text:
The membrane folds of dendritic cells
Dendritic cells have a larger surface area due to extended dendrites (membrane folding into itself). Do other mammalian cells (with functions other than immunological) present these membrane folds?

Yes, these include:

neurons
melanocytes
Merkel cells

In all cases, as you suggested, their function is to extend the surface area of the parent cell. In the case of neurons, the role of dendrites, which receive the vast majority of synapses, is to maximise the number of synapses the cell receives from different pre-synaptic partners (Chklovskii et al. 2002, Chklovksii 2004). In melanocytes, they are used to transfer melanin to keratinocytes. In Merkel cells, they are again used in order to form synapse-like connections with neurons (Mihara et al. 1979).
The word originates from the Greek δένδρον, which means 'tree'. Dendritic structures are found throughout in nature, including in...trees, where presumably they are used to maximise exposure to sunlight. Theoretical studies on the formation of dendritic arborisations in neurons indicate that they are governed by at least these factors: i) repulsion between dendrites (Wen et al. 2009), ii) minimisation of dendritic volume used (Tamori 1993), possibly through resource competition (Graham and van Ooyen 2004). It is an intuitively attractive idea to think that similar processes govern dendrite-like formation in the other biological systems described above as well.

References
- Chklovskii, D. B., Schikorski, T., & Stevens, C. F. (2002). Wiring Optimization in Cortical Circuits. Neuron, 34(3), 341–347. https://doi.org/10.1016/S0896-6273(02)00679-7
- Chklovskii, D. B. (2004). Synaptic Connectivity and Neuronal Morphology: Two Sides of the Same Coin, Neuron, 43(5), 609-617. https://doi.org/10.1016/j.neuron.2004.08.012
- Graham, B. P., & van Ooyen, A. (2004). Transport limited effects in a model of dendritic branching. Journal of Theoretical Biology, 230(3), 421–432. https://doi.org/10.1016/j.jtbi.2004.06.007
- Mihara M., Hashimoto K., Ueda K., Kumakiri M. (1979). The Specialized Junctions between Merkel Cell and Neurite: An Electron Microscopic Study, Journal of Investigative Dermatology, 73(5), 325-334. https://doi.org/10.1111/1523-1747.ep12550322.
- Tamori, Y. (1993). Theory of dendritic morphology. Physical Review E, 48(4), 3124–3129. https://doi.org/10.1103/PhysRevE.48.3124
- Wen, Q., Stepanyants, A., Elston, G. N., Grosberg, A. Y., & Chklovskii, D. B. (2009). Maximization of the connectivity repertoire as a statistical principle governing the shapes of dendritic arbors. Proceedings of the National Academy of Sciences, 106(30), 12536–12541. https://doi.org/10.1073/pnas.0901530106


text:
Why is glucose our primary source of energy?
Is there any evolutionary reason for glucose being the "main" molecule used as a source of energy, beginning with glycolysis and subsequently cellular respiration (after being converted to two pyruvate molecules)? Or did this particular biochemical pathway arise "by fluke" early on in the history of life?
A colleague of mine told me that it was because as shown below, all of beta-D-glucose's hydroxyl substituents are all equatorially positioned (when in the correct chair conformation), which lends to its general stability.

Image taken from the Wikimedia Commons.
Could this have played a factor in the beginnings of energy metabolism, and if so, why?

I don't have a direct answer for you, but you should try to get hold of a copy of Romano AH, Conway T. (1996). "Evolution of carbohydrate metabolic pathways".

I thought this was a great question.  In particular because it hints at two questions.  The first is 'why carbohydrates are used to store energy' in general. The second being 'why glucose rather than other carbohydrates?' in particular.
Glucose metabolism (and glycogen storage) is a core gene pathway - its found in bacteria archaea and eukaryotes.  So probably the most that we can readily say about question one is that as @rwst points out this pathway has proven to be useful at a critical juncture of the formulation of living things on earth.  If you look at glucose metabolism pathways, you can see that glycerate compounds and pyruvate are the actual intermediates that are used to create energy.  The first thing about these molecule worth noting is that they have a good mix of carbon and oxygen, which would make it easier to extract energy - creating CO2 from these compounds may even predates the existence of atmospheric oxygen.  So glucose and fructose (which is actually derived from glucose in the metabolic pathway) are actually storage molecules themselves, easily broken down to smaller molecules.
As to the second question: there are quite a few ways to arrange oxygen around the carbohydrate ring.  why glucose?  The advantages of glucose is probably a subtle one.  The structural properties of glycogen might be a reason that the use of glucose monomer is so important for glycogen. There is no evidence that I can find for this, so its always possible that glucose was just the first hexose carbohydrate to be biologically used.  Its sort of hard to imagine that the structure of glucose does not play some sort of role in cell structure though.

One could argue ATP is used to store energy, glucose is just the means to get this energy into ATP. Semantics, I know.

true - in this case we're trying to dissect the question in terms of which is oldest/ most primal.  from a molecular biology standpoint ATP is often a better answer.

Looking at this question again, ATP does not really store energy - its a high energy currency used throughout the cell, but its used and turned over rapidly in the mitochondria.  a human body has 250 g of ATP at any given moment but uses its own weight of ATP every day: https://en.wikipedia.org/wiki/Adenosine_triphosphate

This is only a guess but I hope somewhat educated, so refute me. The establishment of glucose as nutritional molecule is mainly linked with the availability of carbohydrates in the environment, i.e. plants as nutrition. Before plants evolved however, there were only bacteria and they use glucose as one of many oligosaccharides. But more important than glucose is trehalose because it is less toxic and can be collected in large amounts in the cell. The only reserves for glucose are glycogen and the bacterial cell wall which can be catabolized. So, in my guess, the reason for the mere existence of glycolysis/gluconeogenesis pathways is the bacterial cell wall that has to be synthesized and catabolized. Only later were these pathways differentiated when land plants came up and animals that et them.

that's an interesting argument.  if you could demonstrate somehow that glucose is what plants prefer to make for some good reason, it would really reinforce the hypothesis...

Remember that land plants stem from green algae that were bacteria earlier. Green algae had not much of a glucose preference but they developed starch as an efficient reserve, in addition to glycogen and trehalose. Only when land plants needed thick cell walls and big structures, glucose needed to be produced en masse.

It is simply not true that all living organisms or even most organisms all share some ancestral version of Glycolysis.
Various versions of Glycolysis and Fermentation were later coevolutionary after thoughts which emerged after Respiration; and why?  Glucose was not readily available when life first emerged.
As a matter of fact, many Prokaryotes use two far more ancient alternate pathways to break down Glucose:  The Pentose Phosphate Pathway or the Enter-Duodoroff Pathway.
Gluconeogenesis, now that’s different.  All species can make glucose, and the major part of what many textbooks identify the glycolysis pathway is actually Gluconeogenesis running backwards.
Problem is:  the capture of light energy to produce sucrose and other carbohydrates is a highly specialized phenomenon from an evolutionary POV that's not really part of photophosphorylation and photoreduction in Prokaryotes or even Cyanobacteria.
And how about Respiration in Prokaryotes?  Most do not rely on reserves of Glucose as a precursor.
What about Eukaryotes?  There are many points of entry into aerobic respiration and NOT ONLY Glycolysis.
So why is Glucose given so much emphasis?  Glucose is the precursor of Lignin, Cellulose and Chitin.  Lignocellulose aka plant dry matter (biomass), is the most abundantly available raw material on Earth for transfer to the second trophic level.

Welcome. Can you add sources to your post so that other users can background read on your answer?

source: Stack Exchange

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

sort: votes


text:
In a tumor, why hypoxic regions have access to glucose?
The Warburg effect is ubiquitous in cancer. It consists of the upregulation of glucose uptake, glycolysis, and subsequent lactate secretion, sometimes by over 200 times, in cancer cells as compared to normal cells. A common explanation for this phenomenon is that tumor cells can be oxygen deprived, because they are far away from the diffusive range of oxygen in the blood supply. But if that's the case, then how are they close enough to blood supply to have access to enough glucose? How can glucose diffuse to places where oxygen cannot, even if oxygen is a much smaller molecule?

This is a very good question. I think this is in fact a major problem for the whole glycolysis/hypoxia theory. And I'm not aware of any evidence for rapid glycolysis in hypoxic tumor regions. But note that Warburg's finding was that tumor cells have high glycolysis also in the presence of oxygen; that is completely different from glycolysis in hypoxia.

This is a great systems bio question. You could also take it a step back from cancer and ask something like "what are the absolute fluxes (input - output) of O2 and glucose in healthy tissue, and how does one affect the other?"

I think this is a difficult question for which the answer is not clear --- to my knowledge there is little data on metabolism in solid tumors, and no clear consensus in the scientific community. So I'm not going to attempt to give a definitive answer, but here's at least a few thoughts / opinions.
Why transformed cells engage in aerobic glycolysis, or the "Warburg effect", is a question people have been trying to answer for nearly a hundred years now. There are dozens of hypotheses, but none of them is broadly accepted. One popular hypothesis laid out by Gilles & Gatenby says that transformed cells from solid tumors are glycolytic because they have been selected for anaerobic metabolism in a hypoxic environment, and this selection is somehow irreversible, so that the cells stay glycolytic even after being extracted from the tumor and cultured in aerobic conditions. I think this hypothesis is the origin of the idea of hypoxic and yet glycolytic tumors.
In a way the Gilles & Gatenby hypothesis is a clever idea --- it rests on the well-accepted fact that most cells become glycolytic in hypoxia, and rhymes with the concept of selection for survival in tumors. But the problem with the argument (as you have realized) is that the tumor environment would have to be low in oxygen and at the same time high in glucose. I agree with you that it is unlikely that such an environment could arise due to lack of blood supply, since oxygen diffuses more easily through tissues (and cells) than glucose does. Moreover, considering the high demand for glucose by glycolytic cells, glucose should become limiting long before oxygen runs out. So one can argue that poorly vascularized tumors should be mainly oxidative, not glycolytic!
To my knowledge, there is no data demonstrating existence of (regions of) solid tumors with low oxygen and high glucose. There is of course ample evidence that many solid tumors consume large amounts of glucose, and also many studies showing hypoxic regions in tumors. But most likely these are different types of tumors, or different regions. In an environment with neither oxygen nor glucose, cells will simply die --- which is exactly what happens in the necrotic cores of larger solid tumors.
The best source of further information is probably the tumor physiology literature. This review is a good starting point.
Finally, another issue with Gilles & Gatenby's hypothesis is that aerobic glycolysis can easily be demonstrated in cells that have never been in a tumor. For example, in vitro transformation can increase glycolysis, and normal lymphocytes induce rapid glycolysis when activated by receptor stimulation. So there is no need to assume that glycolytic tumors are hypoxic.

