Why do NK cells not destroy bacteria, even though bacteria don't have MHC-I?

While you’re correct that NK cells are often activated (in part) by the absence of MHC-I, they require other signaling events to become fully activated:

  The Molecular Mechanism of Natural Killer Cells Function and Its Importance in Cancer Immunotherapy. Paul & Lal. Frontiers in Immunology. 2017.

  Activating Receptors on NK Cells

  Lack of MHC class I on the target cell is not sufficient to trigger NK cell activation. Full NK cell activation also requires recognition of stress-induced molecules by NK cell activating receptors.

  Natural cytotoxicity receptors (NCRs) are another immunoglobulin superfamily of activating receptors that utilize extracellular immunoglobulin-like domain for ligand binding. Human NK cells express three distinct types of NCRs... NCRs recognize a wide variety of ligands on target cells ranging from viral, bacterial and parasite proteins to molecules from tumor cells and other host cells.

  Role of natural killer cells in antibacterial immunity. Schmidt et al. Expert Review of Hematology. 2016.

  6 Bacteria fight back and inhibit NK cell activities

  During evolution, many bacteria have developed survival strategies which counteract NK cell activity.

  Both Gram-positive bacteria such as Streptococcus pneumoniae and Gram-negative bacteria such as Salmonella spp and Escherichia coli are able to induce prostaglandin E2 (PGE2), which negatively affects NK cell functions at different levels. PGE2 inhibits the cytolytic activities of NK cells by suppressing their responsiveness to cytokines such as IL-12 and IL-15, and suppresses NK cell mediated activation of macrophages by inhibiting the production of IFN-γ. Similarly, PGE2 has a deleterious effect on homing, migration, and survival of NK cells, as it has been shown in Human Herpes Virus 8 (HHV8) infection.
  Thus, bacteria are able to inhibit both cytotoxic and immunoregulatory effects of NK cells in various ways.

  8 Conclusions

  In conclusion, there is a growing body of evidence that NK cells play an important role in the antibacterial host response. NK cells are able to kill bacteria directly, or to modulate the immune system via cytokines and interferons. Further studies are needed to characterize how NK cells are activated by different bacteria. In addition, the role of NK cells among the other arms of the immune system in the defense against bacteria is poorly understood. Last, bacteria are able to inhibit NK cell activities, and a better understanding of this impairment may be the basis to specifically strengthen the antibacterial host response. Therefore, additional in vitro and in vivo data may open new therapeutic strategies using NK cells to fight bacterial infections.

If you’d like a full-text copy of the Schmidt paper, I can share it with you.


What is delayed compliance in blood vessels?

First let's consider what compliance means:

C = compliance
ΔV = change in volume
ΔP =  change in pressure

Delayed compliance
The response of a blood vessel to a sudden change in pressure. When the volume and so the pressure highers in the blood vessel the vascualar wall will stretch. As the wall of the vessel stretches the pressure inside the vessel will fall. So an increase of compliance is the result(look at the formula ΔV will get higher because the wall stretching will make the vessel larger at so the volume bigger and the pressure less). this change in compliance is what they call delayed compliance.

I don't really think you can speak about permanent because it's a dynamic process.


How long can Cholera bacteria survive in a dead host?

No, I don't think so.

Mostly estuaries (brackish water) and marine biofilms on submerged surfaces are a reservoir for Vibrio cholerae. Vibrio cholerae is isolated from rivers, creeks, washes, irrigation ditches, hulls of ships, etc. (Indeed, cholera spread rapidly throughout the world after the 1817 epidemic, largely due to the inadvertent transport of contaminated bilge water, mainly from British ships.)

  Transmission is by the fecal–oral route. Infections are particularly common after ingesting contaminated water or food. Cases are occasionally seen in people who have eaten raw or undercooked shellfish, particularly oysters, from contaminated waters. V. cholerae is excreted in the feces and vomitus. Viable organisms can be found in feces for up to 50 days, on glass for up to a month, on coins for a week, in soil or dust for up to 16 days and on fingertips for 1 to 2 hours. Bacteria survive well in water and may remain viable in shellfish, algae or plankton in coastal regions.

In 1855, a wave of cholera hit London. Thousands became ill and died before John Snow identified the Broad Street water pump as the single point source of that outbreak. Today, patrons of the John Snow Pub (built on the site) can enjoy local ale, and more importantly, a glass of crystal clear, pathogen-free water.

  V. cholerae [is] an autochthonous aquatic bacterium rather than a human pathogen that is a transient resident of the aquatic environment. V. cholerae has over 200 serogroups, with O1 and O139 being the causative agents of cholera, due to their carriage of the genes encoding cholera toxin (CT) and the toxin co-regulated pilus. ...[A]ssociations with the human host is only one small aspect of the V. cholerae life cycle and is not necessary for environmental persistence. ...[T]his bacterium is a cosmopolitan aquatic species that is capable of causing illness in humans.

Vibrio cholerae attachment is mediated by pili, which promote surface attachment and subsequent biofilm formation. It is rather difficult to believe that an aquatic biofilm was preserved on the hill for all those years, even in a dormant stage.

  ...they could transform into a unique dormant stage that was able to survive for months in the sediment of the estuary. ...These exciting new data enabled investigators to now integrate information regarding the seasonal nature of events surrounding an outbreak in populations living near estuaries.

I have found nowhere that the dormant stage can occur outside of water.

Environmental reservoirs and mechanisms of persistence of Vibrio cholerae

Medical Ecology Main Page

Cholera

 Something goofy going on with these, sorry.


The male has a phenotype XGY BB, and the female, XGXg Bb. Thus the probability is 0.25.


Transmission of epigenetic regulation through surrogate mother

Epigenetic information is information that can be inherited through cell division that is not encoded in the DNA sequence. This includes, but is not limited to, DNA methylation and histone modifications (there is also non-chromatin based epigenetic information). A nice example is the centromere, the chromosomal region that binds the kinetochore and is important to attach chromosomes to the mitotic spindle during cell division. The location of the centromere on the chromosome is encoded by a specific nucleosome composition and does not seem to rely on the DNA that wraps around those nucleosomes: The DNA sequence at centromeres is not even conserved from chromosome to chromosome (with the exception of budding yeast), and there are several known examples of people and families where the centromere is in a different place. However, all the mechanisms for maintaining this epigenetic mark are encoded genetically.

As epigenetic information is transmitted through cell division, it is directly inherited from the biological mother (with the exception of e.g. the centromere, most epigenetic marks from the father's chromosomes are removed when sperm is created).

However, (some) epigenetic information can be modified. This is obviously important during development where gene expression patterns of a liver cell need to be stable but different from gene expression patterns of a neuron, even though both descend from the same cell.

There is evidence that the metabolism of the mother will influence the epigenetic program of the child; diet being one of the determinants. It has also been suggested that epigenetic changes may influence behavior. Thus, it is indeed possible for the surrogate mother's epigenetic state to influence the epigenetic information of the children.


Why can't gametes of one species fuse with that of the other species?

The implied subject of your question is the prezygotic barrier and is one of the possible determining mechanisms of speciation, the others being temporo-spatial (meaning different time or place), behavioral, and mechanical (the organisms don't fit together, physically).

Fundamentally, this means that gamete cells of each organism are chemically incompatible. While the details specific to each species vary, we can take a look at a few examples to illustrate the point.

In order for eggs of Arbacia Punctulata to attract sperm of the same species they secrete a specific chemoattractant peptide we call Resact (a selection of different species' chemoattractants can be found beyond the former link), which is adapted to diffuse well in seawater. Sperm then follow the chemical gradient in the direction of the egg, which is called positive chemotaxis. Resact doubles as an activating peptide for that species' sperm. Pycnopodia helianthoides starfish, which also reproduce through broadcast spawning, use an attractant we call startrak. Internally fertilized animals use roughly the same mechanism to guide sperm through the reproductive tract, though with different chemical adaptations specific to their evolutionary history.

Once the sperm reaches the egg, an acrosome reaction leads to the fusion of the two gametes into a potential zygote (for the reason why I say potential, see  Speciation by polyploidy). The chemistry of this reaction also varies between species.

In summary, the reason is this:

A change in gamete chemistry (chemotaxis, activation, reaction, adhesion) alters the chances of successful fertilization between one or more members of the same species.
Thus, the altered group reproduces more often within itself than it does with the parent group, allowing it to grow in population.
Changes in the altered group further reduce the chance of success with the parent group.
Eventually, the chances of the altered group successfully mating with the parent group are practically zero.

This process is, of course, typically assisted by one or more of the other aforementioned mechanisms. Where two species are capable of producing offspring and successfully do so, you get hybrid speciation.

Further reading

Study.com - Speciation II: Prezygotic Barriers
Recognition of Egg and Sperm
Egg and sperm recognition systems during fertilization


How Scientists sequence, assemble and annotate plant genomes?

Let's try and answer all three parts of your question.

Sequencing
The general method is the same. Sequencing is just sequencing. But as for every single sequencing, there are factors to consider and protocols to be selected.
One important thing is, that you might want comparably long reads to cope with the repeats and the general large size of plant genomes. To get long reads, you need long input DNA sequences. Therefor you would want to follow a suitable protocol for high molecular weight plant DNA. That might be hard, because plant DNA can be difficult to extract based on the plant and tissue you have, as most easily put you have to "crack open" the cell wall in the very beginning.
After that, it is general sequencing. Although, as I already said you might opt for long reads (PacBio) and/or good coverage. If that is not at all feasible, you might choose to do targeted sequencing and only capture the whole exome (or only the genes you are interested in) to reduce both cost and analysis complexity.

