texts:
I am confused about using the ImageQuantTL application as a tool to analyse the Urea Gel. My problem is that I am not sure if the 'shape' for calculation should be the same for all samples (like on picture A) or as close to the band as possible (like on picture B)? And what about the background subtraction? The `Image Rectangle/Ellipse' option says:

  Uses the average pixel intensity in a defined rectangular or elliptical area of the image. To define the area for background calculation, select the background shape in the navigator and then drag with the mouse. Background areas are identified by a broken colored border, and are numbered in the sequence in which they are created. If you have defined several background areas, select the area to use in the Parameters tab.

Does it mean that the shape for the background subtraction not necessarily has to be exactly the same size as the shape for the band? (See Figure C.) I attach some pictures for your convenience.

Thank you very much for any help.


texts: Can you help identify this tree from my garden?

texts:
The picture is an evergreen tree.

I have seen very similar trees in Northern Italy. I would appreciate any help.


texts: Protein that exit from the cell - as marker

texts:
Searching for some protein, that I could use as extracellular marker for mammalian cells. I need to insert mRNA to cell, and to detect the protein outside the cell (not on membrane) if the mRNA successfully enter and been translated. (not GFP, I need protein that exit from the cell in big numbers)

Thank you.


texts: Lower affinity drugs longer time for pathways to rebound?

texts:
Do lower affinity drugs take a longer time for pathways to rebound?

Affinity has to with strength of activating a receptor others options.

Do those with stronger affinities result in more likelihood to rebound?


texts: Is cannibalism part of mainstream food-chain?

texts:
There are some species who sometimes eat their own kinds. Is this cannibalism considered their regular food? Do the link in food-chain for those animals make a loop on themselves?

Can this statement: "Food chains are found within the population of a species." be held true?

Disclosure: The above statement was part of a question that asked to identify the correct among statements. I tried to find relevant content in books and internet but couldn't find any. I'm not trying to get my assignment solved, but I want opinion on cannibalism and it's impact on food chains.


texts: Why is synthesis of tetanospasmin advantageous to C. tetani?

texts:
The tetanospasmin is a neurotoxin synthesised by some strains of C. tetani. It is the factor causing tetanus, but what is its role for the bacteria itself?

I do not believe the main objective of C. tetani is to harm people. I believe that any organism that wastes resources for purposes not related to its reproduction or preservation is being wiped out by the evolution.

As tetanospasmin is encoded by a plasmid gene, it should be pretty easy ro get rid of and there are strains of C. tetani lacking the gene. As protein synthesis costs resourcess, I guess there is some advantage from the neurotoxin synthesis - otherwise it would be a searious handicap, leading to competitive exclusion of tetanospasmin positive strains.


texts: single units vs ensemble recording for signal detection

texts:
I would like to know, when looking (in vivo electrophysiology) at response properties (latency, magnitude) in response to sensory stimuli, is there any advantage to looking at single units over ensembles of neurons? My ensemble data is really good, while my single units are only ok.

Any advice or resources regarding this would be helpful. I've talked to members of my lab, and looked for answers elsewhere, but havent really found what Im looking for.

Best!


texts: What is the appropriate blender speed to maximize nutrition and digestion of fruits and vegetables?

texts:
Blender companies state that a blender for smoothies should have speeds of at least 30000 rpm. They argue that only at 30000 rpm are cells of fruits and vegetables sheared enough to maximize nutrition and ease of digestion.

Would blending at lower speeds, such as 20000 rpm, be sufficient?


texts:
This is an arthropod I found in an apparently abandoned mongoose burrow in the Maasai Mara game reserve, Kenya:

That was the best photo I could get of it. From what I could tell, it had six legs and very long antennae, so I'm guessing it's an insect. It was vaguely orthopteran-like and had striped/banded legs with a dark dorsal side.

Does anyone have any idea what this could be? Even if the species can't be discerned, I'd appreciate knowing what clade this critter belongs to.


texts: Is nutrient absorption different in Hypersensitive I patients?

texts:
I am thinking how the nutrient absorption differs between between patients with allergies (Hypersensitivity I) and those not.

The current guideline about number of eggs in diet is one daily regularly.
My professor says that 1-4 eggs daily can be also ok because cholesterol is inhibited.

However, I am thinking if we have Hypersensitive (allergic) person, what the recommendation should be then.
My hypothesis says that more cholesterol would be absorbed and less inhibited.
However, I cannot find any evidence for this hypothesis.

Hypersensitive response is fast.
I am interested in many responses during long term.

How does nutrient absorption differ in hypersensitive patient and normal patient?


texts: Can 3% hydrogen peroxide be used as effective disinfectant and antiseptic?

texts:
I was curious to see whether 3% hydrogen peroxide can be used as antimicrobial and virucidal product for daily use in home. There are  several disinfecting products in the market claim that use of these wipes for some minutes can disinfect the hard surface. Also, there are quite a few ethyl alcohol based hand sanitizers. Can 3% hydrogen peroxide be used as effective disinfectant and antiseptic - similar efficacy with those of the commercial disinfecting products?

Website https://www.cdc.gov/hicpac/Disinfection_Sterilization/7_0formaldehyde.html discuss use of hydrogen peroxide against a wide range of pathogens. I found that the bottle of 3% hydrogen peroxide lists it as  antiseptic - to use for gargle etc. Can 3% hydrogen peroxide be used as a disinfectant for a broad spectrum of microbes?


texts:
Tl;dr: What is the net joule value of fat if used for energy provision, compared to e.g. carbohydrates. So does 1 Joule Fat intake result in 1 - X Joule energy provided to the cell, or does it work in a completely different way?

My understanding is that if I take in one Joule of fat, my body takes in the energy to move ~100g of mass up by one meter (Wikipedia).

Now for my body to use that energy, it needs to convert it to some sort of Glucose, right?

From the Lipid Metabolism Wikipedia Article I get that my fat needs to become a Triglyceride to serve as energy source.

There are some steps involved, roughly the following:

gastric peristalsis (basically muscle contractions to mix it all up)
peristaltic contractions in the gut (again, mixing is key)
lipase, also working in the gut to finally create Triglyceride
then the fat gets "packaged" in Chylomicrons and put into the bloodstream

releasing energy to the cell involves the following

Lipase unpacking the Chylomicrons
Splitting of the Triglyceride in Glycerin (the stuff we want) and fatty acids

Now this seems like a really cumbersome process to me, and I wonder what the net Joule Value is that arrives at the cell.
Is it significant, or is this process so efficient that it doesn't matter anyways?


texts:
I am new to experimental design and would like to perform the following experiment but I am not sure if my setup is correct or not so far. My idea is below.

Let's say you want to optimise the growth conditions for the small fish. You have been using a standard type of food that has worked reasonably well. But now, three new brands of fish food have become available and you want to conduct an experiment to test which food works best and whether it is worth changing to one of the new food types.
Based on previous experiments, you reckon that you will need 10 replicates to have a good chance
of finding meaningful differences. There are aquaria and tanks of different sizes available so you are not constrained by the equipment.

For this experiment, I assume there will three treatments (the three new brands of fish food). I will call them A, B and C. Since we are testing three different brands of fish food, I will replicate the brands of fish food three times so there will be nine tanks used in this experiment in total. I will label them from 1 to 9. Each tank will randomly receive different food brands of food every day.

But now, how will I find meaningful differences in the growth of the fish if I apply different treatments randomly on the tanks? Also, how many fish do you recommend I use for this experiment and how often should I monitor the growth of the fish? Or do you have another suggestion of how I could set up this experiment, help. Your help will be much appreciated. Thanks in advance.


texts: rRNA colony PCR amplification not working

texts:
We used some universal primers to amplify rDNA in a certain isolated bacterial specie. The problem is that rDNA PCR is not amplifying.

Primers were working well in other strains of same bacterial specie.

Do you know what could be happening? Maybe strain-specific PCR inhibitors? This strain was successfully amplified using ERIC PCR.


texts: What's the meaning of 'plasma' in 'plasma membrane'?

texts: I wonder why is it called plasma membrane - what's the biological meaning of the word 'plasma'?


texts: Recommended books and articles on the origin and evolution of sexual reproduction?

texts: I'm interested in learning about the origin and evolution of life on Earth. In particular, one topic that puzzles me a lot as a layman is the evolution of sexual reproduction, since the DNA mutations have to be such that they affect both female and male in a coordinated way so that their reproductive organs match with each other in order to make the sexual reproduction viable. Would you guys kindly recommend me high quality books and peer-reviewed articles on the matter that hopefully can clear these questions out? Thanks in advance.


texts: Is there any non-human animal social group that punishes members with "imprisonment" or a similar method?

texts:
I was reading this blog on Scientific American, which discusses whether wild animals are happier than domesticated ones. I've also read about strong territorial instincts in some species. This reading led me to ask whether there is any non-human animal social group that punishes members with something similar to "imprisonment".
When I say "imprisonment" I mean restricting the mobility and survival freedom of members, for some social or cultural reason.
By "imprison", obviously I don't mean the use of cages or prisons or any of the manmade ways of imprisoning. I wish to know about whether, in any species, a member acting alone (or acting together with others of their own), build a virtual territorial wall/ring around another member(s) of their own species, acting almost like an imprisonment? This may not be physical exertion of muscle force, but may by making (say, for example) continuous noises as a group to restrict the territory of their own member.
Maybe, one can exclude adult members forcefully protecting their young ones, because that would be in their instinctive interest, even if the young ones' instinct is to violate a restriction. Also please avoid answers on behaviour of one species defending their territory. That's not the same as restricting by "constructing" a limiting threshold in an enclosure-like fashion.


texts: How would blocking Na/K ATPase affect the ability of a neuron to exhibit a series of action potentials?

texts:
Neural firing usually occurs in the form of spike series. Several action potentials are happening in a quick succession. Whereas Na/K pumps (and other pumps) restore ion gradients to allow processes that take place during an action potential.

