Fab fragments of antibodies to fight viral infections

There are three pathways by which soluble antibodies (which is what the Fab fragments arise from) can inactivate viruses (from Janeway's Immunobiology):

What you describe with the Fab binding to the viral receptors is a type of neutralization. Janeway claims that the type of naturally occurring antibody primarily responsibly for neutralization, IgA, is mostly exported to mucous secretions, so presumably it gets digested/excreted along with the rest of the mucous proteins.


Basic Cardiac Rhythms – Identification and Response (The University of Toledo, Medical Center)

This quite thorough one-page source describes:

Basic heart anatomy and physiology
The meaning of the waves in ECG
Examples of ECGs for most arrhythmias with timing, causes, symptoms and treatment

Here's Pocket Guide to Neonatal ECG Interpretation (NICU INK Book Publishers) - an one-page source about arrhythmias in infants.


Yes, these devices and treatment programs are being actively developed. General idea is that epileptic episode follows certain path within the brain. It can start in thalamus, after which sporadic activity spreads into cortical areas, for example motor cortex. There is a number of papers on prediction of epileptic seizure, e.g. Seizure Prediction and its Applications.

The device then will detect initiation of seizure before evident symptoms and provide inhibition via cortical electrodes, microelectrode array (MEA). It seems that currently MEAs are used more for research (recording from tens of neurons), but single electrodes are useful for actual control of epilepsy. Also one can control vagus nerve, which causes parasympathetic response (general inhibition, aka "rest-and-digest"). More you can read here.

Transcranial magnetic stimulation, as I understand, is not portable enough to be useful.


Manual Primer Design for a gene on the reverse strand

Not a stupid question at all. I was just as confused by this as a beginner in molecular biology. You get the hang of it after a while. :)

I find it much more difficult to design primers from just one strand, especially the minus strand, so I always try to get both to work with. If you don't feel like doing that, just one strand is sufficient (plus or minus), but I would recommend at least getting the reverse complement in your case because plus strands are much easier to work with.

For a quick example, let's say I have a ten bp sequence I want to design primers for and this is my plus sequence:

5' ATAACTTCGT 3'

Now let's say I want a three bp primer. So the forward primer would simply be 5' ATA 3', that's easy. The reverse primer, if I just take it from there without flipping it, would be 5' CGT 3'. But if I put that into my PCR reaction, it will not do anything because DNA binds to it's complement strand, meaning that primer would only bind to 3' ACG 5', or 5' GCA 3'. So instead, I'm going to want 3' ACG 5' because it will bind to its compliment, the 5' CGT 3' part of my sequence. (Technical issue here, suppliers usually only give the option to write in 5' to 3', which makes sense, but you must remember to flip your reverse primer before giving it to them because it will be in 3' to 5' originally. In this case, I would ask for 5' GCA 3'.)

This is easier to visualize if I have both the plus and minus strand though, which would look like this:

5' ATAACTTCGT 3'
3' TATTGAAGCA 5'

If you have both strands like the example above, you can find both the forward and reverse primer without much difficulty.

I could give a more comprehensive answer of how this all works out during DNA replication that would involve illustrations, allegories, and maybe a few mildly humorous jokes, but I would hate to bore you unnecessarily, so let me know if you understand now or if you need more. ;)

Edit: Exactly (to your third comment I mean)! Remember, DNA is always read and replicated 5' to 3', so the forward primer will bind to the minus strand and be replicated 5' to 3', so will extend the sequence to the right. The reverse primer is the opposite, 3' to 5', so it will extend the plus strand to the left. After both of those happen, you will end up with two full strands. As promised, here is an illustration:

Now, to your question about Primer-BLAST. You do not have to enter a plus strand, but the tool is assuming that you are entering the plus strand, so you will get the right primers, it will just call them the wrong names (i.e. with the example above, it would give you 5' GCA 3' as your forward primer and 5' ATA 3' as your reverse). The forward and reverse primers are treated exactly the same, so this wouldn't throw off your PCR, but it would be incorrect nonetheless. To avoid confusion, I suggest utilizing a tool to reverse-compliment your minus sequence into plus before running it. It's rather easy to get the reverse compliment of any sequence; here is a good tool for that.

I hope this helps. :)


Why do sparrows jump instead of walk when they are not flying?

As pointed out by @jamesqf in the comment below, there exist many birds like quail and pheasants that run and walk rather than hop. Also, there are several flightless birds like  ostriches, emus, rheas that do the same. But it is also true that sparrows don't walk or run but hop. The question now is- why?

There is an interesting fact- both Quail and Pheasant are ground nesting birds.

Now, the reason why we do not see sparrows running like pheasants is because sparrows rely more on their ability to fly for survival and getting around. So, a sparrow will rather fly the distance than run. The reason for this might be its smaller size which makes it more efficient and safe during flight.

But the question is- why don't sparrows walk? Why do they hop? Quails (video) and Pheasants(video) certainly walk even for short distance.

Just before a flight, all birds jump to power their flight. So, if a sparrow hops around rather than walking around, it can convert any of these jumps into a full flight in the case of an unexpected need. This again comes down to sparrow's heavy reliance on flight to escape danger. Because of their light weight, hopping rather than walking is less costly for a sparrows.

Whereas in a normal situation, Quails and Pheasants would rather run to build the necessary  momentum to initiate a flight. But they walk even for shorter distance because they are heavier than a sparrow, and walking for them is more efficient than hopping. But in worst case scenario, even birds like Quails can simply jump into a flight, as can be seen in this video if you watch it in slow motion.

Edit: another factor that might influence whether a certain bird hops or walks is the irregularity of the terrain with respect to the size of the bird. The terrain is relatively more irregular for smaller birds (there are obstacles like twigs, stones, grass etc), hence making hopping a better option than walking.

There are many kinds of birds that each choose whether to walk or hop. Here i present a small categorization with video evidence to bring out some pattern if any. You might need to watch some of the videos in slow motion.

Birds that hop:

sparrows
American robin
blue jays

Birds that walk

Crow
magpie
Quail
Pheasant
an unknown small bird that the video title says is American robin but which walks


How does a sheep's fleece impact its tolerance for high temperatures?

Wool serves as a good insulator, meaning it doesn't allow warmth to escape the wearer easily allowing the wearer to remain warm. Furthermore, wool helps maintain a dry environment by absorbing moisture from the air (and sweat) which can also keep you cool during summer.
Here's a link that talks more about this for both wool wearers and sheep: https://shepherdsdream.com/blog/wonders-of-wool/how-wool-keeps-us-cool/


Do micro-organisms survive and live normally in a zero-g environment?

Several experiments with microorganisms have been conducted in the ISS (International Space Station), and the results were published in peer-reviewed journals, like this one for instance:

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space

However, two things have to be clarified:

First, the environment at ISS is not really a zero-g environment. Actually, since the ISS is orbiting at only 400 km from the Earth surface, the gravity in the ship is almost the same of what it is here at the planet surface (89%, to be more precise). What happens is that the ISS is constantly falling, and that endless fall simulates a zero-gravity environment.

For this reason, one doesn't need to go to space to conduct micro-gravity experiments: they can be conducted here, on Earth's surface, in rotating containers (Tirumalai et al., 2017). For instance, this is a device to simulate micro gravity on ground, in a common lab:

Second: most of the experiences conducted on ISS focus on bacteria (and not on other groups of microorganisms, like protozoans and algae), and more specifically on their pathogenicity. The way your question was worded ("Are they able to move around in a drop of water like they do on Earth? Are they able to eat and reproduce normally?") make it seems that you are interested in things like locomotion and phagocytosis in unicellular eukaryotes, but that's not their main concern. Their main concern is that bacteria have different selective pressures in space, modifying their gene expression, and such "new" strains could be potentially dangerous for the crew.

According to Tirumalai (2017):

  Microorganisms impact spaceflight in a variety of ways. They play a positive role in biological systems, such as waste water treatment but can be problematic through buildups of biofilms that can affect advanced life support. Of special concern is the possibility that during extended missions, the microgravity environment will provide positive selection for undesirable genomic changes. Such changes could affect microbial antibiotic sensitivity and possibly pathogenicity. (emphases mine)

And according to NASA (2017):

  scientists have observed that in space, some strains of bacteria appear to exhibit enhanced growth and increased virulence (ability to cause disease).

Therefore, experiments like AES-1 (for "Antibiotic Effectiveness in Space-1") were conducted to compare gene expression from a non-pathogenic strain of bacteria (in that case, Escherichia coli) growing in micro gravity with the same bacteria growing on the ground.

NASA Astronaut Rick Mastracchio using a crank to activate a group activation pack (GAP) onboard the ISS for the AES-1 experiment. (source: NASA,
 2017)

The findings so far show that bacteria growing in micro gravity have less availability of nutrients. Still according to NASA (2017):

  On Earth, the movement of bacterial cells through their media is influenced by the physical properties of the medium, including gravity-driven forces like buoyancy and sedimentation, as well as other forces, such as the viscosity of the medium. As the cells move, they interact with fresh media and absorb molecules of nutrients. The cells also excrete waste products that may sediment down, float up, or trail behind the cells if they move, while simultaneously diffusing away. However, in microgravity, these gravity-driven forces are absent, and ALTERED EXTRACELLULAR ENVIRONMENT MODEL the transportation of nutrients to cells and waste products away from cells are limited to diffusion-only transport. The altered extracellular environment model hypothesizes that the resulting reduction in the movement of molecules leads to less interaction of the cells with fresh media and thus reduced availability of nutrient molecules for absorption.

Analysis of those bacteria showed that they changed their gene expression. The genes over-expressed were mainly associated with:

Low glucose environment
Acidic environment

Also, the experiment showed that such bacteria required a higher concentration of antibiotics to be killed, probably because there is a reduced concentration of antibiotics around the cells.

To finish, a curious device is the "test tube" they use in micro gravity. In space you cannot simply manipulate test tubes like we do here, at 1g. It has to be a special device:

  For the AES-1 experiment, the research team prepared 128 bacterial culture samples to send to the ISS National Lab. The samples were each contained in a fluid processing apparatus (FPA), a test tube specially designed by BioServe Space Technologies for use in microgravity.