Assembly
Now you have probably accumulated a lot of sequence and also potentially long sequence. There are multiple tools you could use for assembly and generally you can use the same for plants that you might want to use for example for a human genome assembly. One example that works well on large plant genomes is MaSuRCA, another is Allpaths-LG. There are some assemblers designed to cope with long repeats, but quite often you just assemble and then try figuring out the repeat regions later, for example by improving a shotgun read assembly with long reads from another technique.

Annotation
This one definitely has specific tools for plant genomes. Well, large genomes. The main thing in annotation is finding potential genes and comparing them to databases to annotate them with function. Plants do splice and plants can have long introns, even ones including long repeats.
One gene prediction software example that works on plants is Augustus, but for some model organisms there are even organism-specific pipelines and tools for this task. And of course, on the database part you would choose to rely on a plant specific database (if you do not use NCBI-NR anyway). Those can also be species or genus specific like the ones you find on the TAIR (Arapidopsis) project.

TLDR:
It's in fact complicated. On one hand, there is a need of specific tools and databases, on the other you might go well with standard tools, but would have to adapt parameters, do additional pre- or post-processing steps and so on.


When can I assume individuals marrying into a pedigree are non-carriers?

All the time.

Unless you are specifically told/shown they are carriers, they are assumed to be Wild Type and do not carry the mutation.


Do these large spiders in Taiwan belong to different species?

The following is from Biogeography and Speciation Patterns of the Golden Orb Spider Genus Nephila (Araneae: Nephilidae) in Asia, Yong-Chao Su, Yung-Hau Chang, Deborah Smith, Ming-Sheng Zhu, Matjaž Kuntner and I-Min Tso, Zoological Science, 28(1):47-55. 2011., DOI: 10.2108/zsj.28.47 http://www.bioone.org/doi/full/10.2108/zsj.28.47

Spider 1 seems a good match for C in the images below, and Spider 2 matches A and B. So I propose that both spiders are Nephila pilipes but with different color patterns.

  Fig. 1. Nephila diversity in Asia and Australia and its extreme sexual size dimorphism: (A–E), N. pilipes; (A–B), female of the common color pattern, Taiwan; (C–D), female of the darker color pattern, Taiwan; (E), male (arrow) in copulatory pose on female, Singapore; (F–G), female N. antipodiana, Singapore; (H), female N. plumipes, Australia; (I–J), female N. clavata, Taiwan. Images by M. Kuntner (www.nephilidae.com).


If proteins have an overall charge, how do membrane proteins traverse through the hydrophobic region of the plasma membrane?

Transmembrane proteins are inserted into the membrane in the ER in a rather complicated system, there is a whole chapter about translocation of proteins in "Molecular Biology of the Cell".

The proteins are moved through an aqueous pore in the Sec61 complex, which explains how charged parts of a protein are moved across the membrane.

The parts of a transmembrane protein that remain in the membrane are usually composed of hydrophobic amino acids that aren't charged.

I strongly recommend you to read up on the whole translocation stuff in a cell biology book like the Alberts I linked. There's a lot more to it than what I wrote here.


Is this species a variant of a red flour beetle?

This does not look like a red flour beetle, but more like some species of Melolontha, possibly a cockchafer. For more specific information, we would need to know, where your back garden is and maybe something to scale the bug. I would go for Melolontha melolontha, the common cockchafer.
Of the two other european species of Melolontha, M. hippocastani usually has a black edge of the elytra (see this picture), which this one doesn't seem to have, and M. pectoralis is very rare and mostly (only?) found in Germany.


Why is there a carbon atom without a greek letter in protein residues?

In your context, the "plain-C" labelled carbon is the carbon atom in the carbonyl ($\ce{C=O}$) group.
In organic chemistry, the alpha carbon is the carbon immediately adjacent to a functional group. In general, the greek letters in alphabetical order denote the distance in increasing order from a functional group.  The $\ce{C_\alpha}$ in the case of amino acids is alpha carbon with respect to both the amine and carbonyl.


You are correct in thinking that since the translation of mRNA begins with AUG, which codes for methionine, then all proteins should contain a methionine at their N-terminus (aka start site). But, it is indeed not so. First of all, I want to mention about variations in start codon. As you say, AUG is not the only, but actually the most common, start codon, and it codes for methionine in eukaryotes, or formylmethionine in prokaryotes but only at the start site. But, this start codon can also vary and become GUG or even UUG, coding for valine and leucine respectively. And the twist is, it still codes for methionine or formylmethionine1. In rare cases, such as heat shock, other codons like CUG, ACG, AUA and AUU, are also used for initiation 2. It is so because start codon itself is not sufficient to begin translation, other nearby factors, like the Shine-Dalgarno sequence, or initiation factors, also play a role. One such factor is the initiation tRNA. At the beginning of translation, tRNAMet or tRNAfMet binds to the small subunit of ribosome. So, whatever be the start codon, the first amino acid will be methionine3.

Now, coming back to the main question, N-terminal methionine, although being the first amino acid, is not present at N-terminus of all proteins. This is because of a process that is known as post-translational modification. After a polypeptide is completely translated from mRNA, it is modified at different places by different enzymes, which are regulated by different (internal or external) factors. There are more than a hundred post-translational modifications known4, one of which is the removal of methionine from the N-terminus of a polypeptide. N-terminal methionine is removed from a polypeptide by the enzyme methionine aminopeptidase5.

The question which immediately comes to mind is Why are proteins modified after translation? Well, there can be various different causes of it. First of all, post-translational modifications are regulated by many factors, and this process is called post-translational regulation6. Another point is cell targeting. Attaching different groups to polypeptides makes them more stable at their target location. For example, by attaching lipid molecules to polypeptides (in a process called lipidation) makes the polypeptide more stable and suitable for cell membranes4. A yet another factor is increasing stability. Yes, you read it right, in some cases, N-terminal methionine can destabilize a protein! For example, an extra N-terminal methionine not only destabilizes but also disrupts the native folding configuration of $\alpha$-lactalbumin7. There can be numerous other factors too, which promote removal of N-terminal methionine from polypeptides.

Thus, in short, No, not all proteins contain a methionine at their N-terminus. I hope this helps!

References:

 1. Touriol, C., Bornes, S., Bonnal, S., Audigier, S., Prats, H., Prats, A.-C. and Vagner, S. (2003), Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons. Biology of the Cell, 95: 169–178. doi:10.1016/S0248-4900(03)00033-9

 2. Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Research. 2011;39(10):4220-4234. doi:10.1093/nar/gkr007.

 3. Sherman, F., Stewart, J. W. and Tsunasawa, S. (1985), Methionine or not methionine at the beginning of a protein. Bioessays, 3: 27–31. doi:10.1002/bies.950030108

 4. Post-translational modification - Wikipedia

 5. Liao, Y.-D., Jeng, J.-C., Wang, C.-F., Wang, S.-C. and Chang, S.-T. (2004), Removal of N-terminal methionine from recombinant proteins by engineered E. coli methionine aminopeptidase. Protein Science, 13: 1802–1810. doi:10.1110/ps.04679104

 6. Wolfgang Schumann; Wolfgang Schumann (Prof. Dr. rer. nat.) (2006). Dynamics of the bacterial chromosome: structure and function. Wiley-VCH

 7. Chaudhuri, T. K., Horii, K., Yoda, T., Arai, M., Nagata, S., Terada, T. P., & Kumagai, I. (1999). Effect of the extra N-terminal methionine residue on the stability and folding of recombinant alpha-lactalbumin expressed in Escherichia coli. Journal of Molecular Biology, 285(3), 1179–1194. doi:10.1006/jmbi.1998.2362


Blood urea nitrogen and usage of proteins?

The quotes in the question provide incomplete information at best.

Let's focus on the nitrogen (N) that comes from protein, ignoring for now how metabolism differs among amino acids. We'll assume for simplicity that liver function is OK so that the urea N production rate is a reasonable measure of protein N degradation rate (say in units like moles of N per hour).

First, consider simple conservation of mass:

  Intake = Loss + Net Storage

If you think about this in terms of protein N from the perspective of the whole body, you start to see the limitations in those quotes.

First, loss from the whole body of metabolized protein N in the form of urea N mostly occurs via the urine. Impaired kidney function may lead to less urea being excreted than is being formed. You will then have "Net Storage" of urea N in the blood and body fluids, so BUN can rise even if metabolism of protein is unchanged. In fact, BUN tests can be used with other tests to provide information about kidney function. Thus BUN levels don't necessarily tell you much about the urea N production rate or protein degradation rate.

Second, you have to consider that one "use" of proteins can be "Net Storage" to build muscle mass. That type of "use" won't show up in increased urea N production. Alternatively, body protein in muscle can be broken down to be "used" for metabolism/catabolism during an overnight fast, possibly leading to increased urea N production rate depending on how the mix of protein, fat, and carbohydrate catabolism has changed. Furthermore, the effects on BUN levels will depend on kidney function.

Both storage and degradation/catabolism are important "uses" of protein N, but they have different implications for production of urea N, and BUN levels don't necessarily represent the urea production rate.


What are the most important factors influencing a person’s gut microbes?

Our Unique Microbial Identity (Gilbert 2015) suggests that the gut microbiome is shaped and stablized during infancy and tends to restore equilibrium if it is disturbed later in life. Antibiotics temporarily change the composition of the gut microbiome (by suppressing the growth of certain groups of bacteria more than others), but it tends to drift back to resemble its original (stable) community after treatment is stopped, likely due to the interdependency of individual strains as producers/consumers of particular compounds (i.e., some bacteria will eventually arrive to serve a particular role in the microbial community). A recent study in antibiotic treatment provides some empirical evidence of the long term effects of antibiotic treatment on the human gut microbiome.