Now my question is, what would happen if we completely blocked these pumps and immediately after, we started exciting a neuron? Would the neuron be able to fire a few times before losing the gradients? Or, would one single spike completely diminish the gradients and without restoration by pumps, a second AP would be impossible?


texts: Is it possible to become ambidextrous? i'm 67 and recently and suddenly became ambidextrous about a month ago. I can write w both hands at the same time.


texts: Is Plasmid pGLO a stable or unstable plasmid varient ?

texts: Is plasmid pGLO a stable or unstable plasmid varient?


texts: What is "integrated spindle activity" in plain English?

texts:
From a research article:

  To determine if a combination of spindle parameters allowed for a better group discrimination, integrated spindle activity (ISA) was calculated by integrating over time the amplitude of each detected spindle (and by dividing by non-REM sleep duration). We found that integrated spindle activity was markedly reduced in amplitude and number of detections during the first sleep episode in the schizophrenia group in relation to the comparison and depression groups (Figure 3A).

Is this ISA parameter calculated using integrals? I vaguely recall integrating functions in the university, but by now I've forgotten all - that was too long ago. And I don't know how one would "integrate" not functions (like we did in the university) but spindles. And what is the meaning of "over time"?

In short, I'm curious what this ISA parameter stands for. Is there a way to describe it in plain English?


texts: What is the lifespan of haemonchus contortus in its L5 adult form?

texts: It is well documented that from ingestion to occurrence of eggs in feces for haemonchus contortus can be as little as three weeks.  However, once the parasite reaches L5 in the abomasum, absent external factors (such as treatment of the infected animal with an anthelmintic), how long can it continue to live there?


texts:
A few days ago I observed a corridor built and used by ants that went over a path in fields:

Why do they build it? It seems it doesn't bring any considerable protection from the surrounding environment and it certainly costs them a lot of work.

The picture was taken in the morning when the temperature was low so there is no ant activity visible.


texts: My research on the matter can be summarized in a sentence: "It [sporangium] can be composed of a single cell or can be multicellular" (Source: https://en.wikipedia.org/wiki/Sporangium). Yet there shouldn't be a reply placed between "They are" and "They aren't" test options, speaking of "Are bryophyte sporangia multicellular?". A link to the source where I could ascertain whether the bryophyte sporangia is multicellular (if I could ascertain) is highly appreciated.


texts: I have been quite interested in biology lately,and I would like to know whether it is a good choice to look up taxonomic information there.


texts: Where do i find microbes like tardigrades in winter

texts: Just bought a microscope and i want to see microbes like tardigrades.  Where should i look? I have found many bacteria and what seems to be motionless single celled organism.  I want to see movement and feeding.  Ps snow on the ground and frozen ground


texts: Why does the DNA content of a cell get doubled in interphase? Why doesn't it become tripled or quadrupled? What's stopping it from doing so?


texts:
While doing some biology I came across this question:
The following tables present results of plant crosses involving two linked genes: S is a seed-color gene, and L is a plant-height gene. Each gene has two alleles with one allele exhibiting complete dominance over the other allele. Dominant phenotypes are yellow seeds, and tall plants; recessive phenotypes are green, and short, respectively. Assume that crossing-over between two genes occurs once.

Calculate the map unit between gene L and gene S. (One map unit = distance of 1%
recombination)
This question confuses me because what I understand from the table is that from crossing over we get short flowers with green seeds(0.01) and tall ones with yellow seeds(that 0.01 from 0.51). So as a result from the fertilization we get a 0.02 frequency, that as I understand also equals the recombination rate. And so the map unit would need to be 0.02*100= 2%. But the response I have to get is 20%, which I do no understand how to get to.


texts:
My answer ( after rounding off) is 9% -100( 0.75 X 0.25 X 0.5) but the answer given is 22 %
Am I correct ?


texts: I would like to understand the distribution of metal ion concentrations (such as Mg2+) in the different cell compartments. I tried very hard but still couldn't find such information. Could anyone help?  Also, could you recommend a good reference on this problem? Thank you!


texts: What would be the molar concentration of human DNA in a normal human cell?

texts: A diploid human cell has 46 chromosomes. A haploid cell has DNA approximately 3.2 billion bases long. What is the molar concentration of DNA in the cell then? How would we calculate?


texts: Does unequal dominance mean the X-chromosome should be a coldspot for antagonistic variation?

texts:
Sexually antagonistic genetic variation, in a simple model, will persist if the benefit to one sex is (near) equal to the cost in the other, otherwise the polymorphism will be selected out of the population.

[Rice's theory][1] suggests that sexually antagonistic genetic variance should be over-represented on the X-chromosome, because males are hemizygous (thus express male beneficial alleles more often than females) and females have the X-chromosome 2/3rds of the time (thus female benefit does not need to equal male cost for persistence). This model expands the range of conditions under which SA variation can persist.

[Fry argues here][2] that unequal dominance means the conditions under which sexually antagonistic variation can be maintained in the autosomes. Because of dominance the mean population fitness is increased under conditions of polymorphism (cost of a new allele to one sex < the benefit to the other). This model also expands the range of conditions under which SA variation can persist.

I think Fry concludes that the X-chromosome should therefore be expected to, not only not be a hotspot, but to be a coldspot (a dearth of SA variation on the X).

Conceptually, why does the hypothesis of unequal dominance make the autosomes more permissive to genetic variation than the X-chromosome? (Therefore making the X- a coldspot for SA variation). This is what his abstract says, it seems to suggest that...

  "..such polymorphisms are expected to be more common on the
  X-chromosome... here I show that there are plausible assumptions under
  which the reverse is expected to be true."


texts: Why aren't all strongly self-recognizing T cells made into regulatory T cells?

texts: Negative selection in T cell development is often simply described as preventing effector T cells from recognizing self-antigens. This is complicated by regulatory T cells developing from T cells with moderate affinity for self-antigens. If recognition of self is useful for immune tolerance, why don't T-cells with strong affinity for self-antigens also become regulatory T cells?


texts: A structure determined by X-ray crystallography has a resolution of 1.5 Å. When I look at the coordinates, I find every backbone C-N distance is 1.32 Å.i.e. Accurately predicted. If resolution is not good why every C-N bond distance is accurately predicted?


texts: My question is about these cocoon like things that are all over my house and fence in Florida (USA).


texts: What is the scientific name of this tree?

texts:
The tree flowers prior to the monsoon season and sheds it's leaves in Winter and regrow them in Spring and Summer.
I have seen three different colours of the flower (growing in my neighbourhood): pink, violet and white.
Place-India, Kolkata, West Bengal. Season - Monsoon.


texts: Fish ID? Small, yellow-finned, tropical fish in Thailand

texts:
I have not had any luck finding the yellow fish shown in the photo in any of my fish books. I saw them in many places, so they are fairly common. This observation was at around 15 meter depth.

I hope someone here knows it.


texts: Why do gram-negative bacteria attack the digestive system more than gram-positive ones?

texts: I was researching for a biology project on the subject of contagious infections of the digestive system (mainly the intestines) and almost all of the bacteria that came up (E.coli, Shigella, Cholera, etc.) were gram-negative. Is there is reason that that type effects the digestive system so often or is it coincidental?


texts: Have there been any study that document the evidence of the changing ratio of the biomass of different trophic levels?

texts: You would expect a number such as the producers (photosynthetic) biomass to consumers + decomposers biomass ratio is a very important indicator for sustainability. It is also very probable that the ratio has been changed due to human activities (land clearance, animal agriculture etc.) which have resulted in the likes of climate change (which is in a sense just a problem of excessive mineralization (both industrial and biological) relative to immobilization by producers). Have there been any studies that try to calculate and monitor this number? I can't seem to find any.


texts: Why is the nucleus accumbens in that place?

texts:
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 :)


texts: What is the purpose of THC for a Cannabis plant?

texts: Why does a Cannabis plant produce THC? This question is brought up drawing an analogy to nicotine in tobacco, where nicotine is developed by tobacco plants as a pesticide. Is THC a pesticide as well? I'm imagining that marijuana plants don't have rheumatoid arthritis.


texts: Why is it common to grow microalgae in bottles or canisters?

texts:
I came across many people growing Chlorella or Spirulina types of microalgae, inside bottles or canisters and that that they also bubbled CO2 into these containers artificially.

This question is basically comprised of two questions that will clarify what I am trying to understand:

Why do they use bottles or any type of bottle-like canister?
Why do they insert CO2 to the bottle artificially in cases the bottle doesn't have a cork ? If the claim is that enough CO2 won't be able to get through the bottle neck than why growing the algae inside a bottle\aquarium in the first place, and not in a tub with full exposure to the air?


texts:
De novo conformation predictors usually function by producing candidate conformations (decoys) and then choosing amongst them based on their thermodynamic stability and energy state. Most successful predictors will have the following three factors in common:

  1) An accurate energy function that corresponds the most thermodynamically stable state to the native structure of a protein

This is an excerpt from Wikipedia. I have a very, very limited understanding about de novo protein prediction so here goes.

I asked the post-doc I'm working with about whether there are kinetic barriers to protein folding. Yes, everything wants to be at an energy minimum, but sometimes that just can't happen due to kinetic barriers (the reason your diamond ring doesn't turn into graphite/pencil "lead"). So, why does protein prediction software look for energy minimums? Do they also consider activation energy barriers? Do they take into account the presence of chaperonins? Are there examples where the thermodynamically most stable protein conformation is not the biologically active protein? The post-doc told me that perhaps most proteins do reach their thermodynamically most stable state. True?


texts:
I'm reading this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562283/ , but I cannot make sense of what MPS nor how should I read the pictures that make use of this method.

The authors say

  The MPS, beyond classical representations such as the waveform and spectrogram (Figure 1A and B, upper and middle panels), displays the time-frequency power in modulation across both spectral and temporal dimensions (Figure 1A and B, lower panels). The MPS has become a particularly useful tool in auditory neuroscience because it provides a neurally and ecologically relevant parameterization of sounds

I'm clueless about what the meaning of time-frequency power in modulation across both spectral and temporal dimensions. Can someone provide a brief explanation about this and MPS?


texts:
A picture is worth a thousand words!

