Is there a specific mechanism for the delivery of pain medication? For example, when one takes aspirin or ibuprofen does the chemical get dispersed to all pain receptor? My question really is, how does the chemical know where to target in the body? I figure wherever there is pain in the body that a certain signal is being produced; which possibly acts as a chaperone to direct the medication chemical where to bind and inhibit.

Short answer
No, orally taken painkillers act systemically.

Background
Taking a painkiller orally results in the drug being taken up into the bloodstream by the digestive system. From there it can potentially reach all tissues.

In other words, a pain response does not act as a chaperone. A hypothetical drug that would home in on tissues with a pain response, while avoiding unaffected tissues would be the ultimate painkiller, if it existed.

EDIT: To emphasize that painkillers act systemically I will elaborate on aspirine's pharmacokinetics. Notably, aspirine's actions are not restricted to the pain centers in the brain, and I quote the following excerpt from Wiley's interactive Concepts in Biochemistry]1:

  Aspirin's analgesic and anti-inflammatory effects are due to the drug's ability to stop the production of prostaglandins that cause tissue swelling and pain.

Aspirin's antipyretic (fever-reducing) effect is due to its direct action on the hypothalamus gland, which results in vasodilation of peripheral blood vessels and sweating.

Prostaglandins are also the key mediators of platelet aggregation. By modifying the COX enzymes within platelets, aspirin causes platelets to lose the "stickiness" that is needed to stimulate blood clotting.

Hence, by these examples it can be seen that aspirine works in the periphery (wound swelling and pain), centrally (brain's hypothalamus) as well as in the bloodstream. Hence, aspirine (and other orally administered painkillers) do not target specific areas in the body, and most certainly not only the brain.

There are such targeted drugs, however. An interesting one is carbamezipine, an anti-epileptic that blocks Na+ channels. It blocks Na+ channels only when they are in an active conformation, however (i.e., engaged in action potential firing). Epileptic activity is basically paroxysmal (massive), synchronous over-activity in the brain that is accompanied by massive Na+ channel activity. Hence, epileptic activity will in effect trigger the drug into action.


Is the mutation rate in pseudogenes higher than in coding regions? Coding genes are subject selective pressure that are not present for pseudogenes, that would suggest that pseudogenes have a higher mutation rate than coding regions. If so, how much higher?

It is important to distinguish between the rate of mutation, which is a biochemical process, and the rate of fixation, which is a population process whereby an allele with a particular mutation becomes fixed (present in all individuals) in the population. Relaxed purifying selection, such as that experienced by genes undergoing pseudogenisation, affects the fixation rate of mutations because new variants are not being filtered from the population by purifying selection. The mutation rate itself is probably constant, unless some other factor is at play.

In response to comments, I will say this: if functional constraints on the gene are relaxed to the point where all mutations are selectively neutral, then the process of mutation and substitution can be modelled by neutral theory and the expected rate of substitution (or fixation) is the same as the rate of mutation. This rate is dependent on several factors - lineage, life history, etc., and the difference between this rate and the fixation rate for a given coding region is dependent on the severity of functional constraint on that region.


Understanding muscle tone I am relatively new to Physiology, and I've just learnt about muscle tone.
I however find it difficult to understand the electrical changes that initiate (and/or accompany) muscle tone in smooth muscles .
To be specific, I know that action potentials(AP) cause muscle contraction (just like they cause nerve impulse propagation), and I also know that smooth muscle tone is a result of irregular contractions of the muscles at rest.
How then can these muscles contract when no AP is generated at rest?
PS: This question has been edited to achieve more clarity.

Action potentials usually maintain muscle tone in skeletal muscles, but muscle cells are affected by other influences that can affect their contraction and thus the tone of the muscle.
Smooth muscle occurs in the walls of hollow organs, most notably the blood vessels and the GI tract, and in a few other places.  Contraction of smooth muscle is generally involuntary and can be stimulated by the APs from the autonomic nervous system, but often for the slow maintenance of muscle tone contraction is controlled by hormones, other external molecules, or external pressure.  The mechanisms that cause this contraction generally involve the phosphorylation of myosin light chains. (1) (2)


Has an ape ever drawn/painted something? I know there are plenty of examples of apes making paintings and drawings, but has there ever been a recorded case of one representing something in their art?

Yes. The objective clarity of what constitutes representation is not certain, but here: https://www.youtube.com/watch?v=nSHQyLsPm4Q you can see something relatively convincing. The elephant really slays this, but your question is about apes; I don't know how species-specific you intend to be. I find that non-biologist laypersons assume that finding humanoid traits necessitates searching in human-like animals. Often not so! In fact, I wouldn't be surprised if someone came up with an octopus capable of a transformative masterpiece.


Religion and Genetics Are there studies that investigate the heritability of "believing in supernatural" (or related concepts)?

There are several twin studies showing, that the tendency to be religious has a genetic component. Not which religion you choose, because that is a cultural thing, but how serious you are abot it. I am lazy for a detailed report, but this blog can lead you to the studies: http://www.scilogs.eu/en/blog/biology-of-religion/2011-03-12/religiosity-genes-again-confirmed-by-another-twin-study

Also this article: http://www.popsci.com/science/article/2013-08/what-twins-reveal-about-god-gene

EDIT after a few years - I was informed one link is broken and the other contains no citation. So I checked for new material today and wikipedia has a cool passage how genes and environment affect religion. Wikipedia saves the old version, so this is from March 8 2018, article Religiosity.

"
The contributions of genes and environment to religiosity have been quantified in studies of twins (Bouchard et al., 1999; Kirk et al., 1999) and sociological studies of welfare, availability, and legal regulations [15] (state religions, etc.).

Koenig et al. (2005) report that the contribution of genes to variation in religiosity (called heritability) increases from 12% to 44% and the contribution of shared (family) effects decreases from 56% to 18% between adolescence and adulthood.[16] "

15 Nolan, P., & Lenski, G. E. (2010). Human societies: Introduction to macrosociology. Boulder, CO: Paradigm Publisher.

16 L. B. Koenig, M. McGue, R. F. Krueger and T. J. Bouchard, Jr. (2005). Genetic and environmental influences on religiousness: findings for retrospective and current religiousness ratings. Journal of Personality, 73, 471-88

https://en.m.wikipedia.org/wiki/Religiosity#Genes_and_environment


in order to align genome multi-fasta files, do you ignore the chromosome sections? I want to test my implementation of Needleman-Wunsch on two fasta files downloaded from https://hgdownload.soe.ucsc.edu/.
However, fasta files on this site are multi-fasta and therefore are split into sections each one belonging to a chromosome.
If I want to align the entire genomes in these files:

do I just ignore the chromosomal separation inside these files? thus do I stitch the chromosomes of each file into one big chunk?
or do I align combinations of these chromosomes?

If the fasta really are chromosomes, there will be one per chomosome. Check this in case the multi-fasta you have is an incomplete sequencing of an organism. If incomplete there will be many more fasta. There is a bioinformatics site on Stackexchange now at https://bioinformatics.stackexchange.com .You would get better answers there.


Learn Bioconductor the hard way! I came to analyzing population genetics data from the background of a theoretician and a computer biologist but not with the standard tools that a bioinformatician (or empiricist in population genetics) know of. I have a fairly good knowledge in R and in programming in general.

I am looking for a course/tutorial for learning bioconductor (and other R tools for analyzing genetic data). A course/tutorial that is short, dense and assumes the user has good knowledge in programming. I am happy with both a video or a written tutorial although I would slightly prefer a written tutorial. I typically aim at analyzing data on structured populations such as the average number of pairwise differences among population, or graphing the site frequency spectrum per population, etc..

There are a fair number of such tutorials. Can you please give me recommendations?

I recommend the DESeq2 tutorial at:

http://www.bioconductor.org/help/workflows/rnaseqGene/

I think this is a good start for you because:

DESeq2 is a very popular package. You'll learn how exactly a bioinformatician works.
The workflow starts from alignments, and show you how to connect command-line tools with the R-package
It shows you how to generate MA plot, PCA plot etc. You'll appreciate how easy to do such things in R.
Testing for differential gene expression is very important
You'll learn how R does the programming. For example, in R it's a good idea to create a data set object, and do something like this:

obj <- .... # This is my R-object
obj <- fun1(obj) <- # Function 1 adds information to the object
obj <- fun2(obj) <- # Function 2 adds more information to the object


Is there a difference between polarity and hydrophobicity? From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms?

For example what is the difference in these sentences:

Generally globular protein cores have hydrophobic regions whilst the surface contains hydrophilic exterior facing residues.
Generally globular protein cores have non-polar regions whilst the surface contains polar exterior facing residues.

Hydrophobicity means aversion to water which results because of increase in entropy of the system due to the water-"solute" interaction.

As already pointed out in by inf3rno, polarity of a molecule is because of its net dipole moment. It is true that polar molecules can dissolve in water (because they can interact with water via van der Waals' forces especially Keesom and Debye forces).

CO2 is apolar but dissolves in water (it actually reacts with water). Most apolar substances cannot interact with water via van der Waals forces.

To sum up, usually polar substances are not-hydrophobic (i.e they are hydrophilic), however some polar molecules such as nitriles, ketones and esters can be hydro-neutral (midway between hydrophobic and hydrophilic. See here). Even large polar molecules are insoluble in water such as 1,2 dichlorobenzene and nitrobenzenes (For something to be soluble the solute-solvent interactions should be stronger than solute-solute interactions. "Water insoluble" may not be equivalent to "hydrophobic").

Conversely, apolar substances are hydrophobic (unless they are reactive solutes such as Cl2 and CO2).


What is this plant on the photos? Found in Kustaankartano, Helsinki, Finland in June 2015.

(for closeup view, copy image URL and open in new window and then zoom in)

It is one of the many species and hybrids of Clematis that is grown in gardens. It looks similar to the common Clematis alpina but might be a closely related species or à hybrid.

