texts:
It was found in Hong Kong! Below are a few basic information:

Place: Hong Kong

Habitat: Forest. I live very close to a mountain with lots of forestation.

Where Collected: Found it in my window slit of my apartment.

Coloration: Major body parts are black, but legs are light brown.

Distinguishing characteristics: Appears to have one spine in the mid-body (not sure); Huge mandibles

Length: 14mm to 15mm

Width: 3mm

Anything else distinctive: It could move incredibly fast (like a cockroach). Also, it appears to be quite aggressive. When I put in an ant (male ant with wings) of a different species to its tube, it attacked the introduced ant with its mandibles immediately. During its attack, it shook its abdomen periodically.


texts: If I sent a bag of rice to the bottom of the ocean and brought it back, could I eat it?

texts:
Suppose I filled an oceangoing container with rice and sunk it to the bottom of the ocean… say, a kilometer or so, then brought it back up.

Would it be edible?

Would it retain nutrients?

Do these things depend on how long it's been down there (at very low temperatures, mind you).

Asking for myself because, you know, I think ocean-bottom rice would be tasty.

Thanks!

Edit (after Doctor Whom's answer): I guess I should have mentioned that wrapping it in plastic is an option.  The pressure is what I was most interested in but I did a really poor job conveying that.


texts: How to contract sternocleidomastoid muscle by thought?

texts: If I do not turn my head, how can I contract ( or tighten) the sternocleidomastoid muscle ( like we can intensely tighten muscle in limbs)?


texts: Green Film Build up in Glass Water Bottle

texts:
So I have this Large Water Jug that I fill only water with.
And this is the 2nd time there has been a layer of green film that builds up at the bottom of the bottle. I don't have any way of getting to the bottom to clean this.

I wanted to know.

What does this green film consist of?
What Chemicals or methods can I use to remove the film without having to manually scrub the bottle?

Thanks

ps. not sure if this was the correct place to ask this question.


texts: Is there a macroscopic amoeba-like organism that lives on land?

texts:
In the early 1970s, as a teen, I hiked in Rocky Mountain National Park, going up the base of a mountain. The path went through a deciduous forest (there were brown leaves beneath the trees) and I saw oozing over some of these leaves an organism that looked like an amoeba. It was translucent blue, it had small particles contained in it, and it was about 1.5-2 inches wide (about the size of an oak leaf). It had what looked like pseudopods, and was moving forward by extending one over the leaf ahead of it. It was quite beautiful, as the blue was very clear. I thought it was a slime mold, as we had studied them that year in biology, but find out now that I was mistaken. I googled macroscopic single celled organism and found Gromia sphaerica in Wikipedia, but they seem to be aquatic, like the microscopic ones. Ditto Chaos carolinensis and Polychaos dubium, as far as I can make out.

Any light you can shed on this would be most welcome. I have never forgotten that little guy, and how beautiful it was.


texts: Is it possible to establish a newer animal model completely based on Bioinformatics studies?

texts:
I wanted to know, if it is possible to prove a new organism as an animal model for any human disease by only Bioinformatics methods like NGS and Structural bioinformatics.

For Example, let's say Drosophila is an animal model for Disease X as it have some 60-70% similarity in the gene and protein structure. Can we prove, a newer organism is a better model for X, if it shows a higher similarity, let's say 80-85%, to gene and protein structure of human?

UPDATE
(First I posted it as comment! But I think, this is suited here best!)

@David: Thanks for your answer! Actually, I did looked into it, Large animal models of rare genetic disorders: sheep as phenotypically relevant models of human genetic disease. I am more interested in listing down the problems if we do start this kind of project in our lab. Do NGS is a solution or what part of biology we need to focus so, that we can be more accurate.


texts: What kind of insect eggs are these (found in Malaysia)?

texts:
What kind of eggs are these?

Found outside on a window, when I removed them via scraping, whitish oozy fluid came out. I've seen this before but they've been appearing more frequently, always appear in a straight line and are brown.

This is in Malaysia, in South East Asia. More specifically Johor. The entire line measured about 1 inch, and in terms of individual egg size, 0.3 inches.


texts:
I was recently studying genetics in which  DNase had a crucial role in proving DNA to be the genetic material and I tried to find who discovered DNase (like the discoverer of DNA) but in vain.
Who found the DNA-digesting DNase ?


texts: Can you tell if a corpse was male or female by only examining its skull?

texts:
There are articles that says women have more rounded corner faces than men, than women noses are usually shorter, etc.

But are those (and other features) tendencies or deterministic features that makes you really able to tell if a corpse was male or female, by only examining its skull?


texts: Contracting mouth muscles as reaction to taking in specific food items

texts:
When eating very specific food items, especially confectionery like (salty) liquorice, (it feels as if) the muscles of my mouth contract, right when it hits my tongue.

Does anyone know why this happens?

The process is similar to experiencing relatively high levels of sourness - suggesting it is a similar reaction - but, as far as I know, there is, apart from the glycyrrhizic acid in the liquorice plant, not a lot of acid in this type of confectionery. I imagine other possible causes could be sugar substitutes like steviol or Maltitol.


texts: How do plants intake minerals through their leaves?

texts: How do plants intake the fertilizer when it is sprayed all over the leaf surface as a foliar feed?


texts: Is it theoretically possible to create two humans by splitting one human in two?

texts:
There have been cases where a person has had one of their brain hemispheres removed, and they ended up living a fairly normal life. Could it be possible to split a normal person down the middle and create two people, each with a brain hemisphere? Machines could be used to replace organs that can't be split, like the heart.

