Fields Virology as a general reference for "getting me up to speed" on whatever pathogen I'm currently looking at. I don't know of a similar type of reference for bacteria, but I only became aware of Fields as I was moving out of the field, rather than into it, so it's possible I've simply never heard of a suitable reference.
Any suggestions?

The Manual of Clinical Microbiology from ASM is the bible we use in our Micro lab. It's often our first reference. There are a lot of other useful books in the ASM eStore.
ASM eStore


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What effect has changing pH and salt concentration on protein complexes?
I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt concentration have and what is the physical basis behind this?

I submitted an edit to your question, it was not entirely clear to me if you ask about proteins alone or protein complexes and interactions. If I got it wrong please just edit your post again.

The formation of protein complexes or aggregates in aqueous buffers is determined by a number of factors: physical properties of the protein itself, pH, temperature, type and concentration of the used cosolvent (salt). Solutes are often roughly divided by type into chaotropes ('disorder-making'), which destabilise protein structures and kosmotropes ('order-making'), which stabilize them. [1, 2]
Chaotropic salts interfere with intramolecular interactions mediated by non-covalent forces such as hydrogen bonds, van der Waals forces, and hydrophobic interactions, which, at high cosolvent concentrations, results in protein denaturation.
Kosmotropic salts, on the other hand, cause water molecules to favorably interact, which also stabilizes intermolecular interactions in proteins. The salt molecules readily interact with water from the protein's hydratation shell and remove it from the protein surface, which produces thermodynamically unfavourable interactions that are reduced when proteins associate to form complexes. With increase in salt concentration the protein precipitation (salting out) increases.
Both cations and anions have been ranked separately by their capacity to precipitate proteins, to form a Hofmeister series [3, 4] (first set in 1888 but still hotly debated), e.g.:
SO42− > H2PO4− > CH3COO− > Cl− > Br−
At large salt concentrations protein solubility is given by the empirical Cohn equation [6]:
lnS = α − βc
where S is the protein solubility, c is the salt's ionic strength, α and β are empirical constants characteristic of particular salt.
Salting-out agents are very widely used in protein purification (to concentrate proteins eg. with ammonium sulfate), chromatography or crystalization.
The influence of pH on protein-protein interactions in solution works through altering of the electrostatic properties of protein surfaces. At pH equal to the protein's isoelectric point (pI), where its net charge is neutral, charge repulsions of similar molecules are relatively low and many proteins will aggregate. Very low and very high pH will case proteins to denature; during digestion, for instance, proteins are in extremely low and then extremly high pH that exposes their backbones for enzymatic degradation.
For more information, please refer to:

Martin Chaplin, Kosmotropes and Chaotropes, http://www.lsbu.ac.uk/water/kosmos.html
Zangi R. Can salting-in/salting-out ions be classified as chaotropes/kosmotropes? J Phys Chem B. 2010 Jan 14;114(1):643-50.
Pace CN, Treviño S, Prabhakaran E, Scholtz JM. Protein structure, stability and solubility in water and other solvents. Philos Trans R Soc Lond B Biol Sci. 2004 Aug 29;359(1448):1225-34; discussion 1234-5.
Shimizu S, McLaren WM, Matubayasi N. The Hofmeister series and protein-salt interactions. J Chem Phys. 2006 Jun 21;124(23):234905.
Zhang Y, Cremer PS. Interactions between macromolecules and ions: The Hofmeister series. Curr Opin Chem Biol. 2006 Dec;10(6):658-63. Epub 2006 Oct 10.
Ruckenstein E, Shulgin IL. Effect of salts and organic additives on the solubility of proteins in aqueous solutions. Adv Colloid Interface Sci. 2006 Nov 16;123-126:97-103. Epub 2006 Jun 30.


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Why can cones detect color but rods can't?
I don't know if this question applies to only humans but why can cones see much greater detail than rods? Is it possible to have a rod that can detect light intensity and color?

both useful answers!  sounds like its possible we could have an eye that is both sensitive and seeing color, though summation seems to reduce resolution as well... so to have the same resolution as our eyes, it would have to significantly bigger.

The spectral sensitivity of photoreceptors expressed is the key to color vision. See figure below for the sensitivity of three-types of cone cells (S, M, L) and rod cell (R, dashed line).

From this figure, one can say rod cells provide information about the "blue-greenness" of vision, however, despite their spectral sensitivity, it seems that in human vision rod cells do not contribute to color vision, because they are highly sensitive to intensity, and thus they are mostly saturated in their response (does not induce firing of downstream bipolar cells) during normal daylight conditions. Rod cells specialize for night vision (scotopic conditions) which is crucial for survival, and under this condition the cone cells are pretty much useless.

I would love to see some electrical recordings from cones and rods in response to various light stimuli. Do you know any paper showing that (I would assume some paper archeology would be needed for that)?

@nico I think it will look extremely similar to the graph already posted. There might be quirks because absorbency doesn't have an exactly linear relationship with polarization, but it will be nearly the same. Except, light actually inhibits the cones so mirrored along the X axis.

@nico I'd like to see electrophysiological time series for various intensity and wavelength stimulus as well. Let me know if you find any good source. :)

@Preece: I was speaking of some raw ephys data actually

I wish this chart was taught at primary schools to dispel some of the misconceptions about "primary colors".

@nico There is a large body of literature with that kind of data. King-Wai Yau, Denis Baylor, and W.A.H Rushton are good guys to look out for if you want the historical data. For example, here is a lecture by Baylor with some ephys data. This one has amazing data on the response of rods to single photons! Mike Do and King-Wai Yau have great data on the responses of photosensitive retinal ganglion cells.

Cone cells are each connected to their own neurone.  This allows them a great deal of resolution as the brain can interpret the exact position of the cone cell that was stimulated by a light photon.  However in order to improve low light vision, multiple rod cells are connected to a single neurone - this is called summation.  Whilst it does allow for an action potential to be generated in low light conditions, it greatly reduces resolution as the brain can not know precisely which rod cell was stimulated:

Rods can not detect colour as they only come in one variety - cone cells (in humans) come in a red, green and blue specific form to allow for the perception of colour by the brain due to the relative strength of these signals.

While the answers to date are correct regarding the wiring of rods and cones in the primate (specifically human) eye, they are also fundamentally wrong. Neither rods nor cones perceive color. The brain does. The rods and cones are just the receptors providing signals. The first answer in fact says this in its very last sentence.
As one answer says, during the day the rods are saturated (overstimulated) so the brain ignores them. It uses the components of the cone responses to invent the sensation "color". At night the cones are usually only weakly stimulated, so the brain sees only with the more sensitive rods, and little or no color. This is why brightly colored stars such as Betelgeuse and Rigel still appear only faintly tinged (red and blue respectively).
By the way, some primates have even better color perception than humans with four (or five) kinds of cones. It is speculated that color vision is so good in primates because of the need to judge fruit ripeness to eat. Many mammals have fewer cone types than primates.

