text:
Example of well understood/modeled biological mechanism
I am working on modeling psychiatric disorders, where multivariate time series data - which I think is necessary to do any interesting modeling - is only broadly available recently, due to the availability of surveys via mobile devices.
To get into the dynamic systems modeling literature, I would like to look into a biological mechanism, which is well-modeled, by which I mean that the error/misfit is negligible for many applications. Basically, I am looking for a (historical) example, where I can follow the steps that were taken to get from the observed (maybe experimental) data to a good model, with the hope that I can learn some lessons for my own work. Ideally, it would be an example with about 5 < p < 20 variables.
Any hints and suggestions are greatly appreciated and my apologies if this is a too trivial question.

Assuming you are talking about analytical modelling and not about statistical modelling, you can learn about modelling in general by learning the basics of math. This book from Otto and Day talks about analytical modelling in the fields of evolution and ecology.

while @Remi.b has a good point, I would counter from own experience that getting hands dirty with data is the best learning method for me. there are thousands of examples of biologically interesting mechanisms with data and models, but it would be very helpful to know more about what you want to do. Does it need to be time series data? Or psychiatric data? There is for instance really great data and models on molecular networks running plant circadian clocks from Andrew Millar's group (http://onlinelibrary.wiley.com/doi/10.15252/msb.20145766/abstract).

I would point out that, assuming (as the other commenter noted) you are interested in analytic rather than statistical modelling (which seems a little unlikely to me given your area), most mathematical models are derived from first principles (often from physics) or other assumptions.
This suggests (to me) that looking at models of totally unrelated systems is not so useful; the whole idea of such models is to formalize your domain knowledge!
But I'll give some examples anyway.
For example, consider
 biophysical models of neurons or continuum mechanical models of cardiac tissue, both of which have rich histories of mathematical models developed over decades of work, based on both theoretical and empirical considerations (albeit largely from physics).
Perhaps slightly more related (or at least empirically driven) are the advances in systems biology, which tend to derive from some underlying laws of chemical kinetics, but utilize enormous amounts of (multivariate, temporal) data in fitting (often non-linear stochastic) systems of differential equations. Methods for computational protein structure prediction tend to use a mix of ad hoc rules (for computational time-cost reasons) and physics-based considerations in their models.
Evolutionary biology and population dynamics also have wonderful models (see the book from the commenter above).
My guess, given that your question does not have much detail, is that you would prefer statistical, i.e. probabilistic graphical or stochastic process, models instead.
Let's suppose you have a bunch of variables over time (e.g. the actions or status of a person) but you want to estimate an unobservable quantity (e.g. say, the degree to which they are insane [not my field, sorry]).
One simple probabilistic model is the hidden Markov model.
It has many examples of applications in sequence biology.
It also lets you figure out, in a way, which variables are important, and let's you tune certain parameters (e.g. it's order, which here describes how much the person's state at time $t$ affects their state at time $t+\Delta t$).
In terms of predictive modelling power, though, the state of the art is in deep learning models for time series.
Anyway, I'd consider what your goal is more carefully. If you indeed have a strong idea of an analytic model (motivated by some theory you know), then by all means formalize it. However, if you want the data itself to suggest a model for you, then use a statistical approach.
Note: apologies if this answer was too trivial, I was not sure what you did and did not know.


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How does collaboration on reconstructing metabolic networks work?
I am a researcher in psychology and I am trying to come up with a framework/platform in which psychological phenomena can be studied from a dynamical systems / computational perspective in collaboration with many labs. To be more concrete, the question is how to organize knowledge about psychological variables and how they are coupled by functional relationships on different time-scales that may be a function of additional variables.
My hope was to learn from disciplines that already work with a dynamical systems/computational framework for a long time. The first interesting analogy I came across were metabolic networks. I read this review about their reconstruction and while many things are different, the task is very similar to ours in that a given network of entities and functional relationships is continuously refined by the scientific community.
I saw that there are many data bases with genes, pathways, annotated graphs etc. but my main question is:
How is the scientific process of refining such a metabolic network organized? Are there platforms for this? Is there anything in place to quantify the uncertainty associated with parts of the network or to resolve disagreements? Are there any standards for implementations? Or is each group simply creating their own version based on previous literature and then publishing their new network in a paper?
I realize that this is a rather broad question and I apologize if I posted this in the wrong stackexchange forum. But I didn't know where else it would fit. I'd appreciate a lot if someone could give me some basic insights about how this field works or if someone has some pointers to relevant reading material.

In your comment to the answer from @Nicolai you refer to " a (formalized) dynamical system with many variables and many more parameters which render it impossible for a single research lab to map everything out alone". I don't think this is so. It does not strike me as dynamic and a single person usual writes the program that a single lab uses. One generally works with a network of pathways that is well established and stable, takes a bacterium, sequences it, runs the program to see which enzymes hit the network, and whether they join up to give particular pathways. Game over.

A bit of a preface:
A lot of this large scale collaboration (which I would maybe rather describe as the work of a whole [sub]field over a given time frame) often ends up in some sort of database. Really, there A LOT of those in modern biology - and often with minor but sometimes important differences. One of those would be the level of curation: are results gathered automatically from other sources, or always manually checked before being added? Another thing about databases is that (with certain exceptions of course) they often are only relevant for specific sub field, in some cases this can mean that only one lab maintains a website with a databases that is used by a few others, but that's it.
What I'm trying to get to is that there isn't really a 'one size fits all' solution and that especially the size of your field will impact which kind of solutions are both feasible and actually useful.
Now to answer your actually state question (as far as I can):
Most known biochemical pathways (including the metabolic ones) are described in the KEGG database. Initially this project was started by a single lab (and is still run by that group as far as I can tell), but of course it contains a lot of published information from other sources (I couldn't find information on how they update the networks in the database, you may have to read the papers for this). The database can also be accessed remotely, so it allows people to use the same network for a given reaction, and by incorporating sequence data it also has information on which organisms even contain the given enzymes in the network.
One thing the database does not contain is information about dynamics in the network. In this case I think most groups will generate and publish their own models (e.g. based on ODE's).

I think the poster is talking about computationally determining which metabolic pathways are present in an uncharacterized organism from the genes detected, using the full set of possible pathways in KEGG or the like as a reference. So the info about the KEGG database isn't particularly relevant to the fitting process. I imagine @jmb should try SE Bioinformatics where there may be someone who knows the approaches used in the programmatic fitting..

@ Nicolai thanks for the answer and @David thanks for checking in. I was less interested in the specifics of the field but rather in how efficient collaboration works in fields in which the phenomena of interest is modeled as a (formalized) dynamical system with many variables and many more parameters which render it impossible for a single research lab to map everything out alone.

@jmb — Sorry I misunderstood. I thing you have it wrong, but I'll comment on your question.

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How does high-intensity aerobic exercise affect the brain?
I have been reading articles claiming that serotonin, endorphins and BDNF are produced during exercise, but they never mention the intensity or duration of exercise for this to happen.
To not make this question too broad, I want to narrow it down to, lets say, a 4-5k run over 20 minutes. Also, I want to restrict it to the body's response during these 20 minutes.
How will this affect the brain? Which chemicals do the body produce/release into the blood stream that could have an effect on the brain? And, how much?
I am asking because I am always curious about the mechanisms underlying the effects of exercise on the brain and because it's always difficult to find information regarding results of exercise; Googling mostly results in content marketing articles (like this one for Buffer).

In this article The Effects of Acute Exercise on Mood, Cognition, Neurophysiology, and Neurochemical Pathways: A Review (Brain Plasticity, 2017), there's a comprehensive table The Time Course of Behavioral, Functional, Physiological, and Neurochemical Effects of Acute Exercise (scroll to Fig 1 and zoom it) that shows the duration and intensity of exercise needed for the effective release of cortisol, neurotrophins (BDNF, IGF-1), neurotransmitters (dopamine, norepinephrine, serotonin, acetylcholine, GABA and gltamate) and endogenous opioids.
Examples of effects of exercise on the cognitive function and mood:

Prefrontal-dependent cognitive function (learning, memory): 50 min exercise at 85% of age-predicted mean heart rate
Enhancement of positive mood: low to high intensity exercise 7-70 min
Decrease in negative mood: 60-120 min exercise at ~50% intensity

Cortisol:

In humans, acute exercise stimulates the HPA axis in an
  intensity-dependent fashion, with increases in cortisol occurring
  after a threshold amount of exercise that equates to a duration of 10
  minutes or more at approximately 60% of VO2 max or greater...After
  exercise cessation, peripheral cortisol levels peak around 30 minutes
  and remain elevated for up to two hours.
...cortisol strongly influences learning and memory...The extent
  to which cortisol influences learning and memory processes depends on
  several factors including the intensity of cortisol elevation. For
  example, moderate increases in cortisol enhance working memory...Cortisol elevation over a certain threshold, however, serves to impair memory...
acute exercise also helps mitigate the debilitating effects of stress.

Brain derived neurotrophic factor (BDNF):
Moderate exercise for 30 minutes can release BDNF.

...studies have shown a positive association between acute
  exercise-induced peripheral BDNF levels and short-term memory as
  well as motor skill memory.

But, this does not work in everyone and not in all circumstances...
Dopamine:

Twelve, healthy, regular exercisers underwent PET scans after either
  rest or 30 minutes of treadmill running at 85% of age-predicted MHR.
  Surprisingly, dopamine was not found to increase after acute exercise
  in these humans.

Serotonin:

Acute exercise significantly increased plasma serotonin, with a
  positive linear correlation found between serotonin concentration and
  exercise intensity.
As serotonin regulates mood, emotion, sleep, and appetite, and
  dopamine regulates motivation memory, reward, and attention, the
  central fatigue hypothesis claims that the interaction between these
  two neurotransmitters contributes to exercise-induced fatigue, with a
  high serotonin to dopamine ratio supporting a low activity, exhausted state and a low ratio supporting a high activity, activated
  state.

