text:
Why is ATP the preferred choice for energy carriers?
Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?

the energetics of the phosphate hydrolysis is more or less similar for most NTPs. Compared to GTP, ATP requires one less enzyme for its synthesis. Pyrimidine triphosphates are also high energy molecules but have specialized roles.

It might be worth while having a look at this great article by F. H. Westheimer Why Nature Choose Phosphates, published in Science in 1987

Thats an interesting paper, thanks for recommending it. IF someone wants with no access through a university wants to read this paper, see here: http://academic.evergreen.edu/curricular/m2o2006/seminar/westheimer.pdf

Although ATP is certainly the most common triphosphate synthesized, GTP is quite commonly used to drive reactions: GTP provides 2/3 of the energy for protein synthesis, which is a major energy expenditure for most cells. So I would argue the preference for ATP over other NTPs is not as strong as it might seem at first glance.

The academic.evergreen.edu link is broken, but the Westheimer paper still lives at http://archives.evergreen.edu/webpages/curricular/2006-2007/m2o2006/seminar/westheimer.pdf

I wonder if oxygen has anything to do with it? See MH Zhou's theory here: "Please look at and compare the chemical structures of adenine and ATP vs guanine...the oxygen level on [early] Earth was below 0.1% as compared to 20% nowaday. Therefore, adenine was far earlier than guanine appearred on Earth by billions of years on early Earth. It is because, adenine has no oxygen atom in its structure, whereas guanine has 1 oxygen atom in its structure...."

I really like this question as it is such a fundamental underpinning of all life on the planet, yet there is such sparsity of actual information on its origins and why selection rewarded ATP use over anything else. Here I am talking generally since no specific studies exist in ATP vs other candidates.
A lot of the below information is taken from a relatively old article mentioned in the comments by TomD that discusses: "Why nature chose phosphates." by Westheimer, 1987. The article is very influential and has been cited over a thousand times since publication. Another article that came out in the same year that this question was asked "Why nature really chose phosphate." by Kamerlin et al., 2013
Some of the below arguments are more convincing than others, but all of them should be thought of when attempting to answer this question.
Summary.

ATP has ancestral dominance. Most other reasons derive from this.

Alternative phosphate groups or other molecules may not provide enough energy.

Alternatives may be toxic.

Other molecules, particularly phosphates, are used for inefficient high energy bursts.

Pi is a "good" leaving group.

Phosphates are fundamentally able to be regulated through electrostatic manipulation.

ATP synthase can efficiently reattach the Pi to ADP.

Lots of Pi available to organisms because of it's ancestral dominance ("if it ain't broken, why fix it?" is at play).

ATP can provide more energy if needed; it's scalable to the situation. (ADP becomes AMP + Pi)

Easily usable by a variety of proteins.

Why ATP?
ATP is an efficient and relatively easily biosynthesised molecule that can fulfil multiple biochemical roles. Cells do have alternative energy carriers, some with more specialised roles, however, ATP is ubiquitous throughout our cells and inter-cellular spaces. There aren't a wealth of resources explaining why ATP is any better than other compounds, however, there is plenty of reasons why the phosphates are required.
Why not the alternatives?
Citric acids and their derivatives are a good candidate, with deductible groups and high bioavailability but they simply don't give enough energy to stabilise genetic material.
Another tribasic candidate is arsenic acid. This is a fundamentally toxic compound, though, which isn't particularly great for living things.
There are other phosphates too, and they are used in many organisms. In biology, they have specific functions, and not used as the general energy carrier. For example, creatine triphosphate provides a high energy phospho- anhydride bond, that is often used to quickly and anaerobically regenerate ATP, useful during high rate muscle activity for contraction.
GTP is structurally very similar to ATP. GTPases are used more to initiate cellular signalling pathways. It is sometimes used as an energy source. This is a good example of an alternative energy carrier.
Over the years, many proteins have specialised with a specific shape, and this chance is the primary reason behind ATP over GTP. In other words, the choice of ATP over GTP is primarily down to cellular preference of molecular shape. One of them had to emerge as being more widely used, and it was ATP that 'won'.
Efficiency and simplicity.
The reaction was once thought to be a relatively simple nucleophilic displacement. From the 2013 paper:

...this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalysed reactions.

Traditionally one will be taught that ATP is such a chemically efficient way of storing and transporting energy. This is due to the ATP->ADP & Pi hydrolysis reaction. The phosphate groups in ATP are full of negative charges and these are repelling one another. This means that the third phosphate is a great leaving group and breaking the phospho- anhydride bond is a favourable reaction. ...
...But the story is a lot more complicated than that. The above explanation isn't really satisfying because those same negative charge forces are repulsive of the nucleophile that is attempting to complete ATP->ADP & Pi. A more comprehensive explanation would go along the lines of 'although a negative charge repulsion exists between the nucleophile of the protein and the phosphate, that high energy barrier can be overcome by electrostatic manipulation'. This allows an "on-off switch" for the hydrolytic reaction by tweaking the electrostatic environment. This is another great regulatory tool that the phosphates provide. This regulatory feature is important for signal and metabolic/catabolic cascades.
When it comes to 'rebinding' the Pi to ADP, it is fairly easy since ADP seldom covalently binds to anything, which would require a lot of energy to recover the ADP. This also helps the bioavailability of free ADP to ATP synthase, an incredibly efficient enzyme, that uses membrane proton gradient to drive the production of ATP. Talking about actual numbers is difficult here as there is only data available from Rat hepatocytes. Who is to say mammals are representative of all organisms? The estimates of energy of hydrolysis range from ΔG˚ = -48 kJ mol-1 to -30.5 kJ mol-1. Note that these are considerable, but not exceptional values, so it's easy for many different proteins, that need not be very specialized, to break the bond all over the body. I couldn't even find the numbers for the synthase reaction per ATP, but a single ATP synthase can produce up to 600 ATP per minute.
The final point of this efficiency is that the elements in ATP are very abundant and established in the biosphere making it readily available. This makes the phosphates a convenient biomolecule.
Multi-functionality.
ATP is ubiquitous in the body, but in some cases more energy is needed than there are ATP available. In these times of need, ATP can be used to produce more energy, breaking another phosphoanhydride bond to become AMP+2Pi. AMP however is typically a signalling molecule.
With the low activation energy required to break the phosphoanhydride bond, a multitude of enzymes, far too many to list here, can make use of ATP in order to gain energy towards the activation energy for many other functions.

I think this answer mixes up the advantage of phosphates as energy carriers with the predominance of ATP. The case for phosphates is nicely made by Westheimer's 1987 paper; but there is little reason to suppose that ATP is chemically special compared to, say, GTP --- the prevalence of ATP over other triphosphates is likely just an evolutionary coincidence. And the argument that ATP is "a great biomolecue" because it is "abundant in the biosphere" is obviously circular.

@Roland Great points, but allow me to elaborate that when I say that abundance makes it a "good" biomolecule I am not making a circular argument. Once any compound establishes itself in the primordial soup and is propagated, it is more convenient/probable that molecule is used than an alternative. This is a valuable point, and is less circular than it would first appear.

It seems like you just accidentally explained why AMP is a signalling molecule. AMP signals low energy.

I really like how the top two answers start with their opposing views on whether or whether they do not like the question.

I don’t like this sort of question because I don’t think it can really be answered and I’m very suspicious of arguments that seem to claim ATP is the only or even the best solution to the problem. Nature generally demonstrates that there is more than one way to kill a cat, but if one way works adequately you don’t always need to look for another.
This is not necessarily the case, of course, if we consider an example from the postulated RNA World — which I shall presently — catalysis using RNA was supplanted in most cases by catalysis using proteins. So sometimes a better solution provides an evolutionary advantage, and sometimes if things work well enough they stick as the limiting factor is elsewhere.
So I tend to the view that ATP worked, so it stuck. It was probably chance it wasn’t GTP or CTP or UTP, as these work as energy sources in signal transduction, phospholipid synthesis, and glycogen synthesis, respectively.
But this raises the question of the function or necessity of the purine or pyrimidine ring in the nucleoside triphosphates. As far as I can see the answer is this serves no indispensible function. (Sure, it binds to enzymes — but all sorts of other structure are able to do this.) So I would like to fly the following kite (which must have been flown before, although I am not aware of a reference).

A nucleotide triphosphate (ATP) became the preferred energy source in
  metabolism after a mechanism of RNA synthesis evolved that used NTPs as
  substrates.

When the synthesis of RNA evolved to use the free energy of hyrolysis of a ‘diphosphorylated extension’ of its structural building block (NMP), a system of using a related hydrolysis was extended to metabolism. Note that I say ‘related’, as RNA synthesis (like other macromolecular syntheses) hydrolyses the alpha-beta phosphodiester bond (releasing pyrophosphate), whereas in metabolism it is generally the beta-gamma bond that is hydrolysed (releasing orthophosphate).
The hydrolysis of ATP would have displaced what it is thought to have been a pre-replication system(s) of energy generation because it would presumably have been better and allowed integrated energy metabolism. (The energy demands of replication would have been large.) But that doesn’t mean it’s the best conceivable method — working well and being convenient could have been enough.
Footnote
Although not part of my argument, there is another key molecule in metabolism that has what may be considered a ‘useless’ adenosine component — NAD (and NADP). The redox guts of this is the nicotinamide ring. Did this evolve from a form that was initially part of a ribozyme — perhaps involved in the formation of deoxyribose when the RNA genome was being displaced by the DNA genome?

@rhody  You are quite justified in feeling that the answer to this unanswerable question is not chance. However, what is not justified, in my opinion, is the assumption that a non-chance answer is of the type you assume, namely that NTPs were the best molecule for the job, and that ATP was the best of the NTPs. In the latter case it could be e.g. that ATP was the 'cheapest' to synthesize, or that purines bound better to ribozymes than pyrimidines. And if NTPs were a consequence of the RNA structure of the genome, then selection occured at RNA, i.e. it was not 'pure chance'.