(Picture of C. alpina fr.o.m. Wikipedia)


What is the effect of non-vaccinated people on vaccinated people? Many times have I heard that anti-vaccine people are dangerous even to the vaccinated population. Is that true? If so, how can it be? People say that germs will attack them, and soon they would eventually grow and spread even toward general population which actually got its vaccines.

I mean it's so counter-intuitive: if I'm vaccinated even when disease will spread I shouldn't be in danger.

Biology is rarely black or white, all or nothing. Protective immunity is generally not an on/off switch, where from the moment you're vaccinated you're infinitely resistant for the rest of your life. You shouldn't expect that, having received a smallpox vaccine, you could have billions of smallpox viruses squirted directly into your lungs and shrug it off without noticing.

Given that (fairly obvious) fact, you should immediately think of scenarios where vaccinated people are still at risk of disease following exposure to unvaccinated people. What about older people who were vaccinated 20 years ago, 50 years ago? What about people whose immune systems are slightly weakened through lack of sleep or obesity or stress? Any of these vaccinated people might well be protected against a brief encounter, but not against, say, being in an airplane seat for 18 hours beside an infected child shedding huge amounts of virus, or caring for their sick child.

It's all sliders, not switches. You can have a slight loss of immunity (4 hours sleep last night) and be protected against everything except a large exposure (your baby got infected and won't rest unless you hold him for 8 hours). You can have a moderate loss of immunity (you were vaccinated twenty years ago) and be protected against most exposures, but you're sitting next to someone on the subway for an hour. You may have a significant loss of immunity (you're a frail 80-year-old) and still be protected against a moderate exposure, but your grandchild is visiting for a week.


Is the water-splitting enzyme a component of photosystem II? Can Somone answer a bit bizarre question which is that in light reaction . Photosystem uses enzyme to split the water up to hydrogen ions and electrons and oxygen.But is this water-splitting enzyme in or out of the photosystem 2(PS II)?
Great thanks

The name of the protein (actually, three proteins) you are referring to is Oxygen-evolving Complex.

And yes, it is part of Photosystem II.

According to Lodish (2002):

  An Oxygen-Evolving Complex in PSII Regenerates P680: The splitting of H2O, which provides the electrons for reduction of P680+, is catalyzed by a three-protein complex, the oxygen-evolving complex, located on the luminal surface of the thylakoid membrane. The oxygen-evolving complex contains four manganese (Mn) ions as well as bound Cl- and Ca2+ ions (see Figure 16-44); this is one of the very few cases in which Mn plays a role in a biological system.

You can see the complex in this diagram of PSII, also from Lodish:

Figure 16-44: In a reaction center, two integral proteins, D1 and D2, bind the special-pair chlorophylls (P680), two other chlorophylls (Chl), two pheophytins (Pheo), one Fe atom, and two quinones (QA and QB). All of these are used for electron transport following light absorption by an associated lightharvesting complex (see Figure 16-42). Three extrinsic proteins (33, 23, and 17 kDa) comprise the oxygen-evolving complex; they bind the four Mn2+ ions and the Ca2+ and Cl− ions that function in the splitting of H2O, and they maintain the environment essential for high rates of O2 evolution.

As you can see, all proteins coloured green in the image above are part of PSII. However, since the oxygen-evolving complex is made of extrinsic proteins, it can be easily separated from the rest of PSII:

  The Mn ions together with the three extrinsic proteins can be removed from the reaction center by treatment with solutions of concentrated salts; this abolishes O2 formation but does not affect light absorption or the initial stages of electron transport.

Source:

Lodish, H. (2002). Molecular cell biology. 4th ed. New York, N.Y.: Freeman.


How Ants know about Earthquake? How does an ant know about Earthquake is it because of an organ or due to other factors?

No, they may not sense Earthquake by an organ but due to other reasons. This may be any other physical factors which can be measured.

  "...There is therefore
  little reason to believe that these ants react to earthquake
  precursors other, perhaps, than those that may affect colonies
  directly, by altering physical variables that can be directly measured
  by other means..."

Fascinating though the behavior and physiology of ants may be, they cannot be employed as reliable predictors or even sensors of earthquakes.

Source: Shaken, not stirred: a serendipitous study of ants and earthquakes


What are " temporal kinetics"? I am new to Biology and I am reading some papers about kinase proteins. I know what kinases do in the body. However, I found it hard to understand what are "kinetics". I googled this term but it seems it is a general term and I couldn't understand it.
I came across the following sentence in a paper, and I am not able to understand it:
"many substrates of a given kinase have similar temporal kinetics"
I know what "substrates" and "kinase" means. But I don't know what "temporal kinetics" means here.
I appreciate the chance if somebody let me know the meaning of "temporal kinetics".
Thanks

Temporal kinetics does not refer to the kinetics of kinase phosphorylation reactions and, since it is not standard terminology, you likely wouldn’t find its meaning in any textbook.
The authors of the paper quoted in the question use the phrase temporal kinetics to describe the phosphorylation state of a proteome-wide selection of kinase substrates (ie phosphorylation sites in proteins) over time. The general idea is that since one kinase can phosphorylate many substrates, clustering substrates based on their temporal kinetics (ie the times at which they become phosphorylated or dephosphorylated) can help identify the kinase and signaling pathway involved.
Fig 6B in the paper (shown below), for example, illustrates how 3,178 phosphorylation sites can be clustered based on the time-course of their phosphorylation and/or dephosphorylation after treatment of mouse adipocytes with insulin. As discussed in the paper, each cluster can be associated with one or more kinases based on known kinase-substrate interactions.


Are these bat social calls? I'm currently researching bat social calls (not echolocation calls) and have been given a series of samples (in .wav format) and wanted to know if what I can hear is actually the social calls. Below is a Graph representation of the a sample from the data I have:

This looks fine to me. From this, I can clearly tell where the social calls are. If I play at the specific peaks, then it sounds like a bat "chirping." However, I've been told that social calls cannot be played back, and, therefore humans cannot hear them. I'm just trying to figure out what these noises, or, chirps might actually be.

Here is a link to the .wav file:

Thanks for your help :)

It could not fit in a comment..
You recorded bats. You are interested in social calls. Socials calls can be recorded by your microphone but they cannot be read by standard media player because...

the standard media player are limited to certain frequencies
your speakers cannot produce such high sounds
your ears are not able to hear many of the frequencies emitted
you formatted your records in a format that cannot hold very high frequency (for reason of optimizing data compression)

You might use some program like Adobe Audition in order to easily visualize the frequencies (vs time) of your record. (It might also help you finding all harmonics or performing Fourrier analysis)

This wiki article says :

Social Calls
This is a wide subject and there is still a lot to be discovered about bat social communication and how they use social calls in roosts and when flying. Generally a bat social call is not tonal, in other words it does not consist of a musical type note. Some bat detectors do not produce an accurate recording of a bat social call. Typically bat social calls use a lower frequency range than echolocation calls, and can thus be heard further away. Sometimes a bat will make a social call while echolocating which can cause confusion.
We can see and hear how the lower frequency social calls are heard at a greater distance than the higher echolocation calls as the bat approaches and departs. Zooming in on a spectrogram, social calls are atonal and repeated rapidly about five times in each call. The social calls are interleaved between the echolocation calls. They show a ragged frequency distribution around 20 kHz. Note the FD detector divides frequencies by 10.
The echolocation calls are single "hockey stick" calls at a higher repetition rate. At this scale the hockey stick shape is not very clear, but the end frequency can be measured as 45.2 kHz. A doppler shift is recorded as the bat approaches. The frequency was measured as it passes


Is starch and glycogen digestion intra or extracellular? Do humans have the enzyme for starch intracellular digestion?
Also, do plants have the ability to digest Glycogen? Intra or extracellular, or both?

The problem with your question is that, right now, you have three different questions:

Is the starch/glycogen digestion intra or extracellular?
Do humans have the enzyme for intracellular digestion of starch?
Do plants have the ability to digest glycogen?

Unfortunately, that goes against Bio SE rules: you have to pick one question, otherwise your post will be closed as too broad ("Avoid asking multiple distinct questions at once.").

That being said, I'll address only this question:

  Do humans have the enzyme for intracellular digestion of starch?

The answer is yes. Intracellular digestion in humans (as in any animal) is performed by lysosomes, organelles that contain hydrolytic enzymes.

Lysosomes can digest proteins, lipids, carbohydrates, nucleic acids etc. Regarding digestion of carbohydrates, this is a short list of enzymes (the complete list is way bigger) found in human lysosomes:

alpha-Galactosidase
alpha-L-Fucosidase beta-Galactosidase-1
beta-Glucuronidase Chitinase
Chondroitin B Lyase/Chondroitinase B
Chondroitinase
Cytosolic beta-Glucosidase
Galactosylceramidase
Heparanase
Hyaluronidase
Lysosomal alpha-Glucosidase
O-GlcNAcase
O-Glycosidase

Among the enzymes listed above, this is the one that answers your question:
 Lysosomal alpha-Glucosidase.

That enzyme, which is a α-1,4-glucosidase, breaks down starch (and glycogen) to glucose.

Source:

Lübke, T., Lobel, P. and Sleat, D. (2009). Proteomics of the lysosome. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1793(4), pp.625-635..


How do people actually find codons in a DNA transcript just by looking at it? I was looking at this transcript of a DNA sequence, and the article kept referencing what the first codons are, but a codon like AUG isn't in the sequence...there's no "U" in any sequence. What am I missing?

Codons refer to sequences of nucleotide triplets that translate to amino acids. As you know, polypeptides are translated at the ribosome using a messenger RNA (mRNA) blueprint produced by RNA polymerases from the DNA.

DNA consists of four nucleotides: adenine, guanine, cytosine and thymine. Thus, DNA sequences read, for example, ATAAGC. RNA, however, replaces thymine with uracil. So to transcribe the above DNA nucleotide sequence into mRNA would result in UAUUCG.

The mRNA may also get spliced into various isoforms coming from the same gene. In short, it may be difficult to determine the gene product from the DNA sequence.

