text:
Why do the most structurally well-characterized bacterial RNA polymerases belong to thermophiles?
From Lewin's Genes (11th edition, page 515):

The only bacterial RNA polymerases for which high-resolution crystal structures have been solved, however, are from two thermophilic bacterial species, Thermus aquaticus and Thermus thermophilus.

Is this just a matter of economy? I mean, as X-ray crystallography is exceedingly expensive and complex, did scientists consider enough to resolve the RNA polymerase structure of one species and deduce those belonging to the rest by homology-based folding prediction?
Or is it because thermophilic proteins are inherently more stable and thus easier to crystalize?

I think both of your suggestions have some merit: (1) it appears that Thermus RNAPs are more stable and easier to crystallize (2) RNAP is highly conserved and so it is not critical to crystallize it from every bacterial species.

It might be worth adding that knowledge about thermostable enzymes is generally economically interesting since it is often easier to use them in various experimental settings, especially after optimising/engineering them - which becomes much eaiser with structural information.

The Nature article provided by @canadianer states that they were succesful isolating the core complex (that is, alpha dimer, beta, beta-prime and omega), but not the holoenzyme (the previous ones with sigma). I suggest that is because sigma leaves the RNA pol complex once elongation (the longest phase) begins; so researchers have a shorter window of time to isolate the holoenzyme.


text:
Why don't allergies cause fever?
Allergy
To my understanding, an allergy is a hypersensitivity of the immune system causing a substance in the environment to be identified as pathogenic by the immune system while it is not pathogenic. During an allergic reaction, the immune system triggers histamine, which triggers an inflammatory response just as if the allergen was a pathogen. The resulting symptoms of an allergic response is similar to the symptoms of a cold but without fever.
Fever
To my understanding a fever is an increase in body temperature driven by the body through production of pyrogens, most often in response to a pathogen. This response might be adaptive for various reasons that I am not too interested in discussing here.
Question
According to NIH, an allergic response never causes a fever. Given that the fever is not directly caused by the pathogen but rather is caused by the body, why do allergies not cause fever?
The fact that allergies don't cause fever give me the weird impression that the immune system somewhat "understand" the allergen is not pathogenic otherwise the immune response would be the same in the case of an allergen or a pathogen.
Un-educated guess
Allergic responses implies the firing of IgE. IgE are typically involved in response to parasites such as helminths. Could it be that pathogens leading to an immune responses mediated via IgE never yield to fever. Why would it be the case?
Plasmodium falciparum (which causes malaria) is a pathogen who causes an immune response involving IgE (according to the wikipedia). Malaria's symptoms include high fever (according to Mayo Clinic). Now it would be possible that the pyrogen would be of external origin (not produced by the body but by the pathogen) or it is possible that several immunoglobulin are involved in response to P. falciparum. The same logic hold for Fasciola hepatica (an helminth; common liver fluke) who also causes fever and is who's infection lead to the firing of IgE.

The short answer seems to be that fevers help combat microbes (a term I take herein to include viruses for brevity), which aren't a part of the threat addressed in an allergic reaction. While there's not a full consensus on which benefits, if any, a fever brings to the response to microbes, both humans and other warm-blooded vertebrates fare better with infections when a fever is present.
Fevers appear to mobilise leukocytes and enhance their phagocytosis while suppressing endotoxin effects (see Craven, R and Hirnle, C. (2006). Fundamentals of nursing: Human health and function. Fourth edition. p. 1044) and proliferate T cells (see Lewis, SM, Heitkemper, MM, and Dirksen, SR. (2007). Medical-surgical nursing: Assessment and management of clinical problems. sixth edition. p. 212), rather than mobilising basophils.
Higher temperatures are also more damaging to at least some pathogenic cells than the body's own, as they are typically smaller with higher relative surface area. Note this also explains why fevers wouldn't be as natural a response to such large parasites as helminths. (Even their cells, being eukaryotic, are comparable to human cells.) It is unsurprising that IgE would be a more specialised response, found only in mammals.
On the subject of malarial fever, for which the pathogen is relatively large because it is eukaryotic, there is ongoing research into both the mechanism and function of this fever. It seems to be Plasmodium itself that creates and presumably benefits from the fever, not the host. I'll discuss the evidence in a moment, but note this means the "endogenous fevers follow suspected small pathogens" hypothesis is unthreatened.
According to this 2013 paper, the timing of such ruptures may (I stress may; the paper discusses the uncertainty around a number of ideas about this) serve the function of controlling the time at which the immune response is most active, so the reproductive cycle is unaffected. According to this 2007 paper, the malarial parasite's hemozoin causes the disease's characteristic fever following erythrocyte rupture. The same paper mentions that the timing of the fever has been used as a diagnostic criterion for malaria, and the 1927 Nobel Prize for Medicine was awarded for the now discontinued treatment of syphilis with a malaria-induced fever.

By the same logic, the body doesn't need to "combat" peanuts, pollen, or cat hair with an inflammatory response, yet it does for people with allergies to those things.

@mgkrebbs I'll admit the immune system has to be imperfect whatever explanation one advances, but I think the evidence suggests allergens are mischaracterised as poisons or toxins rather than as pathogenic microbes.

@J.G. I don't think this answer adds much beyond the background already contained in the question - can you provide some citations?

In light of the reference-seeking notice (whose posting I welcome), I've edited my answer to directly reference the relevant primary literature, although in some cases this is a book or a possibly paywalled link.

@BryanKrause Whether or not my answer "adds much beyond the background", I think any answer needs to see the real question to be not "Why do allergies that don't warrant fevers still happen?" but "Given that allergies are clearly a mistake, why aren't they the same kind of mistake they would be if they were feverish?" Adverse reactions to vaccines, which can be feverish, are the microbe-detecting mistake type.

Malaria, which is caused by a helminth, is causing high fever though. I edited my question to add some info on the subject in the "un-educated guess" section.

@Remi.b Since when is Plasmodium a helminth? I can find any number of interesting papers on the interaction between infection types in their shared regions of prevalence, but no evidence Plasmodium is a helminth.

Sorry, I corrected that. According to wikipedia, an infection by P. falciparum lead to the firing of IgE. I wrongly concluded that Plasmodium was an helminth. I added the common liver fluke who is a helminth and cause fever (according to wiki).

@Remi.b I've added a discussion of malarial fevers to my answer, but I couldn't find anything useful on the possible causes of fevers in liver fluke infections. My guess is this may have a different cause again, possibly linked to bile duct infection.

@BryanKrause Please review whether recent edits have addressed the concerns of the notice you posted. I'm sure there's room to improve this answer further, but I'm not sure what, if anything, still needs a reference or citation added.

@J.G. I still don't feel like your answer addresses the actual question in the OP, it's mostly about why fever is useful against some pathogens plus some added speculation. I'll remove the notice, however, because the notice is only meant to draw attention to a lack of references.

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text:
Gene cluster of interest not being amplified in PCR
In a lab, I currently have a sample of Rhizobium sp. NT-26. This bacteria is a chemolithoautotrophic arsenite-oxidizer, and I want to clone the arsenite oxidase genes into another bacteria strain in hopes of expression of those genes and learning more about arsenite oxidation and resistance. My first step of this experiment was to purify the plasmid DNA of a colony of NT-26 that I grew on a TSA plate. For this, I used the Omega Bio-teK E.Z.N.A plasmid mini kit I. After using the kit, I was left with 40 microliters of plasmid DNA solution. Afterwards, I wanted to amplify the genes of interest through PCR. The sequence of this gene cluster is listed on NCBI Nucleotide right here: https://www.ncbi.nlm.nih.gov/nuccore/AY345225. My main challenges for this project are designing the right primers for correct amplification, and the fact that this sequence is 9 kilobases, so I would need a high-fidelity taq polymerase blend. The main problem that I will focus on is the design of the primers.
For one, I knew that I would be cloning this gene cluster into a plasmid expression vector for electroporation into a strain of E. coli. Because of this, I decided that I wanted to design my primers with restriction sites already attached. Long story short, I attempted PCR a total of 17 times, and I have not found the correct length of sequence in electrophoresis. I have tried PCR with many variations in the program and various other changes, and I have come to conclude that there is something wrong with my primers. I would like to go over the details of the project, and maybe I can receive a hint as to what I have done wrong.
The gene sequence that I am wanting to amplify consists of 6 total genes. The first four genes are aroB, aroA, cytC, and moeA1 (Santini et al. 2010). These genes are in one gene cluster. The other two genes are upstream, and they are AroS and aroR. These two gene clusters compose a two-component signal transduction system that encode for the autotrophic oxidation of arsenite. In her original publication, Dr. Joanne Santini added the link to the sequence of all 6 genes on NCBI Nucleotide. I have listed the link in the above paragraph. I went on Addgene's Genome Compiler and found the exact sequence from NCBI, and I have pasted a screenshot of that below. For some reason, the actual genes I am interested in amplifying do not start at the beginning of the sequence on NCBI. Instead, the first gene, aroS, starts at 424th nucleotide. From nucleotides 1-423, the Genome Compiler listed that as "unknown". For that reason, I decided to get rid of those nucleotides, and just amplify the rest of this. The same thing happened at the end of the sequence, where the last gene, moeA1, stopped at nucleotide 8,263. From then on, the Genome Compiler listed the rest as "unknown". I decided not to deal with the unknown regions, and just amplify the genes i am interested in.

