Does the false positive covid-19 PCR % referred to by Surkova & Nikolayevskyy in The Lancet mean % of all tests, or % of positive tests?

Actually, neither A nor B in the example are a correct interpretation of a false positive rate, because there isn't enough information provided to determine a false positive rate. In the terminology of clinical diagnostic testing evaluation, testing outcomes can be classified into one of four fundamental categories: True positive, false positive, true negative, or false negative.
While there are four possible outcomes, any given patient only has two possible test results, positive or negative. And the assessment of that result depends on whether they have the disease or not. So patients with the disease can only have a true positive or a false negative, and patients without the disease can only have a false positive or a true negative.
Since it's not possible for a patient with the disease to have a false positive, we get to ignore them in calculating a false positive rate. So a false positive rate would be the number of false positives out of the total number of possible false positives (or the percentage of patients without the disease who test positive). With an ideal data set in which you knew both the test result and true infection status of each patient, you could calculate it like this:
$$ FPR = \frac {False\ Positives}{False\ Positives + True\ Negatives}$$
The thing is, we don't usually use this in evaluating clinical diagnostics, but rather it's complementary value, which is called "specificity" (for some reason), and is essentially true negative rate.
$$ Specificity = \frac {True\ Negatives}{False\ Positives + True\ Negatives}$$
But note that neither of these values can give you the number of false positives in your example without more information. If you assumed that all 100,000 people tested did not have the disease, then you'd expect 1000 false positives (given your 1% false positive rate). But it gets more complicated when you have a non-zero rate of infection in the tested population. The greater the underlying infection rate, the fewer false positives you expect to see (and vice versa, with a lower infection rate, you expect a greater proportion of positives to be false, which I think is pointed out in the article you linked). Basically, it's really hard to determine something like a false positive rate on the fly and even harder to estimate it's impact in the real word, especially when the test you're trying to evaluate is also the best means you have for determining true infection.
Another consideration is that, for a well designed PCR diagnostic test (most COVID tests are), the majority of false positive results will come from technical errors (i.e. cross contamination, mislabeled specimens, etc.), rather than randomly from the test itself. And the rates of those kinds of errors can vary with the underlying rate of infection, the number of tests being processed by a given lab, the level of training those lab workers have, the number of hours they're putting in (tired people make more mistakes), and probably other factors I'm not considering.


Thalassemia is a genetic disease, in which either the alpha- or the beta-globins are missing or mutated. The hemoglobin of the blood is a protein complex which in adults consists of 2 alpha- and 2 beta-globin subunits. The ratio of these proteins needs to be exactly right, if one of them isn't produced enough or even missing, this leads to non-functional hemoglobin and subsequently abnormal erythrocytes.

These are then removed and broken down in the spleen (which is often abnormally enlarged), which also leads to the breakdown of the non-functional hemoglobin. The main product of the hemoglobin breakdown is Bilirubin, which is yellow. The yellow skin is a sign of jaundice, which is caused by high levels of Bilirubin in the blood.
The cause for the high Bilirubin levels in the blood of Thalassemia patients is the abnormal high rate of Hemoglobin breakdown.


This is the "Acer palmatum" or Japanese maple, which shows a wide variety of different leaf forms (from here):

Specically you found "Acer palmatum dissectum 'Red Dragon'", for more information look here (picture also from this site):


Usually you would want to keep the amount same, not the concentration. However, if you still want the concentration to be the same then you can add suitable amounts of PBS or your lysis buffer.

For e.g. if you have two samples with 1mg/ml and 4mg/ml concentrations and you want to load 20μg of total protein, then you can take 20μl of first sample and add 5μl of 5x loading buffer. For the second sample, you would take 5μl of the sample, 5μl of 5x loading buffer and 15μl PBS.

  Why 1x?

Because researchers before us found this composition to be optimal (or just simply stuck to it as a matter of practice).

  Would it be a problem if the final concentration of the loading buffer is more than 1x?

Apparently not, in my experience if it is up to 1.5x. Never checked higher concentrations.


Bacterial Conjugation/Horizontal Gene Transfer -- how does the plasmid exchange work?

The donor cell retracts it pilus upon contact with another cell and both cells form a pore between the two cells, which allows the transfer of DNA.
Take a look at the image, I think this makes it clearer (from the Wikipedia article on Pili):

This has even be seen in an electron microscope:


How do mosquitoes orientate in the darkness?

What is the purpose of their loud, annoying sound?

Both males and females produce a sound when flying but not at the same frequency. I would think of the male sound as mainly an artefact of flying and don't really know if it has any usefulness. I would note though that before mating both gender tend to synchronize their sound (Gibson and Russel 2006). On the other hand males are very attracted toward the sound of females.

In nature, mosquitoes make swarms. Male's job in the swarm is find find female, courtship and mate. This means that males need a cue to detect them from far away and this cue is their sound. Males evolved large and fluffy antennas (with which they hear) while females only have small antennas Charlwood and Jones 2008.

  How do they avoid obstacles?

They have eyes! It is never complete darkness and they just move around, see things and sometime bump into something and keep flying until they reach their goal.

I can't offer you a citation for that but as I worked with mosquitoes in the past, I think it is a good description.


What is the very hard sphere inside the eye of many common fish made of and how is it called?

From what you describe, it seems the hard sphere is the lens and the semi-liquid substance is the vitreous humour. Like the lens of other vertebrates, the fish lens is made of lens fibres—cells rich in proteins called crystallins.
For more on the anatomy of fish eyes, you could read this page and watch this dissection video.


An expression vector is a (usually circular) piece of DNA which is able to replicate inside a (bacterial) cell independently of the genome. Vectors can be transferred between bacteria and can express proteins from their own DNA sequence. They are used to express proteins inside of bacterial cells which can subsequently be purified. In this case the sequence for an immunogenic peptide is cloned into a vector and expressed in bacteria.
These are antibodies which are directed against a certain peptide. This is one technique of generating these antibodies. Making a (synthetic) peptide and then immunize animals against it. Then you can purify the antibodies from the serum of the animal.
Yes. You make short peptides of 8-12 amino acids (which is the length that the antibodies binds to) and use them for immunization.


Are similar smells usually based on similar chemicals?

With regards to the similar chemicals having similar smells, it does seem that there are trends with smell association and functional group.  This wiki article has a good list of compounds and their smells, and some classes definitely give similar types of smells, amines are rotting/fecal smells (hence the names putrescine and cadaverine), while esters are often fruity.  As you can see its not perfect, but there are definitely patterns.

There are some weird dose-dependent effects like in the case of indole which is labeled as flowery/fecal, which are two pretty distinct smells.  Apparently its fecal at high doses, and smells like jasmine at low doses.  My guess is that this has to do with different binding affinities of the different olfactory receptors (ORs) that are expressed in the olfactory receptor neurons (ORNs).  Many odorants will bind to multiple ORs, which means they will stimulate a characteristic sub-population of ORNs.  The binding to the different ORs will of course have different affinities.  This probably means that at low concentrations of indoles, you stimulate a certain population of ORNs that your brain recognizes as nice flowers, but as you increase the concentration you get the activation of ORNs with ORs that have a weaker binding to indole, changing the population of activated ORNs to one that your brain recognizes as feces.  Its definitely a strange pairing though..

I'm not familiar enough with the literature to know if the similar smelling things have similar ORN activation patterns, but my guess would be that they do.  If you have a population of different ORs that your odorant is binding to, a slightly different odorant will probably bind to a similar subset of ORs, just off by a few if its missing or has gained a functional group that is in the binding pocket of some of the ORs.  This probably means that if you are presented with a chemical that you have never smelled before, it will probably activate a similar ORN population as other similar chemicals, and your brain will probably say it smells like one of those similar chemicals.


How do I clean and calibrate pipettes, and how often should I do it?

How often you should calibrate your pipettes depends on the tolerances of your application. For some applications, like quantitative PCR setup, one may care a great deal; for general lab work, one can probably be less particular. You can get a sense of how accurate your pipettes are by pipetting DI water onto the platform of a sensitive (and calibrated!) balance. Comparing the random and systemic error you get while doing that over several trials to the specifications published by the manufacturer will give you a good idea of whether pipette calibration will help and help give you a sense of how much you care. Note also that the error may vary with the volume; you should test error over the entire volume range you intend to use the pipette for.

How to clean and calibrate pipettes is specific to each design. Some pipettes, like Gilson's, are not intended to be calibrated by the user. Others are. The pipette user guide published by the manufacturer should tell you.

For some demanding applications, even well-calibrated and well-handled micropipettes may not be sufficiently accurate. In particular, I've made standard curves by serial 10-fold dilution for quantitative PCR both a) relying on my micropipettors to be correct and b) trusting pipettes only to get me into the right ballpark, and intentionally undershooting and correcting volumes with sequentially smaller pipettes until the reading on the balance is correct, if that's at all clear. In both cases I was using 900 ul of diluent and 100 ul of the previous dilution, which I feel are comfortably large volumes to handle. I found that the latter curve gave me noticeably better regressions.


It is very easy, use google + pathophysiology and read some articles in the actual topic. There are a lot of pathophysiology books as well (some of them pretty expensive). Another way to do an online course.

Just a simple search about your example:

  It is known that AAAs are characterized by destruction of elastin and
  collagen in the media and adventitia, loss of medial smooth muscle
  cells with thinning of the vessel wall, and transmural infiltration of
  lymphocytes and macrophages. Atherosclerosis is a common underlying
  feature of aneurysms. However, atherosclerosis is not the primary
  driving factor in the development of AAAs. Atherosclerosis is a
  disease that is widespread throughout the vasculature, however
  aneurysms only form in specific locations and only in certain
  individuals. Additionally, atherosclerosis is primarily a disease of
  the intima, while aneurysm formation primarily affects the media and
  adventitia.

2009 - The Pathogenesis of Abdominal Aortic Aneurysms


Can you answer Ray Comfort's question on Biological Evolution?

