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Chromosome position mismatch for SNPs in dna tests
TL;DR: why is the position reported by DNA testing companies for an SNP on a particular chromosome different than the one in dbSNP/SNPedia databases?
I'm analyzing the raw DNA exports for the same person from 2 different companies.
There is, as expected, a small number of discrepancies on the genotype reported.
Strangely, there is also a (smaller) number of discrepancies on the chromosome and position reported for the same SNP (about 0.02% of the rs-ids that are common to both exports).
Trying to find out who is right, I looked at SNPedia and dbSNP. To my surprise, while SNPedia and dbSNP (logically) agree on the positions, they never seem to match the positions reported in the raw DNA exports.
While the two companies that I used agree on the position in the vast majority of SNPs, they are apparently always different from dbSNP. In 75% of the 101 differences between the two companies, the position number only differs by 1.
I'm surprised by this and I feel that I'm missing some underlying piece of information.
What can explain these differences?
Does the "position" in the DNA exports from 23andme and MyHeritage represent some other biological property than the position reported by dbSNP/SNPedia? Or is there a conversion formula? Or is the information from the exports unreliable?

Welcome to Biology.SE! Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. In particular, this question seems like it might be a better fit for the Bioinformatics site. ——— The different companies might be using different versions of the human genome than those online databases — your best bet may be to contact the companies and ask why their numbers are different. Thanks!

Most or all consumer DNA companies doing autosomal SNP tests deliver their raw data (at least by default) based on human reference genome build 37 (GRCh37).  This is effectively the standard for this arena because it is compatible with existing files and other companies, allowing matching and other processing.  dbSNP and SNPedia have changed to use the next major genome update, build 38 (GRCh38).  The major genome builds can be expected to have different position numbers for most all comparable places in the genomes, including of course all SNPs which are defined in both builds (most of them).
So the differences in positions shown in your raw data files and dbSNP/SNPedia are due to this difference in the reference builds they are based on.  I don't know a way of getting build 37 positions on SNPedia, but on dpSNP one way of seeing the build 37 position is to scroll down to "Genomic regions, transcripts, and products", "Choose placement" of GRCh37, and then hover over the blue highlighted SNP name, which will show a drop-down list with the (build 37) position, among other things.


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Stem cell that can pass through blood vessel
I know that blood cells can pass through the smallest of capillaries, but I was wondering is it possible for stem cells to pass through the smallest of capillaries?
In other words, is it possible for a type of stem cell therapy where stem cells are injected into the vein in the arm for example and the stem cell would pass through into the tissue through a type of targeted therapy involving ultrasound or magnetic field.
Thank you very much ,
everyone

What should ultrasound or magnetic fields help here?

yes they can.. unless of course if the stem cell is not very huge..

I am still wondering do the stem cells just simply diffuse through the walls of the capillaries?

I am thinking of some type of encapsulated stem cells where ultrasound, heat or magnetic fields from the MRI would break up the encapsulation releasing the stem cell at the targeted area. Is that plausible?

Yes, stem cells can pass through blood vessels and capillaries (as @WYSIWYG points, these cells should be small enough to fit inside that capillary). The interesting thing is that they posses multiple mechanisms of transmigration. They are attracted by TNF-alpha activated endothelial cells [1] and can pass through by [1]:

leukocyte-like diapedesis
paracellular migration between endothelial cells
transcellular, directly through individual endothelial cells

I am thinking of some type of encapsulated stem cells where ultrasound, heat or magnetic fields from the MRI would break up the encapsulation releasing the stem cell at the targeted area.

Note: I don't know if the following is plausible. It is just something I thought of and I consider it to be more effective than what you suggested.
Then what is the purpose of using stem cells that are capable of chemotactic movements and can go by themselves in targeted areas? The encapsulation you propose could be used to fit inside the cell a drug-containing capsule that would break upon external electromagnetic, ultrasonic (etc.) stimulation. This means that the capsule would also contain a substance capable of inducing cytoplasmic membrane lysis, so the drug could reach the interstitial space. Or the cell could be genetically engineered to secrete that drug, when available in cytoplasm, through exocytosis.
But why not get rid of that capsule? A cell could contain (for example) a cytostatic drug in its cytoplasm and also be fitted with membrane receptors for a specific tumoral marker. When it reaches the tumor, receptor stimulation should trigger exocytosis of drug.

References:

Teo GS, Ankrum JA, Martinelli R, Boetto SE, Simms K, Sciuto TE, Dvorak AM, Karp JM, Carman CV. Mesenchymal stem cells transmigrate between and directly through tumor necrosis factor-α-activated endothelial cells via both leukocyte-like and novel mechanisms. Stem Cells. 2012 Nov;30(11):2472-86. doi: 10.1002/stem.1198. PubMed PMID: 22887987.

A couple of points: there are many kinds of stem cells (hematopoietic, gut epithelium etc etc) and its likely their respective ability to 'home' to a target tissue varies.   Entry into a target tissue occurs when adhesion receptors on the circulating cell bind to ligands on the activated endothelium of the vessel. Another approach is to transduce the cells with an enzyme that acts on a prodrug per this type of approach

source: Stack Exchange

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sort: votes


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Gene Therapy for Cystic Fibrosis
I have another question regarding cystic fibrosis.
I understand that gene therapy is currently being talked about in the cure for cystic fibrosis. I know that Eric Alton at imperial college London is working on delivering genes using liposomes and viruses like lentiviruses but I am confused over the advantages and disadvantages of those two methods.
In addition, is there an alternative 3rd method for injecting genes that don't involved viruses or liposomes. (An alternative type of vector) ?
Thanks

There are many types of non-viral vectors. They generally fall into cationic lipids and cationic polymers. The positive charge binds to the negative charges on DNA and forms stable particles. Getting these to work in the body is harder. I've been working at it for 5.5 years and far better scientists than me have spent far longer. Some researchers working on non-viral gene delivery include Dexi Liu, Leaf Huang, and Mark Kay.

Just thought of a couple guys who are doing research on cystic fibrosis specifically, John Engelhardt has a ferret model and Joseph Zabner is using pigs. Neither animal perfectly replicates the human form of the disease, but they're both better than current mouse models.

Why are the ferret and pig models better than mouse models?

I don't exactly know, but Engelhardt and Zabner have papers describing the animal models. If I remember right the mice don't exhibit the same inflammation and immunity symptoms.

There are many other methods that are used for transfecting cells in culture. These include:

Cationic lipid mediated (as mentioned by user137)
Calcium Phosphate mediated transfection
Biolistic methods
Electroporation

Newer techniques include optical transfection (using lasers to bore a hole through membrane) and impalefection (using nanotubes). Wikipedia page on transfection nicely summarizes these techniques.
Induced pluripotent stem cells can be cultured from a patient, transformed using the plasmid and transplanted back to the tissue where it can replace the old cells with "corrected" cells.
There is another somewhat recent technique called in-vivo electroporation using which Nucleic Acid can be delivered directly in to the desired tissue.
However, to fix a mutation or introduce a transgene, just transfection is not enough; you have to make sure that the desired gene is inserted in the chromosome at the right location. Faulty gene can be replaced by the transfected functional gene via homologous recombination(HR), but rates of recombination are generally very low. Targeted gene insertion methods using genome editing tools such as Zinc-Finger Nuclease (ZFN), TALEN, and Crispr-Cas can increase this rate by introducing a break in the DNA at that region; this causes DNA repair systems to "repair" the break using HR.
There is another type of DNA repair system called NHEJ (Non-Homologous End Joining), and this is not what we are interested in. NHEJ can, in fact cause mutation through indels. Presence of the transfected DNA would shift the preference towards HR, however it has also been shown that different stages of cell cycle have different preference towards HR and NHEJ (cant find the reference as of now but I am sure about it because I was thinking at some point of time, to work on this).
Having said that, I would add that it is essential to screen the cells to see if the gene is incorporated or not. If some optimal protocol is devised then one can proceed to in-vivo electroporation.

Consider adding viral transduction to the delivery methods. If that could be effective to silence the mutation. Then introduce the wt gene by viral delivery again. It's done in vitro, even with CFTR However the pathophysiology behind CF would not allow something this simple to work.  Otherwise +1 for good answer

@rhill45 OP was interested in non-viral methods, that is why I did not include it

Your methods are all in vitro; are there in vivo methods being tested? +1

@ChrisStronks In vivo electroporation has been used for experimental purposes (I have provided a JOVE link for it) but I don't think they have been used for therapeutic purposes. As such gene therapy is still in its inception. Stereotactic injections are also used to deliver a gene to a desired tissue but afaik, they mostly use viral vectors

All of these methods are good for delivery in vitro, but in vivo is a much harder problem, especially for nonviral methods. I've reviewed a paper about endoscopic electroporation in pig intestine, but never heard of it in the lung, which would be where you want the DNA to go for CF. Hydrodynamic Injection is a fun one that works well in mouse liver, but in larger animals it turns into a major surgical hassle, and probably wouldn't translate well to the fragile tissues in the lungs, not to mention pumping them full of fluid.

I think this is that electropration paper, looks like it got published.

@user137 Yeah lung tissue is a little difficult. I think better technique would be to implant corrected epithelial stem cells in the trachea. It will still be very difficult to eliminate the existing population of mutants. It is so much easier for blood cells.
For delivery to lungs inhaling the DNA-complexes might be a solution. I had heard about a paper in which they delivered a small RNA to lungs via inhalation (shown its effects too). I am not very sure if transfections can happen that way.

