texts: "Secondary refractory period" of class 1 neurons?

texts:
In Izhikevich's Dynamical Systems in Neuroscience, p. 199, one learns about a class of neurons that can be forced to fire with maximal frequency:

Injecting a constant current of appropriate size (here: 320pA) a neuron of this class can be forced to fire with maximal frequency. The frequency is determined by the refractory period of the ion channels producing the action potential.

What the picture does not show is what happens beyond the half-of-a-second that is recorded and displayed: Will the neuron continue to fire with maximal frequency forever, as long as the input current is applied? I guess eventually it gets exhausted and must pause or lower its frequency.

My questions:

General: For which injected currents can the neuron continue to fire with the corresponding frequency forever? Beyond which current $I_{critical}$ does it have to make a pause or lower the frequency?
Qualitative: Beyond $I_{critical}$, does it make a pause or does it lower its frequency? Or both?
Quantitative: If it makes a pause, when and how long is it? (This could be called its "secondary refractory period".) If it lowers its frequency, when does it start (to lower its frequency) and by which rate?


texts: Why do mitochondria have a phospholipid bilayer?

texts:
So, a thought came up and I couldn't find all that much info online, so I thought I'd ask some professionals here!
The endosymbiont theory states that: mitochondria came to be ingested by bigger prokaryotic cells about 1.8 bYa, and by chance of luck came to a mutualistic relationship.
Now, mitochondria are said to have been archaea, right? But the mitochondria in our cells have phospholipid bilayers, with ester bonds in them, like all eukaryotes, but when you look at archaea, you see that they have monolayers because of their ether bonds, with rings and all sorts of branching, which is what gives them that extremophile-acclaimed resistance.
Question is if the endosymbiont theory is so widely accepted and mitochondria are meant to be archeae, why do they not present a monolayer with ether bonds?
Thanks for your time!


texts:
In an answer to a recent question on Worldbuilding, I suggested that an organism convert $\ce{H2O}$ into $\ce{H2O2}$. I suggested a few processes that yielded the desired final result ($\ce{2H2O \rightarrow H2O2 + H2}$ and $\ce{H2O + O3 \rightarrow H2O2 + O2}$). I noted that both were mere guesses. The feasibility of it was debated because hydrogen peroxide is a rocket fuel and contains a lot of energy (I heavily modified the answer and set it on an entirely different track after another mistake was pointed out).

Could some process similar to this ever happen in an organism?


texts: How the genome assembly be done after k-mer counting?

texts:
As far I know, before assembly of a genome, all k-mers from read should be counted.

But after that, how the genome assembly be done?
Is there any other thing needed along with k-mer counts?
How the standard value of k is determined for a particular genome assembly? or is it fixed for all kind of assembly?

I just want to know the basic concept that how this actually been done. Explanation with flow char or algorithm is much more appreciated.

I went through some similar question, but those did not help me too much.


texts: How do nicks in the DNA strand affect the success of Long Range PCR?

texts:
Long Range PCR using NEB Master Mix - Hot Start Taq was working fine for me (amplicon sizes of ~10kb) but stopped working all of a sudden. Is it possible that many freeze-thaw cycles on the DNA template introduces nicks into the DNA strand that hamper the polymerase activity ? In certain cases, I am getting no amplification and in some I am getting very weak amplification. Because the integrity of the DNA should be intact over the entire length in case of long range PCR, am I right in thinking nicks in DNA will be especially detrimental if we are trying to amplify large fragments ?

The concentration of the DNA templates I used was 90-140ng/ul in a 10ul PCR reaction, DNA eluted in TE buffer after a magnetic bead method of DNA extraction.


texts:
I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites.

As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this area.

Are there any weaknesses in the ChIP-exo approach?


texts: Is it true that, prior to puberty, there are no physical differences at all between boys and girls (except for their private organs)

texts: And that even their physical appearances are exactly the same? This seems very counterintuitive and goes against many people's personal experiences and observations when they were kids. But i have comes across claims that prior to puberty, there are no differences in size, strength, speed or even physical appearance. How true is this?


texts: How are homing pigeons' "homes" changed?

texts:
Last night I was watching the David Attenborough minidocumentary on animal navigation, and it talked about the homing pigeons used in the two World Wars.

Apparently they were donated by UK pigeon fanciers for the war effort.

However, when used as war messengers, obviously they had to "home" back to HQ, not their original UK roost.

How do you "reprogram" the pigeons to use a new home? I assume that pigeon fanciers have to do this all the time if they move house?

(I couldn't find a pigeon SE site so hope this is on-topic here!)


texts: Which of the following is NOT a type of tropism?

texts:
Which of the following plant movements is NOT a tropism?

Plant stem growing toward light
Plant structure growing away from light
Plant roots growing in response to gravity
Vines coiling around tree trunks
Leaflets folding after losing turgor pressure

Please help, I am stuck!  Thank u :)


texts: What does an allele frequency of 0 mean in gnomAD v3?

texts:
There is a single nucleotide variant: 18-47394-G-A (GRCh38) with an allele count and allele frequency of 0.
As I understand it, this means that there are no alleles in the population with this variant, in which case, why is there a record of it?
Does 0 AF have any biological significance, or is this a quirk of the database?


texts: Growing Mouth Bacteria in a bowl of sugar water

texts:
I want to teach my nephew why brushing in necessary and how sugar in mouth reduced by bacteria to acid.

I plan to put sugar mixed water in bowl and take swab from his mouth and dip in bowl, and test ph using Litmus paper to show him that sugar is converted to acid.

Is it possible to grow mouth acid making bacteria in this solution and will it change pH enough to show in litmus paper?


texts: All-trans-retinal being converted back to 11-cis-retinal or vitamin A

texts:
There are two pathways all-trans-retinal can take after detaching from the scotopsin: (1) it can convert back to 11-cis-retinal, or (2) it can convert to all-trans-retinol (form of vitamin A), which then converts to 11-cis-retinol and then 11-cis-retinal. My question is what factors determine which pathway will occur?

The first sounds like it doesn’t involve vitamin A at all and just recycles the retinal. Hence it wouldn’t be affected by any vitamin A deficiency, yet we know vitamin A deficiency affects the stock of retinal in the eye. Yet I don’t see any disadvantages in simply recycling our retinal; why would we go through the process of converting it to vitamin A and then back to 11-cis-retinal?


texts: How difficult is it for wild birds to find food?

texts: This question came to my mind when I was wondering if my parrots would have it better on the outside than with me. Also, is starvation a significant cause of death at different stages in a bird's life cycle? Obviously, this is an open ended question due to the many species and different habitats, but I wanted to know what the answer is in general.


texts: How can I predict DNA binding affinities from a protein sequence?

texts: Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?


texts: My niece found some caterpillars that we can't identify. Anyone know what these are? They were found in Massachusetts. The look kind of like Luna Moth caterpillars to me, but I'm not sure.


texts: Fibrinous inflammation, exudate and scarring in monotonous movements and ageing

texts:
I have palpated many hard organs during my work and studies.
I have seen many young and old people who have hard organs, like very hard shoulder - very common.
I have interviewed some of them, some points

only one type of weight lifting
no running
no stretching
no stretching before training
no stretching after training
not age dependent only - very old can be healthy
dynamical movement dependent

There are two mechanisms of fibrinous inflammation

trigger the release of fibrinogen
trigger release of fibrinogen-to-fibrin reaction

which both result in the production fibrin in the interstitium:

The area may also be mixed with serous so two variations of fibrinous inflammation

serofibrinous
fibrinous.

I am interested in the mechanism that leads to this hard tissue throughout the organ.
This raised to me an idea about Fibrinous inflammation in the shoulder.
Robbins say that if the exudate cannot be sucked out, it leads to scarring.
I think this is what is making the organ feel hard.

What is the pathogenesis in such monotonous movements without stretching?


texts: How many samples to run an association study on B-Cell receptors

texts:
We are trying to find biomarkers on the B-Cell receptor VDJ regions. To do this we plan to run Single cell RNA-Seq (using the solution from 10x genomics https://www.10xgenomics.com/solutions/vdj/)  to get the transcripts, then assembling these using VDJ Puzzle: https://www.biorxiv.org/content/early/2017/08/26/181156

The output will be a list of about 100k base pairs per patient per cell sequenced. I will then have clinical information ... how can I compute the number of patients needed to establish a statistically significant association between SNPs and clinical outcomes / disease state?

Furthermore how many cells would we need to sequence per patient?


texts: Number of autoregulation and FFL motifs in a network

texts:
Suppose we have a network with N* nodes (N* is the number of internal nodes). Every directed link in this network exists with probability p. What would be the number of:

motifs that are auto-regulatory?
feed-forward loop motifs
feed-back loop motifs


texts: Blue light in a fridge. Is it really beneficial or just marketing?

texts:
Recently while visiting a shop with electronics I saw a fridge with a huge advertisment sticker going more or less like this:

  There's blue light source in this fridge so there will be less bacteria inside and your fruits will have larger quantities of vitamins.

Can it be true? How can dead (picked, transported and refrigerated) fruit produce more vitamins? How does blue light affect this?

Furthermore I thought that only UV light kills bacteria.

Therefore my question is: how much truth was on that sticker?


texts: Why does inbreed produce a higher percentage of abnormal babies?

texts: The babies of close (say, brother and sister, or cousin and niece) family members have a higher chance of being born with an abnormality than babies from non-family related men and women. Why?


texts: Europeans succumbing to diseases they introduced to native Americans

texts:
I am reading a non-fiction account of Spanish first contact with native Americans. The Spaniards were shipwrecked, undernourished, malnourished, and dehydrated upon their arrival. Over 75% of them died within a few months. The author writes that after their numbers were thusly reduced, the natives who they were staying with then began to die of "a sickness of the stomach." The natives blamed the Spaniards for killing them.

I am assuming that the illness the natives contracted was introduced by the Spaniards, and that it was one of the ones for which the Europeans had developed a certain level of immunity, meaning that in effect, the natives were correct that the Spaniards were killing them.

