The ability of bacteria to take up intact environmental DNA is called natural competence.

One problem with trying to take advantage of this in a therapy is that it is not very efficient. Importantly, natural competence is regulated and tends to be activated when bacteria are already stressed. This is also likely part of the answer as to why a bacterium would take up DNA from the outside: if they are already in bad shape, they don't have much to lose. Bacteria growing in non-stressful conditions are less competent, and possibly negligibly so.

Ween et al 2002 compared competence in two bacterial strains, one with a "normal" regulation of competence. At most bacterial concentrations, the "normal" strain showed less than 1% transformation, and this is still in sort of an ideal laboratory condition, where the culture medium is flooded with plasmids. There wouldn't be a feasible way to even approach delivering that much plasmid DNA into a human.

Ween, O., Teigen, S., Gaustad, P., Kilian, M., & Håvarstein, L. S. (2002). Competence without a competence pheromone in a natural isolate of Streptococcus infantis. Journal of bacteriology, 184(13), 3426-3432.

The other big problem is you are working directly against selection pressures. In the case of a plasmid that improves survival (say, one containing a gene that confers antibiotic resistance in the presence of that antibiotic), then the population will more quickly increase the expression of that plasmid, as bacteria with it grow and reproduce while other bacteria die. However, if you have a lethal plasmid, all the bacteria you are able to transform simply die. They don't spread the plasmid by reproducing, and as they die the non-transformed bacteria will continue to reproduce.


The read length has absolutely nothing to do with what you are sequencing. It is a characteristic of the sequencing technology you use. NGS sequencing techniques typically produce this sort of short read you're seeing. The read length does not change because you are sequencing a longer molecule. You would still get ~250nt reads even if you were sequencing an entire genome. Your reads are something like this (image source):

So the vast majority of your 250nt are overlapping and cover slightly different parts of your target sequence. This is one of the reasons why NGS analysis is not trivial. The first step in any NGS analysis is to assemble your reads into a bam file that covers your target region. If you need help on doing that, come on over to http://bioinformatics.stackexchange.com.


Were nicotinic acid/amide or flavin nucleotides ever part of primary RNA sequence?

There are naturally occurring RNAs that contain a NAD "cap" at 5' end (Bird et al., 2018; Wang et al., 2019).
I could not find any papers on natural RNAs with nicotinamide or flavin as a regular base. However, a study with synthetic oligonucleotides reports that NAD containing oligonucleotides can form stable triplex structures (Göckel & Richert,2015).
There are two studies from 1970s that explore base pairing potential of flavin. Raszka and Kaplan (1974) report that FMN can hydrogen-bond with AMP but not other nucleotides. They further explore this finding to show that FAD can form intramolecular hydrogen bonds. Scarbrough et al (1976) show that flavin containing nucleotides can form stacking interaction in addition to base pairing kind of hydrogen bonds. (Compare D-X bonds)

More recently, Julius et al. (2020) have shown that NAD and FAD can act as co-factors of primase to initiate DNA replication.
Overall, it seems plausible for FAD and NAD to be a part of nucleotide chains (more plausibly for RNA as they are already known to contain a variety of unusual bases). However, I cannot comment if they really did play such a role during cellular evolution.


"The rhesus macaque is pretty much the closest thing we have to humans" -- why?

Short answer:

Chimpanzees are indeed closer, but perhaps...too close. Almost all invasive research on non-human great apes has halted for some time over ethical concerns.

Rhesus macaques are the main non-human primate still used in research (some others are also used, like marmosets). "Pretty much the closest" is in reference to which species are available to scientists as a model organism; I assume the researcher quoted included "pretty much" as a bit of a hedge, acknowledging that chimpanzees are closest while not being available for vaccine research. Even then, many countries have limited research using all primates and do not use macaques anymore, either.

Longer answer:

The primates include great apes like gorillas, orangutans, and our closest non-human relatives: chimpanzees. They also include more distant relatives, like Old-world and New-world monkeys, and even more distant lemurs.

Many humans (including influential organizations) have decided that chimpanzees and other apes are too closely related to humans to be eligible for certain types of research for ethical reasons. It has been deemed more ethical to use human subjects, who can consent to participation in studies, or to use other model animals. Apes are also difficult as model organisms: they develop slowly, grow large, and have long life spans with few offspring; all these factors make them expensive research subjects. There is no one biological fact for this distinction between apes and other monkeys, besides their closer relationship to us and the perception that they have more advanced intellectual faculties. Further discussion is outside the scope of this answer.

Old-world monkeys, including rhesus macaques, are the next-closest grouping of primates to the human lineage. Macaque monkeys live and breed fairly well in captivity, and are used in research when other model organisms like mice and rats are unsuitable (like when an aspect of their biology is not sufficiently similar to humans).

Rodents can also be models for vaccine research, but their distance from humans and differing response to certain pathogens may make them less useful for measuring efficacy. Therefore, close relatives like rhesus macaques have been used in past vaccine research.

There is no perfect model organism; even humans aren't always great models for other humans, when they vary by age, sex, pre-existing conditions, etc. There is a balance in risk and ethics in choosing model organisms for research: simpler animals like mice and rats are typically used at earlier stages of research. Primates are used when rodent models don't correlate well enough with humans or when there is a large risk to human trials.

Some references:

https://en.wikipedia.org/wiki/Animal_testing_on_non-human_primates

https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-will-no-longer-support-biomedical-research-chimpanzees

https://www.nature.com/subjects/rhesus-macaque

https://www.sciencemag.org/news/2018/11/record-number-monkeys-being-used-us-research

Nath, B. M., Schumann, K. E., & Boyer, J. D. (2000). The chimpanzee and other non-human-primate models in HIV-1 vaccine research. Trends in microbiology, 8(9), 426-431.


Your tree appears to be from the Genus Dichrostachys.

It has several species, quiet a number of them have been reported only in Madagascar.

There are two species found in India, D. santapaui and D. cinerea.

How have I reached this plant?

The leaves of your plant are bipinnately compound. They gave me the impression of Mimosa pudica.

Of course it is not one. Mimosa pudica become creepers with time
and have short and thin prickly thorns.
Resemblance of an unknown organism with a known one can indicate shared derived character(s) (Synapomorphy), meaning they can be related.

Google's algorithm is often able to trace this relation. Look at the keywords I had used. If it doesn't one needs to experiment with the keyworks, note the word Fabaceae, it is the family to which Mimosa belongs.
Wikipedia  often is just the right place to start one's research.

The description of Dichrostachys cinerea is what I checked next, after having ascertained that is found in India.

  Dichrostachys cinerea is a tree characterized by bark on young branches, dark grey-brown fissures on older branches and stems and smooth on the spines.

  They typically grow up to 7 metres (23 ft) in height and have strong alternate thorns, generally up to 8 cm (3.1 in) long.
  Flowers of the Dichrostachys cinerea are characteristically in bicoloured cylindrical spikes that resemble Chinese lanterns and are 6–8 cm long and fragrant.

  The species tends to grow in rainforest zones.In India, it can occur in dry deciduous forest.

Every thing fits well upto Genus Dichrostachys.

  Dichrostachys is an Old World genus of legumes in the Fabaceae family.

  Their Acacia-like leaves are bi-pinnately compound.

  Unlike Acacia their thorns are hardened branchlets rather than modified stipules. They are native from Africa to Australasia...

The next thing I exhaustively checked were the species under this
    genus. I checked their
    locations,
    out of all two species have only been reported in India; D.
    santapaui and D. cinerea.

The reason behind this unusual format is to show you  how to fish. I will leave the rest of the hard work of digging up the species to you .

Few interesting facts about this genus:

Its name is derived from the Greek words dis (two), chroos (colour) and stachys (grain ear or spike), which in combination suggests their bi-colored inflorescences.

Dichrostachys cinerea, known as Sicklebush, Bell mimosa, Chinese lantern tree or Kalahari Christmas tree (South Africa).
D. cinerea is used in Ayurveda.


The term that most scientists use to describe a synapse's "bias" is synaptic strength. The strengths of synapses depend on their "history".  The change of synaptic strength is called synaptic plasticity. This topic is closely related to memory formation and is a very broad question to answer (groups of wikipedia/scholarpedia pages and tons of reviews, not single publications).

Generally, the strength of a synapse, i.e. the size of the effect of a presynaptic stimulus on the postsynaptic neuron depends on presynaptic and postsynaptic factors. To name just a few:

the number of vesicles released from the terminal,
the expression levels of the neurotransmitter reuptake and/or breakdown enzymes,
the expression level, location and posttranslational modifications of postsynaptic receptors and
uncountable other factors.

Although there have been decades research and a nobel prize (to Eric Kandel) on the topic, there is still a lot to find out.

For a start, you might want to look up
Synaptic plasticity and/or
Spike-timing dependent plasticity (long term potentiation and long term depression).

LTP is also a good example to answer all three of your questions (if I understood them correctly).

third question: yes.
second question: LTP (and other mechanisms).
first question: Different frequencies of spike trains are more or less effective at triggering LTP, making them more or less powerful to the change in synaptic strength, affecting the response of future input to the same synapse.


Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory?