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Superpatients for Cancer resistance
I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer.
The article is
http://www.technologyreview.com/featuredstory/532421/the-search-for-exceptional-genomes/
I had also previously read an article on naked mole rats and the hyaluronan in the ECM.
http://www.wired.com/2013/06/naked-mole-rat-cancer/
Therefore, I am wondering whether there are any current studies, that is trying to discover the genetic outliers for cancers. Ie, humans that have hyaluronan in their ECM that is almost naked mole rat like. Since I understand that with a genetic pool of 7+ billion there has to be at least one outlier.
Thanks


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Why does the HLA show a high degree of polymorphism?
I know how the HLA undergoes high degree of polymorphism (random genetic rearrangements), but I have not understood why it undergoes rearrangements. What is the advantage offered when HLA shows a high degree of polymorphism? What would have happen if all individuals had the same HLA?

There are multiple explanations for the enormous polymorphism in major histocompatibility complex (MHC -- the general term for the equivalent of HLA in all species) proteins. In general they reflect resistance to infectious disease, with the details being mildly debated, and usually not mutually exclusive -- multiple reasons probably apply.
The overall phenomenon is called balancing selection (Wikipedia link), and the most common explanations for the phenomenon in MHC are heterozygote advantage (which is not quite the same as overdominance), frequency-dependent selection, disease-specific selection, sexual selection, maternal-fetal interactions, and drift.
Simplistically, since MHC molecules are involved in protection against infectious disease, if there was only one MHC type then infectious agents that developed resistance to that type would be able to spread throughout the entire population readily. That means you as an individual are better off if your MHC is different from your neighbors', since you're likely to be more resistant to whatever pathogen is infecting them.
Many years ago I wrote a series of blog posts discussing the various evolutionary explanations in some detail, including dozens of references. The posts include:

Evolution of MHC: Elimination round
SEX! (… and MHC diversity)
Heavyweight championship: Overdominance vs. frequency-dependent selection
Testing overdominance in MHC: Can it be done?

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How are sound waves amplified while traveling within the cochlea?
How are sound waves amplified while traveling from the basal membrane to apical membrane within the cochlea? Are they amplified by the movement of the stapes?

Short answer
Sound waves are, technically, not amplified in the cochlea. The answer to your question, however, is that outer hair cells amplify the acoustic signal in the cochlea.
Background
To answer your question what mechanisms exist that amplify sound within the cochlea - none.
What is amplified within the cochlea is the traveling wave that moves across the basilar membrane. The cochlear amplifier is mediated by the outer hair cells. These outer hair cells are thought to be able to contract and extend when the basilar membrane moves and thereby amplifying the traveling wave (Fig. 1).
The middle ear ossicles as you say do amplify the acoustic sound, but they are situated in the middle ear, as is the tympanic membrane, which also amplifies sound by funneling a large contact surface onto the small stapes footplate.This is not the answer to your question, as they are all middle ear structures.

Fig. 1. Inner ear structures (Fettiplace et al., 2001)
Reference
- Fettiplace et al., 24, Trends Neurosci (2001); 3: 169-75

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Which statement is incorrect for Rubisco?
My question is this:
Which of the following is NOT correct for rubisco?
a. It is the most abundant enzyme
b. It catalyzes two different reactions
c. It is involved in photorespiration
d. It is not used by CAM plants
e. It is not efficient in fixing CO2
My issues with picking one are because:
a. It is the most abundant enzyme due to its inefficiency
b. It catalyzes both oxygenase and carboxylase
c. It binds O2 meaning its responsible for photorespiration
d. Malate eventually provides a molecule of CO2 to the calvin cycle where it is bound to rubisco, meaning it is used by CAM plants.
e. It only fixes 3 molecules of CO2 per second, making it inefficient. The only reason why this doesn't matter is because of the abundance of rubisco.

@RozennKeribin, the problem he has is that all five choices seem to be correct (for the reasons he provides in the second list), and thus none of the five choices seens to be NOT correct, and thus the multiple choice question has no solution (as far as he can see).

d) is "it is NOT used by CAM plants". In your following text you say it IS used by CAM plants. Seems incorrect to me.

Your justifications for your answer need rethinking. (a) It is either abundant or not. You are not asked to give a reason, and your reason is contentious. (e) Efficiency is not the same as speed. Again, focus on what efficiency actually means, not on why you think it doesn't matter. You need to state clearly whether you think each alternative is true and then say why.

David, I didn’t have to give reasons, just needed to choose an answer. I was just showing my thought process on why I was stuck.

Rozenn, somehow that literally went right over my head. I was reading it wrong and didn’t even realize I answered the question already. Doh. Thanks.

Short answer
D
Background
A. Is correct, as it is the most abundant enzyme on land, and probably also in marine environments (Raven, 2013).
B. Is correct, as Rubisco catalyzes the carboxylation, or oxygenation reaction depending upon the molecular concentration of CO2 or O2 (Sudhakar et al., 2016).
C. Is correct, as it reveals the inefficiency of Rubisco, as CO2 and O2 compete for the active site. Fixation of O2 during photosynthesis oxidizes ribulose‐1,5‐bisphosphate into 3‐phosphoglycerate and phosphoglycolate - which is basically a waste of energy.
D. Is incorrect and hence the answer to your question: Rubsico is present in CAM plants.
E. Because of the photorespiration described under B & C, Rubisco is indeed regarded to be inefficient.
References
- Raven, New Phytologist (2013); 198(1): 1–3
- Sudhakar et al., Phenotyping Crop Plants for Physiological and Biochemical Traits, 2016


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Confusion over role of current/potential in Nervous system?
I am taking a course on the nervous system and I am do not have any physics background. Therefore, I would like to know, what are we precisely talking about when we talk about current in the nervous system?
At the same time what are we talking about when we talk about potential (i.e membrane potential or action potential.
I once heard an analogy about waterfall and water comparing current and potential (voltage), can someone elaborate on that for me.
Also, I know that electrical activity is the flow of electrons. Therefore does that mean that passive current in an axon/nerve is a flow of electrons? And is it also a flow of electrons when we have action potential.
Thank you in advance for all the help.

Current flow is the movement of charged particles (ions in this case). The membrane potential is the charge difference across the cell membrane. Usually there is more negative charge inside the cell than out, so the membrane potential is said to be negative. When ion channels open, typically positive ions (Na+, K+) will flow into the cell as they are flowing from a medium that is approximately uncharged (extracellular space) into an environment that is highly negatively charged. By analogy, the positive ions can be viewed as water flowing down a gradient (waterfall). Electrical activity is not a flow of electrons per definition, especially not so in nervous tissue where it is ions that move (it is indeed electrons in electric circuits and the likes). During an action potential, therefore, it is not electrons that are moving across the cell membrane, but ions, most notably Na+ and K+, but also Ca+, Cl- among other charged particles.


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Ways to measure effectiveness of a gene therapy trial?
I understand that Fluorescence in situ hybridisation  can be used to measure the effectiveness of a gene therapy experiment/trial.
But what are some other genetics techniques to measure the effectiveness of a gene therapy clinical trial. Would blotting (northern/southern) and PCR be a way to tell if a new genome have been integrated into existing cells.
Thanks

These techniques will not tell you the effectiveness of a gene therapy. They will just let you know if the gene is inserted or not. Effectiveness means to what extent is the disease condition alleviated i.e the final response.

Genomic integration might not be a desired outcome of gene therapy. If not carefully controlled, the inserted DNA could be stuck right in the middle of an important gene, or disrupt a tightly regulated promoter or something else that disrupts the normal gene regulation and cause cancer.

If all you cared about was genomic integration, then your best bet would be some kind of sequencing. If you sequence the modified region and the flanking regions you could be sure that the new sequence was present in the genome.
It would probably be more interesting to look at how the new genes affect the cell. For example you could look at differences between protein expression in modified and unmodified cells. For that you could use RNAseq.


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Physiological function of CFTR gene product?
I just need a clarification.
If I am to talk about the physiological function of the CFTR gene product? Then what should I do research and talk about?
The only physiological function that I can think of is the control of the thickness of mucus.
Is there any other ones?
On top of that, if i am to search for research paper for this topic. Do I just search for comparative study that compare the gene product in normal individuals and CF individuals in terms of mucus thickness?
Thanks

Have you read the wikipedia article on CFTR? It's usually a good start and has plenty of references.

I did. But I don't think it is good enough.

Have you read the answers of this: http://biology.stackexchange.com/questions/23557/functions-of-the-cftr-gene ?
E.g. it helps by absorbing salt after sweating.


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Functions of the CFTR gene?
I am a senior in high school and I am studying cystic fibrosis.
I don't quite get the function of the CFTR gene as this is my first time dealing with this type of heavy scientific  info.
I had searched up its function on a website like this:
http://omim.org/entry/602421?search=cystic%20fibrosis&highlight=fibrosi%20cystic
By reading the gene functions section, I learned that CFTR regulate the formation of a chloride channel, changes the regulation of other transport pathways (i.e increase sodium ion absorption in sodium ion absortion). At the same time it also regulate the chloride-coupled bicarbonate receptor. And that is about all I got from that section.
I would greatly appreciate if someone can summarize all the functions of the CFTR gene listed in layman terms (i.e grandma language)  and also explain to me why decreased  chloride channel leads to thicken mucus or increase sodium ion absorption leads to CF Symptoms. In addition I would also appreciate it if someone can tell me does decreased CFTR gene function also lead to other diseases on top of Cystic fibrosis.
Thanks

I don't have enough expertise to have a real answer right now, and may have some info wrong. CFTR is an ion channel that moves chloride and bicarbonate ions into the extracellular space. This adjusts the viscosity of mucous and other fluids that line the lungs, intestines, pancreas, bile ducts of the liver, and reproductive tracts. In cystic fibrosis, the mucous becomes thick and hard to move. This can trap bacteria in the lungs, obstruct the bowels, cause diabetes and liver failure, infertility, etc. Studies on mice, pigs, and ferrets have also revealed changes in immunity and inflammation.