The first gene of this sequence, aroS, starts with ATGAGCCTTCTCGAGC. I know that for designing primers, the forward primer should match the sequence of the beginning of the gene of interest. For this reason, the forward primer contained ATGAGCCTTCTCGAGC. Since I was cloning it into a vector, pBAD30 (the map is listed here https://www.addgene.org/vector-database/1847/), I wanted to add a restrction site to the forward primer. I found that kpnI would work for my sequence. The sequence of kpnI is "GGTACC", so I added it to my forward primer. The primer so far is typed like this: GGTACCATGAGCCTTCTCGAGC. I also learned that a sitting sequence should be added to the beginning of the primer, so I arbitrarily added four letters to the beggining "GTAT". After all three of these additions, my finalized forward primer is GTATGGTACCATGAGCCTTCTCGAGC.
Designing the reverse primer is where I am not completely sure on the correctness of my design. The last 18 bases for the last gene, moeA1, are GAACCGTTCGCAATGTGA. I knew that the reverse primer should be a reverse compliment, so I found the reverse compliment to be TCACATTGCGAACGGTTC. As for my restriction site, I decided to use xmaI. The sequence for xmaI is "CCCGGG", so I added that sequence onto my reverse primer. The sequence so far is CCCGGGTCACATTGCGAACGGTTC. Just like the last one, I added the bases "GATA" as a sitting sequence. The final reverse primer sequence is "GATACCCGGGTCACATTGCGAACGGTTC".
After I designed both primers, I pasted those sequences into Integrated DNA Technologies and ordered primers in solution (100 mM with IDTE). For a PCR kit, I used the Expand Long Range dNTPack from Millipore-Sigma. This PCR kit included enzymes, nucleotides, and all buffers needed for PCR.
After the primers were delivered, I set up a few mastermixes for PCR. I followed the manufacturer instruction for setting up the mastermixes and the program (https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Roche/Bulletin/1/elongnrobul.pdf). The melting point of my forward primer was 60.5°C, and the melting point of my reverse primer was 64.4°C. Because of this, I chose an annealing temperature of 57.5°C. I am slightly worried about the difference in melting temperature and the effect it could have on annealing, and I realize now that I could have adjusted the GC-content of both of the primers to generate closer melting temperatures. However, I do not think that is causing the lack of amplification. One concern that I have about my mastermixes is that I do not know the concentration of DNA in the purified plasmid solution. Each matermix should have up to 500 ng of DNA, but I have used 1-8 uL of DNA solution in each mastermix. Could there be a possibility of too much DNA? Too little? I have tried many different variations, and none have worked. For the most part, each mastermix has used 3 uL of the given DMSO.
On my 17th run of PCR, I did receive some sort of result. As I mentioned before, I did not mess with the unknown regions of DNA, so our final sequence of the 6 genes should be about 7.8 kilobases long. After PCR, I ran it under a gel, and this is what I saw:

In the third lane, the bands of DNA were the brightest. Suprisingly enough, for the third lane, I added a colony of our bacteria to the mastermix for the DNA source, and a band was produced. Most of the lanes show a band of DNA, but the bands are not quite at the 7.8 kb region, so I'm thinking that it is not our desired product. Could this possibly be our product, but impurities slowed the travel of DNA? If so, I would like to know if I should continue with restriction digestion of the insert and pBAD30, and then ligation.

A few things to consider:
Template:

Are you sure the template you want is on a plasmid, and not in the Rhizobium genomic DNA? (In which case it would not be present in DNA purified with a plasmid miniprep kit - you would need to do some kind of genomic DNA prep instead.)
Have you measured the concentration of your template DNA? I typically put ~2-10 ng of template DNA in a 50 ul PCR reaction. If you are adding undiluted DNA there's a chance it could be way too much template, which can adversely affect amplification.
What is your template dissolved/eluted in? Tris or water should be fine - if there is any EDTA in it (such as in TE buffer), it will interfere with PCR.

Primers:

Your primers look good, except that I would recommend using a longer "sitting sequence" - 5-6 nt.
I would not worry about the melting temps. I always use 55°C for annealing, except in rare cases where there appears to be erroneous/nonspecific annealing.
Do you dilute your primers to 10 mM working stocks? Is "IDTE" a buffer containing EDTA? That would likely interfere with the PCR, even if you dilute it 10-fold in water. I recommend ordering oligos dry, dissolving them to 100 mM in sterile water, then diluting 10-fold to 10 mM, also in water, for your working stocks.
One thing you might consider is amplifying first without any restriction sites on the primers, then cloning the PCR product into a blunt vector or TOPO vector, then PCR'ing from that with your primers with restriction sites. This can sometimes help with tricky PCRs, or when amplifying from complicated templates like genomic DNA or a cDNA library.

Polymerase / PCR cycle

It is advisable to try a couple different polymerases. I have had good results with long products using KOD polymerase.
I also recommend trying several different magnesium concentrations, as well as trying with and without DMSO.

As for the "wrong"-size product - if you have enough of it, you could go ahead with the cloning, in which case you'll find out soon enough if it's the wrong thing. You can also check it's identity by doing some diagnostic restriction digests, or directly sequencing the PCR product with a couple internal primers.

One of the reasons why region may not be amplified via PCR is that the region is much larger than is thought. This may happen if there is a repeat of variable length in the region that may be difficult to sequence precisely, or have a different length in your sample than is shown inside NCBI database.
In the case we hit it was Homo sapiens. I am not sure about Rhizobium but who knows? Repeats seem not uncommon, see here.

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Could a strong magnet field repel the body before damaging it?
Could a magnetic field be strong enough to damage the body or erase the brain?
Blood is slightly diamagnetic, so if the field was strong enough, could it repel a body evenly?
Could a diamagnetic material go through electrolysis with water then ingested to give the body more diamagnetic properties?

A strong magnet can repel a body, but the effect is due to small diamagnetism of every atom.
You can see a picture of a levitating frog and a video here. And a very good explanation and more videos here.

Just to show how strong the magnetic field is: This was filmed with a telescopic camera pointed at a mirror above the container with this tiny frog. Any other setup would ruin their cameras.

While mammalian blood is characterized by diamagnetism (as demonstrated here), as far as I know, the human body as a whole is more or less electrically neutral—that is, with all of its summed components the negative and positive charges balance each other out or there are extremely insignificant differences.
If you want to get strict though, it's theoretically possible to use a super strong magnet to repel or attract someone's entire body to a meaningful degree as long as it's not electrically neutral at a given point in time. But even in the video linked above, the guy is using a super strong magnet to observe its repulsive effects on blood and the blood is just barely moving away; definitely not forceful enough to where someone wouldn't be able to resist moving with just their body weight alone.
So to answer your question: can someone be repulsed or attracted by a magnet practically? No. Can someone be repulsed or attracted by a magnet theoretically? Yes.


text:
When does the brain stem appear in humans?
This article states:

Once the neural tube closes, at around week 6 or week 7 of pregnancy,
  it curves and bulges into three sections, commonly known as the
  forebrain, midbrain and hindbrain. Just to the rear of the hindbrain
  sits the part that will soon turn into your baby's spinal cord. Soon,
  these areas bubble into those five different regions of the brain that
  we're most familiar with: the cerebrum, cerebellum, brain stem,
  pituitary gland and the hypothalamus.

How "soon" after 6 - 7 weeks is this soon the article talks about? When does the brain stem appear in humans?
Fetal Brain Development

To correct the article you referenced the neural tube closure normally occurs by the fourth week of pregnancy (28th day after conception). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279093/
The Brainstem is comprised of three parts:

Medulla (Melincephalon)
The Pons (Metincephalon)
The Midbrain (Mesencephalon)

During fetal development
  the brainstem is formed by:

the myelencephalon (fifth vesicle) which will develop into the medulla (Melincephalon)
the metencephalon (fourth vesicle) which will differentiate into the pons and cerebellum
and the mesencephalon (midbrain)(third vesicle)

An outline of the development of the brain stem is depicted in the image below:

Pansky, B. 146. Introduction to Brainstem Development. Retrieved from https://discovery.lifemapsc.com/library/review-of-medical-embryology/chapter-146-introduction-to-brainstem-development

By the end of the sixth week the rudimentary development of the five brain vesicles is complete. The cerebral hemispheres have grown and now cover the diencephalon, the mesencephalon and the cerebellum, which has only just begun development.

Montfort, G. J., & Boon, R. Stages of Brain Development. Retrieved from https://www.bondingandbirth.org/uploads/5/4/1/5/5415260/06_stages_of_brain_development.pdf

I'm not sure that gives the answer, it jumps from day 39 to day 90 where the parts which eventually will turn into the brainstem parts to the part where they are named as the brainstem parts. Which day do you get from the chart?

@Pablo There is no 'day.' Development is a continuous process.

@BryanKrause days are stated for many other organs/parts. Ie, heart when it starts beating. I'm assuming here when it starts to fullfill the function is meant to.

@pablo the definitions of the 3 different regions that comprise the brain stem should help because they aren't necessarily defined by function but rather structure and/or location with reference to adult brain.

@Pablo Even the "heartbeat" day has nothing to do with a heart beat. It's just when the electrical activity of what will become the heart is detectable from the outside. There is no functioning circulatory system at that time.


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Is the tendon width determined by genetic predisposition, and if so, is genetics the sole factor?
Tendons' widths vary widely across humans. E.g.:

{1}: "the mean patellar tendon width was 26.10mm (SD = 3.31; range 18.33mm-33.33mm)"
{2}: "Size of the patellar tendon width, measured at the same location in each patient, ranged from 24 to 35 mm"

Is the tendon width determined by genetic predisposition, and if so, is genetics the sole factor?
I read on {3}:

Tendon length is determined by genetic predisposition, and has not been shown to either increase or decrease in response to environment, unlike muscles, which can be shortened by trauma, use imbalances and a lack of recovery and stretching.{4}

But it didn't mention the tendon width.

References:

{1} Dundon, J. M., R. J. Markert, and M. W. Lawless. "Correlation between patella and patellar tendon width: an anatomic study." Clinical Anatomy 25, no. 3 (2012): 398-400. https://www.ncbi.nlm.nih.gov/pubmed/21853464; https://doi.org/10.1002/ca.21241
{2} Shelbourne, K. Donald, Richard A. Rubinstein JR, Charles D. VanMeter, John R. McCarroll, and Arthur C. Rettig. "Correlation of remaining patellar tendon width with quadriceps strength after autogenous bone-patellar tendon-bone anterior cruciate ligament reconstruction." The American journal of sports medicine 22, no. 6 (1994): 774-778. https://www.ncbi.nlm.nih.gov/pubmed/7856801; https://doi.org/10.1177/036354659402200608
{3} https://en.wikipedia.org/w/index.php?title=Tendon&oldid=885716020
{4} Young, Michael. "A Review on Postural Realignment and its Muscular and Neural Components" http://www.elitetrack.com/article_files/posture.pdf  (mirror)

My best guess is "We don't know. No study has investigated this question. However, given that tendon length has a non-zero heritability and given that a lot of bone, muscle and tendon properties are heritable , it is probably safe to assume that tendon width is somewhat heritable."