Here are a bunch of cases and specific examples that may interest you

There is a species of ants where both genders evolve to be able to reproduce by parthenogenesis (which means that males might be call females as well). In this species, the two genders mate together to create workers that do not reproduce! Therefore, when you look at the phylogenetic tree you can see that males and females are on two totally separate branches as there is reproductive isolation between the sexes in terms of fertile offspring. There is an article by L. Keller on the subject.
In the amazon molly, there are no males. But it is interesting because females need sperm to start the development of their ovules although they don't even use the genetic material of the sperm. Therefore, the amazon mollies need to find mates in sister species. In consequence, they imitate the females of the other species. There is a recent article from Hanna Kokko that investigate with a mathematical model how such system may be able (not cause the extinction of the amazon molly or of the sister species).
Sex-specific segregation distorter. Nasonia sp. may be an interesting case study
Haplo-diploidy. In ants for example, sons receive genetic material from their mother only. They are haploid.
if the rate of sexual reproduction is different from 1 then, females are responsible for more than half of the inherited genes in the next generation.

I apologize for the lack of references $\ddot \smile$


How do antibiotics combined with a non-Western diet affect weight loss?

I don't believe elevated polyunsatured fatty acid consumption falls under the tendencies of the western diet, and may be more reminiscent of the Mediterranean diet, so hopefully this answers your question. This study took mice with elevated blood and tissue omega-3 levels, and were used to identify if high levels of omega-3's could prevent the deleterious effects of excessive antibiotic use on gut microbiota. Regarding microbiota diversity, antibiotics are known to create an imbalance between bacteroidetes (decreased) and firmucutes (increased) - this study evidenced that the omega-3 mice were able to rapidly recover their bacteroidetes composition and reduce the amount of firmucutes present in comparison to the control, which in short is good news, as this also prevented later-life obesity in the omega-3 mice in contrast to the obese controls.

For skeptics of microbiota-influenced weight loss (and I know there's many), there is quite a bit of literature out there describing the relationship between gut microbiota diversity and energy expenditure. The short description is that elevated bacteroidetes (in proportion to firmucutes) is associated with lean phenotypes, that diet is very much capable of modulating gut microbiota over short periods of time, and transplanting microbiota compositions into obese individuals has definitively shown an effect on metabolism. The only problem to a gung ho microbiota therapy is, no one knows the gold standard for microbiota composition.


Is the lac operon repressed in the presence of both glucose and lactose?

According to Molecular biology of the gene by James Watson, in presence of both glucose and lactose, the lac operon has a basal level of transcription. However, when only lactose is present, the operon has an activated level of transcription, due to the CAP mechanism.


To avoid confusion all species names should be written in full at first, and can then be abbreviated. In this particular example it would probably not be a problem to use the second, shorter version. But what if you had four species divided into three genera with all names starting with 'A'? As for question 2, the full name usually only needs to be used in the title (if relevant) and once in the body text (which includes the abstract), so you can abbreviate after the abstract. However, this is really only a space issue, and you can use the full name at all instances (you may abbreviate, but don't have to), unless of course journal style prohibits this. I find it useful to write the name in full both in the abstract and once in the main text.

See The International Code of Zoological Nomenclature (Appendix B: General Recommendations) for a reference. To be picky, technically, authorship and year of species names should also be included at least once in each paper (e.g. Amphiprion clarkii Bennett, 1830), to clarify exactly what definition of a name you are using. However, this is often not done in practice (in fields outside taxonomy/systematics). What you often see is that people refer to a authoritative source, e.g. "... all species names used in the study follow Doe et al. (2008)."


What cells in mosses behave analogously to mammalian embryonic stem cells?

The growing tips of roots and shoots contain regions of rapidly dividing cells in all plants that are called apical meristems. Apical meristems contain the plant's stem cells, which are not fundamentally different from the stem cells of animals.

You can begin learning more about this subject from this Nature scitable article.


Extreme examples of protein translation/use coupling/decoupling?

Proteins that are membrane localized or secreted would take time to become active or even become poised for activity. Membrane receptors may remain inactive until triggered by the appropriate ligand. Nonetheless proteins won't remain (inactive or active) for a very long time as constant turnover happens in the cell.

One example, similar to what MarchHo mentioned in their answer (pre-proteins) is that of fibrinogen. Fibrinogen gets converted to fibrin when there is an injury and haemostasis reaction cascade is initiated. Fibrinogen has a biological half life (in its latency) of ~100 hours [ref].


Do larger unicellular eukaryotic organisms have larger organelles?

The cell has the amount of organelles necessary to perform its function. If a cell requires a lot of protein, it must have multiple nuclei to produce this protein. If the cell performs many activities that require energy, it needs many mitochondria. So the size and quantity of the organelles will be proportional to their function, not their size. In relation to Acetabularia, it is a single-celled organism visible to the naked eye. The nucleus is visible, but other organelles are not.


How much does a biological experiment to validate a gene function cost?

Wow that can vary from a couple of months and a few thousand dollars to a lifetime and millions of dollars.  I can give a couple of examples, but this is an extremely broad question.  Wet science is not cheap might be the message here.

Gene Ontology terms are meant to cover all biological roles known for genes.  Terms are added and retire regularly.  They embody thousands of person-years of work to establish the framework of what is going on in cells.  At the same time its a limited vocabulary of gene behavior.  It doesn't represent a complete catalog of all known gene behaviors (e.g. in such detail that it could only be the property of a specific gene) and it is also uneven in the level of its detail of its leaf terms.  Its an ontology that is manually assembled and edited and therefore subjective.

I just did an overview of GO 1.2.  there are 34153 unique GO terms.  That's easily 10s of thousands of separate assays, so picking a group of important ones might be useful. There are also lots of orphan GO terms, where only one gene is currently attached to the term.

For GO annotations, a simple and typical case is a metabolic gene which has a high homology to a known gene and you are only trying to verify that biological role, and you have a functioning biological laboratory.

A breakdown might be:

clone the gene ( \$200 to \$1000 and up): order primers, use PCR to insert the gene into a plasmid or get the gene synthesized if you have to, transform it into bacteria,  ideally sequence it to make sure you have it right.
purify the protein ( \$500 maybe).  Run a check culture to see if the protein is produced, then run a full culture with induction, lyse it and then purify on an affinity chromatography column.  you may need to run a second column to get the protein pure.
do a kinetics study with mass spectroscopic validation of the products (minimally about \$300).  Cost involves reagents - if you have an assay you can use a UV/Vis spectrophotometer this can be simple, if not it can be much more expensive. This part will vary with the enzyme you are looking at.

Hopefully you get all these steps right the first time.  Salaries are not included in this cost.

The more complicated the GO term, the more difficult the work will be - they are not all equal.  If the protein function can't be verified in isolation, but must be in situ (i.e. in the living organism). Then you start to get into time.  What if your gene is involved in protein routing through the golgi apparatus and modulates the function of other proteins for instance?  That's going to require a very specialized and difficult set of experiments that should involve someone with experience in that field.

Finding GO annotations which are not clear from sequence similarity - unknown functions or new genes which reflect previously unestablished GO Terms could cost even more and take a good deal longer.

Still, high throughput studies are being done to find and validate electronic GO annotations.  And with that scale, the cost per experiment will go down.  Take a look at Olga Troyanskaya's research for an example of such an effort.


The following chemical equation explains why pH decreases with increased $CO_2$:

$CO_2 + H_2O \rightleftharpoons   H^+ + HCO^{-3}$

pH changes are the reason why oxygen binds to hemoglobin in you lungs and then dissociates from hemoglobin at other parts in your body where the oxygen is low because cellular respiration turned the oxygen into carbon dioxide. The binding of oxygen to hemoglobin is in turn explained by the Bohr effect.


Is it possible to have a mechanism to use carbon dioxide as a source of oxygen in human body?

Most energy in humans is generated by reducing O2 to water and CO2, using something like sugar or fat. Converting CO2 into oxygen would require energy, not generate it.

Plants do have mechanisms to convert CO2 into oxygen, but they use light as an extra energy input to push this energy-costing process.


How high is the energy yield of photovoltaics compared to photosynthesis?

According to wikipedia, plants typically convert around 5% of the energy of the sunlight that hit the leaves into energy usable by the plant.  Sugarcane seems to be the best, it converts up to 8% of the energy into actual biomass.

The best solar panels on the market, according to the Independent, convert 21% of energy from sunlight into usable electricity.  Experimental prototypes do much better, and there are some that get over 40%.  Wikipedia has a nice graph of the most efficient solar cell prototypes.


Why do my muscles move slowly when cold?

Sorry for the delay, I was low on time and didn't want to post a poor answer. Let's get into it step by step. The most important thing here is to understand that every single thing you do is a combination of many highly complicated biochemical and biophysical reactions/processes that slow down as temperature gets lower. Since any chemical reaction is a physical process I won't differentiate physics and chemistry any further. The speed of molecular processes is explained by thermodynamics. And in thermodynamics, all other things being equal, things slow down as the temperature gets lower, because temperature is a measure of thermal motion. Why? We will get to that later.

Now, what are those processes we are talking about? I'm not going to list every single molecular cascade in a eukaryotic cell that has something to do with muscle contraction (there are many, believe me). Instead, I'll give you a beautiful example that is directly related to movement. That is innervation. Everyone knows that neurones use axons for long-range transfer of electric impulses. Although people tend to portrait axons as wires, they really are nothing like metal wires, because the resistance is so high any biologically feasible electric signal won't travel for long. So how do axons work? Let's look at one:

Imagine a chain of Wi-Fi base-stations that retransmit a signal and you have a very good analogy. Any axon is mostly covered by glial cells, forming an isolation-coating (myelin sheath), but there are regular coating-free patches (Ranvier nodes). These nodes are the "base-stations". When a neurone sends a signal, it triggers the depolarisation of its cellular membrane by opening various ion-channels. The first Ranvier node senses the change in the electric potential and opens its own potential-sensitive ion channels, so the signal travels from node to node. In order the neurone to transmit a signal again, it has to recharge all the nodes (obviously, it takes time). The process is done by special active ion-pumps that use energy (ATP) to move ions against the concentration gradient. Now, let's list some thermodynamic processes:

Something senses the change in electric potential and changes its conformation. This is work.
The movement of ions along the concentration gradient. This is diffusion.
Something senses that the membrane is depolarised and triggers recharging. Once again, work.
The movement of ions against the gradient. This is done by molecular machines that require ATP. So here we have at least 2 reactions: 1. an ATPase transforms ATP to ADP; 2. an ion-pump works. Hey, what is work after all? ;)

In fact, a similar list of processes can be given for the actin-myosin system that actually performs the muscle contraction, when the cytoplasmic concentration of Ca ions increases after they are set loose from the intracellular Ca-storage facilities (the reticulum) in response to a neuronal or mechanical signal. It's just another charge-shoot-sharge cycle.