I'm assuming there would exist some very advanced technology to prevent excessive blood loss and other problems with splitting a person down the middle.


texts: what is the modern, molecular explanation of independent assortment of alleles?

texts:
in case it isn't obvious i'll begin by stating that i'm a layman, trying to understand something about this subject from reading books. the books i've looked at so far give murky and confusing accounts of meiosis (example: a schaum's outline refers to chromosomes that are "identical, but not the same"), and they always seem to duck the questions i most want answered. what i'm reaching for right now is a coherent, schematic understanding of meiosis. i'm aware that the real world is messier than that, but there clearly is a simple schema that accounts for the most typical cases of meiosis in an approximative fashion. in particular, there must be some way of deriving the approximate correctness of mendelian independent assortment of alleles from the molecular process of recombination.

here's what i think i can make out so far: if two chromosomes x1...xn and y1...yn get paired together then some number of interstices (spaces between successive loci) get picked and each chromosome gets broken at each interstice. after crossover each of the two resulting chromosomes have x-segments alternating with y-segments. for example if only one interstice is picked, and it's between the k-th and (k+1)-th loci, then the chromosomes that are there after crossover are x[1]...x[k] y[k+1]...y[n] and y[1]...y[k] x[k+1]...x[n]. it also seems clear that all interstices are equally likely to get picked. have i got at least this much right? and if so, how many interstices get picked?

also, if anyone knows a book that might suit my needs i would obviously be glad to hear about it. thanks if you can help

peace
stm


texts:
Thoughout life everyone tells you that brain is essentially a computer but just like computers your brain would create immense amounts of heat by being in use, so if that's the case how does it cool down.

Is like liquid cooling where the blood transfers the heat away? and if so what is the critical temperature when your blood can no longer cool your brain? Also at what temperature are you at risk of brain damage?


texts: Marker validation using transcriptome and genomic sequences derived from a single cell

texts:
I conducted a SSR marker analysis using bioinformatic tool on some RNA-seq data of human tissues. Now, my supervisor believed that we have to validate these SSR on a transcriptomic and genomic sequences derived from single cell.

My question is: why I should do validation on sequences from single cell? Thanks for sharing your idea and experience here.


texts: Are nucleotides at the ends of DNA stripped on aging?

texts:
I had the following understanding (now after reading a popular science article seeming wrong understanding):

DNA in (regular) cells (in human and some other organisms) are protected by telomers. Telomeres are shortened at each division. When telomeres reach zero size, nucleotides of the ends of DNA become "stripped" so that the DNA shortens a little. The shortened DNA does is not fully functional. This leads to aging of the organism.

But in a popular science article I've read that telomeres however shortened seem not to reach zero length. So the DNA nucleotides at the ends of DNA are never stripped. However shortening telomeres leads to the cell to become not divisible or even death of the cell.

So two related questions:

Are coding/regulatory nucleotides (not just telomeres) at the ends of the DNA ever stripped as a result of aging?
If they are not stripped and so the DNA itself is not damaged, how shortening telomeres may lead to aging? That is how aging can be caused by just shortening telomeres which however do not reach zero length?


texts: Frequency of dominant phenotype (Hardy-Weinberg)

texts:
The question is:

The frequency of a recessive allele a is 0.6. If a population is in Hardy-Weinberg equilibrium, what is the frequency of the dominant phenotype?

This question is a bit confusing to me. I'm not sure how to use my knowledge about Hardy-Weinberg in this problem. I know that when q = 0.6, p = 1 - 0.6 = 0.4. But when they are asking for the dominant phenotype, should it be p^2 or the squareroot of p? I have watched several YT-videos about this, but I still can't get the hang of it. There's not much help in my teacher or books. I would be really grateful if someone could clear up my confusions!


texts: Why does high-voltage mostly shock a person, and even small current kill?

texts:
This may be the wrong forum to ask.

For instance several people are known to have survived a direct lightning strike; albeit the number of fatalities are probably far larger. Anyway, I found myself wondering why high-voltage may shock a person and throw them off whereas high-current even small current is, purportedly, a killer.


texts: I came across a bunch of these tiny ball-pen-sized insects that (to me) look like they belong to the beetle family. They are all dead but I do remember seeing it once flying in my apartment. They are as small as fruit flies.


texts: What are the bare minimum nutrients required to survive as a human?

texts:
I am trying to determine the bare minimum nutritional requirements to survive as a human, ignoring energy (caloric) requirements. Another way to ask this question is: What elements can humans not live without? I am not inquiring solely about what nutrients are needed, but also their approximate amounts.

Imagine pills that a person can take that covers all their base nutritional needs and that after taking this pill the person can eat whatever they want to meet their caloric requirements. Hypothetically, this pill could have some amount (how much?) fat, carbohydrates, protein, fiber, minerals, and vitamins, and the person could subsequently eat any other food to meet their caloric requirements knowing their nutritional needs would already be otherwise met. Lets ignore the possibility of the person suffering from health issues due to eating too much of any specific food to meet their caloric requirements (e.g., taking the magic pills and then eating only butter).

A person in this situation could think "Ok I've got most of my bases covered, now I just need to ingest another 1000 calories of (almost) anything I want).

What nutrients are absolutely necessary for humans to survive indefinitely, and how much of these nutrients are required?

I am hoping for a complete list with approximate amounts (e.g., 20g fat, 20g carbohydrates, 1mg Vitamin X, .05mg Vitamin Y, 10mg mineral X).


texts:
I came across the following grasshopper this afternoon while walking to my car. It was initially resting amongst some fallen tree leaves, but as I got closer to my car I must have startled it, as it then ran to the tree, and is also how I noticed it.

It was calm enough for me to temporarily hold it in a cut-in-half water bottle, and I was able to take a few more pictures, and record a brief video. Afterwards, I released the grasshopper back into the grass and it promptly flew away. :)

When searching for its species, I was only able to find a dessert grasshopper, Trimerotropis pallidipennis, but I live in KY, and not out west, so I don't think that's it.

Can someone ID this for me please?

Location: Central KY, USA.


texts: How can you band wheat chromosomes using Giemsa dye?

texts: I am working with wheat chromosomes and trying to stain the chromosomes. However, during staining with Giemsa dye chromosomes appear totally dark. I'm not sure why this might be. Anyone have any ideas?


texts: What parasites would be easiest to examine using a compound microscope?

texts:
I want to find some parasites that are easy to examine under the microscope.
I'm a beginner but I have an olympus microscope with total magnification up to 400x (also 200x, 100x and 10x).