The American Gut Project is currently open to the public for participation, and it has the goal of identifying exactly the factors you describe. They are accepting samples from individuals across the country, along with lifestyle information, including dietary habits. A related publication by the group provides a summary of the common gut bacteria implicated in a variety of diseases.

H. pylori infections are a common gut microbiome health issue. This bacteria is present in about half of gut microbiomes and are not generally harmful unless the stomach lining is already compromised (e.g., due to medication or diet). In those cases, they can become opportunistic pathogens that can persist for decades and cause peptic ulcers which can lead to a variety of difficult to diagnose ailments such as arthritis.


Do any known viruses contain "junk" or parasitic genomic information?

I'm curious if any known viruses can contain parasitic genetic information "along for the ride"

Analogous to the parasitic transposons mentioned in the paper linked by canadianer, phage-inducible chromosomal islands are mobile elements that "hijack" the molecular machinery of bacteriophage during lytic infection of Gram-negative hosts.  PICI elements, as they're called, encode Rpp proteins that complex with the phage TerS homodimer, changing the conformation of the complex such that the PICI cos mimic is preferentially bound and packaged into the empty capsid.  Fillol-Salom et al. 2019 1 discuss in detail the mechanism of PICI propagation and provide a good graphical abstract of the process:

Similar elements exist in Gram-positive bacteria, specifically Staphylococcus aureus, called Staphylococcus aureus pathogenicity islands (SaPIs).  Instead of encoding a separate protein that complexes with the phage TerS, SaPIs encode a homolog of TerS that specifically recognizes and packages SaPI DNA into phage capsids.2
Note that this answer does not directly address the question of "junk" DNA in viruses, as PICI elements are dormant in the genomes of the bacterial hosts rather than the genomes of the viruses themselves.  Though, I believe this is relevant insomuch that they parasitize bacteriophage, and are therefore "along for the ride" in the viral capsid.

Citations

Hijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit
Role of Staphylococcal Phage and SaPI Integrase in Intra- and Interspecies SaPI Transfer


Need help interpreting Western blot data

Answers to each question:

Approximately, yes. In this case, phosphorylated Akt (p-Akt) is supposed to be the active form of the enzyme that goes around the cell doing its job, whereas non-phosphorylated Akt doesn't have activity that they are interested in. The authors do show that targets of Akt show characteristics of Akt activity when Akt is phosphorylated (Fig 2B, 2C).

Note that densitometry is just a way of measuring the intensity of some bands on immunoblots (westerns). In this case, it is normalized by the loading control (non-phospho Akt). So you could interpret the densitometry plots as showing the proportion of Akt that is phosphorylated. It is a little confusing because they subsequently normalize them to a specific timepoint. From the methods:

The results were quantitated by densitometric analysis (ImageQuant, Molecular Dynamics and PDSI, GE Healthcare). The ratio of phosphoprotein to its respective internal control was normalized to the control level at 0.5 h, arbitrarily set to 1.

Loading controls indicate how much protein of interest is present. For example, 1% of 100mg of protein is the same as 10% of 10mg protein (each is 1 mg). However the interpretation of 1% vs. 10% may be quite large. So if what you are interested in is a percentage or proportion, you need to have a loading control to allow unbiased comparison or normalization.

I don't really know what "basal mass quantity" means, but you could look into the molecular weight of proteins (usually measured in kilodaltons). For example the molecular weight of Akt is ~55kda. You can compute this from the protein sequence by adding up the weights of all the amino acids.


What DNA has the most info for getting a person's likeness?

Except for Red Blood Cells, every somatic cell contains two copies of the autosomal chromosomes and a pair of sex chromosomes, either XX or XY (Assuming an average human being) One set is maternal and one is paternal
Some lymphocytes actually recombine their chromosomes, so their DNA will be functionally different to all of the other somatic cells in the body.
Gametes undergo Meiosis and will be haploid, only containing one copy of each autosomal chromosome and one of the sex chromosomes
Cells accumulate mutations over time. The closest you could probably come to an exact clone of a person is if you harvested one of the cells from the eight-cell stage of development. The other seven are able to go on and produce a viable and healthy person. The harvested cells DNA would be the closest to the DNA that combined in the fertilization of the egg. The next closest would likely be stem cells from cord blood. Then probably neurons, as they tend to divide the least.
As the link you posted said, ATCG can be represented in a two bit code, so for about 6 billion bases, you would need about 1.5GB of storage (You need to capture both sets of chromosomes in order to produce a person).

There are places where you could compress the data. Telomeres could be removed and just added back after the fact, as there is likely a standard length for each chromosome of the six nucleotide repeats.
Though you could have a minimum of a two bit code, you would really need a larger data set. You would need metadata, so things like polarity of DNA and chromosome number.
You might also want data about the alleles of each and every gene, that way any errors could be fixed. If you are making the DNA from a data set, there is no sense keeping any genetic defects or diseases in the sequence when you remake it.

Craig Venter, one of the protagonists of the Human Genome Project has a company that is able to produce synthetic DNA for a whole organism. They have reportedly produced a synthetic bacterium, so in theory, they could print DNA from a database and recreate an entire genome, though at what cost and how long I am not sure.
The Original sequencing of the Human Genome did cost Billions of Dollars, however today's sequencing machines can produce an entire genomic sequence more in the range of thousands of dollars. I am not sure if they have broken the $1,000 threshold yet.
Most of the commercial companies do not produce full genomes. They likely do not even sequence a full exome (The areas of all genes that make up the coding sequences of mature mRNAs). They likely do some form of polymorphism analysis to determine if for any given gene you have certain allele other than the Wild Type allele. In this kind of analysis, you do not really need a full sequencing to determine what gene a person has, you only need to identify areas of key differences to determine what is what. That being said, the data collected by a commercial genetics company would likely not be sufficient to recreate an entire genome.
Another important factor is Epigenetics. Just because you have the entire base sequence of the person, doesn't necessarily mean that synthetically creating all 46 of that person's chromosomes would give you the necessary material to transfer into an enucleated oocyte to then produce a new person. You would likely also want to capture the epigenetic encoding as well as the full genome. The epigenetic code that you would likely want would be from one of the cells from the 8-cell stage of development I mentioned earlier. While we have been able to clone adult mammals by nuclear transfer, those animals have had issues with cancer and premature aging. This may have something to do with telomeres, but it also may have something to do with the epigenetic code in early development.
There are other considerations in development as well. There is exchange of nutrients between mother and fetus during development. There is also a sharing of immunity and probably hormonal signals from the mother that can effect development.
Also women are mosaics. A woman would also have the added challenge that every single one of her cells has one of her two X chromosomes inactivated, so depending on which one is inactivated, at random, will determine which of the two X alleles she will be expressing in that cell. It is very possible that her clone would be different from her in appearance.

That is a pretty extensive list. I probably have missed some things. One thing I have definitely left out are all of the structural proteins of chromatin and how to package the DNA into a nucleus. We do not yet understand all of the mechanisms to compact DNA down into a nucleus, so we would have to answer all of those questions before we could figure out how to print and package the DNA to make a clone of a person from a database of their genome.

As we have not currently cloned a human, then it is difficult to say if it is possible. Things that we can do, even in other mammals do not always translate to humans and human cells. There would also be significant ethical hurdles to overcome and based on the current sentiments, it is unlikely, even if we have the technology, that society would allow human clones to be produced.


Regarding the loss of Cas9 activity, you are already touching on the answer in your question. Cas9 as a nuclease/enzyme is always active, and will continue to cleave double-stranded DNA as long as there are complementary target sites and guide RNAs to guide it there. If the target site is not mutated or completely removed after cleavage, Cas9 can indeed cleave the same site again.

However, even if the target gene is mutated, there is likely to remain complementary sequence to the guide RNA, at least upstream of the mutation.

I'm not sure if I misunderstand the point you are trying to make here, but the introduction of mutations is usually enough to prevent recurrent cleavage of the same site (although studies of off-target effects clearly show that this is not always the case):
Both Streptococcus pyogenes and Staphylococcus aureus Cas9 cleave their target sites between positions -3 and -4, counting from the end of the 20-nt guide sequence (see attached figure below). The double-stranded break can then be repaired either via non-homologous end joining (NHEJ), or via template-driven homologous recombination (HR).

In the former case (NHEJ), double-stranded breaks are sometimes repaired with small errors. These errors usually accumulate near the break site (read about NHEJ to understand why), and such mutations will typically destroy the gRNA recognition site. Note, however, that not all (in fact, very few) NHEJ repair events will result in the introduction of mutations, and "perfectly repaired" breaks both can and will be re-cleaved by Cas9. But since repeated cleavage is lethal to the cell, there is a selective advantage for mutations that prevent re-cleavage of a target site. Also note that the introduction of mutations (and thereby gene editing) via NHEJ is a random process, with no direct control by the researcher.
In the latter case (HR), the DNA template used for repairing the double-stranded break can typically be chosen by the researcher. It can for example be a chemically synthesized DNA fragment or PCR product with at least some sequence homology to regions flanking the cleavage site. But since there is no specific sequence requirement for the region in between the homology regions, this interspacing region can be designed such that it partly or completely replaces the original recognition and/or PAM sequence (violet region in figure below).


Can acid-fast M. tubercolosis obstruct alveoli?

Mycobacteria are on the order of 2µm in length and 0.2µm in diameter.  Alveoli are on the order of 200µm in diameter.  Obstruction is possible, but M. tuberculosis grows rather slowly.  Too slowly, in fact, to avoid being engulfed by alveolar macrophages.

Furthermore, obstruction does not sufficiently explain the predominant symptoms of tuberculosis:  bloody sputum and the tubercles themselves.


When DNA is at its uncondensed form, what can it do?