What is an example of a pentachromatic—or even tetrachromatic—primate?

All of the above answers are great, and very informative.  But they are also technically wrong, in certain conditions. Once you understand them, you'll be able to understand this explanation of why.
The canonical answer is that cones are used for color perception in bright light and rods are used in low light. But rods have a peak color sensitivity that is very distinct from the cones (see the chart posted above).  And more importantly, there are light levels at which both rods and cones are equally functional for color perception.
This is known as the "Purkinje effect" or "Purkinje shift".  Basically, when light levels dim, your red color perception diminishes first, but your blue color perception is enhanced (or at least doesn't diminish nearly as fast).  The specific effect is that red objects get darker much faster than blue ones. But the brain isn't yet just perceiving the blue objects as a brighter gray, so it seems there is some color perception built into the brain based on the rods.
http://en.wikipedia.org/wiki/Purkinje_effect

yes you are right.. All chromophores have a wavelength range of absorption.. but Rods are not involved in color perception, it doesn't mean that they are not color-biased

It has been proved that rods do add to color vision at certain conditions, especially at mesopic vision, Purkinje effect. Further testing showed that when only rods and L cones are excited, together they produce identifiable hues, although only two monochromatic lights are being used. One very faint blue light enough for rods to react but too dim for S and M cones to react,  and one red strong enough to excite L cones, but too red to saturate rods. Rods may add some color information during phootopic vision as well, but only at low fotopic levels when rods are not being saturated yet. That part is still being investigated.
I have found this article to be very informative...
http://journal.frontiersin.org/article/10.3389/fpsyg.2014.01594/full


text:
Did researchers evolve multicellular yeast or did they just turn on multicellularity?
In this new paper "Experimental evolution of multicellularity" found via Ars Technica the researchers describe having developed multicellularity and apoptosis within 60 days from a unicellular yeast species.
Is it possible that what they have done is merely turn on an ability of that species that evolved previously and just lay dormant?  Do we know that that yeast species and all its ancestors were never multicellular?  The paper doesn't even mention the possiblity of this.

Well, they put the cells in particular conditions that determined the multicellularity, so they have not specifically given the cells this ability per se. And I do not think they are claiming to have done so.

The conditions they put them under favored multicellularity, and the cells ended up being multicellular, and their abstract claims "These results show that key aspects of multicellular complexity, a subject of central importance to biology, can readily evolve from unicellular eukaryotes."

exactly my point. I don't read "we gave an unicellular organism the ability to become multicellular" in that sentence. I read "we put an unicellular organism in a situation in which it became multicellular". It's like people reprogramming stem cells to become this or that type of cell, they don't give them any ability, they just put them in the good conditions.

You're right:

Within the Fungi, simple linear multicellularity of hyphae occurs in all major clades (see below), but only Ascomycota and Basidomycota display more complex two- and three- dimensional multicellularity in the form of sexual spore- producing fruiting bodies. In both of these groups, reversals to unicellular lifeforms have occurred, for example, Saccharomyces and many other related yeasts in the Saccharomycotina (Ascomycota) or Cryptococcus albidus and related species in the hymenomycete clade of Basidiomycota (de Hoog et al. 2000, p. 130).

Medina, M., A. G. Collins, J. W. Taylor, J. W. Valentine, J. H. Lipps, L. A. Amaral Zettler and M. L. Sogin (2003). "Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa." International Journal of Astrobiology 2(3): 203-211. doi:10.1017/S1473550403001551
(PDF)
Update: The authors responded to criticism like this on The Loom, here's an excerpt:

Our yeast are not utilizing ‘latent’ multicellular genes and reverting back to their wild state. The initial evolution of snowflake yeast is the result of mutations that break the normal mitotic reproductive process, preventing daughter cells from being released as they normally would when division is complete. Again, we know from knockout libraries that this phenotype can be a consequence of many different mutations. This is a loss of function, not a gain of function. You could probably evolve a similar phenotype in nearly any microbe (other than bacteria, binary fission is a fundamentally different process). We find that it is actually much harder to go back to unicellularity once snowflake yeast have evolved, because there are many more ways to break something via mutation than fix it.

Just to reiterate (I am not a biologist): this means that we know of Fungi that reverted from multicellularity to unicellularity, so the same could be true of this particular yeast they used?

The fungus they used, Saccharomyces cerevisiae, is part of the fungi described above. So the part I quote actually refers to this particular yeast (Brewer's yeast).

What are the original multicellular species from which S. cerevisiae evolved? Or are you are talking about organisms which have multicellular components of their lifecycle?


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Which human cell lines do not express the GLP-1 receptor?
I need a human cell line that does not express the GLP-1 (glucagon like peptide-1) receptor.
I'm working with HeLa cells, do those express the GLP-1 receptor? Which other cell lines exist that don't express this specific receptor?
Are there any general resources where I could find this kind of information?

AbCam suggests HeLa cells as positive controls for their antibody to GLP1R. They provide the following pictures of HeLa cells labeled with their antibody:

(The image of the right is treated with synthesized peptide.)
According to Wikipedia, GLP1R is also expressed in pancreatic beta cells and the brain.


text:
Which patterns do I have to avoid when modifying the 3'-UTR?
I want to change a pre-miRNA sequence (in my case the pre-miRNA is encoding in a 3'UTR of a gene) and then put it in a lentivirus to see if it is still processed.
After modification (permutation of ten regions of ~20 nt) which kind of newly appeared pattern I've to be careful about? I do not want to disturb the gene in which the miRNA is encoded

I don't understand what you're doing.  It seems like you're altering 10 pre-miRNA genes in the 3'UTR of a protein-encoding gene.  What do you mean by "which kind of newly appeared pattern I've to be careful about"?  Are you wanting to assure that regulation of the protein-encoding gene is unaffected?  Why?  Are you going to knock out the genomic locus and rescue with your viral copy?

Yes I want to assur that regulation of the protein-encoding gene is un affected. I m gonna pertub the secondary structure of all pre mirna to delete the drosha processing. After that i m gonna put the region into a lentivirus and infect cells, and then check if the mirna are no more expressed.

If your goal is to avoid regulatory elements, I would not believe any prediction program, since new regulatory elements are found every day.  The best way would be empirical and just clone and infect with a mutated 3'UTR and see if your gene's regulation is perturbed.  You could at least swap the entire 3'UTR with that from another gene to see if there are even any gene regulatory elements in the 3'UTR.


text:
Effects of beer on muscle recovery after exercise
I noticed it several times that when I drink beer (even one bottle) after some heavy workout, the next day my muscles are more stiff than other times, and not the same way... Is it because that lactate and NADH levels are raised both due to the anaerobic training and alcohol metabolism?

So acute effects rather than chronic?

Yes, acute effects.

Noticed twice the same effect with two glasses of wine drunk the day before the workout

What does "and not the same way" mean?

