What is the role of CRISPR-dCas9 in gRNA-dCas9 transcription regulator complexes?

so why can't the transcription factor be fused with the gRNA instead,
  so that it can directly affect transcription when the gRNA forms
  complimentary base pairs with the target gene, instead of it being on
  a passive dCas9?

The main reason for that is that both the gRNA and the dCas9-TF (transcription factor) combination can (each) be encoded genetically, while a combination of a gRNA with a transcription factor could only be generated chemically.

The possibility to genetically encode the dCas9-TF + gRNA unit allows one to:
a) use established methods for transferring DNA into cells,so that the cells make the Cas9 and the gRNA by themselves and
b) generate cells that will stably express the whole unit (dCas9-TF + gRNA) forever.

Neither of these options would be possible with a chemically linked gRNA-TF (which is also much harder to make for molecular biology labs that don't have the proper chemistry equipment).


Very carefully.  First remove the stinger, the rest is relatively easy.  In your video, you see the fox quickly bite at the stinger, then back off.  Over and over until the scorpion's abdomen was loose as a rag, unable to launch the stinger at 3:08 minutes.  3:32 - you can see the stinger is almost off.  3:40 - stinger gone, she can now eat it more calmly.


Does Human Female Meiosis II occur after fertilization with sperm?

Primary oocytes are formed prenatally and reain suspended in prophase of meiosis I for years until the onset of puberty. An oocyte completes meiosis I as its follicle matures (during ovulation) resulting in a secondary oocyte and the FIRST polar body. After ovulation, each oocyte continues to metaphase of meiosis II. Meiosis II is completed only if fertilization occurs, resulting in a fertilized mature ovum and the second polar body.

So in short, the egg is stuck in metaphase II until fertilization.


Want to know which insect it is? I often found it in washroom. Is it dangerous and how to control it

That is a house centipede, Scutigera coleoptrata https://en.wikipedia.org/wiki/Scutigera_coleoptrata
They are harmless, unless you are a cockroach or termite. People find them unpleasant and creepy, because they run fast, but they are predators that prey on pests in your home.
https://www.familyhandyman.com/pest-control/heres-why-you-should-never-kill-a-house-centipede/


Can methylation of a promoter induce gene expression in some rare cases?

There is nothing intrinsic to DNA methylation itself that requires it to repress transcription. Simply, it affects sequence recognition by proteins. CpG methylation can prevent transcription factor binding and/or recruit proteins that inhibit transcription, either competitively or through chromatin condensation. This is why it's generally associated with transcriptional repression.

I have found some articles which describe methylation in intergenic regions and introns activating transcription but, since you're asking specifically about promoters, I'll limit the examples to methylation in the 5' flanking region. Please note that I'm grossly oversimplifying these articles, you should actually read them to get the full picture.

Bahar HK, Vana T, Walker MD. 2014. Paradoxical role of DNA methylation in activation of FoxA2 gene expression during endoderm development. J Biol Chem 289(34):23882-23892

This study reports that, during development, high levels of methylation of a CpG island in the FoxA2 promoter is present in expressing tissues and absent in non-expressing tissues. Their hypothesis is that CpG methylation prevents binding of a protein that represses transcription by condensing chromatin through histone modifications.

Hantusch B, Kalt R, Krieger S, Puri C, Kerjaschki D. 2007. Sp1/Sp3 and DNA-methylation contribute to basal transcriptional activation of human podoplanin in MG63 versus Saos-2 osteoblastic cells. BMC Mol Bio 8(20)

Here, PDPN expression was associated with CpG methylation. They hypothesize that methylation could affect chromatin state or recruit, what they term, a methylation dependent factor, which activates transcription.

Niesen MI, Osborne AR, Yang H, Rastogi S, Chellappan S, Cheng JQ, Boss JM, Blanck G. 2005. Activation of a methylated promoter mediated by a sequence-specific DNA-binding protein, RFX. J Biol Chem 280(47):38914-38922

This study describes a DNA binding protein (RFX) that can recognize and activate the methylated promoter of MHC. They suggest that RFX can competitively inhibit binding of methyl-DNA binding domain proteins that condense chromatin.


Open Reading Frames vs Coding Sequences (CDS), are they different?

I (mostly) like the definitions given on this page.

An ORF is a sequence of DNA that starts with start codon “ATG” (not always) and ends with any of the three termination codons (TAA, TAG, TGA). Depending on the starting point, there are six possible ways (three on forward strand and three on complementary strand) of translating any nucleotide sequence into amino acid sequence according to the genetic code. These are called reading frames.
The Coding Sequence (CDS) is the actual region of DNA that is translated to form proteins. While the ORF may contain introns as well, the CDS refers to those nucleotides (concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery.

However, I do not entirely agree with this statement:

In Prokaryotes the ORF and the CDS are the same.

While it’s true that all CDSs are within ORFs, not all ORFs are CDSs. You can have ORFs that are transcribed as noncoding RNA elements, and ORFs that are not transcribed at all. CDS refers specifically to the ORFs whose post-transcriptional fate is to be translated.


Why do parasites sometimes kill their hosts?

I can think of several (non-exclusive and probably non-exhaustive) hypotheses:

Maladaptive. It is maladaptive. Maybe because it is a virus coming from another species (e.g. SIV and HIV) or because it is not adapted to our modern lifespan.
Benefit of the host immune system to the parasite. Some parasites might benefit from host immune defence (e.g. sneezing helps bacteria to spread) and death is a consequence of the selection for increasing disease symptoms to the host.
Pathogen's and host's fate. The pathogen's fate is not linked to the host's fate. This is especially true if the pathogens spread well (easily jump from one host to another) I guess or for parasitoïd because the pathogen leaves its parasitic life after the death of its single host.
intra- and inter-host selection. Among hosts, there might have a selection for reducing resource consumptions and therefore for decreasing the probability for the host to die. But within a host (among individuals of a parasite population or even among parasite species), it is a prisoner's dilemma (tragedy of the commons). The more you invest in foraging, the more competitive you are. This might not be adaptative at the population level but it is at the individual level. We might think of this prisoner's dilemma happening among individuals of a single parasite species or among several parasite species. You may want to have a look at the work of Martin Nowak on the subject incl. Consider for example his book; Evolutionary Dynamics.
Consequence of harming on trade-offs. Harming an individual will cause him not to spend energy into reproduction in order that more energy is available for the pathogen use. Moreover, by causing symptoms, the infected individual will be sexually less attractive and will again have less opportunity to spend energy into reproduction.
The pathogen does not mean much harm. When fighting pathogens, many of the symptoms we experience (such as fever typically) are actually caused by the immune system and not the pathogen itself. A maladaptive overreaction of the immune system can cause our death.

The book Why we get sick by Randolph Nesse and George Williams, will probably interest you.


How is in-vitro fertilization technically achieved?

After following user David's hints, I have collected some videos that answer the questions I posted:

Regarding to needle manufacturing, there exist machines able to create micropipettes (this is how the needles are actually called) by heating glass cilinders and pulling them to create very thin tubes (capillaries). Click for featuring video.
Regarding to the high-precision manipulation, technicians use mechanical devices able to convert macroscopic motion (eg: human manipulation) to microscopic motion (eg: using reduction gears). Click for featuring video.
Regarding to how they keep the egg still, technicians use another type of pipette that slightly "sucks" the egg in a vaccuum-cleaner style. For a full-feature video of how the egg and sperm are manipulated, check this video out.


Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?

I have found that biogps.org has all expression data I need:

https://biogps.org

https://biogps.org/#goto=genereport&id=7015


Why does plasma protein saturation of a drug increase its volume of distribution and clearance rate?

First a couple of clarifications:

You wrote:

For the distribution volume to increase, unbound drug concentration in plasma should stay constant while tissue drug concentration has to increase when more drug is administered.

Actually, it is the total drug concentration in plasma (bound plus unbound) which matters while calculating distribution volume.

Clearance is better defined as $ \frac{\text{Rate of elimination}}{\text{Plasma concentration}}$. The equation you mentioned above is a derived formula for calculation of dosing rates.

Now for the answer. The basic principle is: when plasma proteins get saturated, increasing drug concentration increases both tissue concentration and unbound drug concentration in plasma, because the drug has "nowhere else to go".

Thus your reasoning is correct when you say this:

The reason why volume of distribution increases is because the drug is distributed to tissues other than blood once the plasma proteins are saturated with the drug.

Of course, our understanding here is that the increase in total plasma concentration is marginal as compared to the increase in tissue concentration.

However, the following does not seem to be correct:

As for clearance rate, it increases because the zeroth order reaction is always faster than the first order reaction in Michaelis-Menten kinetics.

(Perhaps you are confusing plasma proteins with drug metabolising enzymes?)

The answer to the clearance part can be obtained when you recall that we are talking of a drug with low hepatic extraction ratio. Thus, clearance is proportional to unbound drug concentration. As already mentioned above, unbound drug concentration increases on increasing drug concentration.

Hope that answers your queries.

Reference:

Buxton ILO. Pharmacokinetics: the dynamics of drug absorption, distribution, metabolism, and elimination. In: Brunton LL, Hilal-Dandan R, Knollmann BC (editors). Goodman & Gilman's the pharmacological basis of therapeutics. 13th ed. New York: McGraw-Hill Professional; 2017. pp 13–29.


Regarding the difference between cDNA library and RNA sequencing (Biochem. technique)

The construction of a cDNA library involves making a DNA 'copy' of the mRNA because the aim is to synthesise a large set of recombinant plasmid molecules, each containing a different cDNA and each propagated in E. coli.

The heyday of cDNA library construction predates the invention of PCR.

The key difference between the two approaches that you are comparing is that one (cDNA library) involves creation of a physical representation of the expressed genome whereas the other is an informational representation.


Some theories:

Dead bodies died of something. In the earliest ages these were generally infection. Burying them protected us from something that could kill us too. This is also why we would be evolutionarily programmed against cannibalism
They make great fertiliser. Burying waste, dead animals etc resulted in the growth of plants etc which not only food we could eat but animals that would then eat the plants we could kill and eat.
Dead bodies are unpleasant. They stink and so we would want to get rid of them. Also they would attract carnivores which are likely to target humans too

All these would be evolutionarily advantageous so any cultures practising burial would be likely to survive and pass on those customs. Whether this is genetic, that's open to debate because I'm not sure.