Now let's return to thermodynamics. First, consider diffusion. Diffusion depends on the speed of the molecules. The speed depends on temperature. So this is clear and simple (if you don't want to know, why it does). Now, let's consider reactions. Any reaction/process is probabilistic. We call reactions "fast" when the probability is so high there is no lag between individual events. Where does that probability come from? Although details, such as free energy distribution model (e.g. Maxwell distribution in ideal gases), depend on the medium you analyse, the basic idea of any reaction is to reduce the potential of a system. Aside from concentrations, there are 3 basic things to consider: 1. the starting free energy, 2. the activation energy, and 3. the resulting free energy. Let's look at a picture.

The higher the difference between 1 and 3, and the lesser the difference between 1 and 2, the higher the probability. Okay, this doesn't completely explain why this stuff is probabilistic. The thing is that the starting free energy of reagents forms a distribution, hence only a fraction of molecules have the energy to break the activation barrier. Any time two molecules (that could possibly react) meet, you play a game called "can we make the jump or not". The game is clearly probabilistic. When you lower the temperature, you shift that distribution, reducing the fraction of molecules that can make the jump.
Now we can go further into details, but I feel like this is already enough to give a sense of why things slow down as you lower the temperature.


The second flower is, I'm guessing by the valentine shaped leaf and violet tubular flowers, a morning glory vine (ipomoea violacea or ipomea tricolor). These plants both are closely related cultivars of ololioqui and tlitlitzen which had a history of shamanic use in southern Mexico.


I wanted to comment because I don't think my answer will be the best, but I can't because of my low reputation... Anyway, here are two suggestions:

Plant Physiology and Development, by Lincoln Taiz, Eduardo Zeiger & al.
Biochemistry and molecular biology of plants, edited by Bob B. Buchanan, Wilhelm Gruissem and Russell L.Jones

These are the two main books we are using in my university (I'm studying biology) and I think that together they cover a lot of topics. You can probably buy the pdf versions online as well. I hope it helps!


How many systemic reactions in inflammation?

There are two systemic reactions in inflammation too: mediated by leucocytes and acute-phase response (proteins).


I don't know about the specific cues that American robins use for migration. This species is also both a short range (e.g. between states or to lower altitudes) and long range migrant (e.g. Florida & Mexico), so the cues that they use can probably differ between overwintering populations. There are also year-round populations of robins in the US, but probably not many (if any) in Massachusetts. There are however at least two papers that show that American robins are arriving earlier and earlier, at least in Wisconsin and Colorado (Inouye et al, 2000 and Jones et al, 2012). The studies find that arrivals dates have shifted ~13 days earlier between 1990 and 2010 in Wisconsin and 14 days earlier between 1981 and 2000 in Colorado. The study from Colorado also shows that the first date of bare ground has not changed, so snow melt has not changed over the time period. As a consequence, the interval between arrival and bare ground has grown by 18 days. This could indicate a phenological mismatch between spring arrival and the resources used by robins, and your observations seems to agree with this pattern.

This are at least some comments and a couple of papers that could be useful for your question. Sorry I cannot say more about the actual cues used for their migration.


Is MHC1 knockout sufficient to prevent transplant rejection?

No, MHCII mismatch can also lead to transplant rejection, though through different mechanisms. CD8+ Tcells (that recognize class I) may become activated and directly kill donor cells*, and some NK subtypes can see the lack of self MHCI and also induce cell death.

MHCII mismatch on antigen presenting cells (APCs) brought along in the tissue may activate CD4+ (helper) Tcells, which do not kill directly. However, they can secrete a lot of pro-inflammatory cytokines which will make a generally hostile environment, and can also activate b-cells to produce antibodies against minor histocompatibility loci.

As to your other question, lacking MHCI entirely would be really rough on an animal in the wild, but under laboratory conditions where pathogens can be managed a bit more, it doesn't matter so much. It's the same reason we can keep mice that have gross immunological deficiencies alive, where humans with the same defects would be screwed.


What is the half-life of dNTPs at 95 °C?

Instead of searching for the stability of dNTPs, consider the stability of their constituent parts.
Caveat: ignoring the bonds between the different parts of dNTPs likely misrepresents the stability of the intact molecule, given that the covalent bonds between the nucleobase, sugar, and phosphate pieces each have their own relative stabilities.

Hydrolysis of Purines and Pyrimidines

In The stability of the RNA bases: implications for the origin of life,1 there is an Arrhenius plot showing the rate of decomposition of the most common nucleobases (A,T,C,G,U) at pH 7 in 50 mM phosphate buffer.  According to ThermoFisher, the pH of PCR buffer is between 8 and 9.5, though the authors of the paper linked above observe that the pH rate profile for the decomposition of purines (A,G) is relatively flat between pH 5 - 10.
At 95° C, the least stable nucleobase has a half life of 10-1 years, or about 1 month.

Fig. 2. Arrhenius plot for the decomposition of A, U, G, C, and
T, pH 7. ∆, data from Garret and Tsau (10). Equations are as follows:
log k(A) = -5902/T + 8.15; log k(U) = -7649/T + 11.76; log k(G) = -6330/T + 9.40; log k(C) = -5620/T + 8.69; log k(T) = -7709/T + 11.24. [red lines added for emphasis]

Decomposition of Pentose Sugars

The same research group investigated the stability of the sugar moieties of nucleic acids in Rates of decomposition of ribose and other sugars: implications
for chemical evolution.2  The analysis is slightly obscured by the use of deuterated water, though the authors observe that the rate of decomposition of ribose in H2O at 100° C and pH 7.0 is identical to that in D2O at 100° C and pD 7.4.
At 100° C and pD 7.4, ribose, the sugar component of RNA, has a half life of less than 2 hours.  Interestingly, the authors note that 2-deoxyribose, the sugar component of DNA, decomposes 2.6 times slower than ribose with a half life just shy of 4 hours.

Fig. 1. Rates of ribose decomposition as a function of pD.
The curves were fitted by assuming a functional form k = k0/(1 +
[H+]/Ka), where Ka and k0 are adjusted constants. [red lines added for emphasis]

Hydrolysis of Triphosphate

Getting to the heart of your question, i.e. at what point are dNTPs no longer "polymerizable", the stability of the triphosphate is vital, as the hydrolysis of the two distal phosphates and the creation of a phosphodiester bond with the remaining proximal phosphate is the rate-limiting step in DNA polymerization.
An older publication, The Hydrolysis of γ-Phenylpropyl Di- and Triphosphates,3 investigates the hydrolysis of nucleotide analogs at 95° C, over a pH range of 0.3 to 10.  For the ATP analog, the rate of spontaneous hydrolysis to ADP is very low, 17.5 × 10−5 s−1 at pH ~5.  Assuming first order kinetics, the half life of the triphosphate form is ~4000 seconds, or a little more than an hour at 95° C.  In a buffered solution closer to a neutral pH, we can expect triphosphate to be even more stable.

Table 5. A Comparison of the Rates of Hydrolysis of γ-Phenylpropyl Di- and Triphosphates and ADP and ATP at 95°

A PCR with one 2-minute initial melting and 20 cycles with 15-second melt steps will expose dNTPs to 420 seconds at 95° C.  Considering only the hydrolysis of triphosphate, which is the least stable component of the 3-component dNTP molecule outlined above, the equation for exponential decay can be used to calculate the proportion of unincorporated dNTPs that are still "polymerizable" at the end of cycling, using the rate constant provided in the "Hydrolysis" paper:
$N_{\text{final}} = N_{\text{initial}} × e^{-kt}$
$N_{\text{final}} = e^{(-17.5 × 10^{-5} s^{-1})(420 s)} = 0.929$
For some perspective, a 50 μL PCR with 0.2 mM dNTPs contains enough raw materials to create 1.51 × 1013 copies of a 200 bp dsDNA amplicon, ignoring the contribution of primers to the amplicon body, and assuming perfect fidelity of the polymerase and primers in excess.  A 20-cycle PCR with 106 molecules of template will yield 1.05 × 1012 amplicons, assuming perfect duplication at each cycle, meaning dNTPs are supplied in more than 10-fold excess and heat decomposition is unlikely to have an effect on PCR fidelity in this system.

References

Levy M, Miller SL. The stability of the RNA bases: implications for the origin of life. Proc Natl Acad Sci USA. 1998 Jul 7;95(14):7933-8.
Larralde R, Robertson MP, Miller SL. Rates of decomposition of ribose and other sugars: implications for chemical evolution. Proc Natl Acad Sci USA. 1995 Aug 29;92(18):8158-60.
Miller DL, Westheimer FH. Hydrolysis of Gamma-Phenylpropyl Di- and Triphosphates. Science. 1965 Apr 30;148(3670):667.