At least in bacteria they can. In optimal conditions, E. coli divides itself about once every 20-30 minutes. Wich is more important, the replication time of its genome is about 40-50 minutes. That means that, in exponential phase, E. coli has at least two active replication bubbles. Since the density of ribosomes must be more or less constant, aswell that the new cells needs to synthetise peptidoglycan and other cell components, that means that replication and transcription occurs simultanously. If not, ribosomes, enzimes, tRNAs and mRNAs would be diluded in every replication event.

In eukarya I see no reason of why that shouldn't be possible. The formation of chromatin is not a random event and some specific proteins are required during short periods of time during some steps of mitosis, so it's logic to assume that some specific parts are not compacted or that transcriptional activity can occur even in chromatin.

The specific region that is duplicating itself in a given time will probably be unable to transcribe, because the polymerase complex is pretty big and they need to open the double helix, and that. But this is somehow like children playing in the train tracks. Once the train aproaches, the children stay apart, and they continue again when the train has gone.


How do mutations come to be shared by all cells?

Goods question! Only mutations that occurred when we were in the early stages of development will affect all cells. That's why pregnant mothers shouldn't smoke. The reason for this is that one cell goes on to divide and become all our cells so any mutations in that cell are passed on to cells formed when it divides. That same principle explains your smoker example. In the lung we have two types of cells which are called Type 1 and Type 2. Type 1 cells are constantly dying as they get old and they get replaced by type 2 cells whose job it is to divide continuously to replace Type 1 cells. So we have lots of type 1 and few type 2. When type 2 divide they make one type 1 cell and one type 2 cell, so type 2 cells never run out. If smoke causes a mutation in type 1 cells generally they're okay because they'll die before enough mutations occur. Of course something that causes lots of mutations could make it cancerous before it dies but that's rare. Now if it occurs in Type 2 cells every subsequent type 1 or type 2 cell that cell makes is mutated.

The last thing you mentioned are mutations that occur to eggs and sperm. When making sperm you have the same as above. One cell makes sperm and a sperm maker cell. The sperm is like type 1 cells and the sperm maker cell is like type 2. So mutations affect them as they do above, where a mutation in a sperm maker cell is way worse. As for eggs women are born with all the eggs they'll ever have and there's no egg maker cells. So mutations just occur, and the older women are the more mutations. That's why the older a mother is the much higher risk of genetic diseases like downs. But an older man only has a slight increase in risk.

Mutations that affect eggs and sperm tend to be really harmful, as they affect every cell, so these cells or "babies" die before the mother even realises she's pregnant or as a miscarriage. I've not given the scientific names for things but if you request them, I'll give you the real names, but hope you enjoy the principles.


Can a person die instantaneously from internal damage to the brain?

Please consider this only as a starting point (although a lengthy one), and a race against an acute onset of  tl:dr ...

A person cannot die instantaneously from internal brain damage (under everyday circumstances). The reason is the non-centralized architecture of the brain and that consciousness is a global phenomenon which underlie the activity of many brain structures.

These brain structures are themselves comprised of a cellular hierarchy, with each cell being self-sufficient for at least a time regime in the order of minutes. As such the brain underlies to some extend the study of networks and robustness thereof. The brain also maintains a scale-free organization . Actual Scale free networks in nature are known to be robust.

Instantaneous in this context means a consciously discernible difference in time, which is on the order of tens of milliseconds (See: Inspection time, mental chronometry).

Also I narrow the medical cause of death down to a intracerebral haemorrhage, systemic shock or hypoxia. I definitely leave out all (rare) CNS-immunological phenomena (e.g. explosive brain death, Immune reconstitution inflammatory syndrome related,... )

But, effects that can mimmick instantaneous brain death are very plausible.

Notably, this question can be answered despite there being no rigorous consensus model of consciousness.

Consider the following just as pointers, but not as qualified, thoroughly sourced information, - contrary to a paper or review ( I will gladly include your resources, or turn this post into a community wiki if demand to do so exists):

**** Consciousness**:

The brain weighs only 2% of the human body mass, yet consumes 20% of the total energy at rest. Crucially the brain can deplete oxygen at a great rate, which is proportional to the brain activity in various regions, giving rise to indirect measurements of brain topology and images like these:

"Visualization of a DTI measurement of a human brain"-2006,
author: Thomas Schultz, DOR: 25/09/2012

Humans have different states of consciousness which show different overall patterns of brain activity. As such the result a scientist would witness through an high-resolution fMRI/PET scanner in a stroking-individual would differ during sleep, sleep/wake transition or various levels of awareness during the days. Stroking and the effects on the brain is studied quite extensively with rats(See: rat, fMRI, stroke).

Moreover the brain activity, fine-anatomy and orchestration of brain utilization differs from individual to individual. In short the brain is what neurologists call "plastic" Neuroplasticity is the change of entire brain structures, and the brain itself from experience and physical stress/trauma (on the brain).

We are biologial enetities which have evolved to be in-sync with the planetary rotation and solar energy influx. As such brain activity changes during the day, in accordance with our circadian rythm or biorhythm, and if it weren't for artificial lightning brain activity would change over the seasons as well.

Connecting all the dots: Describing brain death in a seconds-regime comes down to which areas in an individual brain consume the most oxygen and "shut down" first, and which processes steer brain activity till organic shutdown.

Since Stackexchange has a strong programmatic background, to put it in a somewhat programmatic analogy:

The output of a memory dump and its analytic result depend on the hardware, the software and the state of the application. Unfortunately the software is spread across processors, has multiple threads and applies a genetic algorithm with dynamic recompilation.

Death Definitions:

The notion of instant death is a cultural meme (which one can witness in child's play) and is further propagated in the media.  Additionally "death" is a highly political matter...
"Death" has numerous legal definitions (throughout various cultures) medical definitions and biological definitions depending on the context. Legal definitions depends on the culturally dependent legal corpus, medical definitions on the state of (pragmatic) technologies. The medical definition of human death is influenced by the legal definition. The legal definition in turn is influenced by politics.
The biological definition of death depends on the context and a threshold thereof, which in turn describes the level and and of hierarchical systems or one large system comprised out of systems such as organs. An organ is the collection of units in one structural one to serve a common purpose.

Finally to answer more accurately, a person cannot (under everyday circumstances) shutdown brain activity within the time-interval of one reaction time-unit or 'cycle', but may transition between discernible states of global brain-activity. Such states may only be measurable with functional Imaging techniques and classifiable using computer algorithms.


Is the poly(A) tail added while transcription is still underway?

It's slightly more complicated than the comments above indicate.

  Glover-Cutter, K et al. (2007) RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nature Structural & Molecular Biology 15: 71-78

The authors present evidence that RNA polII pauses 0.5 - 1.5 kb downstream of the poly(A) site where processing factors are recruited (cleavage stimulation factor, or CstF, and cleavage polyadenylation specificity factor, CPSF). So the polymerase is still engaged with the template and the premRNA when processing is initiated, although it may not be actively elongating the transcript.

  "Localisation of the active polII-3' end processing complex well downstream of the poly(A) consensus sequence agrees well with the cleavage of Chironomus BR1 transcripts after 600 bases of downstream sequence has been transcribed. This model is also supported by the fact that efficient poly(A) site cleavage requires an intact RNA tether linking the poly(A) site with the downstream polymerase." (references are cited in the original).

It is a semantic question as to whether you call this cotranscriptional processing.

[Incidentally this is yet another example which contradicts the commonly-stated idea that evolution acts to optimise everything to conserve ATP - here we have the transcription process discarding the energy from approximately 1000 phosphodiester bonds per transcript.]

UPDATE
@WYSIWYG The polymerase goes past the site where the poly(A) will eventually be added, and makes another 1000 bases of RNA before pausing to recruit factors that are needed for the subsequent cleavage at the pol(A) site which now lies "behind it". After that the poly (A) tail is added at the newly created 3' end. So the initiation of poly(A) addition (in the sense that the cleavage is an obligatory first step in the process) is accomplished while the polymerase is still engaged. I agree that the actual addition of the poly(A) cannot in any way be considered to be cotranscriptional.

I was trying to make the point out that it isn't simply a case of the polymerase encountering the cleavage site and dropping off to allow a second unlinked process to take place.


How does cholesterol affect the fluidity of a plasma membrane?

Cholesterol certainly affects plasma membrane fluidity. In 1978 Cooper found that increasing the ratio of cholesterol to phospholipids decreased the membrane fluidity. This also reduces membrane permeability and reduces the survival of the cells (red blood cells in that case). I imagine this is where the textbooks draw their conclusions.

More recently Rog et al., 2008 demonstrated the importance of the hydroxyl group in the cholesterol by replacing it with a ketone. This affected fluidity and flip flop rate.


tl;dr
Like the brain, the receptors commonly called 'pain' receptors aren't in the spinal cord itself, but they are present in the meninges around the cord, and damage to the cord can be perceived as pain in particular because it can increase activity in the pathways carrying 'pain' information to the brain.
Details
Nociceptors, often called pain receptors, are peripheral structures that sense and transmit noxious stimuli to the central nervous system. The cell bodies of afferents from these receptors are found in the dorsal root or trigeminal ganglion. The receptor structures themselves (the afferent terminal of these neurons) are not found in the parenchyma of any central structure, though they do innervate the meninges of both the brain and spinal cord. Despite the lack of peripheral receptors of nociception, damage to the spinal cord is often associated with increased activity in the tracts that carry nociceptive information.
This may be beyond the question you're asking, but I would note that the IASP defines pain as:

a sensory and emotional experience associated with actual or potential tissue damage or described in terms of such damage.