Personally I think aerobic glycolysis is poorly worded (though I know it is common). in my opinion ahypoxic hyperglycolysis describes the phenotype better :)

The outside of the tumor has access to the most nutrients and oxygen, sometimes even the blood supply (angiogenesis). Solid tumors have this microenvironment if you will, and the human tumor microenvironment often suffers from a lack of oxygen and nutrients, and acidosis (Milosevic et al., 2004). The distance from the outside of the tumor to the core has an established diffusion gradient of oxygen, nutrients, etc. (Cristini et al., 2005, especially since blood vessels can't always penetrate to these areas). A take home point is the larger the tumor becomes, the less nutrients available to the inward tumor cells until the cells often become necrotic or necroptotic (Huang et al., 2013). Furthermore, since tumors maintain a constant inward pressure, the dead cells are essentially eaten by the living cells and everything is pushed to the center, thereby providing the interior environment of the tumor materials to work with (Greenspan, 1972).
There are gross metabolic shifts explained below that provide the tumors different ways of obtaining nutrients. I don't think it has so much to do with glucose diffusing as deep into the tumor as oxygen as it does this metabolic reprogramming.
How does the tumor alter it's expression profile to fit it's needs under the stress of starvation? Example based approach

Hypoxia-inducible factors or HIF unfortunately modulate tumor progression. (See Bellot et al., 2009, Zhang et al., 2008 for examples of autophagy induced by HIF, Huang et al., 2014 for a non-exhaustive overview of additional ways HIF modulates cancer progression). Tumor cells suffering chronic hypoxia upregulate their GLUT transporters and glycolytic pathways via action from HIF-1α/ß because they must often begin to produce ATP without oxygen. They also, however, downregulate mitochondrial activity through transactivation of PDK1 and MXI1 Denzo et al., 2008. PDK1 ends up inhibiting PDH, and MXI1 ends up actually reducing the number of mitochondria per cell.
The incorporation, then, of glutamine into the TCA cycle where pyruvate would normally be needed supplements the now-missing carbon requirement (see figure below) where pyruvate would be involved, because referring again to the Denzo paper, in the hypoxic tumor pyruvate is converted into lactate by LDH, in part explaining the acidosis. Incorporation of glutamine however should purportedly be independent of HIF expression, so I looked at papers such as Ma et al., 2013, which showed that starving tumors of glucose ended up making them more aggressive due largely to regulation by PKCζ, and subsequent incorporation of glutamine metabolism.

Fig A. Looking here at alternative fuel pathways during starvation of the tumor, the cells can scavenge from the necrotic center of the tumor, utilize autophagy, other carbon source, etc. to fit their needs.
Source: White, E., 2013
More specifically, there is a paradigm shift in tumor cells deficient in PKCζ that involves (1) upregulation of Phosphoglycerate dehydrogenase (PHGDH) and Phosphoserine aminotransferase (PSAT1), which are normally repressed by PKCζ, (2) uninhibited mTOR activity, which is normally shut down during nutrient depletion, and (3) inhibited AMPK and autophagy pathways, which are normally active in nutrient depletion.

"Genome-wide transcriptome analysis demonstrated that PKCζ-deficient cells displayed gene alterations in pathways consistent with the use of glutamine as a glucose alternative."

In both humans and mice they conclude that with respect to intestinal cancers, PKCζ regularly acts as a tumor suppressor. But the major point here is that multiple pathologic mutations can be implicated here to try and make sense of the Warburg effect.
Leithner et al., 2015 likewise shows that tumor cells (this is specific for lung cancer) can begin to utilize lactate to form glucose building blocks by modifying the gluconeogenesis pathway, mediated largely by a mitochondrial isoform of the phosphoenolpyruvate carboxykinase (PEPCK) known as PCK2:

"Under low glucose, all three carbons from (13)C₃-lactate appeared in the PEP pool, further supporting a conversion of lactate to pyruvate, via pyruvate carboxylase to oxaloacetate, and via PCK2 to phosphoenolpyruvate."

I'd like to bring up again that in the hypoxic tumor, evidence supports that pyruvate is converted to lactate, but now I imply the lactate can potentially be converted to glucose, a positive feedback loop providing the tumor glucose. This is somewhat supported by the clinical study in Koukourakis et al., 2006 that shows tumors overexpressing LDH-5 and HIF-1α/2α that in the malignant tumors, oxygen consumption was low and glucose consumption was high. But I also want to go back to the Denzo paper because they brought up some interesting points, and I recommend reading it: The decreased mitochondrial need for oxygen might be more important than the increased glycolysis.
Some interesting points:
1) The metabolic shift induced by hypoxia lowers the tumor oxygen requirement and heightens it's glucose requirement. This doesn't necessarily mean the tumor is actually getting glucose, and sometimes, it doesn't mean the tumor cell is actually deprived of oxygen, either, rather the hypoxia is induced by simply not enough oxygen to fit the high oxygen requirement, read Takakusagi et al., 2014.
2) By reprogramming it's metabolism and cannibalizing cells that actually did die from deprivation, the tumor can viably "get" energy -though not necessarily directly in the form of glucose- through a number of pathological mutations.
3) Anaerobic glycolysis followed by LDH activity is an efficient adaptation if you look at Koppenol, Bounds & Dang, 2011, the hypoxic tumor cell can produce 26 ATP and 26 lactic acid from 13 glucose in the time it takes oxidative phosp. to produce 36 ATP from one glucose. In a time of starvation efficient energy production is a good thing, and the hypoxic mechanism is fast, especially if we consider the tumor is producing glucose from lactic acid in any capacity. They also point out that tumors become in a way addicted to the Warburg effect,

"... oncogenic deregulation of biomass accumulation for cell proliferation creates an increased, sustained bioenergetic demand that addicts cancer cells to an adequate anabolic supply."

"How can glucose diffuse to places where oxygen cannot, even if oxygen is a much smaller molecule?" I don't have such a definitive answer for this, though I would personally determine that it doesn't, not by much. Where I want to go is it's not really about glucose and oxygen getting to the same place. I suspect that they reach just about equally as deep into the tumor depending on the composition of the tumor itself and the tissue it resides in. I also want to point out that hypoxia is not the same as anoxia, where there is no oxygen and the cells are for the most part dead in those regions. If you read the length of this post, you understand that the tumor cells are experiencing hypoxia, or a deficient amount of oxygen reaching them, and likewise I would assume a deficient amount of glucose, as opposed to a lack thereof. In that sense again, and because there's not a lot of nutrients to go around, we're alluding to the efficient usage of both glucose and oxygen, and beneficial biomass accumulation, which we demonstrated the Warburg effect is key to. Because once you get to the point of anoxia, again, we're looking at anoxic cell death, but those cells get turned into what essentially amounts to recycling material.
Closing Notes

I don't see why glucose wouldn't be able to diffuse along it's gradient into the tumor considering there is a microfluid environment inside the tumor, but where we're talking about in the hypoxic region (not the anoxic regions) I suspect there is still some glucose present just as there's some oxygen. It's important, then, for the tumor cells to have more of the GLUT transporters from the action of HIF, and the efficient usage of whatever metabolites it can get. I generally lack data for how far into a tumor they can actually perfuse, but to me it would be hard to quantify since there are many confounding factors such as what tissue the tumor originated from, irregularities in the microcirculation, etc.

I don’t think any of this answers the question.

Thanks for the useful information, but I agree with Roland, this does not answer my question.

I appreciate your answer. I think the most relevant aspect is that you think somehow there can be a high enough concentration of glucose in places where oxygen is not accessible, thus creating a niche for enhanced glycolysis. This is what I find tough to digest, because oxygen is so small a molecule, it should be very easy for it to diffuse, thus it should be available wherever glucose is available. But if you can find some references supporting your claim that would be great, since that is the essence of my question.

The link to the Milosevic paper is broken. I think you copy/pasted a link that goes through your university proxy or something, which I can't access. Can you fix it please?

Do you have a reference with the diffusion coefficients of glucose and oxygen?

@becko So i tried to find some relevant environments such as extracellular matrix or even tumor tissue. In this they measured for oxygen in carcinoma, and in extracellular matrix here. They took measurement for glucose in sclera here and EMT6 spheroids here. Values tend to range around 10^-5 or 10^-6 for either glucose or oxygen.

I think I finally got where I was going with this answer. There's still lots of data out there that I simply can't incorporate without producing an entire book. The TL;DR is (1) oxygen is still there, just in low amounts, like glucose, (2) the Warburg effect is about efficiently using resources that are getting scarce, and (3) there's a complex crosstalk at the end of things and this answer is far from exhaustive. I hope I was able to constructively direct your research! Please let me know if there's anything to be clarified!