The effects of exercise-induced increase of norepinephrine and acetylcholine on cognitive function are not well known.
Endogenous opioids (ß-endorphins, enkephalins and dynorphins) and endocannabinoids:

Neuromodulators are involved in a variety of processes including pain
  modulation, reward, response to stress, and autonomic control.
In humans, acute exercise causes significant increases in peripheral
  levels of endogenous opioids; this effect is intensity-dependent,
  corresponds to acute exercise-induced changes in HPA axis hormones,
  and is linked to improvements in mood.
Though the endogenous opioids have received much attention in terms of
  their involvement in the “runner’s high”, scientists are beginning to
  understand that endocannabinoids may be equally or perhaps more
  involved.

Other sources:
Effects of physical exercise on anxiety, depression...(Clinical Psychology Review, 2001):

Acutely, emotional effects of exercise remain confusing, both positive
  and negative effects being reported.

...or as Alex Corb, PhD says in Boosting Your Serotonin Activity (Psychology Today):

Interestingly, if you try to do too much exercise, or feel forced into
  doing it, it may not have the right effect. Recognizing that you are
  choosing to exercise changes its neurochemical effect. That may be a
  result of your ancient instincts — the difference between running
  because you're hunting something, and running because it's hunting
  you.

How to increase serotonin in the human brain without drugs (Journal of Psychiatry & Neuroscience, 2007):

Exercise improves mood in subclinical populations as well as in
  patients. The most consistent effect is seen when regular exercisers
  undertake aerobic exercise at a level with which they are familiar.

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If sufficienly many people are born, then is it possible that two persons are genetically identical although they are not twins?
It is my tought experiment.
Since for human, the genome information is finite, if so many many people are born,
then there exist two people who have the same genome although they are not a twin.
Is it true?
And how many people need that this event happens?

3 x 10^614 which is a ridiculously large number. in the time needed to get that many humans the human genome will change enough to make it impossible because the species will have changed, humans would also have to have colonized many many planets. .

At a very crude level, the full human genome contains 6 billion nucleotide pairs. Each of those nucleotide pairs has four possible values: AT, GC, TA, and CG. That means there are $4^{6e9}$ (4^(6 X 10^9)) possible human genomes. This is very crude. Not all human genomes are exactly the same size, some combinations would be phenotypically indistinguishable, and some would not be compatible with life. This crude number is larger than the number of atoms thought to exist in the universe. This means you'd never be able to have all those people exist at the same time. The human genome is finite, but so is the amount of matter in the universe.

Wouldn't you only have to compare the SNPs rather than the whole genome? It's still a big number but less than 6 billion.

I find this number way too crude. You've given the number of unique nucleotide sequences that are 6 billion base pairs long, but only a tiny vanishing minority of those could reasonably be called a "human genome". The odds of two identical genomes spontaneously arising is nigh impossible, but this takes it too far - virtually all of the sequences you're counting here could never be observed in a human.

There are ~600 million SNPs, so only one order of magnitude off from the crude level; still well beyond reality.  Admittedly, most of those are unlikely.  Fine.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750478/ found "that a typical genome differs from the reference human genome at 4.1 million to 5.0 million sites."  4^(4000000) is still beyond any reference.  Indeed, if there are 10^80 atoms, that's equal to roughly 4^133, so you don't need much at all.

My suggest was absolutely an incredibly crude estimate. As @NuclearHoagie rightly point out virtually none of the random 6 billion pair sequences would be a functional human genome. On the other hand just counting SNP would be a massive undercount since by definition a SNP occurs in at least 1% of the population. There are  a lot single base pair mutations floating around transiently that never establish themselves as a SNP. And we aren't even considering things like repeat expansion, monosomies and trisomies. I think we all agree that the number of possible, viable human genomes is huge.


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Why do we use word prime with base pairing in DNA such as 5-3 prime.. prime stand for?
I was reading base pairing sequence in DNA and found 5-3 direction but my question is why we are using word prime with 5 or 3 such as 5 prime 3prime. Prime stand for?

The answer to this requires a proper chemical representation of the sugar and base rings, which is not present in the answer to " What does 5' and 3' mean in DNA and RNA strands?", but can be found in the custom diagram in my answer to another question.

It comes from Lagrange's notation in math, where "prime" denotes a derivative. So if you have a function x and then a derivative function of x, you'd call it x' (x primer) and if you have another one then it's x'' (x prime prime). So basically you are adding prime to say "another one of x". In DNA this refers to Carbons. DNA is composed of nucleotides which are composed themselves of a sugar + a nitrogenous base (or nucleobase) + a phosphate. Both the sugar and the nucleobase have Carbons and those carbons are called with numbers. The nucleobase gets the first "round" of names: Carbon 1, Carbon 2, etc. while the sugar gets the prime ones: Carbon 1 prime (that is, another Carbon 1), Carbon 2 prime (another Carbon 2), etc. So the 5' means Carbon 5 from the sugar in the nucleotide.

Welcome to Biology.SE! Please provide references supporting your assertion that this use in Chemistry is derived from Lagrange's notation — in general, on this site we expect answers to be backed up by supporting references. Thanks!

"Prime" is how you enunciate '.
e.g. "five prime" is the enunciation of the written 5'.


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What is this insect found in an apartment in Brazil?
I found some insects after moving into a new apartment in south eastern Brazil, in an urban center. It is the 11th floor (relatively high up) but very windy region.
Some loose wings can be found around the house. I'm not sure if they are being blown through the windows or if we have an infestation somewhere.
Some individuals were found inside bathroom cabinets. I've found two live ones with wings last night, one of which is shown in the pictures. A dead one without wings was also shown.

I think that these are termites (AKA white ants).
Termites have a flying form known as Alates (meaning "winged ones"), which commonly swarm and then shed their wings to find a place to nest once mated. The head form with the stripy antennae and long wings relative to the body make me think that these are termites.
This does not mean that you have an infestation, it could be that you have a nearby nest that is swarming, but the presence of dropped wings indicates that male and female alates have mated and are now looking for a place to build their nest. You should get your building checked out by a pest control expert.
More information on swarming termites can be found on the linked page from North Carolina State Extension

It's 100% that, I'd just like to share that's common for them to do their nuptial flight when it starts to get hotter here, between August and November (big country, could vary even more than that). So yeah, prepare to see them yearly.

That is what I feared. Well, pest control it is. Thanks for the help.


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Hydrogen Ions — Common, right?
The Wikipedia entry for Ion states "A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle-free space."  Cells pumping ions across membranes is very common so can someone help me understand what context might be implied by the quote?

It's not clear what you mean by "what context might be implied by the quote". What specifically are you asking about?

Welcome to Biology.SE! This appears to be a chemistry question and is almost certainly answered on [Chemistry.SE]. The short answer is that aqueous H+ is actually H3O+. Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. Note in particular the section on "homework" questions. Thanks!

I'm still not entirely sure what specifically you're asking about, but I have a guess. It is true that positively-charged hydrogen ions, or bare protons, are typically only observed in gaseous/plasma states and hard vacuums, and it is also true that cells routinely pump positively-charged hydrogen ions across membranes. This is not a paradox because in aqueous solutions, hydrogen ions exist as $H_3O^+$, also known as hydronium or hydroxonium.

Image from Wikimedia Commons

You are on the right track with your thinking about the paradox of an actual proton being pumped across the membrane, and it's just a problem of how the chemistry is communicated. The protons actually move along what is called the proton channel, which essentially is a row of protonated amino acids like glutamate (glutamic acid) or histidine.
If we think about complex 1 in mitochondria (below), when a proton in the matrix is "pumped" across, it actually "pushes" protons down the proton channel into the matrix (See the light blue line in the figure below). Think of a series of train cars on a track getting pushed.
Finding these proton channels and figuring out how they work is actually a very competitive field. Since they are buried in the membrane, they are challenging to work with, and we don't know much about them.

Even as someone who works in the field, I have to remind myself that all chemistry works this way. If it is water, protons, or electrons, talking about a single molecule is the wrong way of thinking about it.
Citation for Figure https://www.nature.com/articles/s41467-020-17957-0

"talking about a single molecule is the wrong way of thinking about it" super helpful


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Is tumor necrosing factor alpha now properly referred to as "tumor necrosing factor"?
"Because LTα is no longer referred to as TNFβ,[64] TNFα, as the previous gene symbol, is now simply called TNF, as shown in HGNC (HUGO Gene Nomenclature Committee) database." says https://en.wikipedia.org/wiki/Tumor_necrosis_factor#Nomenclature.
Is this correct? What, if anything, does it say about someone if he calls it "tumor necrosing factor factor alpha" ?
So my question is: Is tumor necrosing factor alpha now properly referred to as "tumor necrosing factor"?

This is an old problem when nomenclature changes: People will still use the old nomenclature and it will only cease with time.

@Chris Are there some that refuse to call it by the new name, like those who insist on saying "degrees centigrade", even though they know the new name, but just don't want to be told what to say? Are there people who think the old name is better? Is the old name better?

I think it is simply a habit. I noticed the same with cMyc (old name) and Myc in another field. It took a while, eventually it came through.

@Chris When you say "a while", do you mean years or decades?

I observed this for a few years. But this is only anecdotal evidence.

In papers I've participated in recently we've called it TNFα. No reviewer has corrected us as far as I can recall.
Near as I can tell, we've done this because we do not read the HUGO Gene Nomenclature Committee database any more often than we read the dictionary cover-to-cover. Instead, we read and cite papers in the literature, and since many of those are older than this apparent change, and even more recent ones are in turn citing older papers, TNFα is the only nomenclature I knew of until your question posted here.
I could have guessed that a "TNFβ" or something similar exists/existed at some point, but I really have no knowledge or familiarity with it, certainly far less than with TNFα, so a renaming there is not really of any interest or relevance to me.
Biology is a massive field and every niche has its own set of terminology that is more or less familiar.
If people in the field decide over time to start using the new name, then that will propagate the new usage. I don't see a strong motivating factor to rename in the meantime: the old name isn't misleading or easily confused with something else, it's not derogatory or offensive, the new name doesn't provide additional context or function. If anything, there's a temporary motivation to not change, in that use of the old term far outnumbers use of the new.
I suppose you can think of me however you'd like based on my explanation here - I don't have much control over that.