It's about 1.3cm (1/2") long. We rented a basement and I found this on a machine that was moved in a bit earlier.

I would like to know if there are any mice, rats, etc that could have come in.

We are on the island of Malta, in the Mediterranean sea.
The basement is below a shop that used to sell AC units and the basement was used as a storage. The walls have gaping holes where cables and pipes go in and out, etc. Clearly industrial and not made for the customer to see.


texts: Is there a chemical or process that would dissolve or remove all other tissues in an organ and leave all the vasculature intact? I am planning to make a shelf display of the blood vessels in the heart of a pig for use as a shelf display.


texts:
Hardy Weinberg would predict that the frequency of normal females, to carrier females,
  to affected females for colorblindness is equal to p$^2$ + 2pq + q$^2$=1. You
  were told that q=freq of the recessive allele. If p+q =1 (frequency of the dominant allele +
  frequency of the recessive allele=1 or 100%) and q=.08, what is the frequency of the
  normal allele in the population? What is the frequency of carrier females in the
  population (ie heterozygous females)?

I get that the frequency of the normal allele is p = 1 - .08 so 0.92. However the frequency of carrier females is giving me an unrealistic number. Using p$^2$ + 2pq + q$^2$ =1, the value for pq comes out to be a negative value. Is it safe to just multiply p and q since that is what we're essentially solving for using the full HW equation? This would make the value (.08*.92) = 0.0736. Would that be the way to approach the problem even though it asks for females only?


texts: Why don't primates have galactose-alpha-1,3-galactose (alpha-gal), but other mammals do?

texts:
I read in wikipedia that:

  Galactose-alpha-1,3-galactose, commonly known as alpha gal, is a carbohydrate found in most mammalian cell membranes. It is not found in primates, including humans.

My question is : Why not?

In the sources for the wikipedia article about alpha gal allergy, I spotted the (pay-walled) article Evolution and pathophysiology of the human natural anti-α-galactosyl IgG (anti-Gal) antibody which has this to say in the abstract :

  It is estimated that anti-Gal appeared in ancestral Old World primates less than 28 million years ago, possibly as a result of an evolutionary event which exerted a selective pressure for the suppression of α-galactosyl epitopes expression by inactivation of the gene for the enzyme α1,3 galactosyltransferase.

However this is more than a bit over my head, biology-wise.


texts: When a molecule is being used in some biochemical process it has a certain 3-d structure. Is this maintained throughout it's usage or can one specific molecule change it's 3-d shape while it is being 'used' in the process. Can a specific molecule in all it's interactions in a cell say , take on 4 or 5 distinct 3-d shapes??


texts: Why does our body exhibit bilateral symmetry?

texts:
Externally, we (humans) look symmetrical. However, internal organs don't show the same patterns of symmetry (heart being on the left side while the liver is on the right side, etc.). It is a bit counter-intuitive to me that the exterior of our body seems to be mainly symmetrical while the interior is asymmetrical.

What is the advantage of having bilateral symmetry in our body?
Why don't all of our organs exhibit bilateral symmetry?


texts: What is this brown spider with black and white stripes? (Atlanta, Georgia)

texts:
Location: Atlanta, Georgia

Spider mostly brown, with black and white stripes. Would fit on a teaspoon.  Ran quickly but not very far when I tried to catch it.

Click to zoom in the pictures below:


texts: How does cytochrome c oxidase inhibition cause cell death?

texts:
I realise the inhibition of cytochrome c oxidase prevents the release of H+ ions into the intermembrane space, and that the ion gradient is required for ATP synthase action. However, I'm not sure how this causes cell death.

Does this:

a) Prevent oxidation of Cytochrome C, preventing electron movement the cytochrome bc1 complex, which in turn prevents electron movement from earlier parts in the chain, shutting down the electron transport chain altogether? Thus, no ATP is produced and the cell dies due to lack of ATP.

b) Prevent oxidation of Cytochrome C, but not preventing oxidation in the other protein complexes*, merely reduce the number of H+ ions available for ATP synthase action, lowering the amount of ATP produced, and the cell dies due to low ATP levels.

c) other.

I realise in either case, the ATP count is merely lowered, as ATP is produced by other methods, so my statement 'lack of ATP' is not totally explicit.

*This being the case, how are the released electrons dealt with by the cell? Are there electron acceptors to remove this?


texts: Resources to study the cell as a "mechanism"

texts: I am looking resources that effectively describe the cell as a mechanism. The cell might be irreducibly complex, but the individual components must necessarily have simple functions, locks, keys, switches, gears, membranes, and extruders. Is there any resource that exists that classifies the great many substances in the cell in this manner?


texts: Specificity of Protein Kinases in Signaling Pathways..?

texts: In most of the signaling pathways the activated receptor when activates Protein Kinase through the action of secondary messenger, then these protein kinases almost always phosphorylate on the specific Serine, Threonine, or Tyrosine amino acid residues? what is the reason of phosphorylating specifically these amino acid residues. why not other than these amino acid residues are choosen for phosphorylation ?


texts:
I came across a photo on Wikipedia depicting an Oreocereus celsianus with what looks to me like some kind of harvestman on it. The photo was taken at the San Francisco Botanical Garden.  Can anyone identify the arachnid in the photo?  (See link below for full-size image.)

Source: https://commons.wikimedia.org/wiki/File:Oreocereus_celsianus_1.jpg


texts: Why can't we kill ourselves by holding our breath?

texts:
Is it possible to kill yourself by holding your breath?

This question is obviously copied from Quora, but I had heard it as a fact that we cannot kill ourselves by holding our breath and I'm looking for a referenced answer.


texts:
I did an expression profiling from publicly available RNAseq data for mouse tissues. While for liver and testes I am getting expected proteins in the top highly expressed mRNAs, for brain I am getting ferritin (Ferritin heavy chain 1: Fth1) as the top expressed mRNA!

There are a few studies which report elevated ferritin and iron in neurodegenerative diseases while some others have implicated its role in ageing.

I haven't come across any study on iron metabolism in the normal brain. Does iron metabolism play an important role in the function of the brain?

PS :

The data that I am talking about, has the SRA accession number- SRR652247 (I tried all three runs submitted in SRA)
The mice used in the experiment were 11 weeks old
I used bowtie -> eXpress for quantification of RNAseq reads.


texts: Whole Genome Sequencing and B Chromosomes

texts:
Do whole genome sequencing techniques detect B chromosomes if such chromosomes are present?

My understanding is as follows:

How the DNA material in a B Chromosome is mapped depends on the reference map and not on how the material is packaged into chromosomes for the sample being sequenced.

Is this correct?


texts:
How does the acidic environment in the stomach affect carbohydrate and fast digestion? Does it aid, impede or remain neutral in their digestive process?
Or do the carbohydrates, fats and proteins leave the stomach straight to small intestine once the churning is over?


texts: I have read that non veg food are better for proteins while veg food is deficient in either one or other protein. If it is so are herbivores protein deficient always in case of animals as well as humans?


texts:
It may seem obvious to us humans to hide our excreta, but this is not quite normal behavior for animals.

Interestingly, dogs have the habit to pee all over the place. It's know that they do so to mark their territory. So when they want to mark their territory, why do they cover up their poop?

I found an old web article where someone asks the same question, without getting a credible answer. He quotes a Yahoo Answers answer making the following claim:

  This behavior is natural in dogs. They cover up their "waste" so that
  an enemy does not find them, from the scent of the poop or pee. It is
  an instinct handed down from wolves, who hid their scent by covering
  up their feces in leaves, sticks, soil, or other nearby natural
  materials. They also rolled in animal carcasses to hide the scent of
  them. Your dog is just using her natural instinct to protect herself
  from predators.

  Another things that dogs do, called marking, is when the dog pees in a
  certain area. They do not cover it up, as it is marking a territory as
  their own. Male dogs usually do this on trees, wooden posts,
  furniture, and other things. Female dogs do this in heat. Dogs do not
  poop to mark something, only pee. When you dog pees or poops and then
  covers it up, this does not mean she is marking her territory. Just
  wanted to add it so you don't get confused. :)

I find it hard to believe these two opposite claims. One time dogs want to mark their territory and the other time it's scared from predators. I know many dogs that do not cover their pee, but do cover their poop, sometimes even within the same walk (and so the same territory).

If this is true, why do dogs do both in the same walk?

On Wiki Answers I found this answer:

  The animals are not actually covering up the pee or pooh but spreading
  their scent. This often happens with animals that are dominant (for
  instance show dogs).

It's so that dogs never actually cover their poop anymore, they only perform some random scratches, throwing a little sand on the turd, sometimes even nothing. That fact makes this answer quite more likely than the previous one.

Another take that's similar to the previous one is this one from Dogster:

  So, why do dogs scratch with their hind legs after defecating? You
  might think the dog is trying to cover up his poop like a cat does,
  but it’s actually a way to mark territory, with the scratch marks in
  the ground pointing to the scent the dog has left.

I also found an eHow article on this subject. It seems to agree with the previous two explanations, but is more detailed.

  It is normal for dogs of both sexes to vigorously kick the ground with
  their hind legs after defecating. This is called scraping or peeling
  out. Some dogs will also do it after urinating. Dogs are descended
  from wolves, which also perform this behavior. It is not a bad habit,
  but a vital part of a dog leaving a visual message and scent message
  to any other dogs that happen to pass by.

They also say that the specific reason why they spread scent with their paws is because paws just contain a lot of scent.

  Dog paws contain scent glands. There are also glands in between the
  toes. The action of scraping the paws against the ground helps release
  the scent inside of the glands. Dogs scrape the ground in order to
  increase their scent on the area near the feces pile, according to
  veterinarian Dr. Justine Lee. Before domestication, dogs wandered in
  large territories. One vital way to communicate with other wandering
  dogs is through scent marking. This instinct has not been bred out of
  the domestic dog.