@Remi.b Makes sense,  thanks for the feedback!


text:
How do you interpret the resulting bands of gel zymography?
I would like to clear up some things for gel zymography. I understand that bright bands show proteolytic activity. But which molecular weight do these bands correspond to? Is it the weight of the active enzyme or is it the weight of the digested substrate?


text:
What kind of spider is this? Bolivia
Can anyone help me identify this spider found in Cochabamba, Bolivia. It is quite small. This photo shows it on a normal mortar layer between brick.

It's a (possibly subadult) female Black Widow. Subadult females often have some level of red or red and white markings on the upper surface of the abdomen, and females of some species retain those markings even into adulthood - the notorious Redback (Latrodectus hasselti) being an examnple of that. Black and red is a very common "Danger!" signal in nature, so you should be a little leery when you see it.  This one looks like Latrodectus mirabilis, which Garb, Gonzalez and Gillespie have marked in the area of Bolivia. I know almost nothing of this Widow, but since most Black Widows are pretty similar in their habits and venoms, I feel pretty confident in saying that you probably do not want to get bitten by this spider. It would be extremely painful, and would probably give you a couple of very bad days until the effects eased up. Widows don't usually tend to bite unless physically injured, but you probably want to shake out your boots in the morning before putting them on..
Here's the link to the Garb paper:
Garb, J.E., González, A. and Gillespie, R.G., 2004. The black widow spider genus Latrodectus (Araneae: Theridiidae): phylogeny, biogeography, and invasion history. Molecular phylogenetics and evolution, 31(3), pp.1127-1142.
And here's a nice Spanish language blog
that features this photo of L. mirabilis:


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Base pair and amino acid weights?
How does a base pair weigh approx. 650 Da (which is two paired nucleotides) but an amino acid (3 nucleotides) weighs only approx. 110 Da ?

There seems to be a  misconception: amino acids do not consist of nucleotides, but are coded by them. Please look up the structures of amino acids and nucleotides and read about the process of biological translation. If the question remains, please edit your post  and add your prior research on that topic.

Welcome to SE Biology. Please take the time to take the Tour and consult the Help on asking questions. You will see that you are expected to do some research before posting. Try looking up amino acid on Wikipedia etc. You will discover what an amino acid is. It is not a trinucleotide.

In short: base pairs are not composed of amino acids but nucleotides. Base pairs are parts of the DNA, while chains of amino acids forms proteins.
Certain parts of the DNA (called genes) are transcribed to messenger RNAs (mRNA) which are sequentially translated to amino acids and the chains become proteins. 3 bases (called a codon) code for 1 amino acid.
Please look up the Central dogma, DNA, mRNA, protein and translation for further information

Yours is a question based on a wrong premise.
First, it is very important to note that an amino acid is not made by sticking together 3 nucleotides. However, in the process of translation, the mRNA sequence is read by groups of three nucleotides, named codons. For example, 5'-AAA-3 is a codon that anneals with the 5'-UUU-3' anticodon. So where is this anticodon?
Unlike DNA, which is double-stranded, mRNA is single stranded. Other single-stranded RNAs called tRNA contain these anticodons. In the previous case, the 5'-UUU-3' tRNA always contains the amino acid lysine on its 3' end. This is because there are special enzymes called aminoacyl-tRNA transferases that ensure that a particular tRNA always links to a particular amino acid.
Long story short, the ribosome allows the tRNAs to orientate themselves so that the amino acids they carry react and form a peptide chain. The incoming tRNAs take this growing chain of amino acids, until a special "tRNA" stops the process and the amino acid chain is "set free". Obviously, this chain once complete is not bound to any nucleotide, so once you calculate the average molecular weight of a proteinogenic amino acid you don't have to take them into account.


text:
How to download different kinds of data from NCBI eutils?
I have been researching NCBI eutils and wish to get some 'big data' from it. I know that I can construct queries to query one of (I think) 8 databases, like this:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=nucleotide&id=2765657
which queries the nucleotide database for an id 2765657.
I am looking for a query that will return:

genetics sequences.
functional annotations of the sequences (e.g. exons, introns)
metadata (e.g. chromosome)

Would anyone be able to show an example of how to search the eutils to get samples of records as described above?
I would need to know:

Which database to search?
how to list available records?
how to query for a sample of the records?

Any help would be greatly appreciated.
Many thanks.

The Entrez module in Biopython is able to do all the task written here.

thanks Shred, I am aware of this module - but have not tried it yet. Would it be able to help me in determining which database would be best and which filters would be useful? Many thanks

I am looking for complete protein coding gene sequences, from one organism, preferably expressed in close temporal and spatial proximity, that have have quality annotations (e.g. exons, introns, codons). I have no particular preference on the model organism. Just looking for something to exercise LSTMs on.

ok I got a gff3 file from GENCODE - this looks good

Downloading all this using an E-utils search would be cumbersome as you would have to search against multiple databases. For your specific needs, a GTF/GFF3 file would be good. Basically, a GTF/GFF file has genome annotations (positions of features) and includes features like exons, CDS and in some cases even special codons (such as that for selenocysteine). This file would not have the sequences but you can retrieve the sequences from the corresponding genome sequence fasta file using the co-ordinates described in the GTF file. There are several software tools that can do this; for example gffread and bedtools-getfasta (you can even write your own script which would not be very difficult).
You can download the GTF and the corresponding genome fasta files from these sources:

ENSEMBL (many organisms)
NCBI-RefSeq (many organisms)
UCSC genome browser (many organisms)
GENCODE (for human and mouse) and modENCODE (for Caenorhabditis worms and Drosophila)

You should look at the details of the genome assembly. Different releases/sources may have different extents of curation.


text:
What causes bio electricity?
When it is said that “electrical impulses sent from the brain” how is this charge flow produced?

See wikipedia > action potential


text:
How many neurons do we have in our forearm?
I am developing a neural interface, getting signals from the forearm and mapping them to hand gestures. The question we have at the moment is what is the upper bound of information bandwidth that we could tap into, meaning if we were to engineer an electrode so small that we could listen to every single neuron in the forearm, how many neurons could we listen to?

Welcome to SE BIology. Please take the time to take the Tour and find out about this site. After that, the Help on asking questions should be your next call. You need to show that you have done some research for yourself first. What attempts have you made to answer the question yourself?

Your main contributor to the neuron count are going to be touch sensors. The fingertips are quite dense with them.

Yes, I am aware of the homunculus man, but I haven't succeeded in finding any quantitative estimate whatsoever that supports the representation of the homunculus man as having such a high density of motor and sensory neurons in the hands.


text:
Re-stain slice using a different secondary antibody?
I stained a free-floating ~300uM brian slice using 4 different 1º antibodies (rabbit, chick, mouse, rat).
For the mouse primary, I mistakenly used an Alexa-350 secondary, when I should have used 594.
The microscope we have in lab cannot detect the 350 fluorophore, so I'm wondering if I can re-stain the slice with the anti-mouse 594 secondary.
Thanks for your advice !
[cross-posted in reddit/labrats]

Are they the same clone? You might have blocked all the binding sites so you'll get a poor/no/noisy signal with the 594.

Thanks for your input ! They are both Alexa conjugated anti-mouse secondaries, so I'm guessing they use the same clone to make them. (?)


text:
What is the largest species of polychaete?
My Google searches seemed to avail no results. My question is: What is the largest living species in the class Polychaeta?
That's about it. I understand that there will be few accessible weights for these worms so length will suffice.

According to the Smithsonian:

The longest of all known polychaetes was found in Port Jackson, Australia. It was a member of the family Eunicidae, consisted of approximately 1,500 segments and was nearly 6 meters long when alive.

The Eunicidae consist of numerous species (including the super cool bobbit worm), many of which get fairly large.

Though, typically 3 m in considered quite large for worms in this group (e.g., see Uchida et al. 2009 for a description of a 3 m long Eunice aphroditois).
Polychaetes & Allies: The Southern Synthesis also suggests that members of Eucinidae can reach 6 m in length. From p. 94 of this report from the Australian Biological Resources Study:

Eunicids have many segments and may attain a length of up to 6m...
...Eunicids range from less than 10cm to 6m in length, and consists of up to 1500 segments (Fauchald 1992a).

Supposedly, according to Schulze 2011:

The Australian museum even holds a specimen that reportedly was nearly 6 m long when
collected (Fauchald 1992 and pers. comm.)

Salazar-Vallejo et al. (2011) also cite evidence of 3+ m long polychaetes in the genus Eunice as evidence that the genus is "the largest polychaete species and placing them among the longest benthic invertebrates."

None of these worms compare to a species of ribbon worm (phylum Nemertea) called Lineus longissimus that can reach 55 m in length! [Sources: 1, 2].


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What are primary reasons for the failure to localise/anchor sequences in genome assemblies?
My question concerns the incorporation of individual sequence reads into chromosomes during gene sequencing projects, especially those with larger genomes such as Drosophila melanogaster or Homo sapiens.
There are some sequences or short contigs that it has not yet been possible to incorporate into the larger chromosome assemblies.
What are the reasons for this failure?