I just realized that the Wikipedia article didn't explain why a change in the name of the gene means the name of the protein should be changed. Do I understand it correctly: tumor necrosing factor alpha is a protein? And not a gene?

Tumor necrosis factor alpha is the protein product of the gene TNF in humans, which is also known as TNFA.


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Alzheimer's disease - Hyperexcitability
I am trying to read literature on Alzheimer's disease.
A very important phenomenon that occurs in AD patients, is hyperexcitability in neurons close to A-beta concentrations.
Some authors only describe the phenomenon of hyperexcitability in excitatory cells as an indirect phenomenon, which results due to the suppressed function of inhibitory cells.
Some other authors only describe it as the direct result of excessive concentration of Glutamate in a synaptic cleft which, due to the dysfunction of Astroglia, remains there and causes hyperexcitability and excitotoxicity.
I haven't found yet a paper where both are mentioned as distinct ones. At least I haven't found any that I could comprehend, given that my background is not biomedical.
I would like to know if these two cases I mentioned before, are indeed distinct ones, or if they are the same, and I cannot see it due to lack of knowledge.

The answer would require expertise in that specific field. I would suggest you to get in touch with some of the authors whose papers you mentioned, you read.

We can help, do you have the refs handy? otherwise i will look it from scratch.

@PolypipeWrangler thanks a lot! The references are the following:
as an indirect phenomenon: link
as a direct phenomenon: link

I  might be a week, is this still useful?

of course! many thanks for the willingness to help


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What are the different causes for a snail species to have chiral dimorphism or speciate into a new species of the opposite form?
One way for the snail species to have complete chiral dimorphism where one form is an identical mirror image of the other form is if one form can't reproduce with the other form and it's predator is a species of snake that also has chiral dimorphism. If the snail species has chiral dimorphism and and one form can't reproduce with the other form but the species of snake that eats it does not, that means each individual snake of that species can eat either form and the evolutionary stable strategy is to have a mixture of both forms of snail in unequal proportions; if one form becomes more common, the snake will evolve to change a tiny bit in shape to be better at eating that form and less good at eating the other form so that form will evolve to be less common again. If the species of snail reproduces asexually and has chiral dimorphism and the species of snake that eats it also does, then the evolutionary stable will also be for both forms of each species to be identical mirror images occurring in equal proportions, even if it's very rare for in individual snail of that species to be eaten by a snake. If an asexually reproducing species of snail has chiral dimorphism and the species of snake that eats it doesn't, then both forms of snake will still occurr in equal proportions but the random fluctuations from that equilibrium will be larger because it will be the snake's brain adaption that makes it better at eating the more common form but its brain will already be so well adapted to eating both forms. According to Remi.b's answer at Does the species of snake that eats Amphidromous inversus have chiral dimorphism? and https://www.ncbi.nlm.nih.gov/pubmed/16217668, Amphidroumous inversus has chiral dimorphism occurring in very nearly equal proportions and one form can reproduce with the other form but the species of snake that it's it doesn't have chiral dimorphism. Maybe it can be treated very much like the case where the snail species reproduces asexually and the snake does not have chiral dimorphism but one form isn't quite an identical mirror image of the other form because the identical mirror image of either form would be less able to reproduce with that form and the species of snake that eats it is very close to symmetrical but isn't quite because the two forms of snail aren't identical mirror images. How can predation cause mutants of the rarer form of snail to arise and evolve into a different species entirely? Is it really because no mutants of the predator species of the mirror image form arise getting it into the evolutionary stable strategy where the predator and prey both have chiral dimorphism occurring in equal propertions?

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How to design a ChIP-exo experiment with controls?
Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment?  Is it even necessary to run a control (similar to input DNA for ChIP-seq)?  I'm looking for any references or forums that discuss this issue and experimental design?
This video (https://www.youtube.com/watch?v=8qLRI9Bqtso) briefly touches on this issue (t=32.45), indicating NOT to use an Input sample due to the Exo digestion.  However, I don't know how the community (or reviewers) feel about this?
Thanks for any help!

There is a recently published paper addressing the lack of input controls for ChIP-Exo procedures. https://doi.org/10.1093/nar/gkw741 Hope this helps

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How does a polymerized TruSeq adapter affect sequencing reads?
I am trying to build a NGS library on enriched DNA (DNA length = 93 bp).  I am using PCR amplification with two overhanging primers, both containing Illumina adapter sequences (Universal Adapter & TruSeq Adapter w/ barcode).  My final library should be (~182 bp):
Universal Adapter (-), Enriched DNA (+), TruSeq Adapter(=)
------------------++++++++++++++++++++++==================
After PCR amplification and QC by gel, I am seeing fragments of larger size.  Analysis by Bioanalyzer indicates that I am might be getting some polymerization of the TruSeq adapter on the library.  This is most likely due to bad primer design, with the primer containing two recognition sequences (21-nt), one at the 3' end and one at the 5' end of the TruSeq adapter
My question is:
How would the NGS analysis be affected if a library is submitting for sequencing, containing a mixture of single and dbl TruSeq adaptors?
Single:
Universal Adapter (-), Enriched DNA (+), TruSeq Adapter(=)
------------------++++++++++++++++++++++==================
Double:
Universal Adapter (-), Enriched DNA (+), TruSeq Adapter 1(=),  TruSeq Adapter 2(=)
------------------++++++++++++++++++++++==================\==================
Would the sequencing info from the "double library" be lost or would those fragments be read, just fine?
Thanks,

Remember to upvote answers you find useful. :-)

In short, you stand to lose information from your library due to the length of the fragments you're sequencing.
When you set up your sequencing run, you'll set the parameter for the number of sequencing cycles, which will determine the length of the reads to be sequenced. The longer the fragments contained in your library, the less they'll be fully sequenced.
A good idea would be to sequence your suspected polymerized fragments to verify that primer polymerization is really occurring. Just send your sample for normal sequencing, as you would for plasmids and PCR fragments.
If your primers are polymerizing because of inefficient design, you should fix this before loading your library into the Illumina device. If the primer-dimer effect comprises a significant portion of your library, this will only get amplified during the run and can definitely lead to a significantly less complex library. Sequencing a low-complexity library is a really expensive mistake whose one guaranteed result is to enrage your advisor and make him/her loudly question your competence. Trust me.


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Why aren't "Water Giraffes" a thing?
If we assume that the Brachiosaurus and the modern Giraffe with their long necks both came to be by the need to reach higher-situated vegetable nutrition (which is a somewhat controversial assumption to make, I understand Evolution of long necks in giraffes), what biological reason is there we don't see any kind of modern day equivalent to the Elasmosauri?
Put differently, what environmental factor promoted the evolution of water reptiles with extremely long necks that ceased to exist in a post-cretaceous world? What benefits did Elasmosauri have that later water creatures would not?
Assuming that evolution is shaped by environmental factors, of course.
(And assuming the "water giraffes" weren't simply called "hydras" and extirpated by the ancient greeks. :P )

I think you already visited this Wiki page, but just in case you didn't I'll post it here: Neck movement in Elasmosaurus.

Do we not? https://en.wikipedia.org/wiki/Heron https://en.wikipedia.org/wiki/Hydrophiinae

Are there any existing environments where such long necks would be advantageous, and which are large enough to support a population of Elasmosaurus-sized creatures?  Such necks are certainly common in aquatic birds: not just herons, but geese, swans, cranes, flamingos...

Is your question simply: Given that elasmosaurs went extinct, why did an analogue of elasmosaurs not evolve after the Cretaceous?

@kmm rather late answer to your comment, but yes, that's the question.


text:
Is there any meaningful ratio between the width of a vertebra and its height and depth?
Given the location (i.e. their entry points, but not their trajectories) of two pedicle screws, we are trying to come up with a way to approximate the sagittal distance of the vertebral foramen to the screws' entry points.
I.e. how far "down" (= towards the patient's belly) do you need to go from the screws' entry points until you're at the same height as the approximate center of the vertebral foramen?
And we're trying to do that for all vertebrae into which pedicle screws could reasonably be placed.
We don't know which screws are placed in the Traditional Trajectory (TT) and which are placed in the Cortical Bone Trajectory (CBT) but assume we can ask that, if necessary.
To further complicate the matter, we don't know anything about the patient (data protection). I.e. no age, sex, height, etc. that could help us estimate this.
We hope that we can somehow leverage the distance between the screws to get some rough estimate for the vertebra's height ("head-to-leg" direction) and depth ("belly-to-back" direction), but so far, I don't see how.
Is there any remotely useful ratio between the width of a vertebra and its height or depth?
And does it help at all if we know which vertebra it is (which we don't, but which we could ask, if necessary)?


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Has Darwin's abominable mystery been solved or not?
When I research Darwin's abominable mystery, the abrupt origin and rapid diversification of the flowering plants during the Cretaceous, I read different conclusions about whether it has been solve or not. The following 4 articles are the top results I googled for the subject.

New light shed on Charles Darwin's 'abominable mystery', published 23 January 2021 said "In short, no. "One hundred and forty years later, the mystery's still unsolved," says Prof Buggs. "Of course, we've made lots of progress in our understanding of evolution and in our knowledge of the fossil record, but this mystery is still there."