This is it:

Sources:

Zea, L., Prasad, N., Levy, S., Stodieck, L., Jones, A., Shrestha, S. and Klaus, D. (2016). A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space. PLOS ONE, 11(11), p.e0164359.
Tirumalai, M., Karouia, F., Tran, Q., Stepanov, V., Bruce, R., Ott, C., Pierson, D. and Fox, G. (2017). The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic. npj Microgravity, 3(1). [online] Available at: https://www.nature.com/articles/s41526-017-0020-1
NASA, (2017). [online] Available at: https://www.nasa.gov/sites/default/files/atoms/files/upward_magazine_vol2_issue1.pdf [Accessed 5 Aug. 2017].


Is there a chemical that can be used to subdue ants only temporarily without permanent harm?

CO2 is often used for temporary knockouts of insects. I've used it myself for fruit flies (Drosophila melanogaster), and it's quite straightforward and very effective to hit them with it until they're asleep. However, this was in a rather expensive lab that had CO2 on tap - not a particularly accessible method to the average person.

What I'd recommend instead is to chill the ants. Simply capture them and put them in the fridge for a while. Read this wiki article and go to the part about "quiesence" for more. Quote: "quiescence acts like an anesthetic". It's short term, non-harmful and fully reversible. Also much more accessible to someone who isn't working in a big expensive lab. I assume that the ants will stay still long enough for your measurements - if not: put them back in the fridge for a bit. And better yet, there's no chemicals used, so no need to clean the ant and there's no cost to you.


As @picapica has pointed out, I presume these are scale insects, the first instar of Japanese wax scale, Ceroplastes japonicus.

Laurus sp. is a host of this hemiptera in Italy.

Here is an image showing the second instar from Italy:

These are the adult females :


Feeding behavior of organisms that prey on microorganisms

Use "-vore" and "-vorous" suffix [L. -vorus devouring, eating (cf. vorāre to devour].

For example: bacteriovores, algaevores, and planktivores.

Note: "Microorganism" is an unfortunate, albeit popular (viz. "microbiology") term. How small is "micro"? So small that one needs a microscope to see it? And what kind of microscope: "light" or "electron"? i would drop the term "microorganism" altogether. One can use "bacteria, "archaea," "chromists," "protists," . . .


Fur, wool, and hair are all made of keratins.

To the best of my knowledge wool and fur are separated arbitrarily, based on the properties of the fibres. This arbitrary division allows rabbits to have fur but selective breeding has produced angora rabbits, which have wool. The opposite should be possible, with time you could breed a sheep that has fur.

Length; Wool grows continuously and animals are clipped when the fibres are long. Fur often has a maximum length.

Structure: The structure of the keratin in the wool makes the fibres kinked (crimped). These kinks aid the production of fabrics. I believe the cuticular scales also aid in the production of fabrics.

Fur doesn't have kinks, so even if it's long enough to weave the fabric is likely to lack durability.

Some furs are used in textiles rather than pelts. Possum fur is 'plucked' and woven into fabrics with wool. The resulting fabric is slightly less durable. However, possum fur is hollow and smooth so possum fur fabrics are very soft and warm. The clothing is very good to to wear.

However, fur is generally inferior to wool for textiles and it took a couple of decades to develop techniques to produce textiles from possum fur. This happened because of odd ecological and economic drivers. Possums are are a major pest species in New Zealand where they contribute to the decline of native birds and insects. Millions of possums are killed every year in New Zealand. The market for possum skins is very small. This is why so much effort was put into producing a fabric from possum fur.

So you could shear a fox and produce a fabric but the fabric would likely be poor and there's no reason to do so.


Do DNA footprints vanish in generations?

You seem to be figuring that since $A_1$ has half the genes of $A_0$, and $A_2$ has half the genes of $A_1$, etc throughout the generations, we quickly get to a point where $A_n$ has none of the genes $A_0$ had.

This would be correct, if we assumed no inbreeding among the descendants. And by "inbreeding" I don't mean siblings or first-degree cousins breeding, but any of $A_0$'s $n^{th}$ descendants breeding with another. Which is clearly absurd; at some point you're going to run out of breeding partners who aren't also a descendant of $A_0$, unless the lineage isn't very prolific and the number of descendants $A_0$ has is always a small proportion of the total population. And in that case, sure, those genes are probably going extinct.

The same thing happens the other way around by the way; we (most of us) have two grandparents, four great-grandparents, etc. As we go back in time this exponential growth quickly outstrips the amount of humans that were alive at the time our $n^{th}$ great-grandparents were around. That's because that exponential growth assumes no inbreeding, which there is. There is a point in time in the past beyond which everybody alive today is the descendant of everybody back then who has any descendant at all; that's called the Identical Ancestors Point. See for example:

https://www.nature.com/news/2004/040929/full/news040927-10.html

The end result is that there are really two outcomes for $A_0$'s descendance: either they increase over the long term faster that the overall population grows, or they increase at the same rate or slower. In the first case, we'll reach a point where the whole population is part of $A_0$'s descendance. In the second, unless population growth is huge then $A_0$'s line is probably going extinct. Even if not, and if we assume individuals are breeding randomly throughout the population (not a good assumption, but no gene dilution without it), then the original assumption that $A_0$'s descendants have fewer and fewer of $A_0$'s genes every generation is correct, and $A_0$'s genes will likely go extinct even if their descendants don't.

On the other hand if $A_0$'s descendance end up consisting of the whole population, then no more "dilution" can occur. Say at that point every individual has 1% of $A_0$'s alleles; their offspring will also have 1% of $A_0$'s alleles on average, and same goes for all later generations.

Note that at that point $A_0$'s alleles are distributed throughout the population; even if everyone has 1% of them, they don't all have the same 1%. So the question of whether "what makes $A_0$ unique" is present in the descendants is really hard to interpret. Some of $A_0$'s alleles may be present in everybody at that point (they have become fixed in the population), some may be present in X% of the population, some may have gone extinct. The specific combination of alleles that made $A_0$ is gone, but then it was gone when $A_0$ died. As for the question of whether scientists can investigate the descendants and find traces of $A_0$ after all those generations, the answer is "sure": see the aforelinkedto nature article.

More to the point, consider this sentence you wrote:

  Obviously if $A_0$ is human and $A_n$ is human then they share a great deal of their genes with one another (something like $99.99\%$)

Do you not see how this factoid relates to your question? You are asking whether human $A_n$ still shares some genes with its ancestor human $A_0$, and caveat that "obviously" they already share most of their genes, what with being human. You mean, what with both descending from the common ancestor to all humans. That those $99.99\%$ of identical genes come from. Except of course that not even, given $99.99\%$ of that $99.99\%$ comes from our common ancestors with chimpanzees, and so on. Most of "what made the common ancestor to all life unique" is still in our genes today! So yeah, it will take more than a human-scale $n$ generations for all traces of a human ancestor to be predictably erased from its human descendants (keyword "predictably"; in practice many lineages and alleles do go extinct, but not all do and you can't really tell which in advance). More than that, on those evolutionary timescales natural selection is a strong force and you get phenomena like conserved genes - that is, genes that are important to the organism and are thus selected for to stay the same. At that point there is no "random dilution" phenomenon happening: there are specific forces at work to maintain the gene in all descendants in a more-or-less unchanged state.


What happens after the purification step in Hi-C sequencing?

So, after the restriction digestion, the sample consists of DNA fragments with 5' overhangs. These are filled in by Klenow DNA polymerase, adding biotin-dCTP to both ends of each fragment. Then the fragments are ligated under conditions (ie low DNA concentration) such that ligation between non-crosslinked DNA is less likely. This reduced ligation efficiency (which is already lessened by the use of blunt end fragments) means that all crosslinked fragments may not be ligated, which I imagine is what they are showing in Image 2. Any two molecules which become joined by this reaction are called ligation products (ie they are the products of the ligation reaction).

After this step, the sample is treated with T4 DNA polymerase which, as well as having polymerase activity (obviously), also has 3'->5' exonuclease activity. Thus, any free DNA ends which have not been ligated will be trimmed, removing the biotin. After this step, biotin will mostly be present at ligation junctions, and these molecules can be selectively pulled down by the beads. I say mostly because some of these so-called dangling ends will still retain biotin, but these can be distinguished during mapping (see image below).

As for self circles: because they have been ligated, they will contain biotin and be pulled down with the crosslinked DNA. However, since this DNA is from the same genomic locus, they can also be distinguished from valid interacting pairs during mapping:

[source]

Finally, a quick note on the pull-down mechanism. The beads are coated with a protein called streptavidin (or avidin), which just binds to biotin very tightly. Only one biotin need be attached to any molecule (such as DNA) for it to be captured.


Non-radioactive nucleotide labeling compatible with reverse transcriptase?

Biotin-labeled nucleotides can be incorporated into cDNA by reverse transcriptase.  Jena Bioscience, a provider of biotin-labeled nucleotides, has a table showing which nucleotide chemistries have been successfully used with reverse transcriptase, though you'll have to delve into the data sheets of specific products to get the references.

One reference provided on the product page for biotin-11-dCTP:

APOBEC3G Inhibits Elongation of HIV-1 Reverse Transcripts

This study looks at natural endogenous reverse transcription (nERT) in HIV.  From the methods:

  For this assay, a nERT reaction was performed essentially as above, with the exception of the dNTP addition: pelletted virions were resuspended in PBS, 2.5 mM MgCl2, 15 µg/ml melittin and 0.5mM biotin-11-dCTP (Jena Bioscience), and incubated at 37°C.


Atomic force microscopy: depth penetration?

Taken right from the Wiki page you linked to:

AFM only images the surface of a specimen, to a maximum depth of 10-20 µm and a maximum scan area of 150 µm x 150 µm. Compared with scanning electron microscopy, SEM has a much larger depth of penetration and scanning area (~1 order of magnitude greater). AFM is also a much slower scanning method.


Looks like a Hyoscyamus niger also called stinking nightshade.