Does that make sense?


Are there any documented instances of coronaviruses being directly transmitted from bats to humans? Many human coronaviruses have ancestral host origins in species of bat. However, all instances I am aware of identified other animals as intermediary vectors:

SARS-CoV: Human ← Palm Civet / Raccoon ← Bat
MERS-CoV: Human ← Dromedary Camel ← Bat
HCoV-229E: Human ← Alpaca ← Bat

Are there any known cases of direct bat to human transmission of coronavirus?

Source: Bats and Coronaviruses, Viruses (2019)

It is possible, but unconfirmed, that the first incidents of SARS-CoV were directly infected by bats, and that palm civits were infected parallelly:

  The new study demonstrates that Chinese horseshoe bats harbor a pair of SARS like viruses that are very closely related to the strain that caused the 2003-2004 pandemic and that these strains have the capacity to directly infect human cells and civet cat cells as well as bat cells. These findings suggest that bats may have directly infected humans and that civet cats may have been incidentally infected.

More Evidence Emerges That Bats May Have Spread SARS, JAMA (2013)


Can we use differential equations for population that is discrete? Population dynamics is often modeled using ODE. For example one common model is logistic growth model:

$$\frac{dx}{dt} = k.x.\left(1-\frac{x}{C}\right)$$

where x is population size, k is rate constant for growth, C is carrying capacity.

But population is a discrete variable. It is not continuous. It always takes whole numbers. You can have a population of 3000 fish, but not 3001.2 fish.

Then how can one use population as a dependent variable in a differential equation?

Integration of the ODE, given above, will give me a function to calculate size of population, x(t), at time t, when size of the population at t = 0, was x0. We can specify a whole number for x0. Here, x(t) can be a real number with fraction, but a population size is always a whole number.

How does one tackle this anomaly?

You can make the continuous approximation when the population size is large. As mentioned by arboviral, there are algorithms that allow you to perform stochastic simulations with discrete variables. However, these are computationally much more intensive than integration of ODEs. Moreover, analytical solutions for the master-equations (time evolution of probabilities) are very difficult to calculate. Therefore, whenever possible, people go for ODE-based continuous models.

These models would give incorrect representation of the dynamics for small populations and fail to explain phenomena such as extinction. However, they can explain the dynamics of large populations fairly well. So the choice of the modelling approach depends on the questions you want to ask and the complexity/computational cost of the model.


Why are some scorpion species fluorescent under UV light? It's known for some scorpion species such as Pandinus imperator, Heterometrus Petersii etc. to be shining under UV light. That makes them easier to capture and collect by humans.

Is there any evolutionary advantage for this property?
Usually, in articles you stumble upon the phrase "It is not known" for this matter (example). Maybe someone knows of recent discoveries.

As far as I can see from different articles, this seems to be a study in progress. Dr Kloock from the California state University states that scorpions might be more active when not exposed to UV light. If not fluorescing, they know that they are hidden and have a lesser chance of being preyed on. He argues that scorpions are less active on full moon nights rather than other days. (reference) Dr Kloock has also stated that the pigment could get used up on repeated exposure to UV light. He made an observation that scorpions whose pigments got used up were more active than those still fluorescing when exposed to UV light mimicking the moon and the stars. (reference) Dr Gaffin from the University of Oklahoma, in his studies have reported that scorpions might be converting UV light to turn it into the colour blue-green which is what they see best effectively turning their body into one big eye. His studies are consistent with Dr Kloock in that scorpions try to hide and avoid UV light (reference). Some scientists have also hypothesized that scorpions might glow to warn predators or that the pigments that make it glow are the accidental by products of certain chemical reactions in its body (reference). There is no definite proof on this subject though.


What is the effect of TSH on the calcitonin? I know that TSH is released from the pituitary gland and it motivates the thyroid gland to release thyroxine, and calcitonin is released when the calcium level is high in the blood, but is calcitonin affected by TSH or not, I didn't find a specific answer on google, could you help me please?

I found a paper, where it is postulated that TSH secretion is inhibited by calcitonin. However, the paper is quite old (1984) and I'm not sure if there are any more actual paper.


Do we have enough diversity of antibodies to overcome almost any antigen? I always wonder about the capability of diversity of our antibodies. Do we have enough antibodies to fit to every kind of molecule? Wont't it be easier if our antibodies are like clay and can be molded to any form by antigens? Why to waste energy producing so many types of antibodies?

If some pathogen makes its antigens just like antibodies of our body, (I think) they won't ever be detected. So what would our body do?

As my answer is quite big I've highlighted the different regions I answer your question.

Intro and basic info

I take it you know how antibodies are made, but as a quick recap they're made by VDJ recombination of a limited but still quite numerous pool of genes which are recombined randomly, and then further recombination occurs by hypermutation of certain segments particularly in the regions that identify antigens.

What is Hypermutation?

Hypermutation occurs after the original antibody is made in order to perfect it. The same mechanism I talk about in moulding antigens below. It is exactly what it says: a high rate of mutation compared to that of the low rate in cells normally. When B cells are activated because they've met their antigen to which they respond (cognate antigen), they undergo somatic hypermutation. While the B cells undergo somatic hypermutation, the genes which code for the antibody are mutated so that the antibody binds to its cognate antigen with a different specificity. If it binds better the B cell gets to live, if it doesn't bind or it is worse then the B cell dies.

Moulding antigens

What we cannot do is the other way around. We can't recognise an antigen and then make an antibody to it, because recognising the antigen requires an antibody. What we can do is once we've recognised the antigen, then mould the antibody so it is a better fit. How we do this is by B cells mutating their antibodies and competing which binds better. However, B cells just don't have the knowledge to see an antigen and think a tyrosine residue at this position will be perfect to change my shape to this configuration - that's really complex stuff!

Do antibodies recognise every molecule?

Antibodies are made to essentially every antigen which is very costly in terms of energy as you mentioned. In fact, the number of genes that make antibodies are thought to be the perfect amount as to protect us without being too numerous so that it is not only too costly, but we have so many different antibodies the chance of ever finding the right B cell is so low we die before we manage. This is because of the way antibodies are mass produced, in the typical pathway of new antigens, firstly a T cell must recognise the antigen then B cells that produce an antibody that binds to the antigen (rarely in the same region, and may not even be to a protein antigen).

So these two paragraphs highlight the limitations and answer your first question. Antibodies are so diverse that we can expect quite a few to recognise every pathogen, but not every single possible antigen will have a cognate antibody. Diversity without so much diversity that it becomes redundant. The second limitation is that antibodies will ideally not form if they recognise self (our own proteins etc.) Which leads on to your next question.

What if a pathogen makes antigens that look like our own proteins?

Autoantibodies are made but are typically non-pathogenic (i.e., they don't cause harm). Certain HLA/MHC polymorphisms that make us likely to form autoreactive T cells, also make us make autoreactive antibodies. Interestingly, this increases our risk of autoimmune diabetes but ALSO makes us more resistant to infection by HIV. This can be practically seen in the DQ8 polymorphism. This is a perfect example to illustrate the answer to your second question. Ideally, pathogens which have antigens similar to our own would not be detected. HIV wraps itself with an envelope of our own lipid membrane for this purpose, and the best neutralising antibodies are often self-reactive and therefore are those that failed elimination.

However even these pathogens are going to do something or make something that isn't something our cells usually do. This is how the body finds and targets cancer cells (in a way), they do things our own cells won't typically do like make the wrong proteins or wrong amounts etc. Thus cancer cells and pathogens can be targeted by our cells that find something that isn't self (CD8 cytotoxic/killer T cells). As for pathogens, we all make MHC/HLA which is unique to us and pathogens could never manage to invade and make the specific HLA/MHC that we do, so our body also targets missing HLA/MHC.


Evolutionary conservativeness List the following proteins in the order of decreasing evolutionary
  conservativeness of their primary structure:

  Somatotropin.
  Catalytic subunit of a DNA – polymerase.
  Histone H1.
  Prolamines (storage proteins of cereals).

What I think : I am sure that 4th one should be last. I believe that H1 sequence is not that important as I had read somewhere that a cell can survive even without H1 histone. I also think that catalytic subunit is most important. So, according to me the order should be : 2,1,3,4.

Am I right ?

Even when you can live without Histone H1, its a widely distributed protein which you find in basically all living cells (except for some yeasts if I remember correct). This points to the fact that it must be available for quite a while. The same is true for the catalytic subunit of the DNA polymerase. Somatropin is still pretty important (and can be found in a lot of organisms), prolamines are quite specific to certain cereals. I would group it 2-3-1-4.


Why do some plant species have lobed leaves, while similar species in the same habitat don't? Some plants have lobed leaves, like the English oak (Quercus robur), while other plants growing the same deciduous woodland habitats, and very often growing alongside oaks, such as the European beech (Fagus sylvaticus) don't have lobes. Here are two two leaves side by side for comparison:

These two species should be subject to most of the same evolutionary pressures. Why would one evolve lobed leaves, whilst the other has only tiny serrations?

This is a question for which, I think at the moment, we don't have a clear answer.

It is important to bear in mind that the leaf plays a number of important roles in the plant (photosynthesis, thermoregulation etc.) so leaf shapes probably evolved through a process of successive trade-offs. This may make it difficult to identify the exact selection processes operating on any one species. In contrast, something like the eye has a well-defined single function, which in principle at least, makes it easier to understand the link between form and function.

From Niklas (1988):

  Life history and optimisation theory suggest that the number of
  phenotypic solutions that allow for different equally successful trait
  combinations increases as the number of trade-offs increases – a
  conclusion that applies to traits within the leaf (e.g. for shape) as
  well as to leaf–branch relationships.