Hypoxia does not mean no oxygen reaches the place, it means low oxygen tension when compared to normal well perfused tissue. In my experiments I have observed the exterior of rat glioma models well perfused but not so well inside. We have used MR based methods to study perfusion and IHC to study vasculature. In the same way, I have observed increased MCT-4 expression (indirectly, more lactic acid production) in the outer regions of the tumor but certainly sometimes there are some pockets inside with increased MCT-4. But no matter what, the whole of the tumor and surroundings is acidic. This could be due to lactic acid or maintenance of intracellular pH by proton exchangers. Though there is no clear answer, there are lots of points on which I agree with CMosychuk. Low oxygen tension increases HIF activity which has its repercussions. I also faced another curious situation. I was working with pseudohypoxic tumors. They don't have low oxygen tension but still have activated HIF because HIF is artificially stabilized thanks to some mutations (VHL, SDHB). Now, I expected more GLUT because I could see increased 18F-FDG uptake in these tumors but I saw increased hexokinase-2 expression. Remember, in this case there was no hypoxia, still activation of HIF had its effect that is increased glycolysis! So I too think that low oxygen tension might mean low nutrient supply but it certainly does not mean no nutrient supply. We see tumor parts having low oxygen tension, happily living and metabolizing and making the whole region acidic. I have not even seen a necrotic core in these tumors. When, I killed these cells giving temozolomide to the animals, the acidity was not there anymore. So, acidity was certainly from metabolism of cells. Remember, these are all in vivo studies and we do different kinds of measurements on the same tumor as the rat is alive.

Hello Jyotsna, welcome to Biology.SE and thank you for your contribution to the site. That you posted such an extensive response is great, however it would be very much appreciated if you could list some of the sources for your claims.

You're right that hypoxia (and hypoglycemia) is a matter of degrees, of course. But then you would need to argue from quantitative data. What does "well perfused" mean? What is the oxygen tension in your tumors? Respiration rate? Glucose concentration, glycolytic rate? These values are typically very difficult to determine in vivo.

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


text:
Time spent in phases of cell cycle
I am looking for references to papers containing the time intervals spent in different phases of the cell cycle (ej., G0, G1, S, G2, M for eukaryotes) for different cells. In particular, I am interested in E. coli and CHO (Chinese Hamster Ovary cells), but any reference to studies of this kind for any typical cell will be useful.
I'll accept an answer containing a representative sample of references to the literature on this subject. Preferably recent papers (since 2010).
If you can provide the times spent in each phase but don't have references at hand, that will also be useful.

This is the data for a few cell types:

Cell type   Total      G1      S      G2      M      Ref
----------------------------------------------------------
Neuro2a        9       2       5      1.5    0.5     [1]
Hela         16.2     7.7     7.2     0.8    0.5     [2]
A549          18       7      7.5     2.5     1      [3]
MCF7         21.3      9      9.3      2      1      [4]
CHO           15       6      6.8     1.2    0.65    [5]

The timescale is in hours.

References:

De Laat et al. 1980
Kumei et al. 1989
Orfanoudakis et al. 1989
Taylor et al. 1983
Harada and Morris 1981

+1 Thanks. This is useful, but I am looking for recent papers mostly. If you provide some more recent references (from 2010, preferably reviews), I'll accept this answer. Also, do you have any data on CHO or NS0? And what are the units of time in this table (hours, days)?

its not a popular thing for researchers to reproduce old results... not sure you will find more recent ones.

@shigeta so you're saying that these measurements have not been significantly improved/corrected in 20 years?

Not definitively, but its quite possible.  I'm sure we could measure melting points and osmolarity better now, but I can't recall seeing someone spending their time to do it.  Science famously doesn't even try to reproduce some of their most important cancer research.  I wouldn't fault WYSIWYG if they can't be found.

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


text:
Where can I find a list of common enzyme cofactors and/or co-enzymes?
Where can I find a list of enzyme cofactors and/or co-enzymes, ordered by how common they are?
For example, $O_2$, $H_2O$, $ATP$, $ADP$, $NAD$, should be ranked in the first places, because they participate in most reactions.

$H_2O$ is not a cofactor for any enzyme.

Also oxygen cannot be called a cofactor. It is just an electron acceptor- in a way a co-enzyme.

@WYSIWYG I have edited to include co-enzymes.

Check this out. This resource lists organic cofactors and the associated enzymes.
See the wikipedia page also.
Many metals also serve as prosthetic groups in enzymes. They include- Magnesium, Manganese, Iron, Cobalt, Nickel, Copper, Zinc, Molybdenum.
FeS clusters are also an important part in many important enzymes in mitochondria and plastids.

Cofactor:
coenzymes are organic molecules that are required by certain enzymes to carry out catalysis.
Database:
CoFactor - The organic enzyme cofactor database of EBI
Examples:


text:
Diffusion coefficients of glucose in mammal tissues?
Where can I find estimates/experimental measurements of the diffusion coefficient of glucose in mammal tissues? Specefically I mean the inter-cellular space. I'm not looking for a specific tissue, so some examples of values for some tissues, or a generic estimate, is enough for me.
And the same for lactate, although I presume it will be very similar.

Something to start with! (see table 19.1)

This question cannot be answered as is. What do you mean by tissue ? Inter Cellular space ? Cytoplasm ? Nucleus ? Blood stream ? etc etc All of those media have very different diffusion properties.

@Xqua I mean extracellular glucose, inside a tissue, so it's in the inter cellular space. I edited the question.


text:
Why lactate inhibits growth (or enhances death rate)?
Extracellular lactate tends to inhibit cellular growth or enhance cell death. This happens in the vicinity of tumors and in cell cultures.
See for example this reference: Ozturk, Sadettin S., Mark R. Riley, and Bernhard O. Palsson. "Effects of ammonia and lactate on hybridoma growth, metabolism, and antibody production." Biotechnology and bioengineering 39.4 (1992): 418-431 (available here: https://www.researchgate.net/profile/Mark_Riley5/publication/227705703_Effects_of_ammonia_and_lactate_on_growth_metabolism_and_antibody_production/links/540e0bcb0cf2f2b29a3a765a.pdf)
What is the mechanism behind this effect of lactate? Why lactate has these negative effects?

Are you thinking of effects of lactic acidosis rather than lactate? Note that lactate itself is a base, not an acid. The effects of lactate on cancer cells and tumors is still heavily discussed, can you give some references for your claim? Can you specify what types of tumors or cancer cells you are thinking of?

@Roland Almost all tumor types exhibit lactate secretion (this is called the Warburg effect). I think the cell secretes lactic acid, which once outside the cell, equilibrates with lactate, as any acid/base pair.

Most tumors do secrete lactate, but I'm not aware of any evidence that lactate itself inhibits cellular growth, as you stated in your question. So please provide references for this; or, if you actually mean effects of acidosis (low pH), then please revise and clarify. Glycolytic cells do not actually produce lactic acid; anaerobic metabolism is acidifying because of proton imbalance due to inadequate respiration. See https://en.wikipedia.org/wiki/Lactic_acidosis

@Roland Take this example: Ozturk, Sadettin S., Mark R. Riley, and Bernhard O. Palsson. "Effects of ammonia and lactate on hybridoma growth, metabolism, and antibody production." Biotechnology and bioengineering 39.4 (1992): 418-431. Available here: https://www.researchgate.net/profile/Mark_Riley5/publication/227705703_Effects_of_ammonia_and_lactate_on_growth_metabolism_and_antibody_production/links/540e0bcb0cf2f2b29a3a765a.pdf

They report growth inhibition as well as death rate enhancement when extracellular lactate concentrations go up. There many papers with similar statements. My question is what is the mechanism behind this. I've heard that lactate secretion ends up lowering pH, which seems related to what you're saying, and maybe this is a mechanism, but I can't confirm this.

Hm, that paper concerns bioproduction settings rather than tumors. They state in the introduction that lactate has variably been found to either increase proliferation or have no effect below ~40mM. They themselves use 55mM, on hybridoma cells. Not sure this is physiologically relevant for tumors. 55mM lactate would increase pH somewhat, since lactate is a base. At so high concentrations, lactate dehydrogenase might be also be disturbed ... But okay, now the question is clear I think. Please add the reference.

The cells deaths they observed in the reference paper were due to nutrient depletion and high medium osmolality, both of which delay growth and cause cell death, with glutamine being a key limiting factor.


text:
What is the most genetically simple organism except viruses?
What is the most genetically simple organism (except viruses) on this planet?
By simple I mean the least number of genes.

I did a  google search and got this

I would guess it is a symbiotic bacteria! The mitochondria maybe (if we accept it to be an organism). Here is an article that you will appreciate. If you search for "tiniest genome" on google you will find some stuff

@biogirl So, the smallest organism (except viruses and mits) has 159,662 TACG pairs? No smallest number found so far? Any knowledge about this thing?

In the link I gave you, there is an insect that has only 112k base (112,000 ATCG pairs)

Mycoplasma genitalium

Note that the mitochondrial DNA is 16k base long and contain only 37 genes (Wiki Source). But you might not want to consider it as an organism.

Mycoplasma genitalium is fairly good with 583k base pair Wiki

@Derfder Would you accept to consider the mitochondria (for example) as being an organism?

@Derfder I dunno much about this. So many organisms's dna has not been looked into. So, in the future one may find smaller genomes

Mycoplasma genitalium was one of the first full bacterium genomes sequenced and since its a symbiotic organism that lives on the moist and warm genital skin surface it doesn't need as many genes as many bacteria.  It has a 582 kbp genome sequence with only 521 genes.
But that is so 1995.
The 159 kbp genome of Candidatus carsonella was published in 2006. It is thought to only contain 182 genes.  Its an endosymbiont of some sap eating insects.
But the current record holder, published this year, is Nasuia deltocephalinicola, discovered survey of insect endosymbionts, has only 112 kbp in its genome. Smaller than some viruses.  It's thought to contain 137 protein coding genes with 29 tRNA genes, so its not a lot smaller than Carsonella in terms of gene count.
There's no reason to expect that this is the minimal viable genome by any means.  I'm sure this response will need revision in a year or two.
M. genitalium has become the model system for minimal genome work.  Many of these other bacteria might be difficult to culture, molecular biology lab techniques might have to be developed, so hopping onto newly discovered bacteria isn't always the best idea from a standpoint of producing science.  It does suggest that M gentalium doesn't need all of its genes!  A possible cause for these extra genes might be a more complex immune response in human beings where its found.  It might also be because of the symbiotic requirements of insects is simpler.