I'm going to re-interpret this question slightly to make it easier to answer:
"Why do genome assemblies frequently consist of large numbers of short contigs rather than a relatively small number of long chromosomes (or full replicons of other types)? And how could I make my assembly better?"
De novo sequence assemblies (usually) consist of a set of contiguous sequence fragments ("contigs") that have been derived from shotgun sequencing by some heuristic. If sequence assembly did a perfect job, we would expect that these contigs would be full chromosomes. Instead, what we observe is lots of sequence fragments with uncertain relationships to one another. In this common case, we think that some of the contigs could be stitched together ("localized", "anchored", "scaffolded") meaningfully into chromosomes, but we aren't sure how.
For de novo sequence assembly, there is no ground truth to compare to. So all of the information for generating assemblies comes from the starting sequences (which are usually "reads", small shreds of sequence that come off of a sequencing instrument). The heuristics that generate contigs from reads consist of finding overlaps between different starting reads and trying to extend them into the largest possible partially overlapping groups of reads, using some assumptions about rates of error in the sequence of the reads (and other variables). See wikipedia or this paper (figure inset) for a little more information on this.

It turns out that there is a body of statistical theory that governs how large these overlaps will be, and therefore how big/complete your contigs will be. This body of theory says that the size and number of contigs is predictable to some degree from the size of the genome you're trying to assemble, the length of the reads, and the number of reads you have.
Some genomes, like maize, wheat, or the human genome, are also harder to assemble because they are "repetitive". This means that there are lots of very similar sequences in different places in the genome. So when you take a read from one of these places, you are uncertain which one of these very similar regions it comes from. These repetitive regions are hard to resolve unless you have very long reads or some parallel information, so they also lead to gaps in sequence. Such regions will also tend to be "collapsed", meaning that you only have one contig representing a repeat that should actually be present as several contigs with different locations in the assembly.
Sources of parallel information that are helpful are proximity ligation (methods such as Hi-C), genetic maps from crosses, or optical mapping. These orthogonal sources of information express relationships between contigs in terms of their closeness on a chromosome. Here is a paper with more information on these topics. Recently, long read technologies such as PacBio or nanopore sequencing are starting to read through large repeats, but they are still usually not reliable enough to fully assemble even smallish genomes "telomere-to-telomere".
So, if there is a recipe for localizing/anchoring/scaffolding fragmented assemblies, here is roughly what can be done:

get more reads
get longer reads
get orthogonal information about contig placement (e.g. proximity ligation, genetic maps, a closely related assembly, etc.)

Hope that helps.


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Is it possible to stop more/extra fat from being stored in the body?
I don't mean simply by restricting eating or upping the activities, but a way to basically stop the body from adding more fat on itself down on the bio level. For example, I'm not too knowledgeable on this, but I believe fat is stored when the body can't make any extended use of extra energy put in to it.
Given such, could we simply direct the body to only use the energy needed and dispose of any "extra" while not storing it as fat/triglycerides? I know there are drugs that can speed up metabolism and etc., but this only heightens the body's ability to remove said fat -- not stop the process at which it is stored
This would be a great thing because then we could assure the body only uses the energy on what can be beneficial to us -- all the "rest" can be removed and not stored on us and being a con instead of a pro.
So in summary: Is there any feasible way this could be theoretically possible, given our biochemistry/physiology?

Fat storage comes from conversion of glycogen (a glucose polymer) to triglycerides (fats).  (source: https://en.wikipedia.org/wiki/Glycogen).
Intuitively, the simplest way to prevent fat storage is to block conversion of glycogen to fats. Unfortunately, this will cause a glut of glycogen which can cause an entirely different set of problems (see https://www.hopkinsmedicine.org/health/conditions-and-diseases/glycogen-storage-disease ), so you would want to couple this with a mechanism to eject excess glycogen.
Referencing what user1136 posted: uncoupling oxidation from phosphorylation is a really bad idea. That would basically "burn" fuel while blocking the expected ATP outlet. This will cause a dangerous energy buildup in the mitochondria which has to be unloaded somewhere - provable simply by conservation of energy. Energy can be converted to other forms of energy, but it is never destroyed. Physics is the ultimate anti-cheat tool.
Blocking expected energy outlets is almost always a bad idea in practice. Just to name some practical examples:

In archery class, instructors will warn you never to "dry-fire" a bow (draw the string back and release with no arrow). This can compromise the bow's structural integrity, causing it to splinter, snap, or explode later.
Microwave ovens should never be operated empty with no sink for the electromagnetic radiation they produce - this can damage them. See https://physics.stackexchange.com/questions/309154/what-happens-in-an-empty-microwave-oven for more info.
If you jam the pistons in a standard cylinder-based combustion engine (prevent them from moving), you end up with a lot of energy that needs to go somewhere, which will end up as massive vibration and extra heat - either of which could damage the engine as the design never expected this to happen.


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What type of Caterpillar is this?
What type of Caterpillar is this?

My hand brushed against this last night and it burned and itched immediately. Today it's starting to blister, is red, and itches all around the bumps. I was camping at the John Knox Ranch in Fischer, Texas. It was dark and I reached to grab the chair when I suddenly felt pain. It was about two inches long. This is the reaction I initially got. I didn't even feel when i brushed against it until i started feeling pain.
These were the best pictures I could get.
Any help is appreciated!!

Picture is not very good, but I think this might be an Eastern Buckmoth Hemileuca maia caterpillar.

 Photo credit: Gary L. Spicer ; Source: butterfliesandmoths.org
Description: From the University of Kentucky:

The two-inch long Buck Moth caterpillar is brown to purplish-black with numerous yellow spots. The body is protected with branched reddish spines that may have red or black tips....
Common...from spring to mid-summer.

Reaction: Your wound/reaction would not be an unexpected reaction from touching this caterpillar species. From UFL IAFS:

The spines in the buck moth occur on raised, sclerotized (hardened) portions of the larva's cuticle that are known as tubercles and scoli. The spines found on these structures are associated with venom glands that occur within the caterpillar's body... The sting produces pain immediately, which then spreads to nearby lymphatic nodes. The caterpillar's sting then causes swelling and redness to occur. These symptoms can last for as little as a day to over a week. Wagner (2005) reported that the stings he received from a buck moth caterpillar were still present after ten days and the venom of the caterpillar caused a small hemorrhage where each spine had stung him. According to Diaz (2005), severe reactions to the venom of the buck moth (such as anaphylaxis) are rare.

Treatment: The video here suggests running your hand under cold water, air dry, use tape to get out remaining spines, and then apply some ice. UFL IAFS corroborates this approach as well.

Range: According to the incidence map on butterfliesandmoths.org, H. maia is found in Texas:

Wikipedia corroborates the range of this species to include Texas.

it was spiney/spikey. Thank you for your response.


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What exactly happens to animals that fail mating rituals?
Quite a few animals (usually males) participate in various mating rituals to showcase their fertility as mates. While presumably, the successful ones get a chance to mate with females, it occurred to me that I don't actually know what happens to the ones that fail. I would assume that not all the ones that fail don't mate, as that would result in roughly 50% of the male population being frustrated sexually. But I can't figure out an alternative, do they get another chance to fight other losers? Do they just mate anyway at a lower rate?

I think it follows a bell curve with the most successful individuals having more than average and the less having less, and some having none.

this depends on the species, it ranges from death to try again to alternative mating strategy. Many spiders that fail get eaten.

A bit late to the party here but something important to note is that females aren't always strictly faithful to the "winners" of animals. In many cases losers actually employ a "losing" strategy where, while continuing to lose, mate with females on the side not immediately taken up by the winner. This is very common in social animals as far as I know but I am aware of species, especially individualistic ones, where (as the previous answer says) mating follows a more bellcurve pattern leaning towards winners meaning the females are just looking for the best options, and in rarer cases, only winners mate while losers don't get to at all. If only winners mated, it'd mess up the gene pool pretty fast, so females will mate with winners as a first choice, and then also try with next best options. Hopefully that helps answer your question, but I'm not a doctor in bio (yet) so take it with a grain of salt. Source: my Intro to Evolutionary Bio Cornell class, yada yada, and a few Youtube videos I'm unwilling to dig up.

What exactly do you mean by "if only winners mated, that would mess up the gene pool pretty fast"? Many animals produce huge numbers of offspring, very few of which end up reproducing. E.g. octopuses hatch tens of thousands of eggs. Genetically, it doesn't matter why an animal didn't reproduce; failure at a mating ritual is the same as failure to avoid predation.


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Carbon Dioxide, sea water, diatoms, and oxygen
I recently viewed a documentary called “Flying River Observed in Tallest Structure in South America, National Geographic”  (https://www.youtube.com/watch?v=HjpPsZTwsaM).  In this film, as an aside, it was mentioned that a major source (the major source?) for the oxygen required for life on earth are the diatoms in sea water.
It was mentioned that diatoms have shells.
In a separate article (whose source I do not remember) it was mentioned that the sea, because it is being  exposed to higher and higher atmospheric  carbon dioxide levels, was becoming more and more acidic. This high acidity was making it difficult for sealife to form shells.
Will this decrease the number of diatoms in sea water?
Will this affect the amount of oxygen available to life on earth?

Lower pH (from CO2 reacting with ocean water to form carbonic acid) makes formation of bicarbonate shells more difficult. this would reduce the fitness of any bicarbonate-shell forming organisms. However, diatoms, to the best of my knowledge, usually have shells made of silica, so I am not sure to what degree lower pH water will have on the formation of their shells and their overall fitness. However, communities and competitive interactions would certainly change as other organisms' fitnesses are impacted, which very well could impact diatoms indirectly.


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Which complexes physically pump protons in photosynthesis?
The cytochrome b6f complex is often drawn as pumping protons, but then someone told me that actually there is no pumping, rather the Q cycle.
According to this view, what actually moves the protons is that a PQ takes up 2 H+ from the stroma as it is reduced and another two PQ release 2H+ into the lumen as they reduce PC and partially reduce the first PQ. The complex, therefore, does not physically pump the protons.
I now wonder if any of the photosynthetic complexes pump protons. For example, the PSII complex has PQ reduction with 2H+ removed from the stroma and its oxygen evolving complex releases O2 and 4H+ into the thylakoid lumen, so this could be its ‘pumping’ contribution.

General Approach
Although I am not an expert in this area, as an ex-chemist I find this topic one of the most fascinating and fundamental in chemical biology. I have constructed an answer starting from my copies of the 5th (available on line) and 6th editions of Berg et al. Biochemistry (2003 and 2007, respectively), and then searched the Protein Data Bank for structures of the cytochrome b6f complex, and worked from the papers associated with more recent entries.
Definitions
First, it is important to be clear on the following:

What is meant by a proton pump (physical or otherwise)?