This appears to be an inch-worm, the larval caterpillar stage of a moth (order Lepidoptera) in the  Geometridae family. According to Bugguide (my emphasis):

  Larva - generally have only two pairs of prolegs (at the hind end) rather than the usual five pairs in most lepidoptera; the lack of prolegs in the middle of the body necessitates the peculiar method of locomotion, drawing the hind end up to the thoracic legs to form a loop, and then extending the body forward.

The systematics/taxonomy of this group is unclear, debated, and in flux. However, the majority of stick-like larval forms I could find seemed to be associated with the current Ennominae subfamily, which is also the largest of subfamilies in this family of moths.

Müller et al. (2019) just published the 6th volume of "The Geometrid Moths of Europe", which might be a good starting point for IDing this specimen more precisely. A book description from NHBS:

  More than half of the European Ennominae, a total of 181 species, plus 21 new species for the European fauna are covered in two hardback parts (with text and plates in separate volumes), including difficult genera...

You could also keep an eye on or alternatively submit an ID request over at Wildlife Insight's Illustrated Guide to British Caterpillars.


Why are nucleic acids negatively charged at physiological pH?

The phosphate group/s present in the mononucleotide or nucleic acid result in the structure having an overall slightly negative charge.

Positively charged proteins that are also present in the cell such as histones help to keep the negatively charged nucleic acid stable 'in vivo'.


Is it possible for humans to digest and live on food that isn't based on DNA or RNA?

This might be flagged for being somewhat of a subjective question, but to survey human diet:

Mnemonic SPONCH can be used to sum up the necessary building blocks of life, in the elements Sulfur, Phosphorus, Oxygen, Nitrogen, Carbon, Hydrogen. There are others, trace elements, which are necessary and come from diet (selenium, for example). These elements are used in building our biological macromolecules: Carbohydrates, lipids, nucleic acids, and proteins. The molecular interactions between these macromolecules, their cofactors, etc. are essential for life. Some of these compounds, however, can't be made in the human body from scratch; hence essential amino acids, and the necessity to consume foods which provide metals, carbohydrates, fats/triglycerides, etc.

So, at this point our body is optimized to incorporate terrestrial foods. Sometimes, though, we can see that the body will sometimes accept analogs to normal compounds, although this is often to disastrous effect (like chemotherapy in cancer). The real question, then, would be: does said extraterrestrial food compose of necessary biological elements or analogs in a way our body can actually use this food for sustenance? That, however, is 100% speculation as we have no reference in even a single case to base our assumptions.


Are ribosomes assembled in rough ER and Golgi body, or in the nucleolus?

Ribosome assembly starts in the nucleolus (of eukaryotes) and finishes in the cytoplasm. However, in the cytoplasm the Golgi apparatus is certainly not involved, and, as some cells have little rough endoplasmic reticulum, assembly does not require that. Thus, the abstract of a review by Fromont-Racine et al. in Gene (2003) vol 313  pp. 17–42 starts with the statement:

  Ribosome synthesis is a highly complex and coordinated process that occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.

In the 26 pages of this review there is not a single mention of the words ‘endoplasmic reticulum’ or ‘Golgi’.

A more recent (and freely available) review by Thomson et al. in Journal of Cell Science (2013) vol 126  pp. 4815-4820 is in accord with this. It has a pretty poster insert which presents the assembly as a succession of events, starting in the nucleolus, proceeding to the nucleoplasm, and with some final polishing in the cytoplasm.


How does natural selection affects seasonal polyphenism in animals?

[H]ow can it be that natural selection "favors" a particular coloration during winter and summer?

Camouflage for example. In regions, where it snows some animals would take advantage to have a fur colour that match the substrate in which they live and they may therefore be selected for having a white fur in winter and a non-white fur in summer.

Consider for example Lepus lepus in summer

vs in winter

  How can it be proved, that these animals change their coloration because it is useful for them?

There are a whole lot of possible experimental design.

Considering seasonal coat colour in response to predation, a simple and obvious approach would be to experimentally dye the individuals and see how their survival varies depending on the colour they have been dyed.

Sometimes, you may have a sister clade that is non-plastic which it might be of interest to test against (depending on the exact question at play).

  I'm more interested in ecological impact on coloration [..] I'm looking for the articles providing evidence

Cases of local adaptation (such as Hoesktra 2006 for example) or other evidence of natural selection on coat colour such as differential selection among lineages are probably way more common. But if you are specifically interested in seasonal variation then, here are a few papers I could find with a quick google scholar search showing selection on seasonal variation for fur colour.

Zimova 2013 and Zimova et al. 2016 in snowshoe hares (which is listed in the wikipedia article)
Turner 1961 in pastry larvae
Maybe Ornborg et al. 2002 on blue tits


In transcriptome (RNA-Seq) libraries, unmapped reads are reads that fail to map to known exons. More often than not, they represent genomic DNA. RSeQC has tools to help identify genomic (also sometimes called intergenic) sequences.

For the most part, the percentage of unmapped reads just provides you with QC information, like how much gDNA you purified along with your mRNA. It's unlikely to be very useful beyond that, but it really comes down to what you're looking for in those sequences.

If you're doing DNA-Seq, then unmapped reads generally represent reads that failed to map unambiguously to known sequences. This will depend on a threshold (usually provided by the user) for alignment stringency.


Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?

There is very interesting work in this regard done by Ed Marcotte. An overview of the "machine" and its conservation across species is here. The point here is the machine or network is conserved, but used in different ways in different organisms. Hence, the phenotypes of mutants might be different, but they'd be consistent across many variants in the components of the machine.

One paper of his describes a tool, which uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. This is available at www.functionalnet.org/RIDDLE.

Look at their approach to prioritizing candidate disease genes by network-based boosting of genome-wide association data.

Some specific examples of the conserved "machine" are given in this elegant PNAS paper. It is nice how they tested the genes in Xenopus embryos.


Does artificial high intensity light damage permanently dark ecosystems?

I don't know how harmful the exposure to a camera flash could be to organisms that live in complete darkness. However, since the animals that live in this conditions are usually blind, and the time of exposure is quite short, it's reasonable to assume that the damage produced should be minimal.

In the case of caves, permanent artificial illumination is very destructive to the environment, but the effect is due mainly to temperature changes and the introduction of organisms coming from more illuminated parts of the cave (cave organisms are usually slow and react poorly to light, so they are an easy prey if they're under light). In fact, for tourist activity, the use of lanterns or miner helmets is highly recommended.

In the case of abyssal ecosystems, ecological invasions are less likely, since there still exist a vertical barrier based in temperature, oxygen and carbon dioxide concentration and pressure. However, in this ecosystems there exist many animals which are very sensitive to light, due to the prominence of bioluminescence. Some of this animals could be damaged by the kind of light you describe. However, it's very unlikely that the main functioning of this ecosystems could be affected because of its extensive size. Moreover, the low population densities it has implies that even very long submersions would encounter only a few samples (with the exception of volcanic vents and some other geological curiosities which, in fact, are even more isolated from the rest of the biosphere by physical and chemical barriers), so the global effect should be negligible.


Book on current state of knowledge on the genetics of intelligence

A very recent review has been written on this. See

Plomin, von Stumm (2018): The new genetics of intelligence.

For some of the latest genome-wide association studies, see:

Hill, et al (2017): A combined analysis of genetically correlated traits identifies 187 loci and a role for neurogenesis and myelination in intelligence.

Savage, et al (2017): GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence.

However, as Robert Plomin and Sophie von Stumm report, newer genome-wide association studies are on the way which account for a larger portion of the variance. So there is constant progress at the moment.

If you're interested in the neuroscience aspect of intelligence, I recommend Richard Haier's book The Neuroscience of Intelligence.


What is a good source that will help me classify protists?

While not comprehensive, the Portal to Protistology has many resources for exploring the diversity of protozoa. I especially recommend their videos that are really fascinating, focus on distinguishing features of different protists, and may be helpful for identification to some degree. But given your interest you should just explore all the pages on the site, check out the books they recommend (e.g. the Illustrated Guide to Protozoa), and see what is useful for you!


Plants do not need CO2 for survival. They need it just for photosynthesis; if you supply them with alternate carbon source such as glucose then they would survive (See here for non-CO2 Carbon-source utilization). There are non-photosynthetic plants which are totally dependent on carbon sources other than CO2; some are carnivorous like venus fly-trap.

I am not sure what you intend when you correlate leaf thickness to CO2-dependence. Leaf morphology can affect photosynthesis rates but afaik there is no relationship between leaf morphology and CO2-dependence.

  can we conclude that the plant species that are more dependent on
  CO2 levels, would benefit from the greenhouse effect

Greenhouse effect is not equivalent to increase in CO2; increased CO2 levels can cause greenhouse effect which is a physical phenomenon of entrapment of IR radiation.

CO2 is fixed by an enzyme called Rubisco; like most enzyme catalyzed reactions this will reach a saturation limit i.e. addition of more CO2 will not increase the rate of photosynthesis. However the rate of photosynthesis is limited at the Rubisco step because of low levels of CO2 (See here) and it can be expected that most photosynthetic plants will be benefited by increase in CO2. However, not all plants would be resistant to increased temperatures and moreover the rate of enzyme catalysis would also change with temperature. So it is not that easy to predict.


In this case there are two properties that determine the behaviour of RNA:

Its polarity;
Its acidity.

Because of its polarity, RNA tends to escape the phenol-clorophorm phase; actually, it can go into the aqueous phase even if the pH is neutral [1], but with a lower efficiency than if the pH is acidic. Here comes the second property, RNA acidity. Because of that, when RNA is in a neutral solution, it has a negative charge: the $-OH$s of the phosphate group dissociate to $-O^-$ and $H^+$. However, this does not happen in an acidic solution, where there are already too many $H^+$. Thus, at basic pH the $-OH$ groups are intact and have a neutral charge; this stabilizes the system.
Think about it: if the aqueous phase is at neutral pH and fills up with negatively charged RNA molecules, after a while no more negative molecules can enter that solution. On the other hand, if the RNA molecules that enter the aqueous phase stay electrostatically neutral, the number of molecules which go into the solution will be limited only by the availability of water molecules to dissolve them.