The question is really not well defined for two reasons:

What would you accept to consider being an observation? It seems to me that many creationist would accept to consider something to be an observation only if it is extremely simple to understand it. The methodology of observation in evolutionary biology (just like in most science field) are not always very simple to understand for non biologists.
The word "kind" is not define in the sentence "what is a change of kind?".

Because the question is poorly defined, it makes it impossible to answer. And that is the common problem with creationist arguments. Their arguments are not scientific and therefore cannot really been argued for or against. Just want to say also that evolutionary biologist do not need non-scientist to fight against their work. Scientists create their own criticism. Scientists do not form a political party that fight for one point of view just for the purpose of defending it. They think neutrally and objectively (as much as a human can).

Change of kind

If change of kind = change in DNA sequence

Let's assume change of kind means change in the DNA sequence. Change of kinds have been observed in real time in almost all lineages we looked at (including humans). These changes are not only observable at the genetic level but also at the so-called phenotypic (loosely speaking the phenotype is way the organism looks like) level. We can for example think of disease in humans that are due to de novo mutations.

If change of kind = a population/species adapt to a new environment

If by change of kind, one mean "adaptation", then adaptation to new environment have been observed in tons of lineages again. In a lab it can be observed in bacteria within the course of a month. It has been observed in many mammals, birds, plants and unicellular eukaryotes.

If change of kind = one lineage splits and there is reproductive isolation

If by change of kind, one mean "reproductive isolation", then reproductive isolation has also been observed in real time and many times in nature and in labs (see this post for example)

If change of kind = something else

Just tell me what is this something else and we'll let you know if it has ever been observed. We can also let you know if this something is a prediction from the theory of evolution or not.

Observation

If you accept observation based on slightly more complex method such as molecular clocks and comparative genomics, then you'll find thousands of example of "change of kind", again in roughly speaking all lineages of the tree of life.

Very recently I worked on the speciation of clownfishes. This speciation was dated and we observed morphological and genetic adaptation to specific environments.

P.s. I haven't looked at the video completely but only some randomly selected part for a total duration of about 30 seconds! At first sight I'd like to say: Please don't fall into the trap of the media. One making interviews of people that are sometimes identified and sometimes not and that select for some part of their answer and that ask poorly defined question can really easily say anything from his records.

I welcome editing and I welcome anybody wanting to add references. One can find tons of them!


Easy: look at images of hairless cats. You will see they can be not only all black, but also grey, spotted, pink, and a few other rarer colors.

Also, take an average cat - and shave for surgery:

Note pigmented skin matching dark stripes.


First of all: We are not very different on the genetic level - the identity is somewhere around 99.6 to 99.9%. See here for details. If this wouldn't be like this, things like blood transfusions or organ transplants wouldn't work.

To identify genes there are different routes. "In the old days" (meaning before the possibility of massive high throughput sequencing or DNA microarrays), genes were usually discovered when they were connected to a disease which had a noticable phenotype. Researchers then tried to find out which protein or pathway was affected and from there went backwards to identify the genetic region. This way of discovery was relatively slow. An example for this kind of identification is the identification of the Mitf gene which is important for the development of pigmentation.

If you sequence DNA (doesn't matter here if these are complete genomes or only parts of it) you can identify genes based on homology with already known genes. You can also predict the presence of genes in a certain sequence based on regulatory sequences in the region before the gene (the promoter). These sequences are known and also highly conserved, so this gives a good estimate. Predicted genes usually need to be verified experimentally.

What is done today are the so called "genome wide association studies". Here you take a big cohort of people which all share one phenotype (for example blue eye color). Then you take a second group of people which do not show this phenotype and analyse their genomes (usually by sequencing or SNP genotyping). Then you compare the two groups to find the differences. Ideally you can then more or less directly identify a causative mutation which is responsible for the phenotypic difference between the two study groups. This usually needs also to be verified further.


Practical Question about Evolution, Population Genetics and Speciation

Infertile descendants indeed sound like a disadvantage. Individual must invest a fair amount of resources into making an offspring. Making sterile offspring is just a waste of resources as those offspring aren't going to pass on any gene further to any grandchildren.

If there is an increase of the tredecdssini females, then male tredecim that sing quite late are going to mate with many tredecdssini leading to the production of sterile offspring. There is therefore selection against the allele 'earlybird' leading to an increase in frequency of the 'EARLYBIRD' allele.


How can a heart of human work if one of its valve is not working?

It is not possible that one of the valve is completely closed and the person is still alive without being in ICU. I think what the doctor was trying to communicate to the patient was that one of the valves is in the process of complete closure. There are three main types of diseases associated with heart valves :-

1- Blood flows backwards
2- Heart valve opening becomes narrow
3- upper condition may lead to complete closure

For details see the following link:-

http://www.nhlbi.nih.gov/health/health-topics/topics/hvd
http://en.wikipedia.org/wiki/Pulmonary_atresia

Hope you understand. :)


How does botulinum toxin enter the blood stream from the digestive tract?

Transcytosis is a process by which large macromolecules are transported across a cell, such as those in the intestinal epithelium. It is used by many toxins and even whole organisms to enter the body. Botulinum toxin also apparently uses this mechanism. I'm not sure how detailed of an answer you want, but the linked to-review is pretty in-depth.


What are the max angles of human eyeball rotation?

There shall be slight differences due to physiology. Nevertheless, the average vertical ascending angle is 25 degrees and descending angle, 30 degrees.
Within the x-y plane of which we assume to be coplanar with the central line of vision, the maximal angle of rotation is 35 degrees in the left and right directions respectively.

I attempted to construct an image which depicts these angles - simply a Cartesian diagram.
You can find further clarification of details from this link by Nelson & Associates

Finally, it is important to note that although the eye may be capable of these rotations, the eye may not be able focus on all objects in this field acutely, namely, focusing light on the fovea.

Happy muscular experiments.


I am going to throw this idea out there. I was unable to find it stated anywhere so far.

There are several very ancient parasites that make their homes inside erythrocytes and neutrophils. Plasmodium is one, the causative agent of malaria. Trypanosoma is another. These things are ancient degenerate eukaryotes and their lifestyle as intracellular parasites is probably ancient too.

These things cannot make purines either but they need them and they need a lot of them, because they are reproducing fast. If the host cell does not have the machinery to make purines, that machinery cannot be hijacked by the parasite to really crank out the purines.  The best they can do is hijack the salvage pathways these cells have.

From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC259377/

  The apparent competition between parasites and host cells for available purines suggests that depletion of extracellular purines should be considered as an approach to treating extracellular trypanosome infections.

From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405406/

  Plasmodium species parasites, like many other protozoan parasites, are purine auxotrophs, unable to perform de novo purine biosynthesis. They rely on the host to provide purines

That does not explain brain cells  - unless lack of purine synthesis is a defense of brain cells against Toxoplasma, yet another eukaryotic parasite.

Nothing would please me more than for someone to poke holes in this theory. A prediction from this theory: erythryocytes in all animals should lack purine synthesis - including birds, who suffer from a form of malaria and whose erythrocytes do have nuclei.


Black soldier fly Hermetia illucens. http://en.wikipedia.org/wiki/Hermetia_illucens

There is a good key to the Dipteran families here. Although it is for British families, it is very thorough.


Background binding in this case would be the extent to which two proteins associate together by chance.

A hypothetical example: you may have a mitochondrial protein import complex.  Usually cases there is a specific peptide sequence the import complex binds to , but proteins without an import peptide sequence will occasionally be bound to the import complex.  This is called the background binding for the protein complex.  The experimentalists might have measured this by cutting the import peptide sequence off a mitochondrial protein for instance.

Any candidate would have to bind to the complex more than the background case to be considered a target for mitochondrial import.


What molecules does amylase enzyme work on?

Your incomprehension is due to the fact that both starch and cellulose are polysaccharides.

As it is said in the wiki page. Amylase is active only on alpha linkage like starch or glycogen. If you want to break beta linkage like in cellulose you need a cellulase enzyme, which humans do not have.


Staying underwater: would mutual rebreathing help?

Theoretically:
I'm going to assume that in your scenario, both individuals took a deep breath of regular air before submerging themselves, as this changes quite a lot (you'll see why in a second). Regular air on Earth as you probably know is made up of 78% Nitrogen, 21% Oxygen, and other trace elements like CO2 and ArgonColumbia University. What we care about is oxygen, as this is what our body can't function without.

The air we exhale is approximately 14-16% oxygen [2], which is a significant decrease, but is still very breathable. If we choose 15% as the exhaled percentage and 21% as the inhaled percentage, the percentage decrease is approximately 29%. Thus, with each breath taken by the other individual the amount of oxygen in the shared air decreases drastically. Another problem is the dilemma of CO2, which is exhaled at a 5% percentage increase. I would imagine the two people wouldn't make it more than a minute before the oxygen level in the shared air is too little to be absorbed and the CO2 makes them both lightheaded to the point where they faint and forget about the tube altogether.

If both individuals had breathed in pure 100% oxygen it would delay their impending deaths but it wouldn't prevent it. I love doing this sort of stuff and could calculate the difference in time between both before the air is unbreathable but...

Practically:
It wouldn't work. It may sound like something that would work but think about it this way: the very first breath one of them takes it literally sucking the air out of the other's lungs. No matter how much one tries to synchronize breathing in and out with the other -  based on lung size, lung volume, diaphragm surface area and many other factors - one's breathing in simply cannot equal the other's breathing out. One of them would eventually breathe in too much, leaving the other choking and gasping for air, leading to a tug-of-war of air, that unless they resurface will lead to both of them drowning.

[2]:
P.S.Dhami; G.Chopra; H.N. Shrivastava (2015). A Textbook of Biology. Jalandhar, Punjab: Pradeep Publications. pp. V/101.


How to do western analysis to lung tissue?

