bougainvillea is a qualitative short day plant meaning that it needs long, uninterrupted nights to flower. Most flowring accours when it gets 8hrs of light (=16 hrs of night).
India is a huge country so you need to be more specific or tell us how many hours of light the plant gets. Note that if it's exposed to light from the house/street it may not flower as the light intensity for photoperiod is much smaller than that of photosynthesys.
Flowering requires a lot of energy, even if all conditions are met not enough sunlight might prevent flowering. bougainvillea loves sun, give it as much direct light as possible.
According to fao, Paclobutrazol shortens the time to flowering in long day conditions, meaning that GA might delay flowering. Another way to prevent GA synthesis is to stop watering the plant. Once the leaf start to fall give it water again.
Don't water too much:

these plants need full sun & well-drained soils. After establishing,
minimal watering is needed. Two or more irrigations with 3/4 – 1″ of
water per week would provide too much water for the bougainvillea to
bloom well.

What to do:

Give it more sun
Give it less water
Induce water stress to prevent GA synthesis
shorten the day, you may cover the plant with a dark cloth from the late afternoon to the morning


Insect feeding behaviour is generally triggered by one or more conditions which may include colour, shape, chemical traces or temperature.
Insects generally locate food based on some combination of olfactory, thermal and visual queues (colour and shape). If their minimum criteria are met to specified tolerance, they will attempt to feed on whatever is nearby using their usual feeding method.

When these conditions appear on the 'wrong' target, it attracts insects and triggers feeding attempts. Insects can be triggered to feed on atypical food sources if the relevant aspects of their environment match those of their normal feeding environments. For example, here is a report from a professor of entomology recollecting his observations of being bitten by pea aphids while handling plants, which he assumes is because of the scent on his hands.

We can exploit this in various ways for research. One is for artificial blood-feeding of insects: most systems, like the Hemotek membrane feeding system, warm blood to the body temperature of the host. They do not normally resemble a target host in any other way. Some blood-feeding insects have very specific requirements for temperature (for example they will only feed on blood if it is heated to the body temperature of birds; the same blood heated to mammalian body temperature will be ignored) but we do not need to make the target look or smell like the natural host. Other species may need olfactory cues, which can be provided by researchers rubbing the membranes on their forearms before placing them on the feeding system, or by breathing on cages as you add the food.

A second way we exploit this is for insect traps. Although not all traps work this way, some work by mimicking the host and attracting insects that are looking for a meal. This can be via olfactory/chemical mimicry (for example carbon dioxide baited traps - try Googling "CO2-baited traps") or visual. Different degrees of visual 'deception' may be needed; for instance to attract tsetse flies, colour is important but shape is not:

  [tsetse traps] often use electric blue cloth, since this color attracts the
  flies. Early traps mimicked the form of cattle but this seems
  unnecessary

(https://en.wikipedia.org/wiki/Tsetse_fly#Trapping)

The exact reason why blue is so attractive to tsetse is unclear:

  But, why are tsetse flies attracted to blue and black colors? What is
  the evolutionary advantage for them? It has been hypothesized that
  certain areas on humans, where tsetse like to bite, are a darker
  shade. Or, that the dark color simply identifies the object as not
  plants.

(https://www.acsh.org/news/2016/11/28/do-dark-colors-really-attract-tsetse-flies-10471)

If such behaviour increases the fitness of the insects, there is a selective pressure to change the cues used to identify situations where feeding behaviour is appropriate, which may result in consistent feeding shifts. We can infer by comparing insect taxonomy and feeding modes when shifts in diet have occurred. For instance, the moth family Calpinae has evolved piercing mouthparts to feed on fruit, but species in the genus Calyptra ('vampire moths') have adapted to feed on blood (which generally moths cannot access because their mouthparts cannot pierce the skin).


Genetic engineering for insulin production

In short, because the easiest way to get the protein coding sequence of the gene is to create cDNA based on the mRNA, and insulin mRNA is only expressed in pancreatic cells.

Insulin gene consists of two exons. That means, amplifying the genome will not give us a coding sequence -- two pieces of that sequence will be interrupted by a large, non-coding intron.

On the figure above, you see the translated (i.e., coding a protein) sequences represented as opaque boxes. They are linked by a slightly curving thin line -- this is a fragment of sequence that will get excised during mRNA maturation.

To get the coding sequence in a straightforward manner, one can create cDNA from mRNA using a reverse transcriptase. Processed mRNA does not contain the intron. And clearly, pancreas cells express the insulin gene mRNA at very high levels, enabling such a procedure, whereas it is practically not expressed by other tissues.

EDIT: Since I see these comments upvoted, I need to debunk them here:

There are introns and splicing in both, bacteria and archea. Both type I and type II introns are present in bacteria. See this review on bacterial type II introns.
Bacteria also have post-translational modifications, including glycosylation. Once thought to be rare, there is an increasing body of evidence that it plays a much more important role than previously thought. See a paper from a decade ago here.


Mamizuka et al. (2007) calculated acceleration data of the patellar reflex.

Their study measured the reflex generated in response to the tapping force applied to the patellar tendon with a customized tendon hammer. They measured using a tri-axial accelerometer placed at the ankle joint.

They found:

  the time delay (29.6+/-6.0 ms) and the acceleration time (150.8+/-19.5 ms) of the speed response were quite constant for all participants.

Mamizuka, N., Sakane, M., Kaneoka, K., Hori, N. and Ochiai, N., 2007. Kinematic quantitation of the patellar tendon reflex using a tri-axial accelerometer. Journal of Biomechanics, 40(9): 2107-2111


Are there any viruses that integrate their DNA into organellar DNA?

I'm only aware of one paper that claims to show regular viral integration into mitochondrial DNA, and even there they suggest it might be a host defense rather than a viral life cycle thing:

Interestingly, 69.4% (50/72) of HBV integration sites were observed in human mitochondrial DNA (mtDNA) (Supplementary Table 2). ... However, 32% of HBV integration sites in mtDNA (16/50) were in the displacement loop (D-loop) region, which is known as the major control site for mtDNA expression as it contains the origin of replication for the heavy DNA strand and the major promoters of transcription (Figure 1B). Of note, we repeatedly detected mtDNA integration events through the same micro-homology site in independent mice, indicating the hotspot for HBV integration in mtDNA, which is probably related to replication or transcription. ...
We found that HBV integrations were mediated through MMEJ, which is known as an alternative DNA double-strand break (DSB) repair system and reported as a principal mediator during mitochondrial DNA lesions. This suggests that early-phase HBV integration occurred in mtDNA. Damage in mtDNA is known to induce autophagy and was removed in C. elegans, therefore it is possible that integration of HBV DNA into mtDNA might be a defensive mechanism to protect the nucleus from HBV integration.

--Characterization of HBV integration patterns and timing in liver cancer and HBV-infected livers
I would like to see this replicated and extended before I spent too much time wondering about functions and mechanisms.


I think before discussing "pain", we'd probably have to discuss whether plants actually can "feel".

This is also down to how one wants to define this (hence "opinion based"), but I assume most people (?) would equal the lack of a brain/neurons with the lack of the capability to feel. And I presume so do you, as you show by using the tag "neuroscience".

In which case the answer to your question "Can plants feel pain?" is "no", regardless of whether plants react to damage through the release of chemicals or not, and whether one would like to classify this as "pain" or not.


Examples of points in evolution where two species stopped being interfertile?

Two obvious answers are genome doubling in plants, and Wolbachia-mediated infertility in insects. Both can cause one-generation speciation as measured by lack of interfertility.

  Polyploidy, which arises through complex genetic and ecological processes, is an important mode of plant speciation. This review provides an overview of recent advances in understanding why plant polyploid species are so ubiquitous and diverse. We consider how the modern framework for understanding genetic mechanisms of speciation could be used to study allopolyploid speciation that occurs through hybrid genome doubling, that is, whole genome doubling of interspecific F1 hybrids by the union of male and female unreduced gametes.

--Genetic Mechanisms of Allopolyploid Speciation Through Hybrid Genome Doubling: Novel Insights from Wheat (Triticum and Aegilops) Studies

  Bacteria of the genus Wolbachia are reproductive parasites of arthropods. They are cytoplasmically inherited (i.e. from mothers to daughters, like mitochondria) and their phenotypic effects on their hosts range from induction of parthenogenesis in certain hymenopteran groups, to feminization of genetic males in isopod crustaceans and to induction of cytoplasmic incompatibility in many insects  ... Three ways have been suggested4. The first suggestion is induction of parthenogenesis (assuming that the infection becomes fixed in the species). This process appears to occur in the hymenopteran Encarsia formosa7; males in this species can be obtained when mothers are treated with antibiotics, however, they are incapable of mating. The second way is offered by bidirectional incompatibility (Box 1). If a population is infected with two different strains of Wolbachia that are incompatible with each other, then bidirectional incompatibility will act as a post-zygotic reproductive barrier. A promising candidate is the species complex of the wasp genus Nasonia2, 3. The third way is offered by unidirectional incompatibility (Box 1). In this case, Wolbachia is acting as just one of the reproductive barriers enhancing speciation between two taxa.

--Wolbachia as a speciation agent

In general, though, the question seems to reflect a misunderstanding. Evolutionary theory doesn't suggest, let alone require, a sudden loss of interfertility during speciation. In many cases the lack of interfertility is incidental, and isn't selected; even in cases where it is selected, you expect to see the common gradual changes rather than abrupt transitions.


Why are two forward and reverse priming sites depicted here? what do they do?

It's just extra information that you don't need to understand the part above. You could use these primers for colony PCR or sequencing when you'd use the plasmid (after transforming to E.coli for example), but they're not absolutely required.

Compare it with this map for example. There are also some primer sites listed, but you don't actually need those primers for anything.


Role of the Hypothalmus in the control of Blood Sugar

Your question doesn’t make it clear whether you think that the pancreas must be under the control of the hypothalmus, or whether you are asking whether it has an influence on the pancreas in relation to the secretion of insulin and glucagon, which control the concentration of blood glucose.

First, it has been long known that secretion of insulin can be influenced by the concentration of glucose in isolated pancreatic islets in vitro, so it can not be true that the effects must involve the hypothalmus. This is implicit in most book or general information articles you might find on the web, but for an original reference a review by W.J. Malaisse in Diabetologia 9, 167–173 (1973) seems highly cited.