That is why you use acidic* pH, it is simply a matter of efficiency.

Disclaimer: This answer is based upon a comment by the OP under the OQ.

[1] You would never use a high-pH solution to extract RNA because such condition hydrolyses RNA.


This isn't my field, and I'd love to see my answer surpassed by someone with expert knowledge.  But I should say a recent case report (Pantazis, 2016), though it dealt with an unusual situation, discusses some of the current thinking:

hypothyroidism is characterized by decreased synthesis and degeneration of collagen. Hypothyroidism also inhibits epimerase, which results in reduced chondroitin sulfate and elevated hyaluronic acid, hence weakening the matrix. Moreover, it causes accumulation of glycosaminoglycans (GAGs) in the extracellular matrix (ECM), being involved in the pathogenesis of carpal tunnel syndrome during hypothyroidism and predisposing patients to tendon calcification

THs have known effects at the cellular level on the proliferation and differentiation of bone and cartilage. The hypothyroid state appears to induce abnormalities in these tissues, which results in such clinical manifestations as epiphyseal dysgenesis, aseptic necrosis, possibly crystal-induced arthritis, and an arthropathy characterized by highly viscous non-inflammatory joint effusions primarily affecting the knees, wrists, and hands. Neuropathic and myopathic symptoms accompanying hypothyroidism may manifest as joint region abnormalities when in fact there is no underlying arthropathy.

These paragraphs cite three much older sources.  I don't see a tremendous amount of activity on this narrow issue in PubMed - the broader issue that this case illustrates is whether there are better ways of diagnosing and treating hypothyroidism to restore the balance more effectively; see Midgeley, 2019 for example.


I'm sure there are lots of ways of handling this, but there are only 20 of them (more or less).  I really wanted to figure out how the amino acids resulted in the resulting protein structure.  So I started to break them down into categories.  The categories cannot draw boundaries exactly since one amino acid might belong to several categories in a unique way, but it starts to give you a sense of what the sidechains do.

  Aliphatic : G A L I V M P
  Aromatic : F Y W H
  Polarizable : F Y W H M C R
  Polar: S T Q N D E K C
  Small: A S T G C
  Large : F Y W H R K
  Strong Structural variation: P G

you still have to memorize them eventually, but you can make it easier to put them in categories and in these groups its easier to bring them to mind.


Is the function of adjacent genes correlated?

In bacteria, this is often true.  This is because more than one gene is often transcribed onto a single RNA.  This grouping of genes is called an operon.  It is usually true that these have a related function because they are being translated to protein in very much the same proportion - a convenient way to regulate the function as a whole.

Once you get into eukaryotes this is no longer true (except for v. rare cases most of which are viral genes), one mRNA transcript contains just one translation region.  This is true even for yeast and other single celled organisms.  Gene regulation can be correlated, but the relationship on the genome has little to do with it.

There is some importance to the genomic relationship of two genes because of the crossing over that occurs in meiosis, but this is more of a relationship that is important in speciation and evolution, it doesn't have any recognized importance to how the genes act within the eukaryotic cell.


Is "cell proper" considered a biology term / well defined concept?

This isn't a special biology term, it's just an English usage thing. "The X proper" just means "the X, strictly speaking". As well as the question you quote, see also this question on ELU.SE. I would expect this use to be understood by many biologists who speak English as a first language, but there are certainly clearer ways of saying it.

Regarding this particular example, the author appears to be proposing a way of defining a vacuolated plant cell. It sounds like he is proposing a definition that excludes the cell wall, but he confusingly calls the cell wall the "(cellulose-)membrane" (the 'primordial utricle' is the cytoplasm, I think). However, I am afraid I am not an expert in the history of plant cell biology and can't really comment on whether it is a useful contribution to, or synthesis of, the state of knowledge at the time.


What species of ant is this, and is it a queen?

This ant looks very much like a Camponotus pennsylvanicus queen, but since it was found in a Belgian forest, I could be wrong. I am almost certain it is a Camponotus species though. I hope I could have been helpful to you!


How do nuclear membranes form during Telophase of Mitosis/Meiosis?

According to this book, during disassembly of the nuclear envelope, the nuclear membranes are broken down into vesicles. The nuclear membranes reform at the end of mitosis as the vesicles bind to the surface of chromosomes and fuse with each other to form a double membrane around the chromosomes (how this happens is not clear, except that integral membrane proteins and lamins may be involved, but physical contact is supposedly the first step).


If one of eyes is blind, can that eye still feel pain?

Blindness can be due to a damage of the lens, retina, optic nerve or the visual area at the occipital lobe of the brain, for example.

Sensitivity of the eye cornea is enabled by a different nerve - the ophthalmic nerve, which is a branch of the trigeminal nerve (Yale Journal of Biology and Medicine). As long as this nerve, somatosensory cortex at the parietal lobe of the brain and other neural structures involved in pain sensation are intact, you should be able to feel pain when touching the cornea of the blind eye.


How does the brain fake itself into hearing our own sounds even when we are not speaking?

Our brains treat 'talking to ourselves' very similarly to talking to others. There's a small amount of evidence in studies to suggest that when we talk to ourselves, it's like verbalising the speech out loud.

Before you speak out loud, the part of your brain responsible for creating speech copies that information, and moves it the appropriate verbalising areas of the brain. However, at the same time in a process called efference-copy, it also copies it to the area of the brain responsible for listening to sounds. This process overall means that our brains can distinguish sounds that come from ourselves, and sounds that come from other people.

This also partially goes to explain why people with schizophrenia have difficulty recognising their own internal voices as 'own'. It's likely that this process has gone awry in these people, meaning they're not able to recognise their internal voice as themselves.

Here's a link to some research done in Sydney on this matter.


It would be simpler to simply activate telomerase genes or insert them using some vector virus. However, telomerase is a key component in the process of tumoral transformation. Basically, if you don't let cells die they will stack mutations until they become tumoral.


Will neurons live after the death of a human? If so, how long?

I think that depends somewhat on how the human dies - in particular on the conditions. If they die in a very cold environment (say at the top of some icy mountain range), they'll freeze and metabolic processes will slow down considerably, and so will cell death. But such hypothermia-based slowing down is a special case. Normally, if your heart stops or you are not getting oxygen to your brain (perhaps due to a stroke), your neurons will start dying pretty quickly. Within many minutes there will certainly be considerable permanent cell loss - certainly within hours. If oxygen is significantly depleted, ATP production will also significantly drop. If this happens, the various ATP-dependent processes will slow to a crawl (including the Na/K ATPase and other ion pumps and channels that are needed for maintaining and changing the voltage difference between the inside and outside of the cell). This in itself is bad enough as a lot of the enzymes and mechanisms that are dependent on the voltage difference will fail (and probably enough of a reason for many cells to start dying), but one of the effects of this is apparently an increase in the extracellular glutamate, which ultimately leads to (via NMDA receptors for example) an influx of calcium ions into the neurons. Too much of the calcium ions is once again toxic for a variety of the processes inside the cell and is an additional and big reason for neuronal cell death.

In short, as far as I know, neurons don't have a good time living without sufficient oxygen and therefore after a typical human death.


What kind of spider is this (reddish spider)?

This most likely is Microlinyphia pusilla. Note that this is a male, females look quite different. A picture that closely resembles yours can be found here

https://www.ispotnature.org/node/402405

And in case you want to know, the Dutch name is 'kleine heidehangmatspin'


Why are there different gene expressions that are refered to the same gene in microarray experiments results?

What you are looking at there is a microarray dataset (see the description here).
Microarrays are chips that have many sequence specific probes on them and sometimes they have multiple probes for the same gene.
Readout differences between the probes of the same gene could be caused by either noise in the data or biological effects like expression differences between transcript isoforms - other reasons could be possible as well.


Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?

Both the DNA and the RNA polymerase complexes moves along the DNA molecule like it was a track. While the new mRNA is big, it would never be as big as the whole genome, so the reference point is the DNA molecule. Plus, the functioning of the movement of this enzymes is quite similar to other proteins that move "climbing" long polymers, such as actin polymers or microtubules.

One of the theoretical models that describes the movement of this kind of proteins is the model of rectified thermal diffusion, based on Richard Feynman's idea of the Brownian ratchet. A Brownian ratchet is a device that allows the conversion of Brownian random movements into a directional force.

http://en.wikipedia.org/wiki/Brownian_ratchet

The polymerases consume ATP, which enable them to suffer cyclic conformational changes (one change per ATP consumed), which allows the complex to attach to the molecule and detach. Once the complex has detached, by simple diffusion it moves in a random direction. Then, it attaches again. If the movement has occurred in the right sense, it will stay where it ended, while if it has gone in the wrong sense it will return to its previous position. As only a few movements are allowed, the complex will only move in that sense, even if the motor force is random.

I don't know exactly what conformational changes occurs in the RNA polymerase, but this general process seems to apply to almost any motile protein, including those enzymes that travel across polymers. Since the motor force is simple diffusion, and since the mRNA molecule doesn't need to "travel" with the polymerase (it just floats joined to it, but doesn't "pull"), I think there isn't any trouble with this.


That mushroom is from the Boletus family with sponge gills. A Red Cracked Bolete.

Only one sponge gill toadstool neighbor of the boletus family mushrooms has ever been know to kill a single person, or require a liver transpant, because, if you get an amanite wrong, you can survive, but only with a liver transplant. It is said that: if you found an Amanite, and put a triangle of it in your mouth and spat it out, it may taste fairly scary, but it will not kill you or even make you vomit or Hospitalizeded, although you may experience some discomfort, as long as you spit it out entirely and not swallow it.

In temperate climantes, The only boletus that are quite noxious are the red and beige ones which sometimes smell ghastly are in the family of the devil's bolete. There are other boletes that can make you vomit or ill, i.e. some blue and yellow ones. some boletes are strange and interesting such as the pepper boletus which can be used to flavor a dish because it produces very hot pepper flavor same as capsiacin.

