How can a ligand be an integral membrane protein?

A perfectly reasonable definition of a ligand from Wikipedia:

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose.

A ligand can be anything, so long as it binds to a biomolecule. Often, the ligand is a small molecule or peptide, and the thing that it binds to is a protein. On the other hand, both ligand and binding partner can certainly be proteins (or one could be a Mg$^{2+}$ ion and the other an RNA molecule, etc.). Ligand is a very broad term, and is often used in other biochemical areas aside from signaling. For example, the things that an enzyme binds to (substrates, allosteric regulators, etc) can be called its ligands.
Also, the things you describe in your post:

This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells).

are hormones, which is a much more specific category of thing than is ligand.
Edit
There seem to be some 'ahem'... doubters as to the broadness of the definition of ligand, so, time for some examples from the literature:
From the biochemistry textbook Berg, 7e (emphasis added):

The final step is affinity chromatography with the use of a ligand specific for the target enzyme.

From the paper Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations, Wade et al (emphasis added):

To bind at an enzyme’s active site, a ligand must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it.

From the paper Geometries of functional group interactions in enzyme-ligand
complexes: Guides for receptor modelling, Tintelnot et al (emphasis added):

There are many more examples of arginine-carboxyl interactions that appear to have key functional
roles in enzymes, including some in which an arginine-like structure in the ligand interacts
with a carboxyl group from the binding site (i.e., the reverse of that described above).

It is true that the one particular compound that natively binds to an enzyme's active site is often called a substrate, in part to differentiate it from allosteric regulators and other ligands that can also bind to the enzyme. Thus, the set of all of an enzyme's substrates can be thought of as a subset of the enzyme's ligands. Again, ligand is an extremely broad concept that simply refers to something which binds.
Edit 2
Fun fact! The modern word ligand comes from the latin verb ligāre, meaning "to bind". More specifically, ligand derives from the gerundive form of ligāre, ligandus, which translates to something like "(that which is) to be bound".
Not that this has much bearing on how it's used in the modern scientific literature. I just thought it was cool.


Does *E. coli Dh5 Alpha* strain has the ability to degrade polyethylene?

I am not aware of any wild E.coli strains that have been described to have the ability to degrade polyethylene. However, work to equip E.coli DH5α with the ability to degrade polyethylene, by means of transformation, has been done in the laboratory (Mahalakshmi 2012, Danso et al 2018)

Microorganisms that can be found in the wild/nature that do have the ability to break down polyethylene include (Source: article):

Pseudomonas spp
Bacillus spp
Staphylococcus spp
Aspergillus nidulans
Aspergillus flavus
Streptomyces spp


Why honey bees built hive in perfect hexagonal shape instead of irregular shape?

Why honey bees built hive in perfect hexagonal shape ?

Honeycomb cells (not the hive or the honeycomb itself) are hexagonal, in some species of bees but not all.  The regularity of this shape has puzzled people for a long time, and Darwin (and others before him) addressed the reasons for it.  Darwin did a series of experiments with bees, and summarized his results in Origin of Species.  You can search for "hexagon" in the linked text for his long explanation, or read the (still long) summary 'Evolution of Honeycomb on the Darwin Correspondence Project, but the short explanation is that it's the most efficient way to pack cells without wasting wax, and Darwin identified a bunch of intermediate (less efficient) cell structures in various bee species that supported his hypothetized mode of evolution.

  Thus, as I believe, the most wonderful of all known instincts, that of the hive-bee, can be explained by natural selection having taken advantage of numerous, successive, slight modifications of simpler instincts; natural selection having, by slow degrees, more and more perfectly led the bees to sweep equal spheres at a given distance from each other in a double layer, and to build up and excavate the wax along the planes of intersection. The bees, of course, no more knowing that they swept their spheres at one particular distance from each other, than they know what are the several angles of the hexagonal prisms and of the basal rhombic plates; the motive power of the process of natural selection having been the construction of cells of due strength and of the proper size and shape for the larvae, this being effected with the greatest possible economy of labour and wax; that individual swarm which thus made the best cells with least labour, and least waste of honey in the secretion of wax, having succeeded best, and having transmitted their newly-acquired economical instincts to new swarms, which in their turn will have had the best chance of succeeding in the struggle for existence.


What is this fruit (round, 3 cm diameter, yellow outside, 1 black seed, found on Easter Island)?

I think you are looking at Syzygium jambos in the Myrtaceae.  The first link at Wikipedia has a number of pictures which are quite similar to your pictures.


Why can't we kill ourselves by holding our breath?

Short answer
Healthy people cannot hold their breaths until unconsciousness sets in, let alone commit suicide.

Background
According to Parkes (2005), a normal person cannot even hold their breath to unconsciousness, let alone death. Parkes says:

  Breath‐holding is a voluntary act, but normal subjects appear unable
  to breath‐hold to unconsciousness. A powerful involuntary mechanism
  normally overrides voluntary breath‐holding and causes the breath that
  defines the breakpoint.

Parkes explains that voluntary breath‐holding does not stop the central respiratory rhythm. Instead, breath holding merely suppresses its expression by voluntarily holding the chest at a certain volume. At the time of writing, no simple explanation for the break point existed. It is known to be caused by partial pressures of blood gases activating the carotid arterial chemoreceptors. They are peripheral sensory neurons that detect changes in chemical concentrations, including low oxygen (hypoxia) and high carbon dioxide (hypercapnia). Both hypoxia and hypercapnia are signs of breath holding and both are detected by the chemoreceptors. These receptors send nerve signals to the vasomotor center of the medulla which eventually overrides the conscious breath holding.

The breaking point can be postponed by large lung inflations, hyperoxia and hypocapnia, and it is shortened by increased metabolic rates.

Reference
- Parkes, Exp Physiol (2006); 91(1): 1-15


How different is an introverts brain different from an extroverts?

I am not sure if this answers your question, but according to the article "The Difference Between Introverts and Extroverts" (Gallagher, 1999), the main differences between introverts and extraverts are where the main brain activity occurs (as seen by positron emission tomography (PET) measurements).  The full PET study is in the article "Cerebral Blood Flow and Personality: A Positron Emission Tomography Study " (Johnson et al. 1999).

The conclusion of the Johnson et al. paper states:

  This study revealed a pattern of increased blood flow in the frontal lobes associated with introversion. ... in the present study, there were more cortical regions associated with introversion than with extraversion. ...in the present study, extraverts did show lower blood flow in several regions in the behavioral inhibition system, namely, the frontal lobes and the hippocampus.

Some images of brain activity is included in a more recent article "Differences in regional brain volume related to the extraversion–introversion dimension—A voxel based morphometry study" (Forsman et al. 2012).  Forsman's article looks at activity in  the white and grey matter of the brain.

I hope this helps.


For fundamental mammalian cell biology, and molecular biology, and fundamental biochemistry: "The Molecular Biology of the Cell" by Bruce Alberts and colleagues.

It is mostly written for first semester students at university and thus summarizes the basics in a very clear way. Moreover they state whenever findings have some ambiguity, and they use many nicely drawn pictures to convey abstract concepts.  Despite its approachability it covers most fundamental topics of many domains (also diseases).

While the ~2,000 pages of the complete edition might seem a bit intimidating they rarely provide unnecessary detail, and the individual chapters are written in a very concise way (even allowing you to skip some of them).


Often genes or other DNA fragments are inserted into an expression vector and used to transform bacteria or other cells. When a mixture of vectors is used containing various DNA fragments (e.g. a chopped-up genome), then individual (bacterial) colonies need to be isolated to make sure they carry only one insert. This can be done, e.g., by plating the transformed cell culture such that individual colonies are obtained. Theoretically, one colony represents the offspring of one cell, hence the colony as a whole has one DNA insert and is a clonal isolate.


What spider is this? Is it dangerous to humans?

This is most likely a spider from the genus Argiope, which has a few members native to India. See here for a list, I think this is most likely
Argiope pulchella, see the image from the Wikipedia:

Wikipedia also says that these spiders hunt insects, but are not dangerous for humans.


How is a substance classified as a vitamin?

1) Vitamin D is a bit of an umbrella term that actually refers to a whole group of related molecules. One of these, vitamin D$_3$ (cholecalciferol) is formed spontaneously from ergosterol in the presence of UV radiation, which happens in the skin when exposed to sunlight. Cholecalciferol is then converted to calcitriol, the active form, in the liver. Here is some information on the metabolic pathway.

2) Actually, if you consider the definition carefully, only a few molecules are essential for human growth and nutrition, in the sense that they cannot be replaced with something else, and are required in small amounts. For example, the majority of amino acids can be synthesized by the body from other amino acids, and are therefore nonessential. The remaining amino acids are essential nutrients because there is no synthesis pathway -- but they are required in large amounts and not considered vitamins. This distinction between "large" and "small" might sound strange, but it is important since it tells you if the nutrient is consumed for energy/growth (like amino acids) or has some "supporting" role, such as antioxidants, cofactors for enzymes, or hormones (like the vitamins).

That said, it is sometimes a bit fuzzy if a nutrient is essential or not. Vitamin D is a borderline case: it should perhaps not be called a vitamin, since it can in fact be synthesized by most adults in adequate amounts. However, vitamin D deficiency can occur if one does not get enough exposure to sunlight, and this can cause the disease rickets. Some researchers have suggested that this is one factor behind evolution of lighter skin in northern human populations, since dark skin pigment reduces UV radiation needed for vitamin D synthesis.


Role of Prevalence in Estimating Coronavirus Mortality

I think you're talking (setting aside false-positive/low-specificity testing problems for the moment) about the difference between infection fatality ratio (IFR, fraction of infected people who die from disease) and the case fatality ratio (CFR, fraction of clinically defined "cases" who die from disease). The difference between these two depends completely, as you suggest, on the difference between the population that gets infected and the population that is defined as a "case" (which could vary a lot: is it people who have a cough? fever & cough? request testing? are admitted to the hospital? are admitted to the ICU?).