I think that the question — and the scientific community in general — probably assumes a pump to have some sort of channel or revolving door through which the protons are driven from one side of a membrane to the other. If one were able to tag an individual proton to follow it, one would find that it was physically translocated across the membrane. (A model for this might be the Na+/K+-ATPase. See also Berg et al. Biochemistry in Chapter 13 “Membrane Channels and Pumps” although this does not actually mention pumps in relation to either photosynthesis or oxidative respiration.)
This would be in contrast to the net translocation of protons across a membrane by chemical sleight of hand. A reaction at one side of the membrane would consume protons, and a reaction at the other side would emit protons. However no individual proton would pass through the membrane.
Both these processes would be working against a concentration gradient and require energy, in this case in the form of reducing power — not, of course, ATP.
This difference is illustrated in Berg et al. with respect to cytochrome c oxidase (Fig.18.21) in which both processes occur, where the authors refer to ‘pumped protons’ and ‘chemical protons’:

And the answer is…
That the situation in photosynthesis is similar to that for the oxidative electron transport chain:

Net translocation of protons across the membrane is achieved both
  chemically (in photosystem II) and by ‘pumping’ (in cytochrome b6f).

So the ‘someone’ in the question was correct in saying that the chemical type of net translocation occurs in photosynthesis, but was incorrect in saying that this was at the cytochrome b6f stage.
Structural Evidence
The cartoons shown above (taken from Berg et al.) are based on a wealth of indirect experimental data. However some of us are never convinced until we have seen the stigmata. The structure of the cytochrome b6f complex was reported in Science in 2003 by William Cramer’s group, and in the diagram below (my modifications) there is a channel through which the passage of protons is indicated.

A more recent (2013) paper from the same group considers the proton transfer pathway in cytochrome b6f in more depth, and I reproduce below Fig. 1B from that paper to indicate the type of molecular detail.

Heavy reading, but wonderful stuff!

in my undergrad lectures I thought we were told that Mitochondrial complexes I, III and IV do physically, via internal channels, 'pump' protons across the membrane, mainly in contrast to complex II not doing so. Is this wrong then?

@Mirte — As I commented previously, my initial answer was wrong and has been revised. Apologies. I have only addressed the question of proton pumps in the mitochondrial complexes indirectly, as the final answer was long enough restricted to photosynthesis. But, yes, proton pumping (and some 'chemical' net translocation) is thought to occur in mitochondria. There is a 2011 Annual Review of Biochemistry article on the topic.

Thank you, your revised answer is great and I've accepted it!


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Increase rate of change in coding regions?
If a sequence is under selection will it acquire  more changes over time because of faster fixation than if changes were neutral? Is this true or am I missing something?

Generally speaking, there are sequences that are under purifying selection (where new mutations are often deleterious) and there are sequences that are neutral. Sequences under constant positive selection do not really exist. So, when you ask

If a sequence is under selection will it acquire more changes over time because of faster fixation than if changes were neutral?

No! If a sequence is under selection, then it is under purifying selection. As such the rate of fixation will be lower than for a neutral sequence.
If you have a sequence, where most mutations are beneficial, then it the sequence would fix new mutations at a higher rate then a neutral sequence. However such sequence don't really exist! If it were to exist, then mutations would quickly fix such that new mutations would then be deleterious again.
Of course, a single beneficial mutation has a higher chance of fixation than a neutral mutation. Also, when a mutation is under selection (whether purifying or not), the expected change in heterozygosity in the population is higher than if the mutation is neutral (the expected change in allele frequency is equal to the additive genetic variance for fitness at this locus). But those are not details you are asking about.


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What species is this lizard?

A small green lizard (20 cm in size). It was found in the direct neighboorhood of a house, in a small village in the Hungarian hills south of the Balaton lake. It was found in the middle of the day.
Our first guess would be Lacerta viridis. Is this correct?

By the picture and the official distribution it looks to be as you said a Lacerta viridis.
Some references and distribution here:

https://www.iucnredlist.org/species/61530/12507156
https://commons.wikimedia.org/wiki/Lacerta_viridis
http://reptile-database.reptarium.cz/species?genus=Lacerta&species=viridis

In Western Europe we have a brother specie Lacerta bilineata.
Example in Geneva:

The distribution maps shows that Lacerta viridis is mainly present in Easter Europe (including Hungary) and Lacerta bilineata is present in the Western Europe.
Both species are similar and the male get the throat blue generally during the breeding season.
This site have also a description of the specie.

I think it's the biggest lizard locally in most places, i.e. in France it's the biggest lizard i have seen, up to 40cm. the ones with the most blue are the best, they vary a lot.


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If overcooked hard boiled eggs show these green sulfide rings, why do scrambled/fried eggs not show this?

In the image above, the dark green rings are ferrous sulfide rings, caused when the sulfur from the egg white reacts with the iron in the egg yolk when the egg is overcooked.
I was wondering, given the same circumstances, why do we not see our scrambled/fried eggs coated with this layer of ferrous sulfide?

I'm voting to close this question as off-topic because it is Food Science and not Biology in terms of SE Biology.

Although I htink David's concerns are valid, I disagree with him as our cooking stack doesn't typically attract these types of food science questions that are more focused on science vs food, and it certainly doesn't typically provide an answer that would adequately address the OP's science-leaning question. This question is probably most on topic either here or at Chemistry SE.

@QuIcKmAtHs, I recommend that you do a bit of research on your own and indicate that you've done so more explicitly here. In doing so, you should be able to convince us that this is in fact a biology-related question (regarding biochemistry) and not simply a chemistry question.

It would seem obvious, at least in part. 1) Proper scrambled and fried eggs are not overcooked, and it's a lot easier to determine when they are properly cooked when they're not in the shell.  2) Scrambled eggs are just that - scrambled - so even if ferrous sulfide did form, it would be mixed in rather than forming a visible ring - though I admit I have vague memories of greenish scrambled eggs from boot camp :-(

@theforestecologist thank you for your comments, I will take note of them.

Scrambled eggs can change color, but you perhaps haven't run into a batch that shows discoloration. It is the same chemical reaction:

Why Scrambled Eggs Turn Green
When serving a large group, a buffet can provide enough food for everyone without the need to spend all of your time in the kitchen. Breakfast is a fairly simple buffet to set up, but there are special challenges when it comes to scrambled eggs. When scrambled eggs sit for a while, they tend to turn green or gray. This is a chemical reaction that happens as hydrogen sulfide in the egg white reacts with the iron in the yolk to form iron sulfide.

Via: https://living.thebump.com/lemon-juice-keep-raw-eggs-turning-green-cook-them-8383.html


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Is it correct that the nicotinic acetylcholine receptor has nothing to do with Dopamin?
As I know Dopamine is almost exclusively produced via metabotropic receptors, is it possible for a nicotinic ACH receptor to influence a dopamineric neuron?
Can a nicotinic ACH receptor cause a dopamineric synapse to create dopamine?
Unfortunately I can't find anything about it.
Edit: rephrasing my question:  Do 2-neural systems exist where neuron A has a nACH-R and neuron B has a dopamineric receptor? And do dopamineric nikotinic ACH-R exist (receptors which react to dopamine)?

Your question doesn't make much sense because I think you have a variety of misconceptions all mixed together. Dopamine is not produced by metabotropic receptors, that statement is nonsense. The (general) order of things in the nervous system is: Cell A releases neurotransmitter onto Cell B, causing it to be more or less likely to fire for some period afterwards. If Cell A releases dopamine, it will affect Cell B if it has synapses on Cell B and if Cell B has receptors for dopamine. Cell A could possibly have receptors for any other neurotransmitter.

Thanks for your clarifications. Do 2-neural systems exist where neuron A has a nACH-R and neuron B has a dopamineric receptor? And do dopamineric nikotinic ACH-R exist (receptors which react to dopamine)?

Still doesn't make sense. Are A and B connected? What neurotransmitters do they release? What is a dopaminergic nicotinic ACh receptor to you? Do you know what acetylcholine is?

Yes, A and B are connected, A has n-ACHR and B has dopamineric receptors. is this constellation possible or not? Is it possible for a neuron with n-ACH-R to influence a neuron with a dopamineric receptor directly?

Let's simplify your question with correct terminology: you have a presynaptic neuron and a post-synaptic neuron. The presynaptic neuron can release multiple signals (neurotransmitters) into the synaptic space, or cleft. The postsynaptic neuron can be equipped with multiple sensors (receptors) that are specific to detect certain signals.
The signal and the sensor don't have to match, although this is costly if it's poorly tuned. Most neurons that are entirely unresponsive are pruned. Darwinian selection makes circuits much more efficient than what pure chance alone would produce, but remember that nature can be quite imperfect and stochastic.
However, you can have neurons that have a dopamine sensor (receptor) and provide an acetylcholine signal (neurotransmitter) and vice versa.
Acetylcholonergic and dopaminergic neurons can be connected. Here is an example.
Also, most people forget that neurons not only form chemical synapses but electrical synapses as well. That means the circuitry does not rely on ligands and receptors.

Thank you for giving a straight to the point answer.

"The presynaptic neuron can release multiple signals" - Although technically true, I think this statement is potentially misleading. Almost all neurons release a single principle neurotransmitter. "The signal and the sensor don't have to match, although this is costly if it's poorly tuned." - that's not how synapse development works, synapses are developed in an interplay between pre and post synaptic cells. "Most neurons that are entirely unresponsive are pruned" - did you mean synapses?

The answer he gave is fine, you don't need to downvote  because the ones you gave are complete trash that didn't help at all. Really pathetic that you are most likely the person downvoting both the question and this answer, which exactly provides the answer that I was looking for.

@BryanKrause My friend Bryan! I don't know what to tell you. You are woefully wrong on every count. These are neuroscience fundamentals we are talking about! Where to being? This is textbook from at least two decades ago. I'm also sure you must be aware that in development, a huge number of neurons are pruned through apoptosis, to remove most of the superfluous elements in the CNS. Lastly, I too thought you were uncharacteristically aggravating to the questioner; in my opinion it was counter-productive. After all, the question was very simple!