However, there are a  number of ideas to explain leaf shape diversity which include:

Thermoregulation

It has been shown that by adding lobes to leaves, the rate of heat transfer across a leaf is greater than that of an unlobed leaf of the same area (e.g. Gurevitch and Schuepp 1990). So, lobed leaves may be selected for under certain environmental conditions.

hydromechanical constraints

Lobed leaves may have greater hydraulic efficiency. For smaller veins, hydraulic pressure increases as they present an increased resistance to water flow. This places stress on the deliate outer leaf tissues. If  lobed leaves have relatively less mesophyll tissue than large, highly conductive veins, they may have reduced hydraulic resistance compared  unlobed leaves (Sack and Tyree 2005).

optimization for photosynthesis
adaptations against herbivorous animals
random (non-selected) variation. This is a possibility, although probably unlikely due to the importance of the leaf in plants.

So, some or all of the above possibilities (which are not necessarily mutually exclusive) may shape the leaves of species which may appear to have undergone very similar selective pressures.

This is a good read by Nicotra et al. (2011) which summarizes the state of play.

Gurevitch J, Schuepp PH (1990) Boundary layer properties of highly dissected leaves – an investigation using an electrochemical fluid tunnel. Plant, Cell & Environment 13, 783–792. doi:10.1111/j.1365- 3040.1990.tb01094.x

Nicotra et al., The evolution and functional significance of leaf shape
in the angiosperms, Functional Plant Biology, 2011, 38, 535–552

Niklas KJ (1988) The role of phyllotactic pattern as a developmental constraint on the interception of light by leaf surfaces. Evolution 42, 1–16. doi:10.2307/2409111

Sack L, Tyree MT (2005) Leaf hydraulics and its implications in plant structure and function. In ‘Vascular transport in plants.’ (Eds NM Holbrook, MA Zwieniecki) pp. 93–114. (Elsevier Academic Press: Burlington, MA, USA)


Can signals travel "backwards" in the sensory pathway? My understanding of the "sensory pathway" is that its a linear, directional pipeline as follows:

Nerves (fire various signals depending on the type of sensors they are)
Fibers (transmit signals from nerves to spinal cord)
Spinal cord (transmits signals from fibers to brainstem)
Brainstem (transmits signals from spinal cord to brain)
Brain (the somatosensory cortex register signals as pain/pressure/temperature/etc.)

So again, my understanding is that sensory nerves are 1-way sensors, and that once they fire a signal, its 1 and only ultimate destination is the brain.

So, as a precursor to my question, if anything I have stated is incorrect, please begin by correcting me!

I read that pinched nerves in the back and neck can cause neuropathy ("pins and needles") all over the body: hands, feet, face, etc.

But how can this be? If my understanding of the sensory pathway is correct, then a pinched nerve in one's neck should only send "pins and needles" signals directly to the brain; it should not at any point forward/relay signals on to any other areas of the body.

To state that a pinched nerve in one's neck could possibly cause neuropathy in their arm, then that insinuates there is some connection between the pinched "neck nerve" and the nerve(s) in the arm that are experiencing the pins and needles sensation.

In fact, unless I completely misunderstand the entire sensory pathway and how pain signals transmit, this implies that a pinched nerve sends signals out to the spinal cord, down the spinal cord and into, say, an arm, and that the sensory receptors in the arm subsequently react to these signals.

How is this possible?!? Is there some kind of feedback mechanism at play where nerves in the neck and back can relay signals on to other areas of the body, instead of just feeding directly into the "spinal cord => brainstem => cortex" pipeline?

Reverse signals (dendrite -> axon) do occur in neurons, and are called back propagating action potentials (bAPs). However, whatever role bAPs play in the nervous system at large is subtle/small enough that we don't really understand them at all.
In any case, as @luigi points out, pinched nerves don't have anything to do with bAPs. The reason why a pinch in one place (the neck) feels like it has an effect in another place (the arm) is because some neurons trace long (on the order of several feet) pathways through the body. Ultimately, the sensory input of everything below your head passes through neurons in your neck at some point. If there is a pinch in the neuron in your neck that relays sense information from your arm, that neuron in your neck can activate spuriously, even in the absence of any stimulus acting on your arm. In that case your brain will interpret the spurious activation of that neck neuron as being the result of some kind of strange arm stimulus, and so you feel pins and needles.
See here for more information on the sensory cortex in your brain and the "sense image" it maintains of your body.
Edit
To clarify what I mean by a "pathway",

The part marked "proprioceptors or mechanoreceptors" is what's buried in your skin. If you poke a mechanoreceptor, it evokes a signal in the neuron marked "first-order". In some cases, that first-order neuron will reach all the way to brainstem (as in the picture above), and in some cases that first-order neuron will interface with an intermediate neuron in the spine, but the effect is the same in any case. A first-order neuron stimulates a second-order neuron, which in turn stimulates a third-order neuron, etc., all the way until the original signal arising from the mechanoreceptor reaches the somatosensory cortex. A pinch in any of those first, second, etc. order neurons will potentially send spurious signals to the somatosensory cortex.
Second edit:
Rereading your question, I think a lot of the trouble that you're having has to do with your understanding of how the brain assembles sense information. In order to feel pain in your arm, it is not necessary for anything to be happening to the arm itself. Your arm could be perfectly healthy and normal, but as long as your brain is receiving a signal equivalent to the one produced by a damaged arm you will still feel the same sensation of pain.


Modern research or study on patterns in nerve signals I am trying to find any recent study on pattern recognition in nerve signals. It does not really matter the part of the body where the research is focused on. It can be anything from studying activity of one group of nerves to signals coming from an entire limb.

I was only able to find old (1996) research, which could be much more complete with the modern advancements in computing and manufacturing of micro-instruments. Here is an example of an old paper.

P.S. I am generally looking for information on how nerve signals differ within multiple subjects of same specie. For example, how would nerve response to a stimuli differ for two mice from same offspring and how will they differ from it's parents.

You might want to read about event related potentials (recorded by EEG) or event related fields (recorder by MEG). The idea is simple:

1) Pick some stimulus, e.g. a person touching the hand of a subject. Pick another stimulus, e.g. the subject seeing a person touching the hand of another subject. Record EEG/MEG.

2) Repeat each condition for at least few hundred times. Throw away bad data, and average the repetitions. You do the averaging because the signal-to-noise ratio is low in all non-invasive electrical measurements, and the signals are always riddled with movement, cardiac, and eye-blink artefacts.

3) Compare the conditions in each sensor. Rest is statistics, though not very easy.

Actually, the experiment above would be about mirror neurons, a relatively hot topic in neuroscience. (See e.g. recent issue from Nature)

The more general situation is that using pattern recognition/machine learning algorithms to study brain signals is already a standard thing to do. There are for example graduate/undergraduate programs in computational neuroscience.

If you would study some other signal (e.g. measure from a hand, leg), they are going to dull. Very dull. Mostly because then you have 1 time-series, instead of several hundreds of time-series to analyse.

  For example I would want to know if applying hot/cold object to skin of both right and left limbs would cause the sensory neuron to send the same or similar signal (electrical impulse) to the spinal cord.

This you could too study with the event related fields/potentials.


Oak processionary or what else? We have those caterpillars with some sort of webbing on stinging nettles below some oaks.  Photographs I found in Wikipedia look quite hairier with long white hairs but maybe it's the molting level?

Or those guys are something less notorious.  This is in Germany, Northrhine-Westfalia.

And here is a video in case it helps.

Looks more like aglais io, the European peacock.  At any rate, oak and stinging nettle leaves are quite too dissimilar to make a crossover of comparatively specialized caterpillars likely.


Distribution of the number of clover leaves Being no expert at all in this field I am just interested in emprical studies of the frequency $f(n)$ of clover plants with a given number $n$ of leaves.

I would suspect naively from general considerations that the frequency follows an exponential distribution.

Any hints are greatly appreciated.

I have found a study [1] of 2017 (http://www.sharetheluck.ch/single-post/How-rare-are-four-leaf-clovers-really) which answers a great part my question, and I'd like to show those results together with some additional evaluation.

They have counted 5.7 million clovers and found the following numbers compared to 3-leaflet clover:

4-leaflet clover    1 in 5,076
5-leaflet clover    1 in 24,390
6-leaflet clover    1 in 312,500

For the 4-leaflet clover they have corrected appreciably the common figure of 1 in 10,000 (see e.g. the comment of Untitpoi here).

A logartihmic plot of these relative frequencies shows interesting features

(i) a fairly regular exponential decay of the frequency in the range n=4,5,6
(ii)    a significant "exception" from this rule is the "normal" clover with n=3

How can these observations be explained?

It would also be interesting to extend the study to n>6, and maybe also to the range of "deficient" clover which posesses only one or two leaflets. The latter are most probably very rare so that the complete log-plot would resemble an inverted letter V.

The question of 2-leaflet clover was raised here [2] https://www.quora.com/What-are-the-chances-of-me-finding-a-two-leafed-clover. But no quantitative answer was given.

References

[1] http://www.sharetheluck.ch/single-post/How-rare-are-four-leaf-clovers-really

[2] https://www.quora.com/What-are-the-chances-of-me-finding-a-two-leafed-clover

[3] https://en.wikipedia.org/wiki/Four-leaf_clover#cite_note-auto-6
A comprehensive reference which I have only partially explored up to now


how to solve gap reactions in genome scale metabolic reconstruction I'm making a project about modeling of nannochloropsis metabolism. My model is in the refinement stage. However, it is not running in the FBA test. Then i found there are 87 reactions that did not run. But the reactant/metabolites for those reactions to run are there in the model.

Is there any one know what is the possible reason for this, and how to solve this problem?

Really looking forward to see your answer.

Thanks,

It is common that reactions in stoichiometric models cannot carry flux because there is a "dead end" metabolite somewhere. The problem may not be in the immediate reactants / products, but can be several steps away, and is not always easy to find.

If you have a network visualization tool, one option is to highlight all reactions that cannot carry flux; often this reveals an entire blocked pathway ending in the isolated metabolites.

A more systematic method is to examine the dual solution of the linear program for maximizing flux through a blocked reaction; this shows the active constraints, which are precisely the metabolites that are lacking for the blocked reaction to be able to run.