I know almost nothing about physiology, but on searching the web for the role of the hypothalmus in glucose homeostasis, found a most readable prize-winning postgraduate essay on the topic by Syed Hussein of Imperial College London. I trust that it is in order to append an edited extract of this:

  How does your brain control sugar?
  …altered delivery of glucose to specific parts of the hypothalamus can change insulin, glucagon and glucose levels [2]. …alterations in hormones and nutrient sensing by the brain in rodents leads to marked changes in glucose control. Evidence suggests that distinct regions of the brain have roles in controlling blood glucose in response to changes in glucose, insulin and fatty acids [ref]. These discrete brain nuclei regulate glucose output from the liver, insulin resistance, counter-regulatory responses to hypoglycaemia, glucose-stimulated insulin and glucagon release from the pancreas.
  How does your brain tell the pancreas and liver what to do?
  …blood glucose levels and hormones, such as insulin and glucagon, are influenced by the autonomic nervous system [ref]. This system …consists of two parts: a sympathetic nervous system which deals with ‘fight or flight’ responses such as stress and a parasympathetic nervous system which deals with ‘rest and digest’ and ‘feed and breed’ responses. This system arises in the brainstem of the brain and is under the control of the hypothalamus. Nerves from the autonomic nervous system innervate almost every organ in the body including the cells and blood vessels of the pancreas and liver. The ‘wandering’ vagal nerve, a key component of the parasympathetic nervous system, is shown to play an important role in this. This nerve is necessary for the brain to influence blood glucose. The autonomic nervous system can influence insulin release, glucagon release, liver glucose output and even the size and number of insulin producing cells in the pancreas [ref]. …Exactly how these nerve fibres regulate hormone release is still being slowly unravelled [ref].

The essay cites references which you may wish to follow up for further information.


How do exon tandem exon duplications occur in the genome?

There is a section in the Human Molecular Genetics textbook about how such repeats do occur. Like the commentor said, it is likely a result of recombination. If there are repeats flanking a gene or an exon there can be paring between sister chromatids / chromosomes, which can result in the duplication. See Figure 9.7 here http://www.ncbi.nlm.nih.gov/books/NBK7566/#A1095

As for how does it "know": It doesnt. Its not just the exon that is duplicated though. It is also the DNA before and after the exon, which contains cis-elements that splicing factors bind to, which results in the exon being spliced into the transcript.

Splicing is pretty complicated but if just 50 bp upstream and downstream of the exon was also duplicated, it would probably be enough to cause some splicing of the exon. U1 and U2 snRNP bind immediately at the exon-intron junction, and the polypyrimadine tract is about 30 bp or so upstream from the exon. U1 and U2 and the polypyrimadine tract are all vital to splicing. I dont know of any work that shows the minimum requirement for splicing but if you have those 3 you will probably splice the exon at least part of the time. So in sum, its probably not just the exon that is duplicated. It is probably the exon plus the cis elements involved in splicing.


Why does protein folding not depend on the order in which it is synthesized?

I suspect the author meant something a little different. It's not just that it doesn't matter if a protein is synthesized from N- or C-terminus it's also not important for the end result of folding that the synthesis is gradual at all.

When designing proteins de novo they model the folding on a computer. The gradual addition of amino acid residues to the protein is not part of these models, the computations are made on the entire sequence at once. Still, when the designed proteins are synthesized on ribosomes they fold correctly. So the fact that the proteins are built step by step shouldn't influence how they are folded very much. As long as there is a sufficiently low free energy state it will be achieved.

Also, N-ser-gly-ala-glu-pro-asp-C and N-asp-pro-glu-ala-gly-ser-C are not exactly the mirrored images of each other. They just have terminal amino and carboxyl groups swapped. I imagine this can influence folding a bit.


How pricey does the media need to be for a typical bacterial culture experiment?

It looks like Merck have different levels of quality control for their products. MQ 100 being the lowest up to MQ 600 being the highest. From what I can see the MQ200 product here has defined composition (of salt, tryptone and yeast extract in g/L) whereas the cheaper MQ100 product does not appear to have its composition ensured.
I am sure your cultures will grow in cheaper media but perhaps you would theoretically lose out on some replicability and perhaps if you were doing metabolically focussed experiments you would want to be certain of your media composition.
As for water, I have always used distilled water which is then autoclaved after you add the media with no problems.


Antibiotic resistance comes from selection pressure: any bacteria that are resistant will survive and replicate, so in the next generation of bacteria you will find more resistance.

Bacteria do not simply mutate to form beneficial alleles, the alleles or genes that confer drug resistance must already be in the population; by using antibiotics, however, you're killing off their competition by killing the bacteria that don't have the resistant allele(s)/gene(s).

It's very unlikely that one individual using one antibiotic for one illness will lead to detectable antibiotic resistance. However, antibiotics aren't used in just one individual: they are used repeatedly, in many individuals, often in multiple species, etc. It is this broad use of antibiotics over time that eventually "finds" strains that are antibiotic resistant. Once these strains with resistant alleles become more prevalent, it becomes more likely that they will be present in some quantity to be selected for in the future.


Deducing synaptic strength from electron micrographs?

First of all, definitions. By synaptic strength let's understand ability of post-synapse to elicit current flow/depolarization in response to neurotransmitter appearance in the synapse. How can NT appear? By release from pre-synapse or through uncaging (optical activation of "caged", or inactive NT).
Second, post-synapse contain all sort of stuff, but main sources of current/depolarization are ionotropic receptors of NTs, e.g. NMDA-R or AMPA-R. This molecules are not just floating ion membrane but attached to extensive scaffolding just below of the membrane. Scaffolding includes actin, and more importantly PSD95 (in case of excitatory synapses).

I work in vivo and don't do any EM. But in vivo issue of observing molecules is that you can't label sensitive proteins without disturbing function. Some things are just too delicate to be labeled with fusing GFP.

PSD95 has been used for in vivo labeling with GFP. One paper I will point you to, is this knock-in work in mice: Live Imaging of Endogenous PSD-95 Using ENABLED: A Conditional Strategy to Fluorescently Label Endogenous Proteins, J Neurosc. 2014

This is the figure that shows strong correlation between brightness of synapse (aka number of PSD95 molecules) and current that occurs in cell body when authors uncaged glutamate at different synapses.

Figure description

Now, how does that relates to your image? PSD stands for "post-synaptic density" protein, because in EM synapse is very dark. I don't know links, but I would assume some correlation between brightness of synapse in EM and its strength.


Study on MERS coronavirus and HCoV-229E: "rapidly lost most of the infectivity in fasted-state simulated gastric fluid (FaSSGF; pH 2.0)" but "survived FeSSGF" (fed state, which is less acidic). See Figure 3. IOW, on empty stomach, the gastric acid rapidly deactivate the MERS coronavirus and the 229E coronavirus, but if there is food in the stomach then the virus survives.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5687858/


The grain of corn is known as a caryopsis, which Merriam-Webster defines as:

  a small one-seeded dry indehiscent fruit (as of corn or wheat) in
  which the fruit and seed fuse in a single grain

This image by Encyclopedia Britannica shows that the corn seed, enclosed by the seed coat (testa) is then further surrounded by the pericarp, which consists of the layers of tissue around the fruit.

Therefore, the corn kernel can be described as any of the terms that you have mentioned.


How does a gene "know" what to change to?

Using your example, the gene doesn't know anything. Mutations cause some of the offspring of the red frog to turn green, some to turn blue, some to turn fluorescent yellow, and some stay red. Birds can't see the green ones as well as the others, so more green frogs survive and make more green frogs. The red frogs, the fluorescent yellow ones, the blue ones, mostly get eaten. After a few generations, almost all the frogs are green -- not because the gene knew anything, not because the mutations went in any direction, but because all the other changes were counterproductive and got eaten.

The gene doesn't know anything. It's just a bunch of chemicals that randomly react with cosmic rays, chance, whatever. Most of the changes are irrelevant or actively bad, and the frog that's carrying those particular chemicals doesn't survive. But sometimes the change benefits the frog carrying the particular chemicals and then the frog sends those chemicals down to its progeny.

Obviously this is hugely over-simplified. A short and simple intro to the basics of evolution is Understanding Evolution, by UC Berkeley.


Do sulfate reducing bacteria help during the formation of the mineral dolomite in low temperature environments?

The appropriate answer seems to be that bacteria help somewhat sometimes, maybe.

The evidence for this appears to be mixed, and appears to have been historically controversial.

One old-ish paper claims that bacteria (and more importantly, Archaea) are necessary at least under some conditions. Another somewhat later paper including some of the same authors claims to have found conditions for abiotic dolomite synthesis in the laboratory.

It appears that in terms of mechanisms, the relevant process may involve the proper state of magnesium ions, to which apparently microbes contribute via extracellular polysaccharides:

  Literature values for carboxyl group density are not available for all bacteria involved in dolomite formation, however Braissant et al. (2007) demonstrated disordered dolomite phases forming in the presence of the EPS of sulfate reducing bacteria with a carboxyl group density of ~10-3 moles g-1, similar to our values. We suggest that these carboxyl groups promote desolvation of the Mg ion, known to be a kinetic inhibitor in dolomite precipitation (Wright and Wacey, 2004), but are needed in a high density for nucleation to commence.

However, what process exactly is generating geological dolomites appears to be still a matter of debate, and also here, with some suggestive evidence in favor of microbes affecting that process.


How efficient is the sodium-potassium pump ?

I couldn’t find a value for this but I have calculated an efficiency of 84 %.

Caution: this seems too high to me, so I show below my calculation, fully dissected, in case anyone can spot an error.

First of all the parameters. Ion concentrations are:

internal Na+  = 12 mM;
external Na+ = 140 mM;
internal K+   = 140 mM;
external K+   = 5 mM;
and membrane potential = -60 mV (negative inside the cell)

I use these values for constants:

gas constant R = 2 cal mol-1 K-1

Faraday constant F= 23,062 cal mol-1 V-1

and I’ll assume that the temperature, T, is 37℃ = 310 K

The Na+/K+ pump uses 1 molecule of ATP to move 3 Na+ out of the cell and 2 K+ into the cell.

The efficiency of the pump is therefore energy required to move these ions/energy released by ATP hydrolysis.

How much energy is needed to move the ions? In each case there is a contribution from the fact that the ions are moved along a concentration gradient (the chemical component) and from the movement along a gradient of electrical potential (because of the membrane potential). In considering these components we have to think about whether energy needs to be used when the ions move, or whether it is released.