The author does not ever specifically say whether any of the Spaniards contracted this fatal stomach illness, so it is possible that all of the Spaniards who died, did so from other causes, such as malnutrition. I am basically trying to find out how likely that is.

My questions are, would the Spaniards' immunity from whatever disease this was help them in the presence of an epidemic such as this, or did their immunity only keep them from contracting it when it was in its latent form? Did their weakened and malnourished state make them more susceptible to a contracting a disease they were carrying, yet were previously immune to?

To put it another way, I'm trying to find out whether it is possible for there to have been a "feedback loop" of some sort when it came to European-introduced diseases.


texts: Why are many skin depigmenting agents toxic to the body?

texts:
Coming from a developing country, I know many people who regularly use these creams to lighten their skin and some of them have developed liver and kidney problems as a result.
I know that many contain hydroquinone which is said to cause cancer and mercury which can cause neurological issues. Are these the two main problematic skin lightening ingredients or are there any else?


texts: How to approach identifying Melampsora species?

texts:
I'd like to figure out which species of Melampsora that is growing on this European aspen. What would be the right approach? Would a microscope or other tool help? Is there even more than a single species that attacks aspen?
These photos were taken of an aspen leaf in Stockholm.


texts: Material recommendation: molecular biology for mathematicians and computer scientists

texts:
I am wondering if there are some introductory learning resources on molecular biology designed specifically for scientists with heavily math-oriented curricula (math/physics/computer science).

They should be capable of conveying the main ideas in a concise way; if they could represent some concepts in a mathematical language, that would be a big plus.

Additional details

As it was pointed out in the comment, molecular biology is a very broad field so I should be more specific - although it is difficult for me. Personally, I would like to acquire some basic knowledge to interpret NGS data and go in the direction of system biology.


texts: Why does the sandalwood tree produce a fragrant oil?

texts: Why do sandal trees produce fragrant oil? Is there any purpose for it? Is it to make it unpalatable for other herbivorous animals? If so, why do humans find the fragrance pleasing?


texts: Why is it (allegedly) dangerous to feed ducks with breadcrumbs and pieces of bread?

texts:
I used to go down to the local lake all the time with leftover bread and throw little pieces of it to the hungry duckies, who very eagerly fetched it and ate it while happily quacking away.
I thought I was doing them a favour, but apparently, it's bad for them? Can even kill them?
Is this really true, or is this a false rumor spread by people who don't like ducks and want to deprive them of their favourite food?
Why exactly would bread, especially soaked in water, somehow damage wild ducks? Isn't it a very neutral food which feels filling and nice for the ducks? Nobody says that they have to only eat bread thrown from humans -- they can still eat little insects and algae in the lake or whatever they normally/naturally eat.
What exactly can happen? I never noticed any dead ducks or ducks in pain whenever I visited them. They seemed to love the bread and consider it a luxury dish from a fine restaurant from their perspective.


texts: How does blood react to heat when inside the body

texts:
I was wondering:

What are the possible dangers of being burned on the surface of the skin.
Does it congeal (that's what my intuition tells me)? At which temperature would that happen? How heat-conductive is human flesh?

On the other hand, there's of course been many cases of severely burned people who did obviously not die afterwards.

This question comes from an argument i had the other day, when a friend burned himself by accident and we got into talking about what was actually happening with the affected blood (i.e. at the wrists, neck etc) and if it is dangerous (if you could actually die from an occasion where you burned yourself and then get a stroke or something)


texts: My question is about why aquatic plants have roots. At first they seem a bit superfluous to me because leaves of the plants could just absorb nutrients directly from the water thereby skipping a need for root function that land plants have to pull nutrients from the soil. I then wonder if nutrient trafficking is the reason for the root system as diffusion may not occur efficiently through thick leaves.


texts: Basically this tiny bug plopped on top of my laptop keyboard. And as much as I disdained bugs, this one didn't look like anything I've ever seen. It had something that resembled bits of a dandelion on its back, and its body seemed like half a moth/ whatever insect. After closer inspection, I thought it was just a dying moth, the thing on its back being clipped wings and its body cut in half... but when i tried to shove it off the keyboard with my pen, it jumped about a hundred times its width onto my wall - instantly. Tried to get a second picture but it jumped again/disappeared... no idea where it went, or what it was... Here's the picture I took, and a quick sketch of what it looked like.


texts: PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

texts:
I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors.  I do this by predicting the location of Hydrogens on residues and then calculating how far these Hydrogens are from aromatic rings.  If a certain Hydrogen is <7.0 Angstroms from a certain aromatic ring, then I take it under consideration: I form the N-H vector, which is the vector created by the Hydrogen under question and the Nitrogen in the backbone of the residue that the Hydrogen belongs to.  I test that this N-H vector is pointing toward the plane of the aromatic ring, and I also test that the point of intersection between the plane of the aromatic and the N-H vector is within 6 Angstroms of the center of the aromatic ring.

If all of these conditions are met, then I consider it a Hydrogen bond between the Hydrogen and the aromatic ring.  However, my data must be incorrect, because I am seeing situations where a Hydrogen is < 1.0 Angstrom from the plane of the aromatic.  Atoms should not be getting that close to each other.

I thoroughly tested my method by hand using an example situation where my code identified one of the sidechain Hydrogens on an ASN is 0.3 Angstroms from the plane of the aromatic of a TRP.  Unfortunately, I could not find any bugs.  You can find a PDF of this verification here.

Any suggestions on how my method might be flawed would be greatly appreciated.


texts: How do you compare unpaired biological replicates?

texts:
I have done proteomics and I have obtained genes with ratios. As an small example you can see my data below

Gene    Control1     Control2   Control3    Treated1    Treated2    Treated3
pps-1   324680000   211350000   356350000   269770000   258080000   292830000
R11A8.7 477490000   610780000   539550000   533590000   530810000   578290000
ugt-21  105080000   103430000   74137000    78915000    42381000    31415000
spp-18  1042800000  615030000   332720000   538340000   448280000   412310000

Now My question is that I have Three controls and Three Treated, Control has two biological replicate and Treated has two biological replicate

I am trying to find the pathways which the list of my genes activate it. I use IPA which is a tool for pathway analysis

How can I calculate the fold change for it? If I use the 6 values, IPA will give me 6 different results and then interpretation will lead me to hell.

I appreciate any help.


texts: What does static electricity generated by plastic combs do to our hair?

texts:
It is said that wooden combs should be preferred to comb hair as compared to plastic combs. Reason is that plastic combs generate static electricity.

Question: What does static electricity do to our hair that it is said that we should use wooden combs to prevent that electricity generation?

Is it bad for hair? Does it get generated always when we comb hair?


texts: Does red light preserve your night vision?

texts: A number of companies have started marketing LED lamps that can be switched to a red mode. The claim is that red light is less harmful to one's night vision. Given that our eyes are less sensitive to red light, though, I'm not convinced that that red light is any better than dim white light. So if "equivalent" luminosity is defined where it's equally easy to, say, read a book in both light types, is there some physiological reason that red light is better than the equivalent white light?


texts: Melatonin regulates the wake-sleep cycle by causing drowsiness and lowering body temperature, but which specific chemical pathways lead to this drowsiness?


texts: Why are particular laser-related skin products not recommended for darker skin tones?

texts:
This is about products such as:

The "Theradome" laser helmet (this claims to stimulate hair growth through lasers)

  Theradome™, a biomedical engineering company based in the Silicon Valley, is the proud designer, developer and manufacturer of the Theradome™ LH80 PRO, the first and most powerful FDA cleared OTC wearable laser hair helmet for laser hair growth treatment. At last, millions of people suffering hair loss can enjoy clinically effective laser hair restoration treatments at home, at an affordable price, with a simple push of a button.

Silk'n Flash&Go Hair Removal Device (claims to remove hair using lasers)

  Silk'n Flash&Go™ is a revolutionary light-based system for permanent results at home. Now you can remove unwanted hair forever on your body and face – all with gentle pulses of light that disable hair growth. It's the safe way to get smooth, beautiful skin.

From the information on the website, it would appear that the products are safe for all; however, both products seem to be not recommended for the two darkest skin colors on the Fitzpatrick Skin Tone Classification Scale on a variety of different product feedback websites. What is the reasoning behind this?


texts:
In some cases two species can hybridize. For example, Tigers and lions can hybridize to produce "Ligers".

Would it also be possible for humans and chimpanzees (or any other species) to hybridize ?
If not, what would be the likely cause of failure?

Why do some hybridization matings produce offspring, like the Liger, and some not? What mechanisms prevent hybridizations?


texts: What is the name of these snakes? I saw them in the street and I don't know if they are dangerous for people? Photo is taken near to Tbilisi, Georgia.


texts:
Why does Familial Hypercholesterolemia shows autosomal dominant pattern?

Let us take that there is mutation in LDL receptor gene, it is said that:

  The LDL receptor gene is located on the short arm of chromosome 19 (19p13.1-13.3).[6] It comprises 18 exons and spans 45 kb, and the protein gene product contains 839 amino acids in mature form. A single abnormal copy (heterozygote) of FH causes cardiovascular disease by the age of 50 in about 40% of cases.

Shouldn't the expression of the other normal allele mask the effect of abnormal allele by producing the receptor protein?

So, why does this disease show dominant pattern?

Is there anything extra?

Source: https://en.wikipedia.org/wiki/Familial_hypercholesterolemia


texts: What limits the size of fish compared to marine mammals?

texts:
The largest extant fish species is the whale shark (Rhincodon typus). With a length of 13 meters and a mass of about 20-30 metric tons, the whale shark is relatively small compared to the largest mammals, blue whales (Balaenoptera musculus, 180 tons) and fin whales (Balaenoptera physalus, 120 tons).

Is there a physical, physiological, or anatomical explanation why fish never reached the size of marine mammals?