So, which theory is the most valid? I tent to go for the scent one. Any additions?


texts: Why did the face of human species changed so much during the course of its evolution?

texts:
I recently watched this video which showed the evolution of facial features of the modern man
https://youtu.be/-69K7E0UlBI

I'm wondering what evolutionary advantage did we get by having our face from this-

(reconstruction of the face of Australopithecus)

To this-

(Homo sapien sapien)

"In other words for what advantage did nature selected our present face?"


texts: examples of chromosomal aberrations with lack of sexual chromosomes?

texts: Are there any examples in animals where individuals survive having no copies of their sexual chromosomes?


texts: Why is graft-vs-host so selective against phylogenetically close cells?

texts:
Is there a well established explanation for the phenomena that graft-vs-host is so much more selective against phylogenetically close cells? See historically significant references below,
"This type of aggression of the immune system is thus particularly directed against allo-antigens and is much less in evidence across two animals species. “ - Jerne, 1971
"Normal lymphoid cells obtained from animals that are phylogenetically unrelated or only distantly related to the chicken do not initiate graft versus host reactions when introduced into chicken embryos. " - Lafferty, 1968
References
Lafferty, K., & Jones, M. (1969). REACTIONS OF THE GRAFT VERSUS HOST (GVH) TYPE. Australian Journal of Experimental Biology and Medical Science, 47(1), 17–54. https://doi.org/10.1038/icb.1969.3
Jerne, N. K. (1971). The somatic generation of immune recognition. European Journal of Immunology, 1(1), 1–9. https://doi.org/10.1002/eji.1830010102


texts: How can octopus walk if muscles can only contract?

texts:
From this video it is evident, that octopus can make tentacles push:

https://youtu.be/zaE-LwDowcU

How is it possible, if it is said, that muscles can only contract?

What types of muscles can distract?


texts: What's keeping living species from rotting?

texts:
Why do only corpses of species rot and be eaten by bacteria? What is keeping us from rotting?
Just like fruits, and foods we eat; meat and vegetables rot when left uneaten. Like food, corpses rot and get eaten by maggots. Why?
Why don't these apply to living species?


texts:
I am thinking the more reasons why sitting much lead to thrombosis i.e. clotting of blood in blood vessels and then hypoxia in the deep tissues eventually.

What are the physiological mechanisms for this to happen?

One student said hormones.
It can be right, but I am thinking how.


texts: Does a severed limb/finger experience pain after its separated?

texts: If a person ends up with a severed finger will that finger, after falling off, experience any pain and start writhing? Can a limb kind of have a mind of its own for a few more seconds after separating from the body like for instance the tail of a lizard?


texts: What is the advantage of the way eukaryotes initiate translation?

texts:
The eukaryote and prokaryote mechanism for translation is slightly different. Is there any advantage of the eukaryote translation mechanism ?

Edit : I specifically want to know why eukaryotic ribosome first attaches to tRNA and then to mRNA but prokaryotic ribosome can do this in either order. Is there any advantage of the former ?


texts: How many polynucleotides are there in one molecule of DNA?

texts: I always thought that a molecule of DNA was made of two polynucleotides each making up one strand of the molecule... Is that right?


texts: Is the prostate problem unique to humans?

texts: In human males the urethra goes through the prostate rather than around it, which tends to create problems for older men as the prostate enlarges. Is this only a human problem or do other animals, primates in particular, have the same problem?


texts:
According to articles I read, AGEs (advanced glycation end products) activate RAGEs (receptors for AGEs). This activation increases the ROS (reactive oxygen species) levels in the cells.

2003 - Reactive Oxygen Species-Regulated Signaling Pathways in Diabetic Nephropathy

Free radicals can cause damage in cells, which is definitely not good. What do you think, what is the role of RAGEs, which is more important than cellular damage?


texts: What plant is this? Edible, tastes like cress

texts: My girlfriend got this at a Turkish supermarket in Berlin. It tastes like garden cress or a bit like radish. I looked up cress varieties but couldn't find this particular leaf shape.


texts:
It was just on the news that scientists discovered "Two cubs in Russia's Sakha Republic last August in a near-perfect state".  And the South Koreans and Russians are attempting to clone these extinct Ice Age lion cubs. (Link to one such news coverage)

According to this answer, we seem to be able to sequence its genome but cloning may be difficult.  However, is this find likely to be the rare large chunk of well-preserved material that makes cloning possible?


texts: Which mountain range was formed first (historically) and which the pedigree is correct?

texts:
Source 1:

Source  1 shows a map of a particular area. In this map you will find the  mountain ranges 1 and 2, the species P, Q and R. Two possible pedigrees of  the ancestral history of the species P, Q and R are drawn .
Which mountain range was formed first (historically) and which  pedigree is correct?


texts: Fur genetics - what are the causes of fur colour decision?

texts:
This Australian Shepherd puppy's father is a black-tri; mother is a blue merle. What would cause this dog to have so much white color?

Are there any general explanations as to why this might happen in nature? Other examples of this kind would also be greatly appreciated.


texts: Correlating beta-lactamase expression to absorbance

texts:
When penicillin-resistant bacteria are grown in liquid culture media,
  β-lactamase is secreted into the medium. The supernatant of such a medium can be assayed for β-lactamase activity. Culture supernatants
  different organisms , which are suspected to be penicillin-resistant,
  were obtained and were assayed for β-lactamase activity. The corresponding absorbance value were measured at a certain wavelength.

Let us assume that supernatant from organism 1's culture had absorbance value X and 2 had absorbance value Y.

My question : If X>Y, does that mean that more β-lactamase was being produced by organism 1 ?


texts:
I was reading a manual for kit that requires you to amplify DNA by PCR before analyzing it in the kit. The manual suggests mixing proofreading and non-proofreading polymerases:

  For
  PCR
  products
  >2500
  bp
  in
  length,
  use
  a
  DNA
  polymerase
  blend
  containing
  Taq
  DNA
  polymerase
  supplemented
  with
  a
  proofreading
  DNA
  polymerase

How would this improve the amplification of long products? It suggests using only a proofreading polymerase for fragments below 2500 bases. Does the addition of a non-proofreading polymerase improve speed? I have TAQ and PFU Ultra, but both instructions say to use an extension time of 1 minute per kb.


texts: Why Do Most Humans & Cats Have Blue/Bluish Eyes At Birth?

texts:
I've read that the eye color at birth for most humans and for cats may not always be the the true genetic color at first. This is due to the lack of melanin in the iris. This makes sense as there is no light in the womb to stimulate the production of melanin.

My question(s) though is:

Why does the lack of said melanin produce a blue/bluish colored iris?
Why is it not say green, red, clear, etc?


texts:
Almost every dinosaur book writes that Triceratops maximal length was about 9 meters (29.5-30 ft), see for example Thomas R. Holtz's dinosaur genus list 2011. My question is what specimen is the base or indication for that estimate, and what is its size? It could be a partial skeleton or maybe just a gigantic skull, and not a full vertebral-column specimen.
Also, what is the largest complete (or almost complete) skeleton of Triceratops? Peter Dodson in "The Horned dinosaurs" (1996) notes a 7.9 meters long skeleton at Minnesota's Nature Museum, but since then new almost complete skeletons have been found. If it is on display, please write in which museum it can be seen.
Added in edit:
The following image of EoFauna on DeviantArt and the discussion that follows suggests that Triceratops was as big as Eotriceratops, reaching a length of 9 meters and a mass of about 10 tonnes (10,000 kg) with skull about 2.7 meters long.


texts: How do aerobic Rhizobium bacteria survive in root nodules while fixing atmospheric nitrogen?

texts:
I read that rhizobium carry the enzyme nitrogenase, which is irreversibly damaged upon the exposure of oxygen. Inside the root nodule of legumes leg-haemoglobin keeps a microaerophilic environment where nitrogenase enzyme can function and molecular nitrogen can be fixed (source: Brock's Biology of Microorganisms).

Shouldn't therefore Rhizobium bacteria die in such microaerophilic condition inside the root nodules?


texts: How can I fetch nucleotide sequences based on ENA accession numbers and positions?

texts:
I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that manually.

Is there any existing tool or script that can fetch all those entries from a database and extract the correct subset of the sequence?


texts: Mobile carriers of Light reaction in higher plants

texts:
The hydrogen carrier PQ and the electron carrier PC are the mobile carriers in light reaction facilitating electron transfer from PS II to PS I during non-cyclic process.

My question is -

How do they move in membrane, from PS II to cytochrome for PQ and cytochrome to PS I for PC?
I do know the membrane is quasi-fluid in nature so it'll be easy for carriers to move in it but my question is how do they reach their destination? What's the driving force?

Maybe they're just arranged that way on the membrane and some change like - because of change in density (when PQ accepts the H and converts to PQH2 ; I'm not sure about the density change part) which leads to change in side on which it's present or change in anything else, they reach their target?

Is my thinking correct?


texts: Do larger multicellular organisms have an increased risk of mutation and thus cancer?

texts:
So I was thinking that if each cell has P(X) of becoming cancerous, then the chance of cancer is 1-((1-P(X))^n) where n is the number of cells in the organism.

Since larger organisms have more cells than smaller organisms (I'm guessing that larger organisms simply have more cells than smaller organisms as you can't have larger cells since there is an optimum surface area to volume ratio), does this mean then that larger creatures are more likely to have cancer cause they have more cells?


texts: Can a plant be programmed to produce any arbitrary object?

texts:
I'm wondering if a plant can be programmed (by modifying its genes) to grow into any shape that it's programming instructs.

I understand that a plants genes are its instructions of how to convert the nutrients in the soil into the plant we see. So, instead of producing an apple tree or a giant sequoia, couldn't a plant be programmed to shape itself into a house, desk, or even at a stretch of the imagination, a bioship?

I'm looking for any links, or explanations of why this could/couldn't be done by anyone with more experience than I that could guide my research.

I am hoping that a plant behaves just like any other system. That it has inputs (nutrients, sunlight etc.) a function that describes it (its genes) and an output, the plant that grows. With this in mind, I suppose it would only be a matter of modifying the genes to produce the desired output (with the constraint being the available input).

Thank you,
Paul


texts: Interaction study of oligomeric proteins

texts:
I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system.
I have so far successfully been able to purify both the proteins using IMAC(Ni-NTA) protocol.
Further TEM analysis of the purified protein is showing the presence of oligomeric form(for each of them separately) in the purified sample.