Pain is probably best understood less as a sense that nicely maps the external environment to a conscious representation of that environment, and more as an emotional need state, like hunger. Many different receptor structures and nerves can transmit a signal that can eventually be interpreted as pain, and in fact pain can be experienced without any physical peripheral input at all (as the IASP definition attests). This is one of the reasons nociceptors are typically not called pain receptors by people who treat or study pain.


How is it possible to even hope for an ebola epidemic of this current size to remain contained to a relatively small part of Africa?

This is too long for a comment, so my thoughts about this here. The CDC Director said a few days ago after a visit in Africa "The window of opportunity is closing".

This can happen. However, you are not getting contagious unless you show symptoms. This is different in other diseases like chicken pox or measles where you spread the virus before showing symptoms. So there has to be a lot of awareness. Also doctors need to be very careful with patients showing these symptoms. This is most likely one of the main reasons for the wide spreading of the disease.
Same problem as in 1. Theoretically this is easy to prevent, but in a situation of chaos this can cause problems. But since infected people which show symptoms will not handle large amounts of food, this is most likely less of a problem.
Every crossing of a species-barrier is a rare event. Double-crossings are even less likely. So I don't think this is a problem. Besides this, we already have to independent Ebola outbreaks which has never happened before. One is the one in West-Africa, the other one is happening in the Democratic Republic of Congo. Both are independent cross-overs.
This can cause problems. The advantage of the first world is that we have functional health care systems. They allow better care for the persons and also better isolation of contact persons. I think it is unlikely that it would spread widely. The perspective will be different, if the virus makes the jump into the densely populated regions in South-East Asia. There a lot of people live closely together, this can cause real problems. Fortunately for us the virus is not highly contagious. To infect yourself you need unprotected contact to the body fluids (blood, stool, feces, sweat etc.) of infected persons.


Where does an organism store reserves of amino acids?

In the sense that you have asked the question, humans have no stores of amino acids. Amino acids obtained from the diet are quickly incorporated into new proteins or are metabolised as fuel molecules.

Proteins are subject to continual turnover, and the amino acids that are released by degradation are either reused or metabolised in exactly the same way.

This is one of the reasons why the diet must contain appropriate levels of essential amino acids (those we cannot make for ourselves) since these are continually being released from proteins and used as fuel - we have no mechanism for storing them in case of future dietary deficiency.

During starvation the protein turnover process releases amino acids from muscle and these are mainly used as fuel molecules. This is why muscle wasting occurs in starvation, although the mobilisation of fat reserves helps to delay this as long as possible as tissues, including brain, switch over to relying on ketones (derived from fat breakdown).


With the heterozygous genotype $LlSs$, there are two kinds of linkages possible.
1. Cis=$LS.ls$
2. Trans=$Ls.lS$

All the possible gametes ($LS,lS,Ls,ls$) in both cases are same, but their frequency differs based on the strength of linkage and hence, the distance on the chromosome map. In either case, the frequency of $LS$ and $ls$ will be same, and $Ls$ and $lS$ will be same. This is because, in the Cis linkage, the former pair will constitute the parental linkage and the latter will be the recombinants, but both the gametes within the pair are equally likely to be formed. The same is the case for Trans linkage where the former pair acts as the recombinants.

According to the given table, frequency of $llss$ is $0.01$. $llss$ can only be formed by the combination of two $ls$ gametes. Therefore the probability of an $ls$ gamete will be $\sqrt{(0.01)}=0.1$.
The probability of getting an $ls$ gamete is $0.1$. Therefore, the probability of $LS$ is $0.1$, $lS$ is $0.4$ and $Ls$ is $0.4$.

As $Ls$ and $lS$ are more probable, they are more likely to be linked, and hence the genotype will be in Trans linkage. Then the frequency of recombinants($LS,ls$) is $0.2$. The chromosomal distance is $20 \text{ cM}$ or $20\text{ map units}$.

I am not sure whether my line of arguments are true. If you do find any flaw, please let me know.


That appears to be a species of snakefly and the lack of a long needle-like ovipositor indicates that this specimen is a male.

The "kite" rather than rectangular head shape suggests it is in the Raphidiidae.

From the location I think it could be in the genus Agulla and might be the Idaho Snakefly (Agulla adnixa), but I don't know if that is the only species from this group in that area.

Reference image (Copyright © 2007 by Hartmut Wisch) from BugGuide.net:


Looks very similar to Clathrus ruber fungus.

Be careful, it is poisonous.


What is the difference between natural selection and adaptation?

Natural Selection

Natural selection is the differential in survival and/or reproductive success among different individuals. As such, natural selection also refers to the process by which genotypes associated with greater fitness increase in frequency in the population through time.

More information on wikipedia > Natural Selection

Adaptation

An adaptation (or an adaptive trait) is a trait with a functional role that evolved (and is maintained) by means of natural selection.

More information on wikipedia > adaptation

Usage

Both the terms adaptation and natural selection are extensively used in science (and none of them come from the creationist religious belief). Their definitions are related as one is causing the other but these terms are not synonyms.

Further information

As the question is very introductory in the field of evolutionary biology, you might want to have a look at an introductory course to evolutionary biology. Evolution 101 (a.k.a. Understanding Evolution) by UC Berkeley is short, concise and very accessible even for those that have little a priori knowledge in biology.

Side Note

You said "believe in evolution". It is of course a common phrasing from the creationist ideology. Evolution is a theory (a theory is very different from a hypothesis see this answer for more information) and therefore, the phrasing "to believe in evolution" sounds quite wrong as it wrongfully suggests evolution is a thing on which we could legitimately have different opinion about its existence.


Why is pith of Cucurbits hollow when mature?

Pith autolysis is a phenomenon due to which in some dicotyledonous plants like cucurbits, the pith gets hollowed.

Background: We all know that plants get their Carbon from atmosphere in the form of Carbon-dioxide, and fixes it by photosynthesis. During rapid growth Carbon requirement may not be in pace with rate of carbon fixed by photosynthesis alone, So some plants adopted pith autolysis.

This is useful for a  plant when it is in scarcity of carbon, Scarcity here implies that the plant is not able to get enough carbon for its growth with just photosyntgesis. So the plant autolyses it's pith to get required carbon to maintain its growth.Thereafter this carbon resulting from autolysis ,is transported to growing regions of plant.

Source:https://doi.org/10.1006/anbo.1995.1063


I believe these are some sort of Psocoptera, "booklice", even though they don't really jump much. Could it be that they ran or flew a little bit instead? I won't try an identification of the species, but in general booklice like damp places and most of them aren't considered serous pests.

Example of a booklouse:

Slender legs and antennae, wings, and general appearence close to your specimens.
(Image from Wikipedia)


GWAS: marker map based on old genome assembly - can I use the new assembly to look for SNP positions?

Why haven't you tried using LiftOver to convert the coordinates?

https://genome.ucsc.edu/cgi-bin/hgLiftOver


What is the equivalent of shutter-speed in Human eye?

The light receptor of the eye is a protein called Rhodopsin.  To me the equivalent of shutter speed for the eye is the (de)sensitization of rhodopsin by phosphorylation.  The brighter the light, the more sites on rhodopsin are phosphorylated, diminishing the intensity of the signal coming from the photo receptor via the transducin G protein that conveys the visual signal onward.

This process takes a few seconds, but then its possible to see when stepping into sunlight or in a darkened room.

This is more like a volume knob than a shutter speed since the same signal comes out at the same rate of each light sensor, but it has a similar effect - it modulates the intensity of the image.


Are there issues with filling PCR tubes to capacity?

Too long for a comment: I would say it depends on the PCR. I have personally used maximum volumes of 50ul, if I needed to prepare higher volumes, I made one mix which subsequently got distributed to more tubes with 50ul max.

The problem with big volumes is to get a fast and homogeneous heating and cooling. If the outside of the tube is faster, the reaction there starts already while this may not be the case in the middle. This can lead to uneven denaturation and amplification of your template. The later is especially problematic when you amplify short sequences. There the amplification time might already be over and the PCR program is moving on before the template is finished, which will result in less of your full-length product and the enrichment of shorter versions.

There is another problem that might occur in big reactions: Due to gradients in reactivity because of temperature gradients I think it is possible that reagents (dNTPs, Mg-ions) can form gradients which further inhibit a good yield.

Finally I tested one thing on one of our PCR machines: The PCR tube is set into the heating/cooling block. It is not completely set into the block but stick out partly, so if you fill it up to maximum capacity, the upper 75-100ul (approximately) would be outside the heating block and we have a thermal problem. The reaction mix there would only heat up due convection.


Why does the DNA of Bacillus subtilis not contain DNA families of 20-37 members?

Based on the paper (open access) from which this figure was adapted, the 38-77 group consists of 5 gene families with 38, 47, 57, 64 or 77 members. In contrast, there are 284 “families” with 2 members, 91 with 3 members, 42 with 4 members, 25 with 5 members, etc. This is clearer in the original figure:

Thus the larger gene families are outliers and there simply exists no gene families in B. subtilis with 20-37 genes (at least by the methodology of this paper).


What does it mean to "map the human genome"

So, the very first map of the human genome was of a few pooled samples with a single nucleotide called at each position.

This is basically okay, though, because humans are 99.9 (with possibly a few more 9s) % similar to one another. So you can get a lot of broadly-applicable information out of a single individual's DNA.

Further genome-mapping efforts brought data from new individuals and started to give us information about variants, like in your option 1b. At this point, there are projects like the 1000 Genomes Project that are trying to get 1000 full human genomes from a variety of ethnic groups sequenced and to characterize all the common variations.

Your point 2 was a different project, but was also part of mapping the genome. It's mostly complete now-- in that we know almost all of the RNA sequences that are produced by most cell types and mostly where they come from on the genome, with a few mysteries left around the edges.