According to Einstein's Special Theory of Relativity, moving objects measure shorter in their direction of motion as their velocity increases until, at the speed of light, they disappear. It also tells us that moving clocks run more slowly as their velocity increases until, at the speed of light, they stop running altogether.

Hence,  astronauts traveling at great speeds for long periods of time return to earth younger than had they stayed on earth.

Technology, however, limits the velocities of astronauts, the differences are hence minuscule: after 6 months on the International Space Station (ISS), the astronaut crew had indeed aged less than those on Earth, but only by about 0.005 seconds. Hence, your notion that there are drastic changes do not find solid ground in the light of current technology. The effects would be greater if the astronauts were traveling nearer to the speed of light (299,792,458 m/s).

It is the mere physics behind it. Everything slows down relative to a slower moving observer. Not just metabolism, but time itself.


What are the advantages and disadvantages of being ambidextrous?

I think that the advantages of using both hands with equal ease is quite evident whether it be sports, at your work or while you are doing your household chores.

An obvious advantage is using both hands to write or draw with both at the same time.

I would be focusing on the disadvantages that may be faced.

  1) Ambidextrous people are more prone to suffer from Synaesthesia
  (reference)

  2) They are likely to possess (not necessarily) the LRRTM1 gene which
  is linked with Schizophrenia (reference).

  3) They score lesser in intelligence testing (reference).

  4) Mixed handed children are more likely to suffer from ADHD
  (reference).

  5) Mixed handedness is associated with greater age-related decline
  (reference)

  6) They are easier to anger and influence emotionally (reference).

There are quite a few studies that have pointed out that it may not be all that good a condition but Leonardo da Vinci who was probably the most diversely talented man who ever lived is said to have been ambidextrous. He apparently could draw with one hand and write with the other at the same time, so I would have to say that the positives of the condition are extremely good (reference).

edit:

This probably qualifies as a second question :-D but I just saw a thought by biogirl in the comments section on "whether our ancestors used both the hands and using just one hand is recently evolved" and she has a point there. From a study publlished in 1977 I quote.

  The predominance of the right hand over the left was also reported
  among Egyptian art forms 3,500 to 4,500 years old, where the ratio of
  left- to right-handers was 9:111 and 5:100, respectively. However,
  going further back using the "Draw-a-Man Test," found that ancient
  paleolithic man, from 1,750,000 to 8,000 years B.C., was probably
  either more ambidextrous or that there was a greater proportion of
  left-handers than there are now. (reference)

Also from a study titled "Evolutionary Back Grounds of Human Left Handedness", the authors concluded that

  For most manual tasks, especially those tasks involved in competitive
  activities, increasing performance by the specialization of one hand
  is certainly adaptive. Aggressive interactions are responsible for
  fundamental selection pressures acting during primate and human
  evolution. The higher prevalence of right-handedness might well be due
  to a previously existing cerebral bias. But the specialization of one
  forelimb leading to right or left-handedness is better viewed as the
  result of natural selection. (reference)


Assumptions of the models for haploid and diploid selection

Unless I am missing something the equations you have posted are incorrect. The second equation should be:

$$p' = \frac{p^2 W_{AA} + p(1-p)W_{AB}}{p^2W_{AA}+ 2p(1-p)W_{AB}+(1-p)W_{BB}} $$

$p'$ is not interpreted as $\frac{dp}{dt}.$

$p'$ is the frequency of allele A in the next generation. If zygotic frequencies via random mating are

$p^2(AA) + 2pq(Aa)+q^2(aa) = 1$

then all of AA individuals and 1/2 the Aa gametes bear the A allele. So we can find $p$ in the next generation as

$p^2+pq = p^2+p(1-p) = p^2+p-p^2 = p$ which shows that in a Hardy-Weinberg population the frequencies are stable.

The assumptions here are those underlying the HW model, which includes infinite population size (hence constant).


What happens to our body when we undergo a sudden temperature change from 40℃ to 20℃?

Disclaimer: the answer is very broad and covers both the situations I am confident about, as well as those I understand only superficially.

The outcome depends on particular temperatures.

Example - cold shock response: "Cold shock response is the physiological response of organisms to sudden cold, especially cold water. In humans, cold shock response is perhaps the most common cause of death from immersion in very cold water, such as by falling through thin ice. The cold water can cause heart attack due to vasoconstriction, the heart has to work harder to pump the same volume of blood throughout the body. For people with heart disease, this additional workload can cause the heart to go into arrest. Inhalation of water (and thus drowning) may result from hyperventilation. Some people, due to body type or mental conditioning, are much better able to survive swimming in very cold water." But: " A person who survives the initial minute of trauma (after falling into icy water), can survive for at least thirty minutes provided they don't drown."

Sudden heat at entering sauna - I am not sure, but probably it also may cause heart attacks. Recent heart attack is a contraindication for sauna visits. Healthy individuals do O.K. due to thermoregulation mechanisms in the body.

As we move to more extreme temperatures, where the thermoregulation of human body simply has no chance at all to keep up, you can percieve the human body as a chunk of meat. The proteins denature, the water in the body gets boiled. The meat gets cooked, turns coal like, burns to ashes... Or by freezing, the water forms crystals, damages and breaks the cells. Eventually the meat freezes to be stone hard and does not change for a long time if kept at such temperature.


Why isn't the phosphoglycerate kinase reaction of the glycolysis pathway irreversible?

The free energy change that you quote for the phosphoglycerate kinase (PGK) forward reaction is, of course, the standard free energy change (ΔG0') for the overall reaction. The standard free energy change is defined for all reactants at a concentration of 1M. Note that this value includes the formation of ATP -  the free energy of hydrolysis of 1,3-BPG would be much larger, and some of that energy is 'captured' in the ATP product.

The actual free energy change for the PGK reaction, ΔG,  will differ from this value because of the fact that the actual reactant concentrations are very far from the idealised 1M. You can find a Table here which compares, for each step in glycolysis, the standard free energy change with a true free energy change, calculated on the basis of cellular conditions in erythrocytes (also shown). You will see that for the PGK step the actual free energy change is 0.09 kJ mol-1 rather than the -18.9 kJ mol-1 that you quote in your question.

You can also see from the Table that there are only two reactions in the glycolytic pathway with large negative values for ΔG: those catalysed by phosphofructokinase and by pyruvate kinase. These are of course the two steps that are bypassed in gluconeogenesis because they are essentially irreversible.

So - your reasoning was correct, but it was based on the wrong ΔG values.

added much later

As pointed out in the comments, the 1st step in glycolysis also has a large negative value for ΔG and is also bypassed. Not sure how I forgot to include that!


DNA Sequencing - Sanger termination method: What effects will more ddNTPs in solution have on the resolution on agarose gel via electrophoresis?

You are correct. The greater the ratio of ddNTPs to dNTPs, the more frequently ddNTPs will terminate the reaction, resulting in shorter mean fragment size. However, Sanger sequencing is not done with agarose gels. The result visualizing a Sanger reaction on agarose, using more ddNTPs would result in a smear closer to the bottom. For actually visualizing the sequences on acrylamide, or with capillaries, increasing the ddNTPs would reduce the resolution of longer fragments. It is a balance you need to optimize.


Can we disambiguate competing molecular mechanisms of learning and plasticity by measuring electrical activity of neurons?

Just adding a little bit here. Estimating changes in connectivity based on STDP is hard
http://klab.smpp.northwestern.edu/wiki/images/2/2b/Stevenson_Inferring_Plasticity_2011.pdf

but yes - these questions are enough to keep a big field busy for a long time.


1-6: OK;

prokaryotes. Cytosol is the portion of cytoplasm which is devoid of any organelles, i.e., cytoplasm = cytosol + organelles. As prokaryotes don't have any organelles in their cytoplasm, they have only cytosol. So the answer would be prokaryotes (their cytoplasm consist of cytosol only). For a special case in eukaryotes see Crags answer below.
Double strand;
Glucose? (but not ATP, fat would also be a suitable alternative specially in animal living in cold regions thanks to @CRags);
protein


https://www.researchgate.net/publication/200464654

This is a detailed comparison between two lakes in the Trans-Volga region in Russia, one of them being Lake Pustoye. I'm not sure if the Lake Pustoye in this article is the same lake being referred to by the op as it isn't in Siberia and there's no mention of champagne-like water, but it does bear the same name and has a curious lack of fish. The authors found that while there is an absence of fish, there is by no means an absence of life in the waters of Pustoye. In the article, they catalog the seasonal shifts of biodiversity in the waters of both lakes. The pH was observed to be low in Lake Pustoye which they implicated to be the likely cause for the lack of fish, though they indicated that more research would be needed to determine the exact cause of the acidification.


Short answer: Due to habituation. You do something enough number of times, then that event ceases to be something new, and your body adapts to it.

In this case, you train your body to accept more risks allowing greater lengthening, before it begins to internally signal the muscles that an injury is incoming.

Read below for the slightly longer version:

  The stretching of a muscle fiber begins with the sarcomere, the basic unit of contraction in the muscle fiber. As the sarcomere contracts, the area of overlap between the thick and thin myofilaments increases. As it stretches, this area of overlap decreases, allowing the muscle fiber to elongate. Once the muscle fiber is at its maximum resting length (all the sarcomeres are fully stretched), additional stretching places force on the surrounding connective tissue.

  There are two kinds of muscle fibers: intrafusal muscle fibers and extrafusal muscle fibers. Extrafusil fibers are the ones that contain myofibrils. Intrafusal fibers are also called muscle spindles and lie parallel to the extrafusal fibers and are the primary proprioceptors in the muscle.