Bigger isn't necessarily better, but I was wondering if there is a simple explanation why fish species are so much smaller than marine mammals.


texts: Which point mutations in proteins are OK, and which cause significant change?

texts: I heard that some point mutations in proteins are OK, like from alanine to glycine (I'm not sure, it's just an example), some will change the protein significantly. I want to understand deeper but don't know the right keyword. I have tried some but none of them works. Can you give me a good keyword to start searching? Thank you.


texts: How to correlate survival probability to gene expression profile?

texts:
I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how exactly is the clinical data and the gene expression data merged?

For example, I have a matrix of clinical data (m by n) where there are m patients and n columns related to followup days, death days etc. I also have an gene expression data (m by t) where m is the number of patients and t is the genes. I first find the survival probability using Kaplan Meier method and plot it. Now how do I related the survival probability to the expression data?


texts: What are these little creatures living inside a silk web?

texts:
They are found in Bangladesh. Some of my observations:

They are so small that their legs and appendages look transparent.
Their colour is brown and they have no wings.
My eye sight is not brilliant, but the don't look like spiders. Their head and mouthpart vaguely resemble that of the termite. When I tried to observe them closely, they looked bed-bug-shaped.
They are fragile: when I tried to grab them by pinching, they just squashed.
They seem like living in a big city made of silk strands. The can easily move in, out and within the structure which slightly bigger, potential predators could not.

Unfortunately my mobile camera is not good enough to capture a clear image of them. Click images for larger version.


texts: Is heat released during work due to ATP breakdown or a increased blood flow?

texts: Is heating up of a body during work or exercise an effect of increased speed of blood or is it because of the extra energy released while harvesting energy from the ATP


texts: What happens to female mosquitoes which want to lay egg but couldn't find mammal host for blood, will that mosquito simply die, if no mammals in area would mosquitoes will be absent too?


texts: Do bacteria exist which live exclusively on non-organic matter?

texts:
Are there bacteria which consume exclusively non-organic matter? Meaning that they do not require organic matter from other organisms to stay alive and reproduce? A completely pacifistic bacterium.

Or phrased differently, are there bacteria which can stay alive and reproduce indefinitely with only non-organic matter present (plus sunlight or thermal vents etc.)?

I'm asking specifically, to name one or more bacteria species which can do this.


texts: Are natural daylight lamps for Seasonal Affective Disorder just about the color temperature?

texts: I've seen many expensive lamps made for people who have Seasonal Affective Disorder (SAD) and/or who live in regions where there isn't much daylight during the winter. I'm wondering if the benefit of these lamps is simply the color temperature (typically advertised at 6000K or more), or if there are other aspects of these lights that are meant to be theraputic? Some of these lights are also advertised as "ion therapy lamps".


texts: I found this bug in southern Florida in February. It was approximately 1cm long or less, fully extended.  What type of bug is this?


texts: Can a plastic degrading bacteria project be recreated in a school lab environment?

texts: I am looking for a science fair project and am wondering if this could be a good idea. I am in the 10th grade. I am not exactly sure of the materials needed since this is just the beginning stages of finding a project. From what I've researched, the main objective would be to isolate bacteria from soils, to test these isolates for ability to degrade different types of plastic and to identify these microbes. We have until December 14 to finish experimentation and would have help from a lab technician. Do you know if this type of project would be possible and what we should inform our lab technician with in order to help us? Please reply asap as we don't have much time left to find a project. Anything helps. Thanks!


texts: Are there animal species where some females have greater amounts of male-associated qualities than average males?

texts:
In the human species, some women ( a meaningful, though not large percentage) are taller and stronger than the average man.

Is a similar thing true in the animal kingdom? Are there some meaningful percentage of hens that would make better fighters than the average (game) cock? Cows that would be better at pulling plows than the average bull? Lionesses that could beat the average lion in a stand-up fight?

The point of the question is are there overlapping "bell curves" of size, strength, etc. so that "strong" females, while a clear minority, are nothing freakish. Or is it true in most (mammal) species that male strength is "off the charts" compared to female strength, except for "freaks."


texts: How does Halosulfuron-methyl kill nutsedge, while leaving lawn grass and most weeds undamaged?

texts:
I use Halosulfuron-methyl to control yellow and purple nutsedge in lawns. This chemical acts by interfering with the acetolactate synthase enzyme, which quickly slows cell division, and growth at all points.

How does this work without also interfering with enzymes in the lawn grass?


texts: Can two arms-racing species be stabilized?

texts:
I am trying to build an evolution simulator in which there is group A and group B, each group has 9 members each generation. Each generation, each member of group A will enter a competition (in the form of combat) with a random member of group B, and fitness will be calculated based on how quickly and with how little losses will one member's army destroy the other. The best few members of each group then becomes the parents of the next generation.

(Note that an "individual" of each group is in fact a genetically determine neural network that controls a swarm of robots, think of it as a swarm of ants sharing the same DNA and thus can be effective consider one individual)

Will this end up with both group A and B having phenotype/strategy that do not change very much over many generations, or will it result in strategies that gradually changes throughout generation, with each successful, significant change out-smarting the opponent's old strategy until the opponent develop a counter strategy?


texts: Is every decision we make already "pre-programmed" because of DNA?

texts:
DNA has information about our cells and how every cell should act.

Since I am made entirely of cells, including things that make my mind, aren't decisions coded for by DNA by proxy of our cells.

Even asking this question is a decision that has already been made because that's what my DNA told my cells to do?


texts: What makes cows stop being able to produce milk?

texts: I'm writing a paper about cows and want to discuss why they stop producing milk. Is there a disease that causes them to stop producing milk?


texts: Can genetically engineering the DNA of a human zygote, make it a twin of another human in entirety?

texts: My question is simple. If I wanted to make an exact twin of an individual, will genetically engineering the DNA of the zygote to match with the individual suffice?


texts: How do animals learns seductional behaviour?

texts: I was curious how the gender behaviour, the male role or female role, is known in mammals. Do mammals instinctively know how to do seduce the opposed sex or do the animals learn it from their parents/companion of the same sex (e.g. by imprinting)?


texts:
I have a list of mouse genes, but all our analysis happens for human genes. Is that possible to translate these mouse genes to human genes? and is there any tool that can help me on this?

I am mostly a computer science guy, I am not sure this is even possible. However, according to someone, this could happen, I don't expect a full conversion though.

Thanks.


texts: When can I assume individuals marrying into a pedigree are non-carriers?

texts: If I'm not told that they're non carriers, and if I don't have proof of their geneotype based off of progeny, when can I assume they're non carriers for a trait?


texts: Is Sugar a stimulatant or a weak sedative?

texts:
Quite often, I have heard the remark that children become hyperactive when high amounts of sugar are consumed.

But common websites suggest that sugar is a sedative, and the hyperactivity in children is more likely caused by 'artificial dyes and preservatives'. (http://curezone.com/forums/am.asp?i=1444631)

So, is Sugar a stimulant (for adults and children) or is it a sedative? Is there any conclusive research to validate this theory?


texts:
I'm looking for a book that provides a good overview of primatology, one aimed more at researchers rather than a popular science book. Ideally, I'd like something with an ethology/ecology angle with an eye towards phylogeny.

My preference would be for an e-book.


texts:
Background
I am looking into enterotyping the gut microbiome data, obtained by shotgun sequencing. This essentially means performing the Principal Coordinates Analysis (PCoA) of the beta-diversity matrix (distance matrix), based on the abundance table of species/gene-counts for all possible species/genes in all samples: for sample $i$ the counts of species/genes are $\mathbf{x}_i=(x_{i1}, x_{i2},...,x_{im})$. Such a table necessarily contains many zeros, whenever a species/gene is not present in a sample. Some of the possible beta-diversity measures are listed in table 1 of this article.
Problem
Statisticallys peaking, such data are considered to be an example of compositional data, i.e., the meaningful information is contained only in the ratios of the counts, which makes log-based distances the most suitable ones. These are used in many statistical methods (see, e.g., here). However, the log-transofmation is meaningful only when all the entries in the count table are strictly positive $x_{ik}>0$. One thus faces a problem of dealing with zero entries.
Possible solutions

Using metrics not sensitive to zero entries (excluding alr, ilr and other similar log-transformations, highly recommended by statisticians - this limits the choice of statistical methods)
Imputation of zeros: this requires a principled/biologically-sound way of imputing the zeros, since the results may be potentially very sensitive to this choice.

Question
What are the commongly used imputation methods? What is their advantages/disadvantages and justification for their use?
Some references

Here is a statisticians' view on imputation in compositional data: the methodology may get rather involved, but does not have any specific biological basis.


texts: There aren't any animals like hornets that hunt large prey (like a rabbit, or even up to a deer), right? Why not?

texts:
There aren't any eusocial animals (hives of wasps, ants, termites, etc) that hunt large prey, are there?

I'm thinking prey in the size range of, say, a rabbit, or even a deer.

I can't see a rabbit or a deer having any real effective way to defend against a swarm of hornets, especially if you supposed that the hornets' venom could easily be adapted to be particularly effective against such prey.

Intuitively, this seems like it would be a lucrative little niche.

Like:

A swarm could bring down a kill without risking losing too many members.
The return seems like it could be very high.
There shouldn't be too much of a risk of losing much of the kill to scavengers or whatever.
And after starting down the evolutionary pathway into such a niche, they could easily develop methods of preserving meat (I'm imagining a horrifying hive full of natural ham, here).
Protecting this ham-hive wouldn't be any more difficult than protecting a honey-hive from bears etc.

And such a niche doesn't seem that evolutionarily distant from where hornets already are.

Like:

They already do seriously hurt or even kill large animals that they perceive as threatening their hive.
They already do scavenge large animals they find dead, and even steal the occasional chunk of flesh from living animals.

But as far as I know, nothing like this exists, right?

Why not?