IMO irrespective of country and level (undergrad/Masters), if you can run a job on a High Performance Computing cluster or a supercomputer, you should mention that on your resume. And sure, you can use that in your statement, especially given the fact that not many have access to it, you had the rare opportunity and made full use of it.

In my experience, I haven't seen many undergrads here in the US that can run a job on a HPC - not without prior computing experience!

All the best to you!


DNA glycosylases bind to dsDNA, flip a base out of the base-paired double-helical structure and cleave it off, leaving the sugar-phosphate backbone intact. This base removal renders the DNA susceptible to alkaline cleavage.

In this recent paper:

  Miyazono et al. (2014) A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi. Nature Communications 5: #3178

the authors monitor the activity of a DNA glycosylase using this phenomenon: after treating an oligonucleotide with increasing amounts of the enzyme R.PabI they treat the DNA with NaOH so that the oligo is cleaved, allowing detection of the result of enzyme action on a polyacrylamide gel, as you can see from this image, taken from their Figure 3.

Incidentally the same phenomenon is exploited when DNA is transferred to a membrane for Southern blotting. After electrophoresis the gel is soaked in acid which causes depurination (analogous to DNA glycosylase). It is then transferred to an alkaline solution. Although protocols often refer to this as a neutralisation step it actually breaks the DNA at the apurinic sites and separates the strands. This cleavage is important for effective transfer of larger fragments from the gel to the membrane.


According to Wikipedia:

  A carbon sink is a natural or artificial reservoir that accumulates and stores some carbon-containing chemical compound for an indefinite period.

The key point here is the "indefinite period" part. For example, although my body stores some kg of carbon, I can't qualify as a carbon sink because most of it is likely to be released again in some decades.

On the other hand, soils store large amounts of carbon, and as the soils keep developing that amount tends to grow, making them an effective carbon sink. The mechanism consists mostly on accumulating organic matter, as you say, but as long the amount of that organic matter keeps growing, soil works as a carbon sink.


What could cause sudden deafness and deliriousness on a boat adrift?

He probably had hypernatremia: salt toxicity from drinking seawater.  That definitely can cause delirium.  It was harder to nail down that hypernatremia could cause deafness specifically but I found that for pigs.

http://www.merckvetmanual.com/toxicology/salt-toxicity/overview-of-salt-toxicity

  Affected pigs may be blind, deaf, and oblivious to their surroundings;
  they will not eat, drink, or respond to external stimuli.

It would be easy to think a person was deaf if he were altered / delirious / encephalopathic.  His brain does not process what he hears and so he is oblivious - like these pigs.


Are there any plants that fix their own nitrogen?

There are no known plants that fix their own nitrogen. However, there soon may be!

Because N is the major limiting factor in agricultural productivity, there is huge interest in plant systems which can fix their own. It's important enough that the Bill & Melinda Gates foundation have started a project aimed at reducing dependence on fertilisers by giving plants the ability to fix their own nitrogen. There are several potential strategies, the most obvious being encouraging more species to form symbioses with nitrogen fixing bacteria.

However, there's another proposal which builds on recent discoveries about the mechanism of nitrogen fixing in bacteria: we now know how the crucial enzyme complex is made (Rubio & Ludden, 2008). As a result, there are many people calling for efforts to engineer the system directly into a plant organelle (e.g. Beatty & Good, 2011; Godfray et al., 2010).

So, in 10-15 years time you can check back and the answer to this question might have changed! The most likely answer then will be "just the usual suspects: rice, maize, wheat".

References:

Beatty, P.H. & Good, A.G. (2011) Future Prospects for Cereals That Fix Nitrogen. Science. [Online] 333 (6041), 416 –417. Available from: doi:10.1126/science.1209467 [Accessed: 2 February 2012].
Godfray, H.C.J., Beddington, J.R., Crute, I.R., Haddad, L., Lawrence, D., Muir, J.F., Pretty, J., Robinson, S., Thomas, S.M. & Toulmin, C. (2010) Food Security: The Challenge of Feeding 9 Billion People. Science. [Online] 327 (5967), 812 –818. Available from: doi:10.1126/science.1185383 [Accessed: 2 February 2012].
Rubio, L.M. & Ludden, P.W. (2008) Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase. Annual Review of Microbiology. [Online] 62 (1), 93–111. Available from: doi:10.1146/annurev.micro.62.081307.162737 [Accessed: 2 February 2012].


To understand why satellite cells are genetically inactive in Barr body

DAPI (4',6-diamidino-2-phenylindole) preferentially binds AT-rich DNA (although it binds CG-rich DNA, too), which can give chromosomes distinctive banding patterns if they are polytene or in metaphase.  In interphase condensed chromosomes, such as the inactive X chromosomes of female mammals (Barr Body), the relatively high concentration of tightly-packed DNA makes the chromosome appear as a brighter spot in the nucleus.  When the DNA of a chromosome is decondensed (such as the rest of the chromosomes in interphase), it appears as more-or-less homogeneously stained DNA in the nucleus.

A great picture is here (see below), A is the DAPI staining, B is a protein localized to the Barr Body, C is the RNA (Xist) which binds the Barr Body.

Since the active X is not condensed, it appears as do the rest of the chromosomes, so cannot be identified among the mixture of autosomes.  The difference in DAPI appearance has nothing to do with activity per se, but rather differences in how tightly packaged the chromosomes are.

I do not understand the first part of your question, though.  You cannot tell from a still image that the Barr Body is relatively inactive.  If your were doing experiments on live cells, you could measure RNA production (using a labeled nucleotide), immunofluorescence to show localization of e.g. RNA Polymerase, or reporter genes located on the inactive versus active X chromosomes.  If you clarify your question, I can answer better.


How is the renal osmotic gradient maintained even though the blood osmolarity changes?

The water doesn't get drained.  As blood flows down a vas rectum, in any given section of the arteriole the tonicity is slightly higher outside the arteriole vs inside the arteriole.  This results in a small amount of water flowing out of the arteriole to attempt to equilibrate the osmolarity.  But before this has even finished happening, the blood has flowed down another quarter of a millimeter (or whatever) where the tonicity is even higher outside the arteriole.  In other words, down the entire vas rectum the water is flowing out.  But when the vas rectum comes back up, the situation is reversed, so the same quantity of water ends up diffusing back into the blood vessel.  Thus the osmolarity at any given level of the medulla remains constant.

Correct, the maximum osmolarity of urine is 1,200 mosm/L.  The concentration gradient in the medulla will change very slightly (temporarily), but don't forget that even as the urine in the collecting tubule is being concentrated to that maximum concentration, the whole process of creating the concentration gradient is actively happening in loops of Henle all around the collecting duct.  So even if the initial effect of having a bit more water in the medulla from the collecting tubule would be to slightly lower the extracellular osmolarity, in the grand scheme of things it changes nothing since the rest of the nephron is still actively creating an effective osmolarity gradient.

References

Any physiology textbook... for instance (among others), I have Human Physiology, from Cells to Systems - in the First Canadian Edition it's pp. 553-63.


Some graphs about the ovarian cycle mention only the follicular phase and luteal phase, and the ovulation just as a point in time, not a phase, for example, here:

Source: Differencebetween.com

In this case, the LH surge starts in the follicular phase and peaks at ovulation or shortly before it.

Some other graphs also show the "periovulatory" phase (or "ovulatory phase" or just "ovulation" as a phase):

Source: Nature - Scientific Reports

In this graph, LH surge starts few days before ovulation, so in the follicular phase and peaks in periovulatory phase.

  The first half of the menstrual cycle is comprised by the menstrual
  and follicular phases during which time estrogen levels are low
  (menstrual phase) and rise (follicular phase) and ends with the
  periovulatory phase in which follicular stimulating hormone (FSH) and
  luteinizing hormones (LH) peak.

Now, these graphs are still confusing, but Merck Manual defines the ovulatory phase by the surge of LH and FSH:

  The ovulatory phase begins with a surge in luteinizing hormone and
  follicle-stimulating hormone levels.

In conclusion, LH surge occurs in the ovulatory phase, if the source mentions it as a separate phase, and if not, it occurs in the follicular phase.


Identify these two large, colorful dragonflies in Taiwan?

Looks like this species is Orthetrum triangulare commonly known as blue-tailed forest hawk. It is an Asian fresh water dragon fly species.
As you mentioned that the dragonfly had a bluish hue, it became clear.

The other one looks like Neurothemis ramburri, commonly known as red perch Reference

Neurothemis is a genus of dragonflies in the family Libellulidae. Most Neurothemis species are red in color.
Neurothemis ramburii (Brauer, 1866) is distributed from Sundaland to New Guinea. There are records from Peninsular Malaysia, Taiwan, the Andaman Islands, Sumatra, Java, Borneo (Sarawak, Sabah, Brunei and Kalimantan), the lesser Sunda islands, the Philippines, the Bismarck islands and New Guinea. It is a widely distributed and common species that thrives in disturbed habitats.


Number of elongating RNA polymerases on a gene

Regulation of RNA polymerase II activation by histone acetylation in single living cells by Stasevich et al. provides detail on how they were able to determine the number of elongating RNA polymerase II for a given gene array. The issue I had with the paper is that they used a ~1.8Mbp tandem repeat as their target, so they really upped the probability of seeing activity. You may be able to do similar for your gene of interest, but there may not be enough signal to tease out your data.


What comes out of this bump in this vegetable?

I think your vegetable is a leek, or a closely related allium. If this is the case, you are seeing its flowerbud. Congratulations, it will become quite pretty in some days, I know people who use leeks as decoration plants instead of vegetables.


I am confused, can evolution ( speciation ) really occur in such a short time?

Well, Evolution and Speciation are not the same. Evolution is the adaptation of an existing species to an environment over generations. Speciation is the development of a new species, and the definition of "species" can vary depending on who you talk to - but a very commonly accepted one is that two individuals cannot produce fertile offspring.