Yes I am aware that neurons release more than one substance, but they do not typically release more than one of the typical neurotransmitters. That is, neurons do not release both dopamine and acetylcholine, for example. Your source is talking about corelease of peptides which do not mediate the immediate synaptic response but instead influence the synapse itself. I am worried your answer is misleading to a novice.

My questioning was because the OP showed so little understanding of the underlying structure of the nervous system that I don't think they are ready for this answer.


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Placebo Effect Reactions
Why do some people actually experience measureable effects when given a placebo(fake drugs) versus the actual drug?  Is is the power of suggestion, belief, or something else?

Few examples in which placebo looks effective even if it isn't (Wikipedia):

The condition, for example, common cold heals on its own in participants who received a real drug and in those who receieved a placebo.
In psychological and other conditions in which the participants are asked only how they feel after the treatment, some of them may just think that they feel better.
Sometimes neither the real drug nor the placebo work, but the condition has a naturally fluctuating course, so it looks that they both work.


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What is (probably) the closest living relative of the trilobite?
The trilobites vanished from the fossil record many millions of years ago, but they were obviously arthropods of some sort. Do we know which animals are their closest living relatives? I've heard both Armadillidiidae and horseshoe crabs. Can we tell which is right (or if there is a different answer), and how?

Without their DNA, it's difficult to know the answer to that, from physiology of >250mn year old fossils, perhaps crayfish and scorpions also come from trilobites, also arthropods, they appeared 100 million years afterwards. it's best to content ourselves with a map of genetic distance between shrimps, earwigs, horeshoe crabs, crayfish, and find a map of animals that comes from them. I can't find a genetic distance mapping tool on the web.

There were so many species of trilobites for 300 million years, so perhaps some trilobites species are closer to horseshoe crabs whilst others are closer to woodlice, some trilobites were amphibious and could walk onto the seashore.
If you check this research about horseshoe crabs, there are a dozen fossils that are hybrids between a trilobite and a horseshoe crab, i.e. bellinatus trilobitoides.

 From the family tree you can see some early horseshoe crabs:

this is a harpetida trilobite:

The morphology of the fossils is mostly saved as dorsal morphology and ventral morphology. from the top the are similar to horseshoe crabs, and the different legs are similar to woodlice and bathynomus and horseshoe crabs in different fossils:

There are other living animals that resemble them like Serolina Delaria:

Tadpole Shrimps:

That's from this cool page with images of lots of things like trilobites.
Silverfish:

Bathynomus, similar to woodlice:

The videos of bathynomus are cool: https://www.youtube.com/watch?v=jfnHQPkta-Q

The Tree of Life Web Project is a good resource for these kinds of questions. It looks like we cannot distinguish trilobites' origin from the origin of arthropoda: link. Also, some references on trilobite evolution and systematics from the same source: link.


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Does constant pressure cause muscle atrophy, and if so, why?
I read on https://en.wikipedia.org/w/index.php?title=Gluteal_muscles&oldid=876760828#Clinical_significance:

Sitting for long periods can lead to the gluteal muscles atrophying through constant pressure and disuse.

However, the statement isn't supported by any reference. Does constant pressure cause muscle atrophy, and if so, why?

I tried to find some references stating that constant pressure causes muscle atrophy, but I haven't found any so far. The following information sources don't list constant pressure as a cause of on muscle atrophy:

https://en.wikipedia.org/w/index.php?title=Muscle_atrophy&oldid=884590568
https://vet.uga.edu/ivcvm/courses/VPAT5200/02_injury/atrophy/atrophy01b.htm  (mirror)

I think it's likely you found a scientifically unfounded and (if we want to be very pendantic) inaccurate sentence on Wikipedia. It's unsourced, and colloquially stated. Disuse causes atrophy, and pressure is simply something that doesn't help. Pressure probably does not lead to atrophy; hearts don't atrophy simply due to being exposed to ever-present pressure from circulating blood. The pressure might even slow down atrophy in such cases. One could make a case for sitting restricting blood flow to the muscle, which could be a mild contributor in the long run.

@S Pr: But bedsores are caused by constant pressure on areas of the body, including people in wheelchairs: https://www.hopkinsmedicine.org/health/conditions-and-diseases/bedsores  Though I doubt that normal sitting would be sufficient.


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Assumptions for Nernst Equation
While I am familiar with some of the conditions for the Nernst Equation, for example:
1) "The membrane is only permeable to one ion even if there are several other ions in the system"
there is an assumption/condition that I have yet to see mentioned (and I am pretty sure that it is an essential one that must be included). That assumption is as follows:
The two solutions separated by the selectively permeable membrane must initially have the same total charge...i.e. there is no initial potential difference between the 2 sides of the membrane
I believe this must be true because of the following 3 cases:
for all 3 cases, only potassium is permeable, and there is a "Left Side" and a "Right Side" on either side of the selectively permeable membrane.
A) Left Side: 25 mM K+, 125 mM Na+ |&| Right Side: 125 mM K+, 25 mM Na+
B) Left Side: 25 mM K+, 10000000000 mM Na+ |&| Right Side: 125 mM K+, 25 mM Na+
C) Left Side: 25 mM K+, 0.00000000001 mM Na+ |&| Right Side: 125 mM K+, 25 mM Na+
Without using my proposed assumption, in all 3 cases, the Nernst equation for potassium would be the same:
(RT)/(ZF) * ln (25/125)
However, I fail to see how case B & C could have the same Nernst potential for potassium as case A when the electrical forces on the left side of the membrane are completely different! Let's use case B as an example. Clearly, the potassium concentration differences exist between the two sides (25 mM vs 125 mM), BUT there is an enormous electrical repulsive force imposed by the sodium (1000000000 mM Na+) so there is no way that the same amount of potassium will pass over to the left side as it would in Case A, right?
Could someone please clarify?

Assumption (1) is not really even true. The Nernst equation is always valid to find the reversal potential for a single ion: that is its purpose. To determine the equilibrium potential for a number of ions, you use the Goldman/GHK equation. It happens to be that the Goldman equation reduces to the Nernst in case of single-ion permeability, which of course never happens for real but is a reasonable approximation in some cases.
As far as your additional assumption, no, that assumption is not required. The Nernst equation doesn't tell you which directions ions flow, it tells you what the reversal potential is for an ion. If you add a voltage from some other source (like your example of adding a bunch of mysterious unaccounted for positive charges outside the membrane) that doesn't change the reversal potential, it changes the voltage. If you put a large positive charge on the left side somewhat like your situation (B), potassium would flow up its concentration gradient towards the Nernst potential for potassium.
Note also that your example is utterly ridiculous: if you want to know what happens when you have 10000000 M Na+ ions together on one side of a membrane you need to consult a physicist, not a biologist. I don't know where you put all the other negative charges, but you're probably about to have a) A very expensive electric bill, and b) a very big hole in your lab.
In real biology, the number of charges on each side of the membrane is similar enough that you can call it equal (see for example Why is it possible to calculate the equilibrium potential of an ion using the Nernst equation from empirical measurements in the cell at rest?). In any case where someone describes "adding sodium" to one side of the membrane, they don't mean just sodium, they mean sodium as a salt with some negative ion, it's just that the identity of that negative ion doesn't matter if it isn't membrane permeable (relative to the other ions involved).

Just so other people know, I put this question over in the physics stacks, and the only person that answered stated that each side must be electrically neutral. So, I don't know if your answer is necessarily correct. Further, I don't agree with your logic. The Nernst Equation can also be reinterpreted as the voltage at which the electrical force and diffusive forces are balanced. So if one compartment has a fundamentally different electric potential, then the electrical force experienced by the permeable ion should be fundamentally different.

Yes, that interpretation still holds. My answer fully agrees with the answer posted at physics, you are misunderstanding both answers.


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probability of hairpin vs self-dimer formation?
I have a linear ssDNA oligo that is designed such that the ends are complementary, and conducive to hairpin formation (see attached figure). My question is, which has a higher likelihood of formation, a hairpin, or a self-dimer? Would the likelihood of hairpin formation increase if I decrease the concentration of the ssDNA oligo during the annealing process? If I enter the sequence in IDT oligo analyzer, the gibbs free energy for formation of self-dimer is significantly lower compared to hairpin.
The melting temperature of the complementary part of my oligo is 50 deg. The annealing will be done in nuclease free water, without any Mg+.

I have tested a similar design to this. With a duplex protocol the chance of forming a hairpin is much higher than that of forming self-dimer, even at concentration of 25 μM. You can run a 3-5% agarose gel to test the outcome.

Welcome to SE Biology. Your answer sounds reasonable but we have no way of judging whether it is correct for lack of evidence. Do you have your own gel to illustrate this?

It seems kinetics have more thing to do than thermodynamics.
Intuitively it seems if you take this DNA at a low concentration, then the 2 termini of the same molecule will have more probability to find each other since they are within same molecule, as well the 60 nucleotide intermediate portion will bend. So the hairpin form is likely to form at lower concentration of this ssDNA.
Now from this condition if they have to go to the linear form, they have to first unwind the paired region. That is the "uphill" region of the kinetics, or the energetically unfavourable action.


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Is sugar absorbed into the bloodstream through the walls of the mouth?
If you let a piece of candy melt in your mouth, but did not swallow it, would the sugar be absorbed through the walls of your mouth?

Welcome to SE kindly read tour page about how to ask question and modify yours accordingly. Your question would be downvoted or closEd  as it shows no effort to answer  and any kind of research.

@Chemist Answering questions that are not well-researched rather encourages people to post such questions anyways.

@BryanKrause Answering poorly researched questions isn't to me inherently wrong. The issue is that you cannot tell what the question is. Is this person asking about how digestion works? How sugar is tasted? If sugar can be absorbed directly as well as or instead of absorption in the gut? Is it asking about dissolving sugars? Is it asking about the composition of saliva? There is too much to unpack here to make an answer useful.