(And, like... maybe the most important question: How can we make sure it never comes into existence?)


texts: CML (Chronic Myeloid Leukemia) and blast cell percentage

texts:
I'm trying to understand the oncogenesis of CML. I have a question about CFC cells and blast cells. Are those the same? I know that in the chronic phase of CML there is a blast percentage of 1-10% of blast cells in the blood. Considering that the total amount of WBC is around 1x10–11 cells/l. That means the blast cells should be around the same order of magnitude. Looking on research articles I found that the amount of CFC (which contains according to my understanding all of the blast cells) are only 1x10–8 cells/l. Thus comprising around 0.1% of the blood count.
What cells can be considered as blasts? Only the myeloblasts? Are all blast cells CFC cells?
I also know that the average value of CFC cells in the bone marrow is around 10–5 cells, so how can they be 10–9 cells?
Reference:
https://pubmed.ncbi.nlm.nih.gov/9922073/


texts: What does "This variant falls on 11 transcripts in 3 genes" mean in the output from GnomAD?

texts:
The gnomAD browser provides information on variants of genes (in this link, for the SAMD11 gene.)   The report on a particular variant, like this one,  includes the information in the header that says (for example): "This variant falls on 5 transcripts in 2 genes."

What does this mean? In particular, how can a variant occur on more than one gene? Isn't such a variant a variant of a particular gene -- SAMD11 in this case?


texts: What is the name/type/species of this spider?

texts: Below are images of it, specimen found in the western region of the Pacific Northwest - North America.


texts:
I recently found this in Rincon Puerto Rico on the beach.

I assumed it was a baby sea turtle shell or some kind of turtle. Someone that frequents Puerto Rico said it was not. Does anybody know what this is?


texts: I came across a black cicada in northwest Missouri last week (May 2015). I am only familiar with brown cicadas. What makes this black one different? Is it a different species, or do the brown cicadas change color at some point in adulthood?


texts:
What is this lizard?

Seen in Hollywood, Florida, on a golf course. It may have been an escaped pet and was approximately 17" long.


texts: Why would taking antibiotics increase stamina and energy?

texts:
I often hear that people who are taking antibiotics experience wild fluctuations between feeling full of energy and completely alert but soon after feeling impossibly fatigued and sick.

Does this have anything to do with the antibiotics being used by the body as anything? For example as a hormone or as a source of nutrition?  Is this this a reported side effect when used for other infections?


texts: Is it possible to get infected with HIV from old blood?

texts: Let's say that someone uses a needle which has some old blood infected with HIV. In this case, is it possible for them to get infected with HIV?


texts: What makes a protein structure discernible?

texts: In Lehninger's Principles of Biochemistry, Pg. 116 states that "parts of proteins lack discernable structure." What exactly makes this protein not readable? Is it the complexity of the shape that makes it difficult for scientists to understand the structure?


texts: How does an inhibitory synapse communicate to the cell body of a neuron?

texts:
I picture a neuron as having multiple trees of dendrites attached to the cell body with a single axon leaving the cell body.  I believe the cell body near the axon root makes the decision to fire or not fire an action potential.

If the neuron has both excitatory and inhibitory synapses in the dendrite trees, how do these communicate to the cell body?
Does something like an action potential get transmitted down the dendritic trees to the cell body?
What is the difference between the excitatory and inhibitory signals that are transmitted?


texts:
Contrary to all of the textbook images of mitochondria that I have seen over the years, I had just learned that the mitochondria within a cell form a dynamic branching network along microtubule scaffolding by fusing with each other.

Why would they need to fuse together?

When they fuse, would this involve only the outer mitochondrial membrane?

Would it not behoove a mitochondrion to remain distinct from others both physically and genetically?


texts: Where I can find information about the study of animal vision?

texts: I read a lot of articles on the internet about how dog see the the world. But I can't find the source of these study. I want to know how did scientist setup the experiment to find out animal vision. I don't know which keyword should I use to search for the information on the internet. Can anybody please send me some research paper about the problem?


texts: Expected number of SNPs in a sample of size `k`

texts:
Consider a Wright-Fisher population of constant size N. We sample k haplotypes in this population. What is the expected number of SNPs?
I think the answer should be in Watterson (1975) but it looks like my institution does not pay for access to this journal.


texts: What to call a trait that has current utility but unclear evolutionary origin?

texts:
I'm looking for a commonly used term to describe a trait that has clear current utility but an evolutionary origin that is uncertain and that we do not necessarily wish to emphasize in our description (e.g. to avoid unnecessary speculation):

Adaptation emphasizes an origin driven by natural selection.
Exaptation emphasizes an origin driven by co-option.
"Aptation" fits the bill, but it seems cryptic and rarely used.

Thank you for your help.


texts: Why do cells have an average 'life span'

texts: I've heard of Henrietta Lacks. As a result of a genetic mutation, her cells never died. I've heard/read that overtime, our cells stop multiplying as much, (as an effect of aging). Why? Why do we age? Why do cells eventually die? What causes our bodies to degenerate? It is encoded for in our genes? If we treated our bodies in the highest regard, accounted for accurate diet and sleep, with the introduction of genetic engineering, could everlasting life be possible?


texts: Noticed two grasshoppers jumping together on the porch, and started wondering if they are monogamous? I am aware they have males and females.


texts: Do lysosomes play any role in cell division?

texts:
My biology textbook includes a point that lysosomes stimulates cell division without further elaborating. But studying it, I felt eerie about this function of lysosome. Then, I checked on the internet; found nothing relating cell division to lysosomes.

Maybe, autophagy of lysosomes can play a role in this regard. Killing cells and thus 'stimulating' cell division. But this reasoning doesn't seem plausible as autophagy doesn't occur without extreme conditions.

Nothing else is coming into my mind.

So, is this point included in my book wrong or right?


texts: Can some one give a simple explanation or definition on what a dye-reduction test is.


texts:
I found this small creature in my water bucket which i filled from my water tank. I would like to know what kind of creature I have found here.

Features which ought to help for identification:

Size = 1 cm
2.Transparent or semi Transparent
4 thread like legs
6 tentacles
2 black dots possibly eyes
It can swim
Triangular tail (Fish Like)
Found in Karachi City, Pakistan.


texts: I've searched the internet for several minutes and I've looked at DAT but I'm having trouble finding the DAT binding location. Where (and to which aa) does dopamine and cocaine bind to hDAT1?


texts: I can understand that trees produce oxygen in daylight but why is the area with vegetation much cooler than the environment's temperature?


texts: Are progenies factually half-clones of the parents?

texts:
Given that a "clone" (if anything, in the context of human cloning) is taken to be, as far as I have understood, a specimen possessing the same genome as his "father/mother", aren't all "non-cloned" organisms born out of inter-individual, heterosexual reproduction (i.e. "standard" sons and daughters), effectively "half-clones", under that same definition?*

Are "normal" sons and daughters "half-clones", as a matter of fact?


texts: What would sanitiser fail to do that detergent and warm water would do in cleaning glasses frame that isn't 'visibly soiled'?

texts:
Update (from comment):

It's certainly possible that the manufacturer had that in mind when making their cleaning recommendation, but I'd like to think they would specifically warn against it if it was a common issue.

For an arbitrary glasses frame, specifically the earsocks, can regular alcohol/sanitiser replace detergent and warm water? Apparently some brands of glasses frames recommend really detergent and warm water. I mean, with alcohol and sanitiser, am I perhaps killing only 99% of the germs instead of 99.9% of the germs? (If we wanted planes to be safe "with statistical significance" that is 99% confidence level we'd have between 400 and 2500 crashes a day.)
I couldn't find any videos for this on youtube. Most of what youtube gives is cleaning ears or cleaning the lenses.
Edited to add: I got the following with my new glasses.

Kind of a hassle to do the recommendation especially that I've never cleaned glasses frames in my 13 years of wearing of glasses, except when they were, to borrow a term from WHO, 'visibly soiled':

Clean your hands by rubbing them
with an alcohol-based formulation,
as the preferred mean for routine
hygienic hand antisepsis if hands
are not visibly soiled. It is faster,
more effective, and better tolerated
by your hands than washing with
soap and water.

• Wash your hands with soap and water
when hands are visibly dirty or visibly
soiled with blood or other body fluids
or after using the toilet.

Alcohol is a substitute for soap and water for hands that are not 'visibly soiled'. Is there perhaps some kind of substitute for glasses frame?


texts: Beyond anabolism, what are factors that restrict growth rate?

texts:
Beyond obvious constraints in the case of nutrient limitation, what can explain the relatively slow growth rate of cells in rich media?

Lab strains of E. coli grow really, really fast. The cell cycle in rich media is even faster that the genomic replication (!). But for many other organisms, that is not true. Is there anything else, beyond the lack of food / environmental signals that can act as intrinsinc barriers to the growth rate of cells, assuming that parameters like pH, temperature and oxygenation are properly chosen?

For example some cells have genomes about the same size as S. cerevisiae but divide much, much slower, why is that? Is it necessarily a sign that something in their growth medium is lacking? Maybe checkpoint kinetics (if so, can the issue be fixed by mutating cyclins, for example)?


texts: How animals maintain their body shape after development to maturity?

texts:
I've recently read a book on evolutionary-developmental biology for laymen, and it described how a fetus is progressively divided into more refined zones of genetic activity. These zones, kinda like GPS coordinates define which genes will be activated at which time and at which location.

What interests me is - after development to maturity, what defines how animals maintain their body shape? Is it the same "GPS" system that defines boundaries of an organism? Or is it something else within the specialized cells that tells them to grow in certain directions and avoid others?

To clarify the question with an example - lets take blood vessels - what prevents blood vessel lining from growing forever in all directions, taking up all available internal cavity space?


texts: Why is it $q^2$ for the individual count in hardy weinberg?

texts:
My understanding:

In Hardy-Weinberg problems the frequency of a homozygous recessive genetic occurrence in a population is $q^2$. So if 1 in 100 people in a population have albinism (homozygous recessive disorder) then we say the frequency is $q^2=1/100$.

We then say, to find the frequency of the allele count $q$ that $q=\sqrt{1/100}= 1/10$.

I don't understand why we say this. Why would the allele count be the square root of the population frequency? There's 2 alleles per person. Why isn't it x2 or /2 instead?
I suppose my problem is understand what exactly is p and q.


texts:
Whenever there are minor/major injury to blood vessels, the platelets, fibrin, thrombin, etc. are recruited. They then seal the wound and block bleeding.