However, the answer is still Yes. Evolution can occur in as little as two generations because that's all the time it takes for a change in the DNA to be exhibited in the newest generation. For instance, Lactase Persistence - which allows the bearers to ingest dairy products without digestive stress into adulthood - has evolved at least twice in humans in separate groups. Both are the result of either one or two point mutations (single changes in a Nucleotide within the DNA). The result is that at one point in time for each appearance of lactase persistence, a child was born that could drink milk into adulthood while their parents and cousins could not.

That is evolution; the child was better adapted to the resources available, and because lactase persistence either...

Provided a significant advantage over their kin in the environment (which is likely, as being able to digest milk in an agrarian society opens up a new source of energy)...

or

Didn't hinder the child's ability to grow and produce fertile offspring of their own...

...it has persisted in the populations where it initially evolved.

Speciation is a little trickier, but that's because there isn't a known qualitative way to differentiate species at the genetic level quite yet. It could be a few key gene changes, it could be a whole genome difference of 10%, or a million other factors. Practically speaking, though, Speciation is simply the result of accumulated genome changes that at some point prevent the members of one group from producing fertile offspring with their ancestral group.

Because we simply don't know how much of or where the genome has to change, it's certainly possible that speciation could occur in the same time period as it takes to evolve: Two generations.

Since I'm doubting the wall lizards have a generational time of >37 years (don't mistake it for lifespan, humans can reproduce in our teens - even if we live into our 80's), it's definitely possible that the wall lizards could evolve (and potentially speciate) in such a short amount of time.

With organisms that have a very, very short generational time - like E. coli or other bacteria - you can observe the Evolution of populations in days or hours.


How much influence does toxoplasmosis have on personality and intelligence?

I believe its the other way around - humans may engage in riskier and more novel behavior when infected... which is the most interesting part of the story.  Its not cut and dried, but I think its quite possible that risky behavior increases.

T. gondii is a parasite whose typical life cycle includes both mice and cats as hosts.  The transmission involves the mice being eaten by a cat.  Mice infected with T gondii will tend to lose some interest in being sheltered in close spaces and wander out into open spaces.  They also lose their fear of cats.   That is a permanent change even if the mice are cleared of the parasite.

Other animals, such as humans are secondary hosts - they can become infected by handling or close proximity to cat feces, who have a nearly 50% (45.6%) infection rate themselves. As a result toxoplasmosis is very common in humans.

Toxoplasmosis has been found to increase novelty seeking and increases risk seeking behavior at least in men.  Its been shown to contribute to higher automotive accident rates, schitzophrenia and suicide.

  Thus, the men were more likely to disregard rules and were more expedient, suspicious, jealous, and dogmatic. The personality of infected women, by contrast, showed higher warmth and higher superego strength (factors A and G on Cattell's 16PF), suggesting that they were more warm hearted, outgoing, conscientious, persistent, and moralistic. Both men and women had significantly higher apprehension (factor O) compared with the uninfected controls.

The correlation between toxoplasmosis and lower intelligence is a matter of debate, at least in this review I cite.  Its still not clear whether it is a sociological correlation - do smart people just handle their cat poo more carefully or not at all? This more recent study shows that some factors might make infected humans more intelligent and some researchers see toxoplasmosis as a transformative factor in humans ability to generate and use technologies.

I do see those links suggesting less risky behavior too.  Some say that the increase in traffic accidents is related to lower muscular coordination for instance.  There is evidence on both sides, but looking at what T gondii does to mice, I would bet that some risk behavior will increase.  As such, I'd guess that researchers as such might have a slightly higher rate of toxoplasmosis, but maybe you will do a study and help figure this out!

That being said - anyone who tries to link a single phenomenon; host-parasite interactions; a drug; a gene; a mutation to a phenotype with a simple description is definitely oversimplifying.  The mapping from biological activity to english (or any other language) is hopefully conscious of the caveats of such talk.


Phosphorylation-Dephosphorylation : ATP-driven VS spontaneous

First, I would like to clarify what is meant by "spontaneous". In chemistry, thermodynamically favorable reactions ($\Delta G < 0$) are indeed termed spontaneous because they will eventually occur, regardless of how slowly. But if transition states are unfavorable (high energy barrier), the reaction rate can be extremely slow --- millions of years in some cases. For example, combustion of wood is highly favorable and, chemically speaking, it is spontaneous. But that doesn't mean trees are unstable and likely to catch fire any minute.

Most biologists would probably call a reaction "spontaneous" only if it actually happens on a reasonable time scale, perhaps on the order of hours, depending on the context. So the terminology is a bit messy. But neither chemists nor biologists would call a molecule "unstable" if it has a reasonable half-life, I think.

Now for the actual questions. Dephosphorylations are typically not ATP-driven, because breaking the P-O bonds is usually favorable already (although I'm sure there exceptions). However, the reaction is typically too slow to be useful to cells, so it is not "spontaneous" in this sense, and therefore needs to be catalyzed by phosphatases. A typical example is alkaline phosphatase which dephosphorylates a wide range of proteins and other substrates.

Phosphorylation requires a phosphate source of course, but also an energy source, because forming P-O bonds is not a favorable reaction on its own (the reverse of the above). So adding a lone phosphate would not be favorable, but transfering one from ATP is much better, because this simultaneously involves breaking a P-O bond in ATP, "freeing up" energy to drive the reaction.

Finally, an interesting point is that ATP itself is actually a quite stable molecule, with a half-life of about two weeks. So ATP hydrolysis is not "spontaneous" in the biologist's sense, and enzyme catalysis is required (kinases). In fact, the combination of a high "energy content" and good stability is probably key to the role of ATP as an energy currency in cells: if ATP was indeed unstable, it would randomly phosphorylate everything. Stability means enzyme catalysis can be used to control phosphorylation events. Truly unstable compounds are never used by cells, because their reactivity causes damage and toxicity.


The term isoform has become a little ambiguous over the years (see http://blogs.cornell.edu/collinslab/2012/05/30/protein-isoform/)... still some things are consistent:

In some genetics literature 'isoform' has been used in the place of allele when talking about the allele states at a locus for a gene
Typically a gene isoform is equivalent an alternate transcript. The gene isoforms are the set of mRNAs that can be produced by a gene.
Protein isoform commonly refers to the set of proteins produced by a gene, this can include variations produced by alternative splicing and post-translational modification. Note that in some contexts the set of products from closely related gene duplications can also be included.

Note that databases will typically have a specific definition in mind for their use of isoform in their annotation, check their documentation for details (e.g. in UniProt see What is the canonical sequence? Are all isoforms described in one entry?)


Although this question sounds easy to answer in the first place, it is not. The main problem between humans and the apes we are most closely related to is that we have 46 chromosomes, while the apes all have 48. At some point in the evolution of the humans the ancestral chromosomes 2 and 4 fused together to form our chromosome 2, leaving us with only 46 chromosomes (see reference 1).

This makes offsprings much more complicated, but not completely impossible. A good example for this are crosses between donkey and horses (donkeys have 64 chromosomes, horses 62) to get mules (male donkey crossed with a female horse) or hinnys (male horse crossed with a female donkey) which subsequently have 63 chromosomes and are infertile. There are even crosses possible between horses and zebras which even differ wider. Zebras have between 32 and 46 chromosomes (depending on the species) but still zebroids are possible. See reference 2 for some more details.

So far there has been no successfull attempt to produce such hybrids, although there have been some attempts to make them. Some information can be found in reference 3.

Besides this problems (which are also due to ethical restrictions), there is a study available that at least humans and chimpanzees interbred for at least 1.2 million years after diverging and still produced fertile off-springs. See references 4 (for a summary) and 5 (original paper) for details.

Based on this evidence, I would say it is possible for humans and apes to produces off-springs, however, this is relatively unlikely and they will probably be infertile.

References:

Origin of human chromosome 2: an ancestral telomere-telomere fusion.
The chromosomes of two horse x zebra hybrids; E. cahallus x E.
grevyi and E. hurchelli
Blasts from the past: The Soviet ape-man scandal
Human Ancestors May Have Interbred With Chimpanzees
Genetic evidence for complex speciation of humans and chimpanzees


What makes a metal safe to use for an artificial joint?

There are a number of reasons why a given metal may be toxic to an animal:

Radioactive metals are the easy ones.
Some metals can affect the normal biosynthetic pathways within the body.  Lead is a good example of this, as it can take the place of calcium; I believe beryllium does the same for magnesium.
Some metals themselves are very reactive.  Hexavalent chromium ($Cr(VI)$) is highly reactive, and will cause damage through severe oxidative reactions, whereas $Cr(III)$ is largely okay.
A lot of metals are okay, even required, at some level, but become toxic at too high a concentration.  Iron, for example.
People can simply have allergies to metals.  Nickel in silver jewelry is a good example, although in my experience it can be overcome.

The basic gist is that some metals are required for life, some aren't but aren't too terrible, and some are completely toxic to it.  Different organisms can vary a bit in which metals are useful or not.  A good implant will of course not be toxic at all, and will be strong and long-lasting.  Titanium is often used, given its strength and general nonreactiveness, but so is cobalt, despite being toxic to some degree.

Ref: Metal Sensitivity in Patients with Orthopaedic Implants.  Hallab, et al. J Bone Joint Surg Am, 2001 Mar 01;83(3):428-428


Why do we have no enzyme to digest cellulose?

While it's true that cellulose is full of calories, it's very difficult to get the calories out.

Symbiotic bacteria take ages to digest cellulose, and as a result animals that digest cellulose with specialized symbiotic bacteria have a huge gut to house them in.

It's likely that the reason humans can't digest cellulose is because mammals generally can't. And mammals generally can't because it's way too much work, and we don't need to.


How is instinct carried from one generation to another?

This stuff is hard-wired into either the organism's nervous system, or endocrine signalling pathways (e.g., hormones), or possibly a combination of those two mechanisms.  In that sense, yes it is encoded in the genome, but not in a language that we can understand or interpret yet. Also, don't overlook all of the macromolecules that the female provides to the developing egg during oogenesis, your mother gave you lots of things besides a copy of her genome--you just don't have any of those macromolecules left now--but you wouldn't be here without them.