But, how can I be able to detect or show how the oligomers of protein_a and protein_b is interacting to produce a much larger macromolecular entity ? And how can I be able to quantify that interaction ?

Any ideas regarding this issue would be highly appreciated.


texts: Changes in spongy urethra during tumescence

texts:
How does the columnar cells of spongy urethra expand during tumescence(erection of penis)?
If we assume that the urethra has the length, long enough to sustain tumescence without expansion of cells, then will it form wrinkles on retraction just like skin? Probably latter should not be the case, since accumulation of urine would then take place in the grooves of those wrinkles.


texts: What specific membrane adaptations do cells have for saline-rich environs?

texts:
Are the cells of marine animals and flora equipped with special ion exchange pumps to mitigate the effects of a saline-rich environment?

Or have the cell's membranes adapted through structural changes to counter the osmotic forces?


texts: Do "transcription factor binding site" and "operator" mean the same thing?

texts: Can the terms "transcription factor binding site" and "operator" be used interchangeably in all contexts when referring to a DNA sequence, e.g. regardless of a cell type, whether or not the binding sequence is synthetic or natural etc.? If not, what are the differences?


texts: I found this bug in my closet. Could someone help me identify?

texts:
It looks like it recently died. The shell was shiny and smooth and fairly brittle. I've been having trouble identifying what it is because it doesn't quite look like any of your common house pests.

The bug is at most 4 mm. I live in a relatively old apartment in New York City and my best guess is that this guy crawled out of a crack in my closet wall.


texts: Why are there no fresh water osmoconformers?

texts: I'm just having trouble understanding this. I know that often marine fish are osmoconformers, and freshwater (like bony fish) are often osmoregulators, but why?


texts: How do neurons form new connections in brain plasticity?

texts:
I've been reading about brain plasticity and how the brain can "rewire" itself.

One of the things that is not clear to me - how neurons can establish new connections. Does this rewiring mean that neurons can "disconnect" from other neurons to reuse existing dendrites?  Or do neurons grow new dendrites to make these new connections, adding to existing ones?

Thank you for your input!


texts: Does sunlight Kill Rotavirus? Maybe freezing? Norwalk or similar. Its a practical question for bedding.


texts:
I've been reading up about DNA writing, and it seems there are machines available around the five-figure US dollar mark for DNA synthesis, and I'm considering picking one up for my lab.
We normally order our DNA/oligos from IDT and similar companies, and for cutting down cycle time from a few days with next-day shipping to a few hours with in-house printing, as well as potentially saving on cost with enough scale (how much is enough scale?), this seems really promising for our lab.
Is this a reasonable thing to do?


texts: Are there any disadvantages to HRP conjugated PRIMARY antibodies

texts: I need to detect a FLAG tagged protein on a western blot and have to order an antibody. I'm not expecting to see a massive amount of my protein. To keep analysis time to a minimum  I am considering a HRP-conjugated anti-FLAG. Are there any disadvantages to it (e.g. sensitivity)? First hand experiences/problems?


texts: Is it possible to make a contagious cure to a virus?

texts:
In a TV series I've been watching The Last Ship, - spoiler alert - a scientist develops a cure for himself for a virus, but actually continues to remain a carrier, and sort of weaponizes the virus accidentally, killing 3 billion people. In response, another scientist develops a cure for that virus, a vaccine, and eventually makes that contagious by close contact as well, based on data gathered from the lungs of the scientist that infected/vaccinated himself with the weaponized version.

The science behind this might be totally ridiculous, or potentially realistic / possible I don't know. Is this possible? Can a vaccine / cure to a virus be engineered into a contagious version, to cure everyone in a chain reaction?


texts: I took a picture of a snail whose tracks are not continuous. What is the reason? Does the snail lift itself from the ground during its motion?


texts: Are there any animals that gradually approaches the predator to search for food?

texts:
I was wondering if there is an animal (or insect, bird, etc.) that eventually comes close to its predator to search for food, but only does so if it couldn't find food in the environment it is in. So it first searches part of the environment farthest away from the predator, but gradually comes closer and closer to the predator as it searches for new food. That is, over time it dares more to come closer to a, lets say ambushing predator, since it has ran out of food (or perhaps for other reasons). Similar behavior is ok, but note that the key behavior that I want in the animal is that it "gradually" comes closer and closer to the predator.

Thank you.


texts: Regarding cryonics, why can't you freeze a living body and then thaw it later, fully functional?

texts:
Cryonics is very popular in science fiction today, as a method of preserving animals, including humans, for long time storage and thawing the tissue later in the future. What is the difficulties with this method? Why can't we simply freeze living persons and expect them to be fully functional again later?

I've heard that the membrane potentials get lost in the process and thus all neural activity stops. I've also heard that freezing cells leads to cells imploding, due to the formation of ice crystals, leading to rapid necrosis. Is any of this true or just myths?


texts: How to tell if a given gene is a tumor suppressor or oncogene?

texts:
This is a problem taken from "Concepts of Genetics", Klug et al, 10e. I'm given the following table about the mutations in the BRCA1 gene:
$$\begin{array}{c|c|c|c|c}
\text{Kindred}&\text{Codon}&\text{Nucleotide}&\text{Coding}&\text{Frequency in}\\
&&\text{change}&\text{effect}&\text{control chromosomes}\\
\hline
1&24&-11\text{ bp}&\text{Frameshift or splice}&0/180\\
2&1313&\text{C}\to\text{T}&\text{gln}\to\text{stop}&0/170\\
3&1756&\text{Extra C}&\text{Frameshift}&0/162\\
4&1775&\text{T}\to\text{G}&\text{met}\to\text{arg}&0/120\\
5&\text{N/A}&?&\text{Loss of transcript}&\text{N/A}\end{array}$$
Footnote: "*N/A indicates not applicable, as the regulatory gene is inferred, and the position has not been identified."

Using this information, how can I decide whether the gene is a tumor suppressor or an oncogene?

I already know that BRCA1 is a tumor suppressor, so put another way, how can I arrive at this conclusion given the data above?


texts: Why have a placebo control group when testing a new drug if existing drugs can be used?

texts:
It is general practice to compare a new treatment against a sham treatment (placebo), and then use those results to compare efficacy of the new treatment (call it B) to an existing treatment (call it A), at least when existing treatments are available.

However, it seems reasonable and more ethical to use A and B together in a study, rather than giving one group a sham treatment. In other words, instead of a placebo group and a treatment group, why aren't there two treatment groups, one with A and one with B? Statistical noise such as regression to the mean, natural progression of the disease, etc would all show up in both groups, so if B gave better results than A, we should be able to say directly from that result that B works better than A, and we would be doing so in a more direct way than comparing the effect sizes of B vs placebo to the effect sizes of A vs placebo.


texts: How do people actually find codons in a DNA transcript just by looking at it?

texts: 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?


texts: Are the fossil sites in Hadar geographically separated?

texts:
The Hadar fossil record is made up of, from oldest to youngest, the Basal Member, Sidi Hakoma Member, Denen Dora Member, and Kada Hadar Member.

Are these regions geographically distinct, or, are they layers on top of another on the same geographical region?


texts: How many neurons are stimulated by electrodes in memory engram experiments?

texts:
Researchers have recently identified "engrams" in the mouse hippocampus, "sparse populations of neurons" or "small clusters of cells", stimulation of which elicits a specifically trained fear memory association. For example...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874022/

http://www.nature.com/nature/journal/v484/n7394/full/nature11028.html

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331914/

http://www.smithsonianmag.com/innovation/meet-two-scientists-who-implanted-false-memory-mouse-180953045/

My question: Roughly how big -- how many neurons -- are the regions stimulated in these experiments? I looked through a number of papers and was unable to find this information.

10/18 -- Changing the title and wording to clarify that I am asking just about experimental procedures with electrode implants, not fMRI studies, and not about how engrams might actually work.


texts: In males, why it is difficult to control orgasm?

texts:
Why it is difficult to control orgasm in male humans? How are orgasms controlled and what is different between males and females?

We can control urine for few minutes, but we can't control orgasm for more than a few seconds, but both are discharging though same organ (penis).


texts: Depolarization and hyperpolarization in stereocilia of the inner ear

texts: It’s a well mentioned fact that when the stereocilia of the cochlear hair cells bend in one direction, the hair cell depolarizes, and when the stereocilia bend in the other direction, the cell hyperpolarizes. When the basilar membrane vibrates, the stereocilia are bent back and forth, creating depolarizations in the hair cells followed by hyperpolarizations. What I’m having trouble understanding is why this is significant. This does not determine the frequency of the sound wave, as that is determined by the location along the basilar membrane that the wave impinges on. I don’t see how this would determine amplitude either, seeing as a greater amplitude would only create more drastic bending of a greater number of hair cells. Can anyone shed some light on this?


texts: Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?

texts:
I asked a similar question on Quora before, but did not get any useful answers as the program the one answerer suggested turned out to have the exact same problems as all others I have found so far.

Most programs for the construction of phylogenetic trees—being made for researchers in various biological disciplines—seem to rely on the input of a dataset that is a formulation of collected genetic and/or anatomical data.

Specifically, I am looking for a program that is like this, but with a GUI that allows tree editing (i.e. you can add and remove new taxa), for example, poorly described/novel theoretical species, dubious species, and subspecies and can be used to create simplified versions of charts like these.


texts:
We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic distance is probably less than 200 base pairs.

The two genes are expressed in opposite directions towards each other. Base on the preliminary transcriptomics data, it seems like one gene is over transcribing (3' UTR perhaps?) into the adjacent gene, possibly resulting in some kind of transcriptional regulation of the adjacent gene.

Here is a rough diagram of what we think might be happening:

------------------------==========gene A================>----------------------

----------------------------------------<====gene B=====-----------------------

Of course we need to first confirm this by designing primers to see if this over transcription is actually happening.