Point 3-- no. Lots about the genome we still don't know. We're pretty good about where genes are encoded, but how they're regulated, how they interact... and remember that the part of the genome that codes for genes is a very small percentage of the overall sequence. Something like the the ENCODE Project is trying to figure out the various biochemical interactions present at every position of DNA, but even if that data were complete and reliable, which it's not, it still wouldn't tell us the "purpose" of all DNA.

So, when we say we've "mapped" a genome, we generally mean (A) we have (something pretty close to) full sequence of at least one individual's DNA (or a consensus sequence from a pool) and (B) we know where genes are on it. That's a huge step but only the beginning of understanding genetics. In the case of humans, we're adding on to that understanding by learning where variants are and how common they are.


Requirements for soil sample transportation over long distance

We did a soil sampling expedition around farms in the UK a few years ago.  We took with us some insulated plastic picnic drinks cool boxes, and a lot of pre-frozen camping freezer blocks.  We bagged up the soil samples, and put the bags in the drinks coolers with the frozen blocks.  This worked fine for our 48 hour trips.  If you were going for longer, you could try to arrange access to a rotation of frozen freezer blocks, or buy bags of supermarket ice along the way to top up the drinks coolers.  The idea for us was not to freeze the samples, but just to keep them cold enough that the organismal diversity was not changed too much during the transportation.


Would a shark whip into a frenzy from smelling its own blood?

I'm pretty sure, they can smell their own blood, but they do not attack themselves. Wounding a fish results in the release of chemicals into the water. This is a signal for other fish about potential danger and they will escape (Schreckstoff). Of course, the predator of the wounded fish will not mind. So this seems to work best within the same species. Fishermen and military have apparently used dead or rotten sharks in the past to keep sharks from attacking (Shark repellent). I guess, a similar mechanism plays a role here. Sensing a wounded member of the same or close species (including oneself), would block any feeding behavior.

The Myth Busters have actually done this (not very scientific) experiment: https://youtu.be/E1GenfKR9pk


Quantity of toxin release by pathogen in host

As I commented, a bolus is a single (often large) dose of a drug or compound given (released) all at once. Please read the very next sentence after the one you quoted:

  For example, the lethal and edema toxins of Bacillus anthracis disseminate within the host bloodstream and act upon both immune and nonimmune cells.

This gives an example of a pathogen releasing multiple toxins, although there are other pathogens such as Clostridium tetani which release a bolus that consists of only one toxin. So, it can be one or the other.


In the case of two healthy, viable identical twins, the separation generally occurs at the first division from one zygote to two cells. So they are equal partners in the split, not an original and a clone. During the first several cell divisions in the morula and blastula, there is no significant growth. So these divisions produce smaller and smaller cells. If one of these smaller cells is separated, it is very unlikely to be substantial enough to survive and implant in the uterus.


Is it possible to make bacteria vulnerable to antibiotics it's resistant to?

Perhaps it is useful to first consider how resistance is gained:

If you treat a population of bacteria with an antibiotic, some may die and some may live.

If none die, they are obviously resistant.

If all of them die, then all of them were sensitive, meaning that the size of the population and the variation were not large enough in order for some of the bacteria to be resistant. One approach would be to try to get larger genetic variation by inducing mutations with some mutagen. In addition, you can take a larger population. This would in effect let you sample a larger part of the genetic space to see if you can find a resistant strain. Of course it is possible that this will not work.

If some die and some are resistant, the situation is slightly more complicated. One possibility is that those which lived are genetically resistant (their DNA is different). To see if this is the case, you take those which lived and treat them again with the antibiotic. If they all live, they are resistant. Another possibility is that they are scholastically resistant. This phenomenon is known as bacterial persistence. What happens is that there is a genetic switch that randomly bestows resistance in some fraction of the population, let's say 10 percent. If you now take this population and reapply the antibiotic, only 10% of the population will survive. This interesting mechanism allows the bacteria adapt more quickly, since they do not have to make modifications to their DNA.

I am guessing that if the bacteria are genetically resistant, they will stay resistant. If the bacteria are scholastically resistant, it might be possible to affect the genetic switch which causes the persistence. This, in addition to reducing the size of the population, might cause a situation where none of the bacteria in the population are resistant long enough to survive.


Why can't pyruvate be used directly in the Krebs cycle?

Oxidative decarboxylation of pyruvate to acetyl-CoA by pyruvate dehydrogenase is coupled with reduction of NAD+, which can feed into the electron transport chain.
CoASH activates the acetate: hydrolysis of the thioester is thermodynamically favourable and drives the reaction catalyzed by citrate synthase.
Conversion of pyruvate to acetyl-CoA commits it to a subset of possible fates (including the tricarboxylic acid cycle) and is therefore a key regulatory step.

You can read more about this in most introductory biochemistry texts, like this one.

Also note that pyruvate actually can enter the TCA cycle via carboxylation by pyruvate carboxylase to oxaloacetate. This reaction requires energy in the form of ATP and is used to regenerate TCA cycle intermediates as they are siphoned off for anabolic pathways.


Is there a way to see what representations are currently displayed in PyMOL?

You can use "as" to switch to a particular style (http://pymolwiki.org/index.php/As
):

as cartooon, 11AS and chain a

You can also hide everything, to remove all representations (http://pymolwiki.org/index.php/Hide):

hide every, 11AS and not (n. ca+c+n and resi 5-10)

I'm a fairly expert user of PyMOL and I've never seen an API exposed which will show you what representations are being used. That's not to say that it doesn't exist, there are a variety of undocumented features and commands still.

The problem is it isn't as simple as ribbon,mesh.  Every single atom can be displaying any combination of representations, so as an API call or command, it would have to return the status of every atom in your selection. If the displayed representations are exposed somewhere they're probably in a very low level format like that, and not of use unless you're a programmer.


Is it fine to state every learned behavior has an innate component ? ie. Behavior X is largely/ mostly laerned with an innate component

Think of a cake. Is a cake determined by its ingredients or by its preparation (mixing, baking, etc)? It's a meaningless question. The cake is determined by both.

Now think of two cakes. In principal, we can now begin to talk about the causes of their differences. For example, if they had identical ingredients but were prepared differently, then we could say that the differences in the resulting cakes were due to different preparation.

Humans are baked cakes. Quantitative genetics is a field which tries to estimate to which extend differences between organisms are due to genetic factors. Learned behaviors are consistently found to be heritable in quantitative genetics studies. For example, adult vocabulary size is substantially heritable. It is not that the words are literally transmitted to the offspring, but rather genes that influence the cognitive abilities, interests and personality of the individual. That vocabulary size is "heritable" means that a substantial portion of the differences between individuals' vocabulary sizes are due to genetic differences (although by no means only due to genetic differences).

In short, what I'm trying to get at, is that you can only talk about the relative contributions of genes and environment if you're talking about it in the context of differences between individuals. In that case, yes, learned behaviors have an innate component.


Why are red blood cells considered to be cells?

A very good question, and it is most likely because of the last option.  It had a nucleus for part of its life. After the RBC jettisons its nucleus, it still remains very metabolically active for approximately 3 months.  It maintains its cell membrane integrity, it metabolizes glucose, it interacts constantly with its environment, numerous cellular functions and structure remain intact...  It is extremely specialized for a primary purpose, and no longer requires the nucleus to provide more proteins.  It has limited capacity to heal from injury, so it has a limited life span.

Speculation:  I wonder if it might lose the nucleus early on so that when it is destroyed in the spleen at the end of its life as RBCs are, the spleen macrophages are not overwhelmed with additional processing of nucleic acids?  Macrophage type cells are already working hard in there to clear infectious agents and some immune cells from the blood.


What happens to the mold spores we inhale?

Mold spores are capable of landing and becoming dormant. Unless conditions are severe enough, mold spores will not just simply die off; they will essentially wait for conditions to improve and once those conditions do improve, they will take root and grow. When it comes to the human body, it all depends on the type of mold and the overall health of the host. The body is designed with natural defense mechanisms - mucous, enzymes, beneficial bacteria, filaments, etc. - against airborne particles and microorganisms. Basically, you'll never know if a sneeze or cough - other forms of defense - saved you from a miserable existence as a mold host.

As for whether or not mold spores are expelled from the body, that is not so easily answered. Mold spores can sometimes teem in the millions, especially around a dense infestation (such as grain silos or a house that has structural mold rot). Research has concluded that farmers (who make up 30% of victims who suffer respiratory illness in the U.S. alone), for example, inhale up to 750,000 mold spores per minute. The odds aren't exactly in their favor when it comes to expelling mold spores simply by exhaling.

(I write for MoldBlogger, by the way. If you have anymore questions or are curious about other mold-related scenarios, feel free to check it out.)

Edit:

Here are some of the sources where a lot of this information can be read about.

National Institute for Occupational Safety and Health. Agricultural Safety. Centers for Disease Control and Prevention website. https://www.cdc.gov/niosh/topics/aginjury/. Published June 19, 2014. Updated December 15, 2014. Accessed February 1, 2017.

Glen H. Hetzel, et al. Farmer’s Lung: Causes and Symptoms  of Mold and Dust Induced  Respiratory Illness. National Agriculture Safety Database website. http://nasdonline.org/1853/d001796/farmer-039-s-lung-causes-and-symptoms-of.html. Published 2005. Accessed February 1, 2017.

Dennis J. Murphy. Agricultural Safety and Health: Farm Respiratory Hazards. PennState Extension website. http://extension.psu.edu/business/ag-safety/health/e26. Published 2017. Accessed February 1, 2017

Also, please feel free to check out a simple post that summarizes this type  of information: Occupational Respiratory Diseases: The Farmer, His Lungs, and Mold


What is the diameter of the measles virus?