I would like to choose parasites that are safe for me as an amateur to work with and would like to have one that parasitizes people.

I prefer lets say:
Helminths, mycose (Candida alba) or something that can make people sick and is safe to work for someone who is an amateur.


texts:
When you get a shot for a vaccine (for example, the annual flu vaccine), the nurse frequently indicates that your arm will ache for a day or two, maybe more. This ache is typically not just a pain from having your skin punctured, but is actually an ache of the entire arm.

What mechanism causes the entire arm to ache from a vaccine? Why doesn't that ache extend to other parts of the body, like the hands or the shoulders? Why do non-vaccine arm punctures (such as drawing blood, injecting drugs) not cause the ache?


texts: What is the evolutionary rationale for palm sweating?

texts:
Sweaty palms seems to be a reaction to stress, anxiety, etc. For our forest-inhabiting primate ancestors sweaty palms could cause unwanted side-effects such as slipping off tree branches under stressful conditions, like when being chased by a predator.

Why did palm sweating became a reaction to fear, worry, anxiety etc in the course of human evolution? What is the benefit of sweaty palms?


texts: Is hands-only CPR as effective as traditional CPR?

texts:
Is hands-only CPR as effective as traditional CPR ? Wouldn't 30 chest compressions + 2 rescue breaths be more effective if the person doesn't have a pulse AND not breathing?

From my understanding (correct me if I'm wrong) by doing chest compression you manually make the blood continue to circulate the body in order to deliver oxygen to the organs (and most importantly, to the brain), but after some time (several minutes?) all the oxygen from the blood will be used up, and if the person is not breathing, that means that no new oxygen is entering the bloodstream, so that would mean that chest compressions alone won't provide oxygen to the brain anymore, so they would be useless... am I wrong?


texts: How prominent is the gene-centric view of evolution among professional researchers?

texts:
Richard Dawkins famously advocated a gene-centric (as opposed to organism-centric) viewpoint on natural selection, most notably in The Extended Phenotype. However, I have also heard "on the grapevine" that most professionals in biology and related areas do not take the gene-centric viewpoint altogether seriously.

My question is simple: how prominent is the gene-centric view of evolution among professional researchers in biology and related fields?


texts: Which blood vessel carries the most impure blood?

texts:
There is a question in my Biology textbook:

  "Which blood vessel in the human body carries most impure blood after
  few hours of meal."

The answer is given as Renal artery.

But I think the answer should be Hepatic Vein, because the liver produces urea and other waste materials and then it pours it all in the right ventricle of the heart for oxygenation. And then the heart distributes the blood to various parts of the body. So the impure blood brought by the Hepatic Vein and other blood vessels gets distributed through the aorta. This will automatically imply that the Renal Artery will contain lesser impure blood than the Hepatic Vein.

Impure blood is the blood with urea, uric acid and other components of urine.

It would be good if you give your opinion and also a reason for it.


texts: Please identify this creature found on the beach

texts:
Found on beach in Atlantic Canada in November.

"Sack" is approx. 2" (approx. 5cm) in length.


texts:
I have been trying to wrap my head around the concept of epistasis for a couple of days now, and I think I understand it, at least at a basic level, but I still don't understand some of the ways that the term is used.

What does it mean if gene A is epistatic to gene B? Does this simply mean that gene A masks the phenotype of gene B when expressed? or is there more to it?

Also, what does it mean when genes are in the same epistasis group? I am currently studying the transcriptional up-regulation of PSY3 in yeast as a result of UV treatment. PSY3 codes for a protein that forms the Shu complex along with 3 other proteins. One paper I am reading states that PSY3, is in the same epistasis group as the three other genes that code for these other proteins. What does this mean?


texts: (Why) are polar bears more common in Labrador than in southern Greenland?

texts:
The Labrador Sea is between Greenland, Labrador, and Qikiqtaaluk:

Map source.
A Greenlandic source on polar bears states:

In Greenland the polar bear lives and breeds in the northernmost parts of West Greenland and in Northeast Greenland, but is also occasionally seen elsewhere in Greenland, as it moves with the drifting ice.
However, it is extremely rare for either local inhabitants or tourists to see a living polar bear. The chances of seeing a polar bear are greatest when sailing by ship along the coast.

On the other hand, Parks Canada for Torngat Mountains National Park (northern Labrador) states:

Polar bears are true carnivores and can be a significant risk to human beings. Visitors travelling and camping in the park are in polar bear country and are at high risk of encounters. Polar bears are almost always present along the north Labrador coast.

The observation that polar bears are more common in Labrador than in southern Greenland is supported by Derocher (2010), Nature:

Derocher (2010), Nature
Polar bears like the sea ice edge, but this is very far from either Labrador or Greenland when at its fall minimum.  When sea ice is at its spring maximum, both Labrador and almost all of Greenland are packed deeply in ice (see maps below).
Then why are polar bears so much more common in Labrador than they are in southern Greenland?  Arey they really?  And how do they survive all summer long, when the sea ice is very, very far away?  The occasional tourist might not be enough, I guess.

Arctic minimum sea ice from NSIDC

Arctic maximum sea ice from NSIDC


texts: What is the mechanism through which fractals arise in plants and animals?

texts:
Many biological organisms -- such as trees, broccoli, and the blood vessels in animals -- can be approximately described using fractals.
What is the reason behind such fractals? Specifically, do we know of the way certain cells split that lead to fractals? Do we know if there are specific genes that tend to generate fractals?


texts: How do I find the number of child terms associated with a specific GO term?

texts:
I am trying to figure out how to find the number of child terms associated with a specific Gene Ontology (GO) term using QuickGO, without just counting the amount of terms in a list. For example when I want to find the number of child terms associated with the GO term 'heart development'.

I could just click on the tab 'Child Terms' and count, but what if it would be a very long list, how can I find the correct amount?