Genome of 'Candidatus
Tremblaya princeps' is a bit larger (138931 bp), but contains 116 protein-coding genes: kegg, original paper. It's an insect (P) symbiont and has in turn its own bacterial (S) symbiont.


text:
How is the sequenced genome of a person useful to him in practice, now?
Currently it is possible and not so expensive for a person to have his genome. This is useful in general for understanding how life works. But, in practice, how is this useful for the specific person at this point in time?

A human genome sequence can uncover large deletions and insertions in the genome and would give the genotypes of both common and private (rare to very rare) small polymorphisms (e.g. SNPs) and SSRs (simple sequence repeats). From this information, one can learn about some curiosity traits (say, sensing asparagus metabolites in the urine, slow or fast twitch muscles, curly vs not curly hair) and, more importantly, about disease risk. Ancestry and family relationships can also be learned as in, for example, a half-sibling relationship.
As many diseases are polygenic with numerous loci each making small contributions to the variance, it becomes very difficult to fully describe the level of increased or decreased risk. In other words, we don't yet know all the players and so assessing their contribution to risk of disease can't be done with complete confidence. To further compound this problem are both epistasis and gene-environment interactions. Epistasis is a gene-gene (gene-gene-gene, etc) interaction, such that genes A and B separately make no contribution to the phenotype (disease risk), but do so in combination - say in ab/ab individuals. A gene-environment interaction can be described as when an allele associates with increased risk only when an environmental factor (e.g., exercise, fat in the diet, sun exposure, oxygen tension (altitude), etc), passes a certain threshold.
Still, the most powerful predictor of disease risk, onset and progression is family history. A genome sequence approaches that history (half your genome is from your mother and half from your father, of course), but remains fairly uninterpretable in terms of complex traits. You may carry a couple variants posing increased risk for heart disease, but what about the other hundred or so loci that also make small contributions to this affliction? Sure, if we knew exactly what those other hundred were and how much they each contribute and if they interact with each other or the environment. An incomplete picture emerges.
With rare diseases and altered genomes (say in cancer compared to normal) great strides are being made to either identify the small number of defective genes (rare diseases) or the commandeered pathways exploited for uncontrolled growth (cancer). In this regard, much can be learned and will have quicker, but still measurable in years, applications to the clinic.

This is a good answer, for sure, but my impression is that the OP wants to know what can the man of the street take home from having his genome sequenced. I think that it can do more harm than good, seen that the majority of the population -for instance- does not know the difference between cause and risk factor.

Therein lies the need for a genetic counselor, and thanks for the comment. I do think that cause and risk can be explained simply enough - one is less likely to die in an automobile accident if one does not drive, eg, whereas the cause of that accident could be an icy road + speed + inattentiveness (a combination of controllable factors).

How is the genome sequence useful right now? There are several tests out there that rely on identifying single mutations that will lead to diseases, or that are associated with bad response to medication. Having the entire genome sequenced allows identifying all of them at once, and is cheaper than doing these diagnostic tests one by one. Thus, sequencing the genome gives you information about whether to expect certain diseases, and a list of medication that you shouldn't take, sort of as an insurance.
Sequencing also allows you to learn about your ancestry, which may be of interest especially to people from countries with a long history of immigration, such as the US.
How is the genome sequence useful in the mid-term? Many diseases (including many cancers) are not caused by single mutations, but rather buy a combination of genetic and environmental risk factors that exceed some threshold. Thus, the genome sequence only allows to tell whether a person has increased risk for certain diseases, but not whether they'll get it. By itself, this information is not very useful. However, it has recently been suggested that blanket screening for cancer may not be the best idea due to bad side-effects and cost associated with treatment of false positives (which you'll get if you screen a sufficient number of people). Here, the genome sequence may help to identify who should get screened.
How is the genome sequence useful in the long term? The more genomes are sequenced, and the more phenotypes and diseases get associated with them, the better the predictions become, and the easier it will be for basic science to understand how mutations cause/influence disease. Thus, getting the genome sequenced now may be extremely useful and informative for the people who get their genome sequenced five years from now.

I assume some people would have their genome sequenced not so much for "My family has a history of heart disease - what risk factors have I inherited?" but for "I have my genome on this DVD - isn't that neat?".
The reason I suspect that is that I've heard that there are services that allow Europeans to find out which of the "Seven daughters of Eve" they're from, which seems to be more about curiosity than medical information.

Sure, there is this curiosity factor that is outside health. And such ancestry and other info is a lure that brings customers to 23andMe, eg, where there is a mix of health and ancestry info in the report returned to the customer. I do think more people are interested in real ancestry - land, race, ethnicity - rather than something like the "Seven daughters of Eve."


text:
Are Asians more genetically homogenous than other races?
I've heard that Asians (I'm not entirely sure which subgroup was being referred to) tend to be more genetically homogenous than other races, with people of African lineage being on the other end of the spectrum being the least homogenous.
Is there any truth in the claim that Asians or a specific subcategory such as South East Asians have less genetic variance than other races?
I've seen papers like Extreme mtDNA homogeneity in continental Asian populations for example, but I don't understand enough to know if that answers my question.
If Asians have less genetic variance, would that lead to less variance in phenotypes?

I think you'll find that Africans are the most genetically heterogeneous.

@AlanBoyd That's interesting...do you have a source? I remembered reading it was Caucasians which given how far Caucasians have spread and evolved independently would make sense to me...

This Wikipedia page is a good source http://en.wikipedia.org/wiki/Human_genetic_variation The argument is that during the out-of-Africa migrations only a small sample of the total genetic variation left Africa. Those who remained inherited all of the existing variation. Detailed information at the WP page.

I will side-step the question of 'race', as you seem to be using it (like most people) in the sense that has no scientific basis, but the answer to your question goes something like this:
The amount of genetic variation in a given population is mostly the function of the geographical distance from Africa. Roughly, populations in Africa are most genetically variable as they are the oldest (they have been there for the longest time in human evolutionary history and therefore there was a long time for mutations to accumulate in their genomes). Because all the other populations in the world have originated from these original African populations, they have a subset of that original variation - they are less variable. The further you get from Africa the less variation remains (a very simplistic scenario: a group of Africans left and settled down in the Middle East; then a group of Middle Easterners went further up to Europe and further east to India; then the Indians moved further north and east etc. etc.; in each stage, only a subset of the previous variation would be travelling along).
A famous image depicting this phenomenon is in Ramachandran, S. et al. (2005). Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences of the United States of America, 102(44), 15942–15947. doi:10.1073/pnas.0507611102 figure 1B

On the Y axis you have a measure of genetic relatedness (more relatedness = less variation) and on the X axis you have rough geographic distance that takes into account major geographic barriers (like seas etc.). Green is Eurasia and blue is Australia and Oceania. Red is variation within the groups (so, Europeans only, Australians only etc.) The variation  between the populations explained by this geographic distance is close to 80% - which is huge. If I get this right, it means that most of the genetic differences between people in different populations are a simple consequence of living outside Africa. And the variation within each population is tiny (12%) compared to the between population.
This is a simplified view, because we now know that there were other species of humans that lived when our ancestors left Africa, and that thay had sex together as our ancestors spread around the globe, so a small portion of the others' DNA is still present in us today. Also this picture may be slightly different depending on what region of the genome you're looking at. But the major picture stands.
Going back to your question - "Asians" (populations with ancestry in east Asia) are on average more genetically homogenous than "Australians", "Americans", and "Africans".
EDIT: A paper I like that should explain all this much better: Barbujani, G., & Colonna, V. (2010). Human genome diversity: frequently asked questions. Trends in genetics : TIG, 26(7), 285–295. doi:10.1016/j.tig.2010.04.002 link

a sensible , scientific answer to a sensitive question!

Thankyou, a very interesting answer! I disagree that race has no scientific basis as I think that's being overly PC. Could you clarify if on your last point when you say "Australians" or "Americans" you mean Caucasians, or if you actually mean Australians or Americans?

Answering the second part of the question: I mean people of Australian or American ancestry. The first part: I encourage you to read that Barbujani paper. When people say "race" they tend to mean a social construct that classifies people into groups based on physical appearance (skin color, hair, eyes etc.). You cannot divide people like that based on the DNA, because the variation is continuous and all division of it will be arbitrary. It's like seeing a rainbow: can you tell me exactly where the yellow ends and orange begins?

The reason I think it's being overly PC to assume race has no biological basis is because we have evidence to the contrary. When people say Caucasians or Asians or Black, we genrally know what the people being referred to look alike. That aside, there are different medical issues effecting different races. Race is the subgrouping of people with common characteristics, which we know exists in biology. That's all it has to be, unless you make it into something more. Koreans all have genetic characteristics in common that Caucasians lack, and vice versa. No?

I think your answer would be a lot more useful if You didn't compare races to nationalities, especially nationalities only established in the last half century. Would you say the Asian Race is more genetically homogenous than the Caucasian Race? - http://en.wikipedia.org/wiki/Caucasian_race and http://en.wikipedia.org/wiki/Mongoloid_race

@SonnyOrdell No. I agree that when people say Asians or Black, we generally know what they mean - because we tend to think in general features of appearance. This may be particularly true in the US, where the people of many greatly different ancestries live together (imagine picking only "full" colours from the rainbow). But the gradients are there - in physical appearence and in DNA. And "what people look alike" is just adaptation to the environment (ie skin color is an adaptation to uv radiation). Anwyay, this comment section is probably not a best place for a complex discussion...

@yotiao would you be interested in taking it to chat? My point I guess is that the phenotypes we associate with cultural constructs have a basis in DNA..gradients are there, but I don't see why that takes away from it. If we study ancient human remains we can see the remains, can we not?