For the chemical component we can use

ΔG = RTln(ratio of concentration, inside and outside), where ln = natural logarithm

The sign of this ΔG will depend upon how the ratio is expressed (in/out or out/in) but the absolute value will be the same. So I calculate an absolute value and then deduce the sign of the free energy change.

For Na+ ΔG = modulus(2 x 310 x ln(12/140)) = 1,523 cal mol-1

Since Na+ is being moved up a concentration gradient, work must be done so the free energy change is positive.

Applying the same formula and logic for the movement of K+:

ΔG = 2,065 cal mol-1.

(This value is greater than that for Na+ because the concentration gradient is steeper.)

Next I calculate the electrical components using:

ΔG = zFμ, where z is the charge on the ion = 1 in both cases, and μ is the membrane potential (in volts).

So for both Na+ and K+ the absolute ΔG value is 1,383 cal mol-1.

However, in this case Na+ is moving out, against the membrane potential while K+  is moving in with the membrane potential. Thus the value of ΔG is positive for Na+ but negative for K+.

Now I combine the chemical and electrical components to get the net free energy change per mole of ions moved:

Na+ ΔG = 1,523 + 1,383 = 2,906 cal mol-1

K+ ΔG = 2,065 -1,383 = 682 cal mol-1

Now I consider how to combine these two values. Each cycle of the pump uses 1 ATP to move 3 Na+ and 2 K+. Therefore each mole of ATP moves 3 moles of Na+ and 2 moles of K+.

Energy from 1 mole ATP that is used to move ions = (3 x 2,906) + (2 x 682)

= 10,082 cal

= 10.1 kcal

How much energy is released from hydrolysis of 1 mol of ATP? Estimates vary but a commonly accepted value seems to be 12 kcal mol-1

Thus efficiency of the pump = 100*(10.1/12) = 84%.

I think the free energy of ATP hydrolysis depends on ATP concentration, pH, and the amount of Mg present. For a well-fed brain, this is around 14 kcal/mol (see Journal Of Physical Chemistry B, 114 (49), (2010). 16137-16146). This gives an efficiency of around 70%, still too high but better...


How can Taenia solium (tapeworm) lay 35,000 eggs per proglottid?

The eggs are very small compared to the proglottid.

According to this site:

  T. saginata can be up to 4 to 6 meters long and 12 mm broad; it has a pear-shaped head (scolex) with four suckers but no hooks or neck. It has a long flat body with several hundred segments (proglottids). Each segment is about 18 x 6 mm with a branched uterus (15-30 branches). The egg is 35 x 45 micrometers, roundish and yellow-brown. It has peripheral radial striations and contains an embryo with 3 hooklets.

  T. solium is slightly smaller than T. saginata. It has a globular scolex with four suckers and a circular row of hooks (rostellum) that gives it a solar appearance. There is a neck and it has a long flat body (0.1 meter in length). The proglottids are 5 x 10 mm with a 7-12 branch uterus. The eggs of T. solium and T.  saginata are indistinguishable.

I assume that the measurements given for the T. solium proglottid relate to the dimensions of your diagram, and since this is a tapeworm it is thinner than either of these values, so let's assume 2 mm to make the arithmetic easy.

volume of proglottid = 5 * 10 * 2 * 10-9 = 100 * 10-9 = 10-7 m3.

The egg approximates to a 40 µm sphere = 33,500 * 10-18 m3

So, volume of 35,000 eggs = 1.2 * 10-9 m3

So, volume occupied by eggs = (1.2 * 1010-9 * 100)/1010-7 % of proglottid = 1.2 %

So, not much of an accommodation is required for the volume of the eggs, even allowing for errors in this approximation (e.g. I neglected spherical packing which would add somewhat to the volume occupied by the packed eggs).


How long does it take for a cell to synthesize an enzyme?

In human cells it takes about 20 s to make a 20,000 dalton enzyme.

Assuming that the cells concerned are already making mRNA for the enzyme, there will be two main factors:

(1) The time taken to synthesize the polypeptide

(2) Any time taken to fold the protein

(If the enzyme is secreted from the cell there will also be the time taken for the protein to traverse the secretory pathway - perhaps you want to include this time - if so it could be 10's of minutes.)

Here I will focus on (1). What is the rate of polypeptide elongation?

For bacteria:

  Young & Bremer (1976) Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate Biochem. J. 160: 185-194

They quote values of:
17 s-1 for fast-growing cells
and 12 s-1 for slower-growing cells.

For yeast:

  Bonven & Gullov (1979) Peptide chain elongation rate and ribosomal activity in Saccharomyces cerevisiae as a function of the growth rate. Mol. Gen. Genet. 170: 225-230

minimal glucose 9.3 s-1
minimal acetate 5.5 s-1

In human cells:

  Ramabhadran & Thach (1981) Translational elongation rate changes in encephalomyocarditis virus-infected and interferon-treated cells. J. Virol. 39: 573-583

They measure a control value of 9.4 s-1 and quote (with citations) values of 9-10 s-1 in reticulocytes and CHO cells.

Let's use 9 s-1, and assume 110 daltons per amino acid

Then e.g. a 20.000 dalton enzyme (= 182 amino acids) requires 20 seconds.


What is the scientific name of this lovely orange black flying beetle?

This is a blister beetle from the species Mylabris pustulata.

Here is another photo for comparison:

Source: http://www.knowyourinsects.org/Coleoptera1.html

And, just for fun, the specimen in my link and yours, side by side:

It's worth mentioning that Mylabris has been confused with the Genus Hycleus, and the synonymy is complex.


This looks like some species of Phytolacca to me.

It's possibly Phytolacca americana, which is native to the US (in fact it's an enthusiastic 'volunteer' in my garden) but naturalized in Europe.

If you still have any in the ground, once they ripen, the berries are intensely purple and can be used as dye (or even eaten?)

Mark A. Nienaber & John W. Thieret. Phytolaccaceae.  In: Flora of North America Editorial Committee, eds.  1993+.  Flora of North America North of Mexico. New York and Oxford. (link goes to entry of P. americana)


Parasite vs predators

In terms of ecological interaction, a parasite is essentially a predator. As such, of course the Lotka-Volterra equations apply to host-parasites interactions.

Lotka-Volterra equations

However, Lotka-Volterra equations are very simple and very general. So much so, that in order to make good prediction about the real world, one most often have to build more advanced models.

Host-parasite interaction models

There exist a whole set of models specific to host-parasite interactions. You should have a look at the wikipedia entry for epidemic model which is a pretty good overview and introduction.

Most models of host-parasite interactions fall into the category of the SIR (or SIRS and other derivatives) model. The term SIR comes from Susceptible-Infected-Recovered. The whole point of the SIR models is to categorize host individuals on whether they are Susceptible, Infected of Recovered (hence the abbreviation SIR).

The SIR models are very much used by national and international centers for epidemiology and underly many of the decisions of vaccination and other methods of disease control.

Host-parasite co-evolution

Of course, the Lotka-Volterra model and the SIR models assume absence of evolution and only track changes in population size (within each category for the SIR models). There are models that also take into account that populations also evolve in response to the interaction and demographic events that the interactions are causing. Such models are much more complicated to keep track of and we often (I think) make use of technics such as separation of time scales. These models are essential though typically for to control viral epidemic but not only. But these models are outside the scope of your question.


What does the "Psi" in "Psi broth" stand for?

Psi is the Greek letter ψ.  Psi broth is sometimes referred to as ψ-broth.

Here's an example:

  L-Broth or ψ-broth can be used instead of SOC medium, but efficiency may
  be reduced.

  L-broth： 10 g Bacto tryptone, 5 g Bacto yeast extract, 5 g NaCl, pH to
  7.5 with 1 M NaOH, bring to a final volume of 1 L, and autoclave.
  ψ b-broth： 5 g Bacto yeast extract, 20 g Bacto tryptone, 5 g
  MaSO4･7H2O, pH to 7.5 with 1M KOH, bring to a final
  volume of 1 L and autoclave.


How do you knockout an E. coli gene without disrupting the rest of the gene cluster?

Let's say that we have gene A, followed by gene B so that they overlap with 100 bases. If you want to knock out only gene A, you can do the following:

PCR gene A and clone it into a vector
PCR gene B and clone it into another vector
Insert a antibiotic resistance marker at the overlapping region of gene A and B

now you don't have functional gene A and gene B

Transform your cells only with the vector that contains gene B

Now you have disrupted only gene A but you have a functional gene B.


Has any scientist elaborated on the "selfish neuron" hypothesis?

I would argue that the "selfish neurons" idea is a lot less interesting in terms of biological implications than the similarly-named "selfish gene" hypothesis.

It's basically proposing a bottom-up understanding of neuronal circuits where the developmental design feature is that neurons are individually optimizing their input-output relationships in some way. There isn't really any biological controversy about this suggestion.

Dennett (and probably others) goes a little crazy with it and turns it into a discussion of the agency of individual neurons, etc, but from a biological perspective I would argue that this is a pretty boring type of agency, at least in so far as using this definition pretty much all cells in a biological organism would be argued to have agency, because they are on some level "making decisions," but that's all biology is: organic systems of machines that respond in some way to their environment, and which are subject to selection pressures by which the systems of machines that reproduce best come to predominate.

Where this argument is useful, and Dennett uses this approach as well, is in contrasting biological systems with silicon computers. However, all of today's machine learning algorithms are really based on "selfish" nodes according to Dennett's description.

In summary, the selfish neuron hypothesis is just a philosophical approach to what we already know about biological neurons. It's meant as a way especially for people from a more algorithmic/computational background to think about how biological neural networks differ from algorithms structured from logical first principles. It doesn't make strong hypotheses for biology beyond what is already understood and agreed upon. I think this is probably why you don't see much more study about it.


As you guessed, tryptamine alkaloid biosynthesis is generally associated with herbivore deterrence in plants (see e.g. paper 1, paper 2, paper 3), as these compounds can be toxic to animals. I wasn't able to find a reference specifically related to DMT, as it is only one of a family of tryptamine derivatives. For example, the papers just linked to shows that expression of an enzyme catalyzing the creation of the tryptamine precursor of DMT is associated with lower herbivory by insects and nematodes. The second paper also shows that this seems to have little to do with plant morphogenesis via the auxin pathway, which was an alternate hypothesis for herbivory deterrence.