Preface
I have already provided an answer to this question, addressing one aspect of it: why a nucleotide triphosphate — rather than any other molecule — was the choice for an energy carrier. In that answer I suggest that the choice of ATP, rather than any GTP, CTP or UTP, was mere chance.
This second question has, in fact, been posed, but was regarded — incorrectly in my opinion — as a duplicate. I have recently become aware of research that suggests to me a possible reason for the preference of ATP over other NTPs, and, as it is independent of my previous answer, I would like to present it as a separate answer.
Why ATP rather than other NTPs?
I am starting from the assumption of an RNA world in which some sort of RNA genome had developed the ability to replicate and exhibit enzymic activity. The ribosome, and especially ribosomal RNA, can be regarded as a fossil of such a world. Harry Noller, in a review of this topic in Science in 2005, considers the bases that are involved in base-pairing in the many RNA double-helical loops, and those that are unpaired in such loops. Many of the latter are involved in ternary interactions in the rRNA, which has an overall protein-like structure. A significant fact that he mentions about the bases that are unpaired in the helical secondary structures is their skewed distribution:

“However, the unpaired bases are not distributed evenly among the four bases. In Escherichia coli 16S rRNA, for example, the proportions of unpaired bases for G, C, and U are 31%, 29%, and 33%, respectively, whereas 62% of As are unpaired, a tendency that extends to other functional RNAs.”

It transpires that many of these ‘unpaired As’ are involved in what are called Type II A-minor nucleoside interactions, which are illustrated in Fig 3. of that paper, below:

In the legend to this figure Noller points out that:

These precise lock-and-key minor-groove interactions between (usually) an adenosine and a Watson–Crick base pair are found extensively in 16S and 23S rRNA. They were first observed in crystal packing of the hammerhead ribozyme and in the P4-P6 domain of the group I ribozyme. A-minor interactions play an important functional role in monitoring codon-anticodon interaction by the ribosome via their unique stereo-chemical fit to Watson-Crick base pairs.

From this I conclude that adenine has unique structural properties that would allow it to form a more precise and stronger interaction to base-pairs in a ribozyme RNA than the other three bases. One of the features of any ribozyme involved in using an NTP to drive chemical reactions would have been to bind the NTP. (We see this in contemporary proteins with the Rossman Fold which binds adenine.)
The greater suitability of the adenine of ATP for this role may be why it, rather then GTP, CTP or UTP, became the major (I would assume initial) choice for energy carrier.

If this idea has been expressed before, I apologize for not acknowledging the fact. Let me know. Otherwise, you read it here first.


text:
Are there biochemical differences between the cell membranes of prokaryotes and eukaryotes?
I would like to know if there is any difference in chemical composition of cellular bilayer lipid membrane between eukaryotes and prokaryotes.
Specifically, I would like to know about the action of antimicrobial peptides on these bilayer membranes in context of the different membrane compositions.
It would be helpful if someone points me to some references.

I have given some references that let you discuss variations in membrane compositions. There are many more. I think for a more productive answer you need to talk about specific species.

There are differences. (Except mitochondrial eukaryotic membranes, which are indeed similar to bacterial membranes! (reviewed in van Meer et al., 2008)).
First, bare in mind that it is thought that even different eukaryotes, such as Fungi and Humans, have different cell membrane compositions and that this is reflected in the proteins (Sharpe et al, 2010). The outer membrane of Gram negative bacteria isn't even made of phospholipids, it's made of glycolipids (Kamio & Nikaido, 1976). Archean membranes have the most notable lipid compositions, including a bilayer-like monolayer, to adapt to the conditions they are found in (Oger et al 2013). My point being that saying "there are differences" is indeed an understatement.
This question has probably arisen because anti-microbial peptides seem to act with specificity, and that perhaps this specificity comes from direct peptide-lipid interaction. This is on the right lines. From wikipedia:

The cell membranes of bacteria are rich in acidic phospholipids, such as phosphatidylglycerol and cardiolipin[23][27]. These phospholipid headgroups are heavily negatively charged. Therefore, the outmost leaflets of the bilayer which is exposed to the outside of the bacterial membranes are more attractive to the attack of the positively charged antimicrobial peptides.

Notably, no such charge exists in eukaryotes since the negative charge is found on the inner leaflet of the plasma-membrane rather than the outer leaflet.
There is such a massive variation, even within bacterial membrane composition (Bogdanov et al 2014), that I cannot even really begin to list it here. Furthermore, there are variations in the glycocalyx, surface proteins, and lipid composition dynamics due to lipid rafts.

source: Stack Exchange

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

sort: votes


text:
What's the highest glucose concentration (in mM) anywhere in the human body (tissue, capillaries, tumor microenvironment, etc.)?
Glucose blood levels are around 5mM, or 10mM after meals. In capillaries these levels can rise by about 40 %. I haven't found measurements of glucose concentration in tissues, or in extracellular spaces. I'm wondering what's the highest glucose concentration, anywhere in the human body?

Fasting or prandial state?

@VanceLAlbaugh Highest, any state.

I would guess that the highest glucose concentration would be during the active absorption of a high carbohydrate meal - the carbs would be digested and broken down to glucose. The glucose concentration in the GI capillary beds - which would include both circulating glucose and glucose absorbed from the GI tract would be the highest concentration - not sure if there are any good estimates of the actual concentration

@VanceLAlbaugh I just need an order of magnitude.

Glucose concentration in the blood is a highly regulated biologic variable. From personal laboratory experience, it is very difficult to raise a healthy, non-diabetic individual's blood glucose over about 6.5-7 mM (i.e. 120-130 mg/dl). My best guess at where the highest glucose concentration might be in the body is within the hepatic portal vein that drains the intestines after a high carbohydrate meal. The glucose concentration is probably highest in the prandial state or, in other words, when carbohydrates (i.e. food) is being digested and absorbed by the gastrointestinal tract. Many simple and/or complex carbohydrates are digested to glucose and absorbed through the gastrointestinal tract. Once absorbed the glucose enters the venous mesenteric circulation and then drains into the hepatic portal circulation. This allows high concentrations of glucose and other compounds like amino acids from dietary nutrients to be "buffered" by the liver.
I don't have hard evidence to demonstrate that this is the highest glucose, but I think it's probably a good guess. It is inherently difficult to measure the blood glucose concentration in the portal vein - mostly because it's so difficult to get to that place anatomically during a meal. The dog is probably the most used animal for these types of metabolic studies, because catheters can be placed in the peripheral venous and arterial circulation, as well as in the portal vein and hepatic veins, to measure nutrient uptake by the intestine and nutrient extraction by the liver.
A number of previous studies by Cherrington and colleagues, who have done some of the most comprehensive work in this field, frequently measure glucose concentration and blood flow rates across the liver. In one such paper that is freely available from the American Journal of Physiology by Abumrad et al (1982) entitled, "Absorption and disposition of a glucose load in the conscious dog" you can see from Figure 1 the average plasma glucose concentration in the portal vein from a group of dogs given an oral glucose load of ~40 grams is somewhere in the 250 mg/dl region (i.e. ~14mM). These were otherwise healthy dogs, and similar to healthy humans I would bet the glucose concentration doesn't rise too much further. As you could imagine though, in a diabetic individual who has high peripheral glucose concentrations to start, the portal vein concentration might be expected to be higher. How much higher is another educated guess - maybe 100-200 mg/dl higher on an extreme end (obviously pathologic).
In a healthy human (i.e. non-diabetic) who undergoes a 75-gram oral glucose tolerance test I can't imagine that the portal glucose would go any higher than 300-400 mg/dl (or, 16.5 to 18 mM). But again - these numbers are just educated guesses. This is probably the highest glucose concentration anywhere in the body. Additionally, in diabetic patients the glucose concentrations would be expected to be slightly higher because circulating glucose may be slightly higher, but probably not by too much (definitely not an order of magnitude).

Thanks, these sort of estimates is kind of what I was looking for to get started.

happy to help @becko - in diabetic patients the numbers might be a little higher, but not that much higher (definitely not an order of magnitude)

@becko if this answer is sufficient to answer your question... think about accepting it officially - thanks!

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


text:
Can the Na+/K+ pump backwards to generate ATP?
The standard physiological direction of the Na+/K+ pump is to export 3 Na+, import 2 K+, and hydrolyze one ATP to ADP. Can it be driven backwards, importing 3 Na+, exporting 2 K+, and generating ATP? Does this happen in normal cells, and in what conditions?

related: https://biology.stackexchange.com/q/67418/561

All enzymes can theoretically catalyze the reverse reaction.
Researchers have driven the Na+/K+ ATPase to synthesize ATP with artificial ion concentrations:

We have studied the apparent affinity for K at its intracellular discharge sites by measuring the rate of ATP synthesis as a function of the internal K concentration in resealed red blood cell ghosts, where the Na-K pump is driven in reverse by the downhill efflux of K and influx of Na…

But does it happen physiologically, or for cells in culture?

@becko Oh sorry, I didn't see that part of your question. In the paper they drove the reaction with a very high ADP/ATP ratio which I expect wouldn't be found in cells. Technically it is possible for this reverse reaction to occur physiologically, but the ATPase activity will be dominant.

So it seems that the answer is No. I'll wait a bit more before accepting your answer. Thanks again.


text:
Population where most of the newborns die soon?
Is there an ecological name to describe a population of organisms where most of the newborns die after birth without reproducing? The population as a whole keeps growing, however, because there are enough individuals that manage to reproduce.

Yes, we talk about r/K selection theory:

In ecology, r/K selection theory relates to the selection of combinations of traits in an organism that trade off between quantity and quality of offspring. The focus upon either increased quantity of offspring at the expense of individual parental investment of r-strategists, or reduced quantity of offspring with a corresponding increased parental investment of K-strategists, varies widely, seemingly to promote success in particular environments.