Doing westerns with primary tissue can be tough, especially because of the presence (sometimes at high levels) of extracellular matrix (ECM). This material can be quite resistant to homogenization and some lysis buffers. One method I have found to work is to snap-freeze the tissue in liquid nitrogen (not on dry ice or at -80°C) directly after removal from the animal, or after any sub-dissection you may wish to do. Then, when you are ready to prepare your sample, grind it thoroughly with a mortar and pestle in LN2, collect the dust and add a good lysis buffer like RIPA at 2-3X concentration, along with protease and phosphatase inhibitors, also at 2-3X. Then, instead of simply homogenizing, use a probe-tip sonicator (not a water bath one) and sonicate the lysate on ice with 8-10 pulses of perhaps 3-5 seconds each, ensuring that the lysate does not heat up too much, and making sure it does not froth up by getting the tip too close to the surface. Sonication sends very powerful shearing forces through liquid and is excellent at destroying membranes and breaking apart ECM. From here you can do your protein concentration assay (remember to use the same concentration of lysis buffer as your blank), aliquot the lysate and store at -80, or add SDS sample buffer and run your gel.

I routinely use sonication on all of my western samples, regardless of whether it's tissue or cell lines I'm dealing with, and I almost never get smeared lanes anymore. Sonication reduces the viscosity or "thickness" of the lysate, allowing you to pipette it much more easily and accurately. It is also useful when your sample "coagulates" after adding SDS sample buffer, and in this instance it doesn't matter if the sample gets hot, as you'll just be boiling it anyway.

I hope this helps, please let me know if you're still having problems. I used to do troubleshooting like this for a living :)


Why do human vaccines affect different animals differently?

One big reason for the difference is how close the vaccine's epitopes match the natural epitopes in the animals. When they are similar an attempted immune response to the vaccine will either tend to give an autoimmune response; or no response as the relevant immune cells were destroyed during maturation (to prevent autoimmune diseases).

The reports of autoimmune disease from SARS-Cov-2 (kawasaki disease) would seem to reduce the targets for a successful vaccine.

Sorry no refs on this.


How can I describe running a solution four times through a chromatography unit (in an instruction)?

I would continue to use inject to describe loading samples into the liquid chromatography system and replace

  chromatograph the RNAase solution four times.

with

  inject the RNAase solution another four times.


Stability of DNA double helix conferred by base stacking

When you carefully look at the structure of DNA helix, you will notice that consecutive bases are partially layered i.e. one base is "on-top" of the other base. Stacking is a chemical phenomenon in which the cloud of the pi-electrons in an aromatic molecule interact with that of the other. This interaction is non-covalent. Since the DNA nucleobases are aromatic molecules, they also exhibit stacking which stabilizes the structure of the DNA. A study by Yakovchuk et al. (2006) suggests that base stacking has higher contribution to DNA stability than base pairing. Sponer at al. (1997) found that there is no great difference between the stacking energies of B- and Z- forms of DNA helix.


For starters, your conception of antigen presentation seems a bit off, but that's not the crux of your question. There's around 10^15 different sequence permutations for a peptide 11-mer. Despite that, it's actually likely that highly conserved regions of some proteins will be present in both the pathogen and the host. T cells will not recognize them, however, as they are negatively selected in the thymus.


Parameters that determines the thermal stability of DNA

Although taken in isolation GC bonds should be more stable than AT bonds, due to their higher binding energy (three hydrogen bodns versus two), it is the stacking energy that is considered the stabilizing factor of the DNA:

We find that temperature and salt dependences of the stacking term
fully determine the temperature and the salt dependence of DNA
stability parameters. For all temperatures and salt concentrations
employed in present study, base-stacking is the main stabilizing
factor in the DNA double helix. A•T pairing is always destabilizing
and G•C pairing contributes almost no stabilization. Base-stacking
interaction dominates not only in the duplex overall stability but
also significantly contributes into the dependence of the duplex
stability on its sequence.

The reason for that is that one can have the same number of pairs under many different configurations of strands, which means high entropy and instability, unless there are stacking interactions. This is why most models of DNA and RNA helices are based on adding the stacking energies, although there are some additional contributions, particularly in the case of RNA - initiation energy, energies associated to the inner loops, etc.


Are pseudogene counted as a subtype of long non-coding RNA genes?

A note on nomenclature in modern biology

As it stands, this question seems to assume there is some legal commission, Académie française, or the like that is devoted to continually determining scientific nomenclature, and that those in the field obediently follow it. While organizations like IUPAC — The International Union of Pure and Applied Chemistry — do exist for standardization, they move very slowly, and only come out when the dust has settled (so to speak). So if I write an article about genes I can classify them as suits my purpose. I may wish to distinguish just between coding or non-coding; or between structural, informational, regulatory and junk etc. etc. Nobody is going to throw me in gaol if they disagree.

Is it scientific to classify pseudogenes in this way?

By this, I mean do the genes (for that is what we can compare) for long non-coding RNAs (ncRNAs or lncRNAs) have enough general features shared by pseudogenes that it would be useful to sub-type pseudogenes in this way. In my opinion, No. Pseudogenes are generally regarded as non-functional — remnants of unsuccessful or uncompleted gene duplication, or of reverse transcription of mature mRNAs into the germ-line DNA. In many cases they are not even transcribed.  There may not be a single function for those gene-products termed lncRNAs but in general they are transcribed and thought to have functions concerned with gene regulation. There are no structural similarities with pseudogenes, so that all the genes have in common is that they are, well, long, so to that idea I would say “So long!”

How do the genome annotators regard this?

The people that make the rules, de facto — and revise them as science advances — are the ones with the job of annotating sequenced genomes. I haven’t made a general survey of genomes, and am restricting myself to the genome of the fruit fly, Drosophila melanogaster, with which I am familiar. The distinct Biotypes for genes in the data at FlyBase are currently (2019) as follows:

ncRNA (aka lncRNA)
protein coding
pseudogene
snRNA
tRNA
rRNA
snoRNA
pre miRNA

I suspect that this is standard among the large genome databases, and it can be seen that pseudogene and ncRNA are regarded as distinct categories.

Of course, one can argue with this classification — where are the SINES and LINES and Drosophila-specific mobile elements, for example? But that just illustrates what I have written above.


If oxygen deficiency is bad even for a short while, why do people swim?

In this paper the authors measured decrease of arterial blood oxygen saturation in healthy and patients with sleep apnae (this latter part is not really relevant only the measurements in healthy individuals).

They found that fall of oxygen saturation depends on the initial saturation rate, but is not affected by the breath-holding time. As you can see on the graph at high initial saturation the fall rate per second is quite low. Here is the info in a table format:

At high initial saturation only mean 0.16% saturation drop occurs per second, thus in average a healthy individual looses 1% oxygen saturation approx every 5 seconds (I'd also like to note that the urge to breathe does not come from the lack of oxygen when holding breath, but from the accumulation of CO2). According to wikipedia normal oxygen saturation is between 100-95%, and only below 90% is considered hypoxemia /hypoxia (a medical condition where blood oxygen level is low). So if we look at the data in the table, it is safe to say that it takes approx 20s until the blood saturation level drops from 97% to 93% and another 5-6 seconds until it drops to 90% (with approx 0.5% saturation loss per sec at 93% initial saturation).

People who are conditioned by exercise have larger vital-capacity (they can breathe more air in for a single breath), thus have means to acquire more oxygen can compensate for the excess use of oxygen. During heavy sport activity like swimming it is unlikely that anybody will hold his/her breath for several tens of seconds.


How similar do proteins have to be to trigger the same immune response?

Immunoglobulins don't recognize entire proteins, but rather,specific shapes (called epitopes). These epitopes must also be present on the surface of the invading bacteria or virus for the immunoglobulin to have access. The epitope must be exactly the same. Any change in the amino acid sequence would change the shape. But an epitope is a relatively small part of the larger protein. If the shape is the same between different proteins, it would trigger an immune response.


How do genetic chimeras with different blood types not die?

Since these cells are there by the development of the immune system, the immune cells recognize them as self. By blood transfusion with incompatible blood type, the immune system recognizes the blood cells with different histocompatibility antigens (A,B,Rh etc...) as non-self, that's why it attacks them.


What's the difference between tumor cells and host cells?

This question is a bit broad but I'll try to narrow it to be specific in the terms of "tumor" vs "normal" cells.

 (Source)

Basically a tumor contains cells which have a part of the cell cycle regulation broken (very broad way of saying this). There are literally thousands of things that can cause this. Broad groups of things that cause this could be knockdown of a protein (of which many are involved in replication), mutation of a gene (most likely), etc etc. Basically any type of DNA damage can lead to cancer.

 (Source)

So what creates damaged DNA? Well here is a small list:

UV light (Can cause DSBs)
Carcinogenic chemicals (eg: Ethidium Bromide)
Replication proteins getting stuck or loosing function

 (Source)

Well how does that compare to a "normal" cell. Normal cells have a proper cell cycle with all the "checkpoints" working normally to essentially throw away any cells that detract from the cycle in any way. They also have mechanisms to fix DNA that has been damaged before it gets replicated. If none of that works they have mechanisms to basically commit suicide so they never replicated. When all of that fails you get cancer.

In summary, a cell becomes cancerous when the following things happen:

DNA is damaged by one of the above methods
The DNA damage repair mechanisms fail to fix the damage, or cause further problems by attempting to repair (NHEJ is a repair mechanism for DSBs that is implicated in causing cancer)
The DNA damage causes abnormalities in the cell cycle (replication)
The body fails to recognize the particular cell with abnormalities in order to kill it
The abnormal cell is allowed to replicate without hindrance from the body's checkpoint mechanism
You now have cancer

As for the role of immune cells that question is too broad as there are many different types of immune cells. Their "general" role is to clean the body of foreign agents but there are differences even in that role. There are many different types of them.

 (Source)

While I love teaching this stuff I do feel like you could find A LOT of this by doing google searches. Please try that next time.

EDIT: Updated with plenty of sources.


Practical utility of genes responsible for the biosynthesis of a useful compound in a plant

You essentially gave the answer in your question. By identifying the biosynthetic pathway(s) required to create the compound in the plant, its natural host, those genes can then be cloned and transferred into an expression system like bacteria, yeast, or other plant cells like Arabidopsis thaliana to generate larger quantities of the compound of interest than would be possible from harvesting and processing the original plant itself.