Because most of the people aboard the Diamond Princess cruise ship were tested (3063/3711), we can have a reasonably good idea of the fraction infected (unlike the usual scenario where most asymptomatic cases are never noticed). The authors of this (not yet peer-reviewed) study concluded that:

  the all-age cIFR on the Diamond Princess was 1.2% (0.38–2.7%) and the cCFR was 2.3% (0.75–5.3%)

(where 'c' in cIFR and cCFR stands for 'corrected'; these are estimates that account for the fact that we don't yet know the outcome for all patients).

Other issues to think about:

sensitivity and specificity of testing (false positive/negative rates)
variation with/adjustment for age (discussed in the paper)
variation by medical/social context (e.g. Wuhan vs Iran vs places where cases are caught early and the medical infrastructure isn't overwhelmed)

Russell et al., "Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship". https://cmmid.github.io/topics/covid19/severity/diamond_cruise_cfr_estimates.html


Do factors other than concentration gradient and membrane permeability affect the diffusion potential?

You can determine the diffusion potential mathematically with the Nernst equation. If it's not in the Nernst equation, it's not necessary.
The charge of the ion matters (including valance), the temperature matters. Some universal constants are in the equation but these don't vary.
Other factors that potentially matter are found in the other parameters, like the permability.


Diffusion approximation to genetic drift

It does indeed proceed from the Wright-Fisher model, specifically from its diffusion process approximation.

If the population is size $N$, then at generation $t$ the number of alleles is $A(t)$, and so the frequency of alleles is $x(t) = A(t)/(2N)$, assuming the diploid case. Then Wright-Fisher says that:
$$ A(t+1)\mid A(t) \sim \text{Bin}(2N,x(t)) $$
So the distribution of the next generation's count, given the last one, is binomially distributed (under random mating).
One can find that, for a binomially distributed random variable $b\sim \text{Bin}(m,p)$, the mean and variance are given by:
$$ \mathbb{E}[b]=mp\;\;\;\;\;\;\&\;\;\;\;\;\;\mathbb{V}[b]=mp(1-p) $$
Thus, we get that
$$ \mathbb{E}[A(t+1)\mid A(t)] = 2N x(t)
\;\;\;\;\;\;\&\;\;\;\;\;\;
\mathbb{V}[A(t+1)\mid A(t)] = 2N x(t)[1-x(t)] $$
Applying $x(t)=A(t)/(2N)$, we see that
\begin{align}
\mathbb{E}[x(t+1) \mid x(t)]   &= \frac{1}{2N}\mathbb{E}[A(t+1)\mid A(t)]= x(t) \\
\mathbb{V}[x(t+1)\mid x(t)] &= \frac{1}{(2N)^2}\mathbb{V}[A(t+1)\mid A(t)] = \frac{x(t)[1-x(t)]}{2N}
\end{align}
using the fact that $\mathbb{V}[cX]=c^2\mathbb{V}[X]$.

We can relate this to forward Kolmogorov as follows. Recall that the binomial distribution can be approximated by a normal distribution, with mean $\mu$ and variance $\sigma^2$ given by the mean and variance of the binomial. This tells us that: $$ x(t+\delta t)\mid x(t) \sim \mathcal{N}(x(t),(\delta t)x(t)[1-x(t)]/(2N)) $$
The properties of the normal distribution then imply that $$ \Delta x_t=x(t+\delta t) - x(t)\sim\mathcal{N}(0,\sigma^2(x_t)\delta t) $$
where $\sigma^2(x_t) = x(t)[1-x(t)]/(2N)$.
This implies the following equality (in distribution):
$$ \Delta x_t = \sigma(x_t)\Delta W_t $$
where $\Delta W_t\sim \mathcal{N}(0,\delta t)$. As $\delta t\rightarrow 0$, we get a stochastic differential equation,
$$ dx_t = \sigma(x_t)dW_t $$
where the solutions are Markov random processes (unlike e.g. ODEs where there is only one solution and it is a deterministic path; think of it as a noisy ODE), specifically in this case an Ito diffusion. Note the SDE has no $dt$ component since the increment mean was $0$. If we then consider the density function for the random process $p(x,t)$, it must satisfy the Fokker-Planck (Forward Kolmogorov) equation: $$ \partial_t p(x,t) = -\partial_{xx}[p(x,t)\sigma^2(x)/2] $$
which gives a probability distribution over the allelic frequency value at each time point (given some initial value I've not specified here).
Note that $V(x)=\sigma^2(x)$.

In terms of intuition, I'm not really sure. Essentially $V(x)$ measures how much perturbation in the allelic frequency you can expect to happen each generation due to purely random effects, i.e. genetic drift. Notice that there is no perturbation when $x=0$ or $x=1$, i.e. no random changes can happen if no one or everyone has the allele. Notice also that this variance is exactly the variance of a Bernoulli distribution. It's like we've distilled the individual-level model to a population-level model that simply looks at the frequency of the binary choice of allele presence, I guess.
The variance (noise) is maximal when the frequency is $1/2$. It's sort of pushing the allele away from the middle, by increasing noise when one goes there; one might expect that (if run long enough) any such model will hit and get stuck at $0$ or $1$ (not sure if this is true).
I looked a bit if there were any other interesting interpretations of the sde considered here (e.g. in physics), but couldn't find any. Basically, it would be equivalent to a heat equation, spreading under some potential function controlled by $\sigma$.

Your question is closely related to this one. My answer largely follows Tataru et al, Statistical Inference in the Wright–Fisher Model Using Allele Frequency Data.


Do the mother's genes determine the sons' (heredity) intelligence more than the father's?

You might want to take a look on the wikipedia site for x-linked recessive inheritance. The article by Turner mentions that out of 325 known recessively inherited genes associated with mental retardation, 17 are positioned on the x-chromosome. In case you are a male and have one of these seventeen recessive genes on your x-chromosome causing you in some way to be less intelligent, you must have inherited that gene from your mother. In those cases it is more like you inherit "stupidity" genes from your mother, who might be an unaffected carrier of the stupidity gene due to the fact that she has two X-chromosomes and the gene causing mental retardation is only present in one of those x-chromosomes.

There might of course also be recessive genes on the X-chromosome causing males, who has only one X-chromosome, to be smarter but genes that are not causing disease might not be so interesting to investigate from a medical point of view.

According to wikipedia there are 499 x-linked genes and the total number of "vaguely defined traits" are 983.

I would say that yes, as a man you inherit more genes from your mother than from you father affecting your intelligence due to the fact that some genes on your x-chromosome affect your intelligence. Whatever the 499 x-linked genes do, you could say that traits affected by those genes to a greater extent are determined by your mothers genes than by your fathers, if you are a male.

Technically you would of course also have to take the genes on the y-chromosome, which are much fewer, into account.

If we approximate that the human male genome has a total of 20000 protein coding genes, the x-chromosome has 800 protein coding genes and the y-chromosome has 60 protein coding genes a male gets on average (19940/(19940+19200))*100 = approximately 50.945 percent of his protein coding genes from his mother. Now for a highly polygenic trait depending on genes homogenously distributed on all chromosomes one would naively expect that 50.945 percent of the genes contributing to that trait is inherited from his mother.


In cell division, are daughter cells identical?

Actually, the answer is not obvious. @RoSiv gives the textbook case of symmetric cell division, where the two new cells can indeed be considered identical, and this is valid in many cases. But there are also cases of asymmetric cell division, where the "mother" and "daughter" cell are clearly different.

In asymmetric cell division, the parent cell is polarized already before division by gathering certain proteins at one end of the plasma membrane. Therefore, during replication one of the the two new cells obtains certain proteins while the other does not, which makes them distinct. See this article for details.

Asymmetric cell division occurs among other things during embryo development, where it is important to establish body plan asymmetry. It is also the basis for the stem cell concept: stem cells are thought to divide asymmetrically so that the "mother cell" remains a stem cell (stays immortal) while the "daughter cell" becomes mortal and differentiates.


Does the term "Biophysics" have two different meanings?

Short answer
Biophysics encompasses the study of biological systems in physical terms and the methods involved to achieve that goal.

Background
I'll approach this question first from the area of research I'm actively involved in at the time of this writing -

Psychophysics is

  [...] the scientific study of the relationship between stimuli
  (specified in physical terms) and the sensations and perceptions
  evoked by these stimuli. The term psychophysics is used to denote both
  the substantive study of stimulus-response relationships and the
  methodologies used for this study.

source: (RIT)

In short this would translate as

  The study of the sensation and perception of physical stimuli and the methods involved to accomplish this.

To illustrate I will cite the titles of two well-read articles in this area highlighting the dual use (study & methods):

Issues in psychophysical measurement
Spatial hearing: the psychophysics of human sound localization

And to illustrate a compelling example that merges both uses in one:

Psychophysics: Method and theory

Now to  your question; I've done electrophysiology which might, arguably, be considered biophysics, but I'm less comfortable in the arena of biophysics. But given my reasoning above, you can safely replace Psycho with Bio and say that Biophysics is

  The study of biological systems in physical terms and the methods involved to accomplish this.

For example, the University of Wisconsin describes it as:

  [B]iophysics combines state-of-the-art physical measurements with computational models to understand the detailed physical mechanisms underlying the behavior of complex biological systems.


What advantage does an enzyme serve over catalysis by the addition of heat energy?

Enzymes have two benefits over raising the temperature:

First, reducing the activation energy by reusable enzymes is far more energy-efficient, apart from the fact that the required temperature would vary for different reactions.

Second, enzymes are able to be controlled by allosteric mechanisms, which facilitates metabolic control by feedback loops, feedforward motivs and receptor-mediated processes. In the example of glycolysis this enables the cell to fine-control its supply with energy equivalents (see figure from Wikimedia Commons below). This mechanism may be the most important function of enzymes.

Reference

William C. Plaxton: Principles of Metabolic Control. In Kenneth B. Storey (ed.): Functional Metabolism: Regulation and Adaptation, John Wiley & Sons, Inc. 2004


We can only very indirectly and tentatively ascribe emotions/feelings to animals if we understand their brains functionally, and use functional imaging. This is difficult in practice. There is also a crucial difference in science between the subjective world (happy) and objective world (smiling).