The type of species you describe are the r type.
Please note the following potential confusions:
A species can vary its strategy through time and space
Species can change from K to r (and vice-versa) depending on the environment and number of individuals. Consider humans as an example.
The expression r/K selection theory can be misleading
The term "selection" in "r/K selection theory" can be a bit misleading as it refers more to a demographic reality (which has come to be due to selection pressures) but not to the selection process behind it.
Alternative meaning of 'r/K selection theory'
The terms r and K are sometimes used to mean whether a species has reached carrying capacity (K) or whether they are growing in number (r) which is not exactly the same as the interpretation of whether there is much parental investment in the species presented in the wikipedia article.
This second interpretation is actually closer to the origin of the terms r and K. The most common (and one of the simplest) equation of population growth through time is the logistic equation (see here for an easy explanation and also wiki > Population ecology )
$$\frac{dN}{dt} = rN \left( 1 - \frac{K}{N}\right) $$

, where $N$ is the population size, $t$ is time in generation, $r$ is the maximal growth rate and $K$ is the carrying capacity. On the graph above, $r$ represent the maximal slope (that is the maximal growth rate).
r selected species are those that have a growth rate as indicated at the center of the graph. K selected species are those that have a growth rate of 1 (no increase in $N$) as the ones that are at carrying capacity $K$.

Thanks, very good answer. That's the term I was looking for. On the other hand, is there a synonymous name for it, that is just a word, in use, instead of this name that involves an $r$ from an equation?

You can just talk about an r-selected (or r-strategy) species. I don't think there is another term. If it is not intuitive enough when you talk to lay people, you can talk about species that favour quantity over quality of offspring.

Remi is right the closest you get to a term is r-strategist or K-strategist. Also keep in mind these are ends of spectrum not discrete categories.

@becko They are also said to have a fast life history as described in life history theory which is a theory built upon r/K-selection theory.

@Eff Thanks. Can you point to some references?

@becko I would simply start with the wikipedia article on life history theory. I may be able to find some good references later (I'm not with my computer at the moment). Remember that both r/K-selection and Life history theory are concerned with many traits other than number of surviving offspring. In fact, a whole suite of life history traits are correlated: maturation time, lifespan, number of offspring, size of offspring, amount of parental investment, etc. Fast life history is roughly equal to r-selected, and slow is K-selected.


text:
Generate full dimer from monomer with C2 symmetry?
I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: http://www.rcsb.org/pdb/explore/explore.do?structureId=2PJY.
How can I generate the PDB for the full dimer?
I am comfortable with PyMol, so an answer using PyMol is preferred.

Use SymmDock. It is very easy.

This article will probably be informative for you:
Looking at Structures: Introduction to Biological Assemblies and the PDB Archive
The PDB file contains the asymmetric unit found in a particular crystallographic study. The biological assembly is the quaternary structure known or predicted to be found in living systems. For many proteins (but not 2PJY), the biological assembly can be downloaded directly from RCSB. For other proteins, the PDB file may contain the transformation matrix used to create the biological assembly from the asymmetric unit. If you look at the file in a text editor, this information is found under remark 350:
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 8880 ANGSTROM**2
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000

Note that the actual biological assembly of 2PJY is a hexamer and the asymmetric unit in the PDB file is a trimer. You can see that the first matrix is identity (ie keeps the original asymmetric unit). The second matrix transforms the assymmetric unit to create the full hexamer. This matrix is both author and PISA predicted. You can actually go to the PISA website and have it predict the biological assembly of a particular PDB file, and it will spit out the coordinates of the hexamer (and other predicted assemblies) which you can then load into PyMOL.
PDB files may also contain a CRYST1 record, which gives information about the unit cell and space group of the crystal. Via the symexp command, PyMOL can use this information to recreate neighboring asymmetric units. By limiting the cut-off distance (and this requires trial-and-error), the biological assembly can be recreated. This script, for example, will generate the hexamer:
fetch 2PJY
symexp 2PJY, 2PJY, 2PJY, 2.5
hide everything
show cartoon

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


text:
Density of cells in human tissues?
Where can I find values, or estimates, of the density of cells in human tissues? Maybe an overall estimate, or distinct values for distinct tissues? Or maybe not human, but mammal tissues (which should be similar)?

Good question. I would like to see such estimates as well.

for a comprehensive overview of values, and their sources, please see: http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=density+of+cells&org=

Well, Sender, Fuchs, and Milo wrote a paper to discuss the total number of cells in the body and compare it to the number of bacteria in the body (http://dx.doi.org/10.1101/036103). Their discussion is quite in-depth.
There are a number of ways to calculate it, but an interesting one involved calculating mammalian cell density by a study measuring the DNA obtained from a 25 g mouse. Researchers were able to determine there were 3*109 cells in the mouse (Baserga, 1985). From this study we can simply divide to find a value for "typical" mammalian cell density--1.2*108 cells/g.
If you want to know the number of cells per mL, you'll need the density (g/mL) of the tissue you are measuring. As the comments have mentioned, this is typically around 1 g/mL and varies from person to person. There is a web page that has some tissue densities for various tissues.
Baserga, R. (1985). The Biology of Cell Reproduction (Harvard University Press).

This is close, but not complete. To get from here to cell density, I have to know the weight of a given volume of tissue.

@becko: My wife can drift afloat on water, I can't. I'd say that gives roundabout 1 g/cm^3 for human tissue on average. More for bones, less for fat. ;-)

@DevSolar I updated the answer to reflect your suggestions. Thanks!

The 'cleanest' data I am aware of is on studies using density gradient centrifugation.  In density gradient centrifugation, a preparation of cells is layered on top of a density gradient media which has higher density than water (water=1g/ml).  Centrifugation forces denser cells through the media whereas cells with equal or lower density remain above the solution.   Common values of gradients are 1.084g/ml, 1.077g/ml and 1.073g/ml but a useful overview of the technique can be found here. According to a manual for one density gradient product, Ficoll-Paque PREMIUM (search the GE website), GE Lifesciences says:

Ficoll-Paque PREMIUM 1.073 can be used when isolating lower density
human mononuclear cells, for example mesenchymal stromal/stem cells or
monocytes. The higher density lymphocytes and granulocytes will
sediment through Ficoll-Paque PREMIUM 1.073 to the bottom of the tube,
thereby enriching the lower density cells at the interface.
Ficoll-Paque PREMIUM
1.073 has been found superior to Ficoll-Paque PREMIUM for isolating mesenchymal stem cells from human bone marrow (56).
Ficoll-Paque PREMIUM 1,084 can be used for preparation of cell fractions including
higher density human mononuclear cells or for isolating lymphocytes
that form rosettes with autologous red blood cells (15). It can also
be used for separating blood cells from mice and rats, since the
lymphocytes in rodents have a slightly higher average density than
lymphocytes in humans (50, 51).

If you wanted to try and evaluate density of isolated cells within 'solid' tissues your results would require careful (often enzymatic) release of cells from their integral contact with the extracellular matrix and other cells.   I also presume you could try chunks of tissue.
Density gradient centrifugation can also be performed by layering proportions of gradient media of two densities, resulting in a continuous gradient and more nuanced separation.
TL;DR blood cells are slightly denser than water.

hi guys im new here and i was reading this and would add my own believs to this. and most wont follow this, but... Density is a meassure of complexity. Density equals energy + information. Based on our human build up its only logical our body density is close to that of water but with natural selection law of living things and the reproducing factor of non living things such as stars and galaxy's, i have come to conclude that the thing to understand behind it all is that there is that process, that something that drives energy or matter to change into something else, energy(or equal in matter) + information, that something is the next wheel in our understanding.

Hi and Welcome to Biology Stack exchange. Some of the information contained in this post requires additional references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted. Please also use correct grammar and divide the post into paragraphs. Thanks


text:
Where does the lactate produced by tumors go?
Tumors are known to burn glucose and secrete lactate (this is known as the Warburg effect).  Where does this lactate go?
Does it steadily accumulate in the neighborhood of the tumor? This doesn't seem likely. I mean, eventually an equilibrium concentration of lactate in the neighborhood of the tumor must be reached that is balanced by some process taking lactate away from the tumor. The nature of this lactate drain is what I am asking about.
Does it enter the circulation system and is degraded somewhere else in the body (as a part of the Cori cycle)?
Is it consumed by neighboring non-malignant cells?
A combination of all of the above?
Something else?

Most of the lactate produced by tumors probably enters the circulation and is taken up by other tissues (like the Cori cycle, correct). There are several studies like this one measuring glucose uptake and lactate release by tumors in vivo, and it is clear that a substantial amount of lactate is released into the veins draining the tumor site.
Oxidation of lactate by neighboring cells within tumors has been reported as well, but I don't know of any quantitative data on exactly how much lactate this process can consume. But it seems unlikely that this can remove a major fraction of lactate produced by glycolytic tumors, since glycolysis produces lactate at a much higher rate than respiration consumes it (per ATP generated).
It's also true that tumors can accumulate lactate. Some tumors are poorly perfused, with "disorganized" blood vessels and blood flow, and then waste products may not be cleared away efficiently.
So yes, all of the above :)  There are large differences between individual tumors in all these parameters, so there is no generally valid answer I think.

I guess I'm not expecting to find a general answer. But at least some references in the literature would be nice. The papers you point out are already useful.

"But it seems unlikely that this can remove a major fraction of lactate produced by glycolytic tumors, since glycolysis produces lactate at a much higher rate than respiration consumes it" Has this been measured/estimated?

@becko  I'm not aware of any quantitative data on how much lactate is re-oxidized in tumors.  But given that respiration yields 10--15 times more ATP than glycolysis for the same amount of carbon, it seems that a large population of purely oxidative cells would be needed re-oxidize all surplus lactate from glycolytic cancer cells.  And again, there is plenty of data showing that tumors generally produce lactate. (In some cases even causing life-threatening acidosis: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497494/  )


text:
What is an on-line measurement? What is an off-line measurement?
See it used here: http://en.wikipedia.org/wiki/Fed-batch. In the table giving the different strategies to control growth in a fed-batch culture, one finds, for example: "on-line measurement of glucose". What does it mean? Is there an off-line meassurement? What does it mean?