Is process, opposite for growth, known for mammals?

In humans at least (I'm not sure about other mammals), the thymus grown until puberty and then shrinks gradually, a process called involution. I'm not sure if this meets your criteria. The thymus remains "healthy," but it's function greatly diminishes over time.


How can I perform virus neutralization assay for influenza?

There are a number of different protocols, but the canonical one is published at the WHO Influenza site:

SEROLOGICAL DIAGNOSIS OF INFLUENZA BY MICRONEUTRALIZATION ASSAY

It gives a detailed, step by step protocol.


Why do neurons have a negative resting potential?

Essentially all animal cells maintain an ionic balance causing a resting potential of about -70 mV in order to maintain their internal environment including pH, ion concentrations, osmotic pressure and volume. (Lodish, Molecular Cell Biology)  Neurons developed from existing types of cells and it's unlikely that the cost of maintaining resting potential in the neuron could have driven evolution of an entire alternative system to provide the homeostasis supported by the existing system.

Note that the depolarization of the membrane at any particular place during an impulse is very short so the impact of the ion flows have only limited effect on the cell's overall internal environment beyond requiring adjustment by ion pumps for the losses involved.  It also is not obvious how the wave-like characteristic of a nerve impulse could be generated if the membrane did not carry a nonzero potential; there would be no stored energy (in the form of ion gradients) available to make the pulse swiftly spread across the membrane.

Another point to consider is that the perhaps 15% of a neuron's energy spent on replacing leaking ions may have some hidden usefulness.  This paper suggests that neurons may actually be set up to leak at a rate higher than they would if it were minimized.


Are there journals for theoretical models of protein-protein interactions?

Protein-protein interactions is an area of biophysics, so certainly Biophysical Journal (published by Cell) is a nice place to look.

PNAS has a broad range of areas and they pay a lot of attention to nice biophysics and modeling. But also they require (seems to me) experimental evidence.

The Journal of computational chemistry certainly about a lot of simulations and modeling, so see for yourself.

As for publications, the fact that you are asking for references makes me think you haven't done your homework on literature review, as it is always first and foremost job in a research project.


Mark-recapture is the most frequently used method for small mammals. It's best when combined with uncertainty estimates and population dynamics models (e.g. projection matrix).

The fluctuations of small rodent populations have long fascinated scientists, and various models have been developed. Logistic regression models can be used to estimate likelihood of mice outbreak based on local rainfall data.

Estimates vary.

Rat population in New York city, for example, was thought to be 1 rat to 15 humans in the mid 40s, 1:36 in the late 40s (Davis ratio), 12:1 in 2002.

The population of mice is often estimated per hectare - 0.25-60/ha in buildings and 1-200 in the field, over 1000/ha during outbreaks. 10^9-10^10 hectares of habitable land means
that populations of mice and men are, probably, of the same order of magnitude.


Book suggestion on computational molecular evolution

I would suggest the course of Coursera.org:

Computational Molecular Evolution

By Anders Gorm Pedersen

Technical University of Denmark (DTU)

PS: Do tell us if you found a better book!


In my opinion, it should work by size exclusion. Bacteria are on the size of few microns, whereas the pores in semi-permeable membranes are on the size of nanometers. Therefore, bacteria will not pass through the membrane.

Viruses are usually smaller than bacteria, and so maybe more likely to pass through such a membrane. However, you have not included the pore size of the semipermeable membrane in question, and so I am unable to give a more specific answer at this point. If the pores of the membrane are very small, even viruses will not be able to pass through it.


Which are the last cells of the human body to die?

They found live skeletal muscle stem cells in human corpses 17 days after death (LiveScience, 2012).

They isolated live stem cells from the bone marrow from human fingers 5 days after death and transformed them into cartilage, bone and fat cells (NewScientist, 2013).

The survived cells were in a dormant state with very little metabolic activity.


How standardized is lab-grade skim milk?

There is a degree of variability in milk, and in some cases this cause problems in protein work. Despite being a standard for ELISAs, it's not known to be the most reliable blocking buffer. As far as cryoprotection goes, variability doesn't seem to be a major concern.
Standardization varies depending on manufacturer. The Sigma link you included reports a quality level of MQ 200. The MQ level is something Sigma created in an attempt to increase clarity about quality controls. Products rated MQ 200 are for non-regulated applications. For this level they will provide a site-quality self-assessment, a certificate of quality/analysis, and specifications. They also have a notification system that customers can opt-in to for updates on quality control features. There's information on what each quality level meansand a breakdown of what they will notify you about on the Sigma website.


You asked about eukaryotes. The genome of the yeast Saccharomyces cerevisiae is 12.2 Mb.

The genome of the smallest free-living eukaryote, Ostreococcus tauri (a unicellular green alga) is 12.6 Mb

There are smaller eukaryotic genomes, but these are not free-living organisms they are intracellular parasites.


When in the cell cycle is the number of chromosomes normally reduced?

It is the other way around. Meiosis I (or reductional division) splits chromosome pairs so each cell gets half of the chromosomes of the parent. Meiosis II (or equational division) splits double-chromatid chromosomes (making two single-chromatid chromosomes), so cells retain the number of chromosomes, like in mitosis.

If more clarification needed:

before the S phase: 23 pairs of chromosomes, 46 single-chromatid
chromosomes
before the meiosis I: 23 pairs of chromosomes, 46
double-chromatid chromosomes
before the meiosis II: 23
double-chromatid chromosomes without their homologous other
after the
meiosis II: 23 single-chromatid chromosomes without their homologous
other
after fertilization = before the S phase

(I'm talking about humans here.)


Why is membrane potential not zero at equilibrium?

The value of the membrane potential does not affect the location of the resting potential.  The membrane potential affects only the fraction of channels that are open, thus allowing net current to change, which allows for the depolarization and repolarization of the membrane (the action potential).  During the action potential, the resting potential does not change.

The value of the resting potential is governed only by the distribution of ions (how many are on one side of the membrane vs. how many are on the other).  This is relatively constant even as ions cross the membrane for the action potential; it is really not a very large fraction of ions moving at all compared to the reservoir they are in, so the reversal potentials are preserved over time.


Yes, it contains arginase. Thise enzyme converts arginine to ornithine and is probably part of the urea cycle.

You might notice the arginase is listed as coming from Komagataella phaffii GS115, but this is just another (new?) name for Pichia.


How do bumblebees and hornets avoid the negative effects of inbreeding?

Queens do not generally breed with their brothers, but with males from other nests. In the life cycle of bees (and other social Hymenoptera), new queens are born late in the season along with haploid male drones. These all leave the nest and disperse in the landscape to find mates to reproduce with. After mating, all males die and the queens overwinter to start new colonies next spring. The situation is therefore not all that different compared to other annual, semelparous (single reproductive event) species, since you have population mixing before mating and reproduction.

Here are a couple of mechanisms that bees avoid inbreeding:

Population mixing before reproduction (see above).
Inbreeding avoidance
That queens prefer not to mate with close relatives has been shown in several species, see e.g. Foster (1992) and Whitehorn et al (2009).
Polyandry
Each queen generally mates with several males (regulary more than 10 in honey bees, see Palmer & Oldroyd, 2000) and stores their sperm to fertilize eggs during the next year, which means that workers and the queens of next year will have different fathers (increasing genetic variability).

References:

Foster. 1992. Nestmate Recognition as an Inbreeding Avoidance Mechanism in Bumble Bees (Hymenoptera: Apidae). Journal of the Kansas Entomological Society 65(3)
Whitehorn et al. 2009. Kin recognition and inbreeding reluctance in bumblebees. Apidologie, 40(6)
Palmer & Oldroyd. 2000. Evolution of multiple mating in the genus Apis. Apidologie 31(2)


Firstly, may I suggest 2D electrophoresis as a technique for identifying differences in protein/marker expression levels. This technique will give you greater resolution and ease of comparing your sample in basically one step/experiment. Added bonus once you determine your protein of interest you can easily excise it and send for mass spec analysis to identify your protein. In short, 2D electrophoresis separates protein based on their pI(isoelectric point) in 1st Dimension and then by their size in the 2nd Dimension. Once you identify the protein of interest you can purify it using the below steps.

Image Source

Now onto tackling the problem of separating your proteins for analysis. The general outline you can follow to separate a protein, is a follows:

Ion Exchange Column
Hydrophobic Interaction column (HIC)
Size-exclusion Chromatography (SEC)

Ion Exchange first because you elute the protein off the column using increasing concentration of salt (0 --> 1M of NaCl). Whereas you need a high concentration of salt to load the protein onto HIC column. So, the elute from setup 1 can be easily spiked with a 5M (Nh4)2SO4 and loaded onto HIC column (No dialysis). Also, Ion-exchange and HIC are high capacity columns whose resolution can be improved with shallow salt gradients.Hence my recommendation to be used first. However, if you are certain your marker/protein of interest is small you can directly use SEC column

Ion exchange column, as the name suggests, separates protein on the basis of their charge (Least ---> Most Ionic, also note charge +/- of the protein at that pH matters). The buffer to use for Ion exchange would be:

 1. Binding Buffer
    10-50mM Phosphate Buffer pH7.4 (plasma pH)
    0-25mM NaCl
 2. Elution Buffer
    10-50mM Phosphate Buffer pH7.4
    1M NaCl

Use low salt as possible to get the most efficient binding to the column.
Elution is done with a gradient of NACL from 0% of elution buffer to 100% Elution over about ~20 column Volumes.

HIC column separates the protein on the hydrophobicity of the protein. The order of the elution from the column is least --> most hydrophobic.

1. Binding buffer
    10-50mM Phosphate Buffer
    1M (Nh4)2SO4
 2. Elution Buffer
    10-50mM Phosphate Buffer
    (No Salt)

You can find a good protocol for HIC here. The elution is also done over ~20 CV with a gradient of 0-100% elution buffer, similar to Ion exchange elution.