In ethology, you can only observe behavior and its consequences. Stimuli can be appetitive and aversive, positive or negative. Insects, reptiles and mammals can similarly differentiate between sweet water (which they seek out) and bitter water (which they normally avoid). Those are easier behaviors to identify. Of course, in reality, an emotional state is made up of a complex multi-dimensional spectrum of multiple measures (satiety vs. hunger, anxiety vs. relaxation, happiness vs. unhappiness, fear vs. safety, sadness vs. unsadness, etc.) simultaneously. There is also a difference between the measurement and the internal reality. Additionally, there's the choice of measurement and the internal reality, too. One could measure happiness by width of your smile at a given time, but that would not be a very valid and reliable measurement. This is the general difficulty with measuring and detecting emotion - behavior is a more objective quantification.

If you were studying a new species of human, which could not talk or report to you using a language about how it 'felt', and had a brain significantly different from ours, we would also be unwise to ascribe specific emotions so callously. Not because the specimen would be incapable of feeling emotions, but because we wouldn't have the tools to check and verify internal emotional states, or probe whether the snake was conscious of an emotion regardless of its behavior.

However, we do believe that emotions require a big central nervous system to exist. Snakes certainly have large enough brains to experience fear and pleasure. It seems that most large vertebrates can, certainly mammals can such as mice. Whether reptiles or even insects have the 'cerebral capacity' for non-primitive (read: non-humanlike) is an open question.


Which biological process causes the feeling of having "Butterflies in the body"?

These sorts of behaviors are mediated through activation of the sympathetic pathway of the autonomic nervous system.


Tympanic displacement measurement (TMD) is a well studied field using hi-tech tools (i.e. stroboscopic holography), and complex units:
Vm = volume displacement in nl nanoLiters.
μm/pa (UDTF) = Linear tympanic membrane displacement is known as the umbo displacement transfer function.

The graph on the left gives you a value of 0.8-0.6 = 0.2 microns:

The graph above can be seen as resonances in an images sequence of stroboscopic holograms of tympanum (cool name to call your band) https://i.stack.imgur.com/fD6E9.jpg

According to this graph a 94dB sound wave gives you 0.1 micron displacement and a 100dB sine wave gives you 2pa, 0.2 microns.
https://i.stack.imgur.com/O7nQL.jpg

The first research document on google gave me a volume displacement from -120 to -700 nl.

1000 nano Liter = 1mm3

So the TMD volume displacement when very loud can be 1-2mm3, and eardrum rupture probably occurs from 10 to 100 mm3.

There are even muscles in the ear that can modify the way that you hear, i.e. the stapedius muscle which protects against low fequencies, and perhaps which can focus your eardrum elasticity modulus to let hear different frequencies, perhaps conciously? fascinating, I don't know.

See also pages describing elastic measurement of the eardrum, energy transfer by the tympanum by the cone, through these two google search phrasings: "eardrum response measurement" and "tympanic membrane displacement measurement"

Here is research comparing the eardrum to microphone design which is written easily.


What's the evidence against SARS-CoV-2 being engineered by humans?

At the moment, there is very little scientific literature about this, but I found two papers that address the problem and are fairly easy to understand. You can find them in the references. Reference 1 is probably the most interesting and is the basis for this answer.
Edit: It is also interesting to read reference 2 on the origin of SARS-CoV-2; the article also addresses some of the conspiracy theories.
As far as I can see, there are a few major points taken up by conspiracy theories.
1. SARS-CoV-2 leaked from a lab in which research on the Bat CoV (RaTG13) was done:
Unlikely, since the viruses share only around 96% sequence homology, which translates into more than 1100 sites where the sequence of SARS-CoV-2 viruses is different from RaTG13. The mutations are distributed throughout the viral genome in a natural evolutionary pattern, making it highly unlikely that SARS-CoV-2 is a direct descendant from RaTG13. For comparison, the original SARS-CoV and the intermediate host palm civet SARS-like CoV from which it originated shared 99.8% sequence homology, showing a much closer relation.
2. The S (spike) protein from bat SARS-CoV cannot be used to enter human cells via the human ACE2 receptor and therefore has been adapted in the lab:
This is untrue, since a 2013 study of a novel bat coronavirus was published showing the ability of the virus to enter cells via the ACE2 receptor. See reference 3 for details.
3. The spike protein of SARS-CoV contains a unique inserted sequence (1378 bp) located in the middle of its spike glycoprotein gene that had no match in other coronaviruses:
As shown in reference 4, the sequence comparison of the SARS-CoV-2 with closely related other coronaviruses shows that this sequence is not unique to the new virus but is already present in older strains. It shows some difference due to inserted mutations.
4. The claim that SARS-CoV-2 contains four insertions from HIV-1:
The paper claiming this has now been retracted due to severe criticism, and additionally a renowned HIV expert published an analysis (reference 5) demonstrating that the HIV-1 claimed insertions are random rather than targeted.
5. The claim that the SARS-CoV-2 virus is completely man-made:
To design such a "weapon grade" virus in the lab, the design would usually start from a known virus backbone and then introduce logical changes (for example, complete genes from other viruses). This cannot be seen in the genome of the virus; rather, you see randomly distributed changes throughout the genome coming from virus evolution and not directed cloning. It is more likely that this virus originates from the recombination of a bat CoV (to which it is closely, but not directly related) and another, not yet known CoV in an intermediate host, like the palm civet for the 2003 CoV.
References:

No credible evidence supporting claims of the laboratory engineering
of SARS-CoV-2
The proximal origin of SARS-CoV-2
Isolation and characterization of a bat SARS-like coronavirus that
uses the ACE2 receptor
Is SARS-CoV-2 originated from laboratory? A rebuttal to the claim of
formation via laboratory recombination
HIV-1 did not contribute to the 2019-nCoV genome


Can you please identify this mosquito-like insect?

It is most certainly a fly from Chironomidae, which belongs to the same suborder (Nematocera) as Mosquitoes (Culicidae). They have an overall resemblance to mosquitoes, but lack the large sucking mouthparts, and often have the large feathery antenna that are seen in your pictures. Some species are found in large swarms in early spring (but also later in the summer). Larvae can be found in most freshwater, and are called bloodworms due to red colour (high in hemoglobin, adapted to live in oxygen-poor sediment environments)
I doubt that the exact species can be determined from these pictures though.


Isoleucine only has one delta carbon, which we can just call CD. But it seems like some PDB files still name it CD1, and hence programs map CD1 to CD in this case. (E.g. see this tutorial where this practice is shown.)


How do aminoacyl-tRNA synthases distinguish between similar amino acids?

Aminoacyl-tRNA sythetases are highly specific to their corresponding amino acid. First, the activation site, where the amino acid binds, constitutes a complex network of intermolecular interactions. For example, threonine, catalyzed by  threonyl-tRNA synthetase, is very similar to valine and serine. Valine has a methyl group instead of the hydroxy group of threonine, and serine, on the other side, has no additional methyl side group. Uniquely to threonyl-tRNA synthetase, it contains a Zn2+ ion that exhibits an interaction structure specific to threonine. Nonetheless, the threonyl-tRNA synthetase could still be mischarged with serine because the zinc ion site is not specific enough, leading to 1% mischarged tRNAs. For this purpose, aminoacyl-tRNA synthetases have a second, editing site that proofreads the charged tRNA.  The editing site can recognize serine and cleave it from the tRNA.

Figure: Interaction network of the activation site of the threonyl-tRNA synthetase in A. pernix. The  threonine-AMP  is shown in green.

Sources:

a Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Section 29.2, Aminoacyl-Transfer RNA Synthetases Read the Genetic Code. Available from: https://www.ncbi.nlm.nih.gov/books/NBK22356/

b Nagaoka, Yoshiyuki, et al. "EVOLUTION AND tRNA RECOGNITION OF THREONYL-tRNA SYNTHETASE FROM AN EXTREME THERMOPHILIC ARCHAEON, Aeropyrum pernix K1." Viva Origino 1.31 (2003), http://www.origin-life.gr.jp/3101/3101062/3101062.html


This depends on the technology you're using for the interaction detection.  Surface Plasmon Resonance and Isothermal Titration Calorimetry (and others) don't require tagged proteins of any kind.  Though it doesn't hurt either one.

If you're looking purely at chromotography, any tag that will stably capture. I commonly see GST, FLAG, and MBP in order of occurrence.


What is happening at the electrode interface when the electrical field is modified due to the change of ion concentration after an AP?

There is an art to expressing the nature of any kind of uncertainty in writing, and especially in experimental literature, to stating no more than has been empirically shown.  An electrode interface only measures a one dimensional trace of what actually happens during an action potential cycle or spike, and it could be that in most of the literature, the precise mechanism by which the spike is measurable takes lower priority than the existence (or non-existence) of a particular signal.
According to Hodgkin-Huxley theory, the action potential is controlled through changes to the ionic permeability of certain membranes.  The precise mechanisms by which this happens depend on the molecular structure of channels through which sodium and potassium ions flow.  However, it is not hard to explain how a change in the permeability of a membrane can cause changes to an electric potential gradient (over 'large' length scales); the "deep concept" at work here is the second law of thermodynamics.
Let's suppose that you have two ions, one positive and one negative, confined to one side of a box as shown:

You might notice that there are more negative ions than there are positive ions, so there would be a nonzero electric potential gradient between the left and right hand sides of the container.
Now let's suppose that the confining membrane is replaced with one that allows only negative ions to pass (through the purple or tapered channels.)  You might expect a fraction of the negative charge to flow over to the other side of container where the potential is slightly higher (as shown):

The result is that the original potential gradient (from left to right) is dampened slightly.
The OP is probably aware of this, but it turns out that replacing the membrane with one that allows positive charge to pass through results in a fraction of the total positive ions moving to the left side of the chamber (even though it would be attracted to the right hand side by the net negative charge)*.  The reason for this is that the entropy gained by the first positive charge to move into the (log-macroscopically large) empty chamber vastly outweighs the (microscopic) entropy cost of leaving the occupied chamber with fewer positive ions to offset the negative ones.