On-line means that's it's generally continuous, or constantly taking the measure, through a tube connecting the batch.
Offline is used for things that are taken out of the reactor, or removed from the process.
Thus it's "on" or "off" the system depending on whether it's contained within the normal piping/fludics of the system: "On" is in the system, "Off" is out of the system.

So in an on-line measurement, the sample used to make the measurement is returned to the culture?

@becko Normally what is not expended is returned, but often it's not really sequestered very much to begin with.  Think of a temp probe suspended in a tube of flowing liquid.  It can measure the temperature with very little "diversion" and would be an on-line measurement.


text:
Currency metabolites vs. current metabolites: What's the right term?
I have seen the two terms currency metabolite and current metabolite used interchangeably. Is there a consensus on which is the right term?

Currency refers to anything that is used in any circumstances, as a medium of exchange [1]. That's why ATP and NAD are considered as currency metabolites [2]. So currency metabolite can be used for any metabolite that has multiple uses in different reactions/pathways.
Current refers to something that is prevalent at the present time [3]. So current metabolite is used to refer a metabolite that is already available for a specific reaction/pathway and doesn't need to undergo supplementary transformations to fit for that specific reaction.
The same metabolite can be simultaneously a currency metabolite and a current metabolite for a specific situation.

References:

Wikipedia contributors, "Currency," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Currency&oldid=611672968 (accessed July 12, 2014).
Gerlee P, Lizana L, Sneppen K. Pathway identification by network pruning in the metabolic network of Escherichia coli. Bioinformatics. 2009 Dec 15;25(24):3282-8. doi: 10.1093/bioinformatics/btp575. PubMed PMID: 19808881.
The Free Dictionary by Farlex. http://www.thefreedictionary.com/current

I wonder if 'current metabolite' is not simply a mistake? The second usage does not sound idiomatic.


text:
Where does the carbon in new spring leaves of a deciduous tree come from?
When a leafless deciduous tree 'comes to life' in the spring and puts forth new leaves, where does the mass for these leaves come from? The tree has no leaves to make use of photosynthesis to get the carbon it needs to grow these leaves, so where does the carbon come from: has it been stored in the root system over winter just for this purpose? And if so, has enough been stored for the tree to produce most if not all of its new leaf growth for this season, or only enough to get a few leaves out that will 'take over' the task of providing carbon fixation (making sugars) via photosynthesis to grow the remaining new leaves?
It has been suggested in the comments that the new leaf buds were grown at the end of the previous season. It would seem to me that this strategy for new growth in the spring would be fraught with all sort of dangers from 'winter kill', so these buds would not remain viable come the next spring. So, are the sugars needed for new spring growth coming from the roots or last seasons leaf buds?

Possible duplicate: https://biology.stackexchange.com/questions/1041/how-does-a-plant-grow-before-photosynthesis-is-possible The first answer might be a bit unclear that it is not only talking about seedlings but everything written there applies to wintering trees as well. Though there still may be an additional question here to be answered as far as the precise storage mechanism.

@BryanKrause Thanks for the link. The first answer seems to say that the carbon for new growth comes from stored sugars. Was this sugar supply 'stored' in the plant's roots? Was it stored there to be ready for its new spring growth? How much mass are we talking about, i.e., enough to grow all new leaves for that season, or just enough to get a few leaves out that will take over through photosynthesis?

Leaf buds are usually prepared the preceding summer/autumn.

I think you could edit your question to add what you've learned and clarify what you'd still like to know. I'm not a plant guy so I'm uncertain if some of your questions are too broad across the diversity of deciduous trees. SE questions are supposed to be individual questions rather than multiple but think yours are probably related enough to be part of one question.

@user1136 Answers are not supposed to be posted in comments.

While I can't provide references to actual studies, simple observation suggests that it must be stored in the roots, at least in part.  That observation is the existence of maple syrup (and other tree syrups, such as birch: https://practicalselfreliance.com/trees-species-tap-syrup/ In the spring, before leaves start to grow, sugar-rich sap rises from the roots, and can be collected by tapping the tree.

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


text:
What is the total mass of leaves on an 'average' mid-latitude deciduous tree?
I know that this is a broad question as there are a very large number of different species of tree with all manner of profiles, height, leaf sizes, etc. My ultimate goal is to estimate the total mass of leaves that fall each autumn in both the Northern and Southern Hemispheres, separately. It seems appropriate to ask for a single tree to start with, hence this question. If there is a better way to get to the final 'ultimate' answer, feel free to post it.

You might have better luck asking how much leaf litter falls on a unit area of forested ground on average, I suspect that at least has estimates. Per tree will never give anything reliable due to the wide varieties and sizes of trees.

There's a big difference between the mass of the leaves on the tree, and the mass when they fall and dry out.  Anecdotally, I'd guesstimate that the leaves from my large maple tree that I rake up in fall (when they're quite dry) weigh a couple of kg or so - say maybe 5-20 kg if you count the ones that blow into the neighbors' yards.


text:
Is there a way to isolate bacteria and viruses without a centrifuge?
Is there a way to isolate bacteria and phages from soil samples if you do not have access to a centrifuge? The purpose for which we need to isolate bacteria is for basic phage hunting.

Filtration? https://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_6/b_fdi_33-34/36462.pdf

Would be helpful if we knew for what purpose you need to isolate them.

Thank you. Please see edit.

Filtration is the correct answer - the very first viruses were identified as being filtratable (using the technology at the time) agents that could pass through the filters when bacteria couldn't.
Basically for phage isolation from a mostly water sample you just need to get rid of the sediment and ideally any bacteria that might be there too. Sedimentation (i.e letting it sit, centrifuge to speed up, as in Johan Wikstrom's answer) works well, but the best non-centrifuge method is to let large particulate matter settle, then start with filter papers of different grades to remove particulate matter, fine sediments and then work up to 0.45 micrometre filters to remove bacteria.
Of course you also need suitable plates and liquid media with a suitable host bacterium. E. coli works well for many bacteriophages in the Lambda group, but many other species of bacteria have bacteriophages of their own.

Thank you to everyone!

In the seaphages discovery guide the protocol for direct isolation states:

Allow the sample to sit until particulate matter has mostly settled. This may take as few as 2 minutes or as many as 20 minutes. Alternatively, you can centrifuge these samples to hasten this process. To do this, balance the tubes and centrifuge at 2,000 x g for 10 minutes to pellet (i.e., force to the bottom of the tube) most of the soil.

So filtration is really doing most of the job in separating the phage from the bacteria. Centrifugation mostly just speeds up the process.


text:
Can two protein secondary structures "overlap" in the PDB?
I have a technical question regarding the syntax in Protein Data Bank files.  In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:
HELIX    4   4 MET A 255  ILE A  265  1                                  11

SHEET    2   B 2 ILE A 253  MET A 255 -1  N  ILE A 253   O  ILE A 248

Now, as I understand the documentation, this means there is an alpha helix starting from residue "MET A 255" to the residue "ILE A  265".  There is also a beta strand from "ILE A 253" to "MET A 255".  We see that the alpha helix and beta strand share the residue "MET A 255".
The documentation describes these as:

"Name of the initial residue."
"Name of the terminal residue of the helix."

The wording suggests that the "initial" residue is included, but I'm unsure of whether or not the "terminal" residue would be included.

Question:  Should I consider this residue as belonging to both the alpha helix and beta strand?  Or should I consider the "terminal" residue as not belonging to the secondary structure element?  (Or something else?)

ive seen records like this although it does not seem possible as alpha and beta have distinct ramachandran coordinates.  i'll try to look at the structure and post an answer/opinion. a quick way around this is to find the phi/psi values for the amino acids in question and make the call yourself.

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment.

Ambiguous secondary structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be useful for other proteins.
Default pymol assignment
In PyMol I used fetch 1ae9 and highlighted M at position 255 on the A chain in red. I can see why this isn't a satisfying representation: the beta sheet allocation is very short, and the residue in question is clearly the beginning of a helix.

DSS is more conservative
To run a more conservative secondary structure allocation run dss in pymol (watered down dssp). This reveals that the beta sheets were actually quite putative.

We can see why when we look at the stick model (below). There are only a few (2-4) residue pairs in proximity that would be available for hydrogen bonding, even assuming all 4 form H-bonds, calling this a bona fide beta sheet could be seen as a bit generous.

Dual assignment can be okay.
Looking at this example (1ae9), we see the potential for H-bonding with another putative beta sheet, as well as a backbone angle that starts to form a helix. It's a classic case of ambiguous dual assignment. @AlexanderDScouras draws a reasonable conclusion that both is okay and to directly answer the question: dual assignment is possible, and allowed. I would prefer to rule out beta sheets in this particular case, but on the condition that one highlights that there is plenty of hydrogen bonding in the hairpin loop.
So long as it's reasonable.
So long as you can reasonably justify the assignment it's probably okay. You can manually assign any residue and secondary structure.
# set residue 155 to be alpha-helical
alter 155/, ss='H'

# update the scene in PyMOL to reflect the changes.
rebuild

Evidence is always a good idea to support manual assignments. A quick and thorough way would be to run the sequence through a few secondary structure predictors, or use the genesilico metaserver to save yourself some hassle (you'll need an account) (this does feel like going back a step since you now have a structure, so exercise caution - if the sequence prediction doesn't look correct according to the structure, it's probably not). Another method as suggested by shigeta is running this through a Ramachandran plot (RAMPAGE is a favourite).

If it's very very unclear then discuss it thoroughly and clearly whenever this part of the protein is relevant. These secondary structure assignments have somewhat arbitrary cut-offs after-all, and when things get near the thresholds, it's important to approach the situation with clarity and specificity.

Ramachandran plot image source: By Dcrjsr - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=9105708

A most informative answer! But I'm still surprised PDB allows such overlapping secondary structure markup. Perhaps their attitude is that all that is really important are the coordinates — it's up to the individual how they choose to visualize it.

@David Precisely. The terms α and β are there to help us quickly talk about broad biochemically similar parts of proteins. When the biochemistry get's stretched to the limits of the definition, the biochemical similarities become more vague and perhaps it's time to talk about the specific biochemistry in that protein again. There will be times when this residue example acts more like a helix, and other time when it is more like a sheet.