I believe this paper answers your question or at least comes very close to it: https://www.ncbi.nlm.nih.gov/pubmed/6540797
I'll reproduce the abstract here, with emphasis mine to indicate the relevant portion:

The molecular length of measles virus RNA and the structural organization of measles nucleocapsids.
Full-length measles virus RNA molecules isolated from purified virions or nucleocapsids and examined by electron microscopy were 5.12(+/- 0.12) micron in length, corresponding to a molecular weight of 5.2 (+/- 0.1) X 10(6). Purified virions examined by negative staining in the electron microscope exhibited a pleomorphic range of particle sizes varying in diameter between 300 nm and 1000 nm. Purified nucleocapsids had dimensions of 21 nm (diameter) X 1254(+/- 7) nm (length) and a central core of diameter about 5 nm. Full-length nucleocapsids were composed of 204 (+/- 3) protein discs. The pitch of the nucleocapsid helix was calculated to be 6.1 nm and the helix angle, alpha, to be 8 degrees 16'. Approximate volume calculations indicate that each enveloped virus particle contains multiple nucleocapsids.

In case of unfamiliarity with the term "virion", see: https://www.britannica.com/science/virion
In case of unfamiliarity with the adjective "pleomorphic", see: https://en.wikipedia.org/wiki/Pleomorphism_(microbiology)


What is this brown insect with a large wingspan?

It is a moth from the Sphingidae family (hawk moths). They are generally large, robust and often have lobed wings (like the one in your pictures). I'm not closely familiar with this group of insects, and not with species found in the UK, but the individual you observed is very similar to e.g. Laothoe populi (Poplar hawk moth), which is also found in the UK.

(Laothoe populi, picture from Wikipedia)


What forms this pad on the side of the face?

That padding is apparently from a prominent zygomatic arch also known as high chickbones (pictures).

The bones between the eye, nose and ear are: the zygomatic bone below and behind the eye, the zygomatic process of the frontal bone above/behind the eye and the zygomatic process of the temporal bone, which extends toward the ear canal. It makes sense that when the zygomatic bone is more prominent, the zygomatic processes of the connecting bones will be also more prominent and appear as high cheeks.

Image source: Wikimedia, CC license

Here's the photo of Abraham Lincoln from the Wikipedia's article about zygomatic bones:

A Youtube video The Zygomatic Bones and Ogee Curve


Why does histamine cause bronchoconstriction?

Basics first: Crash Course

We will be introducing:
Autonomic divisions, Histamine and Vasoactivity (or Broncho-)
Starring: Innervation of the Lower Respiratory Tract

Lower respiratory tract is mostly innervated by the parasympathetic division, it has only scarce sympathetic-receptors there.

So, why it matters?

Autonomic divisions serve as fight-or-flight and rest-and-digest mechanism for the body as to respond for sudden changes.

You are having a good picnic, your body is in a state of rest. Your body is absorbing nutrient and enjoying your day. Blood isn't needed so much on your hands, or skin, or muscle.
This is the Parasympathetic Division

Suddenly a snake appeared in front of you, you scream, you panicked, and you flight away (or fight?). Your eyes dilate (where is that snake!), your muscles work, your respiratory tract dilates, as to prepare to avoid being killed by the snake. Blood rushs in to your muscles, but shunts on your digestion part, as what every you eat doesn't matter.
This is the Sympathetic Division

What matters?

Parasympathetic division only knows how to lock down things.
Sympathetic division can lock things, open things, and so, and so, and so.

How does sympathetic division work with so many things?
It has different receptors which reacts differently on input
Imagine people when reacting to clown: NOOOO and YAYYY

Histamine serves as modulation to outputs of autonomic division, directly or indirectly

Histamine is a broad-response chemical used to respond against an infection. As different cells have different ratio of autonomic division, it can cause dilation or constriction on different places.

One thing to note that, in a nutshell, histamine serves to buffer the work of autonomic innervation. It is entirely up to the regular function of the "autonomics" there to do their business.

Vasoactivity (or Broncho-) is achieved by state of balance between innervation by the autonomic division and local signals

Local signals play a part. A balance of signal determines the effect of innervation.
For bronchi, when histamine puddles, local signal sends stronger input than global innervation. Hence, the parasympathetic takes over.

  histamine-caused constriction serve in lungs during allergies

Histamine serves as to protect the lower respiratory tract from inhaled irritants. The lower respiratory tract is innervated by parasympathetic stimulation. Parasympathetic stimulation only knows one command: constrict and strike.
When histamine buffs up the signal, it constricts.

  vasodilator in other parts of body

Indeed it is. The vasodilation effect is achieved by GPCR-mediated sympathetic innervation.
Histamine buffs a diverse response of sympathetic division, hence dilates the blood vessels.

  Wouldn't it be more practical to vasodilate lungs so that white blood cells can arrive and toxins can be flushed more quickly

In line with WYSIGYG, vasodilation is different from bronchodilation (or constriction). We have noted above that the operators are different, and they serve different functions.

As a note, white blood cells can't just come anywhere they want. Ever seen your nasal mucus being very viscous? That will happen your lung when white blood cells arrive.
White blood cells also cause fibrillation, which succumbs people when does.

It has been a reason why pneumonia and lung-infection related diseases, tend to succumb people by drowning them in "their own mucus".

Another part of sending much things down your lower respiratory part is...
How could you clean the mess up?
The upper respiratory part is the defense capable of trapping irritants by mucus and send the mucus to your stomach.
Bronchus? Not so much. More mucus will eventually drown your lungs.

I invested 50 minutes for this.


What species of three-tailed flying insect is this?

Based on this list of mayflies of the UK, your mayfly is from the genus Ephemera.  Of the three species listed at that site for the UK, the closest match is to Ephemera vulgata, and it looks quite close.  The image of E. vulgata below is from Wikipedia here.


Recombination fraction( frequency) in Homozygotes

Welcome to Biology.SE

Your question stems from the confusion between measuring a recombination rate and the actual recombination rate.

In the A/A, B/B individuals you describe, recombinations still occur. Those recombination just don't affect linkage disequilibrium between the Aa and the Bb loci as there is no variance at those loci in the individuals you considered. There is therefore, no way to tell whether or a recombination event occurred in a specific case. You need genetic variance at both loci in order to have a linkage disequilibrium which can be affected by recombination. But it is not because you can't measure the recombination rate that recombinations does not occur.


If you're serious about this (and it appears you are), you'll benefit by starting with a Comparative Osteology book or webiste that discusses all the various characteristics of skulls that give you clues to exactly what you're dealing with.

This page on Amazon has a variety of such books. Pages such as this one begin with the basics and references help you to pursue the subject further.

On your specimen, although the missing teeth would be very helpful, important identifying features include the very large percentage of the cranium given over to the masseters, the eye socket placement, the size, the jaw shape, etc.


Can scientists create totally synthetic life?

In 2010, Dr. Craig Venter actually used a bacterial shell and wrote DNA for it.

Scientists have created the world's first synthetic life form in a landmark experiment that paves the way for designer organisms that are built rather than evolved.
(Snip)
The new organism is based on an existing bacterium that causes mastitis in goats, but at its core is an entirely synthetic genome that was constructed from chemicals in the laboratory.

Keep in mind, this is only a synthetic genome, not a truly unique organism created from scratch.  Although I am confident that the technology will become available in the future.  As has been pointed out, the entire genome wasn't built de novo, but rather most of it was copied from a baseline which was built up from the base chemicals with no biological processes, and then the watermarks were added (still damn impressive since they took inorganic matter and made a living cell function with it). But they are working at building a totally unique genome from scratch (PDF).
This is actually quite an emerging field, so much so that the MIT press has set up an entire series of journalsfor this.  As far as to the purpose of these artificial organisms, most research funded by companies are meant to be for specific purposes that biology hasn't solved yet (such as a bacteria that eats a toxic waste or something).  Although, a lot of people are concerned about scientists venturing into the domain of theology.
In terms of abiogenesis, there are many resources to learn more about this.  Here is a list of 88 papers that discuss the natural mechanisms of abiogenesis (this list is a little old, so I am sure that there are many, many more papers at this time).
I also found this list of links and resources for artificial life.  I cannot verify the usefulness of this since the field is a bit outside my area of expertise.  However, it does seem quite extensive.
EDIT TO ADD:  Now we have "XNA" (a totally synthetic genome) on the way.


Is there a good analogy that illustrates the difference between early DNA sequencing techniques and shotgun sequencing?

The public effort, led by Collins, relied on a physical map of each chromosome.  Very large pieces of genomic DNA were sub cloned into cloning vectors and used to create genomic libraries in cosmids, BACs and YACs.  The sub clones are ordered using hybridization probes from either known genes, or RFLP genetic markers. In this way a physical map of each chromosome was built up, and then the project would march down the ordered clones, sequencing the sub clones.  If the physical map is good then you have a very good idea of where the sequence comes from.

Shotgun sequencing, in contrast, involves randomly fragmenting the entire genome into small fragments (using sonication, for example), sub cloning those pieces and sequencing everything.

In the first method each base is sequenced a minimal number of times, whereas in the second approach each base ends up being sequenced many times (on average).

For a whole genome, shotgun sequencing requires an excellent computer algorithm to "assemble" the resulting data into overlapping contigs.


Can someone help me identify this insect

This guy looks very close to one of the variants of the very dangerous Triatoma.

I'm not sure what you should do in Canada about those guys, but in Brazil you should report them to your Disease Control Center. Triatoma has a very nasty bite and it can trasmit the Chagas Disease.

It is a bit weird to find this one in Canada - they are usually found in tropical places.


No, neurogenesis is not necessary for learning (assuming you are talking about adult neurogenesis: of course you need to generate neurons sometime in development to even have a nervous system).