  When the muscle is stretched, so is the muscle spindle. The muscle spindle records the change in length (and how fast) and sends signals to the spine which convey this information. This triggers the stretch reflex (also called the myotatic reflex) which attempts to resist the change in muscle length by causing the stretched muscle to contract. The more sudden the change in muscle length, the stronger the muscle contractions will be (plyometric, or "jump", training is based on this fact). This basic function of the muscle spindle helps to maintain muscle tone and to protect the body from injury.

  One of the reasons for holding a stretch for a prolonged period of time is that as you hold the muscle in a stretched position, the muscle spindle habituates (becomes accustomed to the new length) and reduces its signaling. Gradually, you can train your stretch receptors to allow greater lengthening of the muscles.

You can read more about it (including the role of the lengthening reaction by the gogli tendon organs) here: http://people.bath.ac.uk/masrjb/Stretch/stretching_2.html#SEC13

It has also been published in a short section in this paper. I am sure you can follow the reference chain if you need to.

Smith, Craig A. "The warm-up procedure: to stretch or not to stretch. A brief review." Journal of Orthopaedic & Sports Physical Therapy 19.1 (1994): 12-17.


Why do organisms excrete nitrogenous wastes?

Some amino acids are essential, that is, they cannot be synthesized.  For all the others, however, you need building blocks.  Nitrogen, and specifically ammonia, is required for non-essential amino acid synthesis, the transfer of which is accomplished through a process called transamination.  Amino acids are also broken down for energy as a metabolic process, producing glutamate (in addition to energy-containing molecules such as pyruvate).  The body has thus produced some amino acids and metabolized others for energy,  but glutamate must be deaminated to remove the nitrogen, which by this point is now in excess.

To evolve a specialized storage unit for highly toxic substances could be useful, I suppose, but it would be unlikely and would pose a huge risk compared to just getting rid of 'em.  I'd rather urinate a few times a day than save a lot of toxic material for later and run the risk of something malfunctioning and killing me; besides, eventually that storage unit would get full.  You could ask the same question for any substance we might eventually want.


Making Cupriavidus metallidurans in laboratory?

You can buy Cupriavidus metallidurans from various culture collections.

See these links below:

Cupriavidus metallidurans (Goris et al. 2001) Vandamme and Coenye 2004 - DSMZ
Cupriavidus metallidurans (Goris et al.) Vandamme and Coenye (ATCC® 43123™) - ATCC

As canadianer has already explained, it will be next to impossible to "find" a pure, viable culture out there in the environment.


difference between blastula and blastocyst

A blastula is a hollow ball of cells, while the blastocyst occurs slightly later in mammalian development and has a defined inner mass and an outer layer of trophoblast.


Summary

Several pathways/metabolic reactions are required for bacteria to convert acetate to pyruvate — or more pertinently to the gluconeogenic pathway — but the key is the glyoxylate cycle or shunt. The sequence of reactions is:

2 acetate → 2 acetyl CoA (acetyl CoA synthetase)
1 acetyl CoA + oxaloacetate → citrate → isocitrate (entry to Krebs TCA cycle)
isocitrate → glyoxylate + succinate (glyoxylate shunt)
succinate → oxaloacetate (Krebs TCA cycle)
1 acetyl CoA + glyoxylate → malate (glyoxylate shunt)
malate → oxaloacetate (Krebs TCA cycle)

Thus, the two molecules of acetate replenish the original molecule of oxaloacetate used for one of them to enter the tricarboxylic acid (TCA) cycle, with — in addition — a second molecule of oxaloacetate. This is available for:

oxaloacetate → phosphoenolpyruvate (PEP carboxykinase of gluconeogenesis)

The phosphoenolpyruvate (PEP) could, in principle, be converted to pyruvate:

phosphoenolpyruvate → pyruvate (pyruvate kinase of glycolysis)

Although this sequence of reactions would normally be used to generate glucose etc via gluconeogenesis.

The link betweeen the TCA cycle and glucose metabolism

In addition to oxidizing acetyl CoA, the Krebs tricarboxylic acid cycle (TCA cycle) can act as source of certain metabolic intermediates for other pathways. As shown below, oxaloacetate (OAA) can be converted to phosophoenol pyruvate (PEP), in a reaction that is part of the gluconeogenic conversion of pyruvate to PEP.

Although certain bacteria can convert acetate into acetyl CoA in a reaction catalysed by acetyl CoA synthetase  the TCA cycle per se does not perform a net conversion acetyl CoA to OAA, because a molecule of OAA is needed for acetylCoA to enter the TCA cycle and must be regenerated. The TCA cycle, in effect, oxidizes acetyl CoA to carbon dioxide. The TCA cycle, per se, can only convert to OAA and PEP those intermediates that enter the cycle directly after the acetyl CoA stage.

The glyoxylate shunt

The foregoing explains why most animals cannot convert fat to glucose. (Acetyl CoA cannot be converted to pyruvate by pyruvate dehydrogenase is this reaction is effectively irreversible.) However plant and certain bacteria (including Escherichia coli) can overcome this limitation by means of the glyoxylate shunt. A text available online that explains this is Berg et al., in a section entitled ‘The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate’. To help clarify this I have prepared my own diagram, below.

This involves the conversion:

oxaloacetate + 2 acetyl CoA → 2 oxaloacetate

i.e. the net conversion of

2 acetyl CoA → oxaloacetate

The glyoxylate shunt reactions are imposed on the TCA cycle with a pink overlay. One molecule of acetyl CoA condenses with OAA to enter the TCA cycle in the normal manner. However the isocitrate formed from citrate, instead of being decarboxylated, is converted to glyoxylate and succinate. The succinate — a dicarboxylic acid — regenerates the original molecule of OAA used to allow acetyl CoA to enter the TCA cycle.

What of the glycoxylate produced in the isocitrate lyase reaction? It reacts with a second molecule of acetyl CoA to produce the dicarboxylic acid malate in a reaction catalysed by malate synthase, the second unique enzyme of the shunt. This TCA cycle intermediate is converted to OAA. This second OAA is a net gain from the metabolism and can be converted to PEP, as indicated in the first diagram.

The poster asks about production of pyruvate from acetate. This is technically possible through the pyruvate kinase reaction. However I do not quite see the point of this. I would normally expect PEP to be channeled allong the gluconeogenic pathway towards glucose.

Coda: Pyruvate:ferredoxin oxidoreductase

The poster suggests a series of reactions to convert acetate to pyruvate, the final one being that catalysed by pyruvate:ferredoxin oxidoreductase. Although the pyruvate:ferredoxin oxidoreductase (EC 1.2.7.1) reaction is reversible, it generally functions to oxidize pyruvate to acetyl CoA. It is used as an alternative to pyruvate dehydrogenase by bacteria under anaerobic conditions (as it does not require NAD+), and this is regarded as its role in E. coli, and to an even greater extent in obligate anaerobes such as Clostridium.

The reverse reaction suggested by the poster, involving the synthesis of pyruvate from acetyl CoA, is restricted to autotrophs


Does the cranial dura consist of the periosteum? and if not, then is there a mistake in my textbook?

First about the terms:

The outer side of the cranial bones is covered by a single layer of  periosteum that is specifically called pericranium.
The inner side of the cranial bones is covered by dura mater that has 2 layers:

the periosteal (or sometimes called endosteal) layer that is attached to the inner side of the bones
the meningeal layer that covers the periosteal layer and, at places, folds into the skull to make extensions

Image 1: Dura mater with its periosteal and meningeal layer (source: Idris Siddiqui, SlideShare)

Image 2: Extensions of the meningeal dura mater (falx cerebri, falx cerebelli, tentorium cerebelli) (source: Wikipedia, CC license)

The cranial dura mater has the periosteal and meningeal layer, but the spinal dura mater has only a meningeal layer, which encloses the spinal cord. Vertebra have no additional periosteal layer. The periosteal layer of the dura mater that covers the cranial bones does not extend to the spinal canal:

  The periosteal or endosteal layer of dura mater is simply a layer of
  periosteum that covers the inner surface of the skull. The layer does
  not extend beyond the foramen magnum to become contiguous with the
  dura mater of the spinal cord. The spinal cord dura mater has no
  periosteal layer.

  The meningeal layer of dura mater is a durable, dense fibrous membrane
  which passes through the foramen magnum and is continuous with the
  dura mater of the spinal cord. (V. Kekere, Dura mater, StatPearls)

Both quotes from the book mentioned in the question suggest that the periosteum and dura are two separate things: periosteum being a part of the bone (as elsewhere in the skeleton) and dura consisting of a single layer. The other  explanation, which I presented here, is that the periosteum on the inner side of the skull is a part of the dura (its periosteal layer) that has another layer (the meningeal layer). So, they are two ways how you can look at the structure of dura mater, and I believe, the second one is more widely accepted.


What happens to fecal matter if it's continually re-eaten?

In a healthy person, stool weight depends mainly on the quality and quantity of the diet. The mean stool weight of a normal defecation is about 320 g [1].

Dry weight of fecal matter contains [2]:

30 % bacteria
30 % undigested food and fiber
10-20 % fat
2-3% protein

Let's do the math (the only nutrients in feces are fats and proteins):

20% * 320g = 64g of fats which can release 64 * 9.3 = 595 kcal of energy
3% * 320 = 9.6g of proteins which can release 9.6 * 4.1 = 40 kcal of energy

That's about 650 kcal. 2,000 kcal is a rough average of what people eat in a day. But your body might need more or less than 2,000 [3].

As you can see, fecal matter can't supply enough nutrients. Continuously (re)eating feces and only feces will lead to denutrition, less feces and death.