K thanks, is the extracellular space the surface of the lumen of the small intestine or bronchi,  in the case of Cystic fibrosis?

Also another clarification, the CFTR gene plays  three roles in the body.  The 3 roles are mucus thickness, minor regulation of inflammation in the body, and a minor regulation of immunity in the body?

Yes, the extracellular space is the lumen of both those organs. And what should be pointed out that I didn't really see in the answers is that almost all people with cystic fibrosis acquire chronic pseudomonas aeruginosa infections in their lungs. These are very hard to kill and if untreated the patient usually dies before 30 years old. With modern medical care, they are living long enough for the other organ problems to become noticeable, but still aren't living normal life spans.

CFTR is the gene which encodes the "Cystic fibrosis transmembrane conductance regulator", which is a membrane protein. Its function is to transport chloride and other negatively charged ion like thiocyanate ions from the inside of the cell to the outside (into the extra cellular space). This happens along a gradient, meaning the ions flow from the place of high concentration (inside the cell) to the place of low concentration (outside the cell). Since this would mean that a negative charge would build up on the outside of the cell, positively charged sodium ions follow the chloride ions by passive diffusion. This ions are secreted into the mucus in the extra cellular space.
This leads to a higher concentrations of electrolytes (salts) outside of the cell, which causes water to leave the cell (following the higher concentration of electrolytes), which makes the mucus thinner.
When the CFTR gene is mutated, this function is impaired and ions cannot be transported across the membrane. This causes a higher electrolyte concentration inside the cell and water stays there. This causes the mucus to get thicker (due to less influx of water), which then can block fine channels of the lung. Additionally bacteria can grow in the thicker mucus, which can cause severe problems as pneumonia. The process functions as shown in the figure below (from here), the sodium ions are not shown here:

If you want to read further about cystic fibrosis, I recommend this website.
Regarding the immune system there are different functions affected. First, the reduced (or prevented) secretion if thiocyanate ions lead to a reduction in the production of Hypothiocyanite ions which kill bacteria. Then different cells which are of importance to a proper immune reaction are impaired in their function, as shown in the figure below (from the first reference):

The function of CFTR is impaired in all cell types, not only in epithelial cells in the lung (although these are the most obvious consequences). In the cells of the immune system (T-cells for example) the intracellular ion concentration is disturbed including Ca2+ which plays an important role in the regulation of other genes. Other observations show that the activation of the immune system itself is also affected.
Further informations can be found in the articles I linked below. They require some knowledge of immunology, but when there are question, ask.
References:

Immune Responses in Cystic Fibrosis
The innate immune system in cystic fibrosis lung disease

The CFTR gene is coding a protein called CFTR (Cystic fibrosis transmembrane conductance regulator). This protein is an ion channel, which allows passive transport of the Cl- ions through the cell membrane in both directions. This allows the cells to transport water due to the active transport of Na+ ions. The Cl- ions follow the Na+ ions with passive transport to even up the electric charges, while the water will follow the higher osmolarity created by both ions. (Something similar happens with glucose when you put grapes into water. The glucose cannot go through the membrane of grape cells, but the water can. So the higher osmolarity in the grape cells will suck in water and the grapes will crack.)
Without working CFTR the cells cannot transport too many Na+ ions, because their membrane potential changes too much when the Cl- ions cannot even up the charges, and so the cells would possibly die because of this. (Another possible explanation that the energy barrier would be too much for the Na+ transporter to send through another Na+ ion.)
Without sufficient ion transport the water transport is not adequate in many regions of the body. By cystic fibrosis the most important affected organs are the skin, the lungs, the pancreas and the reproductive organs.

The skin cannot reabsorb Na+, so it will be salty.
The lungs cannot send water to the mucus, so it will be too sticky, and because of that it prevents the cilias by cleaning out the pathogens from the lungs. The results are infections, probably pneumonia and cysts in the lungs.
The pancreas is usually not able to do its job as well. The result are poor digestion, and due to that vitamin absorption problems, e.g. vitamin-D deficiency (and because of that osteoporosis). In many cases the pancreas is completely cystic, and it loses the ability to produce insulin, which leads to diabetes.
The reproductive organs are affected as well, most of the males with cystic fibrosis are infertile, and about every fifth female as well.

As you already know this is a hereditary disease caused by mutations in the CFTR gene. What you probably don't know that only homozygotes are affected. The prevalence of the mutant alleles is around 1/25 in my country (Hungary), so every 25th person is an asymptomatic carrier and by every 625th marriage there is a 25% chance that the child will be homozygote. The prevalence is dependent on the region, e.g. North- and West Europe is more affected than South- and East Europe.

Figure 1 - cystic fibrosis homozygote prevalence - Epidemiology: Mutational Diversity–Patterns of CFTR Mutations

Because of the region dependent prevalence of the heterozygotes (and homozygotes) there are theories, which claim that probably there is (or was) a negative evolutionary pressure on the CFTR gene, and the heterozygotes have evolutionary advantage, just like by sickle-cell anaemia and malaria. The CFTR is target of many infectious diseases e.g. cholera, typhoid fever, tuberculosis, etc..., so there are many candidates. Afaik there is no decision yet in this topic.


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Negative value on linear gene expression in microarrays
I am starting to use microarrays and maybe this is a dumb question:
Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced?
And, in this case, how to correct them? With scaling (adding the absolute value of the minimum negative value) or flooring (converting negative values to zeros)?
Thanks

I'm not personally familiar with Illumina arrays, but I can give some notes here.  This link is a paper which describes the array quality controls specifically. This presentation describes the calculation of the intensities in bioconductor.
The answer is yes: you will find negative numbers sometimes.  They should be rare.  The Intensities numbers from a scanner which essentially takes an image of the bead fluorescence on the glass slide and tries to subtract a background signal.
The background is the typical level of signal you see on a bead with no sample DNA bound to it.  You will get some pixels lighting up a bit even there.
In expression microarrays, this is not a perfect system as each bead has a different nucleotide sequence on it.  Each bead has a specific DNA sequence has non-specific binding which is pretty much unique on the slide.  That is to say, the oligomer on the bead might bind strongly to DNA from your sample which is not its reverse complement to varying degrees.
I think what happened is that there will be a handful of cases you can find a bead which has less fluorescence than the background controls on the slide.  It's possible that the probe has a design flaw but I would generally assume that the negative number means that there is no detectable target cDNA in the sample for that oligo.
I probably wouldn't convert the number to a zero, but you could probably justify it to yourself in some cases.  Most difference experiments are the logarithm of the ratio so zero is not a great number in those cases.
@Luke 's comments are well said.
I think that negative values can still represent signal because of the variance of sequence-dependent effects for the purposes of scaling, and difference experiments.  But I'd tend to think of them as zero signal in any case.  There are probably genes which express at or below detection threshold all the time, which is not zero information, so the number has some value.

This is pretty spot on. The "intensity" values you end up getting are relative values to the background levels. These tend to be normalized to an arbitrary value - "100" could be the arbitrary threshold for background, above which you see a reliable signal. A probe with very low intensity could therefore be below 0.

do you have any suggestions about what to do with a negative intensity @Luke ? I tend to ignore things with such low values, but it can make a difference in comparing 2 small amplitude measurements i guess.  (i'd still tend to ignore them in that case!)

Anything below the background threshold is by definition an unreliable signal (i.e. detection P-value > 0.05). The 2 options for dealing with this is either to set values below the background threshold to "missing", or to leave them in but be aware that below the background threshold the values are no longer meaningful (you might do this if, for instance, 60% of your sample were below background for this probe, but the rest were above - this is still meaningful because it means that 60% of your sample express less than the 40%, so you do not want to set them as missing, as this may be relevant


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What is the standing genetic variation?
I am reading this review. In the first part, the author introduces Standing Genetic Variation, described as:

STANDING GENETIC VARIATION Allelic variation that is currently
  segregating within a population; as opposed to alleles that appear by
  new mutation events

Does it mean that in adaptation the allelic variation is already present (not created by mutations) and in adaptation it prevails over the others?
Thanks

Standing genetic variation is when there is more than one allele at locus in the population at the time-point in question. When an allele goes to fixation there is no standing genetic variation at the locus until new mutations occur. Loci where alleles are not fixed are described as having standing genetic variation.

"Standing genetic variation: the presence of more than one allele at a locus in a
  population."

from Barrett and Schluter 2007


text:
How to assess if biological measurements follow a normal or a log-normal distribution
I am using a dataset composed by $m$ samples and $n$ features (genes). Each data point is real number.
I want to understand how to preprocess data before analysis, in particular: do data points follow a normal or a log-normal distribution?
I thought about using qqplots and searching for different tests to assess the form of the distribution, but I have a doubt:
Do I have to assess the form of:

each sample distribution
each feature (gene) distribution
the whole dataset ($m$ samples x $n$ features (genes))

?

This might be better suited for [stats.se]

@C_Z_ you are right, but I thought it may be a task well-known for bioinformaticians, e.g. while using microarrays. However, if not, how can I transfer it to CV? Thanks

Have a look at http://biology.stackexchange.com/q/37167/3340

From personal experience, nearly all count data whether from microarray or reads from RNAseq of some kind, requires a log transformation of the counts. Usually a small fraction is added to all values before doing so to zero protect. Log2(counts + 0.5) or some such.   This is independent of the treatments. If you log transform one sample, you will do the same for all samples. To examine for normality, a simple way is to look at the histogram of counts (by all samples or by each sample) before and after transformation. Roughly bell shaped -> proceed.
Pictures below from my data. Although the data are from RNAseq, microarray data should be similar.
R code here:
hist(t$counts,breaks=100,main="Histogram of Raw Counts from RNAseq")
hist(log(t$counts + 0.5,2),breaks=100,main="Histogram of Log2
transformed Counts from RNAseq")

There are ways to statistically check for normality, and I find visually examining the data as I listed above is a good first step.