Your mushroom is clearly a Red-Cracked bolete, which make sludgy, insipid soup, they have no texture, gelatious, flavorless, are extremely common, have yellow gills changing to blueish grey, and small red cracks often appear in the top which has the habit of cracking when ripe, hence the name, red cracked bolete. it is harmless and quite a waste of time to cook. https://www.google.fr/search?q=red+cracked+boletus&num=100&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiWn7Ljg9fVAhXDJlAKHe-HADwQ_AUICigB&biw=895&bih=530

The only boletus: sponge-gill toadstool (tail and cap) mushroom ever implicated for someone's death (by artery malfunction in the gut) was a woody tough red one related to boletus satanicus: https://en.wikipedia.org/wiki/Rubroboletus_pulcherrimus

Anyone trained biologist who can identify species from books, has a good chance of never falling ill from Boletus species, as long as he makes very positive identifications of mushrooms that don't have potential deadly or noxious look alikes. many mushrooms like the death cap are particularly deadly because they can be mistaken for small farm agaricus in field edges. especially angel of death and Panther-Cap, which smell of humus, earth, and apples.

The main identifier on a red cracked bolete is the squishy texture, not fibrous, and the velvet. dryish, textured large sporing body which starts as pine colored and matures to olive or bark colored.


I found an interesting article in Scientific American (Coates, 2005), and I quote part of it:

  The condition of having no more than five fingers or toes [...] probably evolved before the evolutionary divergence of amphibians (frogs, toads, salamanders and caecilians) and amniotes (birds, mammals, and reptiles in the loosest sense of the term). This event dates to approximately 340 million years ago in the Lower Carboniferous Period. Prior to this split, there is evidence of tetrapods from about 360 million years ago having limbs bearing arrays of six, seven and eight digits. Reduction from these polydactylous patterns to the more familiar arrangements of five or fewer digits accompanied the evolution of sophisticated wrist and ankle joints--both in terms of the number of bones present and the complex articulations among the constituent parts.

So Coates states that around 360 million years ago there were tetrapods with more digits (6, 7, 8), but that this was reduced to 5 about 340 million years ago. Losing things in evolution is generally relatively simple, yet re-gaining them is hard. So while there is still a tendency for evolution to create species with less digits, there are no examples of land dwelling species with more than 5 digits.

The author reasons that more digits do no good on land as more digits impair locomotion. Most polydactylous species were indeed found to be aquatic.


You ask two questions:

If a bacteria can get the same characteristics as tumor cells.
If such "bacterial tumor cells" actually can form a "tumor" within the
human body.

I assume that your question is not if bacteria can change in such a way that the can be confused with eukaryotic cells. This they cannot do. Bacteria cannot form organelles. Because they have no organelles they are solely dependent on their membrane for energy production. Because the surface area to volume ratio decreases with cell size there is a physical possible maximum size for bacteria. Here is some more in depth info on the subject.

So what characteristics can bacteria then have that tumor cells also have?
Well, according to wikipedia, a tumor is a mass of abnormal and excessively grown tissue (neoplasm) which may or may not be malignant. According to this definition bacteria could be tumor-like if the could form tissue and if this tissue could then grow abnormally or excessive.

And guess what? If you define tissue as "an ensemble of similar cells and their extracellular matrix from the same origin that together carry out a specific function." like Wikipedia does. Then you could argue that the biofilms some bacteria form are quite tissue-like since biofilms also contain an extracellular matrix, the cells within have the same origin and (in some cases) the bacteria can have differentiated functions.

However, the fact that bacteria can form biofilms does not make them tumor like. For that comparison to work mutated bacteria should be able to outgrow the rest of the biofilm. And while mutation that cause noncooperative/cheating/abnormally growing bacteria in biofilm are known, this kind of mutations cause the biofilm as a whole to grow slower. (source) In this sense comparing a biofilm to a colony of ants may be more appropriate than comparing it to tissue.

So to answer your questions:

Bacteria can form tissue-like formations, but when members of this formation do not cooperate anymore this typically leads to less growth, instead of increased growth.
Biofilms do form within humans. For example the bacterium Pseudomonas aeruginosa is assosiated with cystic fibrosis. And while cheaters exist among these bacteria, biofilms with high ratios of cheaters have a lower fitness. see this paper Therefor you would expect most biofilm within humans to be more tissue-like and less tumor-like.


Why only 6 water molecules are formed in the aerobic degradation of glucose?

Your confusion comes entirely from this equation:

$\ce{C6H12O6 + 6O2 -> 6CO2 + 6H2O}$

This reaction is the combustion of glucose. This is not how glucose is oxidized in cells! Why so many biology texts and courses present this equation when introducing metabolism is beyond me.

Indeed, your tracking of water molecules is correct: starting with one glucose molecule, 2 waters are produced in glycolysis, 4 are consumed in the tricarboxylic acid cycle and 12 are produced during oxidation of NADH/QH2 (ie FADH2). This gives a net total of 10 produced.

Why is this different from the combustion of glucose? The answer lies in the oxygens introduced by inorganic phosphate during substrate level phosphorylation. Consider the balanced net reaction for the biological oxidation of glucose (simplified by ignoring ATP produced by oxidative phosphorylation and substituting ADP/ATP for GDP/GTP):

$\ce{C6H12O6 + 6O2 + 4ADP + 4P_i + 4H+ -> 6CO2 + 4ATP + 10H2O}$

In particular, consider the formation of ATP from ADP and Pi (HPO42-). In both substrate level phosphorylation reactions (catalyzed by GADPH/PGK in glycolysis and succinate-CoA ligase in the tricarboxylic acid cycle), inorganic phosphate nucleophilically attacks the activated carbonyl (thioester) of the substrate and is then transferred to ADP (to form ATP):

The oxygens of the original inorganic phosphate are coloured red. The key point is that an oxygen atom from HPO42- is transferred to the substrate. This oxygen is later removed in the form of carbon dioxide, via oxidative decarboxylation, during the conversion of pyruvate to acetyl-CoA and in the tricarboxylic acid cycle. This occurs four times for each glucose molecule entering glycolysis and is accompanied by the reduction of NAD+ to NADH. Given that NADH is used to reduce molecular oxygen during the electron transport chain:

$\ce{NADH + H+ + 1/2O2 -> NAD+ + H2O}$

...this explains where the four, apparently extra, water molecules come from when comparing the combustion of glucose with its biological oxidation.


How does the bear mother ensure her cubs don't escape during hibernation?

She probably can't, but a bear that wanders out of the den away from it's mother probably won't be doing much reproduction.  Infant wanderlust will be strongly selected against.


Statistically, this is that the maximum mean recombination frequency is 50%.

Recombination defined this way means that Gene A and Gene B from one chromosome are not 'together' on the same chromosome after recombination. That means that the recombination frequency is the probability of an odd number of recombination events between the loci. If there is an even number of recombination events, Gene A and Gene B end up back together again (with some rearrangement between them).

Recombination events can be modeled by a Poisson distribution: that is, recombination events are discrete (you either get an event or you don't) and they don't depend on each other. The rate can be expressed in terms of base pairs, e.g. "mean number of recombinations per base pair" or "mean number of recombinations for 'distance' X."

The probability of getting an "odd" result from a Poisson distribution is always <0.5. See for example this Q&A from Math.SE.

Spoken in plain language, let's start from two loci that are very close where the recombination rate is very low. In most cases, then, we get 0 recombination events so the genes stay together. Now, as we increase the distance, we will get more cases where 1 event occurs. However, as we increase the distance further, we will also start to get cases where 2 events occur. 2 events has the same end result as 0 events: the genes stay together. It turns out mathematically that there is no rate that you can choose where the number of "1"s is more than the combined number of "0"s and "2"s; therefore, the frequency must be <0.5, but will approach 0.5 as the rate approaches infinity. If this doesn't seem intuitive, check the math from Math.SE!


I didn't watch the video, but the answer you're probably looking for is that cytotoxic T cells are for intracellular infections -- that is, CTL target pathogens that grow inside one's own cells.  All viruses grow inside cells. Some bacteria also grow inside cells (e.g. tuberculosis, Listeria); those bacteria can (often) be effectively attacked by CTL. Many bacteria do not replicate inside cells, and for those, CTL aren't effective, but B cells (via antibody) and T helper cells (by recruiting other cell types and modifying inflammation) can still be effective.


What is the structural difference between beta and gamma globin chains of Hb?

Here's a pairwise sequence alignment of the human hemoglobin beta (HBB) and gamma (HBG1) chains:

HBB_HUMAN          1 VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST     50
                     .|.|.|:|:.:|:|||||||::.|||.|||||||||||||||:|||:||:
HBG1_HUMAN         1 GHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSS     50

HBB_HUMAN         51 PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP    100
                     ..|:||||||||||||||.:..|.:.|||:||||||.|||||||||||||
HBG1_HUMAN        51 ASAIMGNPKVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDP    100

HBB_HUMAN        101 ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH    146
                     |||:|||||||.|||.||||||||.|||::||:|..||:||:.:||
HBG1_HUMAN       101 ENFKLLGNVLVTVLAIHFGKEFTPEVQASWQKMVTAVASALSSRYH    146

You can see the H143S (or S143H?) substitution, as well as many more.


How deep could a human swim with SCUBA apparatus?

As far as I can find the current world record for "scuba" diving is 1,090 ft 4.5 in set in 2014.

The previous record was 1,044 ft set in 2005 so (as with most human endurance & physical achievement records nowadays) we're most likely at the limit of the possible there.

Barring a few more feet (or even just inches) of course.

Howsoever, that's only normal scuba diving equipment

Deep diving using hydrox and trimix has reached depths of 1,644 ft (1977) & 1,752 ft (1988).

So the answer depends on if you're asking about with normal commercial scuba gear using bog standard compressed air or if you want to include breathing mixes etc to help alleviate the bends.


Within a bacterial cell exists circular chromosomes, and plasmids. During cellular division, chromosomes are always conserved - passed to both daughter cells.

As you are aware, plasmids can be passed between cells by a form of horizontal gene transfer called conjugation - whereby plasmid DNA is replicated, and passed through a sex-pilli into an adjacent cell.

When a cell divides in to two daughter cells, it is possible that one cell will not receive a plasmid. Thus, the result is one F+ daughter cell, and one F- daughter cell.