Is there an "evolutionary species similarity calculator"? Is there a website where I can input pairs of species and get an "evolutionary similarity score"?

E.g. (numbers are completely made up)

Input: Chimp and Human, Output: 97%
Input: Cat and Human, Output: 85%
Input: Is Cat closer to Human or Chimp, or Snake, Output: Cat is closer to Chimp (87%), second is Human (85%) and Snake is last with 50%.

I have no idea what the actual scale should be, but I imagine there is at least one interesting scale, perhaps several.

Cross posted to Quora

Since the simple value of percentage of nucleic acid identity over whole genomes isn't very useful in taxonomy, you won't find these values published in a database, even if they were computed by someone in the process of other work.

One project that provides ready-for-consumption phylogenetic trees based on similarity metrics, by using orthologous genes between species, is OMA. They compute all orthologous genes between two species, and they are now at 1,235 species:

http://www.biorecipes.com/Orthologues/status.html

You could then read off the "distance" between cat and mouse from the eukaryotes tree. This value would then be more meaningful than the nucleic acid identity percentage.

Apart from the trees, using their OMAbrowser you can get for any species pair the number of common orthology groups, i.e., the number of common genes between those two species.


Neuroscience of mathematicians I've tried to google this but everything that comes up are things like "mathematical neuroscience" rather than the other way around.

Specifically, I'm interested in the workings of a mathematician's brain that sets her apart from others. For example, is there evidence to be found in MRI scans or EEG recordings of mathematicians as to why they excel in math?

Short answer
People competent in mathematics have been shown to have higher activation of the left angular gyrus according to fMRI. EEG recordings have shown larger activity in the posterior parietal cortex.

Background
I think you are interested in what makes a good mathematician. A brain imaging study by Grabner et al. (2011). showed that the left anterior gyrus was more activated in individuals more competent in math. Specifically, the authors argue that the stronger left AG activity in the more competent subjects reflects a higher proficiency in processing mathematical symbols. The anterior gyrus is involved in mathematical symbol processing.

Left angular gyrus, lateral view. Source: Kenhub Neuroanatomy Atlas

ERP studies (event-related potentials deduced from the EEG) have shown higher activity in posterior parietal cortex in subjects excelling in math (Waisman et al., 2014). This region is associated with algebra and handling mathematical functions.

Posterior parietal cortex among other regions not relevant to the question answer. Source: Live Science

References
Grabner et al. Front Hum Neurosci 2011; 5: 130
Waisman et al., Int J Sci Math Edu 2014; 12(3): 669-96


Are there more/less favourable phases of menstrual cycle to donate blood? I was wondering whether it makes a difference when during the menstrual cycle a female is donating blood in terms of:

Blood quality (iron or hormones levels)
Her health/safety

I am aware that females can donate blood during menstruation as the blood they lose does not directly come from circulatory system and the amount is not that big after all. As for the hormones - their levels do change considerably during the cycle and can affect a whole range of things. Can they also affect the blood quality or are such fluctuations rather negligible?

1)

Hormones involved with Menstruation (FSH, LH, Estrogen, Progesterone, etc.) will vary depending in concentration depending on the time-frame:

You are correct in saying that not much blood is actually lost in the menstrual fluid: Less than 80mL (80cc), although the blood's origin is ultimately the circulatory system. Does it affect the quality of the blood? No. Usually not enough iron is lost during menstruation to make a difference between being able to donate blood and not donate. However, women who bleed heavier than the average can experience anemia (iron deficiency) - although anemia attributed to menstruation is often misdiagnosed gastrointestinal issues (up to 86% error rate).

One thing to consider is that common pain medications can affect blood content, and thus a woman taking aspirin cannot donate platelets for 5 days after she stops, and a woman taking NSAIDs (like Ibuprofen) cannot donate for 2 days after she stops.

2)

  ...the combination of blood loss from periods and donation will make iron deficiency anaemia more likely, particularly if the periods are heavy or prolonged. This effect can be minimised by taking supplemental iron.

In general, as long as the woman feels well or the pain is controlled, she is perfectly capable of donating as long as her iron levels reach the minimums. The blood makeup is not significantly different, although hormone and iron levels will minimally fluctuate.

  As always, this response is based upon information during some light research. I am not a doctor, and the information presented in this response may be modified later to increase accuracy or remove errors upon the discovery of new information.


EM Brainwaves VS Brain Wave (EEG) The brain purportedly produces very weak EM waves.

EEG is a method of measuring electrical brain activity, it has classifications for the types of brain wave it can detect: Theta, Alpha, Beta, Gamma etc.

Are these the weak EM waves the brain produces?

If not what is the frequency range of the EM waves that the brain produces and does it vary depending on mental state?

I assume with EM you refer to electromagnetic?

You are right that the EEG (electroencephalogram) is a tiny signal. When about 50.000 neurons fire simultaneously, it possible to see a change in the measured signal. Typical EEG amplitudes are in the microvolt range.

Now, when the EEG is recorded, it is a function of time. You could for example collect data from 64 sensors, using a typical sampling frequency of 1000 Hz, and obtain 100000 samples from each sensor during a 100 second measurement.

So, what are alpha, beta, gamma, etc? When the recorded EEG signals are transformed into the frequency-domain (using the discrete Fourier transform), the signals become represented as a function of frequency. The obtained frequency range is half of the sampling frequency (according to the sampling theorem). So, with $f_s = 1 $ kHz you may observe frequencies from $0$ to $500$ Hz. Now, to make it easier to discuss about specific parts of the frequency range, they have been given names: delta refers to frequencies from 0-4 Hz, alpha to frequencies 7-15 Hz etc. So, these are just arbitrary names for different frequency ranges. (And yes, some processes do occur in quite exact ranges.)

So what effects what the EEG spectra will look like? Just about everything. From a short segment of data, it is rather impossible to say anything. This is why many paradigms do averaging: for example, you are presented a sound 100 times, and the repetitions are averaged to cancel uncorrelated noise. Have a look at the so called oddball paradigm, for example. Single-trial and continuous recording are also done today, but they are more difficult to analyse.

(Side note: since you asked about electromagnetic brain waves, have a look at magnetoencephalography too..)

For reference, see e.g. Luck (2005), An Introduction to the Event-related Potential Technique. Fourier transforms, sampling theorem, and signal averaging are well covered in Wikipedia.


How many primary oocytes in human female body at birth? https://discovery.lifemapsc.com/library/review-of-medical-embryology/chapter-4-gametogenesis-oogenesis

In the above site, I see that:

  About 2 million primary oocytes are found in the ovaries of a newborn
  femal Many regress during childhood so that at puberty about 30-40
  thousand remain. Only about 200-400 of these ever reach full maturity
  after puberty and are expelled at ovulation during the female's
  reproductive life

http://www.pnas.org/content/107/22/10280.full

Also, from this site, I see that

  Human ovaries contain follicles as basic functional units. The total
  number of follicles is determined early in life, and follicle
  depletion leads to reproductive senescence. Human follicles begin
  development during the fourth month of fetal life, and each human
  ovary contains ≈400,000 follicles at birth.

From my understanding, there is one oocyte inside one follicle. So, two number should be the same. Why there is a big difference? Or my understanding is just wrong?

PS. I am doing research for my sci-fi, I didn't learn this topic in any college, sorry if this is a silly question.

Short answer: The developmental process starts from oogonia as follows:

Oogonia(7million) in the foetus develops into primary oocyte(2million) in the foetus prior to gestation which again develops into primordial follicle(700,000-800,000)at birth.

From the second excerpt of your question I could understand that it said, "each ovary contains  approx. 400,000 follicles at birth." which is definitely correct if you consider that total number of follicles in both the ovaries would give 800,000.

Excerpts from the references that lead to the short answer above:

In the developing female fetus, oogonia become primary oocytes that begin the first division of meiosis. However, this division is not completed and the primary oocytes remain “frozen” in the prophase stage of the first meiotic division.
At birth, oogonia are no longer present. Each primary oocyte is surrounded by a single layer of squamous epithelial cells called follicular cells. The primary oocyte together with its follicular cells is called a primordial follicle. There are about two million primordial follicles with their primary oocytes in the ovaries at birth suspended in the first division of meiosis.
As the female grows, primary oocytes begin to die and disappear with their follicular cells. This process continues until puberty when there are only about 400,000 primordial follicles left in the ovaries. The primary oocytes continue the process of oogenesis after puberty begins.[Source]

The total number of primary oocytes at birth is estimated to vary from 700,000 to2 million. During childhood most oocytes become atretic; only approximately400,000 are present by the beginning of puberty, and fewer than 500 will be ovulated.[Source]

Primary oocytes reach their maximum development at ~20[6] weeks of gestational age, when approximately seven million primary oocytes have been created; however, at birth, this number has already been reduced to approximately 1-2 million.Recently, however, two publications have challenged the belief that a finite number of oocytes are set around the time of birth.[Source]

In the human embryo, the thousand or so oogonia divide rapidly from the second to the seventh month of gestation to form roughly 7 million germ cells.[Source]

REFERENCES:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008772


How does repair take place on leading strand in eukaryotes? I am currently reading molecular biology of the gene by Watson to develop an understanding of the mechanism of replication and repair.
Under the topic mismatch repair of DNA, they mentioned that eukaryotes lack a homolog of MutH. The repair takes place from the nicks developed on the lagging strand before ligase acts on Okazaki fragments.
How then does the repair take place on the leading strand as there are no nicks on the leading strand?
And also, because eukaryotes lack Dam Methylase, how does the repair system recognize which nucleotide of the mismatched pair is incorrect?