This results in a slightly larger potential gradient than in the first (impermeable) case, as there are now positive charges in the region of higher electric potential.
The electrode can pick up on changes to the potential gradient by "grounding" the circuit at several points.  In particular, this requires a circuit that is soft or sensitive enough that it does not disturb the ambient potential significantly (a tape measure or height rod adapts to your height, not vice versa.)  That is, whatever current flows between the electrodes should be weak enough that it does not completely drain or equilibrate whatever local potential difference might exist, and other circuit elements should be weak enough that they do not cause flooding or, in a sense, drought of the natural electrodynamic state.  Beyond this, the complex and densely packed environment of neurons would make it a challenge to place electrodes to isolate a single action potential, or even a potentially useful signal across several action potentials.  Also, there is inevitably a certain amount of excessive unnatural current flow below a certain length scale (the scale at which the electrode starts to look like a bulk conductor.) Because of this, neuroscientists probably care more about the presence or absence of noise at this point than about the precise physiological origin of the signal, except insofar as the disturbance from the electrode is correctable and within tolerance.
*If the experiment is performed at nonzero temperature, which seems to be unavoidable.


How does temperature affect photosynthesis?

Your experiment should look something like this: The effect of temperature on photosynthetic rate of Elodea (pondweed). I assume you used Elodea canadensis for your test. Maybe the plant is already a bit "exhausted" - try to take a different branch. Or maybe it needs more time to get used to the new temperature.


Two sets of chromosome and the sequencing output

This is very similar to your previous questions, but apparently you are not understanding the explanations we are giving, so I'll try again, by giving a (hopefully not-too-technical) explanation of how next-generation genomic sequencing works. To avoid confusion, we'll assume we're working with human samples.

First, many individual cells are collected (the number depends on the application, it can range from 1 cell to millions or more), and their DNA is collected. This process destroys the cells, and all of the copies of all of the chromosomes are mixed together. As mentioned in your other question, there is no possible way to determine which chromosomal sequence is maternal, and which is paternal. Scientists typically don't even think about this.

Next, the collected DNA sample is purified and broken down into small pieces, then ligated to certain adapters to label them for the sequencing reaction. The sample is then amplified in a standard PCR to create starting material that is many times more plentiful than before. This is the DNA library.

Finally, the sample is ready for sequencing. What exactly happens next depends on which sequencer you're using - Illumina, Ion Torrent, 454, or SOLiD are the most frequently-used instrument brands. Within each brand, Illumina for example, there are multiple different kinds of sequencing.

However, we'll just gloss over all that and get right to the output - the instrument produces a file consisting of "reads" from the reaction. These reads are DNA sequences consisting of As, Ts, Gs, and Cs - the "letters" (also known as "bases") of DNA. The lengths of the reads vary by technology and instrument, generally in the range of 100 to 700 bases. One machine, though - the PacBio RS II, can produce high-quality reads up to 14,000 bases, although to my knowledge it is not in widespread use.

Here is where the computers come in. The individual reads overlap each other to varying degrees, depending on the quality of information you're seeking and whether or not you're looking for rare events, such as a small population of mutated cells taken from a heterogeneous tumor. For our purposes, we'll say our sequencing run resulted in a 25-fold overlap, meaning each base in the original DNA sequence of the sample donor was sequenced an average of 25 different times. The computers can then "align" the sequences, either just among themselves, without a template, or, more commonly, to a pre-existing sequence template, such as a reference genome. Eventually, the computer will spit out two sequences - the forward and the reverse strand (although typically you'd just pick one strand, and use the reverse strand for error-checking). This sequence is the average sequence of the chromosome, or other region of DNA being targeted.

From Wikimedia Commons: Mapping Reads.png

However, one can pretty easily detect mutations, such as single nucleotide polymorphisms (SNPs), deletions, insertions, etc. In the case of a SNP (pronounced "snip"), one allele of a gene has one sequence on one chromosome (lets say ATTCGTAAC) while another allele of a gene on the other chromosome has a single-base change (ATTCTTAAC, for example, where the G was changed to a T).

The point, directly relating to your question, is this: The final sequence that eventually comes out after all the computer wrangling is a single sequence with certain areas that may differ from chromosome to chromosome, or cell to cell in the original sample. There is no way to determine if the G in our example above was on the maternal or paternal chromosome. There is also no way to tell if, 20,000 bases down the line, another mutation is on the same chromosome as the G, because no single read can (currently) span that entire length. You might have a pretty good chance of determining that if the other mutation is, for example, 300 bases away, because many technologies can perform high-quality reads longer than that, so you'd just have to find the individual ones that contain both positions.

I know this was a little long-winded, but hopefully I was able to answer your question.


Menthol is stimulating action potential at cells which are inducing thermoception. As far as I have found out it does not have any effect beyond that. The patients only feel like they can breath better while it could not be proven that they actual do.

https://www.ncbi.nlm.nih.gov/m/pubmed/18702906/

The blood vessel thing : In general "cold" is a cause for vasoconstriction - that might lead to the conclusion that menthol is doing the same. I have no experental background on that but - after online research :-D- it seems like that menthol causes vasodilatation.


Biological nomenclature can be impenetrable. Almost certainly, at some point in history, there were cyclins designated with these letters. Researchers would have discovered apparently novel cyclins which were subsequently determined to be part of an existing family and renamed. For example, this paper reports the discovery of:

  a new cyclin, cyclin M, which appears to be most closely related to cyclin L. Its biological function is unknown, but it is related to cyclins that regulate transcription.

It is now called cyclin L2.

I hope this answer satisfies you to some extent. I doubt anyone is going to sift through the literature and try and determine why all cyclins are are named as they are; that is certainly a losing proposition. The naming of genes/proteins is rather trivial and doesn't generally follow any specific set of rules. Outside of curiosity, the knowledge of cyclin naming doesn't have much, if any, practical relevance.


Are there examples of human genes using meiotic drive?

Yes! Jeffrey and Neumann 2002 report evidence of meiotic drive at a recombination hot spot in the MHC.

Note that mtDNA could arguably be considered as an extreme case of sex-dependent meiotic drive. Mothers transmit mtDNA at rate of almost 1, while fathers transmit mtDNA at a rate of almost 0.


Why is HIV so large compared to other viruses?

There are many other things inside the HIV capsid besides RNA. The ssRNA is bound to the p7 nucleocapsid protein, the p6 late assembly protein, as well as integrase and reverse transcriptase, both of which are vital for infectivity. Also enclosed within the virion are Vif (Viral Infectivity Factor), protease, Nef (Negative Regulatory Factor), Tat (HIV Transactivator), and Vpr (Viral Protein R). Surrounding the capsid is a matrix formed by the p17 viral protein, and finally the lipid membrane envelope (taken from the host cell upon budding), which contains host cell proteins as well as the vital trimer of gp120/gp41 heterodimers, which bind to the target cell.

From Wikimedia

HIV (and many other viruses) depend on binding to certain cell surface receptors, and a larger total size increases the chances of binding to multiple receptors and potentially triggering receptor-mediated endocytosis, if that is part of the virus's entry strategy.

The naked λ phage binds to the lamB porin of single-celled prokaryotic E. coli by way of the phage's J protein and injects its DNA load into the bacterium, where host factors circularize and supercoil it, allowing for transcription to begin. While the phage's genomic material can be integrated into the host's chromosome, it is not required. Additionally, there is no nuclear barrier to cross.

From Wikimedia, numbers in parentheses are copies per virion.

On the other hand, HIV is a highly complex enveloped lentivirus that targets very specific cells in its multicellular eukaryotic host HIV requires reverse transcription and the assembly of a large pre-integration complex to transport the viral DNA into the nucleus and integrate it into the host's genome, all before it can even start producing new viral proteins.

Trying to compare the "packing efficiency" of HIV to the λ phage isn't just comparing apples to oranges, it's comparing apples to goats. The two viruses are completely different, with the only essential similarities being that they are viruses that infect cells.


Why do plants' leaves become enlarged in low light areas?

I have no idea of the biological mechanisms behind what I'm about to propose. Consider this a hypothesis.

If the purpose of the leave is to collect sunlight for photosynthesis, then the behavior you mention is predictable. I order of trying to maintain a healthy flux of light in dim conditions, the plant adapts by increasing the area of its leaves. Once back in a well-lit environment, the need for larger leaves fades and new leaves are thus smaller, but still catch as much light. Of course, there must be limits to the extent of leaf area variation that one plant can handle.

As for the stem structure, I can only guess it's because plants spend more energy on leaf building than stem maintenance when under such stresses.


Can anyone tell me what type of fish this is?

Not an expert, but an online search for bioluminscent fish led me to a bioluminescent toadfish called Porichthys porosissimus. The ventral angle of your specimen looks a lot like the photos I could find...

 Source: Robertson, R on Fishbase

Like many midshipman fish, P. porosissimus have photophores (those dots in your specimen) that glow to attract prey:

 Source: W. Ward (Rutgers Center for Research and Education in Bioluminescence and Biotechnology)


Relationship between the ambiguity (wobble) at codon position 3 in elongation and codon position 1 in initiation

Summary

The difference in the nature of codon–anticodon ambiguity seen between bacterial initiation and elongation lies not only in the position of the codon at which it occurs (5′ v 3′, respectively), but in the partial or absolute nature of the interactions (only some AUG and GUG etc. codons initiate and insert fMet, whereas all AUU and AUC codons will recognize the Phe-tRNA with anticodon, 3′-UAG-5′. It can be accounted for by the quite different molecular interactions occurring at the ribosomal P-site (for initiation) and the A-site (for elongation) and the importance of the base-pairing between the Shine & Dalgarno (RBS) region of the mRNA for initiation.