Preprocessing will and should always depend upon the biology that you try to answer or discover (e.g.: There might be an experimental rationale to believe that some genes behave differently in individual samples - and that different samples could possibly have different distributions.)
log-transforming your data by itself is usually no problem, and hugely facilitates the simultaneous exploration of different magnitudes (though adding a small value prior log can soon make your analysis misleading, if you intended to quantitatively study variance across samples)
For testing normality you might want to apply the Lilliefors test on raw data and log-transformed data
If you are using a readout of gene-expression you must not anticipate a unimodal distribution, e.g.: Metazoans have two different classes of genes, which overall lead to a bi-modal distribution (Hebenstreit et al. 2011) (If you can fit any unimodal  distribution - such as lognormal - you should become very suspicious and check the quality of the experimental data.)


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What's a segmented copy number profile
I am studying copy-number variation. I am reading

C. H. Mermel, S. E. Schumacher, B. Hill, M. L. Meyerson, R. Beroukhim, and G. Getz, “GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers,” Genome Biol., vol. 12, no. 4, p. R41, 2011.

Here, it is written that

Segmented copy number profiles represent the summed outcome of all the SCNAs [somatic copy number alterations] that occurred during cancer development. Accurate modeling of the background rate of copy-number alteration requires analysis of the individual SCNAs. However, because SCNAs may overlap, it is impossible to directly infer the underlying events from the final segmented copy-number profile alone.

It is not clear to me how a segmented copy number profile represents the summed outcome of all the SCNAs. Is it because different alterations can be present in the same sample, or can alter the copy-number in different moments, or both?
And, do they overlap spatially, temporally, or both?

Yes, one sample can contain different alterations. For each patient there is typically one tumour specimen that is removed. That specimen may be divided up into several samples (e.g. one for DNA sequencing, one for RNA sequencing, one for methylation microarray, and one for copy-number variation microarray), however each sample contains thousands of individual cells and two adjacent cells may have different CNVs (depending on their clonal ancestry, etc.). In other words, a tumour is a heterogeneous collection of cells. For some tumour types there can even be healthy cells mixed in.

Hi, can you please put it in an answer, if it's an answer.. and with references.. so I can accept it.

There you go. Done!

Yes, one sample can contain different alterations. For each patient there is typically one tumour specimen that is removed. That specimen may be divided up into several samples (e.g. one for DNA sequencing, one for RNA sequencing, one for methylation microarray, and one for copy-number variation microarray), however each sample contains thousands of individual cells and two adjacent cells may have different CNVs (depending on their clonal ancestry, etc.). In other words, a tumour is a heterogeneous collection of cells. For some tumour types there can even be healthy cells mixed in.
The term in the literature is clonal evolution, there is a nice image in this article: Tumor Heterogeneity

To directly respond to the quote presented,

Segmented copy number profiles represent the summed outcome of all the SCNAs [somatic copy number alterations] that occurred during cancer development.

As a tumor progresses, genomic instability can often increase.  That is, more and more SCNAs occur.  Because of this, one SCNA can overlap another.

For example, look at the tumor progression of the chromosome above.  Let's say you have a loss on this chromosome (Event 1 the MATERNAL chromosome).  This loss can occur by many mechanisms which I won't go into.  The tumor proliferates, splitting many times, and mutations are accumulating.  These mutations can cause more events to occur, and perhaps on this same chromosome arm, the distal part of the remaining copy is duplicated (Event 2 the PATERNAL chromosome).
In the copy number profile, it will look as though you had a loss on just an interstitial part of the chromosome.  But looking closely at the data, you can see that you've lost heterozygosity on the distal portion of the chromosome as well (we now have two copies of the PATERNAL chromosome, and 0 copies of the MATERNAL).  This is a simplified example, and many events can occur along the same chromosome arm.  If the paternal chromosome holds a mutation, this can mean a selective advantage for the tumor or resistance to drug therapies.
Therefore, the CN profile represents a snapshot in time of what the copy number state was at that moment, with no explicit information on how that copy number state was obtained.


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Effect of pupil responses on the electroretinogram
The electroretinogram (ERG) is a measure of electrical activity of the retina. It is typically recorded from the cornea with a wire electrode or gold-foil electrode. Generally, the the ERG is considered to reflect the retinal processing of a light stimulus, typically a photoreceptor response followed by secondary neuronal activity and electrical activity evoked by supportive Muller cells.
I am wondering if the pupil response will add signal on top of the ERG? Firstly, there is the direct pupil response, which causes the pupil to constrict when the eye is subjected to bright light. Pupil constriction may, perhaps, induce electromyogram (EMG) activity when the smooth sphincter muscle around the pupil contracts, which in turn could theoretically contaminate the ERG. Secondly, there is neuronal activity involved in constricting the pupil, as light is processed in the retina by ganglion cells that in turn drive the pupil reflex. Furthermore, there is the consensual pupil response as well. This response causes the contralateral pupil to constrict when the ipsilateral eye is subjected to bright light. The consensual response is mediated by efferent input from the brain following stimulation of the other eye and causes both eyes to restrict. Hence, neural input arrives in the contralateral retina from the brain. This activity is not directly related to the processing of the light stimulus and may disturb the ERG proper when ERGs are recorded with a flash and both eyes are open.
So my question is

Does a pupil-mediated EMG affects the ERG signal?
Does neuronal activity involved in the pupil reflex affect the ERG, for example the  efferent input involved in the consensual response?

I have had no luck after extensive searches in text books, Scopus, Pubmed, Google, Google Scholar.

Answer version1 (read the comments, I leave v1 for the those who can make the same assumptions in the future)
To answer the question we should clarify some general concepts and processes mentioned it the clause:

EMG is performed by means of direct placement of the electrode (the are two types here - surface-EMG and needle-EMG) on/into the skeletal muscles, this is why there is no such thing  "iris-sphincter-related EMG": the sphincter is inside the eye and there is no way to contact it without eyewall penetration somewhere. Thus, this part of the question is hypothetical.
ERG is performed after pharmacological mydriasis (pupil dilation to ensure retinal mass response or to perform multifocal ERG), so in the standard settings there is no substantial pupils reaction during the test. Thus, this part of the question is hypothetical too.
ERG measures electrical changes when one of the electrodes is directly attached to the cornea - here we should stress "to one cornea", and "reads" the current from only one side. This is why, the reaction of contralateral pupil, skeletal muscles, heart/defibrillator activity are irrelevant since they are out of the electrical loop existing between the electrodes (the second electrode is on the forehead).
ERG measures electrical activity only - there is no muscle contractions in the process, while EMG involves the time needed to acetylcholine to be released and muscle contraction to begin. This means that the time scopes of these tests are different. In addition, as stated, pupils react as an efferent organ (III nerve, mediator related), while retinal photoreceptors react directly to the light stimulation, so there is a clear delay between these two processes. Theoretically, one can perform full cut of the optic nerve with the resultant loss of afferent signal and consequent loss of efferent pupil reaction, but the ERG will still detect the normal curves if the photoreceptors are intact.

Back to question itself: according to the mentioned facts we should state that the question is more hypothetical and theoretical, thus answering it directly is problematic and the answer should not be assessed without facts mentioned above.
So, the final answer - 1+2: No, pupil reaction does not affect the ERG in the real and standard settings and should not be counted as an interfering factor.
Version2
I've found an interesting patent claiming that pupillary responses can contribute to eERG (electrical stimulus instead of light). These influences stated to be artifacts, thus the authors raise the question how to diminish/filter them out.
They say

Eye movements and pupil responses may contribute to the eERG;
Pharmacologic dilation abolished these pupil responses;
Bilateral artifacts, such as pupil responses, in the corneal eERG
  cannot be sufficiently reduced by using dilation drops; Even after
  dilation, a residual, but substantial electrical response persisted in
  the contralateral eye.

So, I should convert my answer to yes/yes. Taking into account the obscure nature of the subject, I hope you will agree that by making mistakes we can learn something new. I personally learnt a lot trying to answer this excellent question.
Patent application number: 20120143080 (if the link will be broken in future, one can find the patent by this number).
Direct link
http://www.faqs.org/patents/app/20120143080

I admire your detective work greatly. In fact, I am one of the authors on that patent. In this patent we are basically making guesses, but we have no answers. I left out any reference to electrical stimulation in this question at Bio.SE to make it more general applicable to light-evoked ERGs. Hence, although I cannot accept your answer, I have started a bounty which is yours to keep in 24 hours - as a token of appreciation (cannot give it away immediately).

@aliced I thought that pupullary elecrical stimuli are filtered out from regular ERG

@AliceD there is an amplifier and some filtering mechanism which should affect the noise in some way - I've read about that while searching information about ERG, but don't have a source now....

Never encountered any mention of filtering of pupil responses. A normal ERG a and b peak develop prior to the pupil response so timing may be brought forward, but not so on long-latency responses. Perhaps this discussion should be proceeded in chat when necessary. Thanks!

@AliceD If I understand you properly, we don't have sufficient sources to support both answers neither  "no", nor "yes".  What can we add to "no" answer is the fact that sphincter has constant tonic efferent current, which is why its consequent rise might be less influential on ERG... In addition, the current for dilator should in some way lessen the ERG curve of the sphincter...