I assume there is some way to do this by going to Protein Annotation and applying a filter, but I do not know how to do this.

Any help?


texts:
My 6 year old daughter asked me 2 biology-related questions yesterday and I tried my best to answer them with the aid of YouTube videos.  One of the questions (I may post the other one too) was

  How do we see colour?

I showed her a video on YouTube where it was explained that light hits an object and if that object is a tangerine then that object will absorb all colours except orange and will reflect orange and that's why we see it as being orange.  I then repeated this explanation and she said.

  But how do we see different colours?

I then showed her a video describing corneas, vitreous humours, lenses, optical nerves and so on.  I think I lost her.  I got a bit lost too.

Now I have two problems, which I'd like to ask to you all as questions

I do not know how to explain to a 6 year old how we are able to perceive colour.  Does anyone know how this can be explained?
I have never quite understood this idea that an object has a colour depending on the light that hits it.  Okay, I understand that in low light objects have a different colour because there is a not much light hitting it and that different objects absorb different wavelengths of light and therefore appear as different colours.  What I don't understand is that if I place a bar of gold a bar of silver side by side in the same lighting conditions they do have different colours, so therefore there must be something inherent in these object that give them different colours.  What is that something?


texts: Why isn't Rh disease present in other mammals?

texts: I have read about Rhesus D Hemolytic Disease of the Newborn, sometimes called "Rh disease". It's rare, but it can happen when an Rh+ baby is conceived by an Rh- mother.  This raises many questions. I have heard this problem only happens with humans; if so, why doesn't it affect other mammals like Rhesus monkeys?  Where along the evolutionary time-line did Rh disease come about in the first place?


texts:
What are best practices for naming newly created plasmids?

For example, a common format is pABC123. What is the exact specification? Must there be 3 letters?

What databases of plasmid names exist? How much care is taken to avoid name collisions?


texts: How does your body ultimately recover from a cold?

texts: Is it the eradication of the virus (assuming rhinovirus) by white blood cells? Or does your body somehow adapt to presence of the virus?


texts: Is there theory that connects longevity, time-scale of environmental disturbance, and adaptation?

texts:
I'm thinking here about environmental disturbance or like climate change-driven warming. It seems as if there are two macroevolutionary ways to deal with environmental change:

1) Have short generation times, and evolve fast. For instance, the mosquito Wyeomyia smithii is under selection by the warming climate in North America and it has shown an evolutionary repsonse. The response is "detectable over a time interval as short as 5 years" (Bradshaw and Holzapfel 2001).

2) Be hardy, and 'try' to wait out changes. No real-world example to cite, but imagine a long-lived tree growing in an area that has become to warm for its seeds to effectively produce seedlings.

It seems intuitively like strategy 1 is better in the case of ongoing climate warming. However, we could easily imagine a 5-year hot spell followed by a return to the normal as part of natural weather variation. Perhaps in this situation strategy 2 is better.

Essentially, having a longevity/generation time/hardiness that matches the time-scale of the disturbance would be important – if the disturbance is long (or unidirectional) compared to your lifespan, evolving fast seems best; if the disturbance is short compared to your life, it seems best to wait it out.

So the question is, is there theory that deals with this? I suspect that I just need to hit the population genetics books again or something; or perhaps there's a massive tome by Gould I should be reading?

 Bradshaw WE, Holzapfel CM. 2001. Genetic shift in photoperiodic response correlated with global warming. PNAS 98: 14509–14511.


texts: Do endocrine cells always lie adjacent to capillaries?

texts: The circulatory system transports plasma contents to the body via the interstitial circulatory system, reabsorbed with the lymphatic system. Cell metabolism "waste products" are transported into the blood via this "sewer system", to for example be excreted by the urinary system. The lymphatic system provides a basic route for interstitial fluid to return into the blood stream. The endocrine system has to be relatively fast, and, lymphatic transportation is relatively slow. Do endocrine cells always lie adjacent to capillaries so that hormones are secreted directly into the blood stream?


texts: Which ICs can I use to amplify electrical signals from plants?

texts: I wanted to record variation potential and action potential generated in plants due to some stimulus. So which are the ICs that I can use for the amplifying the signals and what kind of experimental setup would be best. I was thinking of using Ag/AgCl microelectrodes with 0.1M KCl solution for measuring the electrical impulses in tomato plants.


texts: Are there more true codes found in biology besides the central dogma?

texts: I know each element of the central dogma is a code in the mathematical sense of finite-state machines. That is, DNA is transcribed into RNA, and RNA into proteins.  What other examples are there of codes that exist naturally in organisms?


texts:
I have a matrix two gene expression datasets, one from 10 normal individuals and ten from diseased individuals, which are normalised log fold change values--, i.e., already processed.

My question is: how do I obtain a list of differentially expressed genes?
That is the up and down expressed genes. I was thinking of getting means for each group and then sorting the average fold change values would work, but I am not sure...

Thanks.


texts: Is it possible to stop yourself from going into shock?

texts:
https://en.wikipedia.org/wiki/Shock_(circulatory)

I was helping someone move a refrigerator down steps and it slipped while I was holding a sharp corner and it sliced my finger and there was continuous blood flow. Soon after, I started feeling light-headed and was shaking and felt like I was about to pass out or have an attack, but I could not allow myself to appear weak, so I fought against it mentally and I got past it without anyone observing any signs. Did I avoid circulatory shock? Did pure mental dedication allow me to surpass such a thing?


texts: Identification of an Australian pigeon in the NT

texts: This pigeon was spotted in Darwin, NT, Australia. I am not able to solidly identify it using my books or google searches. My best bet is a Torresian Imperial Pigeon (Birds of the NT website).


texts: This fish was caught in St. Augustine, Florida. What species is it?


texts:
I am having a really hard time trying to understand what cranial nerve nuclei are. I have been reading/watching videos and I keep hearing, "that is where the cranial nerves make connection with the brainstem." Also, I keep hearing that some cranial nerves may have multiple nuclei and some nuclei may have multiple nerve synapsing there; however, this information doesn't really help me understand what they are. Are they a processing center? If so, doesn't information get processed in the cortex?
So the main question is: What is a cranial nerve nucleus and what is it's function? What does it mean by "where nerves make connections"?
I am attaching the image which I've been studying. You may refer to that when answering this question.


texts: Is eradication of the Common Cold possible?

texts:
This is a thought experiment, but everywhere I've read seems to say that colds ALWAYS come from someone else. There's no mention of a cold arising in someone without it coming from another infected being.