References:

Seyed Mohammad Kazem Hosseini Asl MD, Seyed Davood Hosseini MD. Determination of the Mean Daily Stool Weight, Frequency of Defecation and Bowel Transit Time: Assessment of 1000 Healthy Subjects
shigeta's answer on What is the composition of human feces?
HowStuffWorks.com. How many calories does a person need daily?


Why was Achromobacter xerosis removed from the NCBI taxonomy?

For whatever it's worth, I queried NCBI support about this and got a reply:

  To: info@ncbi.nlm.nih.gov
  Subject: Reason for removal of a species from the taxonomy?

  Hi,

  I notice that the species Achromobacter xerosis used to be listed in the NCBI taxonomy at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=216898 but no longer is. I haven't been able to track down any documentation hinting at why a species would ever be removed from the taxonomy. Is there any such documentation that I've missed, and are you able to explain why this species in particular was removed?

  Thanks in advance for your time,
  Mark

Reply:

  Dear Mark Amery:
  The NCBI Taxonomy database records exist to support data that are in other NCBI databases. A review of the Taxonomy database must have identified that we have no records for which Achromobacter xerosis
  is designated as the organism name.

  regards,
  Bonnie L. Maidak, Ph.D.
  NCBI Help Desk
  DHHS/NIH/NLM/NCBI


After reading the paper cited I think the logic goes like this: DNAse I will create free ends at accessible sites in the genome. However shearing during subsequent DNA isolation is also a source of free ends, and these represent noise in the analysis. You have to put in a lot of energy to shear DNA to very small fragments, so I infer that mild shearing during DNA isolation is very unlikely to create a new end that is near to an existing DNase I-generated end. Therefore, under the conditions used, any small fragments are much more likely to have been generated by two closely-spaced DNase I hits. By limiting the analysis to these fragments the noise from shearing is minimised.

Now that I've written this answer it doesn't seem like much more than a rewrite of the emboldened sentence, but I hope it is helpful anyway.


Why is an initiator tRNA required, distinct from the methionine tRNA used in elongation?

I think the key to understanding this is to appreciate how different the initiation process is from the rest of translation.

The 30S ribosomal subunit recognises start codons via an interaction with the Shine-Dalgarno sequence that lies upstream in the mRNA. The remaining steps of initiation involve recruiting fMet-tRNA and, critically, placing it into the P site of the ribosome. In contrast, during elongation, aminoacyl tRNAs enter at the A site before their amino acid cargo is joined to the growing polypeptide which is held in the P site as a peptidyl tRNA. So you can see that the initiation process is special because of the need to prime the whole translation process by placing the first 'peptidyl' tRNA (actually N-formylmethionyl tRNA) into the P site.

There are two tRNAs for methionine, tRNAfMet and tRNAMet, and only the former is a substrate for the enzyme methionyl-tRNA formyltransferase. This effectively partitions the supply of methionine into two separate pools, one for use in initiation and one for use in elongation. In fact you could argue that initiation involves a different amino acid (N-formylmethionine) which is also coded by AUG.

Since an N-formylmethionine is essential for initiation, the simplest alternative would be to have a situation where a single species of methionyl-tRNA was a substrate for the transformylase. This would mean that N-formylmethionine would have to be allowed into the A site, and all those formyl groups would have to be subsequently removed from the internal methionines.

Update in response to comment from the OP

Having re-read the original question, I can see that I jumped the gun and actually answered a different question. The real question is much deeper.

Firstly, although the details differ, both bacteria and eukaryotes feed methionine through separate pathways for initiation and elongation.  Bacteria are discussed above; eukaryotes channel methionine through two different pools of tRNA, tRNAiMet and tRNAMet. Clearly this channelling is a universal feature of translation systems.

Next, let's look at tRNAMet abundances in E. coli. Since all protein-coding genes have a single start codon and, on average, a few internal methionine codons, we might anticipate that there would be more tRNAMet than tRNAfMet. But this isn't the case: according to Dong et al 1996 tRNAfMet is present at around 3x the level of the elongation species.

This suggests to me that there is something inherent to initiation that requires a higher level of the corresponding methionyl tRNA. Now you might say that this discrepancy is rather small but bear in mind that one of the properties of Met-tRNAfMet is that is easily rejected by elongation factors (reference). This is important because any charged tRNA can enter the A site before being compared to the current codon. By being easily recognised as 'wrong' for elongation, Met-tRNAfMet is, to some extent, excluded from the elongation process.

So far I have presented facts -  what follows are my own ideas.
If a single Met-tRNA species was used both for elongation and for initiation it would have to optimised for entry into the elongation process, spending time interacting with ribosomal  A sites. In order to maintain the level of free Met-tRNA required to drive initiation I conclude that much higher levels of this single Met-tRNA would therefore be needed. This in turn would increase the transient entry of this species into all A sites, and it would essentially act as an inhibitor of elongation.


Rate of Evolution of population of long lived individuals

That is true to a certain extent in normal environments, where there is not an excess prevalence of mutagenic elements. The "Generation Time Hypothesis" explains why a smaller generation time and hence a higher reproductive rate ( as in annuals) corresponds to a higher rate of mutation (substitutions in DNA) and therefore have a faster evolutionary rate as compared to slow reproducing and longer generation time individuals(for example, long-lived trees).

Since "fitness"-increasing adaptations produced by somatic variations are very less, the formation of new offsprings giving rise to individuals carrying a DNA which has been subjected to processes (Repeated divisions, replications and translations, amphimixis, and different environment) making it more vulnerable to mutation, becomes mandatory, to propel evolution. This process is much faster in annuals than in long lived trees like Sequoia. Moreover Sexual selection (especially in animals) operates at a much slower rate in longer-generation time individuals. Next, smaller individuals, having higher metabolic rates usually have shorter generation time (more pronounced in case of animals). Higher metabolic activity is linked to greater mutation rate (Due to metabolic intermediates acting as mutagens) and hence faster evolutionary rate. Higher metabolic rate also is linked to higher temperature (faster mutation) and these individuals have a geographic distribution favouring the tropics.(Again increases evolutionary rate)

All these, imply faster evolution for short lived individuals(which usually have higher reproductive rate) as compared to long lived trees. But under "normal" environmental conditions (not drastic and fast changes), the evolutionary rate of large individuals is fast enough to preserve their existence (as the Sequoia prevalence indicates). However, in fast changing environment, larger and long-lived individuals are more likely to be wiped out (probably, this applied to Dinosaurs!).


Is it safe to look indirectly at the Sun?

Behar-Cohen et al. notes the periphery of the cornea has a focusing effect:

  UVR incident from the periphery is refracted into the eye, and due to the focusing effect of the cornea, UV radiation is on average 22-fold stronger at the nasal limbus, which is the typical site for pterygium and pinguecula. Moreover, UV radiation is on average eight times stronger at the nasal lens cortex, the typical site for cortical cataract.

Authors note this in further papers as peripheral light focusing. Essentially, the light is refracted from the periphery of the cornea into the anterior segment of the eye. By this notion, I'd say indirectly looking at the sun is no less damaging than directly looking at it (given there are no other restrictions, such as special lenses, etc.).


Why are skin moles (pigmented spots) circular in shape?

Note: I am not stating that moles are in general circular in shape because there are no statistical studies to conclusively state so. This answer is mostly about default circular shape of cell colonies.

Moles (melanocytic naevi) are not strictly circular but generally have  have a rough circular shape. Moles can have irregular shapes too and you can easily check that by a simple google image search.

The exact causes and mechanisms of mole formation are not known but the somewhat circular shape can be explained by a simple spatiotemporal model of growth.

Moles are formed because of pigmented cells called melanocytes (which contain the dark pigment melanin). A mole would grow when a very small population of these pigmented cells divide and expand. In a 2D surface, cells would continue to divide and expand along both the axis at an equal rate, if there are no specific constraints. Since the expansion is same along both the axes, you get a roughly circular shape. For similar reasons, bacterial colonies (on petri plates) are also more or less circular. Note that there are stochastic factors that would contribute to irregularity.

Triangles and rectangles are very specific geometries. There need to be some constraints that would limit the cell growth to adopt these geometries. So the default shape would be mostly circular.


Why human endometrium doesn't stay constant?

One hypothesis is to protect the uterus and oviducts from sperm-borne pathogens.

Also Beverly Strassmann has proposed that the energy savings of not having to continuously maintain the uterine lining more than offsets energy cost of having to rebuild the lining in the next fertility cycle, even in species such as humans where much of the lining is lost through bleeding (overt menstruation) rather than reabsorbed (covert menstruation).


What is the difference between a viral strain and a viral isolate?

An isolate is a sample. It's this particular virus in this fridge, that was isolated from this, e.g., sputum sample, and cultured. A strain is more abstract -- it is a distinguishable, stable genetic variant of a species. An isolate may be identified as a particular strain of a particular species. That's how I and my colleagues use these terms, in any case, and how they're generally used in the literature. You can read more about this here and here
From the first reference (since it's behind a paywall)
Isolate

An isolate may be defined as “a sample of biological material, especially a microorganism, that has been cultured for study” which is clear, perfectly acceptable and useable by virologists.

Strain

Although there is no official definition of a strain, the strain concept is widely used and a de facto definition states “strains are viruses that belong to the same species and differ in having stable and heritable biological, serological, and/or molecular characters”.


What does the (-) in the molecule name mean?

The minus sign in parentheses here indicates the optical rotation, (+) means the molecule rotates linear polarized light clockwise, (-) means it rotates counterclockwise. Typically you would also write exactly which stereoisomer is meant (R or S), which is generally the more useful information.