Wobble in context

Wobble was the term applied by Crick in 1966 to the non-standard base-pairing between the 3′ position of mRNA codons and the 5′ position of anticodons of certain tRNAs. To avoid violating the genetic code Crick assumed strict base pairing at the first two codon positions and asked the question “If one sRNA [old term for tRNA] codes both XYU and XYC [because of experimental evidence that this might be the case for Phe codons], how is it done?”. And then, given the many ways bases might be paired added the constraint “How many base pairs are there in which glycosidic bonds occur in a position close to the standard one?”.

On the basis of geometry Crick predicted that anticodon 5′-U might be able to pair with a codon 3′-G (in addition to the standard A), and anticodon 5′-G with codon 3′-U (in addition to the standard C). He — unwisely in my opinion — referred to these predictions (and his prediction for inosine, I) as ‘rules’. The predictions are summarized below, together with the actual pattern that has since emerged.

It should be noted that although the two predictions involving G=U base pairs would appear reciprocal, that involving an anticodon 5′-U does not occur except in mitochondria, were it is incorrect in that the interactions are not restricted to Crick’s ‘rules’.

The subsequent elucidation of the structure of phe-tRNA by Quigley and Rich in 1976 suggested why the wobble occurred at the 5′ position of the anticodon. This position (G34 in my modification of their figure, below) lacks the base-stacking that would be expected to constrain the interactions at the other two positions of the anticodon, and which was aided by a modified base (yW37) 3′ to the anticodon.

As the amino acid, methionine, has only a single codon (AUG) in the genetic code, one would expect it to have a tRNA that does not allow wobble at the 5′-codon position. This turns out to be the case:

  Both the tRNAmet for elongation and initiation have
  the anticodon 3′-UAC-5′.

In summary: 5′-codon wobble allows mRNA to be decoded accurately by fewer than the 61 amino acid codons, and one can speculate that its emergence involved evolution of both the structures of tRNAs and the ribosomal A-site.

Initiation and decoding ambiguity

In bacteria (eubacteria) there are two main differences in codon recognition during translation from that in elongation.

There is a single specific tRNA species involved which, uniquely, can interact with initiation factors and be bound to the P-site of the ribosome.
Interaction is required between the 16S rRNA of the 30S ribosomal subunit and a polypurine sequence 5′ of the initiation codon (the Shine & Dalgarno sequence or ribosome-binding site) in addition to the codon–anticodon interaction.

To adopt an extreme position, the situation in initiation may almost be thought of as one in which the fMet-tRNA is bound at the P-site of the small ribosomal subunit waiting for mRNA to bind, in contrast to elongator Met-tRNA binding to an A-site with the elongation codon AUG. The energy provided by the Shine–Dalgarno interactions may thus be enough to allow initiation if one of the initiation codon bases is incorrect. This raises at least two questions:

What advantage would allowing such ambiguous recognition have?
Why is the ambiguity in the first codon position and how does it operate in molecular terms?

I have no answer to the first question. Perhaps it has none, but is tolerated because it has no disadvantages either. The second question is the crux of the poster’s concerns.

First, ambiguity at the 3′-position of the codon would not be expected on grounds of structure or precedent: the table above shows anticodon 5′-C only base-pairs with codon 3′-G.

Second, the anticodon loop of initiator tRNAmet differs from that of elongator tRNAmet in having an internal-facing rather than an external-facing disposition (Woo et al., 1980). Furthermore it lacks a modified base 3′ to the anticodon.

Third, the interactions between initiator and elongator tRNAs with the rRNA at the A- and P-sites, respectively are quite different (Berk et al. 2006), conceivably allowing more flexibility at the 3′-anticodon position.

Despite the fact that the predicted anticodon-U/codon-G wobble never occurs at the A-site, it is reasonable to suppose that structural differences allow it at the P-site, explaining the second bacterial initiation codon, GUG. As regards UUG, U=U base-pairs were considered by Crick but regarded as “rather close together”. Presumably in certain contexts this is not too energetically unfavourable to be prevented.

Finally…

The poster asked:

  Am I interpreting this correctly and there's no "Crick" wobble in the AUG > GUG > UUG start codon, but rather another wobble-like mechanism that explains the start codons' first nucleotide wobble-like behavior?

To which I would reply that:

  There is not and cannot be any wobble at the 3′-position of either initiation or elongation AUG codons of bacteria because it would involve non-standard base-pairing of the anticodon C. To the extent that the ambiguity at the 5′-position of the alternative initiation codons used (GUG>UUG) follows a pattern consistent with the most likely non-standard base-pairing predicted by Crick, it would seem to involve base-pairing achieved by movement (wobble) of the 3′-anticodon residue U of initiator fMet-tRNA.


What does the 4DTv (four-fold synonymous) mean?

After one month of research, I have some insights about it.

First of all, more than "fourfold-synonymous", the correct research is fourfold degeneracy. The genetic code is degenerate, in the sense that there is usually more than 1 codon encoding a certain amino-acid. The degeneracy usually takes place in the third position of the codon, that can be 2-, 3- or 4-fold degenerate. A 4-fold degenerate site would be the third position of a codon, where regardless of which nucleotide you have, the outcome doesn't change. Example: GGT, GGC, GGA, GGG all code for Glycine. As there are four variants at the third site of the codon, the third site is said to be fourfold-degenerate (4D). As the encoded amino-acid does not change, there is virtually no selective pressure on these variants, therefore they can be used as a "clock" to estimate times, given that you know the mutation rates per position.

Now for your other questions:
Yes, the value ranges from 0 to ~0.5, and this can be explained in a simple way. Transversions (Tv) are considered to be more rare than transitions (Ti). Therefore, if you calculate the ratio of Tv among all the variants, you expect this value to be < 0.5 (i.e. to have less Tv than Ti, otherwise it would be >= 0.5). Now, in order to accumulate Tv at 4D sites you need time to pass, so the more of them you have, the more time has passed, and that's why 4DTv ratios define time.


It's a greater bee fly, Bombylius major, a nectar feeder and generalist floral pollinator which pollinates hundreds of species of flowers. It lays eggs near real bee nests and it's larvae feed from the bee larvae.
https://en.wikipedia.org/wiki/Bombylius_major


Are there any structures in mammals that are used only by males?

Some researchers consider the neural circuitry responsible for orgasm vestigial in women. I disagree with this for a number of reasons, but here is a book exploring the hypothesis:

http://www.amazon.com/The-Case-Female-Orgasm-Evolution/dp/0674022467/ref=sr_1_1?ie=UTF8&qid=1336286206&sr=8-1


Why are trichomes important for both the roots and shoots of plants?

Plant leaf hairs, or trichomes are vital for many reasons.
Interestingly in 1975 researchers were correct when they stated:

"It can be argued that essentially the same genetic system should be required for both root hairs and trichomes." [1](Pay-wall)

For example:

C. salvifolius, there are more adaxial trichomes present to avoid UV light from injuring the abaxial surface.[2](Pay-wall)
Increased transpiration [3](Pay-wall)
Protecting against insect herbivores [4](Pay-wall)
Increasing tolerance to freezing [5](Pay-wall)


Why does the formula for blood velocity hold true?

The trick here is that 1 mL = 1 cm3 (or cc).  So if you divide cm3/s by cm2 the result will be in cm/s.  What that means is that the blood volume has three dimensions - if you picture the vessel as a simple "box", then it has widths in two dimensions, which define a cross-sectional area, and then the third dimension is the distance that the blood has moved past, through the vessel, in order to define the three-dimensional "box" of blood that has moved past as the blood moved that distance.
The principle should be familiar from the phrase "still waters run deep".  A stream that flows rapidly in a shallow cascade over rocks can abruptly become quite slow at a deep hole, as a great depth and breadth of water is sharing the work of moving forward.


What is a inhibitory tone when talking about neurons?

Neurons communicate electrochemically. That is, when a signal arrives to a neuron it fires a series of electrical signals, called action potentials.
Action potentials are depolarization events that propagate along the neuronal membrane, down to the neuronal terminal.
The terminal of a neuron is (with some exceptions) in contact with another neuron, via a structure called synapse.
When the depolarization arrives at the terminal, it allows the entry of calcium, which then mediates the release of a chemical substance, a neurotransmitter into the synaptic space. Finally, neurotransmitters act on the postsynaptic neuron, by binding to specific receptors on its cell membrane and can either stimulate it, in which case the postsynaptic neuron will fire more and release more of its neurotransmitter or inhibit it, in which case the opposite happens.

The textbook example of a stimulatory neurotransmitter is glutamate, and the inhibitory one is GABA1.

In various areas of the brain certain neurons are constantly receiving inputs from GABAergic afferents. This means that those neurons are constantly receiving a GABA stimulus that inhibits them, and are thus under a constant inhibitory tone. This will prevent their firing until a sufficiently potent stimulatory stimulus arrives or until the inhibitory tone is somehow released (for instance if the inhibitory GABAergic afferents are themselves inhibited by some of their own afferents).

1note that this is not always true: GABA can also be stimulatory in various situations


Cloning of animals typically involves:

Taking nucleus from healthy adult cell of animal to clone
Taking a healthy egg and replace the egg's nucleus with nucleus from source animal.
Implanting egg in female, stimulating the pregnancy process.

This same process should work on humans BUT:

"Is it really possible to create humans in lab?" No. Animal cloning doesn't work this way, so human cloning wouldn't either. Animals aren't "created" in lab. The one artificial step is the modifying the nucleus of the egg cell before the pregnancy process initiates. The rest of the egg->embryo->infant pregnancy process is traditional nature and there is no working lab process available to replace natural pregnancies.
Cloning animals is very high risk, it involves lots of trial and error, and involves lots of mistakes, botched pregnancies, abortions, and birth defects. The core concept of replacing the nucleus in an egg cell makes sense, but the practical reality of that procedure involves cell damage and pregnancy risks. With non-human animals, no one cares. With humans, purposefully causing lots of botched pregnancies, miscarriages, and birth defects will make most people squeamish.
Donor Eggs: If the process worked perfectly, a single donor egg would suffice. Since the process doesn't work perfectly, many donor eggs are required. Getting those donor eggs is a very invasive process that I would not want my wife, sisters, or daughters to subject themselves to. With lab animals, who cares, scientists can be as invasive as they want, and harvest all the eggs that they need. Humans have rights which really impedes this type of risky work.