Which human cell lines do not express the GLP-1 receptor?

AbCam suggests HeLa cells as positive controls for their antibody to GLP1R. They provide the following pictures of HeLa cells labeled with their antibody:

(The image of the right is treated with synthesized peptide.)

According to Wikipedia, GLP1R is also expressed in pancreatic beta cells and the brain.


Certain organisms and strains of organisms can accumulate certain substances, such as Cd (a toxic heavy metal). If they accumulate those compounds more rapidly and in higher amounts, the organisms can be said to be high-"substance" accumulating organisms, e.g high-Cd accumulating organisms. The genotype which causes being a high-Cd accumulating organism can be described as a high-"x" accumulating genotype, like in this paper. A high-accumulating genotype without reference to a certain substance doesn't make much sense. These genotypic predispositions to accumulation are often used with toxic heavy metals like cadmium and arsenic which persist in the body.

As another "substance" example, high-"x" accumulating organisms is also used in the description of high-plaque accumulating organisms, e.g in this paper.


All-or-nothing-law: law or general principle?

I would argue the all-or-none principle is a rule of thumb. It is generally true if voltage hits a certain threshold then there will be a action potential with the same amplitude regardless the strength of the stimuli. But as you point out with the logic gate example, the threshold is notoriously hard to define mathematically. Furthermore Action Potentials don't always have the same amplitude, but as I will argue that doesn't matter all that much to the function of the neuron.

As most rules in biology we can find exceptions. I'll list some phenomena that confound the all or none principle.

Accommodation is the prime example that not all action potentials have the same voltage amplitude. Accommodation is the when the amplitude of the voltage of successive action potentials drops, and may even stop firing (Depolarization Block). This is usually the result of a too strong of a stimulating current, and occurs under pathological conditions.
Resonating Neurons These neurons fire when a certain frequency of input is achieved and can even fire when hyperpolarizing (negative) currents are injected. The reason I bring this particular neuron  type up is it shows that thresholds are not necessarily more depolarized (positive) than rest. They are complex manifolds (or shapes) relating to the gating variables of Ion channels in the membrane.

Another thing to note, is even though amplitudes of Action potential can change, the difference of a few millivolts in amplitude will not make a difference to the synapse and in that sense the all-or-none principle holds. Recall that voltage gated Calcium entry is required for a synapse to release it's neurotransmitter. Much like the logic gate, it will only enter at sufficiently depolarized (positive values) but the more positive the voltage, does not correspond to more Calcium entry. In other words it saturates at high voltages. In this way, to cause a stronger response at the synapse the neuron increases the firing frequency to stay "on average" depolarized longer. Thus more Calcium entry and thus more neurotransmitter release.


Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

This vocabulary is common in textbook but not in the peer-reviewed literature

First please note that while those terms are often used in intro class to evolutionary biology, they are actually rarely used in the peer-reviewed literature.

No trait value is fundamentally derived / ancestral

Note also that any given set of shared trait could be called ancestral or derived depending on the size of the tree that you consider. A trait is therefore not fundamentally ancestral / derived, it depends upon what other trait value you compare it to. Per consequence, it would easier to have a tree under our eyes to discuss these terms.

Note that there is one exception to that. Traits that are shared with LUCA are fundamentally ancestral!

Two states in different lineages can be fundamentally homologous / homoplastic

In general, when we are interest in a given trait, we display a tree so that all homologous trait states appear ancestral. While it is true that homoplastic trait state are necessarily derived when shown, homologous trait state can be shown as derived from a yet more ancestral trait state.

Analogy vs homoplasy

Many think of an analogy as a synonym of homoplasy. However, have a look at @GerardoFurtado's answer for the subtle difference between the two.


Is it easy to test human Flicker Fusion Threshold?

Flicker-fusion rates are very easy to test in humans: you provide a flickering light-source, set it to flicker at different speeds, and get the people to tell you whether the light is flickering or constant. This paper (from 1952) achieved a flickering light by putting a rotating disc with holes in it in front of a projected light source. A more modern testing unit is demonstrated here.

The human flicker-fusion rate does not appear to be a constant. In addition to being influenced by attributes of the light source (such as its wavelength, how much the brightness changes, etc), it also appears to be influenced by factors such as stress and fatigue (pdf).


What about a bat's immune system protects them from Ebola?

The main reason for this is that fruit bats are most likely (I don't think there has been a direct proof for Ebola so far) the reservoir host for this disease. The reservoir host is adapted to the disease and can harbour it for an indefinite time (with recurring infections) without showing signs of an infection or being affected by it. Although it is not getting sick, the reservoir host can pass the disease to other animals.

There is very little known about the immune system of bats, but they seem to be different, so they are not affected by diseases which cause havoc in humans. The following papers go into some details and they are interesting to read:

Bats: Important Reservoir Hosts of Emerging Viruses
Bats and their virome: an important source of emerging viruses
capable of infecting humans.

These papers give an interesting view of the bats immune system. The first article is a short explanation of the most important findings of the second. It looks into differences between species and analyse how the bats immune system may have evolved. Really interesting.

Of bats, flight and immunity to viruses
Comparative analysis of bat genomes provides insight into the
evolution of flight and immunity.
Antiviral Immune Responses of Bats: A Review


This looks like a black trapdoor spider (I'm guessing male by the size of the abdomen), check out the photos on the page I've linked below and see what you think - and this is a pretty good picture, usually the photos friends send me are far more blurry!

http://www.spiderzrule.com/trapdoor1.htm


What kind of tree is this (Seattle, WA)?

It looks like a Laburnum. Probably a Common Laburnum Laburnum anagyroides, also known as a Golden Chain Tree. It is from central and southern Europe.

The seeds are poisonous.

https://en.wikipedia.org/wiki/Laburnum_anagyroides

Here is a photo of the leaves

From http://www.saps.org.uk/trees/laburnum.htm

And the flower

http://wildflowerfinder.org.uk/Flowers/L/Laburnum/Laburnum.htm


Why do scary situations make our skin crawl? Why do we have goosebumps in such situations?

Goose bumps are based on a pilomotor reflex where tiny muscles at the base of hair follicles contract, which leads to the "bumps" and also raises the hair in the follicle.

It's often explained as a vestigal reflex, dating back when our ancestors had more hair than the modern human. The "puffing up" of fur has two effects, which today still both can be observed:

Raised hair traps air in the fur, thus minimizing heat loss in the cold.
Raised hair (often combined with certain postures) makes an animal appear larger, thus intimidating an opponent or predator. This is the scenario you mention in your question.


The answer to this question depends upon the definition of the word 'promoter'.

In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this process the σ factor recognises the core promoter elements directing the polymerase to bind to the DNA to form the closed complex. The next step is the switch to the open complex involving separation of the DNA strands.

Articles describing investigating the interaction of the σ factor with the DNA (e.g. here) refer to the protein making contacts with base pairs. I conclude therefore that the original question doesn't make sense - a promoter is a dsDNA entity even though we might describe it in terms of the sequence on one or other of those strands. So, for example, in a promoter the consensus -35 sequence - 5'-TTGACA -  would be present on the coding strand (upstream of the coding sequence), but the promoter property of the sequence is due to the presence of this sequence and its complement on the other strand.


difference in genetic instuctions between male and female

The typical Male has a Y-chromosome, which consists of about 100 genes.

Genes are the instruction sets to make proteins, and proteins do the work of the cell.

Those 100 genes out of about 21,000 in the human genome are what differentiate Males from Females.

That being said, because of how signaling works, Males and Females can exhibit different expression patterns, like function calls, even though they have the same instruction sets, for the most part.

Expression patterns are how genes are activated and deactivated, it is basically a regulatory process that controls the functions of the cell, tissues, organs, and organism.


BWA-MEM single strand or doublestrand alignment

BWA-mem (like most aligners), takes a normal single-stranded fasta file (I've never seen one with both strands listed) and aligns to both strand.


Pathogenesis of Group B Streptococci and C5a

I think "neu" must be an abbreviation for "neutrophil".

C3a and C5a are both chemotactic peptides that recruit cells to sites where complement activation is occurring. C5 is a substrate for the C5 convertases formed in one of the three complement pathways (classical, lectin, alternative). C5b, the other product of this cleavage goes on to form the membrane attack complex.

C5a peptidase is a Streptococcal product which destroys the C5a peptide before it can recruit neutrophils and other agents of cell-mediated immunity. Streptococci also produce an inhibitor of the membrane attack complex.


This condition is called 'anosmia', see these two links: Wikipedia and from the british National Health Service. They include a definition and reasons for anosmia.


Do alternative start codons code for methionine after transcription?

I commented that this was a duplicate, but reading the question more carefully you seem to be asking something slightly different.

In the context of a 'start' these codons will be recognised by fMet-tRNA and a formyl-methionine will be inserted as the first amino acid. Subsequent occurrences of the same codon within the open reading frame will be translated normally (e.g. GUG > valine).

The use of GTG as an initiation codon in the E. coli lacI gene

In this paper

  Frottini et al. (2006) The Proteomics of N-terminal Methionine Cleavage. Molec. & Cell. Proteomics 5: 2336-2349

the authors report assays of E. coli methionine aminopeptidase with model peptides showing that when Lys is the 2nd residue, Met removal is very inefficient. They also show that when Pro is the 3rd residue, Met removal is very inefficient.

This explains the fact that when the lacI repressor protein was sequenced:

  Beyreuther et al. (1973) The amino-acid sequence of lac repressor. PNAS 70: 3576-3580

it was found to have a Met residue at its N terminus (sequence Met-Lys-Pro-).

However, when the lacI gene was sequenced:

  Farabaugh (1978) Sequence of the lacI gene. Nature 274: 765-769

the corresponding DNA sequence was GTG AAA CCA, demonstrating that the N-terminal residue is encoded by a GTG(Val) codon. LacI residue Val23 is encoded by a GTG codon, demonstrating the normal use of that codon in the body of the mRNA.


What metabolic activities are performed by a developing human fetus's liver?