What tells them that their job is done?


texts: Why do boys sweat more than girls during exercise?

texts: I noticed that boys sweat more than girls in the PE class performing same physical activity. Is there any other specific reason except muscle mass?


texts: What are evolutionary reasons for humans' limited regeneration abilities?

texts:
As far as I understand (I am not a biologist), a ability of a species arises during the evolution if:

It increases reproduction chances
It is not too energy expensive
It is physically possible

At the same time, if a human loses his/her hand/eye/tooth/almost anything, it won't regrow. However, if such regeneration was possible

It would definitely increase reproduction chances, because it would make it much easier to survive (or maybe something even more direct, like reproduction of sexual organs)
Ability to regenerate isn't supposed to require any energy until the moment such regeneration is needed (and, therefore, energy spending is justified)
It seem to be indeed physically possible, at least for some organs (Wikipedia provides examples of species who can regenerate their teeth, body parts (tails) or even lungs)

This seem to be strong reasons why this ability should have been gained during the evolution, but this didn't happen. Why?


texts: What is the genetic background for fast metabolism?

texts:
I am wondering if it is possible that people with very fast metabolism have some genetic mutation. There are people who can eat a lot while others would definitely get fat with such a diet. In other words, they seem to have very fast digestion and never feel so much full after eating but what's surprising is that they still stay very skinny?

Can it be a result of some disorder/mutation?


texts:
I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have 2 options:

BLAST my DE genes against a database with GO terms (human/mouse) to look for orthologs
Use a program that assigns GO from BLAST results, such as Blast2GO

I've been trying with Blast2GO recently, but find if very slow and generally lacking - does anyone have any experience doing GO in Xenopus or other non-model organisms?


texts: Why can't we propose a solid theory regarding origin of life?

texts: What  information is greatly lacking which does not allow us to propose a  solid theory for origin of life ?


texts: Why do apples taste sweeter at the bottom?

texts:
Sometimes when eating an apple, I notice that the bottom (blossom) end of the apple has a lot more sweetness and flavour to it, whereas the top half (stem) is often more watery, crispier and feels less dense than the bottom part.

A quick search on the internet revealed that I'm not the only one asking this question, but answers seemed to be mainly opinions. The largest discussion I stumbled upon can be found here, but comes to no satisfying conclusion.
Apparently, this phenomenon seems to occur in pears (supposedly even mentioned in a japanese saying, but the article does not provide a solution to the question) and pineapples as well.

I am looking for a more scientific explanation, as I believe that the biology of apples might be more complex than to allow a simple "sugar is denser than water and gathers at the bottom"-solution.

Do apples ripen unevenly (the blossom-end growing first, allowing it to ripen for a longer time)?

Might this phenomenon be the result of how apples meant for long-term controlled atmosphere storage are picked slightly less mature?


texts: Why do neurons have long axons but short dendrites?

texts:
Cian O'Donnell, a British neuroscientist, originally asked this question on Twitter: https://twitter.com/cian_neuro/status/1075432086692089857. I am not a biophysicist by training but I wonder whether there might be existing publications that have shed light on this question.

My primitive back-of-the-envelope analysis involves the following:

If we suppose that most neurons are limited to a volume V, give or take epsilon volume, and the function of axons is to carry a signal over a large distance whereas the function of dendrites is to integrate information from different sources then a semi-spherical radiation of dendrites should be the norm.
This becomes an extremal optimisation problem where there are specific constraints on the minimal axon thickness, the minimal dendrite thickness and an upper-bound on the average number of dendrites that fan out of a given axon.
This becomes an extremal optimisation problem where there are specific constraints on the minimal axon thickness, the minimal dendrite thickness and an upper-bound on the average number of dendrites that fan out of a given axon.

This is a very sloppy analysis which ignores biophysical constraints but I think that we have an extremal optimisation problem here.


texts: What is this? I found it under a bed sheet. I live In Mojave county, AZ, USA, in the middle of the desert. It was probably 1/8 inch long. And narrow.


texts: Most painless method for killing insects

texts:
I'm planning on having a small farm of crickets or grasshoppers.
I would like to cause them as little suffering as possible, so I'm wondering what is the most painless way to kill them?

So far, the plan is to put them into the fridge (+4C) to slowly chill them (that way they will not notice it as much), and then to freeze them in the freezer (once they are chilled and are either unconscious or barely so).

EDIT: It is important to note that I am planning on eating them.


texts: How does the immune system recognize pathogens?

texts: There are useful and pathogenic bacteria in our body. How does the immune system differentiate between them?


texts: This picture is take from my village in Gujarat, India. I think it is a small bird which I have never seen before. It is smaller than an Indian hummingbird and even smaller than a neem tree leaf. You can see the leaf and the flowers. That flower's diameter is maybe a half inch so you can see how small the bird is. This bird has a very little trunk like a butterfly. You can't see this in the picture, but I saw it. This bird sucks liquid from flowers by that trunk.


texts: Why don't the genetic similarities between ‘unrelated’ individuals of the same and different species outweigh the differences?

texts:
Ever since starting to learn about the concept of inclusive fitness during my BSc, I've been bugged by this questions: if inclusive fitness can account for many ‘altruistic’ behaviors, why don't the genetic similarities between ‘unrelated’ individuals of the same and different species outweigh the differences? In other words: when we consider (from a gene-centric perspective) that individuals are temporary vehicles for selfish genes, and if we also consider that the fitness effect of different genes should not be measured in the reproductive success of just single individual, should we not expect to see that genes that promote more broad-scale altrustic behaviour since we share most of our genetic heritage with other individuals?

I understand that my confusion arises from the fact that I fail to sufficiently distinguish between behavioral genes that influence altruism and whose distribution in the population is differentially influenced by different game strategies and genes that have no direct influence on this type of behaviour and are thus not under the same type of selection pressure. However, I cannot seem to manage to produce a clear-cut argument from this distinction.

I'm asking because, when I find myself in the position of having to explain inclusive fitness, I feel a bit awkward when I know in the back of my head that I would not be able to answer this basic question if it comes up.


texts:
Is it possible to select from colonies only cells which are at a certain stage in the cell cycle? E.g. if I was trying to analyse expression of a number of genes during different stages of the cell cycle.

I could imagine that if this is possible, the selection mechanism might target cyclins, or use an artificial gene cassette controlled by them.

So for example, a method may attach some gene to a certain cyclin which protects against a substance that otherwise destroys the cell. We could then use that substance to destroy all cells which were not in the cell cycle stage that we want to look at, wash away their nucleic acids, and then extract the mRNA from remaining cells to analyse expression levels at this particular stage in the cell cycle. If we repeat that for the different stages, we should be able to get a nice picture of what is expressed when. Does any method like this exist or is commonly used?


texts:
Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site.

This ability is harnessed as a tool in research to purify target structures in the cell (e.g. in chromatin immunoprecipitation, ChIP).

Now let’s say that I’ve identified an interesting target structure (such as a particular transcription factor) and I want to design an antibody to use in ChIP against said target. How would I go about producing such an antibody, taking into account that it should be both highly sensitive and specific?


texts:
Could someone please clarify the roles and differences between palaeontology and palaeobotany. My textbook says the palaeobotanists study plant and animal fossils, but other sources say that this is incorrect.

Thanks


texts: Extreme or just rare: evolution of complex life in extreme environments

texts:
Many environments are considered "extreme" (boiling hot springs, acidic/basic water, etc) and those tend to be dominated by Archaea instead of the "usual" mixture of bacteria along with complex plants and animals. But "extreme" is in-part in the eye of the beholder.

Very little of earth (in terms of total energy available) is at 100C or pH 0, etc. Broadly speaking, the more organisms in parallel trying out various mutations the higher the chance there is to come up with something useful. We can't expect a 1km^2 hot-spring cluster or the energy-starved layer of groundwater at the 100C geotherm (about 3km below ground) to evolve as much as a 1000000km^2 rainforest exposed to direct sunlight.

There are large extreme environments. There is plenty of energy available in deserts such as the Sahara or the open surface ocean (an iron desert) but the primary productivity is very low. This means that the environment is harsh enough to stop life from adapting "effectively". Here "effectively" means how much of the available energy is used, i.e. what fraction of the sunlight is absorbed by the plant/algae (the conversion efficiency into glucose is very low, at most 7% and often ~1%, but we are ignoring that). Note that in many cases a desert is actually more hostile to microbial life because larger organisms can store water/nutriants/etc more easily.

On the other hand, there is one example of an "extreme" environment that became widespread and in which life thrived: Oxygen. O2 forms reactive species in a wide variety of biochemistry, which makes it a pretty universal poison. But life found a way around with enzymes such as superoxide-dismutase and was able harness the high energy or these reactions.

To the best of our understanding, to what extent would life have evolved and thrived if the entire Earth's ocean were an extreme environment, such as 100C, pH 0, or 34% salinity?


texts: Differentiating Taenia solium and Taenia saginata Infections

texts:
I have been told that both are spread by pigs and cattle, respectively. I would like to know the complications caused by Taenia solium and Taenia saginata. Also elaborate how dangerous is one as compared to the other, as well as preventive measure.

I googled , and found no relative comparison between these two.

Thank you.


texts: Why is the current flow shown to be flowing from the negative area towards the positive area?

texts:
When I was studying the ECG chapter in the book "Guyton and Hall Textbook of Medical Physiology", I noticed something odd in one of the pictures:

As you can see the current is shown to be flowing from the area with a more negative potential towards the area with a more positive potential.
Also here's the part of the text that alludes to the image:

This process provides electronegativity on the insides of the ventricles and electropositivity on the outer walls of the ventricles, with electrical current flowing through the fluids surrounding the ventricles along elliptical paths, as demonstrated by the curving arrows in the figure.

How is this possible? Isn't the current supposed to flow from an area with a higher potential towards an area with a lower potential?


texts: Do transcripts always start and end with exons?

texts:
I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or downstream of these exons that remain in the nascent RNA.