So my question is, if everyone in the world stayed out of physical contact and air space with everyone else for 2 weeks (or until every cold virus would have completely disappeared), would all variations of the cold virus then be extinct leading to a world without colds?

Or is there somewhere else that colds can arise from?


texts: Can mRNA be used by ribosomes more than once? I mean can mRNA be translated more than one time? If not what will happen to it after translation?


texts: Insertion of an additional base at start codon make the protein still functional?

texts:
So the question is if:

a deletion of a codon for the amino acid lysine (AAG) is more or less likely to cause nonfunctionality of the protein than:

Insertion of an additional base (C) within the start codon for this protein
Mutation of the stop codon (TAG) to an arginine codon (CGC)

My attempt at an answer:

Not more likely. Since the insertion of the “C” base is done at the very start, the reading frame could be shifted and the sequence would remain the same after the first base. Since the most common start codon is “ATG”, the “C” would not affect it and the “reading” of the sequence would start after the “C” and at “ATG”
More severe as the stop codon is what signals that the translation of the sequence has ended, so if the stop codon got modified then the sequence would continue into the untranslated region. More peptides would be added to the sequence which would only stop when the next stop codon is reached. If the next stop codon is relatively close and the length if similar to a normal protein then it would still be functioning. But most cases it would continue for a considerable length and cause it to be non-functional


texts: Why do so many people have group O blood?

texts:
Please forgive me in case my question wouldn't make much sense. I was reading about ABO blood groups on Wikipedia, where I learnt that O is a recessive allele, and that it seems the A allele predates the O allele. My question is, therefore, how is it possible that almost half of the human population is group O?

For instance, I would expect (quite naively I reckon), if only alleles A and O existed, that around 75% of the population should be A, and 25% should be O.


texts: What is the difference between disruptive, divergent and diversifying selection?

texts:
In our lab meeting we were chatting about divergent selection. I was confused at some point because I wasn't sure what was the meaning of this work in comparison to diversifying/disruptive and other types of selection.

Diversifying selection was coined by J. T. Gulick and I haven't found an interesting answer to compare with our contemporary definition of these terms.

The way I understand this is that, divergent selection is broader and include directional selection as well as disruptive selection. Is that correct?


texts: Why do flies "rub" their front legs when resting?

texts: I've noted that every time a house fly is resting on a surface, it appears to "rub" or "scrub" its front legs in a repetitive movement. And they do it continuously. Why?


texts: An experiment to test if a bacterial resistance gene is on the plasmid or chromosome?

texts:
So I have an E.coli strain phenotypicall resistant to the antibiotics ampicillin and rifampicin. How do I test if the AmpR gene is carried on a plasmid and not on the chromosome?

In summary, I thought perhaps you could isolate the plasmid, put it in an ampicillin sensitive bacteria, then see whether or not the bacteria die.

I also thought you could use PCR on the plasmid with primers complementary to sequences adjacent to the AmpR gene. I'd use a positive control with the gene of interest and a negative no template control.

Do these sound about right & are there any other methods or controls I should consider?


texts: Can neurons be inhibited with electric current?

texts: It is well known the electricity can be used to fire neurons. But can it be used to inhibit neuronal firing? This is in the context of extracellular stimulation. In extracellular stimulation, it is known that there is a threshold for stimulation and a threshold for damage(electroporation). Is there a threshold in between these two which inhibits neuron firing without any damage? Please provide reference for your answer.


texts: Is this a bedbug or a book lice or what?

texts:
So basically i found this thing in my home. It's super small so I had to zoom it for you. Whiteish/yellowish colour. We had bedbug problem back in our dorms and I'm worried I somehow managed to transfer them home but I don't know if it's a bedbug nymph or a book lice or what kind of insect, so I'd really appreciate someone's opinion on this.

Edit: It's really small, like. really small. my mother wouldn't even see it and thought me crazy. Just zoom made it look bigger. I'd say 1.5mm maximum at the very best. Moves kinda quickly and I thought it jumped two times when i was trying to capturing but maybe it was just me doing it to it. Living in Europe, Slovakia specifically.


texts: In the PR segment of an ECG, how come there's no current flowing?

texts:
I don't really know how to phrase the question, but to put it as clearly as I can, I don't get why it is the P wave "flattens down" when the atria have completely depolarized. I get that the charge is uniform across the atria, but the ventricles are still polarized (and therefore of a different charge compared to the now completely depolarized atria), wouldn't this create a difference in charge and therefore a voltage to produce a current? I think this GIF can help explain my question better:

At frame 12:

I don't understand why there's no current flow and no deflection on the ECG leads despite the charge difference. Rather, why does the GIF deal with the current and charge difference in the atria and ventricles separately? I thought this all might be because of the fibrous cardiac skeleton, which acts as an electrical insulator, but that doesn't make complete sense either; sure it prevent current flow within the heart, but it wouldn't influence current flow outside of it, right?


texts: Difference between viral and human genetic material

texts:
I have heard that there is a difference between viral and human genetic material. What is that difference?