What is the conversion between r and FST?

I am very unsure but here are my thoughts...

We can work out from

$$R_{XY} = F_{XY}/F_{XX}$$

I do not really understand the concept of coefficient of kinship and the concept of coefficient of kinship with oneself but you say

  According to the paper, kinship with himself is 0.5 in a sexual population

So, let's assume

$$R_{XY} = 2F_{XY}$$

Let's assume that the individual Y is drawn from anywhere in the total population. Again, I don't really understand the concept of coefficient of kinship but let's assume that $F_{XY}$ is the same as the probability of identity by descent between these two individuals, then in Nei (1973) terms, $F_{XY} = J_T = 1 - H_T$. Hence, $R_{XY} = 2\left(1 - H_T\right)$ or $H_T = 1-\frac{R_{XY}}{2}$

Given that

$$F_{ST} = 1 - \frac{H_S}{H_T}$$

it results that

$$H_T = \frac{H_S}{1-F_{ST}}$$

and therefore,

$$1-\frac{R_{XY}}{2} = \frac{H_S}{1-F_{ST}}$$

solving into

$$R_{XY} = \frac{ 1 - \frac{H_S}{1-F_{ST}}  }{2} = \frac{1-F_{ST} - H_T}{2(1-F_{ST})}$$

I would recommend you making some more reading on the coefficient of kinship to ensure that my interpretation here is correct.


What's the technical difference between fainting (and being unconscious) and falling asleep (and sleeping)?

For this answer I assume that we are talking about sleep in healthy individuals as well as fainting as an isolated event without underlying disease or injury.

The most common form of what we call "fainting" is vasovagal syncope. It is caused by a drop in blood flow to the brain (cerebral hypoperfusion) e.g. by (false) activation of the parasympathetic nervous system and inhibition of the sympathetic system, resulting in low blood pressure or drop in heart rate (reviews 1,2,3). This can be triggered by the Bezold-Janisch reflex. Syncope can also be a symptom of underlying diseases or a side effect of drugs.

The reduced blood flow results in a transient loss of consciousness, a 'shut down' of the brain, which we don't really understand. It is sometimes accompanied by a flattening of an EEG signal, even though the data doesn't seem to be very consistent. Consciousness is defined by two factors, arousal and awareness. The fainted person cannot be 'woken up' and is not aware of the situation (as you said, you don't remember the moment of fainting). But this state normally only lasts for a few seconds or 1-2 minutes.

Sleep, on the other hand, is a mechanism highly regulated by the brain, circadian rhythms and hormones. The brain is thought to switch between the states of sleep and wakefulness by an interplay of different sleep-promoting and wake-promoting areas, including the hypothalamus.

You can argue that sleep is not a state of unconsciousness, since dreaming or even lucid dreaming are connected to a conscious experience. While sleeping lasts longer than the unconsciousness during syncope, it can be reversed by an external stimulus. The sleeping person can be woken up, even though the arousal threshold is increased (loud noises from the alarm are needed). The brain, in fact, is highly active during sleeping (as can be seen in characteristic EEG signals), with energy use close to the state of wakefulness in REM sleep and about 85% during non-REM sleep.

Since these are two different mechanisms, you should not be able to switch between them. After fainting you should regain consciousness very fast. Activation of sleep mechanisms is unlikely in a healthy individual, where sleep regulation is normal and syncope is a rare event.


How do I retrieve electronic annotation from Uniprot and GO records that relates to molecular function?

The endonuclease is controlled vocabulary. In this case, it looks like GO actually cites UniProt as the source for the endonuclease keyword.

With the Uniprot url, whenever you want to see where the information comes from for the annotation in Uniprot, type /publications after the ID. For example: http://www.uniprot.org/uniprot/Q13283/publications


Is there one centomere for the two chromatids in a dyad?

Each chromatid has a centRomere. A chromosome is a pair of sister chromatids (general term)... also known as a dyad in meiosis. Tetrads are the precursors to separated dyads in meiosis. Having centromeres is super important for being able to pass down genetic information in eukaryotic cells. Prokaryotes and archaea have similar structures to physically keep track of their DNA.


Laparoscopic surgery: Why did the gas cause pain in my shoulder, and how did it escape my body?

Does CO2 cause pain?

CO2 can cause pain by applying pressure on the diaphragm; also stretching of the diaphragm due to the body position can irritate the phrenic nerve (Indian Journal of Surgery).

ALSO:

  It was once believed the resultant shoulder pain was simply due to
  reaction of the gas combining with water; or that it was merely
  trapped CO2. The actual cause of this irritation is the result of
  cellular death caused by the combination of a temperature change from the gas at 70oF and the drying effect of the gas at
  .0002%. Much of this irritation is centered on the diaphragmatic
  region. Experiments with gases other than CO2 i.e. helium, nitrous
  oxide and argon have all produced the same or similar effect (Center
  for Endometriosis Care).

Why they use CO2?

  To begin, during Laparoscopy, CO2 (carbon dioxide) gas is injected
  through a special needle inserted just below your navel. This is done
  to create and maintain a distended abdomen; a condition called
  "pneumoperitoneum."  For safety, cost and convenience, CO2 is used
  almost exclusively for this purpose (Center for Endometriosis Care).

Why is pain in the right shoulder?

  The mechanism of laparoscopy-induced shoulder pain is mainly derived
  from carbon dioxide retention within the abdomen, subsequently
  irritating the phrenic nerve and causing referred pain in the C4
  dermatome. Moreover, carbon dioxide trapped between the liver and the
  right diaphragm, irritating the diaphragm, also causes upper abdominal pain (JAMA Surgery).

BUT

  In such hiatal surgeries including LAGB and in few gynecological
  surgeries, pain occurs preferentially on the left shoulder. This
  difference suggests that the region of surgery and position of the
  patient have an important influence on the site of pain. The cause is
  that in laparoscopic cholecystectomy the liver is separated from the
  undersurface of the diaphragm because of the reverse Trendelenburg
  with a right side up position of the patient. This leads to
  stretching of the right hemidiaphragm and the gas to be potentially trapped below the right diaphragm. Reverse is true for
  hiatal surgeries (Indian Journal of Surgery).

Where does CO2 go after surgery?

Most of the gas passively leaves the abdominal cavity through the surgical wounds immediately after the procedure. What happens with the rest:

  Carbon dioxide readily dissolves in water and forms carbonic acid.
  Carbonic acid is then absorbed into the intravascular space...(JAMA Surgery)

CO2 is not released through the mouth and is not a direct cause of burping. Burping may result from the pressure of gas applied on the stomach and intestine.


the range of interleukin 2 and 12 that can be used to activate nk-92 cells

If you have the resources you should ideally titrate your cytokines. You'll find that cytokines from different vendors may exhibit varying stability or availability in vitro, but also that you obtain varying levels of activation. Standard NK-92 culture conditions are 100-300 IU/mL IL-2 in RPMI1640 medium, 10% serum and 2mM L-glutamine (or 1X GlutaMAX, life technologies). Activation levels depend on how much you want to activate them. Interleukin-12 I'm fairly certain is standard at 10 ng/mL, but should also be titrated.

There's actually a relevant paper with a fair titration looking at granzyme expression at different concentrations of IL2, IL12 and IL15, and different timepoints. They note that NK92 cells show response at 100, 500 and 1000 IU/mL IL2, and at 10-30ng IL12.


What are those patterns found on the surface of wooden furniture? Are those growth rings of trees?

Thees cut on any angle will reveal growth patterns; not all wood grows exactly the same. Some kinds grow straight and have a very even grain, at the other end is the "black gum", the grain of which seems to follow no organized pattern (it's almost impossible to split.)

Without a close up, it's hard to say exactly what's going on with your table.

Some woods, because of their grain and even density, take up stain very evenly and uniformly. An example would be oak. Some woods take up stain more irregularly, an example being maple.

Your table, though (all this is speculation since there's not a close up or head on view) looks like an example of blotchy stain uptake.

This is an example of blothcy staining wood:

If you look carefully at the grain, you can see that's not the only cause of uneven uptake. Some blotchiness is due to not sanding the table down finely enough. Some is due to the uneven density of the wood. See that diagonal scratch? It takes up color regardless of the grain. As do the ends of the boards.

Your table is made up of younger trees (you could see growth rings on the edge) which will give you more uneven uptake, plus it's a blotchy job. So, the answer is yes and no. Or, a qualified yes.


What's the difference between mutation and substitution rates?

The mutation rate is the rate at which mutations happen — i.e. the rate at which "mistakes" are generated.

The substitution rate is the rate at which mutations are accepted — i.e. the rate at which "mistakes" become incorporated into a genome.

The difference is due to selection — if a mutation happens that results in an essential protein becoming non-functional that mutation will tend to be purged and thus won't be "accepted".

A relatively clear discussion of these differences:

  Box 1
  Mutation rates versus substitution rates
  It is important to distinguish between the rate at which spontaneous mutations occur and the rate at which genetic changes accumulate in a surviving lineage. The MUTATION RATE reflects the probability of a change in genome sequence between a parent and its offspring. It is the compound result of unrepaired DNA damage, polymerase errors, intragenomic recombination events, movements of transposable elements, and other molecular processes that introduce errors during the transmission of genetic information. However, only those mutations in lineages that persist — typically in the face of selection — contribute to the SUBSTITUTION RATE measured by whole-genome sequencing. The failure to carefully distinguish between these two types of rates is a persistent cause of confusion and misconceptions about whether mutations are random. In the same vein, the frequency of a mutant allele in a population generally does not equal the rate at which the corresponding mutational event occurs.

From: Barrick, J. E., & Lenski, R. E. (2013). Genome dynamics during experimental evolution. Nature Reviews Genetics, 14(12), 827-839.

You may also find the following article to be of interest:
Yi, S. (2013) Neutrality and Molecular Clocks. Nature Education Knowledge 4(2):3
.


How to convert PDB file of Amino Acids to rotamer tuples list of all AAs instances

I’m not sure if it is what you are after, but I have used Roland Dunbrack's dihedral perl script to get dihedral angles, the header of which is:

 RL_Dunbrack@fccc.edu

 usage
 dihedral.pl filename [chain]

 dihedral.pl pdb2hla.ent
     will print out all dihedrals from file pdb2hla.ent
 dihedral.pl pdb2hla.ent A
     will print out dihedrals only from chain A

I don’t know if it’s on his website as I got it from him personally. If not, or even if it’s not what you need, email him — he is likely to be able to help you.