Possible duplicate of What nutrients can humans absorb in the mouth?

@James, the title of the question says: "Is sugar absorbed into the bloodstream through the walls of the mouth?" so this is clearly about absorption and the topic is very interesting in the context of treatment of hypoglycemia, as I answered.

@Jan That is a very nice answer! But it doesn't address the question in the context of candy ;). I suggest you edit the question; I think you see the value in this question and how it could be made into a good clear question.

@James, well, the "candy" in the question was just used as an example. OK, I'll edit it.

Simple sugars such as glucose, fructose and galactose will be absorbed.

They are most probably transported by a common carrier, which is why if you present both glucose and galactose, the presence of one will inhibit the absorption rate of the other.
Uptake rate also seems to partly depend on the concentration of sodium ions in the buccal cavity. This was identified and explored subsequently.
It seems that at the cellular level, absorption is not the quickest but there is a lot of vascularization which allows it to enter the bloodstream quickly, regardless.

Here's a back-of-the-envelope calculation: about 10mg is absorbed in 5 minutes when you hold a solution of 3.6g/l in your mouth. A normal gulp volume is around 10ml. That's 36mg of sugar in a mouthful. Result: you can absorb 10mg of sugar from a theoretical maximum of 36mg. In other words, within 5 minutes, you absorb ~30% of all available sugar. That's pretty good, given that a sugar solution is not a more concentrated, solid sugary food!
Worthy to note that most complex sugars will not be absorbed. Note that many complex sugars actually won't be uptaken even in rest of the GI tract, like cellulose.
See other posts already here on the topic.

@Jan Of interest.

Yes, there is sucrase in the mouth, but not human in origin! Bacteria that live in the mouth produce glucansucrase that can break down sucrose.

The absorption of sugar from the mouth is possible and it was successfully tested for treatment of hypoglycemia. In all mentioned studies, they used D-glucose (dextrose), which is a common natural or added sugar in foods and beverages.
1) Sublingual sugar administration as an alternative to intravenous dextrose administration to correct hypoglycemia among children in the tropics (Pediatrics, 2005):

Sixty-nine children with glucose concentrations of < 0.8 g/L were
  assigned randomly to 1 of 4 methods of administration, 1 with 3
  different doses of sugar, as follows: oral group (OG) (n = 15): 2.5 g
  of sugar; sublingual group (SG) (n = 27): 2.5 g of sugar under the
  tongue, with 3 treatment subgroups, ie, 0.1 g/kg, 0.15 g/kg, and 0.2
  g/kg; intravenous group (IG) (n = 8): 8 mL of 30% dextrose in a single
  bolus; water group (n = 11)...Bioavailabilities were 84% and 38% in
  the SG [sublingual group] and OG [oral group], respectively. The
  sublingual administration of sugar proved to be effective among
  moderately hypoglycemic children.

2) Impact of buccal glucose spray, liquid sugars and dextrose tablets on the evolution of plasma glucose concentration in healthy persons (ResearchGate, 2009):

Analysis of regression coefficients after 30 min compared to the
  control session, demonstrated an increase in PG [plasma glucose] with the sachet of
  liquid sugars (0.068 mmol/l/min, p = 0.001) which was greater than a
  single dextrose tablet (0.052 mmol/l/min, p = 0.002), but no
  significant PG increase was found after buccal glucose spray. Liquid
  sugars or dextrose tablets, but not the buccal glucose spray, are
  effective means to increase PG within 10 minutes after ingestion.

3) Dextrose gel for neonatal hypoglycaemia (the Sugar Babies Study): a randomised, double-blind, placebo-controlled trial (The Lancet, 2013):

Our findings show that treatment with 40% dextrose gel is more
  effective than feeding alone for reversal of neonatal hypoglycaemia in
  at-risk late preterm and term babies in the first 48 h after
  birth....Our study is the first report in babies showing that buccal
  dextrose gel is a safe effective treatment for management of
  hypoglycaemia.

4) Sublingual sugar for infant hypoglycaemia (The Lancet, 2014)

We showed that sublingual absorption was faster than the oral route.
  An increase of 2 mmol/L in blood glucose concentration was achieved in
  10 min, and 64% of children had a blood glucose concentration of more
  than 3·3 mmol/L after 20 min.

5) First aid glucose administration routes for symptomatic hypoglycaemia (Cochrane, 2019):

Providing sugar under the tongue (sublingual) resulted in a greater rise in blood glucose after 20 minutes than giving the sugar orally,
  but this was in a specific setting including children with
  hypoglycaemia and symptoms of concomitant malaria or respiratory tract
  infection. On the other hand, giving glucose by the buccal mucosa
  route resulted in a lower plasma glucose concentration than with the
  oral route. For dextrose gel (where uptake of the glucose occurs
  through a combination of oral swallowing and via the buccal mucosa),
  no clear benefit was shown compared to oral glucose administration
  (glucose tablets or glucose solutions).

Important: Currently, buccal glucose is not recommended to treat hypoglycemia, except in uncooperative children who refuse to swallow glucose (International Liaison Committee on Resuscitation, 2019) .


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Does digestion require hydrochloric acid?
Would our digestion function any differently if we secreted something else, like sulfuric or nitric acid, instead? I'd assume an acidic environment may be required, but not sure if chloride is also required as well!
Perhaps we just use it out of convenience—e.g., presumably blood serum $$\left[\ce{SO4^2-}\right] + \left[\ce{NO3-}\right] \ll \left[\ce{Cl-}\right]$$ and channeling polyatomic ions across the membrane may be significantly more difficult than doing the same for chloride as well!
*Edit: In fact, Wikipedia states

In the stomach, chief cells release pepsinogen. This zymogen is activated by hydrochloric acid (HCl), which is released from parietal cells in the stomach lining. The hormone gastrin and the vagus nerve trigger the release of both pepsinogen and HCl from the stomach lining when food is ingested. Hydrochloric acid creates an acidic environment, which allows pepsinogen to unfold and cleave itself in an autocatalytic fashion, thereby generating pepsin (the active form). Pepsin cleaves the 44 amino acids from pepsinogen to create more pepsin.

So, while maybe something like $\ce{H2SO4}$ or $\ce{HNO3}$ could work too, hydrochloric acid is just more convenient to use?

Parietal cells use ion pumps to expel protons and chlorine ions into the lumen, which create the necessary acidic environment to denature pepsinogen into pepsin.
It is the low pH environment that reconfigures or denatures pepsinogen into pepsin. The acid used does not matter. For example, one experiment in classifying properties of pepsinogen used a 3.5 pH solution of 0.5 N sulfuric acid to activate pepsin.
We evolved stomachs with parietal cells that use an energetically expensive process to maintain the acidic gradient necessary for digestion and protection from pathogens.
It may be that biochemical pathways to generate other acids did not evolve, because it is either energetically cheaper for these cells to make HCl, compared with other pathways that would generate other acids of sufficient strength; or the relevant chemical components involved are more abundant than others in what we eat and drink, and thus easier to make in quantities needed for digestion and defense. Chloride ions also serve a role in maintaining intra- and extracellular fluid pressure and thus play a larger part as electrolytes in the normal function of the body — they are available and cells use them.
But to answer your main question, an acidic environment activates pepsin, and it is not chemically necessary for this to be created by hydrochloric acid.

“Why pump chloride ions at all ?” , if our requirement is just acidic environment to denature pepsinogen to pepsin , I think hydrogen ion does a good job at that , by adding chlorine we are effectively slightly reducing acidic strength

@Chemist See https://en.wikipedia.org/wiki/Parietal_cell. Chloride is secreted as an exchange to bicarbonate.


text:
What kind of insect eggs are these (found in Malaysia)?
What kind of eggs are these?
Found outside on a window, when I removed them via scraping, whitish oozy fluid came out. I've seen this before but they've been appearing more frequently, always appear in a straight line and are brown.
This is in Malaysia, in South East Asia. More specifically Johor. The entire line measured about 1 inch, and in terms of individual egg size, 0.3 inches.

This eggs belong to Mictis profana which is a species of insect in the family Coreidae known by the common names crusader bug and holy cross bug. It is distributed in Australia, Indonesia, and the Indo-Pacific.


text:
What is the darkest color human bowel movement can become?
I assume a healthy human, with usual nutrition, without using any drugs or supplements.

I find this question difficult for several reasons. You assume "normal" nutrition - what is normal? A meal with spinach gives different colour than beetroot stew. I assume, this is about healthy human (since blood in stool can result in dark colour).  And how would a proper answer look like - providing a colour hex code, or similar?

Yeah, it's difficult.
For me, ideally, a good answer should contain a colour hex code and the type(s) of nutrition responsible for the dark colour.

Unless you define what normal is, your question would be considered opinion based and hence put on hold.

By normal, I mean that things like drugs and medication should be excluded.
I know that it's not always easy to differentiate between drug, medication and 'normal' nutrition, but there, I'll have to just trust for further specification in the answers.

You can say in a healthy human, with usual nutrition, without using any drugs or supplements...and put this in your question.

@MichaelBauer then can you please [edit] your question to add all the necessary details.

btw, why is this still on hold?