If this is happening, we intend to do some knock down experiments. We have no transgenesis available in our organism, only RNAi by dsRNA. It is possible to specifically knock down geneA by introducing dsRNA to the 5' region of geneA that does not overlap with geneB. Perhaps this will lead to ectopic/over expression of geneB.

Is there anyway to knock down geneB specifically without knocking down geneA? It looks like designing dsRNA for geneB would knock down both A and B.


texts: How difficult is it to adapt an existing vaccine to a virus variant?

texts:
There is (at least in France) an ongoing discussion about the Astra-Zeneca vaccine which is perceived as "outdated" because of the prevalence of new variants (the vaccine was designed based on the initial virus)(*).
How difficult is it to create a new vaccine that targets a new variant of the virus? (specifically adenovirus vector vaccines like the AstraZeneca one, but any general information is welcome as well)
My understanding is that the clinical trials are not needed anymore (in the same way as a flu vaccine is recreated each year without clinical trials because the difference is in the virus variants only) so is there a strictly biological, incompressible delay? (ability to target the new variant)?

My main question, related to biology, is above, the following alternative questions are OT for the site, but I am asking them in case they would be relevant:

Or is there a financial aspect? (too expensive to create a new vaccine)
Or is this because Astra-Zeneca believes that the current vaccine is OK, despite the backslash?

(*)

An example of the reluctance (in French): https://www.dna.fr/sante/2021/02/19/haguenau-la-moitie-des-50-64-ans-refuse-le-vaccin-astrazeneca.
In SA the AZ vaccine was stopped due to concerns about efficacity on the new variant, which influenced the French opinion as we also have SA variants in the wild (again, in French): https://www.midilibre.fr/2021/02/08/coronavirus-lafrique-du-sud-suspend-lutilisation-du-vaccin-dastrazeneca-juge-inefficace-sur-le-variant-9360903.php.

Please note I am not saying this is the case - I am just curious how hard it is to create a new vaccine for a variant.


texts:
So I wrote in a chapter that I will be checking for publications with gene lists in them. I got a comment asking "How would you define a gene list and what criteria did I use". I know that gene lists are usually generated by microarray studies, NGS analysis etc but what is the best way to define a gene list?

I am running blank except maybe say that its a list of genes.

EDIT: "I defined a gene list as a list of genes generated as a result of a microarray analysis or a next generation sequencing study." Sounds good?


texts: The photo was taken in southern Florida.


texts: What are these colonies on my Bacillus pumilus lawn?

texts:
I am growing Bacillus pumilus and I have plated some on agar plates. Now I can see some colonies on top of the lawn.

Does anybody know what they could be? A contaminant? Bacillus pumilus? I have observed some people growing Bacillus pumilus, and the colonies they streaked looked different than mine. Could it be that B. pumilus has several colony phenotypes?


texts: What niche was humanity theorized to fill before we possesd weapons and coordination to hunt & kill large prey?

texts:
I'm really interested in evolution, and for a err 'hobbyist' I think I understand a good bit of evolution and adaptation and the role it has played in many species.

However, I feel I'm rather ignorant about a key period of time in human evolution.  When I try to research it (and I have!) I see discussion of humans-as-ape, right around the time we split off from the bonobo & chimp common ancestor, and then discussion seems to skip to the 'cave-man' era of more advanced stone weapons used to take down larger prey animals along with significant coordination.

There seems to be a time gap between these two points, a time when we did not yet have weapons strong enough to deal lethal damage to fleeing prey, and may not have yet had communication skills to arrange complex ambushes.  I'm trying to figure out what evolutionary niche humans possessed prior to having weaponry for killing large prey.  Were they scavengers, mostly dependent on fruits, hunt smaller prey etc?  I really have no image at all of humanity role or how it evolved during the gap prior to being capable of the coordinated hunts.

The only theory I have heard of is the use of persistence hunting to basically chase prey before it died of exhaustion.  I personally am not that big a fan of that particular theory though (ignoring the massive caloric expense per 'hunt' and difficulty of doing it in stone age, prey species would quickly evolve to not run to exhaustion from otherwise non-dangerous humans rather then constantly letting themselves be killed this way if it was the primary hunting strategy of humans).

I realize that this far in time there is no consensus on exactly how humans evolved or exact roles they may have played.  however, I'm hoping someone could point me to some theories or discussion for how pre-weapon human may have lived?


texts: Were they developed anew or a heritage from fish?


texts: What is the definition of a polybasic cleavage site?

texts: I keep coming across the term "polybasic cleavage site" which is implicated in increasing the virulence of many viruses, but I'm struggling to find a definition. Is it just a sequence of amino acids where more than one has a basic side chain? I'd also love to know why it is so important to the function of a virus.


texts: For my first research project in microbiology I've chosen to determine the effectiveness of sanitizers and soaps in killing bacteria from our hands, however, after putting the bacteria on agar plates using cotton swabs, why do we incubate them? Won't their numbers increase and give us the wrong results?


texts: Why do we squint when tasting very sour things?

texts:
Sometimes while tasting a very sour thing (like tamarind, lemon etc.) our eyes squint immediately and involuntarily for a second, but a little later becomes normal again.

Why, and how, does this reflexive movement occur?


texts: How does the dopamine spike from drugs compare quantitatively to pleasurable non-drug activities?

texts:
I did find this popular press article that quotes a researcher offering the following quantification: "in lab experiments done on animals, sex causes dopamine levels to jump from 100 to 200 units, and cocaine causes them to spike to 350 units. '[With] methamphetamine you get a release from the base level to about 1,250 units...'" [1]

However, I haven't found any research study supporting this claim or providing any details?

[1] http://www.pbs.org/wgbh/pages/frontline/meth/body/


texts: Is a part of the spinal cord from the mesoderm?

texts:
The caudalmost part of the neural tube is formed by the caudal eminence. Isn't this mesodermal? So does it mean that, a part of the spinal cord is mesodermal in origin?

Does it have any significance apart from being something just academic?


texts: Using Transduction to reverse Antibiotic Resistance?

texts: Is it possible to use reverse transduction to reverse antibiotic resistance. Since antibitiotic resistance is causee by transduction of the F factor, is it possible to induce a F+ non antibiotic resistant bacteria into a region of F- resistant bacteria?


texts: Defining: Evolutionary (quantitative) Genetics and Population Genetics

texts:
How do we define the fields that are Evolutionary (quantitative) genetics and population genetics. What set these two fields apart? Can you try to provide definitions?

To my intuitive understanding, I'd tend to think that population genetics is a subfield of evolutionary genetics.


texts:
I enjoy watching birds at a garden bird feeder but have started feeling guilty that it is having a negative impact on the birds. For example this study recently showed that birds in the UK have longer beaks than their European cousins because bird feeders are more common there. This led me to google for more info and several sites list numerous potential negative effects of feeding wild birds from altering their migration patterns to increased spread of diseases.

Should I feel guilty or are bird feeders just a drop in the ocean compared to all the other ways humans are changing the environment?


texts: I know that hybrid animals like mules are infertile. What about clones? Do cloned animals show the same fertility as their original?


texts: Difference between crossover rate and recombination rate?

texts: I am not a biology student and therefore, need clarification if crossover rate and recombination rate are the same thing. So if the text says 'recombination rate per base pair per generation' or 'cross over rate per locus per generation', is it the same thing? And if not then what is the difference? Also, is 'per base pair' and 'per locus' the same thing?


texts: Can boiling water without high temperatures kill bacteria?

texts: If you use a vacuum chamber to reduce the pressure of water such that it can boil at around room temperature will it still have the same effect on reducing harmful bacteria as boiling at the usual 100C?


texts: Difference between tissue compression and compaction

texts: I often see these two terms used when studying models of cell dynamics. Is there a technical difference between the terms "compression" and "compaction" of a cell tissue?


texts:
My understanding, that may be wrong, is that cellulose/fibre has little nutritional value to many animals because it's hard to break down thus making consumption inefficient. However, Ruminating mammals, other mammals such as black bears, and many insects such as grasshoppers digest grasses.

Are there any birds with the gut flora to break down fibre? Or even some that eat grass but digest it in another way?


texts: Can someone who cannot talk still whistle?

texts:
Can someone who has a damaged larynx, which does not allow them to talk, still create a tune when they whistle?

I know that the larynx is what allows a person to manipulate their pitch and volume, but whistling sounds are just air making a noise as they are through the lips.

Would a person with a damaged larynx be able to whistle physically, but it would just be a toneless noise?

If this is so, is there any situation where a human would not be able to talk, but could still whistle with a tune and understand the speech of others perfectly? (i.e. having not suffered brain damage or are deaf)


texts:
Is there any skeletal muscle that does not have an antagonist? Excluding circular muscles such as around eye and mouth.

The reason why I am wondering is because in biology normally nothing is ever just like that, there is always an exception. This would be the first biological rule without exception that I came across.

I am thinking of humans only for a start but feel free to include any other animal if any have skeletal muscles without antagonists :)


texts: What concentration of hydrogen peroxide kills mold?

texts:
There are numerous articles online which claim that household 3% hydrogen peroxide can kill mold growing on household surfaces, yet I haven't managed to find scientific studies that show that. My question is what concentration of hydrogen peroxide is sufficient  for killing household mold (defined usually as a reduction of 99% or some other number)?

I have tried searching online for studies regarding the efficacy of hydrogen peroxide in killing mold, and for the minimum concentration of hydrogen peroxide for killing mold, but I didn't manage to really find information on that, though I am not that skilled in finding such information and also don't have much access to scientific literature.


texts: A mathematician's confusion regarding parametric $t$ tests for gene expression data

texts:
I'm a mathematician trying to test some things on gene expression data, and I'm thus skimming over various articles such as Sotiriou et. al. to understand what is typically done with such data sets. Several things confuse me; in particular, a paragraph in Sotiriou et. al. reads:

"Clinical parameters such as ER status, [...] affect the behavior of breast
cancers. We asked whether these clinical/pathologic characteristics were
associated with differential gene expression. Parametric t tests identified 606
probe elements of 7,650 elements represented in our array that could segregate
ER+ and ER- breast tumors (P < 0.001)."