How do gene locations change during crossing over events?

It depends on the regions of sequence homology between the two chromosomes. Crossing over occurs through pairing of homologous regions. If there's a substantial stretch of chromosome without a matching homologous region on its pair, that non-homologous region should loop out and not be involved in crossing over. Crossovers will occur only in paired homologous regions.
For example, if you have a chromosome I and I' as follows:
I   ABCDEFG
I'  ACDEHFGM
They should pair as:

A-(A)
B
C-(C)
D-(D)
E-(E)
(H)
F-(F)
G-(G)
(M)

Crossovers should not happen in the B, H, or M regions lacking homology with the other chromsome. Crossovers in a homologous region will just result in a new chromosome containing the left end of one crossover partner and the right end of the other.
Using I and I' above, a crossover in region E would produce either:
ABCDEHFGM or ACDEFG
Now, if you have repeated regions of homology in one or both chromosomes, or regions inverted on one chromosome vs. the other, pairing possibilities expand rapidly and all kinds of weird things can happen (and do in real life).


Question in gel chromatography experiment

Within reason, you can basically use any buffer you like with Sephacryl S-100, provided that is suits your purpose in terms of protein/enzyme stability, and phosphate-buffered saline sounds ideal.
There are sometimes a small amount of positively or negatively charged groups associated with a gel-filtration resin, introduced during the manufacturing process, and it is recommended to have some salt present (100mM KCl used to be recommended) in order to counteract anion-exchange and/or cation exchange effects.  In addition, at very high salt concentrations (1M ammonium sulphate or higher), proteins may bind to the resin by a hydrophobic interaction. Furthermore, one or more of your target molecules may be unstable at extremes of pH.  NADH, for example, is unstable in acid.
In other words, you want to set up the experiment where the target molecules are stable, and where separation on the column is by 'molecular sieving' only.
A very common method of measuring protein concentration is to measure the A-280 of each fraction (the absorbance at 280nm). The has the big advantage of being reasonbly sensitive AND is non-destructive (you can fully recover the sample after the measurement).  All you need is access to a spectrophotometer and a quartz cuvette!
In addition, with (pure) BSA the method may be made quantitative as the A(1%, 280),sometimes called the E(1%,280), is known. From memory I think this is about 0.68 for BSA.  That is, a 1mg/ml solution of (pure) BSA will have an absorbance at 280nm of 0.68.  (The 'rule of thumb' for impure protein preparations is that a 1mg/ml solution has an absorbance of 1. But note that many compounds absorb at 280nm, including DNA)
You can, if you wish, calculate the A(1%, 280) from the amino acid sequence of the protein of interest. The refs (Perkins; Gill & von Hippel) are given below.
It should be possible to detect B12 by a similar method, perhaps even at 280nm, but an absorbance spectrum may yield a more sensitive/specific wavelength.
You don't give the pH of the PBS (!important), or the dimensions of the Sephacryl column.
Long, narrow columns work best, but you probably already know that.
Some Refs
Gel Filtration by Reiland (Methods in Enzymology, 1971).  A great article
Protein Purification: Principles and Practice by RK Scopes (Springer Advanced Texts in Chemistry) 3rd Edition
Sober, E. K. & Sober, H. A. (1970). Molar extinction coefficients and E (1%, 280) values for proteins at selected wavelengths of the ultraviolet and visible region. In Handbook of Biochemistry. Selected Data for Molecular Biology, 2nd edn. Sober, H. A., Ed. pp C-71 - C-98. The Chemical Rubber Company, Cleveland, Ohio.
Perkins, S. J. (1986). Protein volumes and hydration effects. The calculation of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences.  Eur. J. Biochem. 157, 169 - 180. [Pubmed]  [pdf]
Gill, S. C. & von Hippel, P. H. (1989). Calculation of protein extinction coefficients from amino acid sequence data.  Anal. Biochem. 182, 319 - 326.  [published erratum appears in Anal. Biochem. (1990) 189, 283].


Doxorubicin's intercalant and topoisomerase inhibition in leukemia?

Doxorubicin is part of chemotherapy drugs. Most of them are targeting proliferation of cells, e.g. by blocking cell division or DNA replication.

Intercalants and topoisomerase inhibitors are powerful in interfering with DNA replication (not DNA activity). Other chemo drugs might inhibit proper operation of cell division machinery, such as through interfering with cytoskeleton functions.


How does the body switch between aerobic and anaerobic respiration?

The simple answer to your question is that in the absence of oxygen the electron transport chain stops. (It can't go backwards, that would generate oxygen.) However your assumption that it stops at the last step is incorrect, all the cytochromes are converted to their reduced form, and there is feedback that diverts the NADH elsewhere.

The situation is complicated because it depends what tissue you are talking about and what sort of exercise and what is the fuel for respiration. However let us consider the skeletal muscle at the start of a non-sprint run. Let us assume that it will be using glycogen as a source of fuel, which is converted to pyruvate and NADH. The pyruvate will enter the tricarboxylic acid (TCA) cycle in the mitochondria and be oxidized there and also produce metabolites. The NADH from glycolysis (produced by reducing NAD+) will enter the mitochondria and be oxidized; however it does not enter directly but via a shuttle, one of which — the malate-aspartate shuttle, show below — will be considered in a more detail lower down.

Now let us suppose there is a sudden need to sprint so that the muscle cannot get sufficient oxygen to deal with the NADH produced in glycolysis. What happens? The key event is that pyruvate is oxidized to lactate. Why? Not because lactate is useful, but because this is an anaerobic means of oxidizing the NADH back to NAD+ to allow glycolysis to continue and ATP to be produced at the substrate level.

Why doesn't the NADH keep going into the mitochondria (where it would be wasted as the electron transport chain has stopped)? Because the shuttle stops — in the case of the malate-aspartate shuttle mitochondrial malate dehydrogenase stops converting malate to oxaloacetate, malate builds up and therefore the malate transporter stops bringing malate into the mitochondrion.

This can be understood at the most general level by the fact that if NADH in the mitochondrion cannot be oxidized it will accumulate, hence slowing and eventually arresting the malate dehydrogenase reaction by simple mass action.

In fact Nature generally uses more sophisticated regulation that allows switch on and switch off to be performed more rapidly and completely, most notably by allosteric regulators. In the case of malate dehydrogenase the situation is not really clear, but there are reports that suggests citrate is an allosteric activator of the enzyme in some tissues (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1131027/). The concentration of citrate falls as the TCA cycle stops because of the lack of NAD+ (this is because TCA cycle intermediates get tapped off for other purposes) so the activating effect of this intermediate would be removed.

(There is another shuttle for reducing power that my be more important in skeletal muscle. This is the glycerol 3-phosphate shuttle. However as this requires the oxidized form of FAD directly in the mitochondrial membrane it will clearly shut down in anoxia.)

The net result is that the NADH stays in the cytosol to be oxidized by pyruvate in the lactate dehydrogenase reaction.

This can only happen if the pyruvate stays in the cytoplasm and does not move to the mitochondrion. Obviously the lack of NADH to reduce it to acetyl-CoA in the pyruvate dehydrogenase reaction would cause its concentration to build up in the mitochondrion and reduce transport across the membrane by simple mass action. However it is likely that the specific mitochondrial pyruvate transporter is regulated by metabolites which change their concentration under these conditions. The evidence here is indirect as the transporter was only identified and cloned in 2012.


What would happen if we place denatured DNA in acidic medium?

Hello and welcome Nandini Yadav,
It is worth mentioning DNA is an acid (Deoxyribonucleic acid) and intracellular pH is most commonly between 7.0 and 7.4.
Alkaline reagent Example

"The sodium hydroxide (NaOH) is a commonly used reagent to denature the DNA by increasing the pH. At an alkaline pH, OH- groups are predominant. They remove the hydrogen- bonds-contributing protons from guanine and thymine, thus breaking the hydrogen bonds between the two oligonucleotides."

Source
You can see in the image below hydrogen bonds between nucleotides Adenine (A), Cytosine (C), Guanine (G) and Thymine (T).

Acid reagent Example

A decrease in the pH was found to deteriorate the thermal stability of DNA

Source
At an acidic pH, the H+ in the surrounding environment of DNA is high and therefore the hydrogen bonds between Adenine (A) and Thymine (T), Cytosine (C) - Guanine (G) will 'break'.
More information here.


Why does heating kidney beans at a low temperature potentiate the toxicity of phytohaemagglutinin?

I am a Snr lecturer and a PhD candidate. Currently, I am putting my theses together. My research area involve in part the kinetic degradation of lectins in neglected and underutilized legumes. I  also looked at the possibility of using irradiation to produce complexed degraded starches  to inactivate lectins during low temperature extruder cooking.I observed in some of the extruded samples that lectins have actually potentiated up to about 50%. I was confused. I know lectins are proteins so they are supposed to denature when heated. I was looking around to see whether someone has made similar observation and I saw that indeed somebody has reported similar observation. I was so over joyed but it was short lived-no explanations were offered.  I now offer a possible explanation. Yes, lectins are proteins(or glycoproteins) and like most proteins their tertiary and quaternary structures are 3D. So the 3D forms have a couple of smaller subunits, woven together into the giant super structure(lectin). In the 3D form, most of the binding sites are "buried" or not fully exposed. It is possible that these smaller units have binding sites for carbs and are best positioned to present their ligands for  exposure and maximal binding when the 3D structure begins to "melt down". This melt down occurs at low temperature when denaturation has actually started.  Thus, the greater the exposure  number of subunits bearing the binding sites, the greater the potentiation. My work used low temperature extrusion cooking and the observation occurred in the extrusion cooking.

I just hope this suggestion is adequate. That is indeed the explanation I am going to offer for my observation anyway. Wish me best of luck!

Bye!


What is the so called "hepatic glucose production"

"Hepatic glucose production" is the gluconeogenesis process (the opposite of the gycolysis process), that is the formation of glucose primarily from lactate and amino acids. This process takes place in the liver's cells and it is regulated by hormones (insulin and glucagon).
Look here and here for a better explanation!