This is almost more a philosophical question about how you would like to define helices and sheets, which I would argue is not so well defined.  shigeta mentions that they have well defined ramachandran coordinates, but that's for the central residues. Terminal residues are far more flexible. The more traditional definition is along the lines of the DSSP algorithm, i.e. what is their main-chain hydrogen bonding pattern.
The DSSP algorithm is a bit conservative about assignments, often leaving out the first and last residues in  both sheets and helices. In deposited structures, you can compare author annotations to DSSP and STRIDE and see the authors will often assign longer runs than either. And I have certainly seen structures where a residue is annotated as both, especially when it lies at the junction between two secondary structure elements.
Looking at the structure, residues 254 and 255 are clearly hydrogen bonding into a beta-sheet on one side and an alpha helix on the other, so I see no reason they shouldn't be annotated into both.


text:
Are tuna fish present in the Baltic sea?
Yesterday my grandmother ate fresh tuna at a friend's party. She swears it was fresh and bought at a local fishmonger. The problem is, that we live in Gdańsk, by the south-eastern side of the Baltic sea and I have never heard of tuna in the Baltic. I told her that the fish couldn't have been local and therefore couldn't have been fresh but frozen and thawed. But the thought still bothers me, maybe tuna fish can reach the Baltic?
I did search a bit and found that tuna may be sometimes found in the Northern sea, so maybe it actually can travel so far east as to reach the Baltic? But the water in the Baltic is hardly saltwater (6-8‰), so would it be able to survive?

There's a newly established Atlantic Bluefin Tuna fishery in Norway, and some bluefin landings as far North as off Greenland, so it's not completely beyond the pale to think there might be some very few that stumble into the Baltic Sea, especially with climate change-- but definitely not enough for a commercial fishery.

A good answer except for the fact that Fish that is shipped all over the world is frozen and never fresh, whatever your local fish shops tells you. Most fish is already frozen on board

I agree with you, @RHA , but I know you can get fish shipped on (dry) ice. I work in a lab that does research on tuna, and we have gotten fresh specimens before from off-shore Hawaii. (We're in MA). -- But it certainly costs more $$$$. I can't imagine getting bluefin fresh.

The big commercial fish trawlers are at sea for weeks at least. Then they return to the harbour and only then.the fish is shipped. This means that fresh fish is weeks old. I wouldn't call that fresh. The fish caught at the last few days is often kept and sold seperately to restaurants etc.

@RHA fair enough! I got rid of that part.

Indeed tuna are present in the Baltic sea, and they can also grow in the Pacific and Indian oceans. A lot of the tuna we see in tuna cans in supermarkets comes from the stocks in the Indian ocean, but it is possible to have fresh tuna from the Baltic.
Sorry, I only found a French answer from a famous French news paper: http://sante.lefigaro.fr/mieux-etre/nutrition-aliments/thon/dou-vient-thon

I know some french, so it's not a big problem. The problem is, that Le Figaro is quite far in the Science News Cycle (http://www.phdcomics.com/comics/archive.php?comicid=1174#), so if it's the only link you can find, is very weak. I searched on ncbi and found nothing on tuna living in the Baltic sea, but I don't know how broad is their database - generally I used it when I was a biotechnology student plus for some medical research for my family - not much of ichtiology.

@jkadlubowska there are no landings of tuna in the Baltic. Your research is correct.


text:
Has a primate species ever weighed the average mass of a tonne (1000 kg)?
I ask because primates are mammals from the euarchontoglires superorder. Most mammals that weigh a tonne are laurasiatherians (except for elephantids and their ancestors) (elephantids are afrotherians). The only mammalian species from the euarchontoglires superorder that I know that weighted a tonne is Josephoartigasia.
So, I wonder why there was possibly never a primate species that weighted the average mass of a tonne.

Biggest one known was 500kg. the biggest bear is 750 kilos. primates are best adapted to forests, and forest animals tend to be smaller than high plain and grassland animals big apes have existed for 20,000 years, it's about one ice age.


text:
Can anatomically modern human siblings have three decades of age gap?
In my story titled La Maison Sapiens, there is a HUGE nuclear family composed of the father, the mother, and their seventeen biological children.
To be exact, the male human being and the female human being, who are the starting members of this nuclear family, were respectively 18 years and 10 months, and 19 years old and 6 months when their first biological child was born. When their second child was born, the father was 22 years and 3 months, and the mother was 22 years old and 11 months. When their third child was born, the father was 26 years old and 5 months, and the mother was 27 years old and 1 month. When their first pair of twins were born, the father was 29 years and 4 months old, and the mother was 30 years and 0 month old. When their second pair of twins were born, the father was 34 years and 1 month old, and the mother was 34 years and 10 months old. When their first set of triplets were born, the father was 39 years and 6 months old, and the mother was 40 years and 2 months old. When their second set of triplets were born, the father was 44 years and 9 months old, and the mother was 45 years and 5 months old. Finally, their last biological children, who are quadruplets, were born when the father was 48 years and 11 months old, and the mother was 49 years and 7 months old.
So, the question is: is it realistic for anatomically modern human siblings to have three decades of age gap?
Note: here is a link about multiple pregnancy : https://www.healthline.com/health/pregnancy/chances-of-having-twins#assisted-reproduction.

Depends what you mean by 'realistic'. Possible - sure, the constraining factor would be the age of the parents, the Mother in particular. Mother's can have children well into their 70s, so the scenario from this story seems totally plausible. Whether it's common, that's another question...

Cross-posted from worldbuilding.

Worth noting, this is a biology site. You should use biological terminology here rather than psychosocial neologisms.

I’m voting to close this question because it: 1) lacks evidence of the expected prior research, 2) is unclear (examples: unneeded detail about the exact timing of fictional births, "anatomically modern siblings" doesn't seem to be meaningful), and 3) is crossposted on a more appropriate site. Please take the [tour] and consult the [help] starting with [ask] for details of what is expected on this site.

49 - 19 = 30
So the 1st Child would be 30 when the last children would be born, as long as the parents stay healthy and the mother delivers the child in a natural way (No Surgical Procedure to deliver the child) and the Mother has not had Menopause (Menopause usually happens around 50 Years of age) the sibling age gap would be very possible, but lets take a look at how many children the mother had, if I am correct they had about 16 Children, many people in countries that have a considerably low life expectancy have many children, lets take a look at the world record for most children born from one mother...a person named Valentina Vassilyev, gave birth to 69 Children! Thats a lot of children, so giving birth to 16 children with a 30 age gap should be very possible and realistic as well.

If you downvote my answer please feel free to say why in the comments. (Somebody Downvoted)

I'm not the downvote, but you could improve this answer by providing some references to some of the topics (menarche and menopause would be good) and you could also provide data on the oldest natural and potentially the youngest mothers (IIRC, 5 years old, not sure how verifiable this is).


text:
How are atoms in benzopyridines and benzopurines numbered?
I am well-aware of the numbering system used for the traditional bases, as seen below.

My question is how are the atoms in the size-expanded bases seen in xDNA and xRNA numbered?

This is a question of chemical nomenclature and the principle source for this is the IUPAC (IUBMB in case of biological molecules; but not in this case). You can find all hetero-ring nomenclature references on the IUPAC web site:
http://www.acdlabs.com/iupac/nomenclature/
http://www.acdlabs.com/iupac/nomenclature/79/r79_702.htm
(I'm skipping the actual naming step)
Numbering is actually done according to
http://www.acdlabs.com/iupac/nomenclature/79/r79_72.htm
That means, if you take the skeleton without hetero atoms, you start

in a clockwise direction commencing with the carbon atom not engaged
  in ring-fusion in the most counter-clockwise position of the uppermost
  ring, or if there is a choice, of the uppermost ring farthest to the
  right, and omitting atoms common to two or more rings.

Now, if there are more than one possibility due to symmetry, you chose the numbering that gives the heteros the smallest possible numbers (this means your purines would be actually wrongly numbered if they weren't an exception---see the List of retained names).
So, we have finally in dxC and dxT the start at the lower nitrogen, going anti-clockwise (the other N at 3, methyl at 6, ribose at 8), and in dxA and dxG similarly the start at the lower right N, going anti-clockwise with other Ns at 3, 6, and 8, and ribose at 8, as well.


text:
Are there any strictly chloroplast/mitochondrion-residing ribozymes?
A simple question that had occurred to me. Considering the small doubt of transcribed genes in both organelles, I would doubt it, but are there any known ribozymes strictly found in either mitochondria or chloroplasts?
UPDATE: Actually, I just thought of rRNA acting as a peptidyl transferase in mitochondrial ribosomes... Any other ideas?

can't we consider ribosomes as colossal ribozymes ?

You've already mentioned rRNA. An interesting review (Tanner, 2006), outlines some more:

Group I Introns - self-splicing; "They are abundant in fungal and plant mitochondria..."
Group II Introns - some have been shown to self-splice; "...they are found in fungal and plant mitochondria, in chloroplasts of plants ... and especially in the chloroplasts of the protist Euglena gracilis."
RNase P - involved in tRNA processing, found in mitochondria

None of these are strictly found in mitochondria or chloroplasts. However, the paper goes on to describe VS RNA ribozyme:

The mitochondria of certain strains of Neurospora contain the Varkud plasmid (a retroplasmid), which encodes a reverse transcriptase, and a small, unrelated, RNA (VS RNA). The VS RNA is transcribed from circular or multimeric VS plasmid DNA by a mitochondrial RNA polymerase, and the resulting transcripts are subsequently site-specifically cleaved and ligated to form circular, 881 nucleotides long, RNA monomers. These monomers are then reverse transcribed and made double stranded to form the mature VS plasmid.
In vitro transcribed VS RNA precursors are cleaved and ligated by the RNA itself and this is presumed to occur in vivo as well. Of all the self-cleaving RNAs, the catalytic properties of VS RNA are the most poorly understood.