As segregation of ER+/- based on gene expressions is one of several things I'm
interested in attempting to achieve through novel methods, I have been trying
to understand what precisely is meant with the above paragrah. To recap the
article, there are 99 patients with 7,650 probe expression values, and one
ER+/- value each. The article sets out to determine which of those 7,650
probes successfully segregate the dataset into ER+ and ER-.

I've run the above paragraph by a nearby statistician, and he could not for
the life of him figure out what was done, and had not even heard of such a
thing as a "parametric t test". This leads me to suspect that the term is
specific to biology, so I ask: what is meant?  It is also unclear to me (and
him) what the P-value means in this context.

I hope the scope of this question isn't too broad. Of course I want to avoid
asking "explain this article to me, the outsider, please"; I do believe the
paragraph above is relatively self-contained in the context of gene
expression.

References:

Sotiriou et. al., Breast cancer classification and prognosis based on gene
expression profiles from a population-based study.


texts: When does a jalapeño begin to produce heat/capsaicin?

texts:
I have a small Jalapeno plant in my apartment. About two weeks ago, it started producing a few flowers. In the last few days, many of them have started to turn into fruit; however, a few of the flowers have fallen off. The flowers do contain some seeds. They look rather like this:

Note this is not a picture of my plant (my flowers are white) but apart from the color it looks quite similar.

I tried munching on the seeds to see if they were hot. They weren't at all. I believe it is a common misconception that the seeds are where capsaicin concentrates, but should there have been any heat? Is there none in the seeds at all? Or was it too early in development?

Related questions: Do you think these seeds were viable at this point, or would they need to develop in an actual pepper fruit?


texts: Clarification regarding a statement in "The Selfish Gene" by Richard Dawkins

texts:
In the third chapter of The Selfish Gene: Immortal coils, Dr.Dawkins makes the following statement while arguing for the case that ultimately "the gene" as he defines it is the unit of natural selection.

  Natural selection in its most general form means the differential
  survival of entities. Some entities live and others die but, in order for
  this selective death to have any impact on the world, an additional
  condition must be met. Each entity must exist in the form of lots of
  copies, and at least some of the entities must be potentially capable of
  surviving—in the form of copies—for a significant period of evolutionary time. Small genetic units have these properties: individuals,
  groups, and species do not.

I am not sure what "impact on the world" he is talking about. Could someone explain this? He then goes on to say..

  An individual body seems discrete enough while it lasts, but alas,
  how long is that? Each individual is unique. You cannot get evolution
  by selecting between entities when there is only one copy of each entity!

Whereas in his other book, The Blind Watchmaker, he describes a computer drawing program EVOLUTION where he does precisely that, i.e, select between entities (here, computer drawn insect-like figures) of which there is only one copy and allows them to evolve. This seems contradictory to his above statement in The Selfish Gene. Could somebody explain?

tl,dr: Why must there be many copies of entities that are being selected for evolution to be possible?


texts: I have been reading about the human liver and zebra fish heart muscle having the ability to regenerate. It seems to me that these organs have very little chance to become damaged or worn out. At the very least their chances of being damaged are comparable to other internal organs. So why those particular organs have the regenerative capability?


texts: A question involving immunoprecipitation to identify interacting proteins?

texts:
Using recombinant Flag-tagged Dcr-2 and His-tagged protein X, pull-down assays were performed to determine whether protein X and Dcr-2 interact directly. The recombinant proteins (either alone or in combination) in binding buffer (150 mM NaCl, 1 mM EDTA, 50 mM Tris pH 7.5, 1% Triton X-100) were pulled-down by Flag antibodies coupled to Sepharose beads. Following extensive washing, the proteins were eluted from the beads with SDS buffer, and duplicate sets of samples were analyzed by SDS PAGE. Samples were also taken of the proteins before they were used in the pull-down assay and these were run on the same gel (input lanes in Figure 2B). One gel was stained with Coomassie blue dye (Figure 2A), and the other was transferred to nitrocellulose for Western Blotting. The membrane was probed with a His-antibody (Figure 2B).

The question asks: Do Dcr‐2 and protein X interact directly?

My reasoning is that they DO interact directly. In Fig 2B: the intense bands on LHS shows that Dcr-2 interacts with protein X-that is bound to anti-His. In Fig 2A: the protein X interacts with the Dcr-2 bound to antibody FLAG. I feel I'm not explaining this very though...Could someone please explain their reasoning? Thank you


texts: Can foxes move their ears independently?

texts: I've read that dogs can do move their ears independently, i.e., point one ear in the direction of a sound without having to point the other one at the same time. Is this a common trait with other canids, such as foxes? Can most eared mammals do this, with humans being an exception (except for a few exceptional humans)?


texts: How migration creates Linkage Disquilibrium

texts: I want to know how admixture and migration creates linkage disequilibrium? I am reading about it but I really don't quite get it.


texts: Can chylomicrons formed in the intestine, with apolipoprotein B48, transport lipids to adipose cells for storage?


texts: does anyone know of a fluorescent protein that upon binding of a substrate its fluorescence is activated? i've been looking on this and perhaps my keywords are not the right  ones. Thanks in advance


texts: Why is ACE2 not used as drug against covid?

texts: Can ACE2 be produced and used as drug against covid? I read it is the receptor molecule. If it is in the organism the virus should bind to it and could not attack cells anymore? Is that right?


texts: Is it possible to determine what tissue a DNA sample came from based solely on its sequence?

texts: All cells have the same genome and differ only by the expression pattern. Is it possible to determine the tissue origin of a cell based on its DNA sequence using short tandem repeat (STR) analysis or copy number variation (CNV) analysis?


texts: Carbohydrates- D-Glucose & L-glucose , alpha and beta

texts:
What's the difference between D-glucose & L-glucose ?

Yes , I know that L-glucose is an isomer of D-glucose . But what differences do they have ? They are the same , they are glucose .

Similarly for alpha and beta glucose ?

Sorry I just started learning on carbohydrates and I'm a little confused about these 2.


texts: EGFR, sialylation, and cancer progression

texts:
EGFR (epidermal growth factor receptor) has been intensively studied in cancer and treatments have been developed to inhibit EGFR signaling.  Sialylation of EGFR is known to block dimerization  and down regulate signaling.  I just read this paper:

Liu et al. 2011. Sialylation and fucosylation of epidermal growth factor receptor suppress its dimerization and activation in lung cancer cells. PNAS 108: 11332–11337. (basically just read conclusion if you don't have time).

What I don't understand is that the authors seem to say that increasing sialylation might be a good thing to prevent cancer progression since it inhibits EGFR dimerization.  However, wouldn't this go against almost 50 or 60 years of research that suggest that increased levels of sialic acid are one of the well known hallmarks of cancer that aid in its progression and metastasis?  What could explain this apparent discrepancy?


texts:
Question

Quite a few plant species can be used for medicinal purposes wiki. As an example, Filipendula ulmaria is rich in acetylsalicylic acid (aspirin).

An allele that produces a substance which is beneficial for a predator should not get fixed in the population! Why are there so many drug-like plants?

Thoughts

Here are some (intuitive, unclear or far-fetched, non-exhaustive and non-exclusive) hypotheses I can think of:

Because plants want their seeds to get ingested in order to propagate
Is it because there are so many substances that affect our homeostasy that many plants are toxic and many are healthy just by chance. Containing healthy substances are not adaptations but by-product of evolution.
The substances that are beneficial for us actually evolved to repulse predators. These substances are toxic at high dosage and therefore are efficient against predators that are small or eat a lot of plants (herbivorous). These substances at low dosage might actually have a benefical effect. For example a substance that make blood thicker is very toxic except if you eat just a bit of it while bleeding.
We (primate or whatever taxon you want to consider) evolved in order to get advantage of the surrounding envirronment. Sbstances that were neutral became beneficial. The advantage of being sensitive to various products cause that, by chosing our food source, we can heal. Therefore, by evolving sentivity to various substances, our behaviour can act as a reinforcement to immunity (and other anti-illness system). If this is true, we might expect that the frequency of presence of a plant species affect the probability that out homeostasy get affected when eating it.
Lineage selection. Lineages that produce substances that are active in predators body in a way or another are undergoing many various selection forces because of these substances. Therefore they get a higher speciation rate than other lineages.
Keeping some non-herbivorous species in large population size (by helping them) is the best way to keep herbivorous species in small population (because of territory competition, predators relationships, etc... )


texts: Why are there "Old World" and "New World" families?

texts:
I've been reading on biological classification of the animal kingdom and have come across the New World and Old World terms a few times when they are applied to ranks (family, as much as I could find). Some examples of what I mean:

Old World porcupine vs. New World porcupine.
Old World rats and mice vs. New World rats and mice.
Old World vulture vs. New World vulture.

Old World X and New World X are usually not considered closely related. I assume this is because (at least partially) they evolved separately long enough to be distinct, if they were even related (at a non-trivial level) to begin with.

Is this naming scheme only thanks to convergent evolution? Researchers found families (or species etc.) in the new world that look like families in the old world and called them New World X, which prompted the other to be Old World X? I understand that a good deal of this classification was done in the 19th century when diagnosis tools were limited and conventions varied.


texts:
I found these creatures stuck to a leaf on my tomato plant in the greenhouse/glasshouse, in early June, in south Oxfordshire in the United Kingdom.

They are each about 1-2mm in size. They didn't move much, even when gently nudged, although some did crawl tentatively.

I would be very interested to know what these are, especially if they are a beneficial species or a pest!


texts: Can someone help me identify this Ficus plant?

texts:
I have a bonsai with me which I grew from a seedling germinated in my backyard. It's been with me for the last 5-6 years. I definitely know its a Ficus, but I am not able to identify which species it belongs to. I have provided pictures of the specimen below:

I need to know if its F.virens (white fig) or F.ingens (Red leaf ficus). This specimen is from Kerala, INDIA.


texts: what benefits does lab procedure Realtime PCR have in gene silencing experiments?

texts: RT-PCR performed in gene silencing but mechanistically what are the benefits of this procedure?


texts:
Why do some biologists refer to single-celled organisms such as Amoeba and Paramecium as
acellular (i.e., without cells) rather than unicellular (i.e., one cell)?


texts: How do viruses such as COVID-9 and flu return in the winter if they disappear in the summer?

texts:
COVID-19 is gone from the body after a short time, and the maximum time of exposure to showing the symptoms is two weeks. So if no one gets sick for two or three months, how would it return in the winter?