Easily the most-accepted theory for learning and memory is that learning happens by changes in the strength of synapses, the connections between cells. The strengths of these connections are also often referred to as "synaptic weights." The primary mechanisms for this learning are long-term potentiation and the related spike-time dependent plasticity, as well as the guiding principle of Hebbian learning often stated as "cells that fire together, wire together."

Briefly, long-term potentiation or LTP describes the increase in post-synaptic receptors that occurs under certain conditions: this is what increases the efficacy or strength of certain synapses. One of the key conditions is that LTP tends to occur at synapses that causally contribute to making the post-synaptic cell fire.

Adult neurogenesis primarily occurs in a few localized area of the brain (Zhao et al.,
 2008). Although it is possible there is neurogenesis outside of these areas, it has not been demonstrated conclusively and is certainly not sufficient to be necessary for learning in a normal, uninjured adult brain.

Neurons born in the subventricular zone continually replace olfactory receptors, which have a relatively short lifespan, probably evolved due to their constant exposure to all sorts of potentially damaging external compounds entering the nose. These cells do have to undergo some "learning" processes to integrate into existing networks, but that isn't what you would colloquially think of as learning in general.

The best candidates for cells that actually impact learning to some degree are the new neurons born in the subgranular zone of the dentate gyrus in the hippocampus. The hippocampus is indeed an important structure for certain types of learning, but new neurons aren't necessary for this learning. Although it is still somewhat unclear what the roles are of the new neurons in the dentate gyrus, it is thought that they contribute to the primary roles of the dentate gyrus, which are to help distinguish between similar patterns of activity (Deng et al., 2010), also called "pattern separation."

Two other hypotheses are that adult neurogenesis helps to encode timing information in memories because the new neurons only participate in new memories, or that they allow for incorporation of novel stimuli once the older neurons have been conditioned and tuned only to stimuli that have been experienced before (Aimone, et al., 2013). There is evidence for all of these hypotheses but none of it is conclusive, and all may be true to some degree.

There are many different types of learning and these different types of learning can occur in different brain regions, most of which do not demonstrate any substantial adult neurogenesis. Often people think about associative learning with operant or classical conditioning. There is also episodic learning: remembering events that have happened (this is the type most closely associated with the hippocampus, where perhaps neurogenesis plays some role). There is also motor learning, and several types of learning in sensory systems like habituation or sensitization. Therefore, it is important to understand that learning isn't just one thing, and although the mechanisms can be related they are not always the same.

How to learn more: I can tell you about courses at institutions I have been affiliated with, but of course these could vary between schools. Learning and memory is usually at least part of a systems-level undergraduate neuroscience course, which is often the second of two overview courses in neuroscience. The most common time for students to take such a course would be as a second-semester junior or a second-semester first-year graduate student, because there is prerequisite knowledge in physics, chemistry, molecular biology, and physiology. There are also graduate-level courses in the molecular mechanisms of learning and memory, and theoretical neuroscience courses that cover the computational considerations of learning and memory rather than just the biological mechanisms. These types of courses might be available to a senior-level undergraduate as well.

Of course you can also read some of the review papers I have included here and follow the references they cite for original research, as well. The Aimone review is particularly readable and has some very excellent illustrations for a novice, and also extensively covers the regulation of neurogenesis by behavior and environment.

References

Aimone, J. B., Li, Y., Lee, S. W., Clemenson, G. D., Deng, W., & Gage, F. H. (2014). Regulation and function of adult neurogenesis: from genes to cognition. Physiological reviews, 94(4), 991-1026.

Deng, W., Aimone, J. B., & Gage, F. H. (2010). New neurons and new memories: how does adult hippocampal neurogenesis affect learning and memory?. Nature Reviews Neuroscience, 11(5), 339-350.

Zhao, C., Deng, W., & Gage, F. H. (2008). Mechanisms and functional implications of adult neurogenesis. Cell, 132(4), 645-660.


Can one conduct “novel” research without an advanced laboratory? Has it been done by school pupils?

I can point to two published papers in which students performed useful experiments.

The present study (on the vision of bumble-bees) goes even further, since it was not only performed outside my laboratory (in a Norman church in the southwest of England), but the ‘games’ were themselves devised in collaboration with 25 8- to 10-year-old children. ... They also drew the figures (in coloured pencil) and wrote the paper.
Principal finding ‘We discovered that bumble-bees can use a combination of colour and spatial relationships in deciding which colour of flower to forage from. We also discovered that science is cool and fun because you get to do stuff that no one has ever done before. (Children from Blackawton)’.

--Blackawton bees

As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate.

--Sequencing artifacts in the type A influenza databases and attempts to correct them
You'll notice that both of these projects were guided by "professional" scientists. The biggest problem with doing your own experiments is that you're very likely to simply repeat something that's already done, or else do something that's not useful or is trivial. It's very difficult even for professional scientists to have a reasonable grasp of even a very focused field of science, and for someone outside the field to try to understand what has and hasn't been done, and what is and isn't considered interesting, is nearly impossible.


Why doesn't human consumption of plants cause infectious diseases the way consumption of animals can?

If you mean if there are viruses, pathogenic bacteria or fungi that may cause diseases both in plants and in animals, the response would be that this is very unlikely (But even so, some fungi and bacteria could do it if some circumstances are given). This is due to some key factors:

First of all, the philogenetic distance between plants and animals is huge. Diseases transmitted by the consumption of animals are called zoonosis, and obviously it is more likely to catch a zoonosis by eating pork than eating shrimps or clams. While it's true that certain parasites have different hosts and use them to transmit themselves (for instance, many platyhelmintha uses mollusks or insects to spread themselves towards mammalian or avian hosts) parasites than have only one kind of host usually are adapted to live inside them, and they usually are unable to infect different organisms. Very few parasites can infect a human and a starfish, and even fewer can infect at the same time a human and a tomato plant.

Second, and related to the first, plant physiology differs completely from animal physiology. Plants usually defend themselves by their natural barriers (cuticles, cell walls), hypersensitive response (programmed cell death in order to limit the spread of a pathogen), isolation and/or outgrowing of the pathogen and accumulation of chemicals. Animals main mechanism is immune system. There are very different strategies and very few organisms can effectively avoid all of them at the same time. In the case of viruses, they would even have to face the fact that animals and plants have huge genetic differences.

Third even if they could, the pathogen will face competition against other pathogens that would be more specialized. Bacteria and fungi can be really hostile towards their microfoes, using a wide array of strategies. This hypothetical pathogen would be very unspecific, so they would have a hard time against more focused microbes. It should be noted, however, that unspecialized organisms usually have a great advantage if the environment have some perturbation, and they also are more resilient toward stress. Many plant pathogens are generalistic organisms that attacks when the plant is harmed or stressed. The same applies to many opportunistic infections in animals.

Despite all of this, there are some diseases that should be mentioned. Some fungi of the Clavyceps genera are plan pathogens, but they produce toxins than can affect the nervous system of animals, causing an intoxication called ergotism (the most famous of this chemicals is the lisergic acid, also known as LSD). Other fungi can produce toxins while they grow in plant tissue. Moreover, there are many fungi that can grow both in plant tissue and as animal parasites (mainly arthropods and nematodes), but in this case the plant pathogenesis usually occurs only when high fungal concentration is achieved or the plant is already damaged. While it's not a real infection, plant pathogens can cause allergic reactions. Finally, phytopathogenic fungi and some bacteria can cause infections in wounds or mucoses in individuals with a compromised immune system, but in this case the source seems to be the spores in the air.


What is the difference between optokinetic and vestibular nystagmus?

The vestibular reflexes are the main cause for stabilizing eye movements. The labyrinth canals in the inner ear detect changes in head direction, movement and acceleration. This is important for balancing body and visual field. These are fast involuntary reflexes thanks to almost direct connections between the sensory hair cells in the ear and the eye muscle innervating neurons.

The optokinetic reflexes are complementing the vestibular reflexes for slow movements or visual field motions independent of head movement (source and further reading). It needs the visual input.

In my studies we actually did this experiment ourselves, measuring the eye muscle activity while rotating with opened or closed eyes. The results were basically the same in both conditions. With opened eyes you try to fixate something in the moving image for longer and have therefore larger jumps in the eye movements, but with closed eyes the saccades are still there.

Edit: The two senses can also be in conflict with each other. For example reading a book in a car (your vestibular system detects motion, while your visual field is steady) or watching a movie in the cinema (your visual system detects motion while your vestibular system doesn't). This causes motion sickness.


Isolating a specific gene (specifically TRAV* series of genes) for sequencing

Restriction enzymes are usually only used when you do molecular cloning using plasmids or other forms of shorter DNA moleclues, since - like you said - using them on genomic DNA would cut it into much more than thousands of pieces.

Instead what you can do is perform your PCR directly on the genomic DNA (or potentially cDNA, if you want to get rid of introns).
Doing PCR on genomic DNA is often a bit tricky (i.e. you'll likely have to try different conditions to get a product), but generally possible. If you want to analyse the whole coding region it might be better to extract mRNA instead of DNA and reverse transcribe it, so that can amplify the coding region as one block, that doesn't contain Introns - PCR on cDNA is also easier than on genomic DNA.

Another thing you need to look out for is that T-Cell-Receptors (similar to antibodies) are different in every T-Cell. This means that you can't use Sanger sequencing, which will only give you a proper result if you input has the exact same sequence. To get the sequences of a mix of T-cells you would need to use next-gen sequencing.


This appears to be a Gastropacha Quercifolia, the Lappet Moth.

    It is found in Europe and Northern and Eastern Asia.

    The wingspan is 50–90 mm. The females are larger than the males. The moth flies from June to July depending on the location. Source