Do pregnancy and breast feeding increase basal metabolic rate?

Basal metabolic rate for a particular organism is determined by the amount of calories that the organism needs for basal metabolic processes (i.e. basal energy demands). Since pregnant and breastfeeding women have increased caloric requirements (i.e. increased energy demands), then that means by definition their basal metabolic rate is increased.


It's common for the human immune system to create antibodies against many proteins, even some human proteins. Hemophiliacs who receive regular doses of clotting factor proteins often develop neutralizing antibodies against the clotting factor proteins, even though they are a human protein1.

Therefore it's not surprising that antibodies would be developed against mouse antibodies. There are differences between mouse and human antibodies, and human antibodies may bind to these different regions. I found the amino acid sequences for human2 and mouse3 immunoglobulin gamma heavy chain constant region and aligned them by hand and marked the matching amino acids:

Human: MELGLSWVFLVAILEGVQCEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVANIKQDGSEKYYVDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARECDNWF DPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT CPPC      PAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
       |   |  |||| || |||||||||||||||| ||||  ||||||||||| | | |||||| ||||||| |       || | |||||||||||||| |  || ||| |||| ||||||      | |||||  ||||| |  ||| ||||    | |    |||||| |||| ||| |||| | | |||||| ||| |||  || ||||||    ||  | | |  | | |||| ||     |   ||||      ||| | |||||| |||  || |||| || |||||||||  || |   | |  |||| | |    | |||| |||| |   ||||  ||| |||| || || ||| |||| ||  | |||| |||    |    ||||||| || | || ||| ||   | ||| | |||||||| | ||||    | |     ||| | || | | |  |  | ||||
Mouse: MDSRLNLVFLVLILKGVQCEVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSGSTTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCARELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQS GLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPNLEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTIRVVSALPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLDIKTSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK

As you can see, there are a lot of matching residues, but several differences. Keep in mind that antibodies also contain light chains, and that there are several other types of antibodies, I just used the IgG heavy chain as an example.


Biological advantage of electric synapses

Having just read this article (http://www.ncbi.nlm.nih.gov/books/NBK11164/) there are several advantages/functional reasons that seem apparent and important in having electrical synapses with gap junctions compared to just a very long neuron.

a) signals in electrical synapse can be bidirectional.
b) electrical synapse synchronize electrical activity among populations of neurons.
c) The large pores in gap junctions allows passage of ATP and other important intracellular metabolites, such as second messengers between neurons.

I'm sure there are plenty of other reasons but these should provide a better picture in terms of the functional significance of having electric synapses.

Hope this helps!


The fed batch culture is a means of bacterial production that is used in industrial setups. Nutrients are fed into the chamber with controlled ideal conditions for growth of a particular species of microorganisms.

Upon reaching the desired yield temperatures can be increased (depending on the species of bacteria) to facilitate spore formation for eventual harvesting.


Cancer biology: Can tumors form from cells that are genetically identical to non-cancerous cells?

This is a very interesting question, and one that has been at the heart of cancer research for a long time. I think it separates into three issues.

Are there non-genetic mechanisms that can induce uncontrolled cell proliferation?

Yes, at least in experimental settings. There are many viruses that induce proliferation in its host cell, and viral genes / proteins have been identified that can disable the host cell's cell cycle regulation machinery. A well-studied example is the SV40 Large-T gene (from Simian Virus 40); this gene can be expressed in cells to cause cell proliferation in a transient, reversible manner, and it does so by interacting with host proteins, without causing genetic changes. See for example this article.

Can such genetically normal cells progress to form tumors?

It depends on what you mean by "tumor". To my knowledge, tumors large enough to be a serious medical problem are always found to be genetically altered in one way or another. There are plenty of viruses that cause tumors in humans, for example Epstein-Barr and papilloma (HPV) virus, but in all cases viral sequences are found integrated into the host genome. This may be because development of large tumors requires many cell division, and any non-genetic change that drives proliferation is likely to be lost on the way.

On the other hand, HPV virus frequently causes warts, which technically are small benign tumors. As far as I know, no genetic modification of the host cell is required for this to happen; rather, the virus replicates from its own separate DNA while simultaneously driving keratinocyte cell proliferation to cause these growths. So this example shows that small "tumors" can be formed without any genetic cause. Perhaps there is a limit on how large tumors can grow without genetic changes.

Can genetically normal cells form cancer, meaning a malignant (invasive) tumors?

No, as far as I know, this has never been observed. Large, malignant tumors without genetic changes are unlikely for the reasons above. There are cases of metastatic cancer where the primary tumor is so small that it cannot be located, but in these cases the metastatic cells are again genetically altered. Experimentally, it is possible to produce invasive behavior in cell lines by expressing oncogenes like ras, but these genes are mutated to begin with. Also, normal cells have mechanisms that detect such alterations, causing senescence, and they must first be inactivated by mutations. Transformation to an invasive phenotype is not usually caused by viruses, probably because it would give no advantage to the virus (unlike cell proliferation).

For more information, Robert Weinberg's Cancer textbook does a good job of discussing these issues. This article also provides a historical perspective of tumor virology with some interesting pointers.


How does vitamin C increase iron uptake?

Vitamin C both enhances iron uptake, and affects iron metabolism:

  in addition to the known ability of dietary ascorbate to enhance nonheme iron absorption in the gut, ascorbate within mammalian systems can regulate cellular iron uptake and metabolism. Ascorbate modulates iron metabolism by stimulating ferritin synthesis, inhibiting lysosomal ferritin degradation, and decreasing cellular iron efflux. ... Importantly, this iron-uptake pathway is of particular relevance to astrocyte brain iron metabolism and tissue iron loading in disorders such as hereditary hemochromatosis and β-thalassemia. Recent evidence also indicates that ascorbate is a novel modulator of the classical transferrin-iron uptake pathway, which provides almost all iron for cellular demands and erythropoiesis under physiological conditions.

--The active role of vitamin C in mammalian iron metabolism: much more than just enhanced iron absorption!


How is the diploid chromosome number maintained at mitosis?

The terminology of "chromosome" during this process is confusing, but here it is:

There are 46 chromosomes in the cell (23 pairs)
Before division, each chromosome has two sister chromatids, joined in the middle (92 chromatids in total)
During division, the chromosomes split and each daughter cell gets 46 chromatids, one from each chromosome
These chromatids are now known as chromosomes
Each one of these new chromosomes only has one "chromatid"
During interphase, the new chromosomes replicate and now they have two chromatids each, joined in the middle

So whether a chromosome has one or two chromatids it is still called a chromosome. I hope this helps.

The following link contains a more complete explanation of mitosis. The first picture explains this point quite succintly: http://biology.tutorvista.com/cell/mitosis.html


Difference between stem cell "expansion", "repopulation", and "self-renewal"?

After an hour of reading the paper (from 2014), if you can I recommend instead reading the below review article (from 2020). the 2014 article uses difficult to understand language.

Eric M. Pietras; Inflammation: a key regulator of hematopoietic stem cell fate in health and disease. Blood 2017; 130 (15): 1693–1698. doi: https://doi.org/10.1182/blood-2017-06-780882

https://ashpublications.org/blood/article/130/15/1693/36384/Inflammation-a-key-regulator-of-hematopoietic-stem

I found this by pasting your article's title into google scholar, hitting "cited by", sorting by date, and browsing until I found a review article.

The point of treating with G-CSF is that the stems cells divide, and can be recovered from the blood for stem cell treatments.

"expansion" . Here means an increase in the numbers of cells. But in plant biology it has the literal meaning of cells growing larger.

"phenotypic HSCs". Using the adjective phenotypic, the cells express the phenotype of HSCs. So the cells behave like HSCs

By itself, G-CSF makes the the HSCs divide for a while, then they stop dividing. That is, they become "quiescent".

This state of quiesence can then be interrupted. If the mice are treated with antibiotics to kill intestinal flora (or if mice are used that are germ-free), then the HSCs continue to divide.
The article calls this process of getting the HSCs to divide again "mitigating the G-CSF-mediated HSC repopulating defect"


First of all, the HERV-K virus is present in the human genome, in fact it is one of the most common endogenous retroviruses there (see references 1 and 2).

In a viral infection, these proviruses get integrated into the human genome and can be found later there. This is a useful tool when you want to find out details about the split of closely related species like the great apes and humans. If you find such a provirus in all analyzed species, the integration must have happened latest at the last common ancestor. If it is only found in a part of them, it happened after the species divided. The figure (from reference 3) shows this shematically:

The authors of "your" article did this and found the integration of the retrovirus in a specific locus in the genome of gorilla, chimpanzee and human and found it only in the first two. From this they conclude that the apes are closer related to each other than to the human.

So in summary it means that the HERV-K is not present at one specific site of the human genome, not in general.

References:

HERV-K: the biologically most active human endogenous retrovirus
family.
HERV-K(HML-2), the Best Preserved Family of HERVs: Endogenization,
Expression, and Implications in Health and Disease
Differences in HERV-K LTR insertions in orthologous loci of humans
and great apes.


The sRNA mediated regulation in bacteria operates via diverse mechanisms. This case of sRNA competing with a mRNA for a protein is a passive kind of regulation. This might be good for finetuning but may not be very efficient. It is much better to actively regulate a mRNA by direct binding. Also, it will work only if the concerned protein is in limiting concentrations.

I haven't come across any examples of what you are interested in. There may be one similar situation in case of a eukaryotic system. miRNAs can be titrated away by long RNAs that bear multiple binding sites for that miRNA, thus making the miRNAs unavailable for binding to the target mRNA. These long RNAs are called ceRNA (competing endogenous RNA) or miRNA-sponges (this term is mostly used if the RNA is exogenous). However this is not really a protein-RNA interaction even though RISC complex contains proteins.


Question on the concept of mitochondrial Eve

As the Wikipedia article says:

  In human genetics, the Mitochondrial Eve (also mt-Eve, mt-MRCA) is the matrilineal most recent common ancestor (MRCA) of all currently living humans

Note the use of the words "most recent".  The mother and grandmother of the actual Mitochondrial Eve were living before Mitochondrial Eve, and thus are less recent than she is.