Does this reflect the biology or is it just a consequence of the spliced read mapping? In other words: Do transcribed regions upstream of the first exon and downstream of the last exon exist in nascent RNA?

These regions, if they exist, cannot be called introns when those are defines as 'spliced sequences between exons'. How would one call them?


texts: Requirement of energy for metabolic processes

texts:
Sorry if this is too elementary, but can someone explain why the following reaction can occur without a net influx of energy from some other process?

  $C_6H_{12}O_6 + 6O_2 \to 6 CO_2+6H_2O$

And why does this one need an influx of energy?

  $6CO_2+6H_2O\to C_6H_{12}O_6+6O_2$


texts:
I've performed an experiment wherein I have stimulated cells (cell line) with a drug across different time-points - in its unmodified (Drug) or modified form (H-Drug or M-Drug).

All cells are seeded at the same concentration and all are harvested for analysis on the same day.

Method:

Cells were seeded on the same day. Cells were stimulated at 3:00 on a Wednesday (24 hour timepoint). Cells were then stimulated at 09:00 am on Thursday (6 hour timepoint) followed by 12:00 pm Thursday (3 hour timepoint) and so on until 3:00 pm on Thursday - at this time ALL cells were harvested and put into separate tubes according to what they were stimulated with and when e.g. 3 hour M-drug.

All tubes were analysed in sequence to measure the percentage of cells in that test tube that stained positive for that drug (i.e. as a means of measuring drug uptake)

Question:
I have measured the percentage uptake of a drug at different time-points (0.5 - 24 hours) for the three drug variants. % uptake is taken as the % of cells that stain positive for that drug

What would the correct stat test be? Would a 3-way ANOVA make sense?


texts:
I'm having a great deal of trouble understanding chromosomal walking, especially in regards to this article:

Control of male sexual behavior and sexual orientation in Drosophila by the fruitless gene.

I can get the fact that you can use recombination frequency analysis with chromosomal markers to assess the relative position of a gene, but I'm just stumped as to what it exactly it means when they say that they cloned the gene using DNA segments flanking the two insertions (fru3 and fru4) as a basis for the chromosomal walk.


texts: How to consider ions charges while calculating ions steady-state equilibrium concentration

texts:
i recently tried to find answer for following problem:

  "Assume that a membrane is permeable to Ca++ , K+ and Cl- but not to a
  large cation R+. The inside concentrations are [RCl] = 100mM and
  [CaCl2] = 200mM, and the outside concentration is [CaCl2] = 300mM. (a)
  Derive the Donnan equilibrium. (b) Find the steady-state equilibrium
  concentration for Ca++."

when i tried to write space charge neutrality equation, i encounter to a new question,
how should i consider that

a:for each Ca++ there is two Cl-

and

b:each Ca++ has 2 positive charge

in the past i only worked with the ions that had same charge or same number of molecule, for example considering we had only cl- and K+ and some large
cation R+ , this situation is simple but the above mentioned problem is totally different.


texts:
Three loci C, D and E are located on the same chromosome in this
  order. We found that the frequency of recombinants between C and D is
  10% and that between D and E it is 20%. Assuming that crossing over
  occurs randomly on the chromosome, what is the expected frequency of
  recombinants between C and E?

I know that it should be less than 30% (10%+20%) but the answer given is 26%. I don't understand how they figured that out.

Edit :

The frequency of recombination is <30% because of the chance that a crossover happens between C and D & also between D and E. The probability of that to happen is 2% (10/100 X 20/ 100)
So, why is it 26% instead of 28% ?

Another posssibility : Am I totally off the track ?


texts:
I was under the impression that the CNS is never penetrated by blood vessels, which explains why one never sees them in histological samples.

However a google search reveals I am wrong. So can someone please tell me what the purpose of Cerebrospinal fluid is?

B) Why one does not find blood vessels in histological slides?


texts: Which viruses still present today caused a deadly pandemic/epidemic in the past?

texts:
The current Covid-19 pandemic and its virus Sars-Cov-2 can be dangerous, especially for vulnerable groups like the elders. But however, I have seen studies that this virus become less dangerous in the future, when human population has built some immunity against it.
There are many other viruses still present and most of them produce only harmless diseases like the cold. But were some of such viruses really dangerous in the past and cause only mild symptoms on infected persons in present day (due to immunity)? Perhaps thousands of years they caused a bad epidemic?


texts: Adaptation by standing genetic variation and fitness variance

texts:
I've read a couple of paper on Fisher's Fundamental Theory of Natural selection that states:
$W(t+1) = W(t) + Var_{W}(t)$

Given a population with some degree of genetic variability, and assuming that no new mutations can appear, eventually the most fit strain will be fixed (discarding the effect of drift). The FFTNS allows to predict, given the mean fitness at any point and the fitness variance, the mean fitness of the population in the next generation.
However, can we predict the variance on fitness for the new population?

Given the possible complexity of the problem, the situation I'm focus have specific conditions, but I would also like to know the general answer. But in my case:

Individuals reproduce asexually
Random mating
Diploids
Expanding population with recurrent bottlenecks (we can approximate to Wrigth-Fisher population with certain effective population size)

More generally, given only the initial mean fitness and variance of the fitness can we predict the trajectory of the mean fitness during adaptation? If not, what do we need more? Number of strains present? Or only the full composition of the population allow for such prediction?

Thanks in advance


texts: How do racing pigeons know the way back to their roost?

texts:
I have read that a standard way to do pigeon racing is that the male and female are separated and the pigeon races to its mate.

My understanding that in these cases the roost is several miles away from the release point. How does the pigeon know how to find the roost?

I have heard that sometimes they will hold up the mate in the air, but at several miles away, how would that help.


texts: Is there a link between brain's energy consumption and human experience?

texts:
I was read the article (in Scientific American Mind)  about energy consumption of brain. There are:

  Say you are learning a new skill—how to juggle or speak Spanish.
  Neuroscientists have made the fascinating observation that when we do
  something completely novel, a broad range of brain areas becomes
  active. As we become more skilled at the task, however, our brain
  becomes more focused: we require only the essential brain regions and
  need increasingly less energy to perform that task. Once we have
  mastered a skill—we become fluent in Spanish—only the brain areas
  directly involved remain active. Thus, learning a new skill requires
  more brainpower than a well-practiced activity.

...

  Overall, though, on an individual level, our brain adapts and becomes
  more efficient as we gain mastery. We build new connections among
  neurons to keep pace with the greater demand on our neural resources.
  As our skill level grows in a particular area, our brain will
  inevitably require less energy to perform that task.

I tried to check what was written there. I tried to find experienced facts that refute or support this article. I did not find anything.

Question: are there experimental scientific data that show a decrease in energy consumption by the brain, while doing a certain activity, as professionalism grows? Or maybe there are experimental data that show the opposite? Or is there really no correlation between energy consumption and the growth of professionalism?


texts: Do humans learn to distinguish different senses?

texts:
Does a human being learn to differentiate between its senses at some stage in their development? Is there a time when it, for example, cannot tell if an input is a taste or a visual image?

The question came to me because food may taste different when the sense of smell is impaired, although these are two separate senses with their own receptor organs. Is it possible for other senses to be mixed up in a similar way?


texts:
How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

The book's answer is $20^{12}$.

However, I disagree. This result distinguishes the following two polypeptides even though they are exactly the same polypeptide:

(Met)x11-Glu

and

Glu-(Met)x11

Am I right? How would I otherwise answer this question? My background in probabilities is very weak.


texts: Evolution of insects, spiders and jellyfish

texts:
Well we all learned at school the classic evolutionarily theory

From:          To:
fish           amphibian
amphibian      reptile
reptile        mammal
reptile        bird

But what always interested me:
What about invertebrates?
Do they also have some evolutionary table like vertebrates or was there evolution never that interesting to begin with?
I can roughly imagine that there are giant evolutionary gaps between an insect and a jellifish but is there any common ancestor of all of them?

So my question has essentially two parts:
1. What is the common ancester between vertebrates, arthropods and molluscs
2. Is there an evolutionary Tree for the last two like for the vertebrates


texts:
I have two groups of patients : Responders to chemotherapy and non-responders to chemotherapy. I treat this as a dichotomous outcome we can call response to chemotherapy.

For a fixed set of cancer driver genes, I have calculated cancer cell fraction (ccf) for each group.

Does anyone know of any interaction or relation of response to chemotherapy and ccf?


texts: Amount of Na+ needed to be transfered in order to depolarize the membrane?

texts:
I found out that the number of $Na^+$ ions that is needed to be transfered across the membrane to make it depolarized is a small number.
In what way its proved? (Goldman equation maybe?)


texts: Looking for the closest example of life forms similar to some mathematical patterns

texts:
Caveat: this is my first question here, it is quite interdisciplinary, but I hope to be in the correct place to ask. I am a user of Mathematics Stack Exchange since some years ago, and this question is related with some questions there (here, here whose general formula is discussed here and here).

Context: I am preparing a mathematical paper regarding a new family of dynamical systems (if you are not familiar with the concept, simplifying the idea it is a mathematical formula in which starting from a initial value, once applied to the formula the resulting value is again applied to the formula, and so on, finally the values are plotted and eventually a -sometimes interesting- pattern emerges) whose attractors (plotted patterns) in the present case seem to have unexpected pareidolic properties.
Basically some of the patterns generated by these systems show similarities with some structures of invertebrate life forms, specially insects, marine jellyfish, and zooplancton and also due to the patterns of the accumulation of points, also with life forms presenting bioluminescence properties.
For each interesting pattern so far I have tried to find the closest life form example, to compare both the model and the life form patterns.
So my target is including in the paper the closest life form similar to each mathematical pattern. Initially it is just a pareidolic coincidence, but it might be interesting if the mathematical formula can resemble models of some organic structures.
These are the ones I have been able to gather, both the model and the closest life form I found.  The pictures I am using at the right side of and below the images are just for the sake of completeness (they belong to their respective owners, I do not own them, if there is any problem I will remove them, so just please let me know). The formula can be verified at the MSE links I have added at the beginning of the question and the Python code to generate them is in this link (please feel free to use it and modify it). The questions are after the examples (click to enlarge):

Patterns similar to thorax and abdomen of Bembicini wasp, head and body of Turritopsis dohrnii (inmortal jellyfish) and Tardigrade limbs:

Patters similar to Drain fly:

Patterns similar to Acherontia atropos (thorax and abdomen and main proportions of body, specially the patterns near the head are interesting):

Patterns similar to Ctenophora (down left) and Mnemiopsis_leidyi (down right):

I would like to ask the following questions:

Are there better examples of life forms for the models I am showing above (1,2,3,4)? If somebody could provide examples or specific names would be very appreciated.