Can't describe it properly but maybe less sharp and less localized, also there is no intense pain when the muscles are moved after some period of rest. I'm talking about my thighs anyway (and cycling).

There are a few studies around related to this. One particular study(1) suggests that:

Neural drive is decreased following eccentric exercise leading to a reduction in muscle force. Alcohol may further reduce the already depressed neural drive.
Alcohol also has been shown to affect the innate immune system by altering the activity of a number of inflammatory proteins. A lot of these play "important roles in the damage and repair processes occurring after eccentric exercise". Alterations in these proteins may affect muscle recovery post-exercise.(2).

The second point is maybe what's relevant to the question at hand? They say more research is required though.
Edit (expanded discussion per comment below). The study itself was carried out using 8 (+/-1) standard drinks immediately following a workout. The article(1) itself doesn't hypothesise the point made earlier regarding inflammatory proteins, it rather points to earlier research(2), to suggest this may be the case.
Whether a dose-dependant relationship exists, or the magnitude of it with regards to the alteration in inflammatory proteins is not discussed (except in the context of chronic versus acute alcohol use). Just that the possible effect on inflammatory proteins exists which may affect muscle recovery post-exercise.

Barnes, et al. Acute alcohol consumption aggravates the decline in muscle performance following strenuous eccentric exercise. Journal of Science and Medicine in Sport. 2010. 1:189-93.

Edit
2. Szabo. Consequences of alcohol consumption on host defence. Alcohol Alcohol. 1999. 1999:830–841.

The reference is not relevant - the title says "acute" but the question refers to "even just one beer"

Yeah David, acute as in immediate effects as opposed to chronic or long term effects.

Sorry, I meant to write this in the above comment. Acute in this context - http://www.medterms.com/script/main/art.asp?articlekey=2133


text:
RNA or ribosome, which one moves during translation?
During translation ribosomes decode the genetic information present in the mRNA and protein synthesis takes place.  During this process which of those two does move, the ribosome or the mRNA?

center of mass says - depends on the size of the RNA.  Also at least with prokaryotes, there are multiple ribosomes per RNA, which probably means less movement as they are probably not synchronous movements.

Shigeta, I think you are right about what you are saying but can you please be more specific about the answer...

@Shigeta. I love the argument but conservation of momentum may not hold in these low-reynolds number systems.

@shigeta low Reynold's numbers say F = ma --> F = bv: there is no mass in the equations of motion inside a cell. It's probably misleading to talk about the center of mass at all.

@Shep point taken.  Reynolds numbers assume a fluid which is not really true at that size, but its also true that the ribosomes are even less likely to move too much on timescales of the reaction as the water would interfere.

http://www.jbc.org/content/269/48/30713.full.pdf

Here's an example in which the ribosome is fixed:
During co-translational translocation, the ribosome is essentially anchored onto the ER membrane through the Sec61 complex. It certainly cannot move along the mRNA. The mRNA is fed through the ribosome and the nascent peptide traverses into the ER lumen.

this is the eukaryotic case, the bacterial case is more like the other descriptions, though i'd bet in that case the viscosity of the cytosol makes it so that the ribosome not move very much at all during translation.

The ribosome moves relative to the mRNA by, in effect, pulling itself along it.  If both the ribosome and the mRNA are freely floating and not attached to anything else (as in jp89's answer), the relative amount of movement should depend on their relative masses.
(Actually, it also depends on how much drag each of them experiences with respect to the surrounding liquid medium, but since I have no idea how much that is, and since it's probably highly conformation-dependent anyway, I'm going to just ignore that and just assume that the drag is also more or less proportional to mass, at least to first order.)
As it happens, a quick Google search and some back of the envelope calculation suggests that the mass of a ribosome and the average mass of an mRNA are both around a megadalton.  Of course, the length (and thus the mass) of an mRNA varies quite a lot, so it would seem likely that sometimes it's the ribosome that moves mostly, sometimes it's the mRNA, and sometimes it's both.
Also, as shigeta and others have pointed out, there can be more than one ribosome attached to the same mRNA strand.  That's going to make the mRNA move more (and, correspondingly, the ribosomes move less), since there are more ribosomes pulling it along.
Then there's also the protein being transcribed, which is attached to the ribosome but also being moved with respect to it.  And I really have no idea how negligible the interactions with the tRNAs and so on are.  It's a mess, but my guess would be that, usually, it's mostly the mRNA that moves, but that the ribosomes aren't completely stationary either (unless they're attached to something, of course).

Ps. Here's an exercise for you, which you may try out if you happen to have a friend who works at a public swimming pool. Otherwise consider it a gedankenexperiment. You know those floating ropes that separate the lanes in the pool? Try getting your friend to let you into the pool when it's not in use and to release one of the ropes from the walls.  Then get in, grab the rope with your arms and legs and try pulling yourself along it.  While doing so, try to decide whether it's you or the rope who moves more. (Also, to more closely approximate the Reynolds numbers involved inside a cell, imagine doing this in treacle instead of water.)

Your swimming pool experiment is right on. I'm not so sure about the talk of "center of mass" though. A low Reynolds numbers, it's far more important to consider the linear drag coefficient than the mass of anything involved. To imagine the inside of a cell, you need to forget newton's laws: objects in motion will stop moving unless acted on by an outside force (at low Reynolds numbers).

You may well be right. As I noted in the parenthetical remark, I based my crude back-of-the-envelope calculations on the relative masses because that was something I could get some data on.  If my guessumption about the drag coefficients being roughly similar is way off, then so may be my conclusion as well.

Movement is relative. The real events happening in translation are the conformational changes of ribosome makes itself continuous reading the base sequentially. Please refer the biochemistry textbook or cell biology textbook.
Indeed, if the ribosome is anchored, you may say the mRNA is moving.

Well, thanks for your response but bit of a problem here.  Certainly movement is relative and depends on perspective or reference frame.  What I meant by movement here is relative to more stationary structures, for example cytoskeletons, which one of the two moves.  precise answer in not clear from the first response.  And I did already consult the text books and obviously didn't find the answer either!

Regarding the second response, ribosomes are certainly not 'anchored' to any part of the mRNA, cos had that be the case, how do other parts get translated then?

@balaka: it does not say ribosomes are anchored to mRNA, just that they are anchored.

True, but with which substratum it is anchored is also not mentioned.  mRNA was just one plausible candidate for me for their obvious proximity.

@balaka: not really a plausible candidate because, as you said, it moves! I'm not an expert on the matter but I would not be surprised if they were anchored to cytoskeleton proteins.

The mRNA moves during translation. It is essentially threaded through the ribosome. This has been known ever since polyribosomes were discovered; see paper here. Polyribosomes are a cluster of ribosomes that read a series of mRNA molecules. Often, the ribosomes in a polyribosome will be translating the same mRNA.