If I take my cells and take DNA out of them and insert only a small part of it having a sequence, say, AGTTC, and viral DNA with the same sequence, can my body distinguish between the two? If so, how?


texts: How do T cells deal with the obstructions in their path of migration?

texts: When T cells move in the blood, are their any obstructions(other cells) while they migrate? If there are then how do the T cells overcome such obstructions in their path? Do they move past them or does their movement lead to displacement of the obstructions?


texts:
A year ago my family and I were in Tanzania on vacation. Upon returning to our home in Alaska my wife found a small stowaway in her luggage. Feeling sorry for the poor creature we put it in a container, gave it some green leafy things to eat, some water and some paper towels pieces to hide/burrow under - thinking that its life span would be a few days/weeks and short of flying back to Tanzania this was the best we could do.
Skip ahead a year and he/she is still with us... every few days we change its food, change its bedding, and make sure it has something moist to get water from. We even took it on vacation this year to Florida and back because trying to explain how and why to take care of our friend to a neighborhood kid may work for pet cats or hamsters but we were afraid Mr. Bug might not survive.
Since we are coming up an a full year of bug sitting we are wondering what is it ? And should my daughter plan on taking it to college with her when she leaves in 6 years ?


texts:
I was reading Developmental biology by Gilbert and stumbled upon a fact that Sertoli cells provide protection to the developing sperms with no futher explanation.

I googled it and found a few books mentioning that it protects sperms from cell mediated immunity and antisperm antibodies. Yet I found a website called fertilitypedia that said:

  Sertoli cells do not only control the process of spermatogenesis, but they are also responsible for creating so called immunologically privileged area in the testicles. It means, that Sertoli cell manage to keep blood separated from seminiferous tubules through the connection between them, called tight junction. Tight junction keeps bloodborne substances from reaching germ cells, so all stages of germ cells are protected from the body immunity. Tight junction also keeps surface antigens found on developing germ cells from eluding into the bloodstream so no autoimmune reaction could happen. Since Sertoli cells form the block between the blood and lumen of seminiferous epithelium, they are also in control of the entry and exit of nutrients, hormones and other chemicals into the tubules of the testis.

I'm unable to verify this explanation from the cited sources as none contain the mentioned information.

So my question, how does it actually protect the sperms?


texts: Is this species a variant of a red flour beetle?

texts:
Found this little guy crawling around the back garden - South Coast of the UK.

The closest things I could find online (with an admittedly weak knowledge of where to look up these things, aside a google search for red beetle) were the red flour beetles. However, it doesn't look quite like what we had, this being more stockier, with a dark head, and more splayed feelers.


texts: Why does so much variation exist within species?

texts:
My last phrasing of this question did not go down well, so I will try again.

The genotype of species is not always the same. If you ask yourself why not all of these possible expressions except one have died out, a natural answer is each genotype occupies a specific niche: For example, different eye colors might be found attractive by different kinds of people. If the the genotype for one eye color became more rare for some reason, other individuals with this genotype had a higher mating chance; the frequency of that genotype would get pushed back up.

But there seem to be genotypes (for example, having zits) that don't occupy any niche at all. Why didn't they die out?


texts: Confusion over role of current/potential in Nervous system?

texts:
I am taking a course on the nervous system and I am do not have any physics background. Therefore, I would like to know, what are we precisely talking about when we talk about current in the nervous system?

At the same time what are we talking about when we talk about potential (i.e membrane potential or action potential.

I once heard an analogy about waterfall and water comparing current and potential (voltage), can someone elaborate on that for me.

Also, I know that electrical activity is the flow of electrons. Therefore does that mean that passive current in an axon/nerve is a flow of electrons? And is it also a flow of electrons when we have action potential.

Thank you in advance for all the help.


texts: Why are antibiotics prescribed with a viral infection like a cold?

texts: I've heard both ways; people going to the doctor for a cold and then getting a prescription for antibiotics and those that go to the doctor and told they have ride it out because it's a viral infection.  Do antibiotics really help in true cases of a viral cold?


texts: Why don't bacterial cell walls prevent bursting when attacked by the complement?

texts:
The complement system creates pores in cell membrane which leads to influx of lots of water thereby causing lysis of bacterial cell.

But what I fail to understand is that if bacteria have cell walls around them, why will they burst ? Shouldn't they simply become turgid just like plant cells do ?


texts:
Sure it's convenient to decide when to urinate but not essential for survival or reproduction, as I understand. But just convenience is not a drive for evolution.

Does the bladder serve any essential purpose? If not why did bladders evolve?


texts: Oncotic (Osmotic Pressure) in the blood pressure

texts: I just wanted to ask, why is the oncotic pressure more negative in the blood plasma even though the hydrostatic pressure is higher since the blood comes from the pumping of the heart?


texts: What is the function of Xylem parenchyma?

texts: why xylem need parenchyma cells ihave read these cells are connected with xylem by plasmodesma i know that plasmodesma is to connect between cytoplasm of two cells and xylem is dead so what is the need of xylem parenchyma ?


texts: Consensus symbols in multiple sequence alignment

texts:
I was using multAlin for multiple aligning a set of sequences. The output I and came across included the following documentation (English corrected):

  Consensus symbols:  ! is any of IV  $ is any of LM
  % is any of FY  # is any of NDQEBZ

I understand what it says but I don't know how to interpret it further. What impact does this have on the sequence alignment?


texts:
I found it in Russia.

Where do they usually live? What do they eat?

Full length is approximately 2 cm.


texts: is there any theory about why life evolved to have DNA with 4 different bases and not 6 or other number like in organisms created with artificial DNA?

texts: If organisms can carry DNA with 6 bases which supposedly stores increased genetic information, why living organisms evolved to have DNA made of 4 bases and not 6 or other number? is there any theory about this, were the chemical process to reach those 2 additional bases much more complex or something?


texts: What's the technical terminology for call-and-respond type behaviour?

texts:
The groups of some species such as water birds display a behavior that once out of line-of-sight a member will periodically initiate an interaction by make some type of sound, which will be followed up by responses from all the other members - presumably to confirm they haven't been silently snatched by a predator. I have observed this in person at a local botanical garden where the water birds sound off like this every 10 minutes or so all day long.