References

Tanner NK. 2006. Ribozymes: the characteristics and properties of catalytic RNAs. FEMS Microbiol Rev. 23(3):257-275.


text:
Average number of gene products in (a) eukaryote(s)
Due to alternative RNA splicing, it isn't uncommon to ultimately find multiple gene products expressed from one gene in eukaryotes. I'm looking for a reference value for the average number of final gene products expressed per gene for:

... a particular eukaryote (preferably humans).

This can't be too hard to do for one species like humans. I would expect the following formula to provide me with a rough answer. Is this correct?
(number of distinct proteins + numbers of distinct non-translated RNAs) / number of genes

... all eukaryotes as a whole.

This one is slightly more problematic.

Are you referring to protein products only? Also, many alternative splicing events do not affect the protein but the untranslated regions (UTRs).

I'm looking for protein products as well as non-translated RNAs.

One answer can be found in the UniProt FAQ:

What is the human complete proteome?
In 2008, a draft of the complete human proteome was released from
  UniProtKB/Swiss-Prot: the approximately 20,000 putative human
  protein-coding genes were represented by one UniProtKB/Swiss-Prot
  entry, tagged with the keyword 'Complete proteome'. This
  UniProtKB/Swiss-Prot complete H. sapiens proteome (manually reviewed)
  can be considered as complete in the sense that it contains one
  representative (canonical) sequence for each currently known human
  gene. Close to 40% of these 20'000 entries contain manually annotated
  alternative isoforms representing over 15'000 additional sequences ...

http://www.uniprot.org/faq/48
So, we have 20,000 genes and 35,000 products yielding about 1.75 gene products per gene. Alternatively, the 8,000 genes undergoing alternative splicing give about 2.88 proteins per gene.

I thought it was much higher than this! More in the region of 100's of thousands, because the majority of genes have at least 2 alternative isoforms, usually more... I'll try to find some evidence. If this is the case then I am surprised (also I'm not getting at you - I realize you have cited UniProt, arguably the authority on this!)

The number given here is very debatable... The sequences considered are only manually curated sequences - generally manual curation is way behind the actual data, so it is a bad idea to look at these numbers. For example, see ENSEMBL: http://useast.ensembl.org/Homo_sapiens/Info/StatsTable?redirect=mirror;source=www.ensembl.org , which mentions ~200,000 transcripts. And as I mention below, protein-coding genes are the easy part: ncRNA are much more difficult to count.

Like the number of genes dwindled in the years after 2000 from 100k to 20k, I expect such unconfirmed numbers to get more close to reality in some years, too.

@Bitwise, just wanted to point out that the number of transcripts is not necessarily correletaed to the number of different, mature, gene products. A lot of alternative splicing events only affect gene regulation (think spliced UTRs).

Well, there are a number of problems. First, the discovery of noncoding RNAs is relatively new and they are difficult to detect, so their number is unknown. In addition, it is unknown how many of them are functional. This has also made it very difficult to define what a gene is and thus made it difficult to count how many genes there are.
Protein coding genes, however, are much easier to deal with, and if you like you can enter any public protein database (at NCBI, for example) and easily query the number of distinct proteins.
Finally, the last problem is that with an organism like human, experimental methods are generally limited by sensitivity (might not detect proteins/RNA at very low concentrations) and the fact that you can't measure all possible cell types/conditions (many gene products will be cell type/condition specific).
Who said life is easy? Somehow things are always complicated in biology...


text:
Advantage of cup-like shape of blood cells, spores?
Mold spores sometimes have the same shape as platelets in blood. If I were designing a spore it would probably be spherical. Is there any advantage to this cup-like shape?
Maybe there is some advantage in flow properties in fluid or air? And maybe the physics of structures on that scale differ from that of everyday objects?
Thanks.

The functional implications of the biconcave shape of human red blood cells are not fully understood. Several hypotheses have been suggested as explanations, including bending energy (1) and effects on oxygen transport (2). More recently, it has been hypothesized that the shape is important for the flow properties of the blood cells in capillaries. Uzoigwe (3) states that

The deleterious nature of turbulent flow on the cardiovascular system
  suggests that the biconcave disc form has evolved out of a necessity
  to maximise laminar flow, minimise platelet scatter which in turn
  suppress atherogenic activity in the large vessels.(...) The biconcave
  profile of the discocyte means that much of the mass is distributed in
  the periphery. This increases the moment of inertia of the cell and
  subsequently renders the erythrocyte less prone to rotation during
  flow in the large vessels. Here it is suggest that this reduction in
  rotation promotes laminar flow and discourages platelet scattering by
  minimising the "Eddy currents" and it thus anti-atherogenic. A number
  of pathological mutations result in the red blood cell adopting a
  spherical shape as opposed to the biconcave disc profile. The sphere
  has a smaller moment of inertia when compared to the discocyte, as
  much of the mass is distributed round the centre. The spherocyte is
  hence much more prone to rotation during flow in the large vessels.

The advantages of various structures do depend on the scale of the system, as you say. For red blood cells, the size of capillaries and veins are of importance. The shape of red blood cells differ in animals that have blood transport systems with different structures than humans. Thus, the red blood cell shape is likely optimized with respect to movement in the human blood transport system, with oxygen diffusion also being a possible factor. To determine what advantages a specific shape of spores would give, you would need to consider the expected environment the spores would live in and their typical lifecycle.


text:
Species ID: What's this mushroom?
So this one is found in white mountain forest in New Hampshire, and I have strong suspicion it is actually just a boletus.

My question would be what's is the name of this fungus?

It actually looks very much like a boletus. It should have pores, which I just can't see on your picture. Is that your kitchen? Mind though that not all Boletus are edible...

There are different types of boletes. For a better answer we would need a picture of the underside and a spore print. Also, specific information about the environment of growth would help.


text:
What plant is this?
It was all along a fence in a downtown core in Ottawa, flowering in November.

I didn't get a better close-up of the flower itself, I had thought the leaves would be pretty important.

where was the picture taken (Down Under November is mid-summer) and a close up of the flower is in place

My bad - I'm new at naming species and what is needed to identify a plant. I'll add a close-up. It's actually in Ottawa, so November can be a tad nippy, hence my surprise.

@SQLiteNoob Can you add the information to the question? Information given in the comments may be missed. Also, it is good if the question is complete in itself.

@SQLiteNoob This is an example of an acceptable species ID question, while your others are not acceptable. This image has a clear single plant species visible (or otherwise pointed out), and you provided information about the location and time the photo was taken. In the future, you should provide these information if you want your plant to be more easily identified.

Given what I can guess of the flower organization and the type of leaves I see on the first photo, they could belong to the Ranunculaceae or Rosaceae family.
Edit
The example of Asteraceae provided by RHA seems more likely to be close to the correct answer, although it seems to me that the leaves don't look exactly the same as the one showed in Wikipedia for Tanacetum parthenium:
https://en.wikipedia.org/wiki/Tanacetum_parthenium#/media/File:Tanacetum_parthenium_Blatt.JPG

Really? It looks like a composite to me

True, it could also be an Asteraceae, but the texture of the yellow part, the low number and the almost-round shape of the white petal-like parts somehow make me prefer the other hypotheses.

thanks so much for the input. It was along a fence, so I was myself trying to determine if it is a spontaneous weed or deliberately planted - it's just that there was nothing else around it that looked to be on purpose

I disagree with @bli. I am pretty sure it is an Asteraceae, and I think I even know what species. It is Matricaria parthenium, also known as Chrysanthemun parthenium or Tanacetum parthenium. It is indigenous in Europe (Palearctic species) and it is also grown in gardens often. It is said to be a medicinal plant that works against fever and migraine. For more info see Wikipedia

This seems to be the correct answer.


text:
What kind of fruit is this?

Just spotted this fruit while walking to school. It's the size of a small coin.The taste is almost sour and tangy and somewhat sweet (I only tried one of them and very little of it).  I admit, I've never seen it before. Does anyone know what this is?
Update: Location is two or three blocks north of UC Berkeley (Berkley, CA, USA).

It's probably Arbutus unedo, strawberry tree. Native to Mediterranean region and some part of western Ireland.
Edit: I've just spot that you found it in California, so it's probably one of north american Arbutus species, eg. Arbutus menziesii.

Awesome! Thanks so much. Now I'll eat the rest of them without fearing dying.

@darksky I've never eaten this kind of fruits so please don't blame me nor the SE community if they appear not edible.

Yes it is Arbutus Unedo. We have several in the garden. In Spain it is called a Madroño. The fruits are edible, but they don't taste that great. They are not very sweet and can have a mushy texture. Use them to make jams.

Definitely not Arbutus menziesii. Very different fruit.


text:
Is it possible to biologically convert potential energy to chemical energy?
To lift an object x meters it is necessary to expend, at a minimum, an amount of energy corresponding to the increase in that objects potential energy associated with the increase in height. When putting the object down, returning it to the position it was moved from, its potential energy with respect to gravity returns to the original amount. However, this potential energy is not returned to the person who did the lifting. On the contrary, putting an object down gently requires additional energy to be expended to slow what would otherwise be a free fall.
Can any organism convert gravitational potential energy to chemical energy? Is it at all biologically feasible?

Yes of course: The ATP synthase :) But it is chemical potential, not gravitational potential.

I originally wrote "potential energy with respect to gravity" in my question, but simplified it to "potential gravity" as I thought it would be clear from the question. I edited it back in.


text:
What type of CCD system is required to take photos of luciferase
I'm working with luciferase and I want to be able to take a photo of it. The trouble is, I can see the luciferase glowing in all of its glory in front of me but no matter how hard I try, I can't take a photo of the luciferase with my DSLR (Nikon D80).
I'm curious if I'm missing a certain lens or if I should be shooting using a different lighting setup. I'm already exposing for 30". Perhaps longer?