The darkest stool in a healthy human is black. It can result from eating black licorice, blueberries, blood sausages, Oreo cookies or grape juice.
Other foods that may cause almost black stools: dark chocolate, beets, cranberries, prunes, dark green leafy vegetables, such as spinach or kale.
They are not nutrients, but natural or artificial dyes in the food, that can turn stool black.
Black, tarry and smelly stool is suspicious for bleeding from the upper gastrointestinal stomach (from mouth to stomach), since the acid in the stomach turns blood black.
Sources: (Medline Plus, OU Medicine, 25Doctors.com)


text:
Issues with Mutant Allele Fraction Preparation
I am currently trying to prepare mutant allele fraction (MAF) solutions for an allele discrimination qPCR assay. I began with plasmids cloned with the different desired alleles. I amplified the the plasmids via PCR using primers flanking the mutation site. The amplicons were purified and quantified using qPCR with primers that flank the mutation site. The quantification was done with an standard curve of Ct values plotted against the log dilution factor of the solutions, with an efficiency of 84.18%.
Based on the Ct values obtained, the mutant allele and wild type allele amplicon solutions were then diluted to the log dilution factor that would give a specific Ct value (using the standard curve).
When I amplified the 100% mutant and 0% mutant solutions, I obtained roughly the same Ct values (values differed by no more than 0.5). When I mixed the 100% and 0% MAF solutions to prepare 5%, 1%, 0.1% MAF solutions and amplified them with the same primers that flank the mutation site, the Ct values from each MAF solution differed by up to 2, when it should differ only very slightly since the total DNA content for each of the different MAF solutions are the same.
Does anyone have any idea why this is happening?


text:
Why does eyebrow growth stop after it reaches a specific length?
When compared to hair that grows forever after we cut it, why do eyebrows stop growing? What genes measure current length of eyebrow to ensure it stops growing after a specific length?

no gene measures the length, all hair grows for a period of time then goes dormant, eyebrow hair just grows for a much shorter period of time and grows slower. even head hair stops growing after a few (2-7) years. https://en.wikipedia.org/wiki/Human_hair_growth for more detail on the genetics You can start here https://www.ncbi.nlm.nih.gov/pubmed/5173315

If we cut it in the middle and in the base, why it regrow to the same length after all. I mean If we cut it in the base then it's need more time to regrow than if we cut it in the middle. But how gene determined this?

short answer, It doesn't

An interesting question, but backwards.  Almost all hair seems to grow only to a certain length (or for a certain length of time), then stop.  Human head hair seems to be one of the few exceptions.  The only others I can think of are wool sheep and horse manes.  As for human head hair stopping growth after a time, why am I still paying to have it cut every couple of months?

Does this answer your question? Why does hair grow after trimming but remains at a constant length after a while?

My eyebrows used to be 1 cm, and after 35 they could easily get to 6 cm, they grow for a specific time and are renewed.

@jamesqf - Stop getting it cut and see if it grows indefinitely. Some kinds of sheep will grow wool until it kills them if not shorn.

@anongoodnurse: I've actually tried that :-)  But I have very fine hair (oops, ambiguious language there, I mean the individual hairs are much thinner than most people's) so it only grows to about shoulder length before the hairs break. Especially considering that everything that sticks out from under a motorcycle helmet gets seriously windblown.  OTOH, I have one or two hairs in each eyebrow that seem to grow indefinitely...

@jamesqf - "I have one or two hairs in each eyebrow that seem to grow indefinitely..." Lol! Ok, you won that one! My hair, when young, made it down to my upper thighs, then stopped. Apparently my follicles had a long growth cycle. Decades later, it stops between my shoulder blades. Strange. Maybe my follicles are tired. :)

Activation of the mammalian gene Lhx2 leads to increased hair growth. Lhx2 is a transcription factor which regulates hair formation.

"...length of the hair is determined by the duration of the growth phase; for example, the growth phase for scalp hair can proceed for a number of years, while the growth phase for eyebrows last a few months."

Other genes that have been associated with hair disorders include: FOXN1, ALX4, HOXC13, MBTPS2, VDR, CDH3, HR and ANTXR.

I'm afraid I don't understand this answer.  People who shave their eyebrows regrow them (over a few months).  But your answer suggests that after an eyebrow hair begins its life, it grows for a few months, and then never ever grows again.  Or the eyebrow hair will once again re-start growth once it has been shaved?  How would the hair root know if the hair was cut?

@cowlinator - When I was a brand new doc, it was customary to shave either side of a laceration that went through the eyebrow before suturing it. But very soon after, the procedure changed, because 1. the rate of infection was no different between shaved and unshaved repairs, and 2. in some people, the shaved eyebrows never grew back. Can't tell you why, though.


text:
which enzyme phosphorylates sodium potassium pump?
I know that Na+/k+ pump possess atp-ase function; so the pump will hydrolyze ATP into ADP + Pi. And I see in a figure that the pump is phosphorylated but couldn't really find which protein catalyzes this.
Does the pump act as a phosphorylase??
Or is there a separate enzyme present nearby that does this?

What figure?  Go figure why a pump needs ATP, or read the associated text. Come back and post when you’ve researched your question better.

Also: Please add a link where you read this.


text:
What is meant by 'fixing' of an antigen presenting cell?
Can someone please explain what does 'fixing' of an antigen presenting cell mean?

In which context did you find this term?

in the chapter of MHC and APC (Kuby).

You can also read about purpose and the procedure of hostological fixation: https://en.m.wikipedia.org/wiki/Fixation_(histology)

According to this paper, fixation of an antigen presenting cell refers to the exposure of antigen presenting cells to paraformaldehyde prior to immunostaining. This treatment is used to aggregate membrane proteins and strengthen the intercellular transient protein-protein interaction.
Resource
Barisas BG, Wade WF, Jovin TM, Arndt-Jovin D, Roess DA. Dynamics of molecules involved in antigen presentation: effects of fixation. Mol Immunol. 1999 Aug;36(11-12):701-8. doi: 10.1016/s0161-5890(99)00091-7. PMID: 10593509.


text:
Absorbance anomaly
The standard concentration for absorbance of 1 for ssDNA is 33 ug/ml, while for RNA it is 40 ug/ml. I can't find the reason for the difference in this value for these two macro-molecules. My professor was unable to answer either. Would really appreciate some hint towards finding its answer.

DNA and RNA have different extinction coefficients - i.e. they absorb different amounts of light - because they have different structures.

This paper points out that uridine and thymine have different absorbances at 260, with uridine being higher. Perhaps that helps to explain the difference in absorbances? There seems to be very little difference between ribonucleotides and deoxyribonucleotides.

Another possibility is the ribose-phosphate and deoxyribose-phosphate backbones force different conformations onto the bases, which affects the base stacking interactions.

Thank you user137 for your response. However as you see in my question that actually ssDNA absorbs more than RNA. The paper points to the fact that at 260 nm the absorbance of uridine is higher than thymidine. It also shows that there is negligible difference in the absorbance between ribonucleotides and deoxyribonucleotides if the base is similar in both. So now I am more puzzled by the fact that uridine is absorbing more than thymidine at 260 nm.


text:
‘Inoculum’ vs ‘inoculant’ – which one is it?
I’m currently writing the report of a study which looked at commercial soil inoculants (Rhizobium sp.). However, I’m confused about the differences between the words inoculum and inoculant and when to use which.

ask on http://english.stackexchange.com/ please

If the dictionary definitions do not tell you which one to use, I doubt anyone at english.se would know either.

In my opinion, dictionary definitions are not helpful in this case as it is an idiomatic problem. Therefore I was hoping to get some information from people who are also using these words in academia. Inoculants are used in a variety of research fields, hence it is likely that I would find help here.

I'm voting to close this question as off-topic because it is a question about the english language.

@GeraldEdgar I disagree. There are a number of people over at english.se who write some excellent answers about usage, suffixes, and the like. I expect that's the best SE site for this question about when to use the direct latin ending inoculum, vs. the suffix -ant

Further to @DeNovo, I would say that on SE English Language and Usage you will be expected to provide a sample sentence in which you wish to use the word. You will also be expected to report what you found in dictionaries and explain why it didn't help. It would help to know what the leading scientific journals are in your field, so that anyone with access to a (e.g. University) subscription can search for actual usage of the word if you cannot. Also Google ngram viewer may be a useful tool for that in relation to books.


text:
Backbone hydrogen bonds between adjacent amino acids in a protein?
Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO?
Are there any examples of such situations in proteins and how common are they?
If such bonds are rare, why is this so?

Are you talking about main-chain hydrogen bonds (i.e. from the CO and NH on the backbone) or side-chain hydrogen bonds (e.g. from serine, aspartate etc.)?

@David Yes, I am talking about the main chain hydrogen bonding.CO--HN of the backbone

The situation you ask about was originally part of the 27 ribbon and 2.27 helix structures considered as possibilities by protein chemists (Linus Pauling?) in the 50s or 60s. The diagram below, showing the ribbon, is from the classic text (long out of print) The Structure and Action of Proteins by Dickerson and Geis.

This turns out to be very rare in proteins. To understand why, one must remind oneself of the conditions for forming hydrogen bonds in proteins. For hydrogen bonds between peptide bonds these would be:

Correct distance between hydrogen of the NH and the O of the CO (too far apart — bond weak, too close — repulsion).
Near(ish) linear angle of the NH and OC.
Lack of steric repulsion of other atoms in the structure

Calculations indicated that a 2.27 helix would be less strained than the 27 ribbon:

Playing with polyglycine in Bosco Ho’s Ramachandran Plot Explorer (Rama) indicates steric repulsion still exists in this structure (white striped connectors):

I could only find one report of this structure, and that was in the artificial peptide Ac-(∆ELeu)5-NHMe, with a model using dihedral angles Φ,Ψ approx. –60°, 30° (as in the Rama simulation) shown below:

It should be noted that this position of the Ramachandran plot is at the margins of stability, and I would expect the bonding only to occur in proteins where it was stabilized by other interactions (as in this artificial peptide) and no lower energy structure were possible.


text:
Do violet potatoes contain more or less solanine than normal potatoes?
What is the solanine content of the violet potatoes? Is it more or less than in the normal potatoes?

What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

@theforestecologist I have googled the Internet for violet/black potato solanine

and what did you find? What websites did you look at? Have you tried Google Scholar?

Seems to be about the same.
In Effect of Genotype and Environment on the Glycoalkaloid Content of Rare, Heritage, and Commercial Potato Varieties, Tables 1 and 2 list 60 different potato varieties showing glycoalkaloid concentration (solanine and chaconine are shown separately); Table 1 indicates the skin color, and Table 2 indicates the flesh color.  "Violet" is not an option, but "Blue" is, and there doesn't seem to be any particular correlation between skin or flesh color and glycoalkaloid concentration. (The potato with the highest concentration of glycoalkaloid in the flesh was a blue one, but other blue varieties were fairly low; the variety with the highest in the skin was "yellow".)