How is it possible for monosomies to occur?

Gametes cannot be compared to regular (id est, somatic) cells for two main reasons:

Their lifetime and...
Their gene expression.

In human beings, gametes have a very short lifetime. Supposing the nondisjunction happened at meiosis I (which is the worst case scenario), a "nulissomic female gamete"1 has to be alive for some days, from the end of the dictyotene to the fertilisation. The male gamete would have to stay alive for a little more time, some weeks, from the spermatogonium stage to the end of meiosis. Those are not big time spans.

But the most important reason is that gametes are basically a structure to "deliver" genes. They normally don't express the genes they have, at least not as a somatic cell would do. Sperm cells, for instance, have densely packed chromosomes and gene expression, if any, is little and poorly understood.

Thus, the problem in your reasoning lies in assumption #2:

  Gametes without a copy of a specific chromosome would also die.

Gametes lacking a given chromosome can and do exist, and they form aneuploid zygotes.

Note 1: the name "gamete" here is a wrong choice, since a primary oocyte is not a gamete, as it is the name "nullisomic", which doesn't apply to haploid cells.


The genetic code and the effect of point mutations on proteins

Nonambiguity refers to the fact that codon X will always code for the same amino acid.

Degeneracy refers to the fact that an amino acid can be coded for by many codons.

I rephrase the question to get to the gist of things:

  Why do certain mutations cause no difference for protein synthesis, while others make a big difference?

Certain mutations can change the codon but still code for the same amino acid, so the resulting peptide sequence is unaltered (synthesis of a functionally identical protein). This is due to degeneracy, explained above. Certain other mutations change the codon in a way that produces a completely different amino acid, and these result in the synthesis of a different, distinct peptide that may be dysfunctional. This due to nonambiguity of the code. Simple!

It's best to refer to our translation guide, the codon table. If you know your codon table, you might have noticed that within a codon frame, changing the 3rd nucleotide often has no effect on the translated amino acid (see outer ring, below). Changing the 1st and 2nd nucleotide produces a more drastic effect in the translation of the codon.

That means that the position of a nucleotide mutation within the reading frame is key to the effect of the mutation on protein synthesis.

  Where I am going wrong?

You are complicating the picture needlessly. You fail to explain that the resulting amino acid depends on its codon, and that the effect of changing the codon in different places (position 1, 2 or 3) has different outcomes. You also have to think about different kinds of mutations; we are discussing substitutions, but you must also consider what deletions and insertions of nucleotides do to the translation of the peptide! You may also get bonus points for discussing the start and stop codons... they are special cases.


We will be needing some additional information to answer your question more completely:

What sequencing platform are you using? Illumina HiSeq/MySeq; Ion proton

What type of sequencing (as noted by @CMosychuk): Exome or Whole Genome?

What type of variant caller (as noted by @CMosychuk): Unified Genotyper; Haplotype Caller; TVC

The QUAL metric is heavily dictated my sequencing depth, so if you use 30 (phred-scaled), that would be an accuracy of 99.9%.

The typical QUAL metric used by most sequencing studies is 20 so using 30 may cause accumulation of false negatives. But again, depends on the type of sequencing and platform used.


Do humans squint more readily at green light?

Yes.  According to Action spectrum for photophobia Journal of the Optical Society of America A, Vol. 20, pp. 1852-1858 (2003), the most squinting-sensitive wavelength is ~510 nm, which is green.  Squinting sensitivity progressively falls above 510nm, and below 510nm squinting falls to a local minimum at 460 nm, and then rises again below 460nm, but did not reach a higher maximum in the range studied, which ended at 420 nm.


What is the ratio of head to waist and waist to floor of the human anatomy?

The study of those measures is called anthropometry. Typing anthropometry on google image returned this

This is definitely not a peer-review source and might eventually be a good approximation only for white males (or whoever they considered to take these measurements on) but if we believe this image, then the ratio head-to-waist over waist-to-floor is $\frac{0.52}{0.485} = 1.072$.


Would salt cause a pistachio nut not to be able to germinate?

This article https://wikifarmer.com/how-to-grow-pistachio-tree-from-nut/

says unsalted.  Lots more on that site about growing them.


Replicator dynamics giving probabilities greater than 1?

This is happening because the fitness for your first strategy can be negative. In the case of the discrete replicator dynamics, the fitness cannot be negative. Otherwise, you can leave the simplex. Note that the continuous replicator dynamics doesn't have this restriction (the fitness can be negative).


How is it that ionic diffusion is independent of other ions?

Most importantly, the whole Goldman-Hodgkin-Katz model is, well, a model. It is a way we would like to find and explain phenomena, given pen and paper.

Often, scientists build models in order to explain data in hand, but even then, they will have to add something from their imagination. For example, early astronomers saw planets moving differently from stars, and came up with the idea that, you know, planets do not circle the earth, but maybe around some points in space, which in turn circle the earth. That didn't work well, so they created the heliocentric model, where planets and the Earth circled the sun. That was still perfectible, and Newton suggested the planets do not move on circles, but on ellipses. Each generation of astronomers had almost the same data in hand, but chose to make some assumptions in their models.

The same goes with the lack of interaction between potassium and sodium ions: it is a theoretical assumption. As models go, the GHK model is quite good, because it fits experimental findings better than any other model. Its assumptions have a great chance of being true, of reflecting the physical world. I guess you really asked what are the physical facts that underlie the assumption of ion independence. The fact is, you are looking for explanations for a fact that may be or may not be - so any response you will receive is, to a degree, speculation.

My thought is that the number of water molecules (55 molar) that may collide with an ion is far greater than the number of cations (up to a few hundred nanomolar, about 100 million rarer). Perhaps the number of ion-ion collisions is negligible. There is one bottleneck, in the actual channels, but there different species do not meet, because each has its own channels.

Another, more factual, is that the model is imperfect, and independence is more of a wish than a complete truth. Quoting from http://books.google.com/books?id=SmJoSwnwSh0C&lpg=PA353&ots=3fvI19Sk5Q&dq=ghk%20ion%20independence%20fails&pg=PA353#v=onepage&q&f=false : "The rich literature on how ion channels fail to obey the independence principle is reviewed in Chapter 14 of Hille (1991), and some specific models will be studied in the following chapter."


Does this look like the same bug to you ?

.

This one is a bulb mite, Rhizoglyphus robini, see here.


What does it mean when a protein has a different excitation spectra than wildtype, but the same emission spectra?

Let me start from short description of fluorescence (since we talk about it here).

Fluorescence is one of the processes through which excited molecule can relax, lose its excessive energy. That is, quantum interaction between atoms in molecule (organic dye or complex GFP) create permitted energy levels. There is "ground state" $S_0$, for example, and excited state $S_1$. You "pump" your molecule with excitation light from $S_0$ to $S_1$. All this can be nicely illustrated as absorption in Jablonski diagram (look at a for now):

via http://micro.magnet.fsu.edu/

"Loss of energy" here is some process via which molecule returns to ground state. In case of GFP energy is released as an emission photon. Nature of fluorophores is that they tend to return to ground state as the state of less energy, and almost all systems tends to go to state with lesser energy.

Now, to your question. Why GFP can has different excitation profile but same emission? Notice, how in (a) molecule get pumped to highest state, then relaxes a bit to lowest of $S_1$ states and then go all the way to $S_0$? That initial relaxation is thermal relaxation. Some energy is lost, essentially, to water molecules around GFP. That is why emission is always "more red", i.e. has lower energy than excitation. Initial relaxation is why your GFP spectra also broad. There are many levels GFP can emit from, as well as be excited to. In crystals of GFP transitions will be very narrow, because much less of excitation energy will go not into fluorescence.

So, my point is following. Nobody prevents one from engineering a mutant molecule of GFP that could be pumped to some even higher level $S_2$, which then relaxes to $S_1$ via non-irradiative process (e.g. gives energy to water, but not into fluorescence!). Only requirement is that for mutant direct pathway from $S_0$ to $S_1$ would be forbidden (see b and c).

Another point is that whether your spectra are different in shape or only intensity. Different shape of spectra means there are differences in those levels and transitions.


Why do doctors use a new thread for each stitch?

Using a single thread for a suture also known as continuous stitching has a major con that it has higher risk of failing if the suture is cut in just one place. So it is generally avoided eventhough it is very easy to do.

On the other hand interrupted stitching ( one thread for each stitch) is favoured because of lesser risk of failing, eventhough it is time consuming than continuous stitch.

Source:https://en.m.wikipedia.org/wiki/Surgical_suture


Could two women have a child through artificial insemination/genetic engineering?

Recently, researchers have been able to produce sperm and ova from germ cells.  It's not been proven yet that the two can produce a viable embryo, but probably the technique will be perfected eventually. [https://www.technologyreview.com/s/608452/a-new-way-to-reproduce/]


This depends on your coverage and the number and relative proportion of species in the mixture.  this seems unlikely to produce results unless the protocol biases the library (rRNA universal primers for instance.)  I think at 25 bp sequences, even 30x coverage would not give full assembly sequences. Typically I believe 25 bp reads are only used to resequence close variants from similar or reference genomes.


Heterochromatin v Euchromatin. Which is more abundant?

Percentage of euchromatin varies between cell types and organisms. It has been shown that upto 88% of the human genome is transcribed; a phenomenon called pervasive transcription [1]. Highly specialized cells may have a lower percentage of transcribed regions and in females one entire X-chromosome is silenced (some regions in the silenced-X do show transcriptional activity).

Euchromatic regions not only constitute the geneic regions but also regulatory intergenic regions such as enhancers, locus control regions (LCR), silencers etc. It has been found that ~97% of these elements fall in the DNAse hypersensitve (DHS) region of the chromatin [2].

DNAse hypersensitivity is directly proportional to the chromatin state such that open/accessible regions are more prone to DNAse-I digestion. You may call these regions as euchromatin.

Though the total DHS density is not reported in the paper [2] or supplementary data, the ENCODE project that the paper concerns, will have all the detailed information. You can can find these datasets here, from which you can calculate DHS density distribution for different cell types. However, most of these cells are actually cell lines and not from primary tissues.