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Identification of black growth on onion skin
I have encountered this black-colored growth on onion skins a lot. It seems to develop over the course of weeks and I have rarely, if ever, encountered the material on fresh ones. If I peel the onion and it streaks the onion flesh, it appears, dark blue-ish. It looks like a fungus, perhaps a bacterium, but I am unsure. It is often found 'hiding' under the outer layer of skin on the deeper skin layers. In the photo the outer layer of skin was peeled off. It never seems to invade the edible parts below, though.
The pictures below are standard white onions from the local supermarket in Canberra, Australia (Canberra [Australia's capitol yes!] lies between Sydney and Melbourne). I must admit, I don't know if they are imported. The pictures below were taken mid-winter. Temperatures in our kitchen plummet during the day because of bad insulation. In the evenings and weekends it's room temp with heating. The onions are stored in the dark, in a kitchen cabinet. Humidity is low and mostly the days are dry and sunny. However, we cook in the kitchen so at times there is plenty of moist.
Also, I wonder, would it be harmful? No self-help medical issues here, I always wash and fry/cook my stuff and no issues whatsoever, just curious.

I understand there is little to go with. However, a general genus or group of fungi would already be cool. I googled and sought for images to no avail.

I think it is Aspergillus niger:

On the second place I'd suggest  Black Mold disease caused by Alternaria species.

Are they bad for your health? Something rings a bell that A. Niger has some bio-active compounds.

@AliceD They will not improve your health definitely. A. niger could produce ochratoxin A (OTA) and fumonisin B2 (FB2) as well as other potentially toxic substances.


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About lack of selective pressure
In [1] it is stated that:

the frequency of comutations in FGFR3 and KRAS or PIK3CA and KRAS was lower than predicted by chance, suggesting ... a lack of selective pressure for both mutations to occur

It is not clear to me how lack of selective pressure may produce a frequency of comutations that is lower than predicted by chance. I'd expect the frequency to be the one predicted by chance, if no selective pressure is applied. What am I missing?
[1]   S. E. Woodman and G. B. Mills, “Are oncogenes sufficient to cause human cancer?,” Proc. Natl. Acad. Sci. U.S.A., vol. 107, no. 48, pp. 20599–20600, Nov. 2010.

Often the phenotype caused by a given allele depends on the alleles present in other genes; this is termed epistasis. In the context of tumors, selective pressure is primarily associated with the ability of cells to grow and divide (without dying). It could be possible for two mutations which each confer some tumorigenic properties to conflict with each other, such that when both mutations are present they interact to either kill the cell or otherwise block the effect of the other mutation. The expected result would be that few tumor cells would exist with that combination of mutations because they would proliferate less than those cells with just one.
However, I suspect they are just addressing an non-significant difference from chance that they felt was too big to ignore entirely in discussion. You left out the rest of the sentence including a key word 'either' which I think is entirely misleading here and I wish you would not have done that (emphasis mine):

frequency of comutations in FGFR3 and KRAS or PIK3CA and KRAS was lower than predicted by chance, suggesting either a lack of selective pressure for both mutations to occur or a negative interaction between the consequences of each mutation

Essentially they are hedging the statement that there could be a negative interaction (i.e., selective pressure against) having both mutations with the possibility that there is just no meaningful positive interaction and the observation of a less than chance co-occurrence is not a true result. Note that they have a very small population because these are clinical tumors, and KRAS analysis was only in 59 patients (with only 12 mutants), making the statistical power for interactions very low.
I agree that this wording is imprecise and a bit unclear, so your confusion is understandable, but I think there are two reasons why it is worded this way. First, I believe they are trying to emphasize a possible future research direction and are trying to do so without making a criticism of the paper they are reviewing, because I don't think they view it as a criticism. Had they said "This study doesn't have enough statistical power to determine if there is a negative interaction between these mutations," that would sound overly critical given they are discussing something that wasn't really the intent of the original study. Second, I think the simplest prior expectation (which they do not state but is implied) is that two mutations that contribute to tumor production individually will be even more tumorigenic when present together. By stating the other outcomes: no selective pressure for the two mutations to cooccur or a negative interaction, they are implicitly stating that the simpler outcome, a positive interaction, does not seem to be occurring.
There is also a definite issue of selection bias here (statistically, not evolutionarily). That is, they are investigating a certain type of tumor. If those tumors can be caused by either a mutation in one gene or a mutation in another, then the chance association of those mutations would be the chance in the general population/other types of tumors/noncancerous tissue, which would be low (because most have neither), rather than the chance in patients.
The article you refer to is just a commentary on another article; you should really read Hafner et al instead (and note the original paper doesn't talk much if at all about these co-occurrences).

Good answer +1. I would add the term epistasis somewhere in here and maybe add that the phrasing is indeed quite misleading.


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Colormetric assay for a phenol product?
I am working on an assay for phenol products created by a colony of bacteria. I have searched up a paper that involves gibbs reageant but the protocol is kind of unclear.
Does any of you know where I can look for a detailed protocol for a gibbs reagent colormetric assay (preferably one that uses cell medium)
Thanks

I have not used the assay myself, but Bhuiya and Liu "A cost-effective colorimetric assay for phenolic O-methyltransferases and characterization of caffeate 3-O-methyltransferases from Populus trichocarpa." Anal Biochem. 2009 384(1):151-8 [link] seems to have a relatively straightforward protocol.
Roughly, you make a 0.4% (w/v) solution of Gibbs reagent in ethanol, and then add one fifth volume of that to your enzymatic reaction mix. You then observe the solution spectrophotometrically.
The biggest issue I see is that it looks like each phenolic compound has its own absorption maximum, and widely varying extinction coefficients. In their protocol it seems they look at full range scans, rather than single wavelength measurements. You'll definitely need a standard curve for your particular phenolics in order to get quantitative results. (Also, any background phenolics or medium absorption in the 400-600 nm range may throw off measurements - use appropriate blanks.)


text:
James Allison's T-cell discovery technique
The excerpt on Wired magazine of The Breakthrough by Charles Graeber has the following description of how James Allison found the T-cell receptor.

Suddenly it seemed so obvious: If Allision could rig up a way to
  compare B cells and T cells, devise a lab experiment that put one
  against the other and let their redundant surface proteins cancel each
  other out, the receptor should be the molecule that didn’t cancel out.
  Essentially, he was looking for a needle in a haystack, and his idea
  was to set fire to the haystack and sift the ashes—or as Allison puts
  it, “pick it out of the weeds.” Whatever was left would be the needle
  he was looking for.

It is a vivid metaphor. But the author does describe in more specific detail how the cancellation actually works. Can someone give such a description?

Well so here's the paper, at least on Dr. Allison's side. Mind you, the discovery is shared by a number of individuals for their combined effort.
So what they did is took mice and immunized them with T-cell lymphoma cells. The mice would essentially produce B cells against the lymphoma cells. And so we know that B cells produce antibodies, and hybridoma methods exploit the B cells to get a lot of that antibody. With their constructed hybridoma library, they could look at reactivity of antibodies produced against the lymphoma cells against the reactivity of the same antibody against other cells. They ended up finding 1/43 antibodies, which they dubbed 124-4O, reacted to their lymphoma line, but not to other cells.
With a pull-down assay, they isolated the receptor and determined it was a heterodimeric glycoprotein. A step further, they looked at both B cells and T cells, then, and were able to detect similar structures in the T cells, but not in the B cells.
Someone correct me If I'm wrong, though.


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Waste generation by embryo
How does an embryo produce waste products even when its organ systems are not developed fully ? How does the placenta identify or differentiate waste materials from embryo ? Which organelle or specific cell acts as excretory organ ?

Embryos still metabolize the nutrients delivered by the mother. The metabolism takes place in the cells, including in the developing organs. Metabolism produces waste products that must be removed. The allantois is the structure that removes waste from the embryo.
I'm not sure what you mean by the placenta identifying or differentiating waste materials from the embryo. The waste simply diffuses passively into the mother's blood from the embryo. The mother's excretory systems then handle it.


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What fraction of biomass is cultivated by humans? Have we increased the number of large animals?
What fraction of "large animals" are domesticated by humans, compared to those who are wild? I mean cows, pigs, sheep, horses, dogs, cats in relation to comparable wild animals. Different measurements to a similar effect would also be of interest. Possibly including even chicken and fisheries.
I wonder if there are more "large animals" alive on Earth today than thousands of years ago when human agriculture was much smaller?
I'd also be interested in some measurement of how large a fraction of vegetable life on Earth consists of our agricultural cereals et cetera.

XKCD did a bit of research on this, though it doesn't handle historic data, and only mammals: http://www.explainxkcd.com/wiki/index.php/1338:_Land_Mammals

@Deruijter That's... amazing! I suspected it would be large, but this is a factor of ten bigger again than I expected. If correct, I suppose that the mass of wild land mammals cannot have decreased nearly as much as human and domesticated land mammals have increased. Is the age of industrialization at the same time the age of the land mammals?

The loss of wild large animals may be worse than you think. In the 1800s, settlers moving west across america described gigantic herds of buffalo, which are all gone now. Their mass has probably been replaced by cattle. One important factor is probably man made fertilizer through the haber process to capture nitrogen from the air and make ammonia. We have more than doubled the mass of bioavailable nitrogen in the last century, allowing us to grow a lot more grain to feed to cattle, pigs, and chickens. The nitrogen also causes algal blooms and dead zones.


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Is emergence connected to nature's transition between fractal regimes at different size scales?
A fractal algorithm like Mandelbrot is self-similar in all size scales. This is not the case in nature. A tree is fractal in the sense that each branch is similar to the tree as a whole. But that is only true at a certain range of scales, about 0.1 - 10 meter. The forest does not look like one tree, nor does the texture at millimeter scale or the cellular structure at microscopic scale. At those scales the tree may or not be fractal, but at least it is not fractal in the same way as on the 1 meter size. Nature breaks the fractal regime after only a couple or so self-similar scales.
Are these transitions between fractal regimes studied by biology?
Are there any ideas around about how different fractal regimes might be connected with emergent phenomena? At very small scales there exists no tree, but only elementary quantum particles/waves. Macromolecules and cells and the tree and the forest each emerge as a phenomena on different size scales. I wonder if this emergence is matched by the different fractal regimes at those scales?