What is the technical term for this behavior and some examples of species that demonstrate it?


texts: How long does foreign DNA stay intact in human blood?

texts:
How aggressively is foreign DNA in blood targeted and degraded by the human body?
I am asking because we have a metagenomics project where we want to detect parasite DNA in the human blood. The process from DNA extraction to sequencing to bioinformatic analysis is not a problem for us. But the question is if we can expect some signal in the data.


texts: Protein function and how it does not get affected with amino acid

texts: How is it possible that a protein's function is not changed when an amino acid within it is replaced?


texts:
I have heard the claim:

  sleeping requires more energy than watching TV.

I have heard the counter-claim - watching TV requires large amounts of energy.

My question is: Is there evidence to suggest that sleeping requires more energy than watching TV?


texts:
It has been my thought for a long time that this is the case, but I am unsure currently, since the parasympathetic tract of colon sigmoideum does not seem to have connection with CN 10. It connects with pelvic splanchnic nerves.
Discussion about it here.

If there is no connection from pelvic splanchnic nerves to CN 10, like CN 10 running within the nerves, then my though must be wrong.

Are CN3, CN7, CN9 and CN10 the only Parasympathetic Cranial Nerves?


texts: Protein-coding introns in mitochondrial genomes

texts: I am studying the mitochondrial genome and have read that some contain introns. However, these introns code for proteins. I cannot really understand this. Could someone tell me what intron in which mitochondria genome this refers to?


texts: Mutation rate breakdown by original and mutated nucleotide for Coronaviridae

texts:
In a discussion of the mutations S:Q677H and S:Q677P in SARS-CoV-2 it was mentioned that the mutations leading to this result are "against the tendency" of preferred mutations on the nucleotide level. It was also stated as a well known fact, that the rate of mutations depends on the original and mutated base.
So I'd like to know the mutations rates for all possible base pairs in Human Coronaviruses, or a pointer to reference where I can look them up. A less specific but still applicable reference is also welcome, as well as relative mutation frequencies given in some arbitrary units.
EDIT in response to comment by @David: This is the relevant part of a preprint by Hodcroft et al. on the top of page 5

The amino acid Q changes to H due to a mutation at nucleotide position 23593. Notably, in four of these six lineages, the mutation changes from G to U, whereas in the other two, it changes from G to C (FIG 2B). In contrast, the S:Q677P variant occurs by virtue of an A to C change at position 23592. All mutations leading to Q677H or Q677P involve transversions. Hence, their spontaneous occurrence is generally disfavored relative to transitions. In SARS-CoV-2 samples from human infections, A to C and G to C transversions occur at only ~10% the frequency of C to U transitions, while G to U mutations are more common, occurring half as frequently as C to U. (Wright, Lakdawala and Cooper, 2020) (Ratcliff and Simmonds, 2021).


texts: What can eating pink mold do to a healthy person (someone whose immune system is not weakened)?

texts:
I've tried searching it up, but my research has yielded nothing very specific.

The following website was the closest I came to finding something about pink mold on bread. It, however, said nothing about the effects of eating pink mold (https://moldcleans.com/pink-mold-on-bread/)

I also found another website, https://lookmold.com/detect/type/pink-mold, which states that healthy (people without compromised/weakened immune systems) people don't get sick right away from exposure to pink mold. Other sources, however, claim that only people with compromised immune systems will get infected by a fungal infection. Hence my question: what can eating mold do to a healthy (healthy immune system) person?

Edit: Thanks to all who responded! The advice was very helpful. I have also edited my question to fit the rules, for I am still curious about the effects of pink mold on a healthy person.


texts: Why does Rigor Mortis occur after death?

texts: After someone dies they become stiff, this is termed Rigor Mortis and happens because the cells run out of ATP (I think). But why do the cells need it to remain flexible?


texts: In the context of heterotrophic theory of abiogenesis, what is an organism that eats other organisms called?

texts:
In the heterotrophic theory for the origin of life, we imagine a primordial soup that is rich in organic compounds and the first organisms emerge eating those compounds. Since these organic compounds are external to this early organism, this early organism is a heterotroph. But it is not like any current heterotroph since it doesn't eat other organisms or their byproducts. Is there a special name for this 'type-0' heterotroph?

At some point, some organisms emerge that eat other organisms (i.e. eat those 'type-0' heterotrophs that are already around). These new organisms are more like the standard heterotrophs of today. Is there a special name for this 'type-1' heterotroph?

I am looking for the terminology that distinguishes the heterotroph that eats only organic compounds that are non-organisms in the primordial soup ('type-0')  versus the heterotroph that eats other organisms ('type-1').

Normally, I could call the 'type-0' a primary heterotroph and the 'type-1' a secondary heterotroph. But we usually think of primary heterotrophs as things that eat autotrophs and at the start of the heterotropic theory, there are no autotrophs to eat. The primordial soup of the environment itself is the 'producer'.

If there is no standard name, would it be strange to call the 'type-0' heterotrophs as 'nullary heterotrophs' and the organisms that eat other organisms as 'non-nullary heterotrophs'?


texts: Why do some plants have the ability to stand frost, while others can't? Does it have to do with the size of the water vacuoles in the plant cells?


texts: Can you force human body to mass produce specific proteins?

texts:
I've had difficulty finding an answer to this question on Google.

From what I've been taught, DNA is used as a "naive blueprint" to synthesize proteins.

If we can manipulate DNA (Which I hear we can) does this not mean we can force cells to produce specific proteins we want? Purely hypothetically, ethics aside.

I also can't quite understand "what" uses that DNA to create proteins, or does it magically just "replicate itself" and turn into a new cell with the same proteins...

Sorry for the vague last question, but these questions were bothering me for a while now and I wanted to have some more references to read or answers.

Thanks ahead of time.


texts:
Today I found a spider in my home that I have never seen before.
I live in Karachi, Pakistan.

I want to know which spider is this and if it is venomous and danger for me or my family ?? Is this spider commonly found in homes. I have seen many home spiders but they were never like that.