How can it survive so long? Nobody got sick from nowhere except the first one and that things happened once to a lot of years.


texts: Do men have more extreme variations than women?

texts:
This question was considered unsuitable for Skeptics and I think it is more suited to BIology than Cognitive Sciences

I was reading this article which I found interesting. It is not supported with references but was an invited address for the American Psychological Association.

It makes the claim that men go to more extremes than women.

People can point to plenty of data that the average IQ of adult men is about the same as the average for women. So to suggest that men are smarter than women is wrong. No wonder some women were offended.

  There are more males than females with really low IQs. Indeed, the
  pattern with mental retardation is the same as with genius, namely
  that as you go from mild to medium to extreme, the preponderance of
  males gets bigger.

[...]

  Almost certainly, it is something biological and genetic. And my guess
  is that the greater proportion of men at both extremes of the IQ
  distribution is part of the same pattern.

[...]

  Nature rolls the dice with men more than women. Men go to extremes
  more than women. It’s true not just with IQ but also with other
  things, even height: The male distribution of height is flatter, with
  more really tall and really short men.

Another notable example of a similar claim was Lawrence Summer's speech regarding the possible reasons for dearth of women in tenured positions in science and engineering at top schools.

Summers outlined 3 possible reasons, with a major kerfuffle erupting - resulting in his firing from the job as a Harvard University President - over his presented second reason [ quotes from Wiki ]:

  The second hypothesis, different availability of aptitude at the high end, caused the most controversy. In his discussion of this hypothesis, Summers said that "even small differences in the standard deviation [between genders] will translate into very large differences in the available pool substantially out [from the mean]

  Summers referenced research that implied differences between the standard deviations of males and females in the top 5% of twelfth graders under various tests. He then went on to argue that, if this research were to be accepted, then "whatever the set of attributes... that are precisely defined to correlate with being an aeronautical engineer at MIT or being a chemist at Berkeley... are probably different in their standard deviations as well".

QUESTION: Are there any studies or evidence to support the claim that men have more extreme variations than women (in other words, that the trait's distribution in males have fatter tails) in a variety of traits?

Possible areas of research can be:

Intelligence (general IQ or specific linguistic or spacial abilities)
Physical attributes (strength, height, weight)
personality traits

for lack of anything better, let's take the FFM's Five:
openness
conscientiousness
extroversion
agreeableness
neuroticism

In order for the answer to be "yes", the research needs to show fat tails in at least 5-6 traits from all 3 of the buckets above (intelligence, physical, and personality), although precise trait mix may be arbitrary and not necessarily limited to my examples, as long as 5-6 somewhat independent traits fit.

In order for the answer to be "no", at least 8 of the 11 traits above should have no fatter tails in men.

Anything else means "inconclusive".


texts:
Triose phosphate isomerase deficiency, a rare condition, is the only glycolytic enzymopathy that is lethal. This deficiency is characterized by severe hemolytic anemia and neurodegeneration.

How can I relate this enzyme deficiency to hemolysis?

My attempt:

1- Accumulation of DHAP is causing intracellular fluid to be more osmotic leading to cell bursting.( Then why don't we see the same in outer cells?)

2-Lack of glucose may lead to less ATP production, Na/K pumps work less, thus disturbing membrane potential, which finally may cause hyper-osmic ICF and then henolysis. ( But why don't RBC take twice the amount of glucose?)

Source: Biochemistry 8th edition by Jeremy M. Berg John L. Tymoczko Gregory J. Gatto, Jr. Lubert Stryer


texts: Across from me there is a large flick of Pigeons and Ravens that like to nest on the roof. They swoop and dive and fly all over. Sometimes the whole flock lifts off at once. My question is, how do they avoid running into each other? Certainly they can't see every bird around them, can they?


texts:
As I write this I've just eaten a fair amount of cacao (not cocoa) powder and it's given me quite a buzz. I've googled the effects and the Internet seems to think it's somehow psychoactive although it's hard to find a reliable source for the details.

Some sites describe the ceremonial preparation of cacao but I'm wondering if someone here knows the actual science behind the effects of cacao.

Can you please help me understand the underlying processes better?


texts: Why exactly does the immune system weaken with age?

texts: Why does the immune system become weaker with age in humans and in some other mammals?  Let's try to be more specific than just "everything degrades with age."


texts: Within and Between Allelic Class Diversity

texts:
I am reading Charlesworth et al. 1997. They talk about diversity within and between allelic classes.

Nucleotide diversities ($π$) at each neutral site were estimated from the mean of $2 \sum z_t (1-z_t)$, over replicated introductions at the site of single variants, where zt is the frequency of the neutral variant at time t, and summation is over all times until either fixation or loss occurs.
The total genetic diversity at the neutral sites ($π_T$) was also decomposed into that within and between allelic classes at the polymorphic locus. Diversity within allelic classes, which will be written here as $π_A$, was estimated from the mean of $2 \sum \left( x_t(1-x_t)+y_t)(1-y_t) \right)$ where $x_t$ and $y_t$ are the frequencies of the neutral variant within the first and second allelic classes, respectively. Diversity between allelic classes with respect to the polymorphic locus was calculated as the difference between the total diversity values and $π_A$

Note that the parentheses don't match up but this this is what is written in the paper!
Why am I confused about this text?
I am confused about the term allelic class. I first think there is anything fancy in here and I think we can simply replace the term "allelic class" by "allele". but then when I saw the equation for $\pi_A$ I realize that the frequency of the two allelic classes does not necessarily adds to 1 (even though we consider only two allelic classes).
I also got also a little confused about the difference between $\pi$ and $\pi_T$ but I think that they just used two notations for the same think ($\pi = \pi_T$)
In population genetics's jargon, diversity just mean expected heterozygosity. $\pi_T$ makes sense to me. It is just the average heterozygosity $\left(2 z(1-z)\right)$ calculated over all time steps. Maybe a more intuitive to put it would to integrate rather than summing over time rather than time steps.
Question
I can read the equation for $\pi_A$ but I fail to get any intuition behind what it means. For example, I have no idea why it should be called within-allelic class diversity. Where does $2(x(1-x)+y)(1-y)$ come from? My whole issue might boil down to the definition of allelic class.
EDIT
The term allelic class is defined in Innan and Tajima (1997)

Suppose that there are two nucleotides, say A and T, in a particular site. Then, we can divide DNA sequences into two classes: one class includes sequences with A and the other includes sequences with T in this site. We call such a class an allelic class

(Slatkin 1996 might help as well).
I am still not quite sure what the within allelic class variance. Maybe it is: Take the most common sequence in the considered allelic class. For each, sequence, calculate the number of pairwise differences to the most common sequence and square this value. Sum over all sequence and divide by the number of sequences. In math form it would be: $\frac{1}{2N}\sum_i^{2N} (D_i)^2$, where $N$ is the population size and $D_i$ is the number of pairwise difference between the sequence $i$ and the most common sequence in the considered allelic class. Does it sound right to you?


texts:
A virus spreads around and usually attaches itself to the host, multiplies & causes diseases. But is there something like an anti-virus? A single celled entity that does the opposite: spreads around 'kills' other viruses and/or cures diseases. Has anybody discovered something like it or is there any research group working on synthesizing one? If so any links to their publications?
Forgive me if I got my facts wrong, I am physical sciences person and know nothing about biology. :)


texts: Are humans evolving since their first appearance?

texts:
Is the evolution a very prolonged progress, or are we going to witness further evolution of the human species?

If so, in which direction? Are there any widely predicted changes for humans?


texts: Why are new vessels more permeable in microvasculature?

texts:
I know for microvasculature

  New microvasculature (arterioles, venules) are always more permeable
  as they lack pericytes.

and then I have this sentence about new blood vessels (not specific)

  New vessels contain initially only proliferative endothelium, the basement membrane has not formed yet, and pericytes are absent.

However, I think pericytes are only around microvasculature.

I think the second statement is correct for microvasculature too.

Why are new vessels more permeable in microasculature?


texts: Questions on mid-2019 Covid-19 Spread in Spain

texts:
I recently read in the news from Reuters that Covid-19 was already present in the Europe in March 2019 as reported by the study by Chavarria-Miró et al (2020). According to  Chavarria-Miró et al they found traces of SARS-CoV-2 in March 12, 2019 sewage samples from Barcelona.
I am interested in this news because I do research on effects of covid-19 pandemic and government responses to covid-19 on macreconomic indicators. In macroeconomcis we are unable to run randomized control trials but sometimes nature can create natural experiments or situations that allow for use of quasi-experimental statistical techniques, and I think I can use the situation above in such way.
Consequently, I have the following questions:

How conclusive is that  Chavarria-Miró et al study? Are there any red flags that would indicate the conclusion drawn from the study should not be taken at face value? Essentially, I am interested in knowing if the study is reliable or if there are possibly other corroborating studies.

Is the SARS-CoV-2 found in march 12 the same SARS-CoV-2 that was circulating in 2020? Or we can't tell? Or to what degree it is similar if it is possible to know (in terms of infectiveness and mortality/morbidity)? If it is not possible to answer this empirically, is it at least possible to answer it theoretically based on how similar viruses mutate? (Here I would also appreciate some references to literature/data if possible).

The reason why I ask this second question is that given how dangerous and infectious is Covid-19 considered, I am surprised that there weren't spikes in deaths in Spain. In fact, according to statistics provided by Statista the number of deaths in 2019 was highest in January and even declined after March. When the number of death is totaled across whole year 2019, and compared to years prior years in data from Statista here, again the number of deaths was comparable to 2018. I realize that just looking at a crude naïve statistics like this is not rigorous but I would expect at least some visible effect if Covid-19 was already spreading in March 2019.