I'm still interested in how Asian genetic homogeneity compares to Caucasian genetic homogeneity, outside of Americans and Australians.

Fine with chat - but I don't know how, I've never used it :-) Give me some time to find relevant papers and we can talk.

@yotiao I've been busy, sorry for the late reply. You still down to chat?

@SonnyOrdell I am, probably later today. My local time is GMT. I think we may do it there: http://chat.stackexchange.com/rooms/11814/genetic-variation-in-humans

Don't worry, caucasians all look the same to Asians too. This is because of the cross-race effect: we are able to effectively distinguish people we are more familiar with.
But as for the most genetically diverse race, this article might be of interest: "Sub-Saharan Africans have greater genetic diversity than other populations." The research paper the quotation is based on is found here.
To be honest, I don't see the point of this question. The answer depends on what classifies under a race: Do Asians include Indians? What qualifies as Caucasian? etc.
The only thing that can be gained by exploring race-specific genetic distinctions is if you want to promote some racial supremist attitude like that guy with the toothbrush mustache.

I'm not really interested in the tired of argument of whether or not race is a valid construct, and I don't see it as relevant to the question. For most people outside of the UK, Asians refers to the peoples of the Asian continent..Chinese, Japanese, Koreans, Thai etc..

The point of the question is that I was curious about it and wanted a detailed answer after being unable to find one myself...isn't that part of why sites like this exist? The cross-race effect is interesting, but doesn't address the question. I'm not asking about the most genetically diverse race, and I think it's naive to say exploring race-specific genetic distinctions is only useful for promoting racial supremacy.


text:
How to quantify quality of vegetables and fruits?
I am interested in knowing if there have been studies in quantifying the quality of vegetables and fruits. By simple examination, it is possible for us to identify if a particular vegetable is 'spoilt'. But does this transitioning from 'edible' to 'spoilt' happen instantaneously? Or is it possible to model this transformation by a random process?
When producers and retailers determine shelf life, is it only based on anecdotal knowledge? Is there a systematic process by which quality can be determined and quantified?
I shall be glad if you could point me to studies that look at time to expiry and hazard rates of vegetables under variously controlled environments. I am happy to have the data for one or more common vegetables or fruits.

What exactly do you mean by "quality"? Do you only mean edible vs spoilt?

@terdon: Spoilt is an extreme case. I am more interested in the 'curve' from edible to spoilt, over time. Is it a step function, where suddenly on a day, it becomes spoilt? Or is it more gradual? Again, is this curve deterministic or random? Such type of questions.

OK, in that case, please [edit] your question and make it more specific. "Quality" can refer to any number of things.

At which level do you want to detect spoilage? By spoilage do you mean decay or just infected by some microbe? Some fruits/vegetables may lose their quality i.e. start degrading by themseleves and this may have not result from exogenous infection. Can you clarify on this. In any case, the assay may vary for different fruits and vegetables.

@WYSIWYG: I am specifically interested in the case when there is no exogenous infection, that is, the natural decay process.

In that case I would suggest that you focus on a specific kind of fruit/vegetable because each one of them can yield different degradation products. Or else, you frame your question like a [tag:reference-request] which means you should mention what all details you are expecting. (Optional but recommended: add some results from your own search [such as this], and indicate what kind of topics you are/aren't expecting)


text:
When do most mammals mate?
Is one part of the day more prevalent then other when it comes to mammal animals mating? Is there an aggregating study that has been done to see if these living beings in nature mate mostly during day or night?

I think this is too vague as written. I think we need a more specific group than "animals."

^ Agree with above. Also, perhaps consider editing the title to read "At what time of day does (inset species name) mate?"

Thanks guys. I am mostly interested in mammals since we can, I guess, consider them most advanced. I've fixed the question title and content to be more specific.

I don't know the answer, but I can help you to restrict your research. With the exception of humans and bonobos that have sex for recreational purposes, all the mammals mate during the estrus. In particular, the female will only allow the male to mate during a restricted time coinciding with ovulation. So if some aggregating study has been done regarding the ovulation, you have your answer.

@96well - ovulations is most likely a few days phenomenon, and I am inquiring especially whether the daylight is accompanying the mating. I suspect that mammals mate only under the day light, but I need someone to confirm it.

Some mammals, including mice, are nocturnal (see a wikipedia list). I know for sure that mice mostly mate during the night (I work with them).

Yes, I have suspected it (about mice), although didn't even bother to check. Thank you again. Now we have one question to answer - are most mammals - daily creatures (non-nocturnal). Most likely yes, right?

I can't vouch for it's accuracy (and can't answer the question), but I found this.
http://answers.yahoo.com/question/index?qid=20090831052348AAOIRCM

Don't have the reference at hand, but I am pretty sure there is a circadian component to it (aside from estral/menstrual cycle obviously)

How are you counting here.  Each mating counts once? Each individual counts once? Each species count once? Each genus counts once?  etc.

Why would it evolve?
No research (that I can find) is consistent with specific time of day mating across many species. I can't think of any reason why even just a few quite different mammals (e.g. mice, bats, lions, whales, and humans) would all find a fitness benefit of mating at the same specific time of day and therefore it is highly unlikely to evolve. I would suggest that if there are consistent patterns they are no reason other than coincidence (correlation over causality).
For example, dawn and dusk peaks in activity...
I have no references to back this idea up but lets see how this goes. The majority of mammals will be awake around dawn and dusk because there is likely an over lap between nocturnal and diurnal species at these times. Given that mating (normally) requires the participants to be awake then this would be a time when more animals are awake it is therefore a more likely time for mating to occur. But, as I already mentioned it would purely be because of the increased numbers awake.
Simple statistical illustration of the dawn & dusk idea...
Imagine a raffle with 2000 winning tickets. You buy 1000 and put 500 hundred of these in a box called nocturnal and the other 500 go in a box called diurnal. The raffle is drawn 24 times (perhaps every hour). The first 14 times it is drawn you can win if the ticket is from the nocturnal box, the latter 14 times you can instead check the diurnal box. This means during the first 10 draws you have a 25% chance of winning, and likewise in the latter 10 hours, but in the middle 4 hours there is a 50% chance every draw.
This comes down to a simple statistical phenomenon, if you don't buy a ticket you can't win the raffle.

Thank you. My idea was to check if there is a corelation between the phases of a Sun (the intensity of light around during different times of the day) and mamal mating activity.

It could be done but choosing which mammals to test would be difficult, they vary substantially in their habitat & behaviour. To get a representative sample of the thousands of different species you would have to sample many of species (from different Orders & Families (biological classification)). It is an infeasible study to do first hand. You could compile data that exists which has been done on single species and conduct a meta-analysis. Again you would have to make sure you capture as much of the behavioural variation as possible. If this answers your question please could you accept it.

also if it does not answer your question then please explain why and maybe I can still answer it


text:
Foveal ganglion cell density (Tay-Sachs Disease)
I’m currently reading on Tay-Sachs disease and have stumbled upon something regarding the typical “cherry red” macula symptom.
On the one hand it is mentioned that the macula is almost devoid of ganglion cells (GCs) and this actually the reason for the high acuity in this region since there is not obstruction of light [Suvarna JC, Hajela SA. Cherry-red spot. J Postgrad Med 2008;54:54-7].
On the other hand google books gives me numerous textbooks that highlight the fovea as the location of highest GC density and conclude that this leads to the high acuity because a GC only receives information from one or two cone cells.
I guess both are correct but how does one fit the other? It seems contradictory to me.
To be precise some sources specifically mention the boundary regions of the central fovea to have the high GC density, this could leave the fovea devoid of them and therefore combine both facts, however if this is correct I still wonder:
1: Where are the GCs that the cones in the central fovea are connected to?
2: Why is the “cherry red” spot in the macula so large on all the pictures. If my explanation is correct only the tiny area of the central fovea should be red and the surroundings the complete opposite due to the high GC density, right?
I’d really appreciate if someone could shed some light into this.

As you've already mentioned, cells near the primate macula tend to make one to one connections.  Due to this lack of convergence they can be somewhat smaller than normal cells (particularly in the size of their dendritic arbors) earning them the moniker "midget" ganglion and bipolar cells (also P cells).  By reducing the magnitude of photoreceptor convergence onto ganglion cells, the retina sacrifices luminal sensitivity for spatial acuity.  Or put another way, a downstream neuron in the LGN/V1 can be more "certain" about which photoreceptor is sending information when light is bright, but less certain that any information is being sent when light is dim.
The other side of the question you bring up is how the retinal ganglion cells themselves alter the image formed onto the photoreceptor layer.  For those that don't already know, photoreceptors are located at the very back of the retina.  Since they're the major light sensitive part of the retina, that means light has to go through the ganglion cells, bipolar cells, amacrine cells, and all of their associated processes before reaching the actual photosensitive part of the eye.  So, why not put photoreceptors at the front of the eye?  One major reason is metabolic, photoreceptors are tightly coupled with the retinal pigment epithelium which helps to re-process used photopigment as part of the retina's vitamin A cycle.
How can those two factors, a one to one correspondence and a decrease in thickness be present at the same time?  For reference, let's locate a cross section of a primate macula

Dark areas are cell nuclei.  The innermost layer of cells (bottom of the image) are ganglion cells, the next layer of cells up is bipolar cells (the inner nuclear layer) and the next layer up is photoreceptor cell bodies.  you can make out the cilial stalks of the photoreceptors pointing upwards toward the RPE.
From this image we can see a few transformations happening in the macula:

The photoreceptor layer is thicker, up to 7 or 8 cell bodies deep.  This means higher photoreceptor density.
The outer plexiform layer (photoreceptors to bipolar cell connections) is considerably thicker.  A single cone should connect to fewer bipolar cells in the retina, so how does this make sense?  We'll find the answer in #3.
The outer nuclear layer is only one cell thick.  This is the first layer that is actually thinner in the foveal region.  The cell bodies for photoreceptors from tis region have been displaced laterally, and the outer plexiform layer from #2 had to be larger to accommodate this lateral shift
The inner plexiform layer, connections between bipolar cells and ganglion cells, is nonexistent.  Also absent is the ganglion cell layer itself.