I think that you are mixing up the causality between fractals and emergent phenomena.
There are LOTS of different types of emergent phenomena, and only some of them are connected to fractals.  Many are instead connected to other physical phenomena like phase transitions (e.g., traffic jams) or feedback loops (e.g. dune formation).
Biology does indeed make use of emergent phenomena at many different scales. This is, however, only what we should expect from an evolutionary process that is building patterns through trial and error selection.  Critically, emergence is the formation of complex patterns from relatively simple local interactions, and these patterns are often highly robust due to the nature of the physics driving them.
This means that emergent phenomena are an evolutionary "shortcut" for achieving many kinds of useful structure. Fractal-generating programs, in particular, are a one very simple way of encoding large-scale space-filling patterns such as tree branches or blood vessels (other space-filling patterns, like hair follicles or shell patterns use different mechanisms). And remember, they typically run "inversely" in biology, starting small and growing rather than starting large and subdividing---thus the natural truncation of iterations by the limit in growing scale.
It is thus unsurprising that organisms would first "discover" fractals rather than something more akin to a human-style blueprints for encoding such phenomena, since the repeated local rule of a fractal is so much less complex. It's just that we discovered fractals later and they are less intuitive to us, so they look more remarkable to human thinkers.

Fractals are by far more ubiquituous than it may appear at a first glance, spanning essentially all the levels of organisation of living organisms; including vascular and neural networks in animals and plants, metabolic networks in bacteria, and the food networks characterizing whole communities. (See, e.g., the answers to this question for more discussion and the relevant links.) All these networks are self-similar, and one cannot really claim that there are transitions between different fractal regimes (at least, such claim is explicitly excluded by one of the postulates of the cited theory.)
That the existence of these fractal networks is an example of an emergent phenomenon (in strict physical sense, as, e.g., described by Anderson), does not cause any doubt. What is less clear is whether 1) these networks are the result a single symmetry-breaking/emergence event that modern organisms inherited from their most recent common ancestor or 2) whether organisms naturally evolve toward fractal structures as a means of increasing their fitness (the theory states that fractals lead to the highest energy efficiency).
The last paragraph in the OP suggests that the question might be posed in more general sense, of the emergence phenomena in biology. Indeed, if we start with atoms, one can treat evolution as a sequence of emergent phenomena in their strict physical definition. To give just a few steps:

emergence of simple molecules and chemical reactions between them
emergence of self-replicating polymers
acquisition of cellular membrane
emergence of multicellular organisms

This question gives links to some more or less readable discussions. Yet, it is fair to say that in terms of exact theory we have not much evolved since Anderson (although a fe succinct results were obtained, e.g., regarding teh tehrmodynamics of self-replicating polymers: here and here.)


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Does any organism use both photosynthesis and respiration?
Chlorophyll and hemoglobin are very similar molecules, as far as I understand. The important difference being one using an iron atom and the other a magnesium atom. Do any organisms use both to get energy from both oxygen and solar rays? If not, is there any good explanation of why?
And do organisms that use chemosynthesis also use macro molecules similar to chlorophyll and hemoglobin?

Plants actually DO respiration and have mitochondria to do it for them as well. It's more or less the same respiratory chain with oxygen as terminal electron acceptor. Hemoglobin is a transport molecule for oxygen that helps distributing the oxygen to all tissues in our bodies. Plants do not really need that as they produce the oxygen on the fly.

Related question on [worldbuilding.SE] (of all places!): Why aren't animals photosynthetic?

Salamander is photosynthetic vertebrate

Also see (on Worldbuilding) : Can a plant evolve to give off CO2?

@AlexDeLarge Well, they don't need hemoglobin because they use diffusion. Pretty much all the important stuff is close to the "body" surface. Don't forget that plants don't produce oxygen in the night - that's when they drain oxygen from air and release carbon dioxide.

Are you asking about "respiration" or "haemoglobin"? The answers will be very different.

I think you have the wrong idea about this site. You have asked a question. If you want a good answer then you need to engage and clarify ambiguities in that question. The question everyone has answered is "Does any organism use both photosynthesis and respiration?". But you might be trying to ask something like "Do any plants use haemoglobin?" or "Do any animals use chlorophyll?".

It seems that the answer by Brian is the one you were looking for.

Besides the unicellular organisms cited by other answers (and the fact that plants actually do respiration), there are some animals who are able to get, although indirectly, energy from photosynthesis through symbiosis with photosynthesizing organisms. You can try the spotted salamander Ambystoma maculatum:

The spotted salamander is similar to the sea-slug [another of these animals] in that in order to be partially photosynthetic, it maintains a symbiotic relationship with algae cells. While it has long been known that a relationship existed between the salamander and the algae, it was presumed to be a relationship in which both organisms worked separately. However, when researcher Ryan Kerney was studying a batch of spotted salamander embryos, he found a bright green color coming from inside their cells.
The chloroplasts were found near the mitochondria within the salamander’s cells, meaning that the mitochondria were likely directly consuming the oxygen and carbohydrates that are created through photosynthesis*. The most amazing part about this relationship is that all vertebrates have strong immune systems that tend to destroy any foreign material found within their cells. Although the reason for this is unknown, this makes the spotted salamander the first vertebrates to be discovered to have the ability to photosynthesize.

And according to its wikipedia page:

Eggs of A. maculatum can have a symbiotic relationship with a green alga, Oophila amblystomatis. Jelly coating prevents the eggs from drying out, but it inhibits oxygen diffusion (required for embryo development). The Oophila alga photosynthesizes and produces oxygen in the jelly. The developing salamander thus metabolizes the oxygen, producing carbon dioxide (which then the alga consumes). Photosynthetic algae are present within the somatic and possibly the germ cells of the salamander.

It should be noted that this animal is not able to directly perform photosynthesis, but it's still able to get energy from the sun and, being a vertebrate (and not a fish from the family Channichthyidae), it has hemoglobin.
Remember that the most plausible theory for the emergence of chloroplasts, the photosynthesizing organelle, in eukaryotes (aka organisms with cellular nucleus) lifeforms is through the addition of an external organism (probably a cyanobacteria) to the cell, since chloroplasts (and mitochondrias) have their own separated DNA:

Mitochondria and chloroplasts likely evolved from engulfed prokaryotes that once lived as independent organisms. At some point, a eukaryotic cell engulfed an aerobic prokaryote, which then formed an endosymbiotic relationship with the host eukaryote, gradually developing into a mitochondrion. Eukaryotic cells containing mitochondria then engulfed photosynthetic prokaryotes, which evolved to become specialized chloroplast organelles

tl;dr: Yes, all plants breathe.—
I'm not sure whether I understand the question correctly; because all plants use respiration! Some of the organic high-energy substances produced by photosynthesis are later "burnt" to produce energy in the same "respiration" process used by animals, producing CO2.
The difference to animals is that green plants synthesize their carbs (including the ones they burn for energy), fat and proteins from thin air, so to speak, while animals must eat them.
These antithetic processes, photosynthesis and respiration, are often tied to the day-night cycle. When light is available, the plants-only photosynthesis dominates so that the plant consumes CO2 and emits oxygen; at night, when photosynthesis becomes impossible, the usual common-place respiration causes the plant to consume oxygen and emit CO2, just like animals.
Only as long as the plant is growing, this cycle is tilted towards photosynthesis so that more oxygen is emitted than absorbed: the excess carbon and hydrogen is sequestered in the plant's growing biomass. But when the plant dies, all this high-energy biomass is burnt by animals and micro-organisms, making the overall balance carbon- and oxygen-neutral.2
So how do plants breathe — or rather, exchange gases with the atmosphere in general — if they don't have lungs or gills? The key is the large surface area of typical plants with leaves. Seen in this light, a tree looks well-designed for filtering stuff out of the atmosphere. Consider these two images. The first one is a lobe of a human lung3. The second one is a tree... or is it?

I found John W. Kimball's page about gas exchange in plants accessible and full of interesting information. Central to our discussion are three facts:

A plant's living cells, including the ones in the stem, are never far from the surface.
The rate (or "speed") of respiration, i.e. oxidizing carbohydrates, is lower than in animals. (Plants do not perform physical labor with muscles and do not have a brain, which are the two main energy consumers in the human body.)
Photosynthesis happens mostly in the thin leaves.

Because of these factors — smaller amounts of gases per time over shorter distances — plants do not need high-volume, long-distance gas transport in the fashion most large animals do, with blood circulation. The gas travels between and through the cells as needed, guided and regulated by mechanisms detailed in Kimball's text. The fluid traveling through the stem provides (lots of) water to the leaves in the upward direction and nutrients to the living cells downward, but apparently does not carry (much) gas.
The Arbor Day Foundation has a nice page detailing a tree trunk's structure with information about each layer's function. (I didn't know that the cells in the heartwood — the inner part of the trunk — are dead and do not participate in the transport of nutrients or water.1)

Your question seems to be triggered by a perceived similarity between the molecule giving blood its red color, hemoglobin, and the molecule which gives plants their green color, chlorophyll.
True, both are organic molecules with metal atoms embedded, but they are quite different, even apart from their color. Hemoglobin is a protein with a fairly complex spatial structure; look at the image on the Wikipedia page. It weighs as much as 64,000 hydrogen atoms, i.e. it has a molar mass of about 64,000 g/mole. Chlorophyll is also an organic molecule, i.e. it has carbon chains and rings, but it is not a protein. (In living cells Chlorophyll molecules are embedded in a protein complex, arranging them to work together; that is a different thing.) It does not fold in space, partly because it is not as big. Its molar mass is only close to 900 g/mole, almost 80 times lighter than hemoglobin. A model of one variety can be found on its Wikipedia page, too.
The jobs the two molecules do also are fairly different, even though both have to do with oxygen.