Today, cloning humans is possible, but at prohibitively high cost and risk. It is inevitably going to happen, but the costs and risks will impede its popularity. Process improvements that deliver more safety and reliability will allow human cloning to become more popular.

UPDATE: "Why cant it be attempted..?" It definitely is being attempted. Panayiotis Zavos is one doctor who has been very public about his attempts to clone humans:

"In April 2009, he claimed to have cloned 14 human embryos and transferred 11 of those to wombs."

AFAIK, none of these efforts led to a live birth. I'm sure other doctors have attempted and even more are considering it and waiting until it's a little more practical and realistic.


Is this "Sympathetic fight response" axis accurate?

The typical axis of the fight response is depicted in Fig. 1.

Fig. 1. HPA axis. Source: Social Psychology principles

This axis is the hypthalamus-pituitary-adrenal axis, or HPA axis. It mediates not only the fight response and is typically referred to as the fight-flight-fright response. It is the central stress response system that prepares the body in a fraction of a second for survival, basically under the influence of adrenalin and cortisol produced by the adrenal glands.

The circuit you are describing, by the looks of it, is more typical for a reflex arc (Fig. 2.).

Fig. 2. Reflex arc. Source: Sweetibnotes

A typical example of a reflex arcs is the pain-withdrawal reflex. Although the sensory stimulus triggering the reflex arc may also trigger the HPA axis, the basic circuitry of a reflex arc does not include the HPA axis. The pain-withdrawal reflex, for example, is basically designed to jerk a limb away as fast as possible in the presence of acute pain as a protective mechanism.


That is a European Millipede.

I found this picture by searching European Millipede. Obviously there are different types - and this is the one you have.
Here is a wiki link I found: https://en.wikipedia.org/wiki/Cylindroiulus

I think your specifically is a Cylindroiulus britannicus

.


Which of this 2 affirmations is more close to the explanation of evolution?

The second is marginally better because it mentions randomness and emphasizes differential survivorship, but the parts about "trying to reach a target" and specifying a particular "task" are misleading at best. I would rewrite the statement as follows (I have edited for grammar, spelling and style as well, but emphasize more substantive deviations with strikeout for omitted parts and boldface for added parts). The substantive edits change the meaning of the statement significantly: most evolutionary biologists would be very uncomfortable with the second statement as written above (setting aside any grammatical issues).

  Evolution is has a random component but the species (or natural selection) tries to reach a target, may result in directional change: each generation has some random variation in traits but only individuals with beneficial traits tends to  are more likely to survive and produce offspring. For example, In order to survive the task is be 10cm taller. taller individuals survive better than smaller ones.  Some offspring are a half cm taller and other children are a half cm smaller; the latter die naturally and only the taller ones survive long enough to produce offspring.

I would probably say "offspring" rather than "children" in a technical context.

Note also that this emphasizes evolution by natural selection; broadly speaking, there are many non-adaptive processes (vicariance, drift ...) that also lead to evolution (change in gene frequencies between generations).


Difficulty in finding protein inhibition drugs

Drug production is very long, tedious and costly process. It generally takes more than 10 years to make entirely new drug. It has various iterative aspects. take a look at following cartoon showing various steps in drug design ( Taken from Anderson 2003 )

Now coming to your questions,

  what is the difficulty in producing drugs that inhibit production by a certain protein?

First of all you need to know other effects of that protein which might be essential for normal cell function. For example, there are many genes overexpression patterns which have correlated with cancer. This suggest excess quantity of these proteins/factors leads to cancer. Now one would like to block these proteins with inhibitors. However if you block these proteins, they might also affect regular cellular function. For example, SHC1 overexpression is correlated with breast cancer. However that protein is very important in apoptosis regulation, EGFR pathway, Oxidative stress and many more functions. Now if you inhibit this protein, your normal cells will also get damaged.

  Isn't it about analyzing the chemical makeup and structure of the protein and finding ways to neutralize it

It is not that simple, for this you need inhibitor which can specifically either bind (it can be competition also) specifically with given protein. Most of the time there are other problems like , there might be other proteins with that structure which can affect other protein's function. There will be other important problems like

Delivery of inhibitor
Specificity (Inhibitor need to act only on target cells)
Sensitivity (Inhibitor need to be sensitive enough to get full response in low concentration)
Side effects (There might be side effects of this inhibitor which should be minimized)
Cell resistance (Many times cell becomes resistant to inhibitor)

Above mentioned points are actually major issues in all cancer treatments like Chemotherapy  , Radiation therapy, Immunotherapy , Hormone therapy etc.


I am no expert in this but I had asked my doctor the same question the last time I fell sick and I'll try to paraphrase his explanation.
"There is this protective lining on our respiratory tract called "Respiratory Mucosa" that acts as the first line of defense against pathogens. But when you consume cold food and beverages , this membrane gets congested or shrinks such that it exposes the respiratory tract to pathogens . This is more prevalent if your body has an elevated temperature such as after spending a lot time outdoors during summer or after a workout. Cold food as such doesn't make you sick but they make it easier for the pathogens."
A quick Google search turned up this
http://www.thehealthsite.com/diseases-conditions/why-does-drinking-chilled-beverages-cause-sore-throat/#
Your cough could be a symptom of having a sore throat from infection.


From which ancestor species did humans inherit orgasm?

Let's assume that pleasure from sexual intercourse might be indicative of some sort of orgasm. Then this would suggest that any evidence of autoerotic behaviour would point to the existence of orgasm, or certanly physical pleasure.

I found this quotation on the Wikipedia page for Animal sexual behavior, amongst a lot of information about mammals :

  Many birds masturbate by mounting and copulating with tufts of grass, leaves or mounds of earth...

apparently from Bruce Bagemihl: Biological Exuberance: Animal Homosexuality and Natural Diversity. St. Martin's Press, 1999. ISBN 0-312-19239-8

If this is taken to imply that the last common ancestor of birds and mammals experienced this pleasure then we have got fairly deep into evolutionary history, although not as far as fish.


What species is this? Seashell from Indonesia

That is a piece broken off of a sea urchin shell.

Without it's spines, it's not possible for me to say which species it is.


Where does my extra blood volume go after giving birth?

The extra volume of fluid is due to the fluid retaining effects of high oestrogen secretion in a pregnant human female. After this high level of oestrogen subsides the extra fluid is mainly eliminated as:

urination
some is lost during parturition (labour)
lactation to some extent as well

Reference:A Textbook of Medical Physiology (South Asian Edition) Guyton and Hall


Help identifying this bird from Southern Brazil

That is Syrigma sibilatrix, the whistling heron. In Brazil we call it "maria-faceira".

Here is Syrigma sibilatrix page in Wiki Aves ("aves" is birds in Portuguese): http://www.wikiaves.com.br/maria-faceira

Wiki Aves is by far the best source for birds in Brazil. It is a very well documented and reliable source, maintained by great ornithologists.

PS: Regarding the Southern lapwings: they are not really attacking, they are just trying to drive off the intruder. And there is a reason: the lapwings nest on the ground. I was "attacked" by them several times (I'm from the Southern Brazil), when I inadvertently approached their nest.


The answers to these questions often boil down to "what do you mean by live forever?".

You've included vegetative cloning, so I infer that counts as one living organism for your purposes. In that case, the answer is absolutely.

Pando is at least 10 thousand years old and only getting larger. The Cavendish banana is about 150 years old, but produces at least 70 million tons of bananas yearly.

See here for other giant clones. Of particular interest is King's Lomatia, represented as a species by a single, sterile, individual. Fossilized triploid leaves are too old for carbon dating(at least 45 thousand years old), so it's essentially unknown how old it is.

I would be comfortable declaring Pando immortal, since it's way too big to be eaten, too resilient to burn down, and has already survived the middle and end(at least!) of an ice age. That just leaves (ha) disease and basically nothing else as possible threats.


Why are sponges sometimes not considered multicellular?

Sponges are generally considered as colonial organisms because there is little cell specialization and little separation of function/role. All cells do pretty much the same thing; it looks more like a pile of individual cells than an actual multicellular organism. In reality it is a little bit in between.

In any case, what one wants to call multicellular or unicellular is a matter of definition and preferences. You cannot find the line between unicellular and multicellular because there is no such line that would not be very arbitrary and filled with special cases.

You can study a little more the physiology of sponges and then decide for yourself if it looks sufficiently like a multicellular organism or more like a colony of cells (a colonial organism).


How many molecules of ATP are actually produced in aerobic respiration?

The discrepancy between 30 and 32 molecules of ATP quoted in the question may well arise from the two possible ways in which the reducing equivalents of the two molecules of NADH generated in glycolysis may be shuttled across the inner mitochondrial membrane into the mitochondrion (suggestion 2).

If one assumes that the malate-aspartate shuttle is used, then NADH is transported into the mitochondrion as such, and the yield of ATP is the same as for those molecules of NADH generated in the mitochondrion — 2.5 ATP per NADH from the most generally accepted measurement.

However, if one assumes the glycerol phosphate shuttle is used then the reducing equivalents are transferred from NADH to FADH2, from which only 1.5 molecules ATP is produced per molecule.

In summary, using the malate–aspartate shuttle a total of 5 molecules of ATP (2 x 2.5) will be produced from the two molecules of glycolytic NADH, whereas using the glycerol phosphate shuttle there will be only 3 molecules of ATP (2 x 2.5). This gives a difference of 2 molecules of ATP, which would cover the range in the question.

As the relative proportions of the two shuttles varies between tissues, a range of values is actually possible.


The shape looks like a leafhopper for sure. There are several species that are known to bite humans though it is not very common. Without a better photo however it may difficult to say what species it is for sure.