You might want to look at photography.se too

That I have done http://photo.stackexchange.com/q/20976/8852

Seem to have got some quite thorough answers there :)

You are looking for a bioluminescence imaging device. These have very sensitive CCD camera and exposure times are around 5 minutes in complete darkness.

here's an example: http://www.berthold.com/ww/en/pub/bioanalytik/produkte/lb981.cfm


text:
How long does it take to stain cells?
I'm never going to run these type of experiments but I do need to have a good idea of their timescale. After I fix my cells, if I stained my cells with histology stains like DAPI, Fluorescein, and various labeled antibodies, how long do I have to wait before I can examine my cells with microscopy?


text:
What is special about the N3 buffer for Qiagen minipreps?
For those who use Qiagen miniprep columns, they may be aware that the P3 buffer is the acetic acid step to neutralize cell lysis. They may also be aware that the Qiagen P3 buffer cannot be interchanged with the proprietary N3 buffer. It is also known that the N3 buffer is particularly unique since it primes the miniprep columns for binding. I was wondering about that priming step and what chemically primes the columns. Would it be appropriate to use QBT buffer to prime the miniprep columns?

The Qiagen manual for the Miniprep Kit states that buffer N3 contains guanidine hydrochloride and acetic acid. The MSDS for buffer N3 gives a bit more information:

Guanidinium hydrochloride 25-50%
Acetic acid 10-25%
pH 4.3

Buffer P3 uses 3M potassium acetate, the potassium is usually important in plasmid preparations as potassium SDS is used to precipitate the proteins in solution.
This information might be enough to create a buffer that should work with the silica-gel columns.
I also found a patent about a method for isolating nucleic acids that states that silica particles can bind nucleic acids in the presence of chaotropic salts, so the guianidinium hydrochloride is probably the important difference in the N3 buffer.
The patent for this method from Qiagen goes into even more detail, according to this the buffer composition  is:

N3: 4.2M guanidinium hydrochloride, 0.9M potassium acetate, pH 4.8

N3 and P3 are different. N3 contain chaotropic agents. P3 does not.
Mainly there are two types of DNA purification kits on the market: silica membrane (glass fiber) based and DEAE anion exchange based. The silica membrane based method requires high concentration of chaotropic agents (salts that can change the water structure dramatically, GuHcl, GuSCN, NaI, are a few of them) present in the mixture before loading on to the spin column. DEAE based method, on the other hand, bind DNA based on the charge property on the DEAE resin which largely depends on the pH and ionic strength of the buffer. Chaotropic agents are not needed for DEAE based method.
In our lab we make our own kit using components and buffer recipe provided by Epoch Life Science for both mini prep and maxi prep. Their mini spin column and maxi DEAE column can be purchased without buffer. Their mini spin column also works perfectly with buffer from Qiagen and Lifetech. That's how we used up our leftover buffer from our old kits.


text:
How would one describe the R-factor in crystallography?
Yes, there is the wikipedia definition, but how would one explain this concept to a non structural biologist?

And what is the background of the person you would like to explain the R-factor concept to?

Crystallography requires the collection of many measurements (could be a few thousand to even millions depending on the size of the molecule and complexity of the crystal (technically speaking, the size of the crystal's unit cell is a major determining factor for the size of the data set).  I'm not going to assume this is a small molecule crystal like a salt or a large molecule like a protein.  its not necessary here.
I'll call this a set of intensity measurements, even though what is actually used is the square root of the intensities measured, called the structure factor.
The only way we really know that the molecular structure model is correct is that it generates as accurately as possible the intensities that were experimentally measured.
R, which I believe stands for residual, is a fractional difference between the measured intensities and what any proposed molecular model gives.
The residual is calculated as the absolute value of F(model)-F(measured).  This means that 0.0 is a perfect match while 1.0 is a perfectly awful fit that shows the model is perfectly awful.
In practice 0.60 is usually as bad as random model will give you (there's a statistical argument as to why it doesn't go higher).  Also the measurements are usually not perfect - they contain errors in measurements or artifacts from imperfect crystals or the detector, so an R value of < 0.20 (20%) is typically what you see in a reasonable paper.  I think its commonly less than 0.15 for most structures now in fact.


text:
How often can you reuse coomassie stain?
I usually heat to boil in the microwave, and stain for 12 minutes. How often can I reuse this buffer?

Since there's a lot of methanol in Coomassie stain, a significant amount would probably evaporate off each time you microwave it. Therefore, it'd be probably a good idea not to reuse it because (1) you're losing methanol, and (2) the concentration of everything else is thrown off.
Why do you boil the stain? I just pour mine at RT right on the gel and it works fine.

Doesn't heating it up make it stain faster?   Also, labs I've worked in have done both: reuse and not.  My impression is that you can reuse some of it, but it's best if mixed 50/50 with fresh stain.  But of course, this is all lab folklore.  I'd be curious to know if there has ever been a systematic study of whether/how much re-use affects results.

I've never boiled it and it always stained my gels fine in 10-15 minutes. (Plus it takes a few minutes to boil anyways... and sniffing those methanol vapours isn't exactly good for you...)

And after I've stained the gel, I just pour it back into the container. I've used the same bottle of stain for 2+ years. Works like a charm.


text:
What are the most important differences between HSP70 and HSP90?
Question originally asked on Quora. These proteins have many functional similarities, so why do cells need both to handle unfolded proteins?

For one, they have different molecular weights (HSP70 = 70kDa, HSP90 = 90kDa).

Often cells have multiple types of the same protein — this redundancy can have different effects for different requirements such as having proteins function under different physiological conditions, or providing specificity to a certain class of ligand proteins or so on.
But here, it seems like the two have some synergistic interaction, a tag team if you will.
 Wegele H, Müller L, Buchner J. 2004. Hsp70 and Hsp90 — a relay team for protein folding. Reviews of physiology, biochemistry and pharmacology 151: 1–44.
Unfortunately this article's full version can only be accessed if you're at a university or somewhere that has a subscription to some of the large research databases, but the abstract is free and it may provide more clarification.

Hsp70 and Hsp90 are not single proteins, but entire protein families. And those two protein families are not the only ones of their kind. There are different groups of heat shock proteins, Hsp70 and Hsp90 are molecular chaperones that assist in protein folding. There are five major families of molecular chaperones: Hsp100, Hsp90, Hsp70, Hsp60 and Hsps.
Hsp70 binds to nonnative, unstructured segments of proteins and helps folding them. Hsp90 doesn't bind to unfolded proteins, but to native-like proteins. Some substrates are also handed over to Hsp90 by Hsp70.
The whole area of chaperones and heat shock response is a very, very large and interesting field. I recommend to you to read the reviews below.

Vabulas, R. M., Raychaudhuri, S., Hayer-Hartl, M. & Hartl, F. U. Protein folding in the cytoplasm and the heat shock response. Cold Spring Harb Perspect Biol 2, (2010).
Richter, K., Haslbeck, M. & Buchner, J. The heat shock response: life on the verge of death. Mol. Cell 40, 253-266 (2010).


text:
What happens when seeds are refrigerated before planting?
My son is doing a science research project at school, and he's chosen to research what happens when seeds are refrigerated before planting.
I cannot provide any information in regards to background research (I couldn't find any), but I want to know if refrigerating seeds before planting them will have any effect at all on the seed (so that my son's experiment can be interesting).
Thanks.

What kind of seeds? Some seeds require cold in order to germinate (search for "cold stratification").

@kmm Sorry - silverbeet seeds, but it would be best if a generalised answer would work.

That might be a good experiment.
I know that before planting bulbs you want to put them in the refrigerator or even the freezer sometimes.
In fact this process of cold treating seeds has a name: Stratification.
To paraphrase: some seeds become inactivated at higher temperatures like lettuce and delphinium.  You can place the seeds in medium and put them in the fridge or freezer for a day or two.
You can see how this makes sense.  The seeds have adapted to start growing when they are freezing because the timing results in the plants breaking ground as early as possible when the temperature is warm enough in the spring.
A quick search doesn't seem to imply that silverbeet needs to be stratified before planting.  The result might be negative, but there is definitely some good expectation that it makes a difference to some plants.

That's the main idea, apparently - that the silverbeet seeds do not need stratification - so my son's testing the results.

i think that's awesome.  nice project really.  Every year I judge science fairs and that one sounds pretty good!


text:
Plant a whole fruit or only seeds?
I'm trying to figure out whether it is better for the plant to reproduce by planting its whole fruits with seeds inside them, or picking the seeds out and planting them without the fruit. In my case it's chili pepper, but I'm also interested in other plants that reproduce through fruits.
I heard that the whole fruit concept is about providing the seeds with some energy in form of their shell (the fruit) to give them a head start in terms of initial growth into a seedling. Is that true? Do all seeds benefit from growing from inside its fruit, or is it not very significant?

If your question is purely practical (which fruits are better to plant as seeds or whole), you might have better luck on gardening.SE. If you are interested in the biology side, then this is the place.

@kmm What if I'm interested in both?

That's fine. I think this question could be edited to get at the biology. And then ask which seeds to plant how over at gardening.

@kmm if you know how to make the question more about the biological aspects, please go ahead and edit. I only have some basic info on that, so I'm not sure I can make the question better myself.

I'd guess that, evolutionary, it would vary greatly depending on the plant. There are many strategies for seed dispersal: some rely on mammals eating your fruiting body, others on birds, others on blowing away in the air or floating in water, usually aided by what we might call the "fruit".

I'd argue that this relates to species-specific strategies of seed dispersal, so the answer depends on which species you're asking about. Here's an answer for chili peppers, which I think illustrates how complex and idiosyncratic these strategies can be.
As I mentioned in this answer, the seedsavers' manual Seed to Seed has great info on most plants, including the genus Capsicum (chili peppers). They say to clean the seeds from the peppers, and then dry them thoroughly but not in direct sun.
The Tewksbury lab has done someone amazing work on Capsicum evolution and seed dispersal from a biological standpoint. As published in Tewksbury and Nabhan 2001 (behind paywall, but described well in this Science in the News article) Capsicum fruits have evolved specifically to be eaten by birds, who do not have the receptors that make the fruits taste spicy to us and other mammals.
Essentially then, what you're trying to do when you hand-germinate seeds is to mimic the process of the fruit being eaten and passing through a bird gut. Tewksbury and Nabhan found that seeds from fruits eaten by birds actually germinated at a slightly higher rate than their control group of hand-processed seeds. In contrast, seeds eaten by mammals (who in normal settings totally avoid these spicy chilis) were destroyed and did not germinate.
Seed dispersal mediated by birds and other animals is one way that plants can be motile.