SCIENTISTS FINALLY SOLVE CHARLES DARWIN'S 'ABOMINABLE MYSTERY', published Jan. 12, 2018 said yes

Darwin's abominable mystery, published May 24, 2017 said "many of the solutions we are seeking for the mystery today - such as pre-Cretaceous angiosperms - even if they were found, would simply restore the mystery to the depth that it appeared to have for Darwin. They wouldn't solve it."

The meaning of Darwin's “abominable mystery”, published 01 January 2009 said "it is worth briefly addressing whether Darwin's “abominable mystery,” specifically with respect to angiosperms, has been “resolved” in the interim between 1882 and the present."

So has Darwin's abominable mystery been solved or not?
BTW, I asked a related question at history SE "How often was the 'abominable mystery' used to attack Darwin's evolution theory?"

Why would you think the rapid diversification a plant that evolved a completely new way to exploit animals, thus decreasing its need for gamete production at the same time drastically increasing the efficiency of its seed spreading mechanism, would need special explanation.   Its like asking why there is a rapid diversification of animals once they evolve the ability to lay eggs on land.

I am a layman and that is why I asked.

Short answer:
No, it has not been solved.
Long answer:
To briefly summarize:

2/4 of your citations (1,3) definitely state that the mystery is unsolved.
1/4 definitely states that the mystery is solved (2).
1/4 does not provide a clear answer (4).

Looking more into your citation (2), it refers to this paper (Simonin and Roddy, 2018, PLOS Biology). However, it does not look like that paper actually resolves the problem, that appears to be a journalistic exaggeration. What the paper actually does is present some hypotheses for how a hypothetical angiosperm ancestor's genome might have been well-disposed for rapid diversification. The pop science article also somewhat misstates what the mystery itself is: "why angiosperms replaced gymnosperms so abruptly", as opposed to "how angiosperms diversified so rapidly" (the paper itself appears to more or less accurately summarize the mystery). So we can probably discount the reference that claims that it is solved, because it is a somewhat overhyped presentation of interesting but incremental work.
I think that your citations 3 and 4 comes the closest to a nuanced view here, neither of which appears to be very optimistic about a solution, and both of which appear to be quite skeptical of claimed solutions of the mystery. This is a classic case where the more you know, the more confused you get.
Overall, it's worth noting that "solving" the mystery is probably not something that we can do beyond a general inferential fashion, at least without a time machine. The early evolution of angiosperms (or dicots, with respect to your citation 4) happened a very long time ago, we can't directly observe or measure it. We are obliged to look at the fossil record and make guesses based on that.
Our guesses might be very good and highly quantitative, but they're still just guesses based on a very incomplete and non-representative dataset. And that's ok! That's what a lot of paleontology is, you can get very far with that kind of analysis (for example, we are now quite sure that birds are dinosaurs). But "how did this extremely complex evolutionary process occur?" is a much more difficult question than "how can I best classify this object?".
For these reasons, we are unlikely to ever get a complete picture of the process by which angiosperm radiation occurred. What we might achieve is a good general idea of when the radiation's major events occurred, what its major lineages are, and a statistical guess at the causal factors behind it.
Based on your references, I think that we have a good idea of the major lineages and the timing of the radiation, but the causes of the radiation are still very up in the air.

Thanks for answering my question but other than my citations is there any consistent conclusion in science community ?

@Qiulang I think that the consistent conclusion is what you've already found: no we have not. The sophisticated commentators that you've found go on to say that we probably can't solve this mystery, you yourself have quoted the relevant passages. We don't know why or how the radiation of angiosperms/dicots happened. As I say in my last sentence, we have more paleontological data points but do not know much about causes. Claiming to solve this kind of question is a good way to hype up your work, so people make those claims (as with your citation 2). But those claims appear to be unfounded.


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choosing the right housekeeping gene for Western Blotting analysis for liver lysates
B- actin is used a great deal for quantitation of liver lysates. What other alternatives are there for WB analysis? should we opt for GAPDH or tubulin?

This is totally up to you, and the antibodies you have on hand. The quality of the antibodies helps as well. There are many so-called "housekeeping" genes whose expression is not necessarily greatly affected by various conditions. Beta-actin, alpha- and beta-tubulin, GAPDH, COX IV, Histone H3... all work well, and some are better in some scenarios than others. For example, H3 would likely be a much better loading control for nuclear lysates than actin or tubulin (even though both do occur in the nucleus in some circumstances), due to its much higher and more stable expression.

So, test what you have, and ensure that it truly isn't affected by your treatment or disease conditions. Also, make sure that the signal isn't saturated, otherwise you can't quantitate results and draw meaningful conclusions about your data.

I'm not posting an answer as I've voted to close this question as opinion-based. This is not a discussion forum; rather it is a Q&A site for biology researchers, academics, and students where specific objective questions relating to biology get specific objective answers. Please take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and how to ask a good question.

@MattDMo, I think there's an objective answer to the question "What other alternatives are there for WB analysis? ".

Use a total protein stain. Irrespective of tissue type, normalising your immunoblot signal using a total protein stain is a good, probably superior, approach (ref1, ref2, ref3). Many journal guidelines now strongly encourage the practice;

Normalize signal intensity to total protein loading (assessed by
staining membranes for total protein) whenever possible.
“House-keeping” proteins should not be used for normalization without
evidence that the experimental manipulations do not affect expression.

If you really need to use single protein loading control, confirm that it's stable in your hands; the abundance of any given protein in a tissue could still be perturbed by your experimental conditions.
Confirming consistent loading of your lanes using a total protein stain can help to confirm that your loading control is consistent in your experiment. I generally collect both total protein signal and a loading control but will only use the latter if a reviewer is being difficult.


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How did birds reduce their tail and fuse the last caudual vertebrae into a pygostyle?
I was just looking at the phylogeny of Avialae and saw that birds go from having long tails made up of many caudal vertebrae (ex: Archaeopteryx, Jixiangornis, Jeholornis) to ones with very few vertebrae and a fused pygostyle (ex: Confuciusornithids, Chongmingia, the opposite birds, etc). Has anyone figured out what mutations caused this to happen?

have you tried googling pygostyle genetics, because I got a lot of good hits with just that.  I am not saying this to be rude but because questions like this are expected to show some attempt to research an answer yourself before asking for help. It is part of the homework question rule. Hint: something like it has evolved in more than just birds.


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Recommendations for Books on Systematic Phylogenetics
I am a physics major and need to study systematic phylogenetics for a research project. Can someone please recommend at least one introductory and one advanced book, please?

What did you find when you searched online? Have you used Google Scholar or some other search engine like NCBI to look for review articles? What did you learn there, and where are the gaps in your understanding? As it stands, this question is opinion-based, which is off-topic on this site.

It would also be helpful to know what aspects of systematics you're interested in. Like, are you wanting to construct a tree? Are you comparing characters across species? Something else?

About which aspects of phylogenetics I'm interested in, mainly comparing characters across species and the methods for constructing trees, but since my knowledge is limited to Hennig's articles and a few youtube videos of a PhD in evolution, anything works, really.

I've managed to pick three books: [Joseph Felsenstein] Inferring Phylogenies, [Baum, David A.; Smith, Stacey D.] Tree Thinking - An Introduction to Phylogenetic Biology, and [Funk, K.A.; Brooks, Daniel R.] Phylogenetic Systematics as the Basis of Comparative Biology

Those books are probably a great start. I'm sure they cover it, but if you're comparing characters you'll need to be aware of phylogenetic comparative methods.


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semantical meaning of positions of letters in genomic sequences
here is a sequence from the human_nontata_promoters.zip dataset that represents a genome.
My question is whether the position in this genome data is consequent. For example, the positional letters at 0 to 10 are in charge of "this" from the position from 10 to 14 for another property.
TCCTGCCTTTCCACTTGCACCAGTTTTCCCACCCCAGCCTCAGGGCGGGGCTGCCTCGTCACTTGTCTCGGGGCAGATCTGCCCTACACACGTTAGCGCCGCGCGCAAAGCAGCCCCGCAGCACCCAGGCGCCTCCTGGCGGCGCCGCGAAGGGGCGGGGCTGTCGGCTGCGCGTTGTGCGCTGTCCCAGGTTGGAAACCAGTGCCCCAGGCGGCGAGGAGAGCGGTGCCTTGCAGGGATGCTGCGGGCGG
My knowledge in biology is almost zero and I would like to use this dataset for some purposes, I appreciate your help!

I would recommend thinking about DNA sequences more like words and sentences in a book than bits in a digital data file.
If you're reading a book and come across:

The quick brown fox jumps over the lazy dog

you don't need to know what character # in the book the sentence started at to interpret it. If you have another edition of the same book and you read:

The lazy brown fox jumps over the quick dog

you wouldn't say "oh, the 12th character used to be a 'w' but now it's an 'o'" (ignoring the spaces): that's true, but it's clear that the way these sequences actually differ is that two of the words got switched around. The rest of the sequence is the same, though, and much of the meaning is, too: there's still a fox jumping over a dog, even though about half of the characters are different if you compare the two strings letter-by-letter.
A promoter is like a word in this sequence, say "jumps"; a transcription factor will find places in the book with the word "jumps", and bind to that chunk of DNA. This will then influence transcription of the words that come after it.
In interpreting DNA sequences (or RNA, or protein) the solution to this general problem is called "sequence alignment", and sometimes it's fairly trivial and other times it's quite complex. There's a whole subfield of bioinformatics dedicated to these sorts of algorithms.

thanks a lot! Promoter seems to have some fixed semantical positions according to these -10 and -35 elements described in Wikipedia, isn't it?

@malocho Yes but remember these are all relative to something, not absolute positions.

ok, got it, thanks!