Hemoglobin has a transport job. It binds oxygen efficiently. The spongy, blood-heavy lung tissue absorbs oxygen, which dissolves in the blood and is bound to the hemoglobin swimming around in it. There is a lot of hemoglobin in our blood, increasing the blood's capacity for oxygen transport by a factor of 70 compared to just dissolving oxygen in water (and it dissolves actually quite well in water!). Thus, hemoglobin does not synthesize anything but simply transports gases, mainly oxygen, through the body to where they are needed. Some athletes dope by collecting their own hemoglobin and re-injecting it before a competition, thus increasing oxygen supply for their muscles.
Chlorophyll does not transport molecules but instead does some heavy chemical lifting. It absorbs light to harvest its energy through the mechanism called photosynthesis. The details are fairly complicated, but the big picture is not: It is a reversal of respiration, or chemically a reversal of oxidation, called reduction: Oxygen is separated from the hydrogen in H2O and carbon in CO2 and given off to the air. Doing this consumes the same amount of energy which is released during oxidation (be it by fire or by metabolization in the plant). The emerging oxygen-poor(er) compounds can be oxidized later elsewhere to release that energy, or can be used as building blocks for new cells.

1 My girlfriend thinks I'm stupid not to know that ;-).
2 Unless it is buried and taken out of the biosphere, fossilizing to peat and eventually coal, tar and mineral oil. Then the net CO2 balance of a plant's life is indeed negative, i.e. the plant has removed CO2 from the atmosphere; until somebody excavates the fossil fuels, re-injects them into the biosphere and and restores former CO2 levels and all the tropical climate which made the old jungles grow so well.
3 From wikipedia, https://upload.wikimedia.org/wikipedia/commons/a/a1/Lungs_diagram_detailed.svg. By Patrick J. Lynch, medical illustrator, via Wikimedia Commons. The "tree" is actually the same lobe, rotated and colored.

This seems more complicated than I imagined.

Well, or it's easier... the basic cellular chemistry is the same between plants and animals (oxidize combustibles to get energy for, well, living); just where the combustibles come from differs.

Tangentially related is the fact that a forest which is in balance (doesn't shrink or grow) does not produce any net oxygen over the course of a year... a common misconception ("hey, we need the forests for our oxygen" -- nope, bury them deep enough and you are fine, at least oxygen-wise). A growing tree does produce net oxygen, but when it eventually falls and gets eaten by the buggy bugs all the nice carbon gets burned back to CO2, using up all the nice oxygen...

@LocalFluff Why do you think plants produce sugars and fats? With the exception of fruit, it's not meant for animal consumption. They're doing it for themselves - for storage and (very slow) metabolism. Note how much we had to breed plants to make them truly useful for us - modern wheat is estimated to have at least ten times more yield (with some estimates going up to a hundred times more) than natural wheat. Only fruit is "designed" to be eaten, as a mechanism to spread seeds.

Chlorophyll and hemoglobin do have structure in common: the chlorin ring in chlorophyll is very similar to the heme ring in hemoglobin. But that's because they both need to ligate a metal atom.  What they do with the assistance of the metal atom is very different.  And there are probably hundreds of other enzymes that use similar rings for the same reason.

Indeed several organisms can do both.
Another good example following the answer from Prince of an organism that can do both photosynthesis and respiration would be cyanobacteria.
Source:
Photosynthesis and
Respiration in
Cyanobacteria

I know this question is a little bit awkward, but how did you provide the source, I've tried to figure that out, but all I could do was to post the website fully and not in words like you did to my answer, that is, how you changed the website I posted into three simple words.

@Prince  [Cool text](complete link)  :)

@Prince You can press edit on my answer and see how the text is written behind, that's how I learned some of that stuff ;)

@Prince If you ever need hovertext, you can add it like this: [Text](link "hovertext")

@trichoplax I don't understand your description on how to do a hovertext. Can you post a site where hovertext was used so that I can check it out there, that is, by trying to edit the question or answer.

@Prince Hover over the "Photosynthesis and Respiration in Cyanobacteria" link in my answer, I've added it :)

@Dart Feld sorry, don't have edit privileges yet. Why not you insert a hover text and I'll check it out. Sorry for the inconvenience.

@Prince you don't have to edit - just hold your mouse pointer over the link in the answer and the hover text will appear.


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Could a biological process organically build solid metal "organs"?
Human ingenuity has made great use of metal tools. But are there any known, or potential, biological processes that might produce sizable solid metal objects like how for example skeletons and shells are being grown? Does solid metal manufacturing require melting point temperatures beyond what biological processes can survive, or could it be grown by proteins more or less atom by atom?

i think that, even if it could be possible to "be grown by proteins more or less atom by atom", there would be two problems. First, metals are already hard to find in a proper manner for consumption, and even if it was easy, in excess they become toxic to the organism. Second, building something like a metal skeleton would mean a great loss in adaptability, as once made, I understand it would be immensely difficult to unmake without using great amounts of energy. So I don't see how metal parts could be biologically used apart from beings with a somewhat developed intelligence and means

You might have better luck on worldbuilding.stackexchange.com if this is for a story. They are more focused on finding ways to make something sound feasible if that is what you're looking for. I'm not giving an opinion either way on if it should be here. That depends on your intention.

That is an excellent question. I was a little confused at first because, without realizing it, you actually cited a perfect example of a biological process that manipulates metal: bone formation.
Bone is made of hydroxyapatite crystal, which is a mineral whose main ingredient is, of course, calcium (metal).
Now, to answer the how of your question; bone is formed, as you eluded, through protein to protein interaction mediated by cells called osteoblasts (osteo- = bone, -blast = immature cell). The osteoblast first locates a site on the bone that is to be expanded, then encases itself in a framework of collagen fibers. When this is done, calcium phosphate and hydroxide bind to the collagen and "harden" as hydroxyapatite (Ca10(PO4)6(OH)2). The osteoblast, now encased in a shell of hydroxyapatite (called the lacuna), transforms into an osteocyte (-cyte = mature cell) and projects long arm-like structures called filopodia which it uses as sensors and to communicate with surrounding osteocytes. All that adds up to look an awful lot like this (with respect to the fact that they are usually fully enclosed, but that would make for quite an insipid picture):

Finally, to put Filipe Rocha's concerns to rest, how is this fully organic and (almost) solid metal structure adapted and "unmade," should the need arise? Well, there is a third type of bone cell called an osteoclast (-clast = to break). Osteoclasts break down bone by secreting hydrogen ions to dissolve the calcium in hydroxyapatite, then cathepsin and other protease to digest the collagen network.
So there you go; a fully biological system with the capability to not only create a non-toxic, solid metal structure, but also maintain it and even manipulate and "unmake" it. Even though bone is not an organ, I'm sure this system could be modified for such an implement if we put our minds to it... :)
Edit:
If calcium isn't "metally" enough for you, you might want to check out limpet teeth, which are comprised of goethite, iron oxide-hydroxide (FeO(OH)). I can go further in depth with the biological processes necessary to produce this mineral if you want; just ask. :)

I did think about bone, but did not include it because Calcium is not a true metal. It is actually an alkaline earth metal, and its properties are somewhat different from true metals. I was going to suggest bone as being an almost perfect example of a biological process that manipulates metal, but did not want to prolong my comment. Also, bone is not a pure metal formation, which is what I think the asker was referring to, but rather a formation that includes "metal" atoms in its composition. Apart from that, your answer is nice and detailed, I just suggest you edit accordingly.

@FilipeRocha I am aware of calcium's peculiar properties, but alkaline metals are still, nonetheless, metals. You have, however, reminded me of a certain marine mollusk with iron (goethite) teeth... I also did outline the constituents of bone, so if the OP would like to specify a more restrictive definition of "solid metal," I will be happy to revise. I assume the OP is not referring to truly pure metal, as it would be necessary, obviously, for an organ to sustain cells, so including minerals such as hydroxyapatite in his research would be largely beneficial.

you interested me with those iron teeth! But not every part of the body has to sustain cells - think hair, or a seashell shell (this one I'm not sure!)

Also since you offered, I would be interested in you going into deeper details about the iron teeth! You can even make a question and answer it yourself!

@FilipeRocha They are quite fascinating! They happen to be the strongest known biological material... but this is not the time nor the place for that conversation; perhaps later :) Thank you for reminding me about them; this discussion would be incomplete without mentioning a biological structure comprised of arguably the most common metal.

Thank you too! I think hemoglobin may be angry at us for forgetting it either! And just to add, I went to reread the question, and he did say "solid metal parts"

@FilipeRocha I believe it would be inappropriate here unless the OP asks about them... If not, I will consider asking and answering a question regarding it. I will definitely tag you in it if I do.

I will be grateful

@FilipeRocha This is what I love about the stack exchange; everyone has something to add to the conversation :) You are right, we mustn't forget about metal blood! ;) I think the confusion here is coming in because of the loose term of "solid metal." Let us await clarification by the OP. If you think there is more to talk about, I believe we should start a discussion in chat... much more of this and we will effectively bogged down the comments section. :)


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Is human blood useful as food?
Lacking other resources, could a healthy adult slit his wrist to feed a starving child with his blood? Would it be nutritional and would a starving dehydrated child eat it?

High amount of minerals ( iron for example) could show their toxic effects.