It's old and I can't get access to this issue of the Annals of the New York Academy of Science, but it looks like it has some relevant information. Sifting through the abstracts it seems the vasculature of the fetal liver is completed at around 8 weeks although is still different to the adult vasculature because of the umbilical vein. The growth of the organ itself goes through different stages with each lobe growing different amounts:

They start the same size
12 weeks the left lobe is twice as large as the right
36 weeks the left is 10% larger than the right
at birth they are the same size
5days after birth the right is 10% larger
adults, they are the same size

And, studies have been conducted with dyes to look at liver function in both its capacity to concentrate the dyes and secrete it into the bile. The fetal liver can carry out bile acid synthesis, despite lacking digestive purposes, from very early on (Suchy et al. 1987). The fetus does however require help in removing the toxic cholephilic organic anions (COAs), which is done via the placenta. This review describes more.

There is also evidence to suggest the newborn's liver is not performing all the usual metabolic processes of children or adults (from looking at drug toxicity and delays in excretion/detoxification), as would be expected. More recent literature notes the fetal liver lobes (right and left) as having differnt biochemical capacities and independent function due to the right one getting less oxygen. Also, a layer of drug metabolising enzymes normally present in adults is missing in the fetal liver, although its capacity for drug metabolism is still better than that of rodents.

  In the adult liver, there is a clear zonation of metabolism of carbohydrates, proteins, lipids, and bile salts. In the livers of fetal rats, mice, and humans, this heterogeneous distribution of enzymes and metabolic function does not exist initially. Towards the end of gestation, the adult pattern of heterogeneity for these processes begins to emerge, and after birth, the adult pattern is rapidly established (Ring et al. 1999)

There is in vitro evidence for the activity of glutathione S-transferase and sulfotransferases in the human fetal liver. Returning to the asymmetry of fetal liver function (albeit in sheep..) it was found that levels of malondialdehyde, an index of lipid peroxidation, oxygen consumption, and CYP levels (a family of oxidative enzymes), are higher in the left lobe than the right lobe of the fetal liver which evens out after birth.

So in conclusion, looks like a variety of metabolic enzymes are present in the human fetal liver from very early on after the organ is formed. We know a varitey of metabolic enzymes are present and the drug/dye metabolism studies show there is some fetal liver activity, albeit reduced from that of an adult or child. The limitation with many of the studies that have been done is that they have to use in vitro data and extrapolate to the in vivo situation, so I guess we still don't really know for sure how metabolically active it is. It is clear though that it remains inefficient and unable to carry out all the functions required of it during childhood/adulthood until after further development after birth when it has stopped growing and adapted to ex utero conditions.

References

Ring JA, Ghabrial H, Ching MS, Smallwood RA, Morgan DJ. Fetal hepatic drug elimination. Pharmacol Ther. 1999 Dec;84(3):429-45.

Suchy FJ, Bucuvalas JC, Novak DA. Determinants of bile formation during development: Ontogeny of hepatic bile acid metabolism and transport. Semin Liver Dis 1987; 7(2): 77-84


Evolutionary history: did any organs start out as autonomous organisms?

Very short answer

No!

Long answer

It is not the nucleus who was an independent organism but the mitochdonrion (organelle) (One might discuss this point and say that both are correct, it is just a philosophical issue of the identiy of the eukaryotic cell). The plastids (the chloroplasts for example) were also independent organism. In consequence, in every cell, we have DNA in the nucleus and DNA in the mitochondria. The mitochondria is contained in every cell of our body and is transmitted via the ovule (and not the spermatozoid) to the offsprings.

Now let's think about your hypothesis that one of our organ (let's say, our liver) might have been an independent organism in the past. Therefore, this organ would contain different DNA than the rest of the cells of our body. How would you transfer the DNA of your liver to your offspring? Well, it is hardly imaginable.

Moreover, it has been argued that because we now have a complex and efficient immune system, a endosymbiose would be very unlikely.

But no, none of the cell in our body come from a previously different organism. But every cell of our body is some kind of chimera of two previous cells. Note: the vast majority of our DNA are present in the nucleus and not in the mitochondrion.

For more information about endosymbiose, have to look to this and this (wiki articles)

It seems much more easy to have two organisms that stay together during reproduction when reproduction is mediated by striking.

You may find some funny examples (border cases) of two organisms that don't separate during reproduction in corals (zooxanthella), leafcutter ants (and their fungus), parasitoid bees (and the virus that females create in their ovary) and lichens


Are there any theories why such an imbalance in chirality of molluscs?

Why so many molluscs exhibit sinistral winding?

The estimates of the number of molluscs vary quite greatly between 50,000 and 200,000 species. Of those molluscs species, about 70'000 are Gasteropoda. Gasteropa is most diverse Mollusca phylum.

The winding you describe is present in all Gasteropoda and is often called the torsion. So the answer to why there are so many molluscs that make a torsion is simply, because of phylogenetic independence. The torsion evolved only once in the gastropods. The answer to the more specific question, why is the torsion right handed rather than left handed in all gastropods is 1) phylogenetic independence again. The torsion evolved only once and was therefore either sinistral or anti-sinistral. There is no need for an explanation of why they are all sinistral because the observations are not independent.

Why has the torsion evolved at first place?

One may ask but why did the torsion evolved at first place?. I think the reasons are still to be discovered. The following is a summary of what I read on wikipedia (torsion#evolution)

"Why torsion is bad"

As a result of this torsion, the anus is found next to the mouth which is an obvious hygiene issue and therefore seems rather deleterious. Moreover, there are a whole bunch of issues about organs spinning around and entwining. Also, ventilation seems to be reduced by the torsion which is pretty deleterious.

"Why torsion is good"

However, because there's no "hole" left in the posterior position, the torsion may help preventing sediments. Some have suggested that the torsion may allow to move sensory organs closer to the head. The most likely explanation is that the torsion might have evolved as a defense mechanisms against predation as torsion allow an organism to hide its head behind its shell. Finally, citing from wikipedia:

  The evolution of an asymmetrical conispiral shell allowed gastropods to grow larger but resulted in an unbalanced shell. Torsion allows repositioning of the shell, bringing the centre of gravity back to the middle of the gastropod’s body, and thus helps prevent the animal or the shell from falling over.

Note also that

  Whatever original advantage resulted in the initial evolutionary success of torsion, subsequent adaptations linked to torsion have provided modern gastropods with further advantages.

Why sinistral rather than anti-sinistral

To repeat myself, we only have one single observation of torsion (as it evolved only once) and this observation is either sinistral or anti-sinistral. It sounds therefore quite likely that stochastic processes have driven the evolution of sinistral (rather than anti-sinistral) torsion. In other words, the first mutation allowing for some degree of torsion was probably causing a sinistral torsion and this is it.

But there might eventually be a more functional reason for why torsion evolved to be sinistral. The reasons would then be related to the already existing asymmetry of organs. For example, anti-sinistral torsion may yield to more entwining between the gut and the respiratory system, or to not squeeze too much the one lung, who'd be smaller than the other one due to the presence of circulatory organs. I don't have enough knowledge in the anatomy of the molluscs ancestors to have a good intuition of whether I'd expect sinistral or anti-sinistral torsion to be more beneficial.


I know this is not what you want to hear back, but I think you should go with all the samples/replicates at once. Only this way you will have the highest possible statistical power to claim the results that (hopefully) you'll have in the end.

When it comes to microarrays and RNASeq, also, it is important to remember that these are mostly whole-transcriptome techniques, therefore the way they are thought to be used is more like "sequence all > analyze all > fish for specifics" than the opposite.

I would use all of them, feed them to a proper pipeline (there are many, not my duty to suggest you one) and see what has a good score/p-value. If you had something in mind before doing the microarrays you probably would have assessed only a subset of the genes, and not the whole transcriptome. So go for both tissues and see what pops out!


Does depolymerisation take place at the minus end of microtubule?

Often microtubule (MT) dynamics and actin dynamics are taught side by side, which can be quite confusing as MTs display unique characteristics relative to actin filaments. Indeed, treadmilling is an in vivo behavior primarily associated with actin, while dynamic instability characterizes MT growth. But why?

Both actin filaments and MTs are "sided" (polar), with actin having barbed- and pointed-ends and MTs having plus- and minus-ends. This polarity emerges from two properties: 1) the energetic state of the individual monomers that make up the filament and 2) the rate of growth.

For actin, the barbed-end is compromised mostly of ATP-actin (high energy), while the pointed-end is made up of ADP-actin (low energy). This composition preferentially adds new ATP-monomers to the ATP-rich barbed-end, yielding a faster rate of growth than at the pointed-end. Disassembly at the pointed-end occurs more readily as ATP-actin is converted to lower energy ADP-actin. Treadmilling occurs when the rate of assembly at the barbed-end is equal to the rate of disassembly at the pointed-end (Pollard and Borisy, 2003).

Similarly to actin filaments, MTs are polar, with their plus-ends made up of GTP-tubulin monomers and GDP-tubulin concentrated at their minus-ends (Desai and Mitchison, 1997). Unlike actin filaments, which can form sporadically almost anywhere in the cell (Pollard and Borisy, 2003), MTs are initiated at what we call a microtubule organizing center, or MTOC (Kollman, 2011).

The bulk of MTs within the cell are attached to the MTOC through their minus-ends, though there are unattached sub-populations. Both in vivo and in vitro data indicate that growth and shrinkage at the minus-ends does occur, but that the rates are slow relative to those occurring at the plus-ends (Hendershott, 2014). In these instances, MTs can undergo treadmilling in a manner similar to that as actin and this behavior is readily observed in vitro (Waterman-Storer, 1997). Recent studies have suggested that MT minus-ends are under tight regulation in vivo, likely limiting their dynamics (Akhmanova, 2015). Therefore, MT growth and shrinkage primarily occurs at thee plus-ends. Enter dynamic instability.

MT plus-ends undergo a cyclical process of growth and shrinkage known as dynamic instability (Mitchison and Kirschner, 1984). The key to this process is the difference in shape between GDP-tubulin and GTP-tubulin (Buey, 2006). One can imagine GTP-tubulin as a rectangle, with perfectly straight lines connecting its angles. On the other hand, GDP-tubulin has a small bend in the center of one of its long ends.