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Evolution equations of a 2-gender age-structure model?
This sounds a bit complicated but I want to grab more feelings on age-structured problems. Less than 2 days to the exam so I appreciate any help.
So suppose we get 4 age classes in a population census and we don't count the people in the eldest age class again. We model females and males separately. Let $u_{i,n}$ and $v_{i,n}$ be the number of females and males in age class $i$ at census $n$, respectively. $s_i$ and $t_i$ are the fraction of females and males, respectively, surviving from age class $i − 1$ to $i$. $m_i$ is the (expected) number of children from a female in age class $i$.
If a fraction $\alpha$ of births are females and $1 − \alpha$ are males, what are the evolution equations for (1) $u_{1, n}$ to $u_{4, n}$ and (2) $v_{1, n}$ to $v_{4, n}$ respectively?

I tried putting forward the Leslie matrix for female: $$\begin{bmatrix} \alpha s_1 m_1 & \alpha s_1 m_2 & \alpha s_1 m_3 & \alpha s_1 m_4 \\ s_2 & 0 & 0 & 0 \\ 0 & s_3 & 0 & 0 \\ 0 & 0 & s_4 & 0 \end{bmatrix}$$ Is this correct?

If I try to repeat the thought process in part 1, we must use $u_{i, n}$ to write out the equations for males in the 1st age group, i.e. $v_{1, n+1}$ (unless both gender can give birth): $$v_{1, n+1} = (1-\alpha)t_1\left(\sum_{j=1}^4 u_{j, n} m_j\right).$$ Is this a way to determine "the evolution equation for $v_{i, n+1}$ in terms of the population structure at census
$n$"?

In case I have to find the gender ratio (e.g. for a certain age class or overall) in census $n+1$ or in long run, should I find the largest eigenvalue of both Leslie matrices for both gender, and proceed to find the respective eigenvectors for both gender, and then add the terms together to compare?

Thanks in advance.

Good luck on your exams! I sure am glad I’m not the one taking them. (I had a dream last night about needing to solve a math problem much simpler than this one. Unfortunately the numbers kept changing!)


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I just do not understand how myelination speeds up action potentials
first off, I've watched like 7 youtube videos, read a bunch of articles, and the explanations for why myelination actually increases action potential propagation differ each time are very vague. I've read and heard that because action potentials only occur on the nodes of Ranvier, that it simply takes less time for them to travel down an axon. I get that, but I was under the impression that increased +ve charge = further generation of action potentials. if that is the case, wouldn't that mean that myelination should slow it down as there is less +ve charge influx? I understand that it takes time for action potentials to be generated, but is the variable affecting the rate at which they occur not the influx of +ve charge, and wouldn't this positive charge be less if there are fewer action potentials generated? it's not like myelination decreases the time taken for particular na+ channels to open, right? ftr, I'm not doubting that myelination speeds up action potential propagation, I just don't get it and the explanations are contradictory (nothing that I've mentioned here is contradictory to my knowledge FYI, I just mean that I have heard other contradictory explanations). I understand that it insulates the neuron, thus preventing k+ leakage. Does the insulation possibly increase the rate of propagation by decreasing the ability of extracellular ions from interacting with intracellular neurons? I would understand that I suppose since then there wouldn't be positively charged particles on the exterior exerting electric force upon the intracellular +vely charged particles, thus making it easier for +ve charge to spread throughout the negatively charged axon. even if there is any truth in that, could that possibly compensate for the decrease in intracellular sodium that the decreased amount of na+ influx channels would imply?
thanks to anyone who responds! a long one for sure, lol.

Hi @William. Good question. Would you care to edit your post for legibility? It may help with getting more people to help you out with an answer! At the moment it's a verbose and hefty chonk of text, I'm sure you'll agree!

I think this is a duplicate; if you're still not following then maybe you can distill it down to some more specific uncertainty, but I'd recommend dropping the things you think you know and trying to relearn how it works from that linked Q&A.


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A career in synthetic biology
So I am thinking about a career in synthetic biology, but I am not sure what route should/needs to be taken. I don't want to do technician work--I want to be involved in the planning. Y'know, the exciting stuff. :)
I'm wondering whether I should go for a Master's or a PhD (or is a Bachelor's enough?)
It's a young field, so I'm having trouble finding this kind of information online. Any help would be much appreciated!

this is off topic here, and is more suitable/appropriate on academia.SE

I'm voting to close this question as off-topic because it's a career question.

Sorry, I was torn on where to put it and thought that academia was more for questions about how academia works. But will move there!

I think that "career in synthetic biology" and "involved in planning" both express very vague ideas. There are significant differences in what you will be able to do with a Bachelor's, Master's or PhD, depending on what exactly you end up doing.
I entered a PhD program in biology for no better reason than that I felt awed and fascinated with science and had done really well in science subjects as an undergrad. Grad school seemed like a natural extension of that effort.
In retrospect, my motivations for pursuing a PhD were horribly naïve and easily the greatest challenge that I faced as a grad student was that of defining why I was there and where I wanted to go with my degree. So, to address the issue of vagueness in your question, my first piece of advice is to have a firmer idea of what you want to do. Plans will change, but simply having a plan (a real plan) might provide an anchor when you need one.
As to what you can do with the various degrees, I can't precisely answer your question, the way you've phrased it, but I can give you a general idea.
A bachelor's degree in biology will not get you far in a lab setting. Among the lab techs I've worked with, even most of them have master's degrees. From what I've seen, this holds just as true for academia as for industry.
It's a little unclear what you mean by "planning", but most of the admin that I work with, who are involved in planning our various projects also hold advanced degrees, typically in science, business or public health. I see a strong representation among the management at my institution (Columbia University) of PhD scientists, who left the bench for something less life-consuming, while still wanting to have a hand in research. These people are frequently grants managers or program directors.
As I mentioned earlier, the lab techs around me generally hold master's degrees. When I was considering quitting my PhD program after the master's component, a friend in industry advised me against it, if I ever thought that I might seek work in industry. The picture that he painted was that in industry, a master's degree makes you overqualified for many of the tasks that you can expect to be hired for, but underqualified for significant future career advancement.
Obviously, you shouldn't feel limited to academic vs industrial research tracks. There are plenty of other options out there. Maybe look up people's blogs that involve synthetic biology or whatever other topics of interest you might have to get a wider view of what people who have expertise in the subject are doing.
Good luck!

Thank you so much! This was very good. (And for clarification, by 'planning' I mean things like, for example, looking at symptoms (assuming we are looking at a person), pinpointing underlying causes, designing a molecule that stimulates X, modifying it to avoid inadvertent binding to Y, etc.)


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Is it possible to separate the binding and catalysis of an enzyme in two steps?
Is it possible to do the following:

Enzyme E binds to its substrate S without catalysis;
Add a controllable stimulus, such as light, adding or removing chemicals;
The enzymatic reaction is triggered by the stimulus.

The word controllable means I can add the stimulus at any time I want. Before I add the stimulus, the enzyme keeps binding to the substrate specifically but no reaction takes place.
This is what I mean by separating binding and catalysis in two steps.
In the case of allosteric regulation, some chemicals will inhibit the activity of an enzyme. For example, ATP will inhibit the activity of phosphofructokinase 1 (PFK1). But I'm not sure whether this allosteric inhibition also hinders PFK1's binding to the substrate, which does'nt satisfy my description above.

Interesting question, but need some more specifics. This depends strongly on the enzyme, are you focusing on FPK1? Do you consider the enzyme substrates themselves as "controllable"? (That gives you more options.) Must the enzyme bind all its substrates irreversibly in the inactive state (for FPK1, ADP and fructose-6P)? Is this for detailed enzyme mechanism studies in vitro, so the molecular dynamics is important? (For simply keeping the enzyme inactive in cells this seems unnecessary.)

@Roland Thank you for your comment. I'm actually focusing on methionine aminopeptidase (MetAP). I mentioned FPK1 because it is a typical example for allostery. The substrate of MetAP is a peptide with methionine as its N termini, which could be controllable if necessary (but how?). It is prefered if the binding is irreversible, but also acceptable if reversible. The assay is designed for an in vitro biotechnology. I don't think such a method is already available for MetAP, but any similar method may be helpful for me to adapt it to MetAP.

In that case you need to review the details of the reaction mechanism for MetAP. Some enzymes bind their substrates and cofactors sequentially, and if the peptide happens to bind first, you might achieve what you want by withholding a cofactor. But if peptide binding is the event that initiates reaction, this may not be possible. If the enzyme requires a posttranslational modificatin for activity (e.g. phosphorylation) that might be another possibility.


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Can aptamers be used to identify the terminal amino acid residue of a peptide?
Suppose there were DNA or RNA aptamers that bind specifically to a certain terminal amino acid residue. Let's name it aaSA (amino acid specific aptamer). For example, the aptamer binding to terminal methionine residue is named as MetSA.
If such 20 aaSA all existed, then they could be applied to identify the terminal amino acid of a peptide. Concretedly, the peptide sample is immobilized to a solid surface, then all 20 aaSA are introduced and bind to the terminal residue. Extra unbinding aaSA will be washed away, and the binding aaSA will be separated later by another approach (like heating). And by sequencing the binding aaSA we can know the terminal residue of the peptide.
Either N-terminal or C-terminal is OK.
I know mass spectrometry is much more powerful in this task than the method I have supposed. But I still want to know if such aptamer exists or not.
I have searched in Google and Google Scholar, only to find aptamers binding to some intact proteins (rather than short peptides with terminal exposed). The binding site is unknown, possibly not in the terminal.

I'm not quite sure what you're asking about. If you're just talking about peptides, then N- or C-terminal sequencing is much easier and more accurate than the method you describe. For large proteins, they're still easier, as the terminal peptides may not even be available to an aptamer in the protein's native conformation.

@MattDMo Thank you for your comment. I have learned many well-developed N- or C-terminal analysis method in biochemistry class such as DNS, PITC, hydrazinolysis and amino/carboxy peptidase. I'm not proposing the first peptide terminal analysis method but just an alternative. Despite this, I think the method by aptamers may still have some advantages. For example, if the peptide is in trace amount, the signal produced by other methods may be too weak to be detected accurately. But for aptamers, they are nucleic acid and can be amplified.