The papers also include a little speculation about the mechanism by which DMT inhibits herbivory on the animal side; it seems to come down again to animal toxicity and behavioral alteration.

So, as with other cases, likely the reason that plants express many secondary metabolic compounds is the same reason that humans use them, namely that they can have strong physiological effects on animals. But I wasn't able to find literature specifically about DMT in plants.

Hope that is helpful.

Update: found an entomology paper that goes into more detail about the effects of a variety of tryptamine derivatives on leaf-cutter ants. The compounds are toxic, but also there are some interesting insights about effects on insect behavior.

Update 2: Looking at question again, realized that I didn't address immune system response.

What's important to note is that plants don't have something homologous to animal immune systems, e.g. antibodies and so forth. They instead substitute various chemical responses, many of which are mediated by signaling factors such as jasmonate and salicylate, that have strong effects and sometimes e.g. kill off pieces of infected tissue (sort of a scorched-earth strategy). This part of plant biology is quite complex and bears further reading.

So in this sense, yeah, sure, tryptamines could be thought of as an immune system, in that their production facilitates resistance to their biotic environment. But that mechanism is completely different from any immunomodulatory effect of DMT or similar compounds in humans.


The cost of transcribing and translating a hypothetical average gene in yeast has been calculated as 551 activated phosphate bonds ~P per second (Wagner, 2005).

  The median length of a yeast RNA molecule is 1,474 nucleotides, and
  the median cost of precursor synthesis per nucleotide (derived from
  the base composition of yeast-coding regions) is 49.3 ∼P. With a
  median mRNA abundance of R = 1.2 mRNA molecules per cell and a median
  mRNA decay constant of dR = 5.6 × 10−4 s−1, the mRNA synthesis costs
  calculates as 49.3 × 1,474 × 1.2 × (5.6 × 10−4) = 48.8 ∼P per second
  and cell. This is a fraction 48.8/1.34 × 107 = 3.6 × 10−6 of the total
  RNA synthesis cost per second. The median length of a yeast protein is
  385 amino acids, with a combined biosynthesis and polymerization cost
  of 30.3 ∼P per amino acid. The median abundance is 2,460 protein
  molecules per cell. No currently available data allows a meaningful
  estimate of the median protein half-life, but a protein of an
  intermediate half-life (see below) of 10 h (decay constant dP = 1.92 ×
  10−5 s−1) yields an overall synthesis cost of 30.3 × 385 × 2,460 ×
  (1.92 × 10−5) = 551 ∼P s−1.

For your question about a single gene, the cost would be 49.3 * 1474 ~P for the mRNA and 30.3 * 385 ~P for the translation, which would result in around 84 thousand ~P. This is probably a very misleading statistic as you can transcribe multiple proteins from a single mRNA.

How the cost of mRNA synthesis and translation are calculated is described in detail in the paper. A large part of the cost comes from the synthesis of the basic building blocks, the nucleotides and the amino acids.

Wagner, A. Energy Constraints on the Evolution of Gene Expression. Mol Biol Evol 22, 1365-1374 (2005).


In replication, both the chromosomal halves (which are simultaneously threaded through the replication complex) have a lagging and a leading strand. A part of the segment will be replicated as leading and a part as lagging.


The hippocampus helps to solidify the pattern of connections that form a memory but the memory itself depends on the solidification of connections between the individual brain cells".

This refers to the phenomenon called Long Term Potentiation which regulates synaptic strength between neurons. Certain patterns of firing (high frequency) causes the post synaptic neuron to strengthen the synapses. One way of doing that is by increasing the number of receptors (Usually NMDA receptors). Due to this, the response would be stronger in the next firing event. You can imagine its effects- more number of times you read a passage better will you remember it.

Hippocampus is involved in this process (it is one region where a lot of synaptic dynamics happens) but consolidation and long term storage of memories is handled by the cortex. Essentially what happens when a memory is formed is strengthening of synapses.


The Next-Gen sequencers cannot sequence a very long stretch of DNA with good reliability (~150 for the recent model- HiSeq2000; even less for older models such as GA (40), GA-II (70), GA-IIx (90)). For increasing the confidence in a certain hit, it was sequenced from both the ends.
For example, if you have selected 500bp DNA fragment, then after ligating adapters to both the ends, it is sequenced from both the direction up to 150bp. This would leave an unsequenced "insert" region of 200bp. (In the example image below, they have sequenced up to 40bp [case of old GA] )

During assembly you stitch together the fragments of DNA to find out the larger DNA from where the fragments arise. In case of RNAseq, these arise from a transcript, and your assembly should give you the complete transcript (mRNA or ncRNA etc). There are two basic types of assembly: reference guided assembly and de-novo assembly. In the former you use a sequence such as the genome as a reference to assemble the transcripts. If such a reference is not available then you have to go for de-novo assembly.

The assembly algorithms use several parameters and since these are computer algorithms and not some kind of magic, their output depends to an extent on the different parameters.

In case of paired end data there are some parameters that are important. Most important is the size of the insert. In case of a 500bp fragment, you'll end up with an unsequenced region of 200bp. This is not much of a problem with reference guided assembly because you can figure out the sequence of the insert based on where the sequenced region align to the reference. The average insert length is important to remove discordant reads (aligning too far apart in the reference). In case of de-novo assembly, the insert will remain unsequenced even if you know that the final transcript looks something like:

frag1-frag6-frag3-frag9-frag4

So, to get the sequence of the assembly, you need to sequence the insert regions. This is not a problem if you at least know the order of fragments in the assembly. However you should know the insert size to get the assembly size correct and as skyminge said, in scaffolding. Obtaining this insert length is not that difficult (You need not provide it as a parameter. Most algorithms can calculate it automatically).

Another parameter in de-novo assembly is k-mer length (the sequence reads are broken down into k-mers for better assembly). I cannot explain the algorithm of assembly here in detail. You can check the manuals/papers of common assembly algorithms like Velvet, SOAPdenovo, Euler [de novo]; cufflinks [reference based]

I have mentioned transcriptome sequencing here but the principles are same for genome sequencing too.

Back to your main question:
Why is assembling paired end illumina without any input parameters an important problem?

Because it is less effort; but tweaking may be difficult. I won't consider it as an important problem. There are other important algorithmic optimizations that are required with de-novo assembly.


Humans can, to some extent, be scaled: While most humans are two meters tall; the human body essentially works throughout the entire range from around a meter to around two and a half meters, although you tend to run into problems at the extremes.

However, outside of that range you run into the tyranny of the square-cube law:

As you scale a creature (or, in fact, anything), it's mass increases proportionally to the cube of the scale, while its surface area increases proportionally to the square of the scale.

This means that as you scale humans down, their mass, and hence their ability to generate heat would drop faster than their skin area, and hence their ability to dissipate heat; meaning that if unaltered, smaller humans would rapidly run into problems of freezing to death.

(Small animals typically solve this through a number of methods: Higher metabolic rates, rounder bodies, and more fur. Small humans, i.e. babies also suffer under this, and solve it by having what is typically referred to as "baby fat", a blubber that, among other things, aids thermoregulation.)

Similarly, as the human body is scaled up, the opposite problem arises: The body becomes unable to dissipate heat quickly enough. Larger animals solve this problems with giant organs specifically suited to radiate heat, such as elephant ears; or through submersion in water, as seen is cetaceans and hippopotamuses; or simply through living in cold climates, such as the polar bear. (All of this is typically augmented by lower metabolic rates.)

Heat economy isn't the only problem with size, however:

Especially when scaling up, the strength of various structures in the body become problematic. Unusually (yet not even freakishly) tall humans generally have some manner of bone problems, and also often have problems with too small hearts, leading to low blood pressure, or too big ones, leading to heart failure.

If the change was gradual enough, with sufficient adaptation, this wouldn't necessarily be a problem. After all, giraffes and elephants get on perfectly well; but a pump-valve heart such as we have cannot be scaled up indefinitely.

With a continuous-flow heart, this limit could probably be stretched, but how that would even begin to work biologically I have no idea.

Further problems with very large humans include getting enough air flow through the lungs, the enormous chore it would be to stand up or sit down, and of course, just getting enough food to drive the enormous body.

The long and short of it is: Anything less than about half a meter would probably leave us freezing to death; and anything more than two and a half meters is quite frankly a stretch (if you'll pardon the pun).

(There are people alive now that are more than two and a half meters tall, but they are not generally speaking in good health, although some do get on.)

Of course, all of this is predicated on the specific gravitational and atmospheric conditions on Earth.

On another planet with a greater or lesser gravity, a different proportion of oxygen in the air, or just a denser atmosphere; many of these limits and limitations would be quite different indeed. (Which is why whales, living in such an alien world as the sea, can be an order of magnitude bigger than any animal that lives on land.)


Are there people cured of HIV by means of HAART?

This very recent (and freely available) review pretty much sums the problem up in the introduction:

http://dx.doi.org/10.1038/clpt.2012.202 (Barton et al., 2013: Prospects for Treatment of Latent HIV)

And here's an update more specifically on the problems with actually curing an individual of HIV infection, if you have access: http://dx.doi.org/10.1016/S0140-6736(13)60104-X (Katlama et al., 2013: Barriers to a cure for HIV: new ways to target and eradicate HIV-1 reservoirs)

Essentially, current antiretroviral therapy (ART) is able to nearly fully suppress active HIV, practically restoring the individual to a healthy status, including the prevention of transmission from them. However, the therapy needs full adherence (missing a dose can already cause viral loads to rise) and is lifelong. The reason for this is because HIV integrates into the genome of host CD4+ T cells, of which there are latent populations in places difficult to reach with therapeutics such as peripheral lymph nodes.

Apparently, some rare individuals actually achieve a "functional cure", i.e. the body is able to suppress viral replication for a given period of time (5 years) without ART. But these patients "are characterised by a favourable HLA profile and potent HIV-specific CD8 T-cell responses that are associated with a low viral DNA reservoir" (Katlama et al). They also mention another group of five patients who did not seem to have a favourable genetic profile and were still able to control HIV following cessation of ART for several years (http://dx.doi.org/10.1097/QAD.0b013e32833b61ba Hocqueloux, 2010: Long-term immunovirologic control following antiretroviral therapy interruption in patients treated at the time of primary HIV-1 infection). So it seems there are plenty reports of people who are able to remain free of detectable viral loads and maintain CD4+ T cell counts for a long time after treatment, but it doesn't seem like any of them stay permanently virus-free.