Finally, size Exclusion or SEC separates proteins based on their sizes. The elution order is biggest ---> smallest size. The column is run in an isocratic mode i.e only one buffer used.
Buffer composition:

1. 50-100 mM Phosphate Buffer
2. 150mM NaCL

The salt in buffer is to prevent non-specific interaction of the protein with column, which might result in protein eluting later than necessary. This might result in poor resolution.

The most important thing to realize is each of the above column have their own sets of cavets. 1) Ion exchange columns are specific to the charge of protein, so you will end up having a lot of protein not binding to the column at all based on type (anion/cation) of column used. 2) Similarly, HIC column might not bind well to your protein as well. Also, adding 1M (Nh4)2SO4 will precipitate proteins which might include your protein of interest. 3) SEC columns have an upper limit on protein size they can accept, above which all the protein elute together at the void volume decreasing the resolution(However, this shouldn't be a problem in your case as you trying to separate out the lower molecular weight protein from the higher weight ones.)

Finally, all the above step work great considering you know the protein you are looking to purify(separate). Since that is not the case you will have to collect and run SDS-gel Electrophoresis of the fractions at each column purification stage. Also, run a side by side comparison of control and sample plasma to figure out which protein is being expressed differently.

In closing, I would like to point out that 2D electrophoresis gives you a gel to compare, as shown in the pic, anyway. So it might be a better solution to your problem. However, I do admit you might have to setup purification to confirm your findings.

Hope that helps, good Luck!


Are original x-ray diffraction data available

In many cases they are available.  One of the establishing principles of the Protein Data Bank (PDB) was to store not only the models (atomic positions and identities) of macromolecules and proteins, but also the originating X-ray data, more recently in structure factors.

If the question is 'why are they giving only the structure factors and not the original data they took' - such a task would require a lot of curation effort for very little scientific benefit.   Scaling the individual sets of data from the detector used to be a bear of a task.  The original myoglobin structure would entail scanned films in an ancient format from the 50s.  Nobody would be able to use that now without hacking the image format, if it wasn't on paper tape or cards.  In fact in that case the structure factors are not available.  Scaling many or several data collections together was often done with custom tweaks into the 70s and then in the 90s data collection became more routine, but several generations of x-ray detectors became popular and then faded from the market.  Each had its own eccentricities and requirements for combining data sets from multiple reads.

The purpose of having structure factors available is to allow anyone to reconstruct the electron density and evaluate the interpretive act which is tracing a peptide through electron density.  Since that format is mainly independent of the detector and has been fairly consistent over the years, it delivers a significant amount of scientific bang for the buck.

If you want raw image data or detector-proprietary data before multiple data sets from different crystals before they were combined you will have to contact the authors, who would probably have to sift through a sea of DVDs to get to it.  In older cases it might be tapes.

So as far as Structure factors, which are essentially the square root value of the combined and scaled Intensity data, they are available and a part of every submission to the pdb:

Look on any X-ray Structure Page at RCSB.  For example this one.

There is a box called "Experimental Details" and you can download the structure factors there by clicking a link.

If you are looking for more than one at a time, there are bulk downloads available through their download page.  Check the "Structure Factors" box.  Raw intensity data should be available if you look around for it as well.

Further Suggestion:  I was thinking that if you look at the scaling software that comes with the X-ray detectors you might find some tutorials with unscaled raw data.  I found one example at Marresearch - hen egg white lysozyme.


Reminds me of Senecio articulatus (Candle Plant; hot dog cactus), a succulent plant in the broad (aka polyphyletic) Senecio genus (Asteraceae).

 Source: U. Wisconsin-Eau Calire

Based on my limited knowledge of the plant and the variable leaf shape, I am not sure if this is your species or not. However, I'm sure some additional searching using this species as a guide will get you to the correct species/cultivar.

World of Succulents provides some additional information on Senecio articulatus.

You can see a video of a Senecio succulent identified as S. articulatus for better comparison to your plant:


Why is the blood pressure in the superior vena cava during inhalation less than during the exhalation?

The diaphragm moves down during inspiration. This leads to air being sucked in, due to the pressure difference created. The converse is true during expiration. As the thoracic space is where the SVC sits, it's pressure decreases during inspiration as it is subjected to the surrounding decrease in pressure.


In a skeletal muscle contraction, what happens after ACh binds to the nicotinic iontropic receptors on sarcolemma?

Acetyl choline, which is released at the neuromuscular junction is continuously broken down by the enzyme acetylcholineesterase into acetate and choline. Choline is once again taken up by the neuron through choline carriers to regenerate acetylcholine. This process continues as long as an the neuron is stimulated.
Source:
Wikepedia


How do CD 8+ Tc cells reach the site of tumors?

I do not remember enough details to share a mechanistic insight.

However, chemotaxis is a likely answer, which basically means moving along concentration gradient of certain ligand of interest.

Also relevant to your question: a hypothesis called 'immune surveillance' gaining support over the past few years.

http://www.biolegend.com/cancerimmunoediting


Can leukopenia in a person with an otherwise normal immune system lead to non-infectious diseases in the long-term?

Leukopenia is just a definition. In medicine, there's a saying:

  Treat the patient, not the numbers.

Numbers can mislead people, sometimes quite seriously. Definitions of leukopenia vary: some define it as less than 5,000 WBCs per µL of blood; others define it as less than 4,000.

Decreases in specific WBCs is usually described as neutropenia, lymphocytopenia, monocytopenia, etc. This, too, is important information, as each cell has a different function, and thus different results are possible.

In leukopenia, bone marrow biopsies are very informative. They reveal if the cause is a decreased production of WBCs due to destruction of precursor cells, replacement of marrow by other tissue, invasion of marrow by cancer, etc. If a bone marrow biopsy is normal, that is very comforting.

  does the condition need to be treated?

Most people with anti-epileptic drug (AED) induced leukopenia are just fine. Some common-sense precautions (such as avoiding other drugs which might also cause leukopenia, and checking a white count if you fall significantly ill) should be heeded. If your doctor is a neurologist, they should be thoroughly versed in the side effects of AEDs, as this constitutes a very large patient population for them. Some of the newer AEDs have a lower incidence of leukopenia. Talk to your doctor about the potential benefits and drawbacks of switching.

  Does leukopenia increase a person's chances of getting some non-infectious diseases too?

Theoretically possible, but not particularly likely.

If you are truly concerned, ask if you can get a referral to see a hematologist. They should be able to give you a real picture of the problems with long-term AED-induced leukopenia.

Remember: treat the patient, not the numbers. If you're healthy now, you're likely to continue to be so. Maybe you'll need more blood tests than others, but that doesn't mean you're not healthy. Talk to your doctors, not the internet.


Why don't neurons die during a stent procedure in the brain?

I am assuming you are asking because of occlusion during balloon angioplasty. If not, please clarify.

Ischemic stroke occurs when a blood vessel to the brain is occuluded by a clot or some other emboli or poor perfusion due to atherosclerosis (a type of narrowing of the vascular lumen). Given enough time, ischemia can produce tissue death, called infarction. It is possible to suffer an ischemic stroke (or ischemia to any tissue) without substantial infarction if reperfusion occurs quickly enough.

Time to tissue death

For stroke, the catchphrase "time is brain" is often used to indicate the importance of occulsion time in stroke. Cell death is not instant upon loss of oxygen, but rather occurs throughout any extended reduction in blood flow as well as during reperfusion.

The brain is more sensitive to ischemia than other tissues like the heart, but there is still a window in which little to no damage is done. By 5 minutes, however, neuron death can begin.

Balloon Angioplasty

When using balloon angioplasty (including during balloon delivery of stents), a single vessel is occluded for ~30-180 seconds. It is also possible for multiple individual inflations. Importantly, this time range is normally kept less than the ~5 minute range for damage to occur.

Embolic protection

One of the dangers during balloon angioplasty is the release of particles from the vascular wall that is being opened up. Those particles can cause distal embolisms. In other organs like the heart, this problem is fairly minor, because only small amounts of myocardial tissue are expected to be impacted which will not have a major impact on heart function. However, loss of small regions of brain could have significant impacts on patient recovery. Therefore, embolic protection strategies are sometimes employed which include devices to block distal flow or capture emboli. The use of these devices is very case-dependent, because if there is already a significant blockage it may not be possible to use particular devices for a particular case.

In any case, pharmacological protection with drugs like aspirin and clopidogrel are standard for interventional angioplasty procedures.

Balloon alternatives

Balloon-mounted stents are standard for coronary procedures, but in the periphery, including carotid and neurovascular implants, there are other stent types, such as nitinol, a shape-metal alloy of nickel and titanium. These are also known as self-expanding stents. They are deployed by removing a protective sheath and they open up on their own. Thus, there is no total occlusion during a nitinol stent deployment. However, balloons can still be used with nitinol stents to open up the original blockage, because the nitinol stents themselves don't "push" nearly as hard against the walls.

In my opinion, the major benefit to nitinol stents is not that occlusion isn't necessary for their deployment, but rather that they are not sensitive to crushing. With a regular stainless steel stent, external pressure would permanently deform the stent. In the heart that isn't a problem, because if someone is poking you in your myocardium you have bigger problems. However, the carotid arteries are fairly exposed in the neck, and a regular metal stent in the neck could be compressed and deformed. Instead, nitinol will snap back into position, like the underlying tissue.

Neurovascular circulation redundancy through collaterals

Although any ischemic tissue can eventually develop collateral circulation pathways to bypass the occlusion (assuming partial and not total occlusion, sufficient to keep the tissue alive in the meantime), the neurovascular system is unique for the high degree of redundancy present even in normal individuals with no blockages. Therefore, occlusion of a single vessel even permanently may not cause substantial symptoms. Of course this will vary from patient to patient and depends on the patency of collaterals, overall vascular health, and specific anatomy at the site of treatment.

Caveats

Of course there are risks in any surgical procedure. It is unlikely that there is zero neuronal death during any neurovascular procedure. Rather, these procedures are used when there is already significant risk or imminent damage without intervention; the intent is to create as little damage as possible while either solving an acute problem that is much worse, or reducing the likelihood of future infarction events.