As a MT grows, GTP-tubulin is added to the plus-end forming a "GTP cap." The role of this cap is to counteract the inherent desire of GDP-tubulin to bend outward, thereby forming a straight filament and ensuring continued growth of the MT (Desai and Mitchison, 1997). However, the MT will lose its cap when the rate of GTP-tubulin addition drops below the rate of GTP to GDP conversion, thereby exposing GDP-tubulin. This event characterizes the "catastrophe" stage of dynamic instability (Mitchison and Kirschner, 1984). The shape of GDP-tubulin is no longer constrained in this stage, and instead, bends outward causing rapid disassembly of the MT. Because the cell is chock full of GTP-tubulin, recovery of the GTP cap rapidly occurs and the MT re-enters productive growth. This cycle of growth-catastrophe-recovery is the hallmark of MT dynamic instability.


Macrophages and dendritic cells generally recognize large foreign complexes. They often do this through the recognition of pathogen or damage-associated molecular patterns (PAMPs or DAMPs). Otherwise, cell-mediated pathways involve cyto/chemokines which direct macrophages and the like in the region. We also have to consider, does the compound in question belong in the region, or is it insoluble amongst the tissue? In these cases, the compounds are also degraded/engulfed. So how does the body go about recognizing small, soluble foreign molecules?

These are called haptens. If these small molecules can bind to a larger carrier complex in your body, so that it now looks like there's something foreign, regardless if the initial carrier complex was foreign or not, this may present cause for immunologic reponse (as in the mechanism of urushiol, the toxin in poison ivy). There are certain T-cells, like NKT and γδ T cells, which can "see" these antigens despite their lacking a type I or II MHC presentation.

The short answer is it depends on what the injected drug does once it begins interacting with your physiology. Vitamins, on the other hand, are regularly uptaken by cells for metabolism, and I wouldn't imagine macrophages engulfing exogenous vitamins outside of it's needs on their own.

Source: Cellular and Molecular Immunology, 8th ED.


I would suggest that the behaviour of the gazelles you are citing is perhaps over simplified. There will likely be temporal and spatial dynamics in their behaviour... Prey will probably spend more time concentrating on observation when they know there are predators around. There will also be likely peak times during which hunting occurs (in savannah systems it tends to be dawn and dusk) and prey would be more cautious at these times.

It seems to me that the prey would not be judging the hunger of the predators but instead they learn the consistent patterns in the level of risk associated with being near predators. This could be genetic in its cause. If there is a gene (or genes) which determine when a prey individual is most likely to be out in the open grazing then the higher probability of predation at certain times would reduce the frequency of the genes which cause that choice.

There could also be fluctuations over time as the predators learn that the prey have become less cautious, which then causes predators to take advantage of unsuspecting prey, which you might be interpreting as the "faking" behaviour... it is not a deliberate fake, more taking advantage of the risk taking behaviour of the prey (as time passes without attack they will become more brazen). To the best of my knowledge there are no examples of the deliberate fake but predator prey dynamics are not my specialism.

Overall, I think you are asking a question based on learning and information use of repetitive patterns in behaviour of predators by prey, and have interpreted these behaviours in an over complex way (see Occams Razor).


What is the difference between the neural tube and the dorsal ventral cord?

The terminology can be confusing, and I suspect the question you meant to ask was: what is the difference between the neural tube and dorsal nerve cord?

In vertebrates, the neural tube and the dorsal nerve cord are two names for the same structure. It develops into the brain and spinal cord.

  Neurulation occurs during the early embryogenesis of chordates, and
  it results in the formation of the neural tube, a dorsal hollow nerve
  cord that constitutes the rudiment of the entire adult central nervous
  system.

Source: Colas J-F and Schoenwolf GC. Towards a cellular and molecular understanding of neurulation. Developmental Dynamics. 2001. vol 221(2): 117–145.

This differs from invertebrates, some of which have a ventral nerve cord that does not invaginate and form a neural tube. As the name suggests, in contrast to vertebrates the nerve cord in these species is located ventrally.

In summary:
Dorsal nerve cord = neural tube
Ventral nerve cord ≠ neural tube


How can I get started in molecular biology?

First develop a background of basic highschool chemistry, basic biochemistry and basic genetics.

What is molecular biology: Molecular biology has 2 definitions. A broader definition is molecular basis of life. That is indistinguishable from biochemistry. The second definition is how does genetic information flows through
 molecular mechanism. The secod one is a more specific definition of molecular biology and how it differs from biochemistry.

Its good to develop some background in biochemistry and genetics because concepts of molecular biology comes from biochemistry and genetics.

A quick start through biochemistry:

Lippincott's illustrated review on biochemistry.
Harpers's illustrated review on biochemistry
Organic chemistry by Solomons and Fryhle (especially stereochemistry portion).

then go through gradually more detailed book, such as biochemistry by Lubert Stryer.

Parallelly go through Genetics book such as

Principle of genetics by Hartl and Jones
Gene IX by Benjamin Lewin
Principles of genetics by Snustad et al.
iGenetics by peter J. Russell
Concept of genetics by Benjamin pearce
Genomes 3 by T A Brown
Principles of gene manipulation and genomics by RM Twyman and Sandy B Primrose.

Each book has a different perspective. it will help a clearer picture of different concepts.

Some basic molecular biology books:

Molecular bioloy- principle of Genome function: by Nancy Craig et al.
Molecular biology by RF Weaver.
Fundamental molecular biology - Lizabeth Allison
Princiles of molecular biology by Barton and Tropp.

For a more cellular approach and bigger picture see cell biology based molecular biology books viz.

Cell biology by Pollard, Earnshaw et al.
Cell biology by Gerald Karp
Lewins' CELL by Plopper et al.
The Cell- a molecular approach- by Geoffrey M. Cooper.


Stem cells can be stored but that is an expensive alternative to generating them freshly. It has been shown that you can make stem cells from skin cells.

Theoretically, it would be much less expensive to store a piece of epidermis from a recently deceased relative than to make fresh stem cells and store those.

However, the research for generating stem cells from deeply frozen tissues is not there yet. Furthermore, the concept of using stem cells to 'combat disease' is not the right paradigm. It might even be said that some diseases (cancer) are the result of dedifferentiation gone awry.

Where stem cell transplants are used is in the replacement of bone marrow after total body radiation/chemotherapy to destroy marrow (in those cases where the disease has arisen in the marrow). In these cases we rely on the poorly defined process that allows cells to target their microenvironment.

For example, it would not work if marrow replacement cells decided to grow wherever they landed (lungs, liver,etc).

So stem cell storage is an option whose time has passed ,as our tech now allows us to make them.


Sodium concentration during action potential generation

Below is a schoolbook example of the membrane potential combined with the individual conductivities of Na+ and K+ during an action potential (AP) (Fig. 1);

Fig. 1. Membrane potential and conductivities of the two most important ions in AP generation. source: Physiology Web

And in Fig. 2 is an example of the currents of Na+ and K+ during an action potential (AP) (Fig. 1). Note that K+ stays high due to amanipulation of ion concetrations.

Fig. 2. Sodium and potassium currents during AP generation.

However, you ask about the concentrations of Na+ in the cell. As far as I know, this has not been investigated directly. Intracellular Ca2+ concentrations, for example, can be imaged with various imaging techniques, but absolute Na+ and K+ concentrations have to be measured with intracellular electrodes. So while the conductivities and the currents are depicted quite clearly in the above figures, they do not show the absolute concentrations of Na+ or K+ and I doubt it can be found anywhere in the literature. It can of course be mathematically deduced, by calculating the number of ions entering the cell using the Nernst equation and correcting that for the background effect of the sodium-potassium pump and other factors that alter Na+ concentration in the cell (protein transporters and what not). It will at least give an approximation of [Na+]i.


Do Tardigrades preserve water or replace water?

neither they are desiccating, some water remains but too little to sustain normal processes, the matrix just preventing all the normally destructive side effects of desiccation that would destroy the cellular machinery, the cellular processes are still essentially stopped.


What are some examples of animals who return to their group when threatened?

The specific description you have made is almost the definition of mobbing behaviour. Some animal species protect each other and especially their offspring by cooperatively attacking and harassing a predator. Individuals can't cope with the predator alone, but by working together they increase the chance of discouraging the predator.

African buffaloes, bison, gulls show mobbing behaviour.

Wikipedia article

The Royal Society for the Protection of Birds article


Before I restrict the answer to human metabolism, I recon it is important to mention that
CO2 is the source of the carbon atoms of glucose in photosynthesis (in the Calvin cycle). [In photosynthesis CO2 is 'fixed'].

Even with the above restriction, I am certain I  cannnot do justice to every helpful aspect of CO2 in mammalian metabolism, and I'll restrict myself to just one area that came to mind on reading your question: the requirement for carbon dioxide (in the form of bicarbonate) for fatty acid biosynthesis (FAS) and, in a bit more general sense, mammalian/bacterial biotin-dependent carboxylation reactions. Depeding on other contributions, I might be able to extend this a bit later.

Salih Wakil showed that CO2 is an absolute requiement for fatty acid biosynthesis, but carbon atoms from CO2 do not appear in the fatty acid product.

We now know that FAS begins with the carboxylation of acetyl-CoA to malonyl-CoA, catalyzed by the enzyme acetyl-CoA carboxylase. Acetyl-CoA, ATP and bicarbonate are the substrates for this enzyme, and malonyl-CoA is a key product. One of the many interesting properties of this enzyme is that it contains biotin, which (in this case) may be considered a carrier of 'active' CO2.

This explains the requriement for carbon dioxide but why no carbon from CO2 in the final product?

It is now known that in subsequent FAS reactions, a derivative of malonyl-CoA condenses with a derivative of acetyl-CoA (I am simplifying here) to give a four-carbon compound with loss of CO2.

Thus, carbon dioxide (in the form of bicarbonate) is an obligate requiement for mammalian fatty acid biosynthesis, but no CO2-derived carbon is incorporated into fatty acids.