What are the blue and white things on this Sunburst lichen?

The small blue creatures coould possibly be (oribatid) mites.
I have them under my the binocular when I study lichen pretty often.
Their asociation with lichen is well documented


What is the overall end result of proteins and enzymes binding together?

At a high level, points 1 to 3 are reasonably correct, but 4 is only a special case.

Say we're at end of point 3. You get a protein. Some proteins are enzymes (the majority of enzymes are proteins), others are not. Example of proteins that are not enzymes would be, for example, hemoglobin, which is "just" a (very high-tech) carrier.

Now, each enzyme catalyzes (at a very high level) one reaction, which may or may not involve other proteins:

Reactions without protein other than the enzyme: for example, the cleavage of sucrose into glucose and galactose (two small sugars) performed by an enzyme called sucrase. Such reactions can assemble, cut and modify small molecules or large organic molecules that are not proteins (for example, starch, which is a large polymer of sugar, or even DNA itself)
Reactions mediated by enzymes, that act on non-enzyme proteins: for example, your digestive enzymes can cut proteins from food into building blocks (amino acids) that your body can use to build its own proteins. Similarly, some proteins can ligate proteins together, or add things on them (the proteins on the surface of cells are commonly modified with small sugar chains that control their activity).
Enzymes that catalyze reactions that involve other enzymes: since enzymes are proteins, they can be the target of other enzymes. A very well described example is the cascade of enzymes called kinases. When a cell is stimulated by a hormone, a kinase gets activated by addition of a small phosphate group. Once it is activated, the kinase phosphorylates (i.e. it adds a phosphate group on) another type of kinase, which phosphorylates yet another type of kinase etc; that's a way to amplify small signals.

So the overall result of an enzymatic reaction, regardless of whether it acts on other proteins or not, is usually either

The conversion of a molecule into some other molecule (1 to 1)
The assembly of several molecules into a larger, new molecule (N to 1)
The separation of a large molecule into smaller fragments (1 to N)
The transfer of a fragment of molecule on another molecule (N to N)

Examples of these four types of processes when enzymes act on other proteins:

1 to 1: a "protein disulfide isomerase" can rearrange the topology of the so-called disulfide bridges, that connect cysteine amino acids together in the target protein. This allows a misfolded, non-functional protein to turn into a functional molecular machine.
2 to 1: a "ubiquitin ligase" can covalently attach small proteins (ubiquitin) to old, broken proteins and target them for recycling, thereby preventing the accumulation of dysfunctional proteins in the cell.
1 to 2: a "protease" can cut another protein into two smaller proteins
2 to 2: a "protein kinase" removes the phosphate from a small molecule called ATP, and sticks it on another protein


Can anyone identify this caterpillar / cocoon?

It's carpet beetle larvae.
It's a serious pest, right behind the bedbug. The larvae were found on an old mattress.

I found about 4 more afterwards.


The answer here lies in epidemiology and the pathogenic nature of the virus. Humans infected with Ebola have a range of recovery rates of 5-75%, meaning that most of those infected will not survive infection. Given the combination of preparedness factors at first recognizing a true outbreak in Ebola and viral load which had already been spread by the point healthcare workers have organized an efficient response, it is not surprising that some outbreaks are worse than others. I think attempting to correlate the virulence to the type, size with the extent of the viral spread is not pertinent, but rather, as you mentioned breaking "protocol" can have more deleterious effect than simply explaining it by a mutation.

That is not to say that this strain of Ebola is not different from those detected in other outbreaks--in fact it is likely to be quite different and accumulated several mutations.


What is the term for "technical extinction" of yet alive animals?

This is technically called Functional extinction. With no viable reproducing population the species will almost certainly become extinct. Note that humans could potentially mess with this through the use of reproductive technologies.


I'm just skimming through it now, but this 2011 review in Nature Reviews Cancer looks like it has everything you could possibly want to know about the BRCA1/BRCA2 pathway. If you don't have access to the journal, the first page of this Google search should have a PDF link to Researchgate down near the bottom, or you can try this direct link.

I apologize for the "link-only" answer, but there is a ton of info in the paper, and it would be rather difficult to summarize it in just a few paragraphs. This is a rather broad question, so perhaps you could read through the review and references, and if you still have specific questions about the pathways or interactions you can ask another question.


No, it cannot. Viruses infect cells, in order to use the cellular machinery to replicate themselves - viruses themselves do not possess such a machinery, so speaking of one virus infecting another is meaningless.
This does not mean that viruses do not interact: when two viruses co-infect the same cell, the progeny virions may contain parts of the genomes of both viruses. This is how genetic recombination occurs in HIV.
An even more famous example is gene reshuffling of influenza viruses, where an animal virus exchanges its genes with a human virus, producing a new human strain. In the popular culture some of these a famously named after animals whose virus contributed or animals where the reshuffling has occured (bird's flu, swine flu, etc.)
Update
It is worth mentioning the satellite viruses, which are viruses that lack the proteins necessary to catalize the replication and possibly even the genes coding for their capsid proteins (in which case they are more properly called satellite nucleic acids rather than satellite viruses). These viruses are dependent on a helper virus to carry the missing genes. This is not characterized as parasitism, but it is rather close.
Update 2
A special type of satellite viruses, called virophages, actually do exhibit characteristics of parasitism in respect to the helper virus:
Unlike satellite viruses, virophages have a parasitic
effect on their co-infecting virus. Virophages have been
observed to render a giant virus inactive and thereby
improve the condition of the host organism.


How is vitamin B12 stored in the body although it is water-soluble?

Vitamin B12 (cobalamin) is a cofactor required by the enzymes methionine synthase (MTR) and methylmalonyl-CoA mutase (MUT). These are the only known enzymes that use B12 in humans, and are abundant in the liver. Since it is a cofactor, B12 is not consumed by any reactions, and hence there is no need to store large amounts of B12 beyond that bound to MTR and MUT. (In contrast to major nutrients like glucose and fats, which are stored in large amounts.)

Early biochemical studies showed that B12 isolated from cells was bound to an unknown large protein complex, called the intracellular cobalamin binding protein (ICB). It was later found that ICB actually consisted two separate proteins, and that these were identical to MTR and MUT.

So B12 is "stored" by simply being attached to the enzymes that require it. But, as @jzx also pointed out, perhaps "storage" is not an accurate description --- cobalamin is an integral part of these enzymes; it is not present in excess, and not kept in some storage compartment from where it can be mobilized (like glycogen, for example).


Is there a Pharmacology Textbook that Satisfies the Conditions listed in the Body of this Question?

A title called Essentials of Medical Pharmacology fulfills these criteria and is quite popular in India.

Reference to the current edition:

Tripathi KD. Essentials of medical pharmacology. 8th ed. New Delhi: Jaypee. 2019; 1064 p.


How can a drink contain 1.8 kcal energy while 0 g fat/carbs/protein?

The list of ingredients on the can mentions "Zuckerkulör," which is caramel colour, which can have 2 kcal/g, according to one producer.

Next, there is "Citronensäure," which is citric acid, which can, as other organic acids, have 2-3 kcal/g, according to this source.

There is also taurine, which is an amino acid-like compound, so it could, like proteins, have 4 kcal/g, but is, according to Taurine Metabolism in Man (Journal of Nutrition), poorly metabolized and probably has less than 0.2 kcal/g.

It is sometimes allowed, at least by U.S. Food and Drug Administration, to round the amounts of macronutrients (carbs, proteins, fats) smaller than 0.5 g per serving to zero, which is what they obviously did in this case, but they decided to keep the summary of calorie values of all ingredients exact.

It is usually said that only 3 types of nutrients contain energy: carbohydrates, proteins and fats.

Digestible carbohydrates (sugars and starch) provide 4 kcal/g. Undigestible, but fermentable, carbohydrates, such as soluble dietary fiber, sugar alcohols or polyols (maltitol, mannitol, sorbitol, xylitol, isomalt) and organic acids (citric, acetic acid, etc.), can provide 2 kcal/g of energy in average. On the other hand, some carbohydrates (such as "Sucralose" from the ingredient list) are neither digestible nor fermentable, so they do not provide any calories.

The "fourth" nutrient that can provide energy (7 kcal/g) is alcohol (ethanol), but is not considered a nutrient by some authors.

According to Food Label Accuracy of Common Snack Foods
 article (Obesity, 2014), the calories on the food labels should represent usable calories (metabolizable energy):

  Of note, it is important to distinguish that food label calories
  actually represent metabolizable energy, which is total caloric
  content minus calories that are presumably not absorbed by the body
  and excreted as waste.


Do action potentials cause the neuron to heat up as well as its environment?

While it is possible that action potentials themselves result in waste heat, there are other processes within the neuron likely to contribute much more to energy lost as heat. The action potential itself uses energy that's been stored in chemical and electrical gradients that are the result of numerous sodium-potassium pumps which require the energy in ATP. There would be some loss of energy in the operation of these pumps.

But far more heat is likely generated by the mitochondria within the neurons. These are the structures that convert most of the energy in the breakdown products of carbohydrates and fats into the ATP the Na-K pumps require. Generous estimates put the efficiency of this production at roughly 50%. That means about half the energy from the food-stuffs used to create the ATP is lost as heat.


what is the principle behind Allele Frequency Net Database

Allele frequency is simply the frequency at which a specific allele is found in members of a population. Let's take the following example from the site you referenced:

The first column merely has the name of the allele, A*01. The second column is the population from which individuals were genotyped. Skipping ahead, the fifth column is the number of people genotyped from the population, 187 in this instance. Of those 187 people, 14.8% of them have at least one copy of the allele as stated in the third column. It's important to remember that each individual could potentially have two copies of the allele.

The fourth column gives the actual allele frequency, calculated by the number of A*01 alleles/number of total alleles (374, assuming no serious mutations). Of those 374 total alleles, 7.4% (0.074) of them are the A*01 allele, meaning 27-28 of the 187 total people had the allele. Since 14.8% of people had the allele, but the frequency of the allele was only 7.4%, we know that each person who has the allele only has one copy of it.


What is the common diet of food-related IBS patients? Besides most patients being lactose intolerant, what other intolerances do they face?