References

Kulik, T., Kusano, Y., Aronhime, S., Sandler, A. L., & Winn, H. R. (2008). Regulation of cerebral vasculature in normal and ischemic brain. Neuropharmacology, 55(3), 281-288.

Lee, J. M., Grabb, M. C., Zipfel, G. J., & Choi, D. W. (2000). Brain tissue responses to ischemia. The Journal of clinical investigation, 106(6), 723-731.

Mousa, A. Y., Campbell, J. E., AbuRahma, A. F., & Bates, M. C. (2012). Current update of cerebral embolic protection devices. Journal of vascular surgery, 56(5), 1429-1437.

Pan, Jie, et al. "Reperfusion injury following cerebral ischemia: pathophysiology, MR imaging, and potential therapies." Neuroradiology 49.2 (2007): 93-102.

Saver, J. L. (2006). Time is brain—quantified. Stroke, 37(1), 263-266.

(disclaimer: I worked for a major manufacturer of intravascular catheters and stents for about 4 years. I was last employed by that company ~8 years ago and no longer have any financial relationship with that company. Everything in this post represents my own personal views. I am not a medical doctor; this information should not be taken as medical advice. Only your doctors/interventionalist can give appropriate medical advice according to your specific case)


When should I use cryofixation and chemical fixation?

Cryofixation usually preserves the organelles inside the cells better, but is more work and usually results in TEM images that are lower contrast. Chemical fixation is easier and gives good contrast, but is more likely to destroy details in delicate samples. Chemical fixation will usually be used unless it is found or expected to not work well for a particular sample. It is possible to mix the methods, for example by including glutaraldehyde in freeze substitution solutions. Here is an article that describes everything you asked about in more detail, if you can access it: A comparison of cryo- versus chemical fixation in the soil green algae Jaagiella


Modeling intracellular interactions between sender and receiver bacteria

You can start with deterministic model using ODEs for reaction rates.

However, if you are considering diffusion then you would have to use Partial differential equations for Fick's diffusion law.

You can, however, assume that there is no "diffusion" but just transport of the signal molecule from a well mixed system (medium) to another well mixed system (cytosol). In this case you can use an ODE for "conversion" of extracellular signal to intracellular signal.

The model becomes simple and easy to analyze if you reduce the number of steps. Certain steps can be removed by making certain assumptions such as Equilibrium approximation (EA) or Quasi-Steady-State approximation (QSSA). If a reversible reaction is extremely fast compared to all other reactions (such as binding-unbinding of the activator to DNA), you can assume that reaction to be in equilibrium and represent the concentration of some species using equilibrium constants.
In Quasi-Steady-State approximation, you assume that certain species are in steady state with respect to others i.e their concentrations do not change over time. In the model you just set $\frac{d[X]}{dt}=0$ for that species. Then obtain the concentration relationships as a function of reaction rate parameters. I'll explain QSSA and EA using the Michaelis-Menten (MM) kinetics.

MM considers following steps:

Enzyme-Substrate binding (Reversible): $ E + S \rightleftharpoons ES $ with forward rate constant k1 and reverse rate constant k2
Enzyme-Substate complex converting to Product and Enzyme (Irreversible): $ ES \to P + E$ with rate constant k3

EA (The actual MM model):
Assuming step 1 is in equilibrium. $k_1[E][S]=k_2[ES]$
 Get [ES] in terms of [E] and [S]

QSSA (The revised MM mddel):
Assuming [ES] is in steady state. ${\Large \frac{d[ES]}{dt}}=k_1[E][S]-k_2[ES]-k_3[ES] = 0$  which means $[ES] = \Large \frac{k_1[E][S]}{k_2+k_3}$

This way you have removed certain reactions from the model.

You can do stochastic modeling as well.

For simulations you can use Matlab or Fortran.


Continuous selection is not a term; it would not be bolded in a textbook.

When studying the history of a genome/lineage, you could have two very broad hypotheses about a given trait:

1) The trait was not present in a lineage, then appeared fairly suddenly (at least on a long time scale, it could still be hundreds, thousands, or millions of generations), and since then did not change much.

2) The trait was not present in a lineage, then the trait appeared in part of that lineage, and since then, the trait has continued to change substantially among different descendants of that lineage.

You could find evidence towards (1) if, for example, you observe a trait that is fairly constant among a diverse modern taxon but you don't see a similar trait in the cousins of that taxon.

You could find evidence towards (2) if you see a lot of diversity even among recently speciated members of a taxon.

The statement in the article is just saying in plain English, rather than using a scientific terminology, that they see evidence towards (2).


Is there natural occurrence of induced pluripotency / expression of Yamanaka factors and what is the evolutionary explanation of that?

What is a pluripotent stem cell?

A pluripotent stem cell is a cell that can differentiate into any of the major tissue categories. Every animal exists as a collection of pluripotent stem cells at an early stage of development: if you are looking for an evolutionary purpose, that's where you should start, and the purpose is pretty obvious: you start as a single fertilized egg and end up as a complex collection of tissues, so at some point that one cell has to become a collection of tissues, and there is an intermediate step which is a pluripotent cell.

None of this has anything to do with induced pluripotency, however.

What makes a cell pluripotent?

The answer to this question isn't really all that unique to stem cells: all cell types are differentiated from others based on their expression of transcription factors. Transcription factors determine what proteins get produced (including other transcription factors), which in turn determines how a cell functions and what role it plays.

Pluripotent stem cells express pluripotent stem cell transcription factors. Yamanaka started with embryonic stem cells, and looked for transcription factors that were special to those cells.

What does it mean to make a pluripotent stem cell?

Given that the identity of a cell is based on the transcription factors it expresses, the way to make one cell type act like another cell type is to change those transcription factors. A cell is a pretty complicated environment: there are lots of different transcription factors and lots of other types of proteins, so it's possible that it wouldn't be feasible to reprogram a cell this way.

However, Yamanaka and colleagues tried to artificially make an adult cell produce those transcription factors observed in embryonic stem cells. Indeed, they found that if they used the right combination of transcription factors in the right environment, the cells started to behave like embryonic cells, and they could further make those cells differentiate into different tissue types. These transcription factors are the so-called Yamanaka factors.

Summary

An induced pluripotent stem cell is a cell that has been transformed to produce transcription factors that are found in embryonic cells. Transcription factors are what make different cell types different from each other, by controlling everything else that the cell produces. All of this machinery is ubiquitous in development, the only intervention that the humans are doing is to make a cell express genes it would normally only express if it was an embryonic cell.

All of this information is already present in the Wikipedia article you linked.

Takahashi K, Yamanaka S (2006). "Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors". Cell. 126 (4): 663–76.

Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S (2007). "Induction of pluripotent stem cells from adult human fibroblasts by defined factors". Cell. 131 (5): 861–72.

Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA (2007). "Induced pluripotent stem cell lines derived from human somatic cells". Science. 318 (5858): 1917–20.


Dominance and recessive relationship of alleles

Phenotype determines dominance. The "rules" you state are just general possibilities that are most likely; they are not correct definitions. "dominant as wild type most circulated" is just completely totally false.

It's common to have mutations that cause loss of function. These often end up as recessive alleles, because the second copy still makes a functional protein. It's not about the allele being suppressed necessarily, and doesn't have anything to do with benefit or not, it's just that the other copy is able to do the job, so you don't see much effect. Because there are often feedback mechanisms for gene expression, having 1 less copy in the genome often means much less than a 50% reduction in protein.

It's also common to have mutations that cause negative gain-of-function: these are often dominant, because you only need one copy for that negative effect to be observed.

However, as you point out, these aren't always the case. You could have an allele where loss of a single copy causes a deleterious phenotype. Sometimes these might more appropriately be considered "incomplete dominance."

I think it's important to note that these terms are really labels based on phenotypes, they are not biological realities. An allele could be thought to be completely dominant, but under further study actually demonstrates a form of incomplete dominance or co-dominance.

The Wikipedia page on dominance has some better definitions for you.


What is this marmot-like animal (Tigray, Ethiopia)?

This looks like some sort of ground squirrel. Especially in the second picture, the posture is  very characteristic of squirrels in general. The tail also looks very squirrel-like to my eyes. My best guess, without better pictures, is the Striped Ground Squirrel (Xerus erythropus).

See the images at:
http://www.flickriver.com/photos/8834404@N02/2902284598/
http://www.flickriver.com/photos/kpzaremba/5094580855/


Nature versus nurture regarding aggression in specific dog breeds

It seems that there are some important differences in dog aggression depending on the dog breed (towards strangers, owners, and other dogs):

That being said, it seems that a significant proportion of a dog's behavior can be due to its environment (training, etc), according to a study, this 'nurture' component might explain up to 80% in the variation in aggression (which should be considered when interpreting the other study I cite).


Why was it initially thought that Mendel's findings were contradictory to Darwin's natural selection?

It's thought that Mendel's communications were anti-Darwinist, and some argue that his original paper was written specifically as a refutation of Darwin's descent with modification. Mendel believed species were created by God and not Darwinian evolution. Because of this, when he found a law defining constant probabilities of heredity, he saw it as more of an argument for the consitency of genetic information and thus species. To him this was in contrast to the ability of heritable traits to vary slightly in progeny, leading to selective advantages. Source I paraphrased: http://jhered.oxfordjournals.org/content/87/3/205.full.pdf


Oxygen uptake with gills from water vs lungs from atmosphere

The assumption in the question was corroborated by this article here, and is correct. The downvote is unnecessary, it is a valid question, and was easily answered with strong scientific consensus.