Are there papers or references in the Biology field regarding mathematical models of this kind?

In the case I would like to add images from internet in the paper, I know that in the case of Wikipedia there is a standard way to add the reference in the bibliography. Apart from Wikipedia, are there other sources of images which I could use without problems in a paper (thinking about the kind of life forms that are the target of the patterns)? Thanks in advance.


texts:
I had a colleague ask me recently whether mRNAs could be sequenced directly. I found this Nature paper[1] published by Helicos in 2009, in which they describe their developments in the area. It's been several years since this was published, and yet RNAseq and most other transcriptomic analysis is still done by first reverse transcribing RNA into complementary DNA.

What is the current state of RNA sequencing? Has Helicos failed to deliver on their technology? Have any other platforms risen to the challenge (or attempted to do so)? Or is the technology successfully in production and still simply overshadowed by the wide adoption of traditional cDNA-based sequencing methods?

Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF,  Bowers J, Jarosz M, Milos PM. 2009. Direct RNA sequencing. Nature, 461, 814-818, doi:10.1038/nature08390.


texts: What is the main challenge in creating a chemical male contraceptive?

texts: More than 50 years after hormonal contraception for women was invented, a contraceptive pill for males is still not available. With the obvious major biological differences in mind, why does it appear more difficult to create a chemical contraceptive for males? What are the main challenges that must be overcome to create a viable, reliable and marketable contraceptive pill for men?


texts: Does aneuploidy include the loss of chromosome arms?

texts:
I'm wondering if the definition of aneuploidy includes loss of a chromosome arm (telosomy) or arms (ditelosomy).

I'm aware that aneuploidy normally depends on the number of discrete chromosomes (so a chromosome without an arm would be treated as one chromosome), but in the genetics course I'm taking, telosomy and ditelosomy were listed in 'types of aneuploidy'. Was this just for convenience, or does the definition include them?


texts: I read recently that humans have an innate preference for sweet-tasting foods. That seems feasible since carbohydrates are necessary for cells to undergo cellular respiration, but why then is water not similarly good-tasting? The thirst mechanism is a very long, multi-step process that ensures that humans intake a sufficient amount of water, and it can be really satisfying to drink water when you're really thirsty, but why is it flavorless if it's so vital to life?


texts: Why do new atypical antipsychotics like Zyprexa cause TD at lower rates?

texts:
When the d2 receptors are blocked for long periods of time they tend to up regulate.  This is what causes tardive dyskinesia.

Why do the newer atypical anti psychotics cause such at a lower rate?  Added tables for clarification of receptors I am referring to.

Zyprexa

D1  35–118  Antagonist
D2  3.00–106    Antagonist
D2L 31–38   Antagonist
D2S 21–52   Antagonist
D3  7.8–91  Antagonist
D4  1.6–50  Antagonist
D4.2    17–102  Antagonist
D4.4    21–60   Antagonist
D5  74–90   Antagonist

Abilify

D1  265–1,170   ND
D2  0.45–3.3    Partial agonist
D2L 0.34–0.74   Partial agonist
D3  0.8–9.7 Partial agonist
D4  44–514  Partial agonist
D5  95–2,590    ND

Haldol(typical antipsychotic)

D1 (silent antagonist) — Unknown efficiency[citation needed]
D5 (silent antagonist) — Unknown efficiency[citation needed]
D2 (inverse agonist) — 1.55 nM
D3 (inverse agonist) — 0.74 nM


texts: What does z in lac z, y in lac y and a in lac a gene stand for?

texts: In lac operon the 3 structural genes lacz, lacy and laca must have some reason behind their names. While lac refers to lactose but what does z, y and a refer to?


texts: Why don't we keep evolving until we are super-human?

texts:
Humans (homo sapiens) have been on the earth for thousands of generations, and we have kept evolving throughout that time. Why don't we just keep evolving so that, let's say, we live for an average of 300 years? Or why don't we evolve so that we don't need to sleep?

This could also apply to many other species.


texts: Electron balance for biomass synthesis: is my professor right?

texts:
I'm studying for my exam and I came across these notes written by the professor himself. He's talking about the general reaction of biomass production in a bioreactor:

$$\ce{C6H12O6 + NH4+ + O2 -> $\mathrm{C_wH_xO_yN_z}$ + CO2 + H2O + H+}
\\\text{(not balanced)}$$

At some point he proceeds to do the "reduction balance" for this reaction: he calculates the "reduction degree" of the elements (which he defines the same way I define the oxidation number) and here comes the problem.

He states the "reduction degree" of C in glucose is +4 and the one of O in O2 is -2.

Is "reduction degree" different from oxidation number? Are there any particular ways to calculate oxidation numbers when you talk about biomass?

Thank you for your help.


texts:
I have some questions regarding building microtubules:

Do alpha and beta monomers always exist as dimers when they are bonding to form tubulin?
When tubulin structure is destroyed, do alpha and beta monomers fall apart as dimers or monomers? and does it happen at the positive or negative end?


texts: There are two alleles that determine the sensitivity of a person to Coumadin (a medicine for blood thinners used to treat a stroke etc). Sometimes you encounter the terminology that one has a mutation on both alleles (father's and mother's side). But why is that called a mutation and not just a variation? Does a mutation mean that it changed during lifetime, or is the difference between mutation and variation arbitrarily defined? Or is there really a kind of standard taken where deviations are considered to be mutations?


texts:
I'm a curious person, I've never had any medical training, but I wish to know some more about aneurysms. Aneurysms are basically weakened spots in the elastic artery wall. This can eventually result in a blood-filled balloon bulging from the artery wall due to the high blood pressure in these vessels. Aneurysms can rupture and this can lead to brain damage when it occurs in the brain. Aneurysms can be detected by injecting contrast material into the bloodstream and making an X-ray (called an angiogram). Now I was reading a wikipedia article about aneurysms where I saw the following picture of an angiogram where reportedly an aneurysm should be visble:

Now, as I said, I know nothing about biology so I would really appreciate it if someone could download the picture and reupload it with the aneurysm circled.

Is it the really dark spot or the big soft spot to the right? Thanks!


texts: How many systemic reactions in inflammation?

texts:
I have this sentence in my notes

  Inflammation consists of two local reactions and one systemic reactions.

which is difficult for me to accept.
Two local reactions are vascular and cellular.
I think there are two systemic reactions too:

White blood cell response
Acute-phase response

How many systemic reactions there are in the inflammation?


texts:
In arabidopsis, 2 cell types arise in the root epidermis : root hair cells and hairless epidermal cells.

The immature epidermal cells that are in contact with 2 underlying cells of root cortex differentiate into root hair cells whereas the immature epidermal cells having contact with only one cortical cell do not develop root hair.

What is the advantage of this ?


texts: If  an arteriole leading to a capillary bed is dilated will the pressure in the vein coming out from the bed decrease ? Will the velocity of blood in the vein change ?


texts: What part, roughly, of the carbon in a plant comes from the soil? As opposed to the atmosphere?

texts:
C4 plants contain a slightly higher percentage of carbon-13 than C3 plants. Is this because of carbon obtained from the soil or the atmosphere?
I have read that plants using different chemical pathways, such as millet and wheat, incorporate distinctive proportions of stable carbon isotopes from the SOIL.
Do C4 plants need more carbon-13, or does that process just happen to result in accumulation of more carbon-13?


texts: Identification of a red arachnida (?) (picture and video)

texts:
I found this in a greenhouse in Norway. It is a few millimeters in size, I could fit 5-6 of them on my thumbnail.

It looks a lot like this one from Wikipedia https://en.wikipedia.org/wiki/Trombidiformes
Can someone help me identify it? Is it a parasite or a harmless creature?
Also a video of it moving around
https://1drv.ms/v/s!AlmW2TG6jr_7ga4eTDLz7qzKM4W_8w
Update:
I found a link description which makes me think it is a mite (same as the Wikipedia link).

One of the most common sources of confusion between ticks and mites is color. No known species of naturally occurring red tick exists. But ticks can sometimes appear to be red if they’re in the act of feeding. However, the spider mite, red velvet mite, clover mite and the larvae of the harvest mite—known colloquially as chiggers—all take various shades of red.


texts:
The major nutritional mechanisms include chemoautotrophy, heterotrophy (including parasitism and saprotrophy) and photoautotrophy. All of these modes of nutrition developed first in prokaryotic ancestors, and gradually, through the course of evolution, these prokaryotes formed complex eukaryotic, multicellular organisms. Some of these complex descendants (the majority of Kingdom Plantae) possessed the photoautotrophic mode and some (the majority of Kingdom Animalia, some of Kingdom Protista & Kingdom Fungi) possessed the heterotrophic mode.

My question is, since all the three modes developed quite early in evolutionary history, why didn't any chemoautotrophic multicellular, eukaryotic organism develop? (Or, if they did, why did they not form a wide-diverse group as the organisms with other two modes of nutrition did.)