The following are all valid names for the natural stereoisomer of norepinephrine:

D-norepinephrine
D-(-)-norepinephrine
(R)-norepinephrine
(R)-(-)-norepinephrine

I'd recommend that you take a look at the concept of Chirality if you're not already familiar with it.


What are the characteristics of a living organism?

First of all, you have to note that there is no such thing as a scientific, objective definition of life, and that many scientists disagree on a given definition, and that every definition has it's limits.

However, the one from wikipedia

  Since there is no unequivocal definition of life, most current definitions in biology are descriptive. Life is considered a characteristic of something that exhibits all or most of the following traits:[10][12][13][14][15][16][17]

  Homeostasis: regulation of the internal environment to maintain a constant state; for example, sweating to reduce temperature

  Organization: being structurally composed of one or more cells — the basic units of life

  Metabolism: transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.

  Growth: maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.

  Adaptation: the ability to change over time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity, diet, and external factors.

  Response to stimuli: a response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion; for example, the leaves of a plant turning toward the sun (phototropism), and chemotaxis.

  Reproduction: the ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms.

Encyclopedia Britannica

  Metabolism
  Respiration
  Sensitivity (responding to stimuli like gravity and sunlight)
  Nutrition
  Excretion (getting rid of CO2)
  Growth
  Reproduction
  Homeostasis


This is one of my favorite charts demonstrating the complexity of amino acid properties:

http://www.jalview.org/help/html/misc/aaproperties.html

Histidine is probably the most complicated amino acid in this regard (just compare how many circles it falls into).  But don't undersell Cysteine and Methionine; those sulfurs exhibit some surprising behavior, especially when coordinated properly.  Cysteine of course forming disulfide bonds, Methionine occasionally functioning as a methyl-transferase.

Biochemistry text books make some over simplifications because presenting the full messiness of these classifications is pretty confusing. Lehninger itself is the worst about this (and especially when presenting math).  Voet and Voet is probably the most reliable about presenting this complexity. I still think Lehninger is a better teaching textbook overall (I was first taught Biochemistry from the 3rd edition), but I also recall spending a week being confused about a topic before someone pointed me at V&V and I realized Lehninger was oversimplified to the point of being wrong, in that case.


How many plants arise from a polyembryonic seed?

In plants due to programmed cell death only one plant arises.

Here is a good article

  The enigma of plant monozygotic polyembryony is that only one embryo in a polyembryonic seed usually survives while the others are eliminated at an early stage.


Chromosomal structures in S phase and Prophase

A comment by user AlwaysConfused has answered one part of the question, but I think that the OP's confusion is related to a point of language or teaching. The number of chromosomes doubles during S phase (C number), but the ploidy of the cell does not change (N number). That's what your textbook is trying to tell you, it's just stating it fairly confusingly.

When we say that there are the same number of chromosomes before and after S phase, that's just a lie that we tell ourselves to keep from getting confused. We have invented the C vs. N terminology that AlwaysConfused mentions to try to handle this: we say that the 2N of a diploid cell remains constant across the cell cycle, while the C number alternates between 2C (before S phase) and 4C (after S phase).

For you, this confusion seems to be worse because how we represent chromosomes is not what chromosomes actually look like, and this has gotten mixed up with the definitions of chromosomes.

When we draw pictures of chromosomes we draw them neatly like they are in mitosis, but that is not at all what they look like in interphase. They are still chromosomes during that time, they just aren't pretty and neat ("condensed").

To sum it up more, here is a diagram of chromosomes in interphase (most of the time) vs. during mitosis:

It is only during a very specific part of the cell cycle (mitosis) that the chromosomes are packaged up ("condensed") in such a way that we can readily see them as discrete entities. The rest of the time they're all glommed together and are organized instead according to transcriptional activity etc. rather than according to which molecule they're part of. Remember: chromosomes are very big molecules and if they are "loose" they have a total length that is many orders of magnitude larger than the diameter of the nucleus; so the nucleus is like a big bowl of noodles in interphase.

In S phase it will just be a bowl with twice as many noodles in it as before, because there are twice as many DNA molecules ("chromosomes"; "chromatid" is a term that only applies to the condensed form in mitosis).


What does it mean for there to be no correlation between phylogenetic independent contrast?

Your first option is the correct interpretation. The correlation you observe in the raw data is the effect of phylogeny.

Without using PICs, you might expect to see phylogenetic autocorrelation, i.e. your raw data correlate as a function of the amount of shared evolutionary history between different species. Using PICs is one way of testing whether the correlation still exists when the effect of phylogenetic autocorrelation is removed. This is exactly what you observe—you see the correlation in raw data (which are not phylogenetically independent) but it disappears when you use PICs. Without knowing any details of your study beyond what's in the question, it sounds like a textbook case of phylogenetic autocorrelation.

The PIC method originates with Felsenstein (1985). I'd encourage checking that paper out for further details on the method and interpretation of the results.


These look like crystallization structures when liquids dry up. But if it were to be a living thing, I'd go with fungal colonies. In my opinion, the best methods to tell is to scrape off a small piece, flood with KOH, and observe under a microscope, if you see filaments then it is definitely a fungus, and alternatively you can inoculate an agar (Sabouraud agar could work, or LB agar) to see if something grows. If its a fungus, it can take from 4 days up to 3 weeks to grow depending on the species and the growth conditions provided.

Good luck.

Here's a ref that might help you.

Microscopic potassium hydroxide preparation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994805/


Role of microvilli in cell volume regulation

Microvilli, are cellular protrusions on the membrane and hence they increase the total surface area of the cell in context.

If we evaluate the characteristics of microvilli and the structural appearance, we know that; they have many small folds; strengthened and lined by the protein filament actin; bedded in a terminal web of alpha-actinin and keratin. All of these characteristics, work in harmony to support its ability, for it to do its function. That being, to allow greater diffusion whilst controlling the cells integrity. Evidently, the microvilli do help resist the hydrostatic pressure within a cell as a result to the distribution of pressure and the microfilaments present.

Most animal cells have microvilli so, there is a huge excess of factual evidence to support what happens to them in under specific conditions. Knowing this, it confuses me why you even asked this question. It just takes a simple comparison.

I'm presuming, a normal cell is a cuboidal cell, too. So, yes, if they were both placed in a variable hypotonic solutions, with gradual increases in concentrations for comparison, the cuboidal cell would rupture much earlier rather, the cell with the microvilli would be still standing at a further stage (concentration). However, the cell with the microvilli will nearly all of the time still lyse despite it's additions. Microvilli don't sorround the entire cell, if they did, the integrity of the cell in greater hypotonic solutions would be more applaudable vs a plant cell (cell wall containing pectin).

Yes

References:

**
http://www.histology.leeds.ac.uk/cell/cell_cytoskel.php ; 'keratin is a type intermediate filament in cells' [...] 'The nucleation of actin fibers occurs as a response to external stimuli, allowing a cell to alter its shape to suit a particular situation.'

**
http://www.westfield.ma.edu/personalpages/draker/edcom/final/webprojects/sp10/cell/Ross44.jpg; 'A hypotonic solution has decreased solute concentration, and a net movement of water inside the cell, causing swelling or breakage.'

**
http://www.histology.leeds.ac.uk/cell/cell_cytoskel.php ; 'Intermediate filaments are inserted into desmosomes at cell-cell junctions, and help to maintain cell-cell connectivity, as well as the structural integrity of the cell itself.'

P.s. Most of the answer was achieved by the application of knowledge so, direct references cannot be found!


Why are human feces riskier than urine with regard to spreading diseases?

Many gut microbes are pathobionts or opportunistic pathogens — these organisms can be part of the normal gut flora (microbiome) of healthy individuals, but under the right (for them) circumstances (e.g.s: when introduced into the bloodstream by a cut, or due to immunosuppression) they can cause disease.1,2

As for urine, there are many fewer microbes present (>400 species and 109 to 1011 bacteria/g of contents in the large intestine vs. <100 species and on the order of 105 bacteria per mL of urine).3-5  Note, however, it is still far from sterile!5-7

You might also find the following of interest:
https://www.who.int/water_sanitation_health/dwq/iwachap5.pdf

References:
1: Hornef, M. (2015). Pathogens, commensal symbionts, and pathobionts: discovery and functional effects on the host. ILAR journal, 56(2), 159-162.

2: Price, L. B., Hungate, B. A., Koch, B. J., Davis, G. S., & Liu, C. M. (2017). Colonizing opportunistic pathogens (COPs): the beasts in all of us. PLoS pathogens, 13(8), e1006369.

3: Davis, C. P. (1996). Normal flora. In Medical Microbiology. 4th edition. University of Texas Medical Branch at Galveston.

4: Barnett, B. J., & Stephens, D. S. (1997). Urinary tract infection: an overview. The American journal of the medical sciences, 314(4), 245-249.

5: Lewis, D. A., Brown, R., Williams, J., White, P., Jacobson, S. K., Marchesi, J., & Drake, M. J. (2013). The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Frontiers in cellular and infection microbiology, 3, 41.

6: Hilt, E. E., McKinley, K., Pearce, M. M., Rosenfeld, A. B., Zilliox, M. J., Mueller, E. R., ... & Schreckenberger, P. C. (2014). Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. Journal of clinical microbiology, 52(3), 871-876.

7: Whiteside, S. A., Razvi, H., Dave, S., Reid, G., & Burton, J. P. (2015). The microbiome of the urinary tract—a role beyond infection. Nature Reviews Urology, 12(2), 81.


How do racing pigeons know the way back to their roost?