I'll keep the answer to this as concise as possible. The major mismatch repair (MMR) pathway used by eukaryotes is the MutS$\alpha$-MutL$\alpha$-dependent MMR. See the diagram below for its mechanism:

The pathway initiates when MutS$\alpha$ (Msh2–Msh6) binds to a mismatch. This is followed by binding of MutL$\alpha$ (Mlh1 and Pms2). PCNA then activates MutL$\alpha$ to incise the nascent strand and the DNA ends are used for removing the replication error. After this, the repair is completed by correct DNA synthesis and ligation (note that this pathway works in both leading and lagging strands). DNA replication and MMR are temporally coupled in a manner that may be related to the regulation or appearance of the signals used for MMR. Also, pay attention to the point that the opposite strand is used as reference strand for repair and the strand to which MutL$\alpha$ binds is the one at which Pol$\epsilon$ (or Pol$\delta$) replicates as the DNA polymerase and the PCNA act as the signal for MutL$\alpha$ activity.

See this paper (also the image source) by Kunkel and Erie (2015), they describe this process and a lot of things related to it, including its regulation and signals, in much more detail. I haven't talked much about the details here as the paper is a much better source to understand them.

References:

Kunkel TA, Erie DA. Eukaryotic Mismatch Repair in Relation to DNA Replication. Annu Rev Genet. 2015;49:291–313. doi:10.1146/annurev-genet-112414-054722


Can Fluoride be absorbed into the blood from within the mouth without swallowing? I'm having a discussion with somebody regarding Fluoride usage. I told him that even if he doesn't like the idea of ingesting it, brushing and spitting it out will do you no harm. He then said this:

You have missed the point of ingestion massively! Brushing with fluoridated paste is NOT fine.
The mouth, with its gum entry and under tongue glands are the PERFECT entry point to the blood, without even swallowing? What do you think oil pulling is all about? Fluoride passes those barriers as easy as the shit that resides in your blood can!"

Now I call BS on this, but I'd just like an expert opinion with cited sources if possible. Can Fluoride be absorbed purely by the mouth without ingestion?

Although I'm having a hard time finding a source that provides specific information on fluoride in toothpaste, this review explains that fluoride is most readily absorbed through intestinal epithelia and that fluoride absorption through other tissues, such as oral epithelia, depends strongly on other chemical properties of fluoride-containing compounds: their

  "reactivity and structure, solubility, and ability to release fluoride
  ions."

This suggests that you would need additional information concerning the overall toothpaste formula.

This review shows the rates at which fluoride ions are released from various toothpaste formulations. Figures 2 and 3 show that the highest discharge rate is roughly 1.7ppm and the lowest was just under 0.5ppm, both occurring after a 24hr period. The authors note in the discussion that these measurements are likely higher than what would occur in the mouth, since they had to use deionized water for their experiments, in which fluoride is more soluble than in saliva.

Wikipedia lists fluoride toxicity levels as being between 0.5 and 1.0mg/L. Fluoride's molar mass is 18.9984 g/mol and this calculator shows that 0.5mg/L of fluoride translates to about 0.5ppm. While at first this makes the above results sound a dire, it's important to note that toothpaste remains on your teeth for far less than 24hrs and to remember that less fluoride is released into saliva than into deionized water.

Wish I could find better results on how much fluoride might be released during a typical toothbrushing session, but I'm inferring from the linked review that it would be small enough to not merit a health concern.

I emailed a dentist friend for more info and will update this post as I hear back from him.

As for the comment about glands, it's important to understand that the glands found in the mouth are secretory glands, which means that they are optimized for discharging fluids and not for accepting them.

--Update--

My dentist friend wrote back, confirming that no significant fluoride absorption occurs through the gums. From him:

  the only significant absorption would be through swallowing fluoride.
  Any that was just in the mouth would not be well absorbed...
  that is why we do the high dose swish and spit treatments is to avoid
  fluorosis but deliver sufficient fluoride to the teeth.

In short, it looks like the answer to your question is: no, fluoride is not significantly absorbed into the blood from within the mouth without swallowing.


What is this Sacrificial Reproductive Strategy Called? The reproductive strategy of salmon is 'suicidal'. Before breeding the males metamorph permanently into a form suited for the breeding season but unsuited for survival. The females devote so much of their biomass to producing eggs that they do not survive long after spawning.

Does such a breeding strategy have a name? Where the parents die shortly after breeding, or indeed during the mating process. I'm sure the latter, more specialised, case could only occur in particularly simple organisms (think polyps, think deep sea). But does there exist an organism which as part of its reproductive strategy, after breeding, devote such a portion of its biomass into the production of eggs that it literally dissolves into  cloud of spawn?

It is called Semelparity.

From wikipedia:

  Semelparity and iteroparity refer to the reproductive strategy of an organism. A species is considered semelparous if it is characterized by a single reproductive episode before death, and iteroparous if it is characterized by multiple reproductive cycles over the course of its lifetime.

You see semelparity as suicidal but it is more interesting to generalize survival after reproduction in all kind of species and ask why would an individual survive if it won't reproduce anymore anyway?

Why would an individual survive if it won't reproduce anymore?

From an evolutionary point of view, there is no point to keep living after the reproductive age. You will note a few interesting exceptions to the rule though, including Homo sapiens, where the female keep living relatively long after her reproductive age. Of course, modern medicine is part of the explanation but we tend to think that modern medicine alone is not sufficient. Another explanation is based on kin selection and is called the grandmother hypothesis. In consequence, semelparous species die right after reproduction.

Evolution of semelparity/ieroparity

I don't think this point can be summarized in a few words. In consequence, I will just invite you to have a look at wikipedia for an introduction on the subject.

How common is semelparity?

Iteroparity is more common. However it would be wrong to think semelparity is extremely rare or that it exists only in salmon species (in plural).

In invertebrates, Many insects (butterflies, cicadas, and mayflies) are semelparous as well as some arachnids and moluscs (some squids and octopus). In vertebrates, semelparity is rarer, but there are some frogs (i.e. gladiator frog), fishes (smelt, capelin), lizards (i.e. Labord's chameleon) and marsupials (such as the famous opossum). Finally there are semelparous plants (some agave and some bamboos). In unicellular species (and some multicellular species, such as some trees for example), the concept of semelparity/iteroparity may well not apply easily and depend on a philosophical discussion of the identity of an individual.


Evolution - The ability to control ear muscles Among animals the ability to control ear muscles is pretty common, but only a few humans have the ability. Is it because we in general lost this ability ?

Yes, humans have lost the ability to move their ears toward sounds like many other animals such as cats and rabbits.

It is thought that our ancestors lost the ability to move their ears around 30 million years ago when

  Ear size decreased and the associated musculature changed 1 (Steven Hackley).

A review from Steven Hackley outlines the evidence that the neural circuit remains in modern human brains. Apparently, the neural circuit still responds to directional sounds and may cause our ears to curl slightly (2 - 3 mm).


How to statistically test the predictability of evolution? Can anyone recommend me an experimental study which tries to test the predictability of evolution? The closest works I found are the studies of fluctuation tests (f.e. classical study of Luria & Delbrück, 1943) which demonstrates that in bacteria, genetic mutations arise in the absence of selection, rather than being a response to selection. Is there any other point of view from which the predictability of evolution can be studied?

  Luria & Delbrück (1943) Mutations of bacteria from virus
  sensitivity to virus resistance. Genetics 28: 491–511.

I think Lenski's evolutionary long-term experiment should be a good example, without being familiar with Luria & Delbrück (1943). There they use replicated populations of E-coli to study (among other things) the "repeatability" (historical contingency) of evolutionary changes. Nice overviews of the project are given in Blount et al. (2008) and Philippe et al (2008), where they study to what extent certain mutations are repeated in replicate populations, in relation to citrate metabolism and size/shape.

References:

Blount, Borland & Lenski. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. PNAS vol. 105 no. 23
Philippe et al (2008). Evolution of Penicillin-Binding Protein 2 Concentration and Cell Shape during a Long-Term Experiment with Escherichia coli. Journal of Bacteriology 191(3):909-21


Which immunosuppression caused by long-term usage of these antibiotics in untreated celiac disease? These antibiotics include

amoxicillin + acidum clavulanicum (beta-lactam, inhibit cell wall synthesis, broad specturm, 3rd gen aminopenicillin) / last part preventing the resistance
ceftriaxone (3rd gen cephalosporine, inhibit cell wall synthesis, broad spectrum)
clarithromycin (macrolide, inhibit protein synthesis by binding to ribosomal subunit S50)

used regularly for cyclic middle ear infections for years during the childhood - ages 2-10 for a patient with untreated celiac disease.

I am thinking what kind of immunosuppression can this lead to.
I think it mostly conquered by suppression of adaptive immune system.
Little lowered innate immunity lowered too.

I am especially interested in the antigen-presenting cells (mostly dendritic cells) and their function in an immunosuppressed patients of the antibiotics.

There may be other factors which I have not mentioned related to this kind of immunosuppression.
Feel, free to propose.

How can dendritic cells work in an immunosuppressed patients?

You can assume any combination of cases for the three antibiotics: 8 possible cases.
For instance,

(1) and (2) high antibiotic resistance, and only susceptible to (3)
High antibiotic resistance to (1)-(3)
...

Possible cases which reminds

this immunosuppression can remind this one: immune reconstitution syndrome like in HIV but milder

One possibility is that these antibiotics could disrupt your normal gut bacteria. Given that your gut has the surface area of a tennis court and is typically coated with symbiotic microbes, antimicrobial therapies could dramatically change the population dynamics of your gut ecosystem. One might imagine that the immune system of the gut is in homeostasis with these gut microbes, and if they all die off all at once because you're taking some sort of 'cillin, your immune system might suffer for lack of stimulation. Fewer immune cytokines released by your intestinal immune cells into your blood => systemic reduction in immune function.

Other possibilities could include: the drug just randomly fits into a bad spot on some important immune protein; the drug targets bacterial-related genes in the mitochondrial genome and disrupts the metabolism of the immune cells; the drug disrupts your ability to absorb nutrients required for immune function...the list of potential mechanisms is undoubtedly long.


How does the pancreatic beta-cell know how much insulin to secrete in response to glucose? How do $\ce\beta$-cells know how much glucose is in the blood?

I know that when glucose enters a beta cell it triggers the cell to produce insulin. $\ce\beta$-cells trap glucose by converting it into glucose-6-phosphate, this means $\ce\beta$-cells actually consumes glucose.