Yes, blood is nutritious, and whether a child would drink it is up to the child. It's not exactly palatable in large quantities; it's warm, and coagulation renders it gooey relatively quickly. It should help in dehydration (the degree depending on the cause of dehydration) because it's isotonic. The Maasai drink blood from their cattle instead of slaughtering them for meat. All that being said, the adult, if not pretty careful, will not be able to care for the child, and they'll both die.

@AlwaysConfused do human enterocytes have receptors also for other classes of Ig, than for IgA? Do you believe that the number of Ab resorbed this way could cause a life threatening problem?
Also, Ig are quite stable molecules, but wouldn't most of the platelet compounds get digested in stomach?
Just a note: in our culture (middle-east europe) it's common to eat pre-cooked blood from swine and it's considered quite nutritious and delicious meal. (pre-cooking however means that most of the mentioned proteins are probably already denatured )


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Which matched normal(s) to use when computing CNAs from exome data with a Read-Depth approach
I want to use a Read-Depth algorithm to call copy number alterations (CNAs) from Whole Exome Sequencing data (WES) of a specific tumor.
I have a set of WES tumor samples, some of which also have the matched normal sample. My question is: would be more effective, to call CNAs for each tumor, the whole set of matched normals or, if available, only the corresponding matched normal sample?
I thought that using only the single matched normal could spot only somatic variations, while using the whole set of normals would also add germline variations into account. Is that right?
Which best strategy do you suggest?

For the detection of somatic copy nuber alterations it is best to compare each tumour sample with its matched normal. If you want to call CNVs for all your tumour samples and some don't have matched normals, then pooling together all the normal BAMs to create a reference may be the best way to standardise your calling.


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How do fully dioecious plants determine sex?
I know that a minority of plants are fully dioecious, with adult plants producing either only male or only female flowers. When is this sexual differentiation determined? Is the seed of such a plant already male or female? Is it a simple genetic difference?

The short answer is that in dioecious plants the sex of an individual plant is determined by its chromosomes.
Several familiar crop plants are dioecious: asparagus, kiwi, hop, papaya, spinach and yam. The evidence indicates that dioecy has evolved independently in different plant families. I refer you to

Matsunuga & Kawano (2001) Sex determination by sex chromosomes in dioecius plants. Plant Biol 3: 481-488.

I have summarised below some of the introductory information in this review.
First some background for context: In mammals there is an XY system in which maleness is determined by an active Y chromosome i.e. the Y chromosome carries male sex determination gene(s). Males are said to be heterogametic. In Drosophila there is also an XY system, with heterogametic males, but in this case what determines sex is the ratio of X chromosomes to autosomes. This ratio exerts its effects through the Sxl gene. In this system the Y chromosome does not carry male-determining genes.
In flowering plants, in dioecious species, the usual situation is that males are heterogametic. However, there is variability in the underlying mechanism of sex determination.  So for example in hop (Humulus lupulus) there is a pair of sex chromosomes that can be distinguished by their appearance. However there is no active male determination but rather the X to autosomal ratio determines sex (as in Drosophila). Conversely, in asparagus (Asparagus officinalis), sex is determined by a pair of chromosomes designated pair 5. The two chromosomes are morphologically indistinguishable but genetic evidence indicates that there is active sex determination in this species - one member of pair 5 acts like the mammalian Y chromosome.


text:
What bird species is this? (Heron-like waterfowl from China)
I need help identifying this bird.  (Some sort of heron?)
It was seen in Wuhan, Hubei, China, in September.
It is very common there.  It can also swim like a duck, but I've only seen it do this once (it's not something they commonly do).  I can supply more photos upon request.
These are two different individuals:

I'd also be grateful for tips on websites I could use to look up these birds.  Most of what I can find is for North-America only, and I'm having a hard time finding Chinese birds.

My two guesses were Striated heron or Night heron, as the juveniles of both look similar to this.  But I haven't seen any birds that would look like the adults of either species.

juvenile night heron (Nycticorax nycticorax) INDEED good pics, cheers

Based on some external advice, I believe it might be a juvenile night heron (Nycticorax nycticorax), the only remaining question being why I didn't see any adults.
Link to Google Image search results
Update: I went back to the same location today and saw some adult night herons, which convinced me that these were juveniles of the same species.

I'd go with juvenile striated heron. I ruled out others such as the chinese pond heron because of the spotted wing plumage and slightly different shape of the patch around the eye. The night heron seems to have a more red eye than the striated heron and appears to have a stubbier beak.
Arkive is a good place to see a lot of pictures of birds, this is a good birding site, and otherwise I use generic google searching (e.g. start with "herons china" or "herons asia") - this at least helps narrow down the search quite substantially and is considerably cheaper than having a library of the worlds bird books!

It does look very similar to the juvenile of the striated heron (so +1), but how would you explain that all the birds I saw were like this?  (I have tens of photos of several individuals so I don't have to rely on my memory.) Could they all be juveniles, with no adults around?


text:
Are insects attracted to near infrared light?
Do insects see near infrared light?  If yes, are they attracted to it at night, as they are to visible light sources?
I am building something similar to a home-made trailcam with a Raspberry Pi camera.  Currently I use an incandescent light source.  Obviously, it attracts lots of bugs.  I was wondering if the same is going to happen when I switch to an infrared light source.  This would be 850 nm or 940 nm, as these types of LEDs are commonly available.

Just to avoid misunderstandings: the insects are not the reason why I'll switch to an IR light source, but I'd like to know if insects are still likely to be a problem after that.

I tried to build an IR light source for my raspberry pi and IR camera board. I used 24 NIR LEDS, and it worked, but I was dissapointed with the range. What light source were you planning to use?

See this.

In general, insects are most attracted to UV light. If you switch to a light source without UV-light, the amount of insects attracted will reduce to almost zero.
It has been hypothesized that this sensitivity to UV-light is because direct light sources (sun, moon) contains more UV than objects that reflect light. In this way, it may help insects to distinguish between open spaces and shelter.
It has long been thought that insects are blind to red and IR light. However, there is evidence that some insects do see, and are attracted to, IR light, at least up till 740 nm. However, red or IR light will attract far less insects compared to ypur incandescent light source.

Mosquitos use it to find warm animals from afar, and then to home in on warm zones with good circulation. I slept on an inflatable water bladder that was at 35 degrees from absorbing sunlight in summer, the 1 meter long water bed type things. the mozzies did not find me. other insects don't.


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Do thymine and uracil ever appear in the same strand of RNA?
Wikipedia says that "in RNA, thymine is replaced with uracil in most cases."  I'm curious what are the cases when this does not happen?  Does this ever occur in normal functioning, or is it an error?  Do T and U ever appear in the same strands of RNA together, or does a single strand just use T or just use U?

tRNA molecules contain a T in the T arm. I believe that this results from post-transcriptional modification of a U by uridine methylase.

just curious:  can RNA polymerase incorporate thymine from TTP against Adenine ?

Do cells make TTP? (or 5-methyl UTP, as it is usually referred to)

I am not sure.. UMP is the first product of de-novo pyrimidine synthesis. The ribose is reduced and uracil is methylated to produce dTTP.  I dont know if the order of the reactions is unchangeable ?
I guess if artificially provided, Thymine can be incorported in RNA. (Sorry, i should have looked it up instead of commenting)


text:
What is the number of influenza strains occurring at a given time?
My question was initiated by reading on mock-up influenza vaccines. I understand that the manufacturer pre-prepares a certain vaccine and tries to get it tested and ready before it is actually needed, by taking a novel virus strain that has infected a few people, and could potentially cause a pandemic.
My questions:

How many different influenza strains are there at any given time at one geographical spot (say, one US state? - narrow down at will). I always thought there would be just one novel strain appearing each year, explaining why people get sick time and again of the 'same' virus. However, the mock-up virus vaccine production seems to imply there are various strains occurring at once?
Do influenza strains vary on an annual basis, or is it a continuous process (like evolution), and is a new strain re-named after it becomes potentially dangerous (like speciation?) - i.e., what is an influenza strain? It seems, given the vaccine preps, that various strains occur at once, and strains survive for extended periods? Any hard evidence for these indirect assumptions?

And as a side -

Do vaccine manufacturers prepare a whole bunch of mock-up influenza vaccines on a yearly basis just awaiting to identify a dangerous strain and start manufacturing it once people get sick? Or are mock-up vaccines combined into a cocktail mix containing many strains and are these cocktails re-vamped annually? Or is a yearly shot necessary because immunity only lasts a year?
I might have to re-post this last question at Health.SE as a dedicated question, but since related to above I prefer to leave it here for now. Grab me in chat if need be!

Antigenic drift in the coding portions of the genes that involve antibody binding sites accounts for the seasonal variability of flu strains, i.e. they mutated enough that the antigens require new antibodies, hence a new strain. The process is as you said constant, like evolution, and in an analysis of pandemic H1N1 the authors are able to note 1 - 18.1 mutations per genome per replication cycle (ref). Because of this, flu vaccines tend to have more A strains than B strains due to the greater mutability of influenza A, at approx. 30% more mutations per site per infectious cycle (ref). At current It will take me time to research the remaining questions.
Interestingly enough, however, and I've never looked at this but CDC offers weekly influenza reports that detail by region what they're finding (CDC):

Source: CDC's so-called FluView
Beyond that, I'm pretty sure they take this weekly data, see what strain is on the rise in hospitals, and manufacture the vaccine to mirror the "popular" cocktail of strains.


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Estimation of cases with dominant inheritance
I am reading [1] and I didn't understand this passage:

All bilateral cases should be counted as hereditary because the proportion of affected offspring closely approximates the 50% expected with dominant inheritance.

Shouldn't the percentage be 75% with dominant inheritance?
[1]: Knudson, Alfred G. "Mutation and cancer: statistical study of retinoblastoma." Proceedings of the National Academy of Sciences 68.4 (1971): 820-823.