@MattDMo And after searching in the Google, I found it seemed that nobody had done it. So I'm wondering if I have read enough paper or someone already did it.

Two places I'd definitely recommend looking are the US and EU patent and trademark office websites. If someone has developed something like this, they almost surely have filed for patent protection. If you end up doing it, you should get a lawyer and patent ASAP.


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Will the interaction of two proteins vary across different tissues?
Suppose protein A and B is both abundant in tissue X an tissue Y. Will A and B interact in X but not interact in Y?
I guess A and B could be biomarkers of a certain disease, and in the pathological tissues their amount remains relatively unchanged but no longer interact, thus losing their functionality and causing the disease.
One possible condition would be that A and B don't interact directly but require a third protein C to act as the scaffold to form the complex A-C-B. So when C is expressed in tissue X but not in Y, we would observe this phenomenon.
Are there other mechanisms or examples?

Your example of an interaction mediated by a scaffold protein is certainly one way of controlling protein interactions. This doesn't just happen in different tissues either, it is also used to fine-control the interaction of certain proteins within one cell, the most notable example for this are the kinases in the MAP pathway (see for example this paper).
Another possibility I can see is that A and B can interact, but only if (at least) one of them is modified, e.g. by phosphorylation - so the actual interaction happens with A-p and B. In a case like this it's not unlikely that the protein that modifies A is only expressed (or active) in certain tissues, which then mean A(-p) and B can only interact in these tissues.


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How bacteria respond to toxic viral proteins?
The lysis-lysogeny state of bacteriophage lambda is well known. Under certain conditions, the phage will enter the lysogenic state after infection of a bacterium. Then, after a while, the phage switches to the lytic state and breaks the bacterium. I forgot the details but the phage must expressed some proteins toxic to the bacteria, e.g., a protease, to lyse the bacteria.
Here is the question: Did bacteria have any immune strategies to defend themselves in face of these toxic proteins? In mammals, both nucleic acid and protein can induce immunological responses and activate T/B cells. In bacteria, I know that the CRISPR system is an immune strategy to degrade viral nucleic acids, but seemingly not proteins.
So if the CRISPR system has missed cutting the viral DNA, the phage has switched to lytic state and begun to produce toxic proteins, did the host bacteria still have weapons to defend? Obviously, most of the time the bacteria failed and died. However, after billions of years' evolution, how could bacteria just give up in face of the toxic proteins?

I don't know of any direct defenses available to bacteria once a prophage genome has been integrated. If a prophage has induced and carried out its program to the point that lysis proteins are being produced, it is far too late for the host cell.
However, an indirect defense for the bacteria is to simply survive and replicate faster than its prophages induce. You seem to be thinking about this as a purely antagonistic relationship, but once the viral genome is integrated into the bacteria, their reproductive fitness becomes intertwined. When the host replicates, both genomes are copied, so the phage can produce far more progeny by delaying activation until the host builds up its numbers. Phage that boost the fitness of their lysogenic hosts will be even more successful. Prophage can defend against infection by other viruses, confer antibiotic resistance, or provide toxins against eukaryotes or rival bacteria. After many generations, mutations that destroy the prophage's ability to induce and kill the host cell but preserve the beneficial genes are selected for; bacterial "domestication" of integrated viral genomes appears to be common. A thorough discussion of bacterial/prophage co-evolution could fill a textbook, but is mostly beyond the scope of this question. The links in this answer should provide a good starting point if you'd like to know more.

Thanks very much for your inspiring answer! Actually I wanted to seek molecular tools for proteins as CRISPR, the bacteria's immune system against nucleic acids, has been so useful.

Yes I realize my answer doesn't really address the main part of your question. I don't think there is anything like CRISPR for proteins.


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Why is inhibition of inhibition (reciprocal inhibition) such a common motif in cell signalling?
In transcriptional regulation, you often find that positive signals proceed by inhibiting or destroying a protein that is in turn inhibiting or destroying the effector protein. This can be seen in the retinoblastoma - E2F signalling pathway, and many others. I was wondering if there was any direct biological utility, and if so what this utility was.

You might be interested in reading Uri Alon's take on network motifs: https://doi.org/10.1038/nrg2102

This reminds me, somehow, of the Dining Philosophers Problem, which is about avoiding deadlock in distributed systems.

This feels like a my philosophical question...
Direct regulation of proteins would have to have biological utility - such a gene has to be driven by positive selection to adapt that ability.  The question is more about learning what might be driving its role.
I would hazard that protein deactivation and degradation would be important to make sure that these inhibitors could be down-regulated fast enough - if they were left to degrade via a general pathway, the specific signal would not be available for too long a time.


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Why does tetracycline have such a broad spectrum of activity?
What are the structural and chemical characteristics that make tetracycline uniquely broad spectrum? I understand it acts on the A-site of the prokaryotic ribosome, but there exist many ribosome-targeted drugs that are relatively narrow spectrum. I assume it has something to do with its permeability in several different classes of bacterial cell walls and/or membranes - but I can't find any literature that links some characteristic part of its structure to this permeability.

This is a tricky question. First of all, I wouldn't call tetracyclines "uniquely" broad spectrum. They are broad spectrum, but there are other drugs with equally broad coverage absent acquired resistance (e.g., imipenem and chloramphenicol), and current clinical use of tetracyclines is limited somewhat by the spread of resistance.  They don't have any major class limitations, though. Again, absent acquired resistance, tetracyclines are effective against gram positive aerobes and anaerobes, and gram negative organisms, as you seem to be aware.
Tetracylines access their target on the 30S subunit of the bacterial ribosome (blocking the A site, as you said) by passive diffusion through porins of the outer membrane of gram negative bacteria, and active transport across the cytoplasmic membrane of gram negative and gram positive bacteria, but the mechanism for that active transport is still unknown. This is quite a good review despite being quite old. Now, some 30 years later, we have still not identified the exact mechanism, as you can read in Goodman & Gillman's most recent edition (13th), Ch. 59, crossing the cytoplasmic membrane requires metabolic energy, but the process is not well understood. Because of this, we can't point to a specific structural or chemical characteristic. For chloramphenicol, it would be the ability to diffuse across the cytoplasmic membrane; for tetracycline, we don't know. I suspect part of the reason for this is that people are now more interested in pumps removing tetracyclines from the cell than those that accumulate it, so it's more of a question about research priorities than some transport mechanism that is particularly difficult to detect.


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Why are aminoglycoside antibiotics particularly effective for aerobic gram negative bacteria?
Aminoglycosides are short chains of sugar molecules with some -OH groups substituted with amine groups. As far as I understand they function by causing bacterial ribosomes to misread RNA and create non-functioning proteins. These proteins both stop providing essential functions of the cell and increase permeability of the cell to aminoglycosides, eventually leading to the death of the cell. What I don't understand is why this mechanism is specific to aerobic, gram-negative bacteria. Surely membrane permeability would be roughly the same for both classes? And also ribosome structure? Any help would be much appreciated.

Anaerobiosis is incompatible  with effective intracellular accumulation of aminoglycoside antibiotics such as streptomycin and gentamycin.

After an initial binding step involving outer membrane lipopolysaccharide the kinetics of the uptake of aminoglycosides exhibit two energy-dependent processes (EDP I AND II). EDP I  is the slow, rate-limiting stage and is dependent upon the membrane potential ΔΨ, but the details of the process are unclear. EDP II is more rapid and may be triggered by membrane changes arising as a result of translation errors caused by the antibiotic accumulated in EDP I since protein synthesis inhibitors block the transition from EDP I to EDP II.
EDP I requires  a threshold value of ΔΨ, and there is evidence that this threshold often cannot be achieved under anaerobic conditions.
This summary is based on information in this review from 1987.  I haven't been able to find any more recent information.

Aminoglycosides are positively charged and hence more drawn towards the the Gram negative bacteria as the LP in their outer membrane is negative.

Welcome to Bio. Could you add some more background and some sources behind your interesting answer? As of now your post is more of a short comment. Thanks.


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In mitochondria, what is the mechanism by which electrons are transferred between different cytochromes?
And how is the energy gained from the lowering of the "energy level" of the electron used to generate the chemiosmotic gradient?

I think this is a completely reasonable question, why the close votes? Can someone at least comment on what the problem is, and give the OP a chance to edit, before voting to close?

Good question. The common picture of the electron transport chain as a sequence of molecular machines that pass along a "high energy electron" is biochemically rather misleading I think. What is really going on is just a series of energy-releasing (exothermic) redox reactions. The respiratory complexes are enzymes that catalyze these reactions and couple the energy released in each reaction to proton pumping against a gradient.
As an example, lets consider the reaction carried out by Complex I, where NADH is oxidized:
NADH + H$^+$ + CoQ $\iff$ NAD$^+$ + CoQH$_2$
This reaction transfers a hydride ion (H$^-$) carrying two electrons from NADH, which is accepted by CoQ. Since CoQ is a much better electron acceptor than NAD$^+$, this reaction is highly favorable with a $\Delta G$ of about
-85 kJ. So quite a bit of energy is released, and part of this energy is captured by Complex I to pump four protons across the inner memberane.
Note that electrons are not "traveling" on their own through Complex I somehow. The electrons are bound to molecules that participate in a redox reaction. And it doesn't make much sense to say that a specific electron's "energy level" is decreased. Rather, the compounds on the right hand side have a lower free energy $G$ in total than those on the left hand side, and therefore the reaction overall releases energy (the free energy difference $\Delta G$ is negative). Also, if you look at the chemical structures of CoQ and CoQH2 --- and you absolutely should look at structures in biochemistry, the names alone are not very helpful --- you will find that the electrons involved are actually delocalized in CoQH2, so there's no way to figure out which electron goes where.
The same reasoning goes for the other respiratory complexes. Complex III oxidizes CoQH$_2$ back to CoQ by coupling it to reduction of cytochrome C,
CoQH$_2$ + 2 Ferricytochrome-C   $\iff$   CoQ + 2 Ferrocytochrome-C + 2 H$^+$
This reaction is also favorable, and again the energy released is used to pump protons. Finally, Complex IV oxidizes cytochrome C back and transfers electrons to O$_2$, also an energy-releasing redox reaction. The reaction mechanisms are much more complicated of course, involving various chemical groups bound to the enzymes, but this is the net result.
So the "respiratory chain" is not some conveyor belt for electrons; it is a sequence of coupled redox reactions. The net result of the Complex I + III + IV reactions is that NADH has lost electrons and oxygen has gained electrons, but it's not necessarily the same electrons, and it doesn't make sense to speak of "energy level" of electrons in this context. To understand the energetics, we must look at all the compounds and reactions involved.