So how do these observations resolve your question?  Quite simply, the lateral movement of information from the foveal/macular photoreceptors happens predominantly in the outer plexiform layer.  That buys the inner plexiform layer considerably more space to further spread those signals laterally to ganglion cells, and avoids the problematic situation you suggested of having an extra-thick ring of ganglion cells immediately around the fovea.  The end result is that ganglion cells that respond to photoreceptors in the foveal region of space are even further out from the retina than the bipolar cells they connect to, which are themselves displaced.
As far as why a cherry red spot looks so large, that honestly depends on two factors: the disease or disorder in question and the zoom used.  Bear in mind that the red color comes from, as far as I know, the blood vessels in the choroid itself.  It would therefore not necessarily correspond exactly to the size of the macula, but instead to any area which is thinned in that vicinity.  I think you'll become more comfortable with that idea if you look back at the thickness of the total retina in the above figure and notice that even outside of the foveal region it is still growing thicker.
I think your question shows good instincts, because I believe that if the eye evolved to have a larger "true" fovea then you would get exactly what you describe: a large area of super high density vision surrounded by a region with non-linearly worse vision designed to support the central region.  Instead it appears that the primate macula is just large enough that we have a moderate sized central acute region and a (relatively) linear drop in spatial acuity moving out from it.

+1 This appears to be an excellent and thorough answer, although it is a lot of material to post without citing any primary literature.


text:
Turn off multithreading in pymol
By default, pymol seems to grab the number of cores on the system for rendering. How can I force it to only use one core?
Motivation:
I have a large collection time-series of of coordinate data from a computational protein folding experiment. I'd like batch render the generated pdb files into a movie in a programmatic way. Pymol however likes to eat up as many cores as it finds available. I'd like to retain some control of the computational burden (required for some computational cluster jobs). How can I force pymol to only use one (or n) core(s)?
Solution:
While the question was closed (as it was decided to not fit into biological criteria of the site) future visitors might find it useful to know the answer:
set max_threads, 1

The solution was found in a Biostars question.

I'm all for bioinformatics questions, but this one has absolutely no biological component to it.

@DanielStandage I'm sorry, and I'll happily move the question somewhere else. I don't think this belongs on SO, however. Do you have a good suggestion where?

@DanielStandage I only posted this question since I saw a high voted question here on pymol scripting: http://biology.stackexchange.com/q/732/822 Again let me know if this is not the intention of the site.

Try http://www.biostars.org/.

I think bioinformatics questions can definitely be on-topic for this site, assuming they include a significant biological component (or at least some biological component). The question you refer to includes as least a minimal description of a biological question being addressed, whereas this one focuses entirely on the software aspect.

@DanielStandage I've given some motivation for the question. I think that the question in general might be useful for others working with pymol scripts, so I'm going to leave it up. If the community decides to close, I'll understand.

@Danielstandage, lets take this to the meta.

@Hooked - what platform are you running? Linux?

@Luke Yes, this is on a Ubuntu 12.04 machine. Though I think the clusters run on a non-Debian distribution.

@DanielStandage So on the (fictional) Builders.SE site, "How do I fix my circular saw?" should be closed because it's not about building anything?

@NickT It would depend on what the scope of the Builders.SE site was, as per their FAQ. Our FAQ states: "Questions on interdisciplinary subjects like bioinformatics are also welcome, as long as they focus on the biological part of the subject."


text:
determining genome-wide exogenous binding of pathogens to host genome?
I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice genome to the advantage of the pathogen.
It's an interesting concept but left me wondering how one would determine de novo the binding of these pathogen effectors into the host if one didn't know them. What would be the steps to determine where are the pathogen's TFs binding the host genome?
Edit: there is the possibility of not knowing which proteins bind to the host genome, so what would be the way of developing the antibodies in this case?
Reference:

 Li T, Liu B, Spalding MH, Weeks DP, Yang B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology 30: 390–2.

The techniques used to do this are ChIP-seq and ChIP-chip.
Basically, you

let the pathogen bind to the (highly replicated) DNA
cut up the DNA into little random pieces by sonication
enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen
sequence the thus enriched DNA
map the sequenced fragments back to their original location on the genome.

Wikipedia has a nice picture explaining this process in a little more detail:

A colleague of mine discovered the cipher that determines TAL effector DNA specificities, which is described in this short paper. These specificities were determined by observing TAL effectors bound to DNA and recording how often a given repeat-variable diresidue (RVD) would correspond to a given nucleotide (using a weight matrix).
Now that the specificities have been determined, identifying TAL effector target sites is simply a matter of measuring the probability of that TAL effector's RVD sequence aligning to a novel sequence. Some applications are described here and here.
The TALENT 2.0 server (invited paper under review) provides tools for designing custom TAL effectors to target specific DNA sequences, or for identifying potential off-target binding sites in a given sequence or genome.
References:

 Moscou MJ, Bogdanove AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science (New York, NY) 326: 1501.
 Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757–61.
 Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic acids research 39: e82.


text:
Are prions an important driver in evolution?
I understand that prions have been implicated in the passing on of epigentic information[1]. Are prions thought to play a significant role in the evolution of organisms?

 Alberti S, Halfmann R, King O, Kapila A, Lindquist S. 2009. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137: 146–58.

@aland Thanks for your effort to improve the quality of citations in the questions and answers on this site. You may be interested in this thread in the meta regarding the best location for complete/verbose references.

It is proposed that prions are a good mechanism for "testing" phenotypic variation.
There are many identified proteins with prion-determining domains (PrD) in the yeast genome that can spontaneously switch between conformations with some low probability (eg: check SUP35 for one example, and [1] for a good overview of more). The theory is that:

the low probability of switching from non-prion to prion state allows for many more mutations and variations to accumulate -- generating greater genetic diversity than in standard expressed gene variability where most mutations are silent or detrimental
the prions provide a ready form of non-permanent inheritability that can be "trialed" by offspring and others in a colony of organisms -- this can be especially beneficial during say temporary changes in environment
if the prion phenotype is widely successful, selective pressure can easily mutate it into a more permanent fixture in the genome.

Check out the excellent paper published just last week in Nature exploring this this topic [2]. To give a sense of just how evolutionarily-advantageous prions can be, in the author's experiments and analysis they note that 40% of the prion traits they analyzed were beneficial to growth (eg:  in the paper strain UCD939 gains additional resistance to acidic conditions from the prion [PSI+]).
Assuming these hypothesis, prions would thus play a significant role in the evolution and variability of organisms.
[1] Crow, et. al. 2011. doi:10.1016/j.semcdb.2011.03.003
[2] Halfmann, et. al. 2012. doi:10.1038/nature10875


text:
Why is propanoic acid often added to the diet of C. elegans?
And what are its effects on C. elegans?
The paper is  Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.. 2011. Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila. Nature 477: 482–5.

Propanoic acid is toxic against many types of mold, fungi and bacteria (wiki), but same time has almost no effect to C. elegans ("fivefold less", reference). This is why propanoic acids and (more commmon) its salts are used as conservants for C.elegans cultures (as well as for other animals, like Drosophila).

We use nystatin. I don't think the use of propanoic acid with C elegans is that common. Fly people use it a lot.


text:
Could an "overactive" brain increase the chances of Alzheimer's Disease?
From  Raichle ME. 2010. Two views of brain function. Trends in cognitive sciences 14: 180–90:

Alzheimer’s disease (AD) is the most common cause of progressive
  cognitive decline and dementia in adults. While the amyloid cascade
  hypothesis of AD posits an initiating role for the β-amyloid (Aβ)
  protein, there is limited understanding of why Aβ is deposited. A
  growing body of evidence based on in vitro, animal studies and human
  imaging work suggests that synaptic activity increases Aβ, which is
  deposited preferentially in multimodal brain regions that show
  continuous levels of heightened activation and plasticity across the
  lifespan. Imaging studies of people with genetic predispositions to AD
  are consistent with these findings, suggesting a mechanism whereby
  neural efficiency or cognitive reserve may diminish Aβ deposition. The
  aggregated findings unify observations from cellular and molecular
  studies with human cognitive neuroscience to reveal potential
  mechanisms of AD development.

High synaptic activity doesn't necessarily mean hyperactivity. You can have an high inhibitory tone, for instance.

I think the article that quoted(1) is different to what the link shows now(2). However, both the article quoted and the one in the link are relevant to the question.
Alzheimer's Disease : In a nutshell, AD is the most common form of dementia. Although the exact cause is still under investigation, several genes have been implicated in the development of AD. One of the things you see in the brain with disease progression is beta amyloid plaque deposition which disrupts brain activity.
Brain Activity : While the brain consumes around 20% of our body's energy at a baseline, an increase in brain activity only increases this consumption by around 5%. Hans Berger, the first to record an EEG stated that "mental work, as I explained elsewhere, adds only a small increment to the cortical work which is going on continuously and not only in the waking state".(2)
However, there are a few 'intrinsic' networks or regions that perform functions such as "information processing for interpreting, responding to and predicting environmental demands". One of the areas active in this state of the brain is referred to as the 'default mode network' (DMN). It's thought that DMN is the main target of the amyloid plaques responsible for Alzheimer's Disease.(2)
However, there are other multimodal regions of the brain that perform processing of various types of information. It's now suggested that "regions vulnerable to Ab deposition do not simply involve the DMN, but rather comprise multimodal brain regions that are highly interconnected, plastic, and capable of rapid ATP generation"(1).
So it's a variation of activity in these particular areas - not all - that are implicated with Alzheimer's Disease. When you are performing a task, activity in these areas diminish.
Why keep the brain intentionally active : The reason for the hypothesis that actively engaging in challenging activity may reduce the risk of AD is that individuals with a high cognitive reserve have been shown to cope with the pathological changes such as beta amyloid deposition better. Cognitive reserve has been linked to a bunch of factors including "education, occupation, socioeconomic status, social networks and lifelong participation in cognitive and physical activity" and reflects "lifelong patterns of behaviors, endogenous factors (including genetics) and exposure to environmental factors"(1).
Moreover, it's suggested that perhaps higher cognitive reserve increases neuronal efficiency which has been shown to reduce plaque deposition.(1).
So InquilineKea's question and jp89's answer aren't really contradictory.