They find their way back even if they have been moved in complete darkness by using, indeed, magnetoreception. They can sense the direction of where they come from using the earth magnetic field. I believe there is still some debate about how magnetic fields are sensed by pigeons, the latest fashionable idea being that this is through a "warm" quantum process. I don't know if that's correct, but there is clear evidence that there are magnetic-sensitive cells in the pigeons nervous system (Wu & Dickman, 2007). This will only lead pigeons to the approximate location of their home, but once they are close enough they can recognize where they live visually. Pigeons are released everyday so they know the local environment of their home.

I'm quite sure this has nothing to do with the pigeons mates. This is probably some ridiculous idea people had in the middle-age and people kept repeating it because that sort of intuitively makes sense, but when you think carefully about it, it really doesn't.

Wu, L. Q., & Dickman, J. D. (2012). Neural correlates of a magnetic sense. science, 336(6084), 1054-1057.


It there any experimental approach to determine the electronic structure of a given aminoacid inside a protein?

The two most often used methods used to determine protein structures are X-Ray crystallography and NMR (nuclear magnetic resonance spectroscopy). Both of these allow some deductions of electron configuration, but don't actually measure it directly (and as far as I know there is no method available that can do that, but physicists might know more about that).

X-Ray crystallography essentially detects the electron density of a protein crystal. Usually this density is 'only' used to calculate the structure of the protein, but using good controls and smart math might allow one to also detect charges or specific electron configurations (I haven't checked if anyone ever tried something like this). One general caveat of protein crystallography is that the protein structure/configuration in a crystal may not actually correspond 100% to the state of the protein in its normal environment.

NMR measures the chemical shifts and coupling (quantum) spin of atom nuclei (usually H, N & sometimes C), which is more or less directly depend on its electronic micro-environment. Since structural biology usually doesn't care about things like orbitals, protein NMR data is then used to determine the distance of specific nuclei, which allows derivation of a protein structure.
Since NMR data directly measures atomic properties of single nuclei, I think it is probably the closest to what you are looking for, but asking actual NMR experts will be necessary to figure out whether determining specific orbital configurations could be possible (and even then it would likely be a multi-year interdisciplinary research project).

Another approach, that was mentioned in the comments on the question, would be determining charges on specific amino acids, which could be done using biochemical or spectroscopy assays, if one is only looking at one (or a few) specific amino acids in a protein. These assays need to specifically designed for your protein and amino acid of interest - I can't give specific sources here, but reading up on how people (started to) figure out the chemical mechanisms of enzymes might give you some insights on possible experiments.


Wouldn't a non-poisonous variety of a mutant plant be at selective advantage?

Your question is very sensible; we would indeed expect this kind of negative frequency-dependent selection: i.e., if toxin-producing plants are common, non-toxin-producing plants should gain an advantage because they don't pay the costs of producing toxins but they do (or may) gain an advantage from herbivore deterrence. (Conversely, if toxin-producing plants are rare, they could gain an individual-level benefit by being the only ones in the population to deter herbivores.)
As of 2007, however, it seems that the empirical evidence for this phenomenon was pretty weak. In the following, "resistant genotypes" means genotypes that have some kind of anti-herbivore trait (typically production of secondary compounds that deter herbivory) [emphasis added]:

... Only a few studies have examined the role of frequency-dependent selection on plant defenses against herbivory (i.e., Berenbaum & Zangerl 1998, Roy 1998, Siemens & Roy 2005). ...  No study has manipulated the frequency of resistant/tolerant host genotypes explicitly to examine if the evolution of plant defensive strategies is subject to frequency-dependent selection. However, some studies tested some of the predictions of the frequency-dependence selection hypothesis (Berenbaum & Zangerl 1998, Roy 1998).
The study by Berenbaum and Zangerl (1998) found that in Pastinaca sativa, the range of variation in the level of a resistance component (coumarin) against its consumer Depressaria pastinacella did not change from 1873 to present, suggesting a cyclical dynamic promoted by frequency-dependent selection. In a reciprocal transplant experiment Roy (1998) did not find evidence that common hosts are eaten more and have lower fitness than rare hosts.  In a recent paper, Siemens and Roy (2005) evaluated the following: (a) if the amount of damage experienced by the most common host genotype was higher than that expected by its frequency, and the amount of damage experienced by the most rare host genotypes was lower than that expected by its frequency (assortative damage hypothesis); (b) if the most common host
genotype had higher levels of damage and lower average fitness compared with the more rare host genotypes; and (c) if the amount of damage correlated positively with the frequency of the most common host genotype. ... Unfortunately, their results provide little support for the hypothesis of frequency-dependent selection acting on plant defenses against herbivory.
... Although two studies have explored the potential for
frequency-dependent selection on plant resistance, no study has yet
examined this possibility on plant tolerance. Before
frequency-dependent selection can be put aside as an explanation of
the maintenance of variation on tolerance and resistance, explicit
experimental tests of the hypothesis are required.

(I haven't followed up the more recent literature to see if there is more recent evidence ...)
There is a related phenomenon that's much better documented: toxin-producing bacteria produce antibiotics to kill other bacteria of their own and other species, to minimize competition for resources. In "rock-paper-scissors" systems (2), cheaters (bacteria that are resistant to toxin but don't produce it themselves) invade toxin producers; then non-resistant bacteria invade the cheaters (because there's no toxin being produced any more); then toxin producers reinvade (because nobody's resistant any more, so there is once again an advantage to producing toxin).
I would say that the connection between this type of frequency-dependent selection and the selection that maintains polymorphism for the sickle-cell allele is loose. Sickle-cell is usually cited as an example of heterozygote advantage. It is loosely speaking a form of negative frequency-dependent selection at the level of alleles rather than genotypes; a gamete carrying a sickle-cell allele is more likely to end up in a heterozygote (and thus gain an advantage via malaria resistance) when it's rare and more likely to end up in a homozygote (and lose fitness due to sickle-cell disease) when it's common. It's also theoretically possible (although I haven't seen it discussed, and I would guess that it's not very important in practice) that increasing frequency of sickle-cell heterozygotes could also feed back at the population level to reduce the incidence of malaria, lower the advantage of resistance, and hence generate a more analogous form of negative frequency dependent selection.

Núñez-Farfán et al. "The Evolution of Resistance and Tolerance to Herbivores", Annual Review of Ecology, Evolution, and Systematics, Vol. 38 (2007), pp. 541-566 http://www.jstor.org/stable/30033871
Kirkup and Riley, "Antibiotic-mediated antagonism leads to a bacterial game of rock–paper–scissors in vivo", Nature 428, 412-414 (25 March 2004) .


Why do most organisms have negative supercoiled DNA?

One important notion in DNA topology is the linking number ($Lk$) which is the sum of right-handed twisting # and left-handed writhing # ($Tw+Wr$). Say the $Lk = x$ for relaxed DNA. If $Lk<x$ then you have negative supercoiling while positive supercoiling happens when $Lk>x$.

The higher the $Lk$ value the higher the helical energy of the DNA and the harder it is to separate it meaning the DNA is now more stable. In so-called "extreme" conditions (e.g. high acidity or high T˚) the organism must protect his DNA from degradation. Therefore those organisms require a more stable form of their DNA which can be achieve by positive-supercoiling and/or high GC content.

Now why do the vast majority of the organisms have negatively-supercoiled DNAs? If you let the DNA by itself, it will adopt an $Lk=x$, i.e. it will be in his "relaxed"-form. Negative supercoiling arose because of the presence of Topoisomerases (type I and II), which are proteins that cleave the DNA and release the helical tensions and which cumulatively provokes the DNA to be slightly underwinded compared to it's relax-form. Is this good for the organism, if living in non aggressive conditions? Yes it is because a decrease of the $Lk$ will make the DNA easier to separate. This means replication and transcription can occur more easily or in proper terms, they now require less energy to perform their functions.

Here an excellent reference on this subject as well as a Youtube video that explains those concepts using strings. The latter is really helpful as those concepts are easier to understand visually than in writing.

I hope this helps.


What is this New Zealand insect and what is it in?

The quality of the pictures is not the best one, but due to the fact that this is NZ, it's probably a moth from the species Liothula omnivora.

It's a kiwi insect (that is, endemic to New Zealand). Its English common name is bagworm, and its Maori common name is pū a Raukatauri. The English name explains your question ("what is it in?"). According to Farm Forestry New Zealand:

  The common name of this insect refers to the strong silk bag made as a refuge by the caterpillar. The bag is brown to greyish, often covered with fragments of vegetation, and so tough it cannot be torn open.

Here is a picture of it:

And here is the adult, for comparison:


Can stress-induced cortisol reduce diabetes type I?

Short answer
Stress is not a good candidate to treat autoimmune disease like diabetes type I.

Background
Stress indeed weakens the immune system, and diabetes type I is indeed caused by an auto-immune response against the insulin-producing beta cells in the islets of Langerhans. However, autoimmune diseases like diabetes type I need chronic treatment (i.e., insulin treatment and dietary changes).

Even if stress would help reduce diabetes type I (admittedly, theoretically it could), chronic stress would also reduce the immune response against viral and bacterial infections, it would reduce wound healing and perhaps even increase the risk of contracting cancer (Glaser & Kiecolt-Glaser (2005), as well as increase the risk of depression and cardiovascular disease (Cohen et al., 2007).

Hence, it is safe to say that deploying chronic stress as a treatment against auto-immune disease effectively means substituting one life-threatening condition with another.

References
- Cohen et al., JAMA (2007); 298(14): 1685-7
- Glaser & Kiecolt-Glaser, Nature Rev Immunol (2005); 5: 243-51