Of course it all depends on your reference system. If an observer were on the mRNA then he would see the ribosome moving :)

If you think of the cell as a universal 3D space, the relevant reference point would be a fixed coordinate in this space outside of the mRNA and the ribosome. Why would a cell biologist use either the ribosome or the mRNA as the reference point!? If you adopt your attitude, there would be no motivation to identify motile features. Does the Earth revolve around the Sun, or the Sun around the Earth? By your reasoning it doesn't matter, after all it's just relative.

I think any anyone who has seen relativity understands Nico's point. As for the paper, Warner et al. fix the ribosomes onto the surface. It's an artificial surface that forces the mRNA to be threaded through the polyribosomes. One can't make a conclusion from this study.

The fact that ribosomes can collide with each other on the polysome during the translation process shows clearly that the ribosome is moving along on the mRNA.

Welcome to SE Biology. We are looking for comprehensive answers supported by evidence on this site. It is not enough to state something is a “fact”, you need to document it with reference(s). So please provide evidence that ribosomes collide with each other. You may well be right, be I am not aware of this and can assure you that 99% of list members will be in a similar position.


text:
How much time do INS1-E and MIN6 cells need after splitting?
I am currently doing an experiment on cells to test the internalization of a protein.
Normally, I seeded my cells the day before the incubation. This worked well for Hela, CHL or PANC1 cells. However, when I did the same with INS1-E and MIN6 (both beta-cells) after the incubation and the washing step the majority of the cells were gone. This was better in the control where I did not put in the compound, but still a lot of cells were detached.
Therefore, I wonder if I should seed the INS1-E and MIN6 cells earlier, more like 2-3 days before. Do these cell lines need more time after splitting to attach again?

I think that to adequately answer this question, we need to know the composition of your culture medium and any additive with which you supplement it. I'll assume 37 oC and normal oxygen levels. The size of the cultures makes a difference - spinner flasks are not the same as tissue culture plates.

I've worked with MIN6 cells in the past, and have found that they can take at least 12-24 hours to fully seed (if they are being cultured on polystyrine).  Depending on the specifics of your experiment, and whether doing so would complicate your controls, you might also want to try coating the surface you are attempting to seed on with laminin.  MIN6 cells seem to like growing on that over uncoated polystyrine and other ECM proteins.


text:
What's a good reference for choosing histological staining chemicals?
It's often difficult to find the appropriate or best stain to use when I want to examine a new type of tissue. I think that's partly because many histological techniques were developed a long time ago, so the papers don't turn up in Google Scholar. Is there a standard reference which links tissues, cell types or states and their corresponding best stain?
I'm mostly interested in a reference text or website covering plant histology, but general references are welcome too.

Did you try the websites of vendors? They usually want this kind of info front and center so people buy from them.

Vendors tend to expect you to already know what chemicals you want. I'm looking for something which covers modern (e.g. fluoro) histology as well as traditional (e.g. nuclear stains, differential stains).

If you want to go way back, google books has Methods in Plant Histology (Chamberlin, 1905) with a PDF. It details stains and the tissues they are used for and even has a section titled "Selection of a Stain."


text:
Can a new Y-chromosome be created?
The major gene of the Y-chromosome is SRY. Would it be possible to get the X-chromosome and add SRY to create a "fuller" Y-chromosome?
What advantage does the skinny Y-chromosome give an individual anyway? Females only use one X-chromosome (via the Barr body) so they don't seem to gain as much from having the pair.

Females do not always use only one X chromosome - eg Drosophila. And why would an X with SRY be better than the current Y? It is not junk - it is now being found to affect many genes through epigenetics.

SRY translocation to the X chromosome clinically exists and characterizes the De La Chapelle Syndrome. The phenotype associated to this syndrome demonstrates the necessity of other components on the Y chromosome to develop full masculine characteristics.

Would it be possible to get the X-chromosome and add SRY to create a "fuller" Y-chromosome?

Possible? Sure. You could sequence both chromosomes and then create some artificial DNA that included the combined sequences.
Would it be viable? Probably not.

What advantage does the skinny Y-chromosome give an individual anyway?

If there is a genetic condition in the father's X-chromosome, the male child is spared from it.
If there is a genetic condition in the mother's X-chromosome, the male child has a 50/50 shot at being spared from it.
If the genetic condition requires two homogenous X-chromosomes, the male child is spared.
If the genetic condition requires two heterozygous X-chromosomes, the male child is spared.
These are all advantages of simply requiring a Y-Chromosome, and there are certainly disadvantages to having a Y-Chromosome as well; X-linked genetic disorders will definitely affect any male heirs, unlike...

Females only use one X-chromosome (via the Barr body) so they don't seem to gain as much from having the pair.

...Female offspring. Because women have two X-chromosomes they have redundancy. If there is a bad gene on the extra X-chromosome that is deactivated, then it doesn't matter - where for a man with the same X-chromosome it would definitely affect them.
Also, because of the redundancy, what X-linked conditions do exist usually affect women less-so. If both X-chromosomes are utilized for a specific gene, then one bad protein product is partially made-up for with the one good protein product.

If the genetic condition requires two homogenous X-chromosomes, the male child is spared..... hmmm can you point to an example of that? If the condition is recessive the male child is definitely not spared.

Nope, as I'm not sure if one exists. I was being hypothetical.

Further points> Y chromosomes, contrary to popular belief, are not junk - they contain very few genes but these can have epigenetic effects (for example via regulation of other genes). This gives a huge benefit to even "skinny" Y chromosomes because it offers the opportunity to resolve intralocus sexual conflict as it is male limited. Another point is that females do not always use just one of the X chromosomes (X inactivation). Some species use other methods of dosage compensation - drosophila males double the transcription of their X to match the output of both in the females.

Would it be possible to get the X-chromosome and add SRY to create a
  "fuller" Y-chromosome?

Yes. Nature has done that. https://en.wikipedia.org/wiki/XX_male_syndrome
However there are more there is more than just the SRY gene on the Y chromosomes. As such XX males with SRY translocations are sterile.

What advantage does the skinny Y-chromosome give an individual anyway?

To an individual nothing much (as far as we know). However Y bearing sperms swim faster as they have smaller heads than X bearing sperm. So much so that for every 100 girls conceived, there are 140-160 boys conceived.

Females only use one X-chromosome (via the Barr body) so they don't seem to gain as much from having the pair.

Actually there is a lot to gain. X inactivation is random. So female tissue is composed of a mosaic of cells expressing one or the other X chromosome. So if there is deficiency in one allele, the other allele can compensate at the tissue level. This is why despite so many boys being conceived, only 106 boys for every 100 girls are born.
Also why women have smaller standard deviation in intelligence than men (as many of the genes regulating intelligence are on the X)...So while there are fewer women with super high IQ, there are also fewer women with super low IQ.


text:
Mitosis in human body
I've heard that stomach lining has the fastest reproducing cells and the brain has the slowest.
Where in the human body does mitosis occur and at what rates do these cell reproduce? Is there a chart for the whole body available?