Health effect of electromagnetic and acoustic waves on brain function

The question is extremely broad.
Electro Magnetic signals
Even this subquestion is very broad. Electro magnetic signals encompass a lot of phenomenon, some of them represent health risks, some of them don't. It is funny to wish to limit the health effect to brain in your question as to reduce the scope of the question given how variable are difference electro magnetic waves can have on matter overall.
Ionizing radiations
Ionizing radiations will obviously represent health risks. But even non-ionizing radiation can pose health risk.
Non Ionizing radiations
Microwave
You are probably aware that you should not put your cat in a microwave!
Retina damage
Intense light can cause photochemical damage to the retina. See here.
Intense infra-red
High intensity infra-red affect cells (see König et al. 1997)
Cell Phone
Overall, there is likely no impact of cell phone radiation on our health. If there were any, it would be minimal.
See this Veritasium video: Do Cell Phones Cause Brain Tumors?. You should also have a look at the skeptics.SE post Do mobile phones have anything to do with brain cancer?.
Cell phone towers
Likely has no health effect. See Do cellphone towers cause health issues?
Other electro magnetic signals
For more information, you should have a look at WHO > Electromagnetic fields and public health: radars and human health
Sound wave
Some sound can cause hearing loss. The frequency of this sound, the intensity and duration of exposure to the sound are all important in determining the degree of the hearing loss. Have a look at this article from the American Hearing Society for more information.


How does PCR mutagenesis add restriction site near the gene of interest?

This diagram would be easier for you to conceptualize if you instead used the actual nucleotides in the restriction sites and green GGAGAA region along with your gene of interest (GOI). I recommend working with the DNA sequences when learning about primer design for various applications. I believe it has led you to be slightly confused with what is the restriction site and what is not in this diagram so I'll walk through it.
At the first step shown, you have your annealing region of the forward and reverse primers binding to the GOI. The overhanging region on each primer contain your restriction sites, which are flanked by the GGAGAA region for these restriction enzymes to have a sequence to "grab on" when you perform a restriction enzyme digest. Note that the annealing region of your primer anneals to the GOI because it has homology to the DNA sequence. Your restriction sites and green "clamping" region do not have homology to your DNA template so they are considered the overhanging regions. It is important to have your annealing regions of both primers of similar annealing temperatures when designing this or you may not have an efficient PCR reaction. I typically use this tool from NEB to design annealing regions of my primers. https://tmcalculator.neb.com/#!/main
Moving forward, these primers are both going to be used in one PCR reaction, not separate. Thus, when the reaction begins, the double stranded DNA template will denature, giving your forward and reverse primers the opportunity to anneal during the annealing phase of a PCR reaction. During the elongation phase, your DNA Polymerase will add complementary nucleotides in the 3' direction of your primers. Now after the first cycle, you have two different products. The forward primer's product has the GOI with a single stranded BamHI overhang on the 5' end, while the reverse primer's product has the GOI with a single stranded NotI overhang on the 5' end.
During the second cycle, after denaturation, the reverse primer with a NotI overhang anneals to the forward primer's previous product with a BamHI overhang. The DNA polymerase then adds nucleotides in the 3' direction of the primer, eventually adding complementary bases to the BamHI overhang. The same is done vice versa with the forward primer and the reverse primer's previous product.
Now after the second cycle, you have the desired products which will be amplified exponentially. Your GOI flanked by NotI and BamHI restriction sites with the GGAGAA region on both sides. This product is ready for a restriction enzyme digest.


Quantifying the Genetic Basis of Complex Diseases

I'm not sure what you mean by "complex", but many diseases are known to arise due to exposure to toxins or to an absence of essential nutrients in the environment.
Toxic metals:
A good example of this is exposure to some metals including arsenic, lead, and mercury.  See for example this information from the US NIH and the wikipedia article on metal toxicity.
In the case of arsenic, some of this poisoning is even "natural" — i.e. due to toxic levels of this metal in ground water that hasn't been contaminated by human activity.
Diseases that have been linked to such exposures include cancer, heart disease, diabetes, and anemia.1,2
Deficiencies:
Another class of diseases that are more-or-less purely environmental are those due to nutrient deficiencies — i.e. a diet lacking in minerals or vitamins.

References:

Byrns, M. C., & Penning, T. M. (2011). Environmental toxicology: carcinogens and heavy metals. The pharmacological basis of therapeutics. McGraw Hill, New York, 1853-1878.
Tolins, M., Ruchirawat, M., & Landrigan, P. (2014). The developmental neurotoxicity of arsenic: cognitive and behavioral consequences of early life exposure. Annals of global health, 80(4), 303-314.


Why is the mosquito a definitive host in malaria?

Plasmodium falciparum (the main causative agent of malaria) and other Plasmodium species have a very complex life cycle, with stages in the female host Anopheles mosquito, in the human liver, and in the human circulatory system, where it primarily resides in the erythrocytes (red blood cells, or RBCs):

During a blood meal, a malaria-infected mosquito injects sporozoites in its saliva into the human host (1). Sporozoites travel through the circulatory system and first infect hepatocytes (liver cells) (2, stage A) and mature into schizonts (3), which rupture and release merozoites (4). After this initial replication in the liver (exo-erythrocytic schizogony (A), which can last a minimum of 5.5 days), the parasites undergo asexual multiplication in the erythrocytes (erythrocytic schizogony (stage B)). Merozoites leave the liver and enter the circulatory system where they infect red blood cells (5). The ring stage trophozoites mature into schizonts, which rupture releasing more merozoites, which continue the cycle of infection of RBCs (6). Some immature trophozoites, in the so-called "ring stage," differentiate into sexual erythrocytic stages (gametocytes) (7). Blood stage parasites are responsible for the clinical manifestations of the disease.

It is important to note here (in answer to your question) that while the male and female gametocytes are formed at this stage in the human (the equivalent of meiosis), sexual reproduction does not occur until the micro and macrogametocytes are taken up by a mosquito.

The male (microgametocytes) and female (macrogametocytes) gametocytes are ingested by a female Anopheles mosquito during a blood meal (8) - only female mosquitoes (of pretty much any species) drink blood. The parasites' multiplication in the mosquito is known as the sporogonic cycle (stage C). While in the mosquito's stomach, the microgametes penetrate the macrogametes generating zygotes (9). The zygotes in turn become motile and elongated (ookinetes) (10) which invade the midgut wall of the mosquito where they develop into oocysts (11). The oocysts grow, rupture, and release sporozoites (12), which make their way to the mosquito's salivary glands. Inoculation of the sporozoites into a new human host perpetuates the malaria life cycle (1).

Sources

The Centers for Disease Control and Prevention: Malaria
Wikipedia: Plasmodium falciparum biology


What happens to the human ear as it naturally goes deaf?

Hearing loss is caused by different things, but your probably thinking of age-related hearing loss.

When people go deaf, it is be because "hair cells" in the ear break.

This breakage results from overly loud frequencies, or just random damage to cells over a lifetime.

If your last remaining hair cell that is tuned to a certain frequency after all the other ones have died gets killed somehow, it will depolarize and send an action potential to your brain telling it to hear that sound.

But that would be a very faint sound, since only one or a couple hair cells die off.

But in reality, it usually isn't that you hear a sound for the last time before going deaf, you have a faulty premise hear!

it's NOT like the ubiquitous "seeing the light" that happens when your heart stops.


What buffer should I choose for IEX chromatography for purifying IgY

Your column manual will probably come with buffer recommendations (these manuals are also often available online). You can also search for publications that have purified IgY by anion exchange chromatography and use their procedure as a starting point.

Some generalities to keep in mind for buffer selection:

Buffers are most effective when the desired pH is close to their pKa. A rule of thumb is to choose a buffer with a pKa within 1 unit of the desired pH.
For anion exchange, the pH should be higher than the pI of the protein so that it carries an overall negative charge and will bind to the positively charged column. Another rule of thumb is to keep the pH about 1 unit above the pI. If the pH is too low, the protein will not bind. If the pH is too high, the protein will require more salt to elute, which can cause instability/precipitation.
For anion exchange, the buffer itself should be neutral or positively charged so it does not bind to the column. This can affect binding of the target protein both by its ionic strength and localized changes in pH.
Choice of pH depends on whether your column is "strong" or "weak". The charge on the functional group of a strong ion exchanger will not appreciably change over a wide range of pH whereas the charge on a weak ion exchanger is only maintained over a relatively narrow pH range.
This may go without saying, but make sure that your protein is stable in the buffer and pH you select. You may also want to keep in mind the buffer requirements of any downstream applications and choose one that is compatible to simplify purification.

Elution is generally done with a salt gradient, though a pH gradient can also be used. In a typical setup, you would have two solutions, both with the same buffer and pH but one with high salt (let's call it B) and one with no salt (let's call it A). The sample is applied in buffer A and then a gradient from 0 to 100% buffer B is applied to the column with fractions collected periodically. The most commonly used salt for ion exchange is sodium chloride (so the counterion for anion exchange would be chloride). Since relatively high concentrations of salt are often used for elution, in general you want to avoid counterions like sulfate that have a stronger salting-out effect.


What is the correct model for enzyme-substrate complementarity?

This is true of all protein binding as well as the special case of enzyme-substrate interaction:

Various proteins are more dynamic than others: some have only one or two overall conformations and are relatively implastic otherwise. An example would be a receptor tyrosine kinase like Kit (or CD117, or Mast Stem Cell Growth Factor Receptor, whatever you want to call it), which has a very stable structure and binds its substrates in a lock and key manner.

Others, for example p53 (not an enzyme), have much more structural placiticity - even to the point of being mostly disordered when not bound. They tend to be induced fit binders (of other proteins, not catalytic substrates) and often exploit that to bind a broader range of possible targets than lock and key proteins.

The point is, it is a continuum between lock and key <-----> induced fit rather than discrete classes you can sort proteins into.


Yes it is still true for all of biology, of course physics has expanded a bit, and likewise we have discovered cases of biology exploiting these new parts, for instance photosynthesis might involve quantum tunneling.

Feynman's quote basically restating that there is no magic or supernatural aspect to biology, no vital essence or spirit required to explain how it works or seperate living matter from non-living, it is all just chemistry and physics. The most complex chemical process ever discovered but still just chemistry and physics. Of course he does not mention chemistry becasue of course chemistry is just physics as well, the laws of physics control both, so saying it is a result of atoms obeying the laws of physics expresses both.