  As a precondition for the coevolution of eurythermy and life with high energy turnover, oxygen availability had to be maximized and the
  capacity of oxygen supply mechanisms selected high (Fig. 2). Such
  preconditions were met with atmospheric oxygen levels always above a
  minimum of 13%–15% during animal evolution (Fig. 4). Moreover, such
  preconditions were most ideally met in terrestrial environments since
  breathing air rather than water implies a reduction by one order of
  magnitude in the energy cost of ventilation at 30–35 times higher
  levels of ambient oxygen and about 103 times lower viscosity of the
  respiratory medium. However, new and largely different ventilatory
  systems had to be developed in air (lungs instead of gills in
  vertebrates) in most cases (except for terrestrial crabs) to exploit
  the excess amount of oxygen. At the same time, thermal conductivity in
  air is more than 20 times less and specific heat about four times less
  than in water, reflecting that thermal buffering is much less in the
  968 H. O. Po¨rtner terrestrial than in the aquatic environment. As a
  consequence, temperature changes occur on shorter timescales and at
  larger amplitudes in terrestrial than in aquatic environments.
  Therefore, terrestrial organisms at the same latitude are likely to
  experience much larger temperature fluctuations than aquatic
  organisms. Opposite to the marine realm, where temperature
  oscillations are less in polar and tropical than in temperate areas,
  those in air increase at high, especially Northern, latitudes, as
  estimated for mainland locations in the Americas (Gaston and Chown
  1999). According to these considerations, extreme stenotherms
  comparable to Antarctic marine species are highly unlikely to exist in
  (cold) terrestrial environments. Eurytherms will predominate instead.

Pörtner, H. O. (2004). Climate Variability and the Energetic Pathways of Evolution: The Origin of Endothermy in Mammals and Birds. Physiological and Biochemical Zoology, 77(6), 959–981. https://doi.org/10.1086/423742


Disclaimer: the shortest answer still remains we don't know...yet.

Talking from the evolutionary perspective, I have found as many as 8 theories about the purpose of dreaming, some of which even contradict each other(!). But I'll describe them one at a time.

One obvious theory is that we dream about something we dream of. So, dream is basically a way of wish-fulfillment; what we are dying to achieve, we get that in our dreams. Though it has been made quite scientific by Freud et al, it still doesn't look much scientific, at least from evolutionary perspective.
Another idea, made popular mainly by Hobson et al, is that dreams are purely because of accidental firing of neurons. In what they call activation-synthesis theory, they claim that during sleeping, neurons in areas of brain, including brain stem, limbic system, secondary visual cortex, etc. fire accidentally. When the brain tries to interpret those signals, the result comes out as dreams.
Another theory, proposed by Zhang et al, is that dreams are our brain's way of converting short-term moemory into long-term memory. This quite explains why some people reommend a power nap after learning something new, it helps the brain in storing the knowledge as long-term memory. Also, recent studies have concluded that it is better to remain awake for hours after a traumatic experience rather than sleeping right off, if you want to forget that experience faster.
Another theory, popularly called reverse learning theory, basically says that we dream to forget things. Dreaming is a way for our brain to prevent information overload so that memorizing new things becomes easier. Seems the opposite of Zhang et al and most likely answers why Sometimes we can't even recall what we dreamt of.
Yet another theory, seemingly more sound from evolutionary viewpoint, says that dreams are just like the playing-dead response of our body. When we dream, the neurotransmitters related to movement are shut down, resulting in what seems like a dead body. So, our body preferred to retain this mechanism because it could've helped in a way like the freeze response did.
A theory, proposed by Revonusuo et al, says that dreams are to make people ready for real-life situations. According to it, people who often dream about being chased by a tiger will learn how to overcome that situation and eventually will be able to survive such case. Seemingly answers your question Why do we sometimes get weird and unusual dreams?
Barrett et al, based on Revonusuo's theory, proposed that dreams are a way for solving problems for humans, partly because dreaming mind makes connections faster than awake one. Though this explains how Kekulé predicted benzene's structure, it doesn't look very much scientific.
A yet another one, by Coutts et al, says dreams are a way for "natural selection" of best possible method to solve a problem, including emotional situations, and is called Oneiric Darwinism. A much similar idea by Hartmann et al is called contemporary theory of dreaming.

I will not discuss the mechanism of dreaming, not only because it will make the answer too long or because others have delved into that point in their answers, but because it will answer the How? part rather than the Why? part, and also because that part would be better suited for cogsci.SE.


What is this hairy, striped orange-black caterpillar?

It's a woolly bear caterpillar which will later grow to become Isabella tiger moth.


Is it unusual for populations of archaea to be found living inside trees?

The exact term — wetwood, is used only once in the original article (Yip et al., 2018).

Others have found that water content of heartwood tissue was the best
predictor of methane flux across multiple plant species (Machacova et
al., 2016; Wang et al., 2017), however this was not a strong predictor
of methanogen relative abundance in our analyses. It is possible that
within trees characterized by wetwood such as Populus deltoides,
other factors may become more important than water content above a
certain moisture threshold.

However, if you look at these lines from the introduction of the paper, it seems that wetwood just means wood that has a high water content. It definitely does not refer to a disease or infection.

Indeed, both mechanisms may be important depending on tree species
(e.g. those containing dry and dense vs wet and porous wood) and
ecosystem under study (e.g. wetland vs upland forest soils).

Based upon past work and our own informal observations of odors
associated with tree coring at these sites indicative of fermentative
environments, we hypothesized that an anaerobic community including
methanogenic archaea would dominate woody tissue, particularly in
heartwood tissue which is often water‐soaked.

Now coming to your question on whether it is unusual for populations of archaea to be found living inside trees.
Roots have been known to harbour microbes; plants establish this symbiotic relationship with the microbes for nitrogen fixation (See mycorrhiza and root nodules). So, it may not be very unusual that archaea interact with plants but it may possibly be unusual that they are living inside this part of the tree. Yip et al. (2018) highlight that although microbial composition of the wood has been studied in the past, these studies have been done ex situ. This means they are the first to study these microbes in situ.

Microbiological investigations of living wood have been conducted in
the past (Zeikus & Ward, 1974; Zeikus & Henning, 1975; Ward & Zeikus,
1980; Schink et al., 1981a,b, 1982), but these studies primarily
focused on ex situ wood incubations and the isolation of microbial
representatives, rather than overall community characterization across
tree conditions. For example, Zeikus & Ward (1974) demonstrated that
methane production occurred from extracted wood tissue from Populus
deltoides and were able to isolate pure cultures of a new species,
Methanobacterium arborphilicum (Zeikus & Henning, 1975), later
reclassified as Methanobrevibacter arboriphilus (Balch et al., 1979).

So, it seems that people have been working on this area since 1970s.
However, it also appears that there is not much research on archaea as a part of the plant microbiome (Taffner et al., 2018).

IMPORTANCE: Archaea are still an underdetected and little-studied part
of the plant microbiome. We provide first and novel insights into
Archaea as a functional component of the plant microbiome obtained by
metagenomic analyses. Archaea were found to have the potential to
interact with plants by (i) plant growth promotion through auxin
biosynthesis, (ii) nutrient supply, and (iii) protection against
abiotic stress.

So whether this is unusual or not depends on whom you are asking (hence a bit opinion based).


Evolution from Mating types to different sexes

Another important reason to have mating types is to prevent self-fertilization or self-polination that produces less capable offspring. Because of this requirement, mating types may evolve also for species that produce both types of gametes, or does not differentiate them into male and female gametes. Fertilization is only possible if gametes have different mating types.

It may be more than two mating types, but if there are only two, they are probably similar to "sexes" even if gametes do not look different.


Help identify this awesome climbing plant with velcro like stem

I think this might be Japanese hops. Well, what I have in my yard is Japanese hops.

As I said, it's horrible.
Description and Biology:

Plant: herbaceous annual, twining, shallow-rooted vine that can climb to heights of ten or more feet with the help of rough-textured stems covered with short, sharp, downward pointing prickles that can be very irritating to the skin.

Leaves: leaves are rough-textured, paired, simple, palmate (like a hand) with typically 5-7 lobes; leaf margins are toothed.

Flowers, fruits and seeds: flowering occurs in July and August; male and female flowers are borne on separate plants; male flowers are very small, greenish yellow and occur in branched panicles; female flowers are in pale green, plump, drooping, cone-like structures with overlapping scales that become ‘hops’; hop scales and the seeds are covered with yellow glands; seeds are about 1/8 in. in diameter, roundish with a blunt tip, and light brown with darker specks; seeds mature through September.

Spreads: by seed which begins to germinate in early spring, but new plants may continue to emerge as the season progresses if sunlight and moisture are available; seeds are dispersed by animals (including people), machinery and floodwaters.

Look-alikes: native common hop (Humulus lupulus) looks very much like Japanese hop but it is usually 3-lobed or unlobed; native bur cucumber (Sicyos angulatus) lacks prickles, has tendrils, and the leaves have much less pronounced lobes.

Prevention and Control: Do not purchase, plant or transplant this species.


Why does 4-thiouracil labelling to map RNA-binding proteins cause a T-C change?

The technique used in that paper is called PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation; see Ascano et al., 2012 and Spitzer et al, 2014). This technique involves substituting uridine (U) with 4-thiouridine (4SU) or substituting guanosine (G) with 6-thioguanosine (6SG). The rationale behind using these modified bases is that they improve the efficiency of RNA-protein crosslinking. Moreover, PAR-CLIP uses 365nm UV instead of the 254nm UV used in the conventional crosslinking. However, the crosslinking process causes the loss of the sulphur atom causing the U to be read as C during reverse transcription. Likewise, 6SG gets read as A.

  Ascano et al., 2012


Which patterns do I have to avoid when modifying the 3'-UTR?

If your goal is to avoid regulatory elements, I would not believe any prediction program, since new regulatory elements are found every day.  The best way would be empirical and just clone and infect with a mutated 3'UTR and see if your gene's regulation is perturbed.  You could at least swap the entire 3'UTR with that from another gene to see if there are even any gene regulatory elements in the 3'UTR.


Why is warm water comfortable, but warm air uncomfortable?

You constantly generate heat from metabolism.  The ability of this heat to be transferred to your surroundings from your skin is tremendously different in air vs. water. This is known as thermal conductivity.

The ability of water to remove heat from your skin is roughly 24 times that of air. See list of materials and their thermal conductivity rates here

In water of close to body temp, you can still bleed off heat to water. Your ability to do so in air that is close to body temperature is greatly reduced, so much so that in order to keep up, you sweat and increase the cooling ability through the evaporation of that sweat at temperatures well below 98.6F.