August, et al. Lifespan brain activity, β-amyloid, and Alzheimer's disease.
Trends in Cognitive Sciences. 2011. 15(11):520-526.

Raiche. Two views of the brain.
Trends in Cognitive Sciences. 2010. 14(4):180-190.

Hafkemeijer, et al. Imaging the default mode network in aging and dementia.
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2012. 1822(3):431-441.

Harrison's Principles of Internal Medicine. 16th Ed. McGraw Hill.


text:
Why would we overexpress Sir2 by overexpressing its hypomorph (dSir2-EP2300) in C. elegans?
Can't we just overexpress regular Sir2 in the paper? Rather than overexpress a reduced-function gene?
The paper is  Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.. 2011. Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila. Nature 477: 482–5.

That's an interesting paper.

could you point out exactly where they say this is a reduced function gene?  it seems as if they are characterizing a worm which has many copies of the sir-2.1 gene.

I think hypomorph implies reduced-function?

I have had a little time to look over this paper.
They do overexpress a native sir2 clone in high doses, called sir2.1 OE.  Which seems to be native and also appears in high copy numbers. This strain was found in previous publication to have a high lifespan... that is old news.
This paper sees sir2.1 expression levels as an oversimplification of the causes of longevity.  When they create crosses of the sir2.1 OE strain with wildtype, you can see the Outcross, which is verified to have a high level of sir2 expressed no longer has an extraordinary lifespan.
This can be seen in Figure 1.  http://www.nature.com/nature/journal/v477/n7365/fig_tab/nature10296_F1.html
So this paper is now asking, if sir2 levels do not convey the information that creates an extended lifespan, then what does?  It must be some modulation of some protein that sir2 affects.  They implies that the actual cause of the lifespan increase may have been a mutation somewhere else in the organism.
"However, longevity was not suppressed by sir-2.1 RNA interference (RNAi) ... indicating causation by factors other than sir-2.1, either on mDp4 or elsewhere in the genome."
"This implies that lifespan extension is due to transgene-linked genetic effects other than the overexpression of dSir2."
In the second half of the paper (figure2) the investigators have moved on to drosophila work, where they look at how expressing constructs or inhibiting sir2 protein levels might affect lifespan.  Although the dSir(EP2300) / + construct (drosophila sir2) with a wild type gene promoter did not live quite as long as dSir2(EP2300) with a fancy promoter (dSir2(EP2300) / tub-GAL4), the promoter construct (tub-GAL4/+) alone also had just as long a lifespan.  How can this be?  Not sure, but the expression of sir2 is clearly not the panacea we had hoped.  Note however that the reduced power gene still gave the same boost to lifetime.   This shows dramatically that sir2 activity alone does not drive the longer lifetime.
Lastly, deletion constructs (dSir4.5/1.7) , which should have lower than wild type protein levels for sir2 had completely normal lifetimes.
So the answer to your question; you need to test a hypothesis going in both directions - does increase of the protein really create a strong effect?  Does decreasing it have a negative effect then?  There are lots of other reasons to use knockouts and non functional genes in such an experiment, but those are the broad strokes.


text:
protocol for pulldown of DNA breakpoints?
Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination events:
 Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV. 2012. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome research 22: 957–65.
I would like to know if there is something like that which will work on any status of the cell cycle, not only meiosis.

The paper you cite says that the break points are single stranded DNA which have specific proteins bound to them.
I'm not an expert here, but if thats the cause of meitotic break points there are some interesting possibilities for detecting them:
you could detect them with a tiling array.  - that's an micro array which has an oligomer every 40 bp or so of the genome.  The array could be used in a CHP experiment that detects the same proteins as in this paper.
Its possible that the array could possibly hybridize the single stranded DNA from the genome too if the conditions were right.  This sounds noisy though.
On the cheap side it might be possible to use PCR to copy the single stranded DNA from a chromosomal DNA prep.  if the oligos you use are labelled with streptavidin say, you could isolate it , re amplify it and sequence cheaply.
any of these sound like a good bit of work :)

The answer is yes, not only meiotic, but any DNA double-strand breaks will be detected as long as they are processed by homologous recombination. This method (SSDS) is based on the detection of resected ssDNA ends at DSBs. The only difference for the mitotic breaks will be that you cannot use anti-DMC1 for ChIP. Instead, you should use either anti-Rad51 or anti-RPA in ChIP.


text:
variation in expression accounted for a SNP -- what's a usual percent?
I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the variation in the nearby gene expression. 55% sounds like a lot to me, what is the usual percent accounted for a significant SNP in a study like this?

 Dunlop MG, Dobbins SE, Farrington SM, Jones AM, Palles C, Whiffin N, Tenesa A, Spain S, Broderick P, Ooi L-Y, et al.. 2012. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nature genetics 44: 770–776.

eQTLs (expression quantitative trait loci) are variants that affect the expression of one or more genes.
There have been several 'genome-wide' studies of SNPs that directly affect expression. The actual effect sizes are hard to pin down in most of them, but in the supplementary data for this paper is a list of the SNPs with the largest effects and coefficients of determination.
There are several common SNPs (cis-acting) that account for >50% of the variation in that genes expression in this (European) population cohort. That being said, that vast majority of variants account for much less variation in the expression, but this is to be expected.
I therefore can fully suppose that a disease-linked SNP could affect the expression of a gene to that degree, particularly if it is an oncogene or tumour suppressor.
Reference:

 Wood AR, Hernandez DG, Nalls MA, Yaghootkar H, Gibbs JR, Harries LW, Chong S, Moore M, Weedon MN, Guralnik JM, et al.. 2011. Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. Human molecular genetics 20: 4082–92.


text:
How to DIY preserve pet DNA today so that it can be used in 20 years
I know that there are companies that offer a kit+storage of your pet DNA for around $2k.
My question is if there is any other option for doing this yourself with a thought in mind that in 20+ years the technology will get so advanced that even this DIY sample can be utilized.
Any ideas? Maybe drying a blood drop or mixing blood with alcohol/acetone?
Also, I read somewhere that it is better if the pet is still very young, because if you take old pet DNA the clone will exhibit mature signs even as a youngster. Is this true? If yes then what is the top age that is safe?

Make it have babies?

Freezing sounds kinda primitive.

You asked for DIY methods. Surely that means you are looking for as "primitive" methods as possible?

Heard a news story a couple of days ago about a couple who had their dog cloned after it died. @leonardo Amy had some brief suggestions.  Also your last paragraph might be better posed as a seperate quesiton.

@RegisteredUser Hmm. How else would you store DNA? Dehydration? As far as I know, freezing (at very low temperature, way below home appliance freezers) is what’s done in “professional” labs.

I can't consider freezing as a long term option. What will happen if I get a power outage or will have to move apartment...

@leonardo DNA requires constant maintenance to remain 'stable' in your cells at 37 degrees, although DNA can be found in fossil remains, so a synthetic version of this may be theoretically possible. Typically we store extracted samples at -80 degrees celcius, which you're unlikely to be able to achieve at home, unless you invest in a specialist freezer - this is unlikely to be cheaper than the company the OP refers to. And RegisteredUser, I'm afraid that freezing is the only long-term option that I'm aware of! Certainly when you're considering 20 years

Freezing in TE buffer might also help (10 mM Tris pH 8, 1mM EDTA). If you have a biologist friend, I'm sure you can get him or her to let you "borrow" some.

Any idea if this work for blood as well? http://www.ncbi.nlm.nih.gov/pubmed/10620236

preserving DNA for cloning is entirely a different issue than just any old DNA - making sure all the chromosomes are there and intact and useful for injection for in vitro insertion makes this a difficult question...

For the impatient, I'm going to say that probably if you only have a regular home freezer, its unlikely that you will be able to do this. If you have access to a -80C or liquid nitrogen storage its possible, but also less likely.
Cloning an animal typically starts with the transplantation of a nucleus into an egg cell whose nucleus has been removed.  So unless things change drastically in the next 20 years, just purifying DNA and keeping it in a tube of the fridge is not enough - you need to preserve epithelial (skin cells) or some other tissue in a state which can be revived to produce a live and intact cell when you want to do the cloning.
Its possible that we will have machines that can take DNA from a DNA prep and produce a living cell - this is what we hope to do with the mammoth and other extinct animals from fossil tissue some day.  But whether that will be the case in 20 years is just a guess, whether it is affordable is also just a guess.
So from what we know now, you will need to preserve a piece of tissue from the animal when it is alive.  I'm not an expert on how to do this, but you might be able to get the skin cells to sort of turn into a cell line and then freeze them for not too much money.
If you do this, regular freezers are not cold enough to prevent freezer burn.  This is what happens when you put a steak in to the freezer, wrapped in plastic even it will shrivel up and start to dry out as the water in the ice starts to sublime out of the package (the dry air in the freezer basically sucks the water out of the food).  If this happens to your animal tissue, its probably not going to revive.
Scientific labs use -80C freezers and liquid nitrogen storage because the water turns into a glass and all biochemical reactions are basically stopped. (besides drying out, the enzymes like DNAse are still nominally functioning in the cells at -20C and even simple bacterial cells don't live for more than a year at -20C, much less mammalian cells).  For preserving cell lines, liquid nitrogen is much more preferred.  I would say that properly produced cell lines can theoretically revive after indefinite liquid nitrogen storage.
So that's a quick answer.  Sorry to be a party pooper - things could change quite a bit in the next 20 years, but we just don't know how much.  popping a paw in a baggie or some DNA extract into the freezer might work, but its hard to say for sure.
As far as the choice of where the DNA comes from in the animal, its true that skin cell lines are often producing imperfect animals - the DNA may be modified in the skin in various ways that cause the animal to be smaller, weaker, or even deformed compared to the donor.  At this time all the protocols I see (and i could be wrong) are skin cells.  I would expect that there is a better tissue to preserve, but that might be just a guess at this point.  Its likely that in the next 20 years the choice of cell line from the donor will change quite a bit as well.