He is saying biology is still obeys the laws of physics and are made of atoms, this is true for all of biology, but as Feynman points out took some time to be accepted, keep in mind this is the time of the Miller–Urey experiment which showed organic molecules could form through entirely non-biotic means, which was not as widely accepted at the time as many think, especially to a general audience. Many similar discoveries a t the time were showing the same thing, there was nothing special about biological molecules or their interaction. things like evolution is the inevitable result of the interaction of basic properties (reproduction and heredity)just as a salt crystal is the inevitable result of the interaction of charge of sodium and chlorine. Vitalism still hung around in the popular mind and a few corners of academia at the time Feynman was growing up so taking a few moments to help dispel this notion in his lectures makes a lot of sense, especially given how much advancement was done by abandoning it.


Quite simply, because chromosome pairing is sequence specific. Holliday Junctions, which are the functional structures of a cross-over, occur through a process called "strand invasion," during which a region of one chromosome physically base-pairs with that of another.  Thus one locus cannot pair with a random locus, as there is generally insufficient sequence complimentarity between two random regions to form a functional Holliday Junction.  One interesting consequence of this mechanism is gene duplication and deletion in repetitious regions of the chromosome.  For example, genes with large repeated regions, such as the gene responsible for Huntington's disease, can expand and contract during homologous recombination due to strand invasion occurring at non-equivalent, but still homologous, sites.  Wikipedia does a nice job going over homologous recombination.  I also recommend looking over the relevant sections in Molecular Biology of the Cell, available on the PubMed Bookshelf.


Is there a practical upper limit to amount of nucleotides or genes in a transformed plasmid?

From my experience in the mammalian world (and this may apply to bacterial systems as well), it's not so much the number of genes in the plasmid as its actual size. The larger the construct is, the more difficult it will be to get it into your target cells in one piece, without degradation or shearing. Since the transformation efficiency is lower, you are getting fewer whole constructs per cell, so depending on how you've set up your promoters, the overall expression level can be significantly lower. The trouble with splitting your genes amongst two or more plasmids is that each will have different transformation efficiencies, and there will be a certain (perhaps large) number of cells that don't get the full complement of genes, interfering with phenotype analysis. And again, you'll also have to consider differential expression rates.

However, once you get your vector into the cells in one piece, theoretically they should all get expressed at approximately equal levels (assuming identical promoters). It's possible that steric hindrance among multiple transcription complexes may occur - I just don't know enough about bacterial transcription and the effects of circular plasmids to say.

One way to get around many of these factors would be to use a bacterial artificial chromosome or BAC. BACs are 7-10 kb vectors that can have inserts of up to 1 million bp cloned into them and are then electroporated into cells. One of (the many) cool things about them is they control their own duplication and partitioning at cell division, so succeeding generations should have essentially the same copy number as the original. They were heavily used during the Human Genome Project to amplify large sections of DNA for sequencing, but they are also used in many other studies, including synthetic biology. OpenWetWare has a list of some common ones, and NEB sells pBeloBAC11 systems.


It looks like a species from the Arachnid order Amblypygi (Tail-less whip scorpions), which are closely related to Thelyphonida (Whip Scorpions). As part of Arachnids, both of these taxa are related to spiders and scorpions, but belong to a separate order.

Even if they look scary, they are harmless to humans, even if they can sometimes bite.

According to this checklist/site only three species are listed from the Philippines, so if you want to determine it more closely, it might be useful to start from this list. The list includes: Sarax brachydactylus, Phrynus grayi and Charon grayi.

Here is an example picture (from wikipedia):

Charon grayi (giant whip-spider) from biotagua.org:


Gene of interest number of copies in transformed K. pastoris

To predict the number integrations is probably not possible, but you can favor multiple integrations, if that's what you are after. At least in Saccharomyces cerevisiae integration of a first plasmid appears to stimulate the insertion of additional plasmids at the same site (1). It is therefore possible to favor multiple integrations (2) by increasing the DNA-to-cell ratio in the transformation, thereby increasing the chance that any competent cell receives more than one copy of the plasmid, which could then integrate in tandem. The easiest way is to simply use more DNA, but depending on your cell competence you might need to compensate this increase by using less cells for your transformation (or simply plate less cells on each plate) as you will probably also increase the overall colony yield.
One way to actively select for multiple integrations is to use a competitive inhibitor for the selection marker. Again, in Saccharomyces cerevisiae transformations with HIS3 selection can be combined with 3-AT (3). This allows you to inhibit HIS3 activity just enough to only permit the growth of cells that have integrated a desired number of copies of the plasmid. Of course, this method is far from fool-proof, as you might also select for mutants that have increased HIS3 expression for other reasons. Edit: I actually found one paper doing this in K. pastoris (4).
Finally, if your implementation allows it you can facilitate the screening for multiple integrations by including a fluorescent protein-expressing cassette in your plasmid. That way you can easily screen for different numbers of integrations by fluorescence microscopy or FACS.
Sources:

Orr-Weaver et al. (1983): https://mcb.asm.org/content/3/4/747
Plessis and Dujon (1993): https://doi.org/10.1016/0378-1119(93)90172-Y
Wikipedia (retrieved 15 Aug 2020): https://en.wikipedia.org/wiki/3-Amino-1,2,4-triazole
Menéndez et al. (2018): https://doi.org/10.2144/00295rr05


Synthetic construct with multiple ORFs not expressing

I'm afraid there's not much of answer but back to the bench with you! (That's why it's called re-search).

There are several factors that could be playing a role here.  You could have transcriptional or translational read through.   You should check your sequence and the cells you are going into to make sure you aren't getting Amber (UAG) suppression.

Before you do anything, you should check your DNA of all your groups.  Run it uncut on a gel and make sure the majority of the DNA is super coil.  The next easiest thing to check is translation problems.  Get an GFP antibody, possibly a few that recognize different epitopes, and see if your GFP is coming out the right size.  It may not be processed correctly or folded correctly.

You can run into problems by optimizing the sequence.  First, synonymous mutations can cause folding variants (1).  Second, you might be causing a hair pen or other disadvantageous secondary or tertiary structure.  If you can't detect any problems in your Western, you might consider doing a Northern to trouble shoot the transcription.

If you rule everything else out, and you are just getting poor expression, then the only way I know to boost over CMV is to use T7.  The problem with T7 is always going to be what use for a source.  If you can use BSR/T7 cells and you can get your hands on them, they work great.  Otherwise you're looking at a T7 plasmid or MVA-T7 as common sources.  The plasmids never lead to a great deal of expression in anyone's hands I've ever known.  MVA-T7 works, but to say that it confounds things would be the under statement of the year.


Spironolactone's role with adrenergic agents in heart failure?

Spironolactone works through a mechanism different than the adrenergics.

You said of the ABC approach, "This includes also diuretics." That's why Spironolactone was included.

Spironolactone is a specific pharmacologic antagonist of aldosterone, acting primarily through competitive binding of receptors at the aldosterone-dependent sodium-potassium exchange site in the distal convoluted renal tubule. Spironolactone causes increased amounts of sodium and water to be excreted, while potassium is retained. Spironolactone acts both as a diuretic and as an antihypertensive drug by this mechanism. It may be given alone or with other diuretic agents which act more proximally in the renal tubule. Aldosterone interacts with a cytoplasmic mineralocorticoid receptor to enhance the expression of the Na+, K+-ATPase and the Na+ channel involved in a Na+ K+ transport in the distal tubule . Spironolactone bind to this mineralcorticoid receptor, blocking the actions of aldosterone on gene expression. Aldosterone is a hormone; its primary function is to retain sodium and excrete potassium in the kidneys.

  The lack of a decrease in the neuroendocrine prognostic markers, norepinephrine and endothelin-1, suggests that the beneficial effects of spironolactone are mainly related to mechanisms independent of the adrenergic and endothelin systems. The escape of AII and aldosterone, probably reflecting activated feedback mechanisms, confirms the specific activity of spironolactone on the renin-angiotensin-aldosterone system and supports the hypothesis that the beneficial effects of spironolactone on the progression of heart failure are mediated by the blockade of aldosterone receptors.

PubChem
Beneficial neurohormonal profile of spironolactone in severe congestive heart failure: Results from the RALES neurohormonal substudy


If the xylem of a woody plant is composed of dead tissue, how does sapwood become heartwood?

I'm no expert, but I liked this question and did a quick literature search:

Xylem cells are certainly dead at maturity, and it is these cells that make up the majority of what we call wood. However, wood also contains other tissue types, some of which have live cells at maturity. From what I can glean here and here, it is ray parenchyma tissue that is responsible for many of the changes that take place during the transition from sapwood to heartwood. Ray parenchyma is formed at the vascular cambium, along with xylem, during stem secondary growth (wood formation). Ray parenchyma cells remain alive for years after the xylem cells in the sapwood die. Their functions are transporting nutrients radially in the stem, and storage of carbohydrates.

As the stem grows in diameter, there is a zone of transition from sapwood to heartwood where the ray parenchyma tissue begins to die. Before it dies, the cells undergo some metabolic changes and begin to synthesize secondary phenolic compounds (many different kinds) from stored starch or sugars. Then, as ray parenchyma cells die, they dump these phenolics into the surrounding xylem tissue, and the accumulation of these durable, decay-resistant compounds in the xylem leads to the formation of heartwood. In many hardwood trees this parenchyma death and phenolic accumulation is preceded by vessel-plugging, in which the ray parenchyma cells form balloon-like growths that block the flow of water through the xylem. So, once sapwood changes to heartwood there should be no living cells left, and the water transport capacity of its xylem is gone or greatly diminished.

There appears to be quite a bit of variability between species in when heartwood formation occurs and what triggers it. From what I could see in my brief literature search, it is all under fairly complex genetic and hormonal control that remains an area of active research. I would suggest (and speculate a bit) that the trigger has something to do with maintaining an optimum amount of sapwood as the tree grows in leaf area (which increases demand for water transport) and height (which increases demand for support, or stem diameter).