IBS stands for Irritable Bowel Syndrome. The IBS symptoms include belly pain, diarrhea, bloating and constipation. Different persons have an intolerance to different food items. You can know what's causing trouble in you by taking a test at http://intolerancelab.co.uk/intolerance-2.

The most common diets that you can prefer to get rid of IBS symptoms are:

High Fiber Diets can help prevent constipation.
For some people, high fiber diet is intolerant. They should switch to a low fiber diet.
You should prefer a gluten-free diet.
Have a low-fat diet and get rid of a number of health problems.

Some food items that can cause food intolerance are:

Dairy products
Soy products
Fructose
Wheat
Gluten


How were genes located before the development of bioinformatics?

The earliest genome maps were constructed from Escherichia coli by abusing conjugation of special Hfr-mutants. I'm assuming you are somewhat familiar with bacterial conjugation - the process of transferring genetic material between bacterial cells.

Usually, only mobile plasmids are transferred. They carry the necessary tra-genes for the construction of the sex-pilus, replication and transfer system. They also need the oriT-site (origin of transfer), at which transfer is initiated. A famous mobile plasmid is the F-plasmid.

Some mutant cells integrated the F-plasmid into their main chromosome via recombination. Thus, they are able to transfer their whole genome to a recipient cell. These strains are called Hfr-strains (high frequency of recombination) and they were used intensely in early genome mapping.

They discovered, that it takes roughly 100 minutes for a Hfr strain to transfer its entire genome to another cell. By interrupting conjugation (e.g. by vigorous shaking) the transfer was interruped and the genome could be divided into sections by transfer time (10min, 20min, 30min and so on).

The function of the genes (or genome sections) was revealed by mating Hfr strains with defective mutants. If the mutant was unable to grow on saccharose for example, several conjugation experiments with different mating times were conducted. When a mutant was able to grow on saccharose again after mating, the transfer time was checked. If the strain was able to grow again after 30 minutes of conjugation, but not after 20, they knew the genes necessary for saccharose growth lay in the 20 - 30 min region.

It took a painstaking amount of experiments with a wide range of mutants to construct the first map of E. coli genes, but it was achieved before even the nucleotide sequences were known.


Why do eggs lack an endoplasmic reticulum?

I could find no indication that eggs are lacking an endoplasmic reticulum. On the contrary, I could find papers written on the ER in eggs of several species.

Mouse: The onset of activation responsiveness during maturation coincides with the formation of the cortical endoplasmic reticulum in oocytes of Xenopus laevis

Sea urchin: Structural changes of the endoplasmic reticulum of sea urchin eggs during fertilization

Human: The relationship between pregnancy outcome and smooth endoplasmic reticulum clusters in MII human oocytes

Frogs: The onset of activation responsiveness during maturation coincides with the formation of the cortical endoplasmic reticulum in oocytes of Xenopus laevis

However, as can be read in the sea urchin paper, the ER changes after fertilization:

  We interpret these observations to indicate that in the first few minutes after fertilization, the egg's ER is fragmented

For other species, I could only find evidence that the ER reorganizes after fertilization because of changed calcium signaling needs


Reason for variation in the site of onset of edema

We should first recall how plasma (intravascular) fluids moves to the extravascular space. It can be approximated by Starling equation. Briefly:

  The rate at which fluid is filtered across vascular endothelium (transendothelial filtration) is determined by the sum of two outward forces: capillary pressure ($P_c$) and interstitial protein osmotic pressure ($\pi _{i}$), and two absorptive forces: plasma protein osmotic pressure ($\pi _{p}$) and interstitial pressure ($P_i$).

See more: Starling equation

Primary edema localisation depends on the underlying pathophysiological mechanism that disturb the balance between aforementioned forces pushing fluid outside the vessels. Whether the Starling forces are alerted globally or locally, how long the edema develops etc.

Example from Harisson's Principles of Internal Medicine (I recommend the whole section regarding the edema):

  Edema due to an increase in capillary pressure may result from an elevation of venous pressure caused by obstruction to venous and/ or lymphatic drainage. An increase in capillary pressure may be generalized, as occurs in heart failure, or it may be localized to one extremity when venous pressure is elevated due to unilateral thrombophlebitis.

In Congestive Heart Failure edema usually appears in places, where intravascular hydrostatic pressure is the highest. When the individual walks it is typically seen as ankle swelling, when the individual lies down, it is lumbar region edema.
While there is a decrease in osmotic pressure (like in nephrotic syndrome), the fluid moves toward extracellular tissues of relatively "loose"  structure (so for example periorbital region).

What is important, in some medical condition (eg. renal failure) different mechanisms may coexists and change the clinical picture.


why a testosterone pill can't be effective?

As stated in the comments by Eliane B., testosterone can actually be administered orally when an undecanoate ester is attached. The reason regular testosterone cannot be adminstered orally is because it undergoes extensive first pass metabolism (oxidation of the 17b-hydroxyl group to a 17-keto group, catalyzed by 17b-hydroxysteroid dehydrogenase enzymes, which are active in the liver). The undecanoate ester makes the substance lipophilic enough to be transported by the lymphatic system to the circulation after absorption by the intestines. Without the ester it will first reach the liver via the portal vein, thus exposing it to first pass metabolism. Nevertheless, bioavailability of oral testosterone undecanoate is estimated to be less than 10% [1].

Besides that, there are also derivates of testosterone which have a high oral bioavailability. These derivates have an alpha-oriented alkyl group, usually methyl, at position C-17, which retards hepatic metabolism. However, this can lead to hepatotoxicity [2].

https://www.ncbi.nlm.nih.gov/pubmed/3770015 (note, the subjects were women, but in the literature it is assumed that similiar bioavailability is obtained in men)
https://www.ncbi.nlm.nih.gov/pubmed/27372877


You will find here on the UN World Population Prospects plenty of data and visualization about change in life expectancy over time (among other things). The data also include predictions until year 2100.

For example, here is the life expectancy data and predictions over time for men in Morocco.

and here it is for women in Norway (note that x-axis range differs between the two graphs)

I picked two random countries but the general trend is very consistent among countries.

  Is the human lifespan still expanding?

Yes, life expectancy is still increasing in pretty much all countries and is expected to keep increasing.


Base Substitution Probabilities Derivation

(1) There are two cases. For the first equation (6), the case $i \neq j,$

$$(1) \hspace{13mm} P_{ij}(dt) = u~dt ~\pi_j $$ if we have a transition from one base to another (for example G to C). In the case $i = j,$

$$(2)\hspace{10mm} P_{jj}(dt) = (1 - u~dt) + u~dt~\pi_j $$ holds for a same-base transition (G to G) or a non-transition (say, G and no change). Intuitively, we expect that, all things being equal, the probability of a base to same-base situation is slightly higher: it is the sum of probability that the base changes to itself plus the probability the base sits and does nothing in time $dt$ (with the same net result).

(2) Now we look at the equation(s) (7). Again there are two cases.

$$(1a) \hspace{10mm} P_{ij}(t) = (1 - e^{-ut})\pi_j $$

For case 2 (base to same base transition, $i = j$):

$$(2a)\hspace{13mm} P_{jj}(t) = e^{-ut} + (1 - e^{-ut})\pi_j. $$

(3) The author uses  $P(dt),$ $P$ at a very small (infinitesimal) quantity $dt.$ He tells us the leap from (1) to (1a) follows "almost immediately" when we see that $e^{-ut}$ is the probability that no base transition occurs. Well, then $(1 - e^{-ut})$ is the probability that a transition occurs.

Now $e^{-ut} \approx (1 - ut) $ (a truncated Taylor series) or $ut\approx (1 - e^{ut}).$ So for short times $dt$ we have $u~dt \approx (1 - e^{-u dt})$ and this explains his first equality $P(dt) = u~dt~\pi_j.$

So we have to recognize when he tells us about $e^{-ut}$ that $u t$ is the [truncated] Taylor series representation of $(1-e^{-ut})$ for $t$ very near 0. That is how he gets from 1 to 1a and (6) to (7).

(4) $(1 - u)$ is the probability that no transition from one base to another occurs in some short time $t_i.$ The probability that this happens over n consecutive time intervals is $(1 - u)^{(nt_i)}.$ Let $nt_i = T.$

Note that  $u \ll 1.$ We can write $(1 - u)^T = (1 - \frac{uT}{T})^T $ and
$$\lim_{T \to \infty} (1 - \frac{uT}{T})^T= e^{-uT}.  $$ This reasoning comes directly from that used to derive the Poisson distribution which is used to study rare events. See, for example, Deonier, Computational Genome Analysis, p.74.


Why do chickens continuously lay unfertilized eggs?

Chickens are domesticated Red Jungle Fowl. In the wild, Red Jungle Fowl live in flocks with one rooster for every few hens (where "few" is probably less than five in the wild, though in zoos flocks may be larger and have a higher rooster:hen ratio).  Since one rooster can fertilize many hens, in the wild virtually all eggs will be fertilized.  Since jungle fowl, of course, lay far fewer eggs than domestic chickens, the cost of the extremely rare unfertilized egg will be low.

In principle, there could be a molecular mechanism that checked for evidence of fertilization before allowing an egg to be laid, but of course such a mechanism would have its own costs, and would almost never actually be useful.


What is the proper naming of Aminoacyl-tRNAs?