It's not that they have different rates. The stomach epithelium just has a lot of stem cells that can divide non-stop, the brain has very few. Usually, the specialized cells in the body don't divide themselves; a small reservoir of undifferentiated stem cells (maintained for just this purpose) divides and some of the new stem cells differentiate to make more specialized cells. Specialized cells can de-differentiate and revert to stem cells sometimes, too.

In many cases cell division depends on the stage of development an organism is in. The rate of cell division is obviously much faster in a developing organism and from what I understand fully differentiated cells such as neuron and those in skeletal muscles don't divide (correct me if I'm wrong here).
In early development totipotent cells (stem cells that can become anything) begin to differentiate dependent on environmental factors, turning into multipotent (partially differentiated) cells that can only lead to certain cell types. For example: mesodermal precursors can differentiate to myoblasts, which can go on to differentiate into myotubes, later forming muscles.
Epithelial and and blood cells are the two of the main types of cells that need to be constantly replaced in developed organisms. As far as I know cells lining the gut epithelium are fastest to divide. They are created from stem cells in 'crypts' (pockets) in the lining and are pushed outwards, where they are later broken down (by what I would assume would be abrasion and intestinal juices). My book gives them a lifespan of 3-5 days. External skin cells are much slower to divide (though I'n not sure by exactly how much).
Red blood cells have have a lifespan of approximately 120 days. They are replenished by stem cells in the marrow of certain bones (e.g. a femur). Neutrophils are the next most common blood cell, with a circulating life of 8 hours (but lifespan may be a few days). Per day, roughly equal numbers of RBCs and neutrophils are created and are most numerous new cells created per day. Lymphocytes, another white blood cell, are responsible for immune 'memory' can persist for years. The fastest recorded mitotic cycle for a mammalian cell (in culture) is ~8-10hrs.

But from how I understand it, blood cells are not really cells in the sense that they are just bags of haemoglobin without the standard internal organelles found in cells.

That's right, but they do develop from precursor cells that contain a nucleus. To be honest, I don't know of many other cells that continue dividing at a steady rate. As far as I know cells such as fibroblasts and macrophages are mainly produced in response to stimulus. There are probably other types that I am missing however...

Nice answer.   Can you expand the abbrvtn IIRC (not everyone would know). Red blood cells have a lifespan of approx 120days. Neutrophils are the next most common blood cell, with a circulating life of 8 hours (but lifespan may be a few days).  Per day, roughly equal numbers of RBCs and neutrophils are created and are most numerous new cells created per day. Lymphocytes, another white blood cell, are responsible for immune 'memory' can persist for years.  The fastest recorded mitotic cycle for a mammalian cell (in culture) is ~8-10hrs. Feel free add this in, if helpful.

Yeah sure, done :)

Question is two years old, and the answer is approx 20 yo, but I believe both are still pertinent: According to Jared Diamond on pg 12 of his Harper paper version (1993 -- but reissued in 2006) of The Third Chimpanzee, we replace intestinal lining epithelium every few days, urinary bladder lining every two months, and replace every red blood cell about every four months. So though blood cells are fast (and probably more numerous) they are slow compared to the intestinal cells!
It seems amazing that the telomeres of the intestinal walls' cells don't wear out and begin cancerous changes much earlier than they do...if the statements above are all accurate. I do find Diamond an incredibly insightful writer and think you can trust him.

Can you add a link (or a proper citation, First author, Journal, Volume, Issue, and page number) to the answer? It makes finding the reference much easier.


text:
High sequence similarity but start codon isn't methionine
I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(>80%) with known proteins. However, the start is not a methionine. Is this a dysfunctional 'protein' sequence? Or are there alternative codons which translate those regions without a Met or fMet for that matter?
Technically, do all annotations of proteins have to start with a methionine?

Which prokaryote are you referring to? This could be important for answering this question.

There are alternative start codons to AUG used in prokaryotes: GUG and UUG. Those still match the initiation tRNA and encode N-formylmethionine. The rare start codons are matched by wobble pairing.

As far as I know it is a universal rule that the initializing sequence codes the amino acid Methionine (or, as you mentioned fMet in prokaryotes).
However, in very rare cases it is possible that Met is not coded by the expected sequence of AUG. This happens more often in mitochondria and prokaryotes, for example E. coli which uses GUG quite frequent.
For an overview check Wikipedia here. Papers to follow up are listed there.


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Why are pili more common in Gram negative bacteria than in Gram positive?
Although pili have been observed in some species of Gram positive bacteria, the preliminary research that I have done indicates that pili are significantly more common in Gram negative bacteria.
Is this an accurate assessment of the current body of scientific knowledge? If so, do we know (or have any leading theories on) why this is the case?

Pili were at least discovered more recently in gram-positive bacteria.
Pili are formed differently in gram-positive and gram-negative bacteria.  Here's a pretty good review on the differences: http://www.ncbi.nlm.nih.gov/pubmed/18953686
Researchers seem to think that pili might be involved in adhesion/formation of biofilms (adhesion is important for pathogenicity).  Certain types of pili are specifically involved in gene transfer. This is a good review on pili and pathogencity in gram-positive bacteria: http://www.nature.com/nrmicro/journal/v4/n7/pdf/nrmicro1443.pdf. If you can't access it, let me know, and I'll do my best to summarize.
EDIT:
The Wikipedia entry for pilin interprets the second paper I linked as saying that pili are more common in gram-negative bacteria and that pili are implicated in pathogenicity.
Straight from the paper:
Prevalence:

Over the past five decades, several distinct pilus types
  have been identified, most of which were described
  and characterized in Gram-negative bacteria.

Function:

A common feature of Gram-negative pili, however, is their role in adhesion to eukaryotic cells. It has been
  proposed that bacteria use these structures to form an
  initial association with host cells, which can then be
  followed by a more ‘intimate’ attachment that brings
  the bacterium into proximity to the host-cell surface.

and

Pilus-like structures on the surface of Gram-positive
  bacteria were first detected in Corynebacterium renale,
  by electron microscopy. More recently, surface
  appendages were reported to be present in Actinomyces naeslundii
   and were subsequently found in other
  species, including Corynebacterium diphtheriae, Streptococcus parasanguis (Streptococcus parasanguinis), Streptococcus salivarius
   and Streptococcus sanguis (Streptococcus sanguinis). Finally, in the past
  year, pili were also characterized in all three of the
  principal streptococcal pathogens that cause invasive
  disease in humans — group A Streptococcus (GAS; that
  is, Streptococcus pyogenes), group B Streptococcus (GBS;
  that is, Streptococcus agalactiae) and Streptococcus
  pneumoniae — in which they have been shown to
  have key roles in the adhesion and invasion process and
  in pathogenesis. [emphasis added by me]

this doesn't precisely answer the question.  are they more common in gram negative bacteria, and if so, why?