@tomd,  as I interpreted the question, the OP was aware of the chemoosmotic principle but was unclear about the energetics that provide the energy for proton pumping.

All of the members of the Electron Transport System (ETS) are organized in "complexes", clusters of enzymes and other proteins. These complexes are in proximity to one another such that electrons can be passed between them. The different cytochromes, and other electron handlers, have different affinities (attractions) for electrons. Those at the beginning of the ETS have less affinity for electrons than those at the end. The reason the electrons move through the ETS is due to that greater attraction of electrons by the subsequent complexes in the pathway. These complexes are positioned with respect to one another so that no "short circuits" occur; the electrons skip no steps down the ETS. Finally, the "low energy" electron from the last complex is mopped up by that great electron-hog oxygen.
The energy lost by the electron as it passes between carriers is not directly harvested to pump protons. The importance of this "loss of energy" is that it makes the transfer of the electrons a spontaneous process insuring their passage down the ETS. Typical entry into the ETS involves NADH donating a hydrogen ion to the matrix and a pair of electrons to NADH dehydrogenase. The electrons are eventually transferred to the mobile coenzyme Q. This now attracts a pair of hydrogen ions from the mitochondrial matrix which then induces the operation of a proton pump. This pumps hydrogen ions into the inner-membrane space creating the electrochemical gradient.
So, in general the arrival of electrons, with the attendant hydrogen ions, changes the conformation (shape) of pumps which translocate the protons to build up the gradient. The electrons are ultimately passed on to oxygen, forming water with the help of some spare hydrogen ions. This removal of the electrons allows the ETS members to be receptive to another load of electrons from the NADH.
Reference 2nd paragraph: http://www.physiologymodels.info/metabolism/ETSOXPHOS/ets.htm
This is a good site to read more and view some diagrams, especially focus on the second panel, "Complex I".
Reference 1st paragraph: Molecular Biology of the Cell; Alperts, Watson, et.al.

Thanks for the really detailed answer - the link was very interesting; it's just that I'm in the dark as to how these electrons are transferred between complexes? It seems counter intuitive that they can just hop between molecules when all other electron transfers in biochemistry require some kind of enzyme-mediated redox reaction.

@user30109. These are oxidation-reduction reactions. And some of the members of the complexes are appropriately called enzymes.


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How does DNA damage increase the activity of p53?
I understand the steps leading up to the halting of the S-cdK checkpoint from there, but I can't find the mechanism by which DNA damage actually increases the activity of p53.

p53 is expressed constitutively but, in unstressed cells, it is an inactive conformation and its level is kept low by proteasomal degradation. Proteins which are recruited to double strand breaks can start a signalling cascade of protein kinases which leads to 1) stabilization of p53 and 2) activation by phosphorylation. If I find the time, I'll try and write a proper answer.


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What are the chemical characteristics of cofactors that functionally differentiate them from the side chains of amino acids?
Cofactors are essential for the function of many enzymes, such as NAD+ in the glycolytic pathway - I was wondering how the chemical properties of these cofactors allow them to fulfil their function and/or what it is about the chemical properties of amino acid side chains that limits their utility in the kind of reactions that require cofactors.

Are you interested in all cofactors, or only organic ones? (see also: https://biology.stackexchange.com/questions/19896/where-can-i-find-a-list-of-common-enzyme-cofactors-and-or-co-enzymes)


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What might earlier versions of caddisfly shelter-building behavior have looked like?
The caddisfly has an amazing ability to build armor for itself by using a self-produced underwater glue to hold together pebbles: https://www.youtube.com/watch?v=Z3BHrzDHoYo.
How could this behavior and the ability to produce the glue have evolved? The survival advantage of the current level of the caddisfly's ability is clear, but how were the incremental stages advantageous? How could it have developed its armor-building ability without a strong enough glue? And how could it have developed a stronger glue without the armor-building ability that would make it useful?
My guess would be that before it was building a full shell like it does now, it started just by holding a pebble or two to itself. Then perhaps the bodily fluid that is now used as glue gradually increased in stickiness and helped the organism keep hold of the rocks or keep them together. It seems, however, like any modest amount of increase in stickiness that could occur due to mutations wouldn't have been enough to keep the rocks together.

Your intuition seems fairly correct. Mouro et al 2016 show some findings relevant to your question...

Caddisflies have been around for a very long time. Much of the fossil record of their existence is of preserved shelter cases rather than the insects themselves.
Early cases seem to be made up of more variety of materials, whereas selective cases made of very specific materials are observed more recently in the fossil record and today. This suggests that they first just collected random pebbles and organic materials, and later evolved more refined construction techniques.

As far as evolution of their silk, I think it's important to recognize that these insects are closely related to Lepidoptera, the moths and butterflies. Many Lepidoptera species, like caddisflies, spin silk cocoons as part of their development cycle, so it can be inferred that the silk and many of its properties precedes any construction behavior using other materials.

Mouro, L. D., Zatoń, M., Fernandes, A. C., & Waichel, B. L. (2016). Larval cases of caddisfly (Insecta: Trichoptera) affinity in Early Permian marine environments of Gondwana. Scientific reports, 6, 19215.

Beyond what is shown in the fossil record and in genomic analysis, the evolutionary advantage of a phenotypic feature can only be guessed at and its plausibility gauged.
That said, here's a guess that seems plausible: the sticky silk might have first served as a way to tether the caddisfly larvae to stationary rocks in a river current.  The tether would have naturally and coincidentally picked up small rock grains, sticks, and the like.  If the tether broke, the grains would stay attached to the remaining silk strand and, if "reeled in" by the larva, might have served as makeshift armor as the larva tumbled downstream in the current.  This would open up a new adaptive opportunity, channeling adaptations in the direction of improving the shell-constructing behaviors and physiological tweaks that support shell construction.


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Dreaming after passing out
I'll have few questions about passing out and dreaming. English is not my native language, and my biology knowledge is very limited. So bear with me.

What exactly is blackout? (in a really simple way)
Are there different types of blackout? (see below)
Do fainting, passing out, and blacking out mean the same thing?
Can someone have a dream/vision after loosing consciousness? (during blackout?)

I'm asking these because I had a similar experience and I'm trying to make sense of it.
We were goofing around and a friend of mine had me in an arm triangle. I suspect he choked me, because I lost consciousness for a few seconds, max 3. While in that state, I kind of had a dream or vision, whatever it is called. It felt like hours. This was a long time ago and I still remember the dream, but can't make sense of it. What I've seen was really interesting and I couldn't just let it go.
I'm not asking for dream analysis or anything, but the biological/neurological aspect of what happened, so don't get me wrong.

I'm also new in here, though not to stackexchange, so the tags might need a modification.

Fainting, passing out, and blacking out are all common terms for the same thing, a sudden loss of consciousness of short duration.  The medical term for this is syncope. It is caused by a decrease in blood flow to the brain, limiting the the availability of oxygen and nutrients to the brain cells.  Brain cells have high energy requirements, so this causes them to stop functioning, causing loss of consciousness and muscle tone.
There are many causes of syncope.  In the situation mentioned, a likely possibility is a pressure change in the carotid sinus which is located at the side of the neck. When sensed by a nerve, this can cause primitive parts of the nervous system to change the dilation of blood vessels and the beating of the heart in a manner that brings on syncope.
Dreaming during syncope is not uncommon and that fact may be useful in distinguishing syncope from epileptic seizures according to research by Chiesa et al..


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Why does our mouth "water"?
Whenever we see something delicious, rapid salivation starts in our mouth. Also, it doesn't happen for all other food, which we eat regularly.
So, Is there any particular use of "rapid salivation"? and why doesn't it happen for everyday foods?

Basic biology: saliva in digestion is used to digest starches and fats.  It also lubricates food so that it is easier to move down the esophagus.  It is the first response your body has to food entering your digestive system and occurs in advance of food arrival. Pavlov's dog is a demonstration of this.
Rapid salivation occurs most often in two cases.  The easy example is seeing or smelling something like cake or pie, though this applies to any highly desirable food to the individual.  The case we think less of is that of starvation or even deep hunger.  In this case, even "everyday foods" cause rapid salivation as the body needs any calories it can get.


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Are fishes evolving?
As far as I know, Fishing has been one of the important occupation since early ages, and infinite number of fishes have already been captured.
As the time passes, they must've developed some sort of knowledge about the fish-nets, and should've figured out a way to escape from them. But, still now, we are able to capture them at the same rate(I guess)
So, Are they developing any sort of hereditary memory to escape from us?
P.S. I'm not sure whether this is the right SE to ask.

There is no knowledge or hereditary memory involved.

"No hereditary memory involved"? How can we say that for sure?

Pretty much the same reason we don't think the fish are developing psychic powers. There's no evidence for it, the mechanisms by which evolution is known to operate wouldn't produce such a thing, and it wouldn't explain any observed phenomena better than the existing explanations.