Minimal Answer
If all you want to do is exactly what you have specified, on the basis of a 2013 paper on the human tRNAs identified in the 1000 genes project, the format would seem to be:

Met-tRNAMet(CAU)
or
methionyl-tRNAMet(CAU)

Notice that the anticodon is written in the 5ʹ→3ʹ direction, as in the paper, and that Met is capitalized, as recommended in this IUPAC publication of 1970 (sic).
I do have reservations about this as I have been unable to find tRNA nomenclature recommendations (not even in RNA journals), and the paper concerns genes (although a different nomenclature is used there — transfer RNA-Met (CAT) 1-1 etc.). Furthermore, my recommendation to use CAU, rather than CAT (used in the quoted paper) is only based on my experience of scientists who work on tRNA, rather than their genes would use (although it can be justified in a broader context: see below).
A variation on this is to be found in a 2017 paper:
$\mathrm{Met\text{-}tRNA^{Met}{}_{CAU}}$
So I suspect there is no ‘official’ nomenclature.
Problems in giving a more comprehensive answer
The answer above is adequate in certain circumstances, e.g. in differentiating in a paper or a lecture between two species (e.g. with different anticodons, although this does not occur with methionine). The problems occur when you wish to distinguish one tRNA from all other tRNAs present in a cell or encoded in a genome. I list some potential ambiguities:

Initiating v. elongating Met-tRNAs (in the case cited)
Anticodons containing modified bases
Distinct tRNAs with the same amino acid specificity and the same anticodon
Cytoplasmic v. mitochondrial tRNAs in eukaryotes
tRNAs from different species

Possible solutions
Different Met-tRNAs
This is often most important as both initiating and elongating Met-tRNAs have the same anticodon but are structurally and functionally distinct. Differentiation is generally done by way of a subscript: originally ‘f’ or ‘m’, respectively, but for eukaryotes now generally ‘i’ or no subscript:
$\mathrm{Met\text{-}tRNA^{met}_f} \quad or \quad \mathrm{Met\text{-}tRNA^{met}_m}$
$\mathrm{Met\text{-}tRNA^{met}_i} \quad or \quad \mathrm{Met\text{-}tRNA^{met}}$
Anticodons containing modified bases
It was observed early on that the anticodons of tRNA contained modified bases — e.g. inosine, which had particular patterns of ‘wobble’ codon recognition (see my answer to another SE question). Therefore, in many cases it would be important to specifiy these — which is why I recommend using U, rather than T, e.g.

Tyr-tRNATyr(GΨA)

tRNAs with same anticodon
Gene duplication often results in tRNAs with the same specificity and the same anticodon. In some cases the sequences are identical, so there is no way of distinguishing them, but in other cases mutations will occur that do not change the function. To distinguish such species with a single base (here at position 40) the 1000 genomes paper uses the following style:

(G40) tRNAArg(GCA)
or
(C40) tRNAArg(GCA)

At the genetic level arbitrary numbering is used for human tRNAs, e.g.

transfer RNA-Met (CAT) 1-1
transfer RNA-Met (CAT) 1-2

whereas in Drosophila a variant of this style is used, e.g.

transfer RNA:Methionine-CAT 1-1
transfer RNA:Methionine-CAT 1-2

Cytoplasmic v. mitochondrial tRNAs
It is important to remember that the mitochondria of eukaryotes contain their own set of tRNAs, and to distinguish these if necessary by a preceeding ‘mitochondrial’. In Drosophila the symbol would be ‘mt:tRNA:Met-CAT’, and the name ‘mitochondrial transfer RNA:Methionine-CAT’.
Species
Obviously, one can specify the species by a preceeding adjective. I mention this to point out that set of tRNAs is different for different species.


Is tactile perception two-dimensional or three-dimensional?

It's not 2D: Tactile perception can very simply understand a ring around your finger. If you projected the skin of your body onto a 2D plane there would be a way to represent this sensation, but only as an irregular shape. So you need a third dimension to cognitively process this sensation.

But Phantom pain tells us the brain doesn't always register tactile perception from a true 3D mapping. For example a person without an arm could feel pain in a finger that doesn't exist. Not always, but sometimes.

So it's greater than two, and sometimes three doesn't fully describe the known phenomena. Therefore it's (at least) 4-D.


In this context, euthyroidism refers to the amount of hormone present.

What is a goiter:

  The term “goiter” simply refers to the abnormal enlargement of the thyroid gland. It is important to know that the presence of a goiter does not necessarily mean that the thyroid gland is malfunctioning. A goiter can occur in a gland that is producing too much hormone (hyperthyroidism), too little hormone (hypothyroidism), or the correct amount of hormone (euthyroidism). A goiter indicates there is a condition present which is causing the thyroid to grow abnormally.

See also here and here for more of the same info.

ETA: According to this:

  Chronic lymphocytic thyroiditis (CLT), also known as Hashimoto thyroiditis, is an autoimmune, inflammatory process that causes up to 55% to 65% of all euthyroid goitres...

Although, as the link I already gave above state, regular ol' iodine deficiency can still cause euthyroid goiter.


Why are some vegetables/fruits seasonal?

Many plants start flowering (and subsequent seed / fruit production) based on light, temperature, and / or humidity changes, which tell them summer is near. That is when they need to grow fruit. Surely, there are plants trying to look for sunlight, pollinators, good conditions for seedlings, in the winter, but they are specially adapted, and thrive in their niche only through some season sensing similar to the summer-flowering plants.
At the Equator there isn't much difference between seasons and days, and there  should be no need for such mechanism. Bananas are suited to the Equator, meaning banana trees don't know what seasons are.
Plants in temperate climates care about seasons a lot. We put them in greenhouses and we play with their light, in order to force off-season flowering. Tomatoes are kept in the greenhouse not because we don't like them shivering outside, but because we want to fool their temperature-sensing organs that summer is here.
At the Tropics there is an important difference in the amount of rain water and a smaller change in day duration. Mangoes are more suited to the Tropics, meaning they care about seasons. People who grow mangoes in greenhouses try to fool them by adjusting humidity, but I couldn't find any evidence that it is humidity rather than day length.


1/R0 is the threshold fraction. If fraction of population vulnerable to particular infection is  more than 1/R0, only then infection can spread further. And if it is less than 1/R0 then infection can not progress and eventually goes away

And, 1-1/R0 is the fraction of population which requires vaccination so that we can have herd immunity.

(Reference
http://home.iitk.ac.in/~peeyush/mth426/Epidemiology.pdf

https://www.slideshare.net/singh_br1762/r0-value-herd-immunity)


Where can I find DNA Sequence data for colon cancer

You may try the data for "Colon Adenocarcinoma" made by the TCGA project:
http://gdac.broadinstitute.org/runs/analyses__2015_04_02/reports/cancer/COAD/

The file with mutations called by the tumor against a matched normal,
http://gdac.broadinstitute.org/runs/analyses__2015_04_02/reports/cancer/COAD/MutSigNozzleReport2.0/COAD-TP.final_analysis_set.maf

What you need are column 11, 12 and 13. Column 11 is the reference allele (your so-call good DNA). For each row, the alternative allele (bad DNA) is column 12 if column 12 does not equal column 11, otherwise it is column 13. -- It would be a piece of cake to make by coding :)

In case you are interested, column 16 and 17 are the tumor and normal sample IDs.


Why do I see different hues of colors between each of my eyes?

This is an interesting phenomenon which I have been aware of for several years, but I haven't yet come across any official description of it or explanation for it.

Nonetheless, the phenomenon is easy to explain. It is a result of light adaptation in your retina responding to different levels of light being received by each eye.

Background

The level of ambient light present over the course of the day varies by as much as 10 orders of magnitude, and our visual systems have evolved to account for this. The human retina and later visual processing centers have a number of ways to adapt to the light level present in the environment. They are constantly doing this, but these adaptation mechanisms take a little bit of time to adjust to a different light level, usually on the order of fifteen seconds to a few minutes. This is why when you step out of a dark room into the sunshine, you are momentarily blinded by the (relatively) bright light.

Some of these adaptation mechanisms are color-specific, such as those that occur in the cone cells themselves.

Explanation

TL;DR-ers, just read this section

Most of the time, both of your eyes experience roughly the same levels of light intensity, both in general and for each color of light. But this is not always the case.

If you have one eye covered for a period of time, such as when you've been laying down, then your two eyes will be adapted to two different sources of light. If you then uncover that eye, then for a short period of time that eye will perceive the world to be brighter than the other eye. If the light level present in the environment has a tint to it as well, then the just-uncovered eye will perceive that tint more strongly than the other eye.

DIY Science Time

You can verify this yourself, like I have been doing over the past hour, with nothing more than a makeshift eyepatch and nothing better to do.

First, check your initial state by closing one eye and then the other and switching back and forth rapidly while looking at something white. If you've been awake and active, the images from each eye should appear to have roughly the same hue and intensity.
Cover one eye completely (without pressing on it) for a period of about five minutes, while leaving the other eye open.
Then, remove the eyepatch and alternate closing each of your eyes again.

If my hypothesis and explanation is correct, the previously-covered eye should see the world as slightly brighter and more strongly tinted than the uncovered eye does (the hue of this tint should depend on your light source).

If you guys actually do this, you should report your results in the comments, especially if your results demonstrate a flaw with my hypothesis. Let's do some science, people.


We can take a look at the following picture (from wikipedia):

The regions are then:

intergenic: everything outside of the shown gene region
<5 Kb downstream: outside of the transcribed region, but possibly part of the promoter or an enhancer (yellow boxes before coding region).
UTR 5′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box before coding region).
intronic: In the Introns, as shown in the picture (grey boxes)
intragenic: These have to be mutations inside the coding region (red boxes), which is confusing since the authors specifically describe them as 'non-coding' mutations. If you read that as 'mutations that don't change the protein sequence', these could be silent mutations
UTR 3′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box after coding region)
<5 Kb upstream: outside of the transcribed region, but possibly part of an enhancer (yellow boxes after coding region)


Are all 23 chromosomes connected as one long strand of DNA?

According to what I've learnt, we have 23 independent pairs of chromosomes. Each of them contains 2 chromosomes and different kinds of genes. The genes are connected in one strand. So it is the latter one. And the 23rd pair of chromosome is used to determine our gender actually. Females got XX and males got XY


Biological validation of computationally determined gene-gene interaction

Hang in there, this answer will grow over time.

Just off the top of my head, I think we could write a small book (or a very long review article) to cover both the depth and the breadth of your question(s).

First, we need to define, and/or clarify, some terms.  The term interaction probably means different things to different authors at different times.  In fact, one author may use this term to mean different things at different times.  So I would like to propose that we make some distinctions.  For example, I would make a distinction between a genetic interaction between two genes (which is typically detected in one of the model organisms, using a genetic test between two loss-of-function alleles) versus a protein-protein interaction (sometimes called a PPI) between the two proteins encoded by those same two genes.  PPIs have been detected classically by co-sedimentation in a sucrose density gradient, or co-immunoprecipitation (co-IP), or by affinity chromatography.  More recently PPIs have been detected by mass spectrometry (MS) (sometimes coupled with affinity chromatography).  PPIs have been inferred by using proxy assays, such as the yeast two hybrid (Y2H) assay.

PPIs can also be detected by surface plasmon resonance (SPR) assays, and there may well be others.

So, when you say gene-gene interactions, what precisely do you mean?


Can anyone identify this bird - small flock in ireland?