 Tewksbury JJJ, Nabhan GPG. 2001. Seed dispersal. Directed deterrence by capsaicin in chilies. Nature 412: 403–404.

Whealy K. 2012. Seed to Seed. Chelsea Green Publishing (p. 152)

I realize that I've come down hard on the "dispersal" side of the issue and that OP also mentions the possibility that fruits help in seed development. I'd love to read/upvote an answer that explores that aspect of the question.

Thanks, this is the kind of info I was looking for. Let's see if somebody else can answer the "seeds in fruit" part.

I'm not aware of any plants where the fruit provisions energy to the developing embryo. Generally this type of energy and nutrient storage would be done within the seed. Think of an avocado: both the large pit and the flesh contain a lot of energy, but flesh only serves to attract animals for dispersal, while the developing embryo only gets energy from the pit.
Generally, if you have a big fleshy fruit, it's because there was an adaptation to attract an animal to eat the fruit and disperse the seeds (plus extra breeding by humans to make our common edible fruits). Rather than the flesh of the fruit serving as a fertilizer, the scat associated with that dispersal may serve that purpose.
However, there is an astonishing array of fruits and fruit strategies, and many species do have their seeds dispersed along with their fruits. For example, all grass "seeds" are essentially tiny fruits, where the fruit part is reduced to some protective layers. Sunflower seeds are another example, where the hard shell will protect the seed until it can germinate. Many fruits aid in dispersal by the environment, such as wind or water, or by animals without being eaten, as in burrs.


text:
Are these spider eggs?
I was pulling weeds in my backyard in Southern California, when I saw a spider over a white area on the underside of one of the leaves. It's staying right near the white spot. Are those spider eggs? Also, what kind of spider is this?

Yes, those are definitely eggs.  And I believe that is a female grass spider (Genus: Agelenopsis).

Eggs are typically laid in late summer or fall and spiderlings emerge
the following spring....A female that has mated with a male can produce more
than one egg sac. For some species,  it’s common to see two sacs at a
time, side by side, attached to a surface (such as the underside of a
rock, piece of wood in a wood pile, or in a rolled up leaf, for
example). Each different species of Agelenopsis may create a slightly
different egg sac, but typically each one contains anywhere from 50 to
200 individual eggs. The mother spider will remain near her eggs,
dutifully guarding them, until she dies around the onset of winter.

This seems to fit the picture to a T.  I'm not 100% about the species, but I believe it is either A. aperta or A. oregonensis.
Edit:
As user Xan pointed out, this could likely be a lynx spider (Genus: Oxyopes; likely species: Oxyopes salticus - female).  This would explain the defined setae (bristles) on the legs.  To really decide, you would need to check the following characteristics:

Eye pattern: Lynx spider eyes form an octoganal pattern, while grass spider eyes form two, parallel, curved rows.
Spinnerets: You would have to search for spinnerets on a lynx spider, while grass spiders have two very prominent hind spinnerets that you can visibly see from above.

I originally thought those were spinnerets in picture 3, but upon closer inspection it looks like one of the hind legs folded underneath.

Yes, that does seem to be about right. But the pattern on the spider doesn't quite match those species.

Can't say the species, but it seems to be a lynx spider (genus Oxyopes)


text:
Mystery Plant ID
I found this odd rooty thing growing in one of the pots on my patio - any idea what it might be? I'm in Cape Town, South Africa, and it's the tail end of winter here.

Has this grown at all? If you have pictures of newer growth, it might help someone ID this plant...

This is possibly some species in the subfamily Scilloideae. (sometimes considered as separate family called Hyacinthaceae). This group of plants is a subfamily of bulbous plants within the family Asparagaceae.

Scilloideae are distributed mostly in Mediterranean climates, including South Africa

This subfamily contains many popular spring-flowering garden bulbs, so it would not be unlikely to see these growing up toward the very end of winter.
Drimiopsis maculata seems like a fair guess at the species (or closely related to the species in the question).

According to here, info pertaining to Drimiopsis maculata includes:

Distribution: widespread in eastern South Africa
Bulb description: Globose, fleshy, mostly exposed at the surface of the ground, about 2.5 cm in diameter and have large visible scales
Leaves: mottled, but typically lose color to become all green.

I'm hesitant to provide more info because I'm still not sure about this identification. Figured I'd throw it up to see if others could rabbit-hole their way to a better answer...

@AlwaysConfused right?! except for the mottled leaves.... However, I assume since the spots fade in most specimens, they could possibly be absent altogether in specific cultivars? I looked into other species in this genus (and similar ledebouria) but didn't find anything that looked as similar to the OP's pic...


text:
How important is dead wood to the ecology of a forest and how much dead wood should remain?
I have a local 'forest management group' in my area. One of the jobs they do is to thin out the forest by removing some of the trees. They then sell the wood for firewood.
I want to tell them to leave the dead wood in the forest, as it is part of the food chain.
Can anyone give me an estimate of how much energy dead wood provides for the food chain in a temperate forest, as a percentage of the overall energy generated by the forest?
Also how biodiverse is a forest with the dead wood left alone compared to one with the dead wood removed?

It's going to depend on your area.  From my observation, in much of the US west dead wood does not seem to form a major part of the food chain.  It is removed by fires.

@jamesqf I live in the UK. It is too wet here for forest fires.

my rspb woodsman left wood heaps of any size and height as animal nests.     depends on climate. they can favor ants hhogs mammals  parasite ichnumanae and uncommon beetles. a wild forest has much more detrital ecology biomass and insects.

Dead wood is indeed very important to the food chain, and to the ecology and biodiversity of a forest. Lots of biota depend on the presence of dead wood; many species of insects and fungi only live on dead wood. See for example this study of fungi in Danish Beech forests.
The amount of dead wood present depends, apart from management, on the type of forest, the climate (and hence altitude!) and the age of the forest. This study provides a preliminary estimate of the amount of dead wood in British forests and might be very interesting to you. This study gives a review of dead wood in European (incl UK) Beech forest reserves.
I hope this will help you in the right direction. If you want any more information, please let us know. And preferably include some more information on the specific forest (type of trees, location) that you are interested in.
EDIT:
I recently stumbled across this project,
 that resulted in a systematic review of interventions that affected the occurrence of dead wood and saproxylic species in boreal and temperate forests.


text:
What is this insect in this picture?
I recently found this insect  near our veranda wall. What insect is this ?
Is it poisonous?

As you can see, it has multiple legs fine as hair, but it is not like a common millipede or centipede.
I searched for this insect by reverse Google image search without result.
Location: Kolkata, India
Nature: fast-moving, aggressive.
Unlike earthworms, this insect loves basking in sunlight.

It looks like Scutigera coleoptrata. From Wikipedia: Bites are uncommon, and the forcipules of house centipedes are not strong enough to easily penetrate human skin. Bites are similar to a bee's sting, with its venom causing redness and mild to severe swelling.

I think it's Scutigera coleoptrata.

Source of the image.

About copy righted image. Also if an image is not your own work it's source needs to be mentioned.

While using copyrighted image on SE it is advisable (as in the link)  that the copy right allows sharing image as being done, if not it is right to replace it with one that allows.

@SanjuktaGhosh, I edited the post.


text:
When analyzing whether selection favors an allele that allocates indiscriminately, should the initial frequency of the allele be considered?
For example, Refardt, Bergmiller & Kummerli (Proceedings Royal Society-B, 2013; http://rspb.royalsocietypublishing.org/content/royprsb/280/1759/20123035.full.pdf)
model bacteria that have been infected and that commit suicide  in order to prevent the spreading infection to the rest of the population.  They do so even though relatedness is low, approaching zero.
Two questions:

In section 3c, they write

(A)ltruistic host suicide cannot evolve with $r=0$ because populations
  go extinct before invasion of the Abi trait is possible.  Thus, we
  predict marginal relatedness ($r < 0$) to be required for successful
  invasion.

I am assuming this is a typo and they mean $r>0$?
In a situation in which altruism is not directed toward any particular individual(s) but is rather allocated to the whole population, doesn't $r$ depend upon the frequency of the allele that is engaging in the altruism?  If it is a new mutation and there is no other allele in the population to receive the benefit, then r=0.  If the allele has gained fixation, $r=1$ and selection is much more likely to favor the altruism.

What is a way of modeling whether selection will favor fixation of a new mutation that allocates benefits to the population but not any particular individual (e.g., by committing suicide), given that the new mutation is not shared by (m)any other individuals and consequently, $r$ is initially very low?  I would think there is a way of determining the odds that genetic drift would lead the new mutation to develop a substantial enough frequency to increase the odds that the resources would benefit holders of the allele.  But I am unfamiliar.

I have not read the paper but here is my guess and a hint

Is it a typo?

Yes, I think so

In a situation in which altruism is not directed toward any particular individual(s) but is rather allocated to the whole population, doesn't r depend upon the frequency of the allele that is engaging in the altruism?

Yes

f it is a new mutation and there is no other allele in the population to receive the benefit, then r=0. If the allele has gained fixation, r=1 and selection is much more likely to favor the altruism.

If the allele that is causing altruism has reached fixation, then there is no more selection as there is no genetic variance in the population.

"If the allele that is causing altruism has reached fixation, then there is no more selection as there is no genetic variance in the population."
You're right.  I apologize.  That was a mistake.  But the question still stands:  If it's a new mutation, r=0.  If the allele has substantial frequency, r is closer to 1, and it is more likely to be selected.
The ways of modeling drift and selection that I have seen involve stable fitness.  Is there a way of modeling the effects of drift and selection when fitness is frequency dependent?