No, what I meant was that fish should've developed some sort of hereditary memory that we're one of Predators, atleast when they saw fellow fish being captured by us, and should've learned to tackle the "fish-nets"(or whatever). But, this isn't happening even after 40,000 years. Why?

Evolution just doesn't work like that. Here, have a link to an explanation of how it does work.

How's this hypothesis @user2357112 - the effect of man's overfishing is to catch shoals and individual fish that are easier to catch. Therefore the more reclusive/cautious fish survive, which means those characteristics are passed one.  I'd say that would be a reasonable approximation of inherited memory.

@geotheory that's not a hereditary memory, that's an acquired trait.

I don't think its necessarily very different from cats fearing cucumbers - possibly an inherited fear of snakes.

@geotheory +1, just for the reference

I'd be curious to see an answer that addresses indirect pressure through habitat change, like what happened with pigeons and highways.

@geotheory: That's not memory, that's behavior.

That's just fudging.

Yet another question that underestimates the length of evolutionary timesceles compared to industrialisation of people.

Fish are definitely evolving to avoid fishing pressure. For example, largemouth bass evolve toward avoiding hooks.  More broadly, since fishing selectively removes larger fish from the population, there's selection toward fish evolving smaller size.  A brief review, linking to many studies demonstrating this, is Evolutionary impacts of fishing: overfishing's ‘Darwinian debt’.

I would disagree with the phrasing "to avoid" and replace it with "in response to". The old adage about evolution not assuming a purpose applies here.

"in response to" implies a purpose as much as "to avoid" from my point of view. I'd rather use "as a consequence of".

I understand the urge to avoid teleological words, but I think it's pointless and futile to worry about it once we're actually discussing  real evolution.  I realize that it's hammered into students at the very early introductory stage, but once the concept that there's no goal to evolution is solid -- which should be about a week after natural selection is first mentioned -- it simply becomes an exercise in semantics.  If you read actual papers by actual evolutionary biologists, they pretty much all use shorthand language like this.  We're all grownups here.

@iayork: I don't think it's safe to assume the questioner is past that very early introductory stage. Even if they are, this answer will probably be read by people who aren't past that stage.


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sodium chloride and amylase activity
So, I did an experiment on the effect of sodium chloride on amylase. and I found out the higher the concentration, the slower the activity.
Therefore, is it valid to make the assumption that when we consume food with starch and high salt concentration, it can affect our digestion of starch? like slower break down of starch?

I highly suggest you actually look at studies that analyze this and there should be a good number since amylase is a well defined enzyme. (Bailey K, Hopkins RH, Dolby DE)
Not only that but applying this type of logic to any problem results in bad conclusions and therefore is bad science. (Berkeley)
The process of proving something scientifically is something that follows a somewhat predictable route. I only say that because not everything follows this exact path.
There is usually a nicer looking picture though I cannot seem to find it.
(Source)
So to answer bluntly, no. You cannot make that conclusion with any stretch of the imagination.
Being that amylases are so well studied you may have your answer after a few google searches, but the case remains that it took many years of research to reliably say so.

I found that the higher the concentration of NaCl, the higher the rate of reaction
Why is this different to yours?

Welcome to Biology.SE! Please take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site and then delete or [edit] your answer accordingly. In particular what you have posted is a comment, but you posted it as an answer. Answer are much more likely to receive a favorable response if they are actually answers and include supporting references (primary literature is best). Without that support, an answer is indistinguishable from opinion. Thanks!


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Why my proteins are migrating like this on SDS-page?
I'm trying to make a SDS-page of total proteins extracted from algae but I'm encountering two problems. First, when I depose my proteins in the wells the sample goes down and then it starts to move up the sides of the well. Second the result of my run looks like this:

so my bands are not visible and I have like a vertical smear on the sides of the lane.
The buffer used to extract proteins contains Tris, NaCl, EDTA DTT and Glycerol and my loading buffer is a 5x commercial dye with B-mer.
Thank you!

What did you expect? Single bands clearly visible? How much total protein did you load?

I loaded 10 ug of total protein extract and I expected to see at least some neat bands. Honestly I don't know if the "smear" effect is normal (but I've never seen that with bacterial protein extract), or if it can be related to the degradation of my sample or if it is just a problem in the migration.

10ug is not very much - you could load more (20-30). Simply do this as a side by side comparison. Additionally: This is pretty much how I would expext a raw cell extract stained with coomassie to look like. There are hundreds of different proteins of different sizes in there, you would only see bands for really strongly expressed ones. Or for ones which you can enrich for. Otherwise I woud use Western blot to stain for specific proteins, which usually gives very nice bands even from raw extracts.

Indeed my goal is to perform a western blot but I'm not seeing a nice band where it should be, that's why I tried to compare my samples with a coomassie staining.  :-)
Ok, I'll try to load a bit more protein and I also tried to change the extraction buffer to solve the "moving up" problem.

You don't have to see a nice band on the coomassie stained gels to get nice bands in western blots. I do this all the time (doing whole cell extracts and use them for western), I can post the protocol I am using later today as an answer.

I'm running a gel right now and with the new buffer I solved the problem of the sample moving up the wells. Later I will see if I also have sharper bands.

@Ying Zeng  In the end I changed the protein extraction buffer with a new one, I really don't know why the other one wasn't working. In this moment I don't remember the recipe and what is different from the previous buffer but I can post it here if you want.

It's a guess, as I haven't run a algae sample on SDS-PAGE, but your migration problems might be due the algal polysaccharides that are present in your sample. Check if your protein purification protocol is specific for algal proteins and see if there is any step dealing with the algal polysaccharides.


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Estimate mutation rate in UVC treated cells
I am wondering how to get a coarse estimate of the number of mutation I obtain doing UVC treatment on eukaryotic cells (microalgae) starting from information such as the survival rate, genome size, number of genes or gene density... I heard about a similar estimation for EMS mutagenesis (I don't remember the exact details but it was a correlation between number of colonies surviving the treatment and the number of point mutations per kb of genome). I cannot find the source of this kind of estimate so I really appreciate any help!

Could you give us some more information about the kind of data and experiment you have please, as it will help people give you a better answer. If you have genotyped your colonies, then I would imagine it's not too hard to estimate the number of mutations which have occured.

I just did UV mutagenesis on my cells and determined a kill curve, that's all. I do not have genotyped my WT or MUT colonies (I'm not looking at a specific gene).
My question is if there is a way to have a very very rough idea of how many changes I introduced in the genome by just correlating the survival at a specific dose to the genome size / number of essential genes or similar ( I know this requres lots of assuptions but that will be fine).


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Is this a bed bug??? Small insect with tail thing found in bed

Couldn’t find any other ones, no bites, is very very very small like almost fruit fly size

Nah, not a bedbug, those are round and weirdly flat, as shown in the photos in the posting Tyersome linked.  What you have there is a beetle of some sort.  You can tell by the hard shell divided into two halves along the back - only beetles have those.  The wings are folded up underneath there.  I couldn't say what species of beetle exactly, there are many kinds of tiny brown beetle and the photo is fuzzy.  It's harmless, anyway, whatever it is.
Beetles have no tails.  Looking at the photo, I think what you thought was a tail is actually the end of its wing poking out from under its shell.  I often see that.
Update: I found this, which has photos that look a lot like yours.  One of the photos of one of the beetles even has a nub which looks a bit like a tail.
UK Natural History Museum forum: Is this a biscuit beetle or furniture beetle?
The rest of the above is from memory from reading wildlife books, but I was asked to provide some references so here are some websites that confirm the beetle facts I mentioned.
https://www.woodlandtrust.org.uk/blog/2017/11/common-uk-insect-identification/
http://www.oum.ox.ac.uk/thezone/insects/instant/index.htm
https://www.coleoptera.org.uk/beetle-morphology
https://www.coleoptera.org.uk/what-are-beetles


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Cell location co-ordinates
I have just had the nails on both my big toes removed.  I am much happier.  But it got me to thinking, as there is no 'root structure' from which the nail grows, is there an x,y,z, type co-ordinate system in the genome which says the nail cell structure starts from here or what is the determining factor which says these skin related cells stop forming here and now nail cells start forming but only in this narrow band.

Why do you say there's no 'root structure' from which the nail grows? Have you read anything about the anatomy of nail growth which leads you to believe there's no root structure?


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Does Chewing Food Properly Ensure that we gain Less Fat?
We recently went to a fast-food corner and I was told by my sibling that even if we chew a burger properly(slowly) converting it into a fine bolus, then it would not affect the amount of fat gained by the body as much as we gain when we normally(hastily) eat a burger.
I ,on the other hand, don't believe in the above statements. I think that it will at least have a better impact with regards to weight loss.
So who ,among the two of us, is correct ?

the only result of chewing for a longer time is that the food on your plate will be colder at the end of your meal.

I think you are misunderstanding reasons for weight loss advice for slow eating/excessive chewing. Slow chewing is promoted because it reduces apetite not because slowly chewed food is digested differently. Slow chewing reduces the objective amount of food people eat before thay subjectively feel full. For standard sized meal it reduces amount of snacks later.


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What is the purpose of putting multiple blanks on a microplate reader?
I am new to biology and I saw that in the software that controls the microplate reader several targets are set, what is the purpose of this?

What do you mean by "targets"? Do you mean standards - things of known quantity used to compare your sample to? Blanks usually mean a control which has a baseline reading so that you know any value above this is "positive" for your assay (statistical significance needed!) - replicates help with this.


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How to fix outliers in Ramachandran plot using Coot
I have the following Ramachandran plot generated by Coot:

Notice that it has high outliers content (red dots). I want to manually drag those
red dots into some part of the region. Eventually, I expect it to be reflected
in the coordinates so that I can save it as a new PDB file.
How can I achieve this?
G.V.

Surely the first place to ask would be the mailing list for this very specialized software. Have you done this?

https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2207&L=COOT&O=D&P=2725

This was asked also on chemistry and mattermodelling