Carbon dioxide is also required for oxaloacetate formation from pyruvate. This reaction may be though of a method of 'filling up' a key Krebs Cycle intermediate (a  so-called anapleurotic reaction).  The enzyme here is pyruvate carboxylase and the substrates for the reaction are pyruvate, bicarbonate and ATP, with oxaloacetate being a key product.  This enzyme also contains biotin and (like acetyl CoA carboxylase), CO2 becomes covalently bound to biotin during the reaction cycle.

Pyruvate-CoA carboxylase was discovered by Harland.G Wood and C. Werkman in bacteria (See here for a good reference on the early work on pyruvate carboxylase). Its discovery was very controversial because at the time it was thought that animal/bacterial cells could not 'fix' CO2; that is it was though that CO2 is only 'fixed' in photosynthesis.  This discovery disproved that piece of dogmatism.

A third enzyme that requires CO2  as substrate (in the form of bicarbonate) is propionyl-CoA carboxylase.  This enzyme occurs in mitochondria and functions in odd-chain fatty acid metabolism.  It also contains biotin.

I have concentrated on some biochemical aspects of your question.  The three enzymes mentioned, acety-CoA carboxylase, pyruvate carboxylase and propionyl-CoA carboxylase all require CO2 in the form of bicarbonate as substrate, all contain biotin, and (as far as I am aware) all play very central roles in mammalian metabolism.  (They also all require ATP as substrate).

Of the many interesting aspects of biotin, I'll mention just one.  Egg white contains a protein, avidin, which binds biotin very, very tightly.  In fact the biotin-avidin interaction is one of the strongest non-covalent interactions known.  As far as I am aware, no-one knows the function of avidin in egg white.  Some bacteria contain a similar  (but evolutionarily unrelated) protein called streptavidin. No one knows the function of steptavidin either (again, as far as I am aware).

The original Wood & Werkman paper: was published in the the Biochemical Journal in 1936

The utilisation of CO2 in the dissimilation of glycerol by the propionic acid bacteria.

Harland Goff Wood and Chester Hamlin Werkman.

Biochemical Journal, Volume 30, January 1936, pp 48-53


Get "DNA" of one parent based on its children

Ok, I think I can answer somewhat usefully with the update.
It's helpful in this case to think in terms of sampling alleles. It's true that the cases that you give are not 100% unambiguous, but it is not true that we can't give a somewhat confident estimate. We can still make a statistical prediction of the most probable genotype.
The first thing to note is that you are working with pedigrees. That is, you have parents and multiple children. Pedigrees are great because they allow you to pool information across individuals.
The next thing to note is that your alleles are almost certainly not of uniform frequency in the population. In other words, If I sample a random cow from the herd, the probability of allele $A$ at some arbitrary locus is almost certainly not the same as the probability of allele $G$. You can use that information in inferring the most likely allele. Moreover, you can put a precise number on the probability of any given allele.
The simplest method I can think of is to use genotype likelihoods, to account for pedigree information, and to incorporate the background allele frequency as a prior probability (h/t Vadim for the Bayesian approach).
A likelihood is the probability of some dataset given a specific hypothesis. In other words, your data is your offspring genotypes and your hypothesis would be the different offspring.
In your first example, we can logically rule out alleles other than $AG$. (That's actually not true; you should account for the possibility of genotyping error, but we'll ignore that for now.)
In your second example, we can't logically rule out all but one genotype. But we can say some things nonetheless:

you have said that there are only 2 alleles per locus (i.e. $A$ and $G$ are the only possible alleles).
$A$ and $G$ have distinct frequencies in the population.
we now at least one paternal allele ($G$).

Let's take a simple case of the likelihood application, in which we say that frequency of $Pr(A) = 0.9$ and $Pr(G) = 0.1$ (I am making these numbers up). Now in the ambiguous case:
$$Pr(paternal=GG | offspring\_genotypes=GG,AG) = \\
Pr(offspring\_genotypes = GG,AG|paternal=GG) * Pr(paternal=GG) = \\
Pr(offspring=GG | paternal=GG, maternal=GG) \\
* Pr(offspring=AG | paternal=GG, maternal=AG) * Pr(paternal=GG)
$$
and
$$Pr(paternal=AG | offspring\_genotypes=GG,AG) = \\
Pr(offspring\_genotypes = GG,AG | paternal=AG) * Pr(paternal=AG) = \\
Pr(offspring=GG | paternal=AG, maternal=GG) \\
* Pr(offspring AG | paternal=AG, maternal=AG) * Pr(paternal=AG)
$$
Which evaluate to:
$Pr(paternal GG) = 1.0 * (0.5 * 0.5 + 0.5 * 0.5) * (0.1 * 0.1) = 0.005$
and
$Pr(paternal AG) = (1.0 * 0.5) * (0.5 * 0.5 + 0.5 * 0.5) * (0.5 * 0.1) = 0.0125$
You can see that there are multiple ways for the offspring to get genotypes in the paternal $AG$ case, which is what leads to the terms with addition. Note also that the $Pr(paternal genotype)$ at the end handles the genotype frequency, as all the other terms are conditioned on the parental genotypes.
So in this highly artificial example, we prefer genotype of $AG$ somewhat (note that these likelihoods do not sum to 1.0). But, if we were to alter the genotype frequencies to 50% frequency of each allele, we would get:
$Pr(paternal GG) = 1.0 * (0.5 * 0.5 + 0.5 * 0.5) * (0.5 * 0.5) = 0.125$
and
$Pr(paternal AG) = (1.0 * 0.5) * (0.5 * 0.5 + 0.5 * 0.5) * (0.5 * 0.5) = 0.0625$
and you would come to the opposite conclusion!
So it really matters what the background frequency is, if you choose to consider that term.
You could also think about genotyping error or whatever as part of these calculations.
I am certain that there is a more sophisticated way to do this, that takes better advantage of available information, etc. Maybe I've even made a mistake in the computation- but this is an approach that you might use to infer paternal genotypes.


What is the effect of reduced gravity on human height?

As far as I am aware, no one has ever been born in space, so your answer cannot be answered directly. However, it is known that the absence of gravity results in an increase in body height by a few centimeters. This is due to stretching of the vertebral column, which is no longer being pressed together by the downward pull of gravity1. For example, the astronaut Richard Hieb, who spent 2 weeks in space, found that his height had increased by 1 inch (~2.5 centimeters)2. Loss of gravity also causes the blood and other fluids to migrate from the legs to the upper part of the body, resulting in swelling of the face and protrusion of the veins of the neck1. I assume that these effects reported at zero gravity at least partially apply to 10% gravity.

Sources
- Airbus Defence & Space
- NASA


Although tinnitus is usually described as a ringing in the ear, there's a whole range of tunes, buzzes, whooshing sounds, humming and hissing sounds that are described of as tinnitus. The sounds can either genuinely be there or be perceived to be there. If it is genuinely there it suggests muscles ate at play or some blood vessel disease if the sounds are in time with your pulse, but usually its the latter perceived to be there that presents.

Tinnitus that is perceived and permanent usually suggests damage to your hearing nerve (called the auditory nerve or cranial nerve 8 or vestibulocochlear nerve). The common cause for this we see is patients that have been exposed to loud noises or drugs like certain strong antibiotics which cause damage to the nerve. Other drugs also have a side effect of causing tinnitus. However any ear problems really may cause tinnitus including ear infections, too much wax, getting older, a disease called Mennieres, tumours, neurological diseases, vitamin deficiencies and lots more.

If you're really interested, keep reading. There's a number of reasons why it might occur. Usually patients presenting with it have some degree of hearing loss. Its thought that somewhere along the line the structures are getting more sensitive to sound because through a feedback mechanism. Think of it this way, you speak to someone but they can't hear you so you speak louder and louder until they can. In the same way its thought that the sensitivity is increased and increased to try to restore hearing but the result is audible nonsense sound from abnormal activity i.e. tinnitus.

If anything doesn't make sense, please do say :)


Can humans survive without consuming life?

The answer to your question is yes it is certainly possible.

At one time it was thought that there was something special about "organic" chemicals which meant that they could not be artificially synthesised out of fundamental elements. In 1828 Frederick Wöhler synthesised urea (CO(NH2)2) which is often taken as the first demonstration that the organic v inorganic distinction was not a sound one (for more on this see the Wikipedia article on Wöhler synthesis.

As far as we know all essential human nutrients can be synthesised from inorganic ingredients, even complex molecules such as Vitamin B12.

Other contributors have pointed out that organic pathways for synthesising our food have evolved over long periods to be very efficient - at least in the conditions prevailing on Earth. You haven't ruled out copying biochemical pathways using chemicals that are entirely of inorganic origin. Anyone trying to do this seriously could create glucose (for example) by artificially creating enzymes (perhaps via artificial DNA) to do the job. The thing is that we already have self-replicating and repairing machines to do that already (plants).

There might be circumstances when we needed to use artificial synthesis. I can think of two science-fiction stories that deal with this question, the first of which goes into some detail:

The Moon is Hell by John W. Campbell, in which astronauts are stranded on the moon and forced to make food from what they find there.
Technical Error by Arthur C. Clarke, in which a man is accidentally rotated through the fourth dimension. His employers contemplate the difficulty caused by the "handedness" of many biological molecules meaning they would have to artificially synthesise many of his foods.

It may be that a future expedition to Mars (say) might have to think about these things.

A little searching fails to come up with standard inorganic syntheses of glucose and similar substances. The reason for this is almost certainly because it is so easy to use organic inputs. Glucose is easily made by the hydrolysis of starch. Starch is very common and cheap. Even l-glucose is usually made out of organically derived precursors (or sometimes even using d-glucose).

UPDATE: sources etc
One problematic question is: where do you get your input for making nutrients? As others have pointed out, exactly where to draw the line is difficult.