(One possible reason could be lesser availability of chemoautotrophic substrates, but I have no proof, nor any argument to support this.)


texts: Organism and plants reduce radioactivity?

texts: I would like to ask if there are organisms or plants that could help in reducing any one of types radioactive contamination?


texts: Does suffocation pain involve nociceptors?

texts: I never suffocated myself so not entirely sure, but when you suffocate, it's painful, right? But of course different kind of pain than being injured or sick. What I'm wondering is, if the "painful" (or suffering) experience of suffocation involves the standard pain pathway mediated by nociceptors? Or is it some other kind of pain pathway due to a lack of oxygen? I don't mean psychological pain.


texts:
Can we Manufacture bio molecules say e.g. the simplest Sugar, C12,H22,O11 the way we do with any other mechanical component. So, we know all about the Structure and arrangement of Atoms in Sugar - so do the design send the commands to the manufacturing machine which will use C,H and O elements and put them in them specified order !

If it's not doable today, what's the reason? -
1. Our lack of understanding of the Structure of Sugar atoms  or
2. The specialized method which will put nascent atoms into the configuration of Sugar. Are people anywhere in the world trying to work this way? Please give references.


texts:
Are there cases where Zipf Law appears in epidemiology?

I ranked provinces of China by their coronavirus confirmed cases (2020-01-30 14:29):

  4586, 428, 311, 278, 277, 200, 165, 162, 145, 142, 129, 114, 101, 101, 78, 70, 65, 63
  ...

Then I tried fitting the Zipf Law to it. I managed to get a good fit for a segment of it by using $x_n = 1600/n$:

  4586, 428, 311, 278, 277, 200, 165, 162, 145, 142, 129, 114, 101, 101, 78, 70, 65, 63 ...

  1600, 800, 533, 400, 320, 266, 229, 200, 178, 160, 146, 133, 123, 114, 107, 100, 94, 89 ...

The fit isn't very good, but good enough to be interesting. It makes me think there might be situations in infectious diseases where a Zipf Law appears. And by (Cristelli et al, 2012), I expect this situation to be particularly likely in places with a lot of economic and social integration.

I searched on Google Scholar with phrases like "Zipf infectious disease", but did not get anything interesting.


texts: Imagine you somehow got a cup of pure cytosol.  What would be its consistency?  That is, how thick, how sticky, and how viscous would it be?


texts: In some willows, there is a clear distinction between floriferous buds (out of which the catkins grow) and vegetative buds. I have observed this phenomenon myself on numerous occasions (in fact, I can ID several species and hybrids on floriferous buds alone). However, I never took it further and there are things I still don't understand. What about those vegetative buds. What grows out of them: twigs with leaves on them out of some and single leaves out of others? And would there be any noticeable difference between these two types of vegetative buds (if they both existed)?


texts: How do you calculate the charge on a polypeptide chain with changing pH?

texts:
I understand the charge placement on the N & C-terminus and also the utilization of the R-side groups in the amino acids.

For example,
What is the overall charge for a chain Glu-Cys-Arg-Asp with pH 11.0 buffer?


texts: Effect of recombination on the rate of loss of genetic variation

texts:
Following up from this question: Does recombination increase the additive genetic variance for fitness?

(I'm thinking about the evolution of additive genetic variance and differences between the sex chromosomes and autosomes. Assume males are heterogametic (XY) and females XX, recombination occurs on the X in females, but not between X and Y in males. This means X chromosomes recombine at 2/3rds the rate of autosomes. Answers need not necessarily relate to sex chromosomes as many other factors should be affecting their evolution and additive genetic variance)

As far as I can tell, recombination should improve the efficiency of selection as variance in fitness of the population of chromosomes increases (because favourable mutations can combine more easily and deleterious ones do too) which should in turn reduce additive genetic variance (right?). But then recombination means many more combinations occurs which means additive genetic variance might be higher.

So, if I sample the additive genetic variance in a trait in a population where chromosomes that do recombine and a population where chromosomes do not recombine, where should we see the most variance (the recombiners or non-recombiners)?


texts: Lizards are sometimes called cold-blooded because they depend on their surrounding temperatures to keep them warm.

texts:
Predict how the composition of the cell membrane of a lizard might change from winter to summer. Justify predictions.

Can someone please help me figure this out. Does it have to do with fluidity?


texts:
My histology textbook says the following:

  The pluripotential hemopoietic stemm cell (which resembles a lymphocyte) is a member of the null cell population of lymphocytes.

It then goes on to add:

There are three types of lymphocytes:

T cells
B cells
Null cells:

Pluripotential hemopoietic stem cells
Natural Killer cells

However, this is the only text I find that classifies Pluripotential hemopoietic stem cells as null cells.
My question is: what are null cells? (and is this textbook accurate)

Thank you,
jsx


texts: how long after death can a body exhibit an immune response

texts:
I suppose this is part of a larger question - at what point do the body's coordinated systems (Endocrine, Autonomic nervous system etc) begin to fail? Within hours? Days? Minutes?

Of course this must vary widely with the means of death but let's assume for the moment a sudden brain embolism or some such that would leave the organs intact.


texts: Why are mice with a single X chromosome and no Y chromosome males?

texts:
I was searching online and I read this article Mice can be male without Y chromosome and this is a part of it:

  The experiments demonstrate that there are multiple ways to make males, says Richard Behringer, a developmental geneticist at MD Anderson Cancer Center in Houston. “They’ve done it without any Y chromosome gene information,” he says. “There’s not even a sniff of the Y around.”

I know that mouses are separated to males and females, and they both necessary for reproduction. Can someone please explain to me how could this possibly be? there's a lot of biology specific terms that i did not understand well


texts: Help identifying an insect (I think it was an insect)

texts:
While I realize this may be difficult without a photo, I'm hoping someone can say "This is a list of possible species given your location and description" and I can attempt to find a photo that matches from there.

I'm in NE Indiana. I think it was an insect. The species in question looked a bit like a leech, black and shiny but wasn't segmented and it was a bit flattened out (but not entirely), maybe an inch long. It wasn't tapered. Also I don't believe it made any attempt to bite me (or just wasn't around long enough to). Unfortunately it startled me so I smashed it pretty quickly so I didn't get a picture, but I got a good look and couldn't identify any legs, eyes, antennae. It moved fairly quickly, almost in a pulsating motion.
When I smashed it, there was only a bit of white, mealy paste left behind, the body almost seemed to liquefy.

If it hadn't moved so quickly and wasn't so small I'd have thought it was a baby slug. It's possible it could have been some sort of larvae.

I also don't think it was a leech because I found it on my body but I was in my home and can't think where I could have been that would have exposed me to one. I noticed it when after removing my shirt and lying in bed. So it was either inside my shirt for several hours without me noticing, fell out from the covers when I got in bed, or fell from somewhere after I got in bed.


texts: what are the plausible reasons as to why the HRPO-conjugated donkey anti-human immunoglobulin and the chromogen/substrate were added from the right to the left of the microtiter plate?


texts:
In the Theory of Evolution, two main factors take place:
One is random, which are the different mutations that organisms' DNA suffer. This process adds genetic variability to a given population.
The other one is not random, which is natural selection. It is not random because it will only select  those organisms which are better capable of surviving to the conditions of their environment.
Most likely I am wrong and I would like to be corrected, but I was thinking that, since natural selection depends on mutations and the conditions of the environment, and since those conditions can be formed by random processes, wouldn't it make natural selection as actually random?
I mean, this is probably an over simplistic analogy, but take a group of mammals which suffer a great series of mutations in a short period of time, and separate into two species of mammals: one group of animals with hair and the other group has no hair at all. Suddenly, one day starts to snow. We could expect that the second group would most likely go extinct, while the mammals with hair would survive. Since the weather is based on random processes and since natural selection in this example would be based on the mutations that the animals suffered and the weather as well, wouldn't natural selection be a fundamentally random process?


texts: What differentiates diseases like Covid-19 and Polio from the common cold

texts: Why are vaccines required for our body's immune system to destroy viruses that cause the likes of Covid-19 or Polio, while viruses that cause the common-cold are self-limiting (go away on their own)? What is so different about viruses that cause diseases requiring vaccines?


texts: During interphase II, there is no S phase in which DNA replicates. However, in this stage, do the chromosomes remain wound? Or have they unwound into chromatin form, and recondense during prophase II?


texts: Do bigger animals have more testosterone?

texts:
I was wondering the other day outside, thinking about varieties of species and their aggression levels, etc.

I had a theory that since these highly aggressive, powerful, and viciously advantageous animals in fights with humans, such as lions, tigers, rhinos, elephants, etc. are so strong and aggressive in the wild compared to us humans and smaller animals, do they have more testosterone?

Like, in animals, does testosterone correlate with size, possibly explaining why a lion is heaps more slender, muscular, fit, agile, aggressive, and vicious than a typical human?

Basically, does the bigger size and aggression in wild animals correlate to their higher testosterone, such as larger size equal to larger testosterone in comparison to other smalelr or less aggressive animals, or is it different?


texts: Is the minicolumn the unit of the neocortex?

texts:
There are many arguments for what the unit of the neocortex is. "Columns" seem to be the standard, but what exactly those are is extremely contradictory between individuals, cortical regions, and species. Often times, when a column is referred to, it's actually a functional column without any anatomical borders (such as Hubel and Wiesels ocular dominance columns). Sometimes, the "column" is semi anatomical, such as the rat barrel cortex. Other times, these functional columns are confabulated into anatomical units, without any evidence for a border.

So my question is, could Mountcastle's "minicolumns" be the actual anatomical unit of the cortex? I've heard arguments that they are mere developmental relics. But they seem like the only reliable and consistent unit in the cortex.


texts: Density of neurons/cells in the mouse brain

texts: Could someone point out some relevant papers or resources (an online DB maybe?) describing the density of neurons (or, more in general, of cells) in different areas of the mouse brain?


texts: Does Cas9 require a nuclear localization signal (NLS) for it to work in a Eukaryote?

texts: I'm trying to establish if it's required to add a NLS to Cas9 when expressed (or transfected) in a Eukaryotic cell.   Several papers report using a viral NLS, but is it absolutely necessary?   Could Cas9 be trafficked to nucleus without addition of a NLS?


texts: Do siblings have a bias toward believing they look different from each other?

texts: Anecdotally, I have observed (myself included) that siblings tend to think that they look less similar to each other than an unrelated observer would say. Is there any experimental data to back this up, or am I completely wrong?