I don't have a -80C freezer and was hoping for some type of room temp preservation, but thanks anyway.

sorry I couldn't be more positive.  we still have a ways to go before we are like "Bladerunner".  i'm trying to help a biohacker lab get started and the cost of -80C refrigeration is a stumbling block to citizen bioscience.

Well if you are optimistic, which isn't outrageous, you could store some skin tissue taken from the pet.  flash freeze in liquid N2, then seal it in a solid piece of plastic (keeping cold) and pop it in the freezer.  Might work... store in the ice cube tray so that defrost cycles in the fridge don't heat the sample up.

Its possible that we will have machines that can take DNA from a DNA prep and produce a living cell... well, we can do that for bacteria!

If you believe that all you would need is a DNA sample, then I suggest that you store a decent amount of hair in a -20 freezer and hoe for the best. The reason I recommend hair is that it has previously been used to obtain the genome of an 4500year old human. If left at room temperature hair may still produce a genome but probaly only for a couple of hundred years with the current sequencing technology.

To clone something you need a living cell, not just DNA. Although DNA could someday be used to make a clone, it would require technology that is a long way off. You can store DNA indefinitely by extracting it from a cell and storing it in alcohol.
To preserve a live cell indefinitely requires very cold temperature, below -50F, otherwise the cell will deteriorate in various ways. Normal freezing temperatures will damage the cell due to the way water crystallizes at near freezing temperatures. If a cell is fully dessicated somehow without damaging it, then possibly it could be preserved in alcohol at room temperature, but it would be hard to dessicate the cell without damaging it.
You can, of course, experiment to try to do it. Get some cells, and first learn how to grow them so they reproduce. Once you can do that, try freeze drying them with different solvents. Once the cell is dried, store it in alcohol, then try to revive the cell by re-hydrating it. If you can cause the cell to divide again after re-hydration then, congratulations!, you have figured out how to preserve a live cell indefinitely at room temperature and can potentially publish a paper about it. Obviously, this would require many weeks of devoted effort to accomplish.

This is an old Q/A; an answer discussing cryopreservation techniques is missing and would improve it if you want something to work on here.


text:
What constitutes the determination of a normal blood glucose level?
Several on-line resources (e.g. MedlinePlus) suggest:
Normal range for non-diabetic people who are fasting should range between: 70 and 100 milligrams per deciliter (mg/dL)
Non-diabetic people who are not fasting should have a blood glucose level below 125 mg/dL
What I am interested in however, is the coverage interval of the population that was used to determine these 'normal' values.
Also are there differences based on age, sex or any other factors.

Determining what is considered to be "normal" is quite challenging indeed. Both the ADA and the WHO look at upgrading diagnosis limits and both have a conservative approach, primarily due to the difficulties in conducting large scale studies and the anomalies between assumptions of plasma glucose distribution and what is probably actually present in populations. Digging through, I found a very good WHO document here:
http://www.who.int/diabetes/publications/Definition%20and%20diagnosis%20of%20diabetes_new.pdf
I am not going to regurgitate from this document, but I believe Issue 2 provides a detailed answer to your question detailing several determination methodologies.
As to your second question on age/sex variations, are you asking if the criteria are different? At least with reference to FPG, they don't appear to be so.

Summarising some of the bare bones of the document would actually improve your answer - admittedly the WHO website isn't likely to disappear overnight but files can be moved/renamed etc.

I am a layman in Biology. Recommendation 2 at the end of Issue 2 of the WHO document seems to suggest that the normal level should be assiciated with DM and CVD risk. This is hard for me to swallow. Would you also give us the link of ADA document if there is any? Some summaries will also be greatly appreciated. Thanks.


text:
Vigorous shaking for HFR interrupted mating
I am trying to reproduce E. coli interrupted mating using an HFR strain, and I read that the cultures should be vigorously shaken  at times to interrupt the DNA transfer from the F+(HFR) donors to the F- cells.
How vigorously(I'm OK with a qualitative answer) should I shake the culture for optimal results?

I remember doing this experiment many years ago in an undergraduate practical where we used vigorous vortexing of culture samples in glass tubes to achieve interruption and separation.
According to Griffiths AJF, Gelbart WM, Miller JH, et al. Modern Genetic Analysis. Bacterial Conjugation:

... sampling is accomplished by using a kitchen blender to separate
  the joined cells, resulting in interrupted conjugation.


text:
Why is urobilinogen reabsorbed from the gut just to be excreted via the kidneys?
The Wikipedia article on Urobilin states:

Bilirubin is... excreted as bile, which is further degraded by microbes present in the large intestine to urobilinogen... Some is reabsorbed into the bloodstream and then delivered to [the] kidney.

This process is puzzling to me since it doesn't mention any function or reason for urobilinogen to be absorbed into the body, aside from it being there so it can be removed by the kidneys.
The only reasons I can speculate are that:

Urobilinogen shares a transporter/receptor with a similar, useful compound.
It has a direct useful function when in the bloodstream, not mentioned on the wikipedia article or a few other sources I've skimmed.
High urobilinogen is harmful to the gut and it's necessary to remove it via the blood to the kidneys.
Urobilinogen is inherently able to diffuse across the intestinal barrier into blood as a result of its chemical structure

Is it one of the above, or some other reason I haven't taken into account?

I think that it is missing some details. Note that the vast majority of urobilinogen (~80%) is actually eliminated via fecal elimination. I would recommend looking at the article on enterohepatic circulation, which provides more context on this issue. Basically, bile salts can be useful (even or especially after metabolism by bacteria), so a fraction is reabsorbed by the large intestine and then dumped back into the digestive system:

However, just like bile, some of the urobilinogen reabsorbed is resecreted in the bile which is also part of enterohepatic circulation. The rest of the reabsorbed urobilinogen is excreted in the urine where it is converted to an oxidized form, urobilin, which gives urine its characteristic yellow color.

...

The net effect of enterohepatic recirculation is that each bile salt molecule is reused about 20 times, often multiple times during a single digestive phase.

Obviously urobilinogen isn't one of the salts recirculated that much if most of it gets excreted in feces, but apparently it still happens (possibly just because it is chemically similar to the other bile salts, as you suggest).
I think that the mechanism which is emphasized in the urobilinogen wiki page is a secondary mechanism for excretion when urobilinogen is at toxic levels in the bloodstream (e.g. jaundice). These high levels come for example from blood breakdown as pointed out in the article, which may be emphasized because it is a common medical issue (which is of course not a focus of SE Biology).
So, in other words, the wiki article is targeted towards the potential medical problems (toxic levels requiring elimination via kidney) rather than the normal physiology (mostly eliminated in feces, sometimes-useful salt that helps digest stuff), possibly leading to confusion. This flash card resource succinctly notes the functions of bile salts such as bilirubin and its derivatives and may be helpful for other basic info:

Functions:
(1) Digestion and absorption of lipids and fat-soluble vitamins
(2) Cholesterol excretion (body's only means of eliminating cholesterol)
(3) Antimicrobial activity (via membrane disruption)

More about (unfortunately medical focused) physiology of bilirubin etc. can be found here.

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


text:
How does the choice of blood draw site influence the possible specificity of a serological test?
The news has reported that a new serological test for the presence of anti-SARS-CoV-2 antibodies has received an emergency use authorization from the FDA, and notably has a higher specificity than other tests (99.8%).
The new test requires blood to be drawn from a vein, rather than a finger prick, and a quote from the test's manufacturer reads, "If you take blood from a finger prick, you will never be able to achieve the same level of specificity that you will achieve … when you take blood from the vein" (non-scientific news outlet source). Although the question is prompted by news related to COVID-19, I'm interested in the general case as well.
It is unclear to me why this would be the case, since antibodies should be present in capillary blood taken from the fingertip. I would suspect one of two reasons, but I don't have enough of a biology background to verify whether they make sense:
1) The volume of blood which can be drawn from a vein is much larger. This would make sense if it improved the sensitivity to a low-concentration antibody of interest, since there may not be enough antibodies in a fingertip sample to bind to antigens in the test. However, it's not clear why having a larger sample would help with specificity.
2) Fingertip blood samples are contaminated with lymph, matter from the skin surface, and so on. I'm not sure how it would affect the specificity of the test. In my naive understanding of serology tests, the reagent would consist of a synthetic antigen of interest, plus either anti-human-Ig or a second moonoclonal antibody for the antigen that would be used to detect any bound antibodies from the sample. It's not clear to me how these sorts of contamination could cause false positives for this sort of binding.

This ref, https://academic.oup.com/ajcp/article/144/6/885/1761216
show that drops of finger prick blood vary more than venous blood.
The main reason for using venous blood is licensing. A test is licensed only for an exact procedure and materials. If you vary any conditions the license is invalid.
However, I would not expect a test for antibodies (present vs. absent) to show much variation except for detecting the lowest levels of antibodies. (Sorry I cannot find a ref for this).

Thanks. I'm still a bit confused by the licensing aspect: it makes sense that a test is licensed for a certain procedure, but here the choice of procedure was justified by a difference in specificity. The reference about fingertip sample variation is nice, and I'm still trying to wrap my head around any mechanisms by which it can affect specificity.