This problem starts in defining what is alive in the first place. Do you count viruses (which can go down to a few thousand base pairs of RNA) or satellite viruses (STobRV has only 359 base pairs) or prions? In a sense these are "just" very large molecules. But then really simple bacteria are not many orders of magnitude more complex. As an aside most systems of ethics that do not permit eating meat do not make an alive/non-alive distinction, choosing some other aspect such as sentience, though Jainism comes close to doing so.

The second problem is, if we reject living things as sources of food, how far removed from those living things are we allowed to get? You say no cells in any state including "dead". That would exclude (say) fruit even though most fruits are expressly created by plants in order to be eaten (and in some cases must be eaten) - something that vegans, jains, fruitarians and others would be happy with eating. If we could use dead material things would be much easier.

But would you also include hydrocarbons (coal, oil, gas) which were once living organisms? If you do, then you are in difficulty because terrestrial carbon is recycled through the biosphere. All CO2 was (to a close approximation) once a part of a living thing. If you take that position then of course you are going to have to go off-planet to find your source chemicals and your problem becomes very much harder.

I was assuming that you were restricting yourself to consuming cells that retain some of their cell structure but had not completely degraded. If that is where you draw the line then there are ample sources of raw materials on earth.

Genetic modification is much more science fiction though not entirely impossible. Some nutrients could be made by humans without much difficulty. Our inability to manufacture vitamin C is down to one missing enzyme (L-gulono-gamma-lactone oxidase) which is present in most vertebrates (I think of mammals only guinea pigs, humans and some bats are unable to synthesise it). You could certainly imagine some very careful genetic modification changing humans so they no longer need to consume vitamin C.

But photosynthesis would be much harder. Chloroplasts (which do the job in most plants) are really a very primitive form of life living in plant cells which may independently reproduce  (and for that reason might be excluded by you - they aren't "cells" but they have membranes). They could easily end up in conflict with our mitochondria (since intracellular conflict between organelles is possible) and you would need to do enormous amounts of work to make human cells co-operate with them properly.

More in keeping with your theme would be adding photosynthetic systems directly to human cells along with a suite of enzymes to manufacture all the things we cannot. That is of course in principle scientifically possible (since plants do it) but much harder than it looks. Living systems are very complicated and small changes can have unexpected consequences. Even very minor genetic modifications are problematic. The human autotroph is likely to be some way off.


What fraction of bacterial proteins are membrane bound?

As a proxy for asking which bacterial proteins are membrane-bound, we can ask which proteins harbor transmembrane domains. A popular tool for detecting transmembrane domains is TMHMM, which looks for transmembrane helices in protein sequences using a hidden Markov model.1
For E. coli strain K12, UniProt reports 4,391 protein sequences corresponding to unique genes. Of these, TMHMM predicts 1,072 proteins have at least 1 transmembrane helix (24.4%), and 775 proteins have 2 or more transmembrane helices (17.6%).  Expanding this analysis to the E. coli pan proteome, which contains 165,127 non-redundant protein sequences, TMHMM predicts 28,369 proteins have at least 1 transmembrane helix (17.2%), and 16,105 proteins have 2 or more transmembrane helices (9.8%).
For B. subtilis strain 168, UniProt reports 4,260 protein sequences corresponding to unique genes. Of these, TMHMM predicts 1,175 proteins have at least 1 transmembrane helix (27.6%), and 845 proteins have 2 or more transmembrane helices (19.8%). Looking at the pan proteome for this species, which contains 18,046 non-redundant protein sequences, TMHMM predicts 3,967 proteins have at least 1 transmembrane helix (22.0%), and 2,463 proteins have 2 or more transmembrane helices (13.6%).
The relative depletion of transmembrane domain-containing proteins in the pan genomes of both species relative to their reference genomes could point to a functional skew of accessory genomes towards proteins that are less likely to be membrane-associated, such as strain-specific virulence factors, antibiotic resistance genes, integrated phage proteins, and proteins involved in niche-specific metabolism.2,3 Additionally, the relative enrichment of transmembrane domain-containing proteins in B. subtilis compared to E. coli could reflect the different membrane compositions of Gram positive and Gram negative bacteria, though it's hard to say without sampling more species.
One important caveat to TMHMM -- predicted transmembrane segments in the N-terminal region are sometimes just signal peptides. Signal peptides are likely to appear as single transmembrane domains, which is why I've also reported the fraction of proteins with 2 or more transmembrane helices, above.  A more complete analysis may run the same protein sets through SignalP 4 and cross-reference the TMHMM hits to identify transmembrane domain-containing proteins that also contain signal peptides.
Note that the cited publication by Almen et al. uses TMHMM and directly references the results of the original TMHMM paper,1 which reports transmembrane protein abundance in the proteomes of several species.

One of the most referenced papers regarding the percentage of membrane proteins in proteomes is from 2001 where the membrane topology prediction method TMHMM was applied on a number of proteomes from different species to estimate the membrane protein content, for example, Caenorhabditis elegans (31%), Escherichia coli (21%) and Drosophila melanogaster (20%).

Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001 Jan 19;305(3):567-80.
Kung VL, Ozer EA, Hauser AR. The accessory genome of Pseudomonas aeruginosa. Microbiol Mol Biol Rev. 2010 Dec;74(4):621-41.
Álvarez VE, Quiroga MP, Galán AV, Vilacoba E, Quiroga C, Ramírez MS, Centrón D. Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1. Front Microbiol. 2020 Mar 18;11:342.
Nielsen H, Brunak S, von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 1999 Jan;12(1):3-9.


List of the biggest companies that work in selective breeding

This varies by the kind of animal or plant. I think one company would rarely do both.

For plants Monsanto comes to mind.  And Syngenta.

I'm not sure for animals.  For beef cattle in the US, this is done by individual ranchers (who may be corporations) that collectively share their genetic data creating a market which can predict the value of a bull.  The market for bull semen can be worth hundreds of dollars per impregnation.

Why are bulls valued at such a greater rate than cows?  Because semen can be preserved, transported and used thousands of times while a cow can only calf one at a time.


What does it mean to be a fully human monoclonal antibody?

I found this small article that seems to cover all your questions:

https://www.sciencedirect.com/topics/medicine-and-dentistry/human-monoclonal-antibody

Summary:

Being considered a human monoclonal (many of the identical antibody, as opposed to different antibodies for the same target) antibody does not mean it is produced by a human body; it means that the fc-region of the antibody is human-like, which aims at avoiding immune reactions against that antibody if injected into humans.
So the human antibody can originate from animals (e.g. rats or rabbits) with humanized antibody genes or from immortalized human cell-lines (lymphocytes).


Is Plasmid pGLO a stable or unstable plasmid varient ?

The pGLO plasmid uses a stable version of GFP. This is stated in the pGLO education series protocol, and wiki.

I could however, engineer to be unstable if wanted.

https://en.wikipedia.org/wiki/PGLO


What does this sentence about toxemia and Clostridium tetani mean?

Clostridium tetani produces a protein toxin, tetanospasmin which causes the major symptom of tetanus, namely involuntary muscle spasms. C. tetani is an aerobic species, does not infect the blood, and apparently only produces toxin in anaerobic conditions.

If a pathogenic bacterium propagates through the bloodstream this condition is referred to as bacteraemia. In the case of C. tetani it is the toxin which enters the bloodstream, not the bacteria, hence toxaemia. The bacteria, being anaerobic, are inhibited from spreading through aerobic tissues.


Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

It is highly unlikely that there exist any protein that is made from completely identical nucleotide sequences across the entire human population. There will certainly be regions within a gene that are highly conserved, but there is little evolutionary pressure to conserve an entire gene's nucleotide sequence across the population.

This is in part due to the fact that different codons can translate into the same amino acid. So, even if a protein is (phenotypically) identical across the human population, the genes making that protein can use different sequences to code for the same amino acids. This alone can allow for an incredibly large number of possible gene variations that can code for an identical protein.

Related resources: Neutral mutation (wikipedia) and the neutral theory of molecular evolution (wikipedia)


I am voting to close as homework question.

I felt like I would give you a few hints though.

  is it possible for other animals to live without us?

Life on earth have existed for almost 4 billions years. Animals have existed for about 600 millions years. Modern human (AMHS) have existed for 0.2 million years.

  Do humans have a huge impact on the ecosystem?

Here are just a few pictures taken by airplane of agricultural lands

and a koala searching its home after a rapid man-made deforestation


"Junk DNA" is more aptly named noncoding DNA. This is defined as any DNA region that does not encode for a gene or more precisely is not within an open reading frame. In the human genome over 98% consists of noncoding DNA. However the more we learn about molecular biology the more we understand the biological function and importance of noncoding DNA. Examples for important functions are:

Regulatory regions that control the expression of a gene
Regions coding for regulatory RNA
Regions where epigenetic regulation takes place

However, there are also regions which likely do not have beneficial biological function, which may rightfully be called junk:

Transposons are genetic regions that can copy themselves (either by an enzymatically active RNA or by encoding for the protein transposase). They are believed to have evolved as "selfish genes" and several known defense mechanisms against rogue transposons exist (siRNA, RNAi). Transposons and the defense mechanisms have now become powerful tools in molecular biology research.
Endogenous retrovirus sequences which are remainders of retroviruses which have inserted themselves into the germ line and become inactive through mutation.

However, even these "junk" regions are believed to have important evolutionary functions such as protection from mutation through retroviruses: Because there are large DNA regions where the precise order and function is not important, a retrovirus that inserts itself at random positions of the genome is less likely to cause permanent damage.


What are the factors on which protein-protein interaction depend?

It depends both on structure and charge. Binding sites of proteins are essentially formed by amino acids placed in a particular conformations such that it will match the binding site of their counterpart protein or substrate. This is commonly referred to as the lock and key model of protein binding. This is similar to how two puzzle pieces fit together, the pieces are exactly the same shape at the point at which the puzzle pieces connect. At a protein binding site amino acids are clustered together to form the matching shape to the appropriate binding partner. This however is not just dictated by 'physical shape' of each amino acid but also their charges. This is important because negatively charged amino acids will repel other negatively charged amino acids, and attract to positive amino acids, thereby modulating the exact 'shape' of the protein binding site.