So my question is: how do $\ce\beta$-cells decide when to stop producing insulin? (To do that the cells must know the level of glucose in blood, right?)

Yes, pancreatic beta cells can indeed sense the level of blood glucose. They respond to high glucose concentrations by secreting insulin, and stop (or reduce) secreting insulin when glucose concentration falls. This is a classic example of feedback regulation (homeostasis) in physiology.

Exactly how the glucose sensing in beta cells has been the subject of much research for decades; a freely available review is here. You are correct that phosphorylation and further metabolism of glucose by the beta cells is required for sensing. The current theory is that mitochondrial oxidation of glucose leads to increased ATP levels, which is detected by ATP-sensitive potassium channels at the plasma membrane, which in turn leads to secretion of insulin.

When glucose levels fall, beta cells reduce their glucose metabolism because they use the glucokinase enzyme to phosphorylate glucose, and glucokinase is a low-affinity enzyme that becomes inactive at lower glucose levels. Therefore, uptake and oxidation of glucose is reduced, ATP levels fall, and insulin secretion stops.

This is the current consensus I believe. But these metabolic processes are difficult to study, and the precise nature of the connection between glucose metabolism and the ATP-sensitive channels is still somewhat controversial.


If post transcriptional modification happens , how can a gene code for amino acids in a particular order? Post transcription, introns are removed and exons are rearranged randomly. If that's the case (which it is according to the book EDEXCEL SNAB A2 topic 6) then shouldn't the protein produced be different every time? Shouldn't the order of amino acids be different? And if it is, doesn't that mean that the protein produced is different?

To quote : "When mRNA is produced, its introns are removed by spliceosomes and a different number of exons is put together at different orders which changes the sequence of amino acids in proteins."

Quote from the book:

  Genes contain sections that don't code for amino acids.

  These sections of DNA are called introns. All the bits that do code for amino acids are called exons.
  During transcription both introns and exons are copied into mRNA.
  The introns are then removed by a process called splicing -- introns are removed and exons joined forming mRNA strands. This takes
  place in the nucleus.
  The exons can be joined together in different orders to form different mRNA strands.

If this process happens,how can a gene code for a specific protein? This process means that exons are arranged differently, and this means that amino acids are arranged differently, and doesn't that mean that different proteins are going to be produced than the one coded for?

"then shouldn't the protein produced be different every time? Shouldn't the order of amino acids be different? And if it is, doesn't that mean that the protein produced is different?"

It is not different every single time, but it is different depending on what kind of post transcriptional modification takes place. The proteome is larger than the genome thanks to this, genes can code for many different proteins thanks to post transcriptional and post translational modification as well.

So as I understand it, gene segment = same order of nucleotides = same primary mrna

post transcriptional modification to primary mrna = different mature mrna = different order of amino acids = different polypeptide chain (then different protein later on)

Hope this helps


What is the evolutionary relationship between heme, chlorophyll and other tetrapyrroles? As a non-biologist, I have searched the Internet and found dozens of papers discussing the similarity between the structures of heme and chlorophyll molecules, but I could not find any discussion of their evolutionary relationship.

To be more specific, I would like to know whether the use of tetrapyrrole in the blood and in photosynthesis can be traced to the earliest organisms in which tetrapyrrole had some function, and then the molecule evolved to be capable of the different functions it currently performs in animals and plants.

Note the molecules are not that similar, only one portion is similar.

The similar portion in each molecule is a cyclic tetrapyrroles. Cyclic tetrapyrroles and porphyrins in particular are a fairly common structure in biology they have several functional uses and are fairly easy to construct from existing simpler biological molecules. The fact that they are functionally good at binding metals makes them a reoccuring solution, although not all Cyclic tetrapyrroles bind metals. Many many biological molecules contain Cyclic tetrapyrroles.

Many biological molecules have similar structures to other molecules, especially ones that perform similar tasks, there are only so many shapes you can make with carbon atoms, the shape of a molecule affects its chemical properties and that shape is simple and has useful properties. Heme itself is a functional component of many proteins called hemoproteins, basically whenever they need to bind iron. Another cyclic tetrapyrroles would be cobalamin otherwise known as vitamin B12 which binds cobalt.

Its the same reason hammer handles look very similar even in very different cultures, just attaching a stick is a simple easy to discover solution, so it is the one that gets found most of the time. Functionally that is the shape that works. Or to put it another way they are only so many shapes you can make a wheel.

https://www.sciencedirect.com/science/article/pii/S0167488912001000

http://www.org-chem.org/yuuki/porphyrin/porphyrin.html

https://www.cpp.edu/~lsstarkey/courses/CHM-Lab/PorphyrinBasics.pdf

https://www.mdpi.com/journal/molecules/special_issues/porphyrin_chemistry

To address the updated question. I honestly don't know if they share an evolutionary origin. But given that they are synthesised in different organelles (mitochondria for heme and chloroplast for chlorophyll, I would guess no.


Molecularly, why can you straighten or perm hair? I'm aware that hair can be curly because of the disulfide bond interactions in between cysteine amino acids in alpha-keratin filaments. However, I'm curious as to the biochemistry involved in straightening hair with a straightening iron, as well as with "perming" hair.

What happens at the molecular level? I suspect that a straightening iron simply disrupts the present disulfide bonds, but I'm only speculating.

For straightening hair with a flat iron:

This source provided by bobthejoe states that temporarily straightening hair involves the breaking of hydrogen bonds between keratin molecules within hair.

  One of the reasons hair is curly is because of hydrogen bonds between the proteins (keratin) that make up your hair [...]. Another way to alter hydrogen bonds is with heat; electric straighteners work because of this principle. The platters on electric straighteners are flat so that when your hair cools it takes the shape of "flat" as the hydrogen bonds reform. The same thing occurs with curling irons, but since the heating element is circular, the hair stays curled as it cools. The effect of heat, however, is temporary, over time the hydrogen bonds eventually return to their original form and the hairs goes back to the way they were. This rearrangement happens because moisture in the air hydrates the proteins.

This source provides a similar explanation.

  Running a flat iron through blown-dry hair breaks the hair’s hydrogen bonds. It flattens hair until water or water vapor (from humidity, drizzle or the shower) penetrates the hair fiber and allows the hydrogen bonds to revert to their natural positions.

Thus, the straightening of hair with an flat iron does not involve the breakage of disulfide bonds as I had originally hypothesized.

For perming hair:

This article suggests that perming involves the chemical treatment of hair with reducing agents to break the present disulfide bonds between cysteine amino acids, followed by the reformation of the disulfide bonds in the desired curled shape.

  In a standard “cold” perm, hair is put into curlers and the reducing agent ammonium thioglycolate is added. The disulfide bonds break and keratin molecules are now free to move around and adjust to the shape of the curl. Then a “neutralizer,” such as hydrogen peroxide, is added to reverse the effect of the reducing agent. New disulfide bonds form so the keratin molecules are locked into the shape of the curls.

This Wikipedia article also suggests that the chemical straightening of hair is obtained with the same process.


Why is the nucleus accumbens in that place? This description of where the nucleus accumbens is (Ac) says that it should be near the lateral ventricle, when it is quite clearly very far away? How is this?

  the region surrounding the tip of the lateral ventricle, at the ventromedial margin of the rostral pole of the medial striatum (MSt) in birds is marked as the nucleus accumbens

    (from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481519/)

Furthermore the lateral ventricle seems to be in very different places in both diagrams although they are both avian brains?

(https://avianbrain.org/papers/RevisedNomenclature.pdf figure 2)

(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481519/ figure 1)

thank you for any help :)

The ventricle looks in a different place simply because the first image is a transverse section whereas the second one is a sagittal section.
In the sagittal version the striatum looks very far from the ventricle because it is a quite lateral slide, more medially it would look closer to it as it does in the first figure you show.

Here you can see a representation showing also a more medial transverse section.
source: Vertebrate brains and evolutionary connectomics: on the origins of the mammalian ‘neocortex’. Harvey J. Karten. (2015) DOI: 10.1098/rstb.2015.0060


How is bacterial plasma membrane made? Eukaryotes have ER which manufactures plasma membrane of cells. How is prokaryotic plasma membrane made ? What is the pathway and which enzymes are involved ?

The processes that occur at the ER membrane in eukaryotic cells take place directly at the bacterial plasma membrane. Phospholipids are synthesised and inserted at the plasma membrane, and there is a protein translocation apparatus for translocation of proteins into the periplasmic space and insertion of transmembrane proteins into the plasma membrane.


Significance of having goosebumps? What help does goosebumps do to us? I don't think it helps us noticeably when we are scared or shivering.

As a general rule, you might want to check wikipedia before posting here. On the other hand, I am glad you made me look the answer up.

Goose-bumps warm you up a little. "During the formation of goose bumps, the body is warmed from the muscle tension in piloerection."

There are other reasons, which do not directly serve humans, but may be a remnant from evolution. In animals with fur, the erected hair makes thicker insulation and further protection from cold. "Goose bumps can also be a response to anger or fear: the erect hairs make the animal appear larger, in order to intimidate enemies."

More on wikipedia: http://en.wikipedia.org/wiki/Goose_bumps


Modeling intracellular interactions between sender and receiver bacteria I am involved in a modelling task of a biological process described as follows:

--
"Objective: to model behavior of a sender receiver type system

The process goes as follows

Pre-signal [PS] is in media
Pre-signal diffuses into bacteria
Pre-signal binds to activator as a co-activator
Co-activator activator complex binds to DNA and starts transcription of enzyme mRNA
Enzyme mRNA is transcribed then translated into enzyme
Enzyme begins converting Pre-signal to signal [S]
Signal diffuses out of the cell into media
Signal diffuses into receiver cell from media
Signal binds to repressor inducing activation of reporter gene

Questions for model:

What concentrations of signal will be required to get a response from receiver cell?"