@shigeta: see my edited answer.  Given the diversity of pili structure and function (see the first article I posted), I don't know if you'll get a "why" that explains pili prevalence in gram-negative bacteria.

of course perfect answers aren't always going to happen with biology, but it helps the site to give the answer here.  thanks!


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Where are doxycycline's anti-inflammatory properties derived from?
I have been looking at this antibiotic called doxycycline which is used mainly as an antibiotic. It has however some interesting anti-inflammatory properties. Does anyone know where these anti-inflammatory properties come from, chemically?

See this page for information on how to merge your accounts.

Doxycyline inhibits iNOS and TNF-alpha expression.   It also influences secretion of IL-1beta, IL-8, and TNF-alpha, as well as other inflammatory cytokines.
[These are results collected from multiple systems.]
For appropriate references, see: Leite et al (2011). Anti-inflammatory properties of Doxycycline and Minocycline in experimental models: an in vivo and in vitro comparative study. Inflammopharmocology.
As for the chemistry of how doxycycline accomplishes these things, I'm afraid I don't know the answer, but hopefully, this gives you a place to start.


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Extreme examples of protein translation/use coupling/decoupling?
What are known extreme examples of protein translation/effect coupling/decoupling? For example, examples of proteins that are immediately used at the time the have been translated and vice versa, cases of proteins that are translated but then only used much later in time in/outside the cell?

Is this similar? http://biology.stackexchange.com/q/2240/389

@bobthejoe, it is not similar. The OP is asking about cases where a protein is functional just after translation or, conversely, long after it.

Proteins that are membrane localized or secreted would take time to become active or even become poised for activity. Membrane receptors may remain inactive until triggered by the appropriate ligand. Nonetheless proteins won't remain (inactive or active) for a very long time as constant turnover happens in the cell.
One example, similar to what MarchHo mentioned in their answer (pre-proteins) is that of fibrinogen. Fibrinogen gets converted to fibrin when there is an injury and haemostasis reaction cascade is initiated. Fibrinogen has a biological half life (in its latency) of ~100 hours [ref].

A specific example would be great.

@MarchHo There are several. This is essentially a principle based answer. More the number of steps to final destination, more will be the latent period.

Chymotrypsinogen is a proteolytic protein that is translated and stored in the pancreas in an inactive form. They are only activated when they are secreted from the pancreas.
Other zymogens such as apoptotic caspases have similar lengths of time between translation and use.

One example that may interest you Rory M are the so-called toxin - antitoxin pairs in bacteria. Interestingly enough, many bacterial species need a way to protect themselves from their own toxins. Thus, for a particular toxin, a corresponding antitoxin is synthesized (most often both are proteins, but the antitoxin may be RNA as well, three types of toxin - antitoxin systems are known; check out http://en.wikipedia.org/wiki/Toxin-antitoxin_system). The antitoxin remains bound to the toxin until the latter is secreted into its designated location. If the antitoxin decouples prematurely, cellular death may occur. I'm not too sure how long the two are "stored" within the cell; I imagine this could vary greatly between species.


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What are treatable foetal conditions during pregnancy?
What are different foetal conditions during pregnancy that could be treated with appropriate prenatal genetic testing?
I only know that pregnant women are encouraged to take certain supplements to make sure certain conditions won't develop in the foetus, and which are apparently also the case for deficiencies in human growth hormone, but I imagine there must be other specific cases that are treatable for specific conditions diagnosed to only a small number of cases?

this question seems like it would require a full book to respond to it.  there must be scores or even hundreds of such conditions.  Could you maybe be more specific and focused - break the question up?  dietary conditions?  genetic tests?

Your question probably expresses a subtle confusion about the prenatal diagnostics and genetic testing.
So, genetic testing is one of the diagnostic methods in prenatal diagnostics (among with the other methods, see the list) which is used to diagnose genetic disorders of the foetus, whereas the disorders that are diagnosed on this stage are mostly genetic anomalies with dramatic impact on the feotus development, for example chromosome aberrations (like Down or Turner Syndromes). Should these conditions be diagnosed, the woman is given a choice to interrupt the pregnancy prematurely.
Less dramatic conditions (like sickle-cell disease) can be diagnosed at this time too, but are not treated before the birth.
The genetic disorders that are amenable to the dietary or medical treatment (like phenylketonuria or congenital hypothyroidism) are usually diagnosed in the newborn screening tests (newborn heel prickle test), because these screening is more precise and less dangerous compared to the pre-born diagnostics.

So are there any prenatal diagnostics that can be treated during pregnancy?


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Formal definition of a 'genetic trait reservoir'?
I've read the tomato genome paper in Nature published recently, and they describe the tomato genetic resource as a rich trait reservoir that will provide biological knowledge and empower biodiversity-based breeding. What would be a formal definition of trait reservoir in this context?

In this context, "trait reservoir" refers to the set of all possible alleles for all the different genes in the organism. The more different alleles the organism has, the more possible genotypes it might have. The Nature paper might have referred specifically to the set of known allelic variants.


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How would one calculate the availability of nucleotides to an enzyme?
How would one calculate the availability of nucleotides to an enzyme like a polymerase ?
I imagine an answer in units like nucleotides per second per enzyme, but I'm also imagining an answer that is not a simple rate of reaction. k_on calculations and k_off do not offer mechanistic explanation.
I'd like to know, specifically, if there is a theoretical approach to this question:  how does a polymerase reject an incorrect nucleotide?

All nucleotides or a specific nucleotide?

All nucleotides. I will revise the question to reflect better my intention.

The second question on DNA proofreading is probably worth an entire question by itself. You might as well ask it and get more reputation ;)

Wouldn't this be a mass-transport related question? I think that transport rate/flux of nucleotides can be described entirely by the diffusion coefficient given the cellular environment.

@bobthejoe things like temp, pH, salts, etc. should also make a difference to nucleotide incorporation by a polymerase. I think a thorough answer would cover it all, and will be really impressed if we get something that comprehensive.

I could read this question more than one way.  Are you talking about an enzyme in a cell or in a reaction in vitro?  Kinetics and mechanical explanations can overlap, but are not entirely the same and are usually dealt with separately - kinetics with watching the rate of reactions in a tube and mechanism in a crystal structure or possibly Nuclear Magnetic Resonance.
Protein structures are usually static- you only get a time lapse snapshot of the reaction in most cases. kinetics allows you to see how fast these things go and can help you understand the order of binding when more than one component is needed for the reaction, etc.
The polymerase has a binding pocket where the template strand and the growing strand are used to build a double helix together.  if the base being introduced does not form Watson Crick base pair bonds, the geometry of the reaction will not allow the base to be added to the growing strand.
Hope this helps? If I can make this clearer, can you drop me a comment and I'll revise...


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Is there a limit to acceptable brightness for plants?
Can overly bright artificial light harm plants? Is it possible to achieve a level of brightness so high that it does more harm than good to plants?
If sunlight can be filtered of infrared light spectrum, so the plants don't burn from high temperature, but if it's possible, then that too.