With the new image it is still hard, but I think I identified the bird. I think this is a Willow warbler (Phylloscopus trochilus) which is pretty common in Europe.

The drawing from the Royal Bird Protection Society (source here) is pretty similar.

Unfortunately, there are two pretty similar birds living in Ireland which can be confused with the Willow warbler. These are the Chiffchaff and the Wood warbler. Differences are small, the Chiffchaff has dark legs and a smaller eye stripe (both of which the bird in your image has not), while the wood warbler lives in woods and has a more yellow breast (and is also much more rare). The links provide audio files with the songs of each bird, this should help you making a final decision, as they are pretty distinct.


There must be charge considerations in the movement of molecules in the lipid membrane. There is also a consideration that some species of phospholipids will migrate to portions of the membrane with sharper or smoother curvature.

Waves of electrical potential can propagate along a lipid bilayer as well, which is very important to nerve axons and extended structures like that.

In general though the membrane is held together by vanDerWaals forces like other non-polar solvents.  As such, the movements of lipids and proteins and other amphipathic molecules in the membrane are still largely Brownian (random) in the 2D surface of the membrane.


Why does the heart use lipids (and not glucose)?

Lipids require more oxygen to burn, but also they are cheaper to store (since they have great calorific power than carbohydrates and they're hydrophobic, thus not requiring water for their storage). The body can store so much lipids that it becomes an almost everlasting energy source (A normal adult have enough energy stored as fat to allow basal metabolism for weeks to months), which cannot apply to glucose. If fat is not present, glucose would have vanished from the body long time ago. Glucose levels must be maintained at a certain level, because it's the main energy source for the brain (which cannot use lipids ). The brain can use ketone bodies (product of fat oxidation) as a last resort.

For all the previous reasons, the heart (and many other organs, like the liver) uses fat while possible. If possible just means when not starving to death and with sufficient oxygen supply. This second condition doesn't apply to heart failure. In this case, oxygen supply fails and the tissue switch to glucose just because they can use it without oxygen (glycolysis and lactic fermentation).


Yes, T cells -- including T helper cells and cytotoxic T cells -- form memory cells.

CD4 memory T cells: what are they and what can they do?
Origins of CD4+ effector and central memory T cells
Immunological memory
Control of innate immunity by memory CD4 T cells


The third column doesn't contain distinguishing characteristics at all -- they are the first word of the vernacular (or common) names for those groups on Bug Guide. Specifically, Bug Guide lists order Entomobryomorpha as Elongate-bodied Springtails, and family Entomobryidae as Slender Springtails -- so I think you're just looking at truncated data that's misleading you!

What you're looking for a taxonomic or identification key, which gives you set of yes-or-no questions that will allow you to identify an individual to a particular taxonomic group. Know Your Insect has a taxonomic key that allows you to identify insects to order Collembola, which provides exactly the sort of distinguishing characteristics you're looking for: "This illustration shows two characteristic features of members of this order: the collophore (center), a tube-like structure used to secrete fluids; and the furculum (lower left arrow)." Note that this resource refers to this group as an order, not a class -- that's not uncommon among different taxonomic resources. Wikipedia refers to this group as subclass Collembola!

Unfortunately, it doesn't look like there's a freely available taxonomic key for species within this group, unless you buy a specialized guide like A Key to the Collembola (Springtails) of Britain and Ireland.


Why was polyploidy not lethal in certain octodontid rodents?

Actually, that is not what is discussed in the question you linked to. The following is a quote from the very comprehensive accepted answer (emphasis mine):

  Polyploidy arises easily in both animals and plants, but reproductive
  strategies might prevent it from propagating in certain circumstances,
  rather than any reduction in fitness resulting from the genome
  duplication.

In fact, try rereading that answer and the references therein, it answers your general question.

There is a popular theory (mostly accepted) that there have been whole genome duplication events (WGDs) in the vertebrate ancestry. If true, it means that all mammals are the descendents of polyploid ancestors. For a very nice review of WGDs in vertebrate evolution, see here [1]. Octomys is simply the only known mammal with a more recent WGD event. As for what makes it special (taken from [2]):

  Our data demonstrate that parental-specific silencing of at least one
  gene and normal X chromosomal dosage mechanism are conserved in the
  tetraploid genome. We hypothesize a concerted action of genetic and
  epigenetic mechanisms during the process of functional diploidization
  of this tetraploid genome.

1) Van de Peer Y, Maere S, Meyer A., The evolutionary significance of ancient genome duplications., Nat Rev Genet. 2009 Oct;10(10):725-32.

2) Bacquet C, et al., Epigenetic processes in a tetraploid mammal, Mamm Genome. 2008 Jun;19(6):439-47.


What are the exact differences between stereocilia and microvilli?

Stereocilia are basically modified microvilli. They are much longer than microvilli, and lack the villin protein.

According to Ross histology textbook, they both contain actin filaments.


Can growth rate be used as an indicator of fitness in fish populations?

Welcome to Biology.SE!

Possible confusion

When talking about growth rate as a proxy for fitness, most authors think of population growth rate (whether in terms of the Malthusian parameter or the net reproductive rate). Such methods are typically used for unicellular that have very short generation time. You seem to be referring to the individual growth rate.

Possible proxies for fitness

There are a number of different proxies for fitness one can use.

growth rate
Some phenotypic trait correlated with fitness such as:

seed production
body size
etc..

Competitive abilities
Experimental evolution

How to chose a proxy

The proxy you want to use depends:

The accuracy you need
The organism you are working with
The a priori knowledge on the biology of the organism of interest.

For example, if you have little knowledge of what phenotypic trait could be correlated with fitness and if the organism of interest have a very short generation time, then growth rate might be good (and accurate) proxy to use indeed.

Ressource

You should probably read some papers that have used a method of potential interest before doing it yourself.

At page 1232 of Kawecki and Ebert 2002, there are a few paragraphs reviewing the different proxies and their usage. They cite key papers you might want to have a look at.

Proxy for fitness in fishes

I know little about fish biology in general but I doubt there is such thing as a generalization of whether "individual growth rate" is a good proxy or not. As you don't specify what species of fish you are working on, I don't think it is possible to answer this question accurately.

You should look at previous work done on the species (or related species) you are working on in order to figure out what would be a good proxy.

Issue in your post

I think it is clear from above that you should indicate what species you are working on.
The paper you link should come with more explanation. You say a paper is a review but a review about what?
You cannot say "I would like to do something like them" and link a paper. You should describe with you own word what you are trying to achieve.


Is the ringing sound in the ears caused by dying ear cells?

Short answer:

That MAY be the sound of the damaged hairs dying. You MAY not hear that frequency again but that's unlikely.

Long answer:

Okay, so tinnitus, or ringing in the ears, can happen because of many reasons. There are three real kinds:
1) Spontaneous tinnitus can happen because of slight shifts in the acoustic systems of the ears, some of the hairs in the cochlea may amplify wrong and create a tiny feedback loop and ring for no reason. see this article about that kind of tinnitus here

However, that's not the kind of tinnitus you're referencing. That kind, post acoustic trauma, is more serious.  This kind (which can result in hearing loss) results from either 2) one really loud noise OR 3) prolonged repetitive exposure to certain frequencies (like how your mom told you to turn your headphones down or you'd go deaf. Lower frequencies move a lot of air and can indeed be dangerous to your hearing.) Just how serious the damage from a single acoustic trauma event like the explosion from Children of Man would be to you would depend on just how loud the noise was you were exposed to, the frequencies of it, and how close you were.

So now that we've gone over the different kinds of ringing-in-the-ears (tinnitus), we can talk about how it works in this situation.

This is a great article on acoustic trauma tinnitus.

So these characters didn't rupture their eardrums or they'd be in a lot of pain and unable to hear at all in one side. Instead what happened was the tiny hairs that send electrical signals to the brain were probably bent and crushed (see awesome images on the article above of before, at, and ten days after acoustic trauma.) Three possibilities from here: either the hairs recover, they partially recover, or they don't recover at all. The most likely situation is that they do recover in a matter of days, leaving the characters with undamaged hearing. Some of the hairs (usually lower frequencies) may be more damaged that others. Those may dim or cut out frequency ranges in hearing. Multiple hairs cover the same range, so some of them may be out of commission while others survive, leaving you with diminished hearing of that frequency. However, that is not likely to be related to the buzzing/ringing frequency we first hear after acoustic trama, which is the sound of all damaged hairs freaking out and sending signals at once.

Great article on how we hear frequencies

source: Sound engineer. Protect your ears, guys!


Do individual (free) nucleotides base-pair with other free nucleotides?

The base-pairing in solution only provides 2-3 hydrogen bonds, which the nucleotides could also form with water itself. There are no stacking interactions between bases in water like in a DNA helix. So I strongly doubt that the nucleotides would form a significant amount of dimers in water.
I found a paper confirming my assumption:

Short nucleotide fragments such as mono- and dinucleotides are
generally unable to form stable hydrogen-bonded base pairs or duplexes
in water.
Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts.

An easy way to confirm this would be to observe the proton NMR spectra of free nucleotides. Base-pairing in nucleic acids shows characteristic signals in the imino proton region (around 10-15 ppm), which are not visible in unpaired nucleobases due to chemical exchange.


Pathway mediates nitroglycerin-induced relief from angina pectoris

The effect of nitroglycerin on the cardiac tissue is similar to nitric oxide (NO),  which forms in the endothelium of blood vessels from arginin metabolism products.

So, the general scheme can look like this:

R-NO2 is converted to R-NO outside of the cell (glutathion-SH-dependent reaction). NO is lipophilic and rapidly penetrates into the cell where it activates guanylate cyclase. From this moment you can see the resulting influence on myosin and actin on this picture:


ratio between heat transfer coefficient and thermal conductivity

Most likely, you can't assume that $h/k$ might be constant. Reason is that those parameters are characteristics of two very separate systems.

Thermal conductivity shows how fast heat can be propagated through material. That is, it answers question: if block of metal has $T_0$ temperature on its surface A, and you apply temperature $T_1$ (higher) to opposite surface B, how long it will take for whole block to get to temperature $T_1$.

Heat transfer coefficient is a characteristic of a system. For example, when you have coolant on one side of metal plate, and heated air on the other. Question is how efficiently heat will be transferred from one side to the other. For more you can check this link. As you can see, transfer coefficient $U$ is a function of conductivity of the metal plate $k$. Hence, generally, relationship is non-linear.