--

My questions are: what kind of mathematical/computational model or simulation tool is more suitable for this task? is it neccesary to model every step, or can some of these be ignored? I know the basics of ODEs, so I wonder if these are enough or something else would be required. Any other advice about how to go through the modelling is welcome.

You can start with deterministic model using ODEs for reaction rates.

However, if you are considering diffusion then you would have to use Partial differential equations for Fick's diffusion law.

You can, however, assume that there is no "diffusion" but just transport of the signal molecule from a well mixed system (medium) to another well mixed system (cytosol). In this case you can use an ODE for "conversion" of extracellular signal to intracellular signal.

The model becomes simple and easy to analyze if you reduce the number of steps. Certain steps can be removed by making certain assumptions such as Equilibrium approximation (EA) or Quasi-Steady-State approximation (QSSA). If a reversible reaction is extremely fast compared to all other reactions (such as binding-unbinding of the activator to DNA), you can assume that reaction to be in equilibrium and represent the concentration of some species using equilibrium constants.
In Quasi-Steady-State approximation, you assume that certain species are in steady state with respect to others i.e their concentrations do not change over time. In the model you just set $\frac{d[X]}{dt}=0$ for that species. Then obtain the concentration relationships as a function of reaction rate parameters. I'll explain QSSA and EA using the Michaelis-Menten (MM) kinetics.

MM considers following steps:

Enzyme-Substrate binding (Reversible): $ E + S \rightleftharpoons ES $ with forward rate constant k1 and reverse rate constant k2
Enzyme-Substate complex converting to Product and Enzyme (Irreversible): $ ES \to P + E$ with rate constant k3

EA (The actual MM model):
Assuming step 1 is in equilibrium. $k_1[E][S]=k_2[ES]$
 Get [ES] in terms of [E] and [S]

QSSA (The revised MM mddel):
Assuming [ES] is in steady state. ${\Large \frac{d[ES]}{dt}}=k_1[E][S]-k_2[ES]-k_3[ES] = 0$  which means $[ES] = \Large \frac{k_1[E][S]}{k_2+k_3}$

This way you have removed certain reactions from the model.

You can do stochastic modeling as well.

For simulations you can use Matlab or Fortran.


Do the majority of fish lack scales on their heads? Based on pictures, it seems to me that a vast majority of fish species that have scales do NOT have scales on their heads.

Is that fact true?

To make this properly answerable:

lets' define a "majority" as >70% of fish species. But frankly, I'm more interested in actual numerical answer than whether it passes some arbitrary threshold or not.
The universe which I'm interested in measuring the percentage are fish species that have "normal" (Cycloid and ctenoid is the technical term, I believe?) scales on their bodies.

If that's not specific enough, you can restrict the universe to species in Actinopterygii (ray-finned) that have scales.

I certainly agree with your general observation, but not being an ichthyologist, I can only offer a partial answer, based on a particular family of fish. Within the family Tripterygiidae, most species lack scales on their head, or have highly modified types of scales. A comparative study of 48 species showed that only 2 have "normal" scales of their head (Jawad, 2005).

  The squamation pattern of the bases of the fins
  varies among species. The head is usually devoid of scales
  except for two species that have squamation with body-
  type scales (Matanui bathytaton (Hardy, 1989) and
  Norfolkia clarkei). Several species have head ctenoid scales
  modified into tiny spicules of different shapes (Acantha-
  nectes rufus Holleman & Buxton, 1993, Apopterygion
  oculus Fricke & Roberts, 1994, Axoclinus carminalis,
  Ceratobregma acanthops, Cremnochorites capensis, Ennea-
  nectes boehlkei Rosenblatt, 1960, Forsterygion malcolmi
  Hardy, 1987, Forsterygion varium (Forster, 1801), Karalepis
  stewarti, Matanui bathytaton, Norfolkia clarkei, Notoclinops
  caerulepunctus Hardy, 1989).

So far, I haven't found a broader comparative study, to support your general question. Someone more knowledge in the area and the literature can perhaps offer a more general answer. This is at least an indication that your observation might be correct.

Reference
Jawad. 2005. Comparative scale morphology and squamation patterns in triplefins (Pisces: Teleostei: Perciformes: Tripterygiidae). Tuhinga 16 (1), 137-168


Gene duplication and subfunctionalization I’ve been intrigued by gene duplication and want to learn more about it.

I’ve read the following from here:

  several studies suggest that the proportion of duplicated genes
  retained in vertebrate genomes is much higher than is predicted by
  this model [4-6]. This has led to the suggestion of an alternative
  model whereby complementary degenerative mutations in independent
  subfunctions of each gene copy permits their preservation in the
  genome, as both copies of the gene are now required to recapitulate
  the full range of functions present in the single ancestral gene. This
  was formalized in the Duplication-Degeneration-Complementation (DDC)
  model [7] in a process referred to as subfunctionalization.

Can someone explain this?  What is meant by “both copies of the gene are now required to recapitulate the full range of functions present in the single ancestral gene”?

Can you suggest any other good articles on gene duplication?

Suppose a gene performs two distinct functions 1 and 2, both of which are essential. We'll call this gene A, for ancestral gene.

A duplication copies A to another locus. Now there are two genes, A and B, that perform the same two functions. At this point, if either A or B is deleted, the organism is fine.

Over evolutionary time, A and B undergo genetic drift to become A' and B', respectively. Let's say that B' loses function 1, and that A' loses function 2. This isn't a problem for the organism since A' still performs function 1, and B' still performs function 2. In other words, the two genes complement each other.

However, now A' can't be deleted without losing function 1, and, similarly, B' can't be deleted without losing function 2. The result is that both genes are fixed in the genome by evolution.

This means that now, after hundreds of millions of years of relevant evolution and genetic drift, we many duplications like A' and B'. The key to this is that through genetic drift with no selective pressure, it's very easy to lose function but extremely difficult to gain it.

As for your second question, I'll look for a paper on gene duplications that I think would be the most helpful, but there are many.


How to find the enhancer region of a specific gene? I am new to these concepts in biology and need some help understanding. My main concern is how to find the enhancer of my gene of interest, specifically the sequence of the enhancer. I am working on a project where I will be attempting to use CRISPR- mediated deletion of the promoter region and enhancer region in my gene of interest FOXN2, in MCF7 Tamoxifen resistant breast cancer cells. I already have the sequence for the promoter region from UCSC's GenomeBrowser, but I'm not sure if the enhancer region sequence can just be looked up on there or anywhere else. Do I need to do a protocol to find the enhancer region myself? I have seen many things about ChIP-Seq and that I may need to do that to get data to find my enhancer but I am just not sure. I plan to use the sequences of the enhancer and promoter region of my gene of interest to create gRNA for CRISPR. Thank you to anyone who can help.

There are several ways to identify enhancers:

(1) Chip seq / chip-chip recognize transcription factor binding sites,

(2) Enhancer specific factors can also be used to identify enhancers, such as EP300, the binding sites of EP300 are often used to predict enhancers;

(3) RNA polymerase II can bind thousands of enhancers, so POLR2A2a, the largest subunit of RNA polymerase II, can also be used to search for enhancer sites;

(4) The high sensitive site of deoxyribonuclease I (DHS) represents the open chromatin region, many of which are covered with enhancers;

(5) A large number of active regulatory elements, including enhancers, can be identified by formaldehyde assisted separation regulatory elements (face) combined with sequencing;

(6) Some histone modification patterns reflect different chromatin states, such as the binding of h3k4me1 and h3k27ac, which are widely used for enhancer labeling;

(7) Enhancer sequence can be transcribed, and the transcriptional enhancer RNA (enrna) is also a marker of enhancer activation;

(8) The method of chromosome 3D conformation (e.g. 5C and Chia pet, capture-c) can also provide the information of enhancer promoter interaction.


Are endorphins addictive? Endorphins are among the brain chemicals known as neurotransmitters, which function to transmit electrical signals within the nervous system. Stress and pain are the two most common factors leading to the release of endorphins. I wanted to know if they are addictive, and found some contradicting answers:

  If people can get addicted to risky sports just for the thrills they
  provide, they can also get addicted to painful activities where
  endorphins provide relief, "despite the harm to self and/or others,"
  says Dr. Anna Lembke, chief of addiction medicine at Stanford
  University School of Medicine in an email interview. "For example,
  someone who compulsively cuts herself for the endorphin release is
  causing self-harm. Someone who compulsively runs, even to the point of
  causing musculoskeletal injury, is causing self-harm."

Source:
https://science.howstuffworks.com/life/inside-the-mind/human-brain/can-be-addicted-to-endorphins.htm

  In contrast to the opiate drugs, however, activation of the opiate receptors by the body's endorphins does not lead to addiction or dependence.

Source: https://www.medicinenet.com/endorphins_natural_pain_and_stress_fighters/views.htm#

If they are not, how can we explain the 'love' for pain in (this content might be sensitive for some of you) some people?

Addiction specialists and others who study human behavior often catageorize addiction into the two broad categories of physical dependence and psycological dependence. They are not always mutually exclusive, and they can both manifest in serious or mild cases of addiction depending on the person and a number of other factors.

What differentiates them is how they affect your physiology. A person severly addicted to alcohol or opioids can become extremely ill or even die from the withdrawl of those substances, due to the strong physical dependence their body has developed. To my knowledge, people do not experience a physical withdrawl after cessation of compulsive pain seeking behaviors. Since they didn't cite any source, we can only guess as to the intended meaning of your second source, but it's probably related to this lack of withdrawl. A quick search on PubMed shows publications referring to certain endorphins as mediating this type of addiction. Meaning that the endorphin is not addictive per se, but a compulsive or addictive behavior can be communicated to the brain in terms of a native neurochemical pathway which is otherwise a normal part of a healthy brain.

I think the lesson here is to be somewhat skeptical of online sources that don't link to peer-reviewed science. Attempts to simplify a topic for the purposes of communicating with a lay audience often result in more confusion than clarity. And if you search something on PubMed or google scholar, you'll probably find an answer in the same amount of time it took you to post your question here.