Have you done any initial research/litterature searches? If so, it is useful if you post this info.

The wikipedia page on photosynthetic efficiency has some useful insight here:

Photosynthesis increases linearly with light intensity at low intensity, but at higher intensity this is no longer the case. Above about 10,000 lux or ~100 watts/square meter the rate no longer increases. Thus, most plants can only utilize ~10% of full mid-day sunlight intensity. (5)

and

If photosynthesis is inefficient, excess light energy must be dissipated to avoid damaging the photosynthetic apparatus. Energy can be dissipated as heat (non-photochemical quenching), or emitted as chlorophyll fluorescence.

So, briefly, yes. Too much light can harm plants.
To answer the second question: yes, there exist filters for a large variety of wavelengths of light. You could certainly filter out infrared light, just as most sunglasses filter out some UV light wavelengths. However, just filtering out infrared light would not filter out all photons that could cause damage; likewise, all wavelengths of light have the capacity to heat up what they hit, not just infrared wavelengths.


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What is the meaning of a reported OD600 value?
I can't find a reference that explains what, for example, OD600 = 0.1 means.
For example, Wikipedia states

OD600 is an abbreviation indicating the absorbance, or optical density, of a sample measured at a wavelength of 600 nm.

In other words, the OD600 value reports (a function of) what percent of light goes through a sample. But that depends on the thickness of the sample. More light will go through 1 millimeter of fluid than through 1 meter of the same fluid. So what is the thickness of the sample involved when reporting OD600? Or is the OD600 independent of that, so that it actually has units that people simply omit? In that case, what are the units? What is a precise physical interpretation of what is meant by the measurement OD600 = 0.1?
Suppose OD600 = 0.1 for some sample. I shine 1 mW of 600nm laser light through a 1 cm path length of the sample. What is the transmitted power?

related: http://biology.stackexchange.com/q/47973/3340

For most laboratory spectrophotometers the path length in cuvette that holds your sample is 1 cm, and unless another path length for the light is specified you can always assume that the Beer-Lambert Law for absorption of light is using 1  cm.
When growing a bacterial liquid culture in an incubator, the OD (wavelength is usually 550 nm or 600 nm) is a approximation of the number of cells, or colony forming units, or cfu, per mL of culture.
The recipe, or protocol, will normally specify the bacterial strain to use, and the desired OD (at which point one either harvests the growing cells, or possibly adds something else to the culture, like a drug, or a viral stock).
To actually know the number of cfu/mL for a specific bacterial strain one needs to construct a growth curve by taking aliquots at defined time points, and reading the OD, and also plating out some serial dilutions.  After incubating the plates at the correct temperature one can count the number of cells per mL and plot cfu/mL vs. OD600 (for example).

Nitpick: I believe that OD600 correlates better with total biomass than with the number of cells (e.g. growing but non-dividing cells do show continued increase in OD). This also makes more sense intuitively (at least to me).

OD600 is usually used in molecular biology as a measurement of the density of bacteria in a sample.  That frequency of light typically has little other scattering and the bacterial bodies
The interpretation of a specific absorbance is by Beer's law:
A = abc
a = specific absorbance of the light at that frequency by the specimin
b = the concentration of the specimen
c = the path length; the length of sample along the path of light shining through the sample
In practice for OD600 an absorbance of 0.1 is usually not converted but is understood as a low concentration of bacteria in the sample.  Typically E coli and most bacteria will start growing in logarithmic fashion, dividing regularly so the OD600 doubles in a period ranging from 10 minutes on up, depending on the bacteria.
Around OD600 = 1.0 the bacteria will stop dividing, which is called 'stationary phase'.  In practice most measurements of OD600 are not accurate above this level in most instruments since Beer's Law is only accurate in linear form in dilute samples.

Suppose OD600 = 0.1 for some sample. I shine 1 mW of 600nm laser light through a 1 cm path length of the sample. What is the transmitted power?


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Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?
Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?
Do other species have that part of DNA?

Please when you downvote explain why you do it, I see nothing specifically wrong with this question, sex differences in size are well known throughout the animal kingdom.

Are they really so much bigger? M. religiosa (75 vs. 60mm), T. sinensis (130 vs. 100mm), S. carolina (47-60 vs. 54mm) from english/german Wikipedia. As the numbers show this is a wrong statement, so I will downvote, too.

@rwst: 1) without reporting standard deviations those numbers are useless. Are they statistically different? 2) Sex differences in size/weight are a very well reported and have been studied for decades. I am no expert in insects but definitely for mammals it depends on the fact that the patterns of GH secretion are sexually dimorphic and result in different IGF-1 production by the liver.

@rwst: by the way, even if we don't care about SD (which is wrong) 75 vs 60 is a 25% increase which I would consider very relevant.

Insects and spiders have tremendous sexual dimorphism, with males often being much smaller than females.  They are pretty much just sperm carriers and sometimes do not eat.  Insects may have two or one sex chromosome, where males my have only one chromosome.   As is pointed out in the comments, not all mantis' species display this dimorphism.
Since such dimorphism is probably due to small changes in the genome due to environmental selection pressures and the genetic mechanisms of control are probably not simple.
Its difficult to say which genes are responsible for size per-se.  Recent studies of human height indicate that scores of genes may be involved in human size and insects have at least as many genes as humans do; it is pretty hard to look at a human genome sequence and say what height that person is without some other help.  I imagine for specific insect species this too would be difficult.

+1: however, as I was saying in the comments, in mammals the sexual dimorphism of the somatotroph axis is probably the main driver of sexual dimorphism in terms of size/weight.

@nico interesting... would love to see a reference - this is new to me :)

Any [neuro]endocrinology book should do. The literature about GH/IGF-1 is immense and obviously many substances are involved, such as steroid hormones (like testosterone). I guess the seminal paper to look at would be: http://www.ncbi.nlm.nih.gov/pubmed/2861084 Subsequent papers have investigated the story more in detail, see for instance studies like: http://www.ncbi.nlm.nih.gov/pubmed/7768925 and http://www.ncbi.nlm.nih.gov/pubmed/9207075 (and references within)

From the abstract of the Jannson paper: "The results suggest that high, infrequent GH pulses with low plasma GH levels in between (i.e. a masculine plasma GH pattern) promotes growth more effectively than an intermediate, rather constant level of plasma GH (i.e. a feminine plasma GH pattern). Since male sex steroids masculinize the secretory pattern of GH and have only minor growth-promoting effects in hypophysectomized animals it appears that the growth promoting effect of androgens is indirect and is due to an altered secretory pattern of GH."

nice reference!  I see that there is some possibility that insects have an IGF gene as well.  In any event, the same methods could uncover an insect's sexual growth pattern...


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On which date did the official name change of Lactobacillus sanfranciscensis change?
When did the change of official name from Lactobacillus sanfrancisco to Lactobacillus sanfranciscensis happen? An answer ((to the exact day OR within a few days) AND the name of the conference at which it happened) would be appreciated.

Most rule of nomenclature that I am aware of require that changes be made formally print and not at conferences.

Lactobacillus sanfranciscensis first shows up in pubmed in Gänzle et al. (1998). They reference Trüper and De'Clari (1997) for the name Lactobacillus sanfranciscensis. The latter say:

As none of them makes sense in the nominative apposition construction,
  we hereby correct these names to forms that are in agreement with Rule
  12c as follows.
...
Lactobacillus sanfrancisco ("the city San Francisco") is corrected to Lactobacillus sanfranciscensis (adjective: "from San Francisco").

That issue of Int J Syst Bacteriol was published 1 July 1997, so I guess that's your date.
References
Gänzle M G, M Ehmann, and W P Hammes. 1998. Modeling of growth of Lactobacillus sanfranciscensis and Candida milleri in response to process parameters of sourdough fermentation. Appl Environ Microbiol 64(7):2616–2623.
Trüper H G, De'Clari L. 1997. Taxonomic note: necessary correction of specific epithets formed as substantives (nouns) "in apposition." Int J Syst Bacteriol 47:908–909.


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How is the exogenous DNA protected from degradation during bacterial transformation?
During transformation, a bacterium can take up DNA from its environment. A small fraction of bacterial species are known to be naturally competent, meaning that they can engage in this sort of horizontal gene transfer in their natural environments.
As I understand it, naturally competent bacteria carry genes that encode the machinery necessary to facilitate the transport of this DNA across the membrane and into the cell. The exogenous DNA binds to a receptor located on the surface of competent cells, gets fragmented into small pieces, and then one strand is degraded while the other strand is transported across the membrane into the cytoplasm with the aid of a DNA translocase enzyme. Ultimately, assuming a sufficient degree of homology, it incorporates into the host genome via recombination.
During this process, however, the DNA has to be protected from degradative nucleases. I remember reading something about a transformation-specific DNA binding protein that coats the entire length of the DNA strand and prevents degradation. Is it the same translocase enzyme that facilitates movement across the membrane that is responsible for this? Or is there another protein involved?
And then, regardless of which protein is responsible in the case of natural competence, how does that protein get expressed and activated in the case of artificial competence? When we induce competence in the laboratory through one of various methods (e.g., electroporation), the DNA is essentially forced into the cell through openings in the membrane, so no transferase protein is needed. What signals the bacterium, then, to express the protective binding protein? What keeps the exogenous DNA from being readily degraded by endogenous nucleases? Whatever signals induced the expression of this protein in the case of natural competence would seem to be absent when competence is induced artificially, and it doesn't make any sense that the bacterium would constitutively express such a protein.

As an aside, one of the reasons that plasmids are circular no doubt is to prevent natural degradation of the sort you are talking about.

Different bacteria have different modes of transformation and as I understand it is Haemophilus influenzae that takes up the single strand whereas ?Streptococcus [i am not sure which bacteria it is] takes up dsDNA.
I intuitively think that DNAses are not that common like RNAses. Moreover, natural competence is associated with stress and is even triggered by DNA damage. Therefore we can speculate that DNA repair proteins will be prevalent and DNAses will be low in the cell, under these conditions. The chance of foreign DNA being damaged goes down.
In the case of artificial transformation, I guess the entire concept of heat shock is a way of providing stress. Moreover, the lab strains such as DH5alpha have certain mutations which disable them from recognizing a plasmid as "foreign".


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How much does the Vitamin D3 concentration of the blood of a human change over the course of a day?
Are there studies that measured how much the blood concentration of Vitamin D3 changes over the course of a day? If so, how strongly does it change? Does it change in predictable patterns?

Did you check on Pubmed?


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Does ChEMBL have a specific definition for what they mean with "Max phase for indication"?
ChEMBL lists various properties at pages for substances. I would like to copy some of the data that resides under "Max phase for indication" over to Wikidata. For that it would be good to know the exact definition that ChEMBL uses for "Max phase for indication". Unfortunately I can't find it on their website. Is a definition available somewhere?

@Gerhard OK, I see your point. I'll retract my close vote.

This refers to the phase a compound has "achieved" in a clinical trial.
Phases are typically ordered from 1 to 4
(although phases 1-3 are most talked about, as they are needed to bring a drug to market):

Phase 1: Testing of drug on healthy volunteers for dose-ranging
Phase 2: Initial testing of drug on patients to assess efficacy and
  safety
Phase 3: Testing of drug on patients to assess efficacy, effectiveness
  and safety (larger test group)
Finally, there is Phase 4 (referred to in your example), which is
  after a drug has been approved (by e.g. the FDA or the EMEA): here,
  the effects of a drug while used on the general patient population are
  monitored.

See also https://en.wikipedia.org/wiki/Phases_of_clinical_research
Your example has been approved (i.e. it can be brought to market, or might already be available), while others might still be in ongoing clinical trials. Others might have been "killed" earlier due to e.g. toxicity or side effects. Or have not even entered clinical trials (which would be the majority of compounds).
https://en.wikipedia.org/wiki/Phases_of_clinical_research

This answer partly tells me what I already know and partly is wrong and doesn't answer the question. The "max phase" is "4 (Approved)" but that's not what's written in the "Max phase for indication" line. My example scores differently for different illnesses for the "Max phase for indication". More importantly the Wikipedia article doesn't tell me whether ChEMBL only counts FDA or EMA registered trials or whether it counts trials more broadly.

@Christian: I'd suggest emailing EBI's helpdesk in this case, as they will be the only ones who can give you a definite answer.

@Christian This post got a community bump so I'll weigh in with my understanding: Gerhard's answer seems to be right on, and I don't see anything besides numbers 1-4 in the column you are talking about. Indeed, this is different for different indications: in your example, Risperidone has been in phase 4 trials for anorexia, but only in a phase 2 trial for cocaine dependence.


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Under which circumstances does muscle hyperplasia happen in humans?
What circumstances allow humans to have muscle hyperplasia in the prenatal and immediately postnatal period that doesn't exist later?
Is it about specific hormones that follow through our veins?

IMHO, this question would be a better fit on Health.SE.

@Remi.b : Given that it's about developmental biology I don't see how it's better at Health.SE

You're talking about a medical condition at birth. It sure is related to human developmental biology but also human health. The fact that you phrase your question as "Under which circumstances" make the question sounds like a medical question to me. But that was just my opinion and I tend to be willing to migrate more things to Health.SE than most users I think. Other users might disagree with me.


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How specific are Vitamin D promotors in the DNA?
As far as I understand there are genes that get regulated by the amount of Vitamin D that comes in contact with DNA. How specific are those promoters? Are there promotors that for example only get activated by calcifediol but not by calcitriol or cholecalciferol?

https://www.ncbi.nlm.nih.gov/m/pubmed/19944755/

https://www.ncbi.nlm.nih.gov/m/pubmed/21397016/

I’ll try and turn those into an answer later.

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