The spider is around 2cm long (front legs to back legs span as shown in 1st image)


texts: question about fast/slow muscle twitch fibers

texts:
Here are my questions (I have several)

1) Are the fast twitch muscle fibers dominant or recessive as opposed to the slow?

2) Are people of mixed race/greatest genetic diversity in their background, tend to be the best athletes and the healthiest in general?

Allow me to clarify the first point:  Obviously no one in the world is either 100% fast twitch or 100% slow twitch.  Let's put this another way:  (and I'm just using random numbers here that are probably unrealistic, bear with me).  Let's say someone who is 80% fast twitch and 20% slow twitch has a baby with someone who is precisely the other way.  Would the child develop more of the fast twitch or more of the slow twitch?


texts: How does P-protein (phloem) help in sealing of wounds?

texts:
While I was reading a book I found that "P-proteins in the sieve elements of phloem help in sealing  of wounds along with callose".

So how does p-protein do that, moreover how can it reach to other parts of plant body in order to seal the wounds?


texts: Is there a word that describes symmetrical correlations between a damaged brain region and behavioral disability?

texts: Specifically, I'm looking to address phenomena such as (1) how damage to only one side of the substantia nigra leads to Parkinson's symptoms on only one side of the body, or (2) retinotopy, how adjacent points of the visual field are processed in adjacent areas of the primary visual cortex, and how damage to one area in the cortex results in loss of perception in the related area in the visual field.


texts: What is this worm or larva I found in my walls

texts:
We were recently doing some major remodeling in our 1920s era home and found what looks like a nest of small meal worms. I am wondering if anybody can identify them! Here are some photos:

Our home is in Denver CO. I didn't see any living examples so it is possible they have been there for nearly 100 years.


texts: What of Gould's contributions to evolutionary biology are still accepted in the mainstream?

texts:
I have been reading Daniel Dennett's Darwin's Dangerous Idea, in which he picks apart many of Stephen Jay Gould's criticisms of neo-Darwinism, particularly in the chapter 'Bully for Brontosaurus'. Turns out Gould wrote a lengthy refutation back, and they ended up throwing slurs at each other for a few years afterwards.

I am interested to know what the current state of mainstream opinion is on Gould's interpretations, particularly on panadaptationism and gradualism. Has the field yet come to any firm conclusions on who was right after all?


texts: Mass spectrometry versus western blotting for validation

texts:
I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In addition to some of the bioinformatics analysis I am doing, I will have to validate some of the fold-changes from the mass spectrometry by Western blot in order to have my results published.

Some of the proteins I have chosen to to validate work very nicely by Western blot which captures the same trend as the mass spectrometry. However, other proteins that I have attempted to validate go in the exact opposite direction.

My questions:

In general, how accurate is mass spectrometry compared to Western blotting?
Is it unusual to have a lot of variability between the results of the two methods? I am worried that I might have to try multiple proteins before I see the results replicated and this seems problematic to me. That leads me to the third question.
Which result should I trust?

Other information - Some of the proteins I have chosen for validation come from lower in the list where not as many peptide fragments were detected. In some cases, fragments were detected in only 2 of the 3 biological replicates. I did not chose to validate proteins where the 2 or 3 replicates varied widely in normalized spectral count values so I would expect these readings to be accurate. Additionally, the mass spectrometry part of the experiment was performed by a reputable lab that has filtered erroneous data using FDR cutoffs. There is a high correlation overall between all three replicates for a particular treatment and low standard error between samples across the population so, statistically, I trust the mass spec results.

If you need more information please ask - I don't know what exactly will be useful to answer my questions.

EDIT :

This article discusses the justification for using western blotting to validate mass spec results. It suggests using selected reaction monitoring assays as an alternative. Some of the points made by commenters in this thread are reiterated in this article.


texts:
Camels have a hump as an adaptation to the heat. They store fat so that it minimizes the insulating effect the fat would have if distributed over the rest of their bodies.

Why do buffaloes/ oxen/ bulls have a hump then? The climates they are found in, I assume, are not as hot as that of the camels.


texts: Questions about what a productive cough actually is and where it comes from

texts: When I'm sick with a productive cough, what is the stuff I'm coughing up, is it coming from my lungs, and if so how come it doesn't hurt a lot and trigger a violent cough like if I got even a single drop of water down the wrong hole.


texts:
I can't find a definition for 'refractile' (not 'refractory', and not explicitly in an optical context).

As in:

  A tumour cell phenotype features increased proliferation, anchorage- and growth factor-independenth growth and ‘refractile’ cell morphology

It's not in any of the dictionaries I can access online, nor in the Oxford Dictionary of Biochemistry and Molecular Biology. Any help would be appreciated, thanks.


texts: Is it possible to knock out a gene in adults?

texts: gene knockout is mainly used in creating newborn animals... right? Well can you do it to already-adult animals or humans so that they themselves would experience change in their body and not just their off springs?


texts: Why estimate linear and full (linear, quadratic, and correlational) selection coefficients separately?

texts:
"We then fitted a linear regression including all three life-history
  traits to estimate the vector of linear selection gradients, β, for
  each sex (Lande and Arnold 1983). A quadratic regression model
  incorporating all linear, quadratic, and cross-product terms was then
  used to estimate the matrix of nonlinear selection gradients, γ, for
  each sex. "

This is from the paper Evidence for strong intralocus sexual conflict in the Indian meal moth, Ploida interpunctella. I am not sure why they estimate these gradients separetly rather than taking them just from the one full model - any suggestions? Is this normal or have they done it for a reason?

For some similar work see these two papers:

Gosden et al which seems to use only the linear gradients from one model with sex as an effect.
Stearns et al which uses linear, quadratic and correlational estimated from one multiple regressions model per sex (similar to the main paper I cite first but not using a linear terms only model for the linear coefficient).

I have mailed the corresponding author on the quoted paper to ask why, I will let you know what he says if he replies


texts: Are the intestinal microbiota substantially different within a diverticulum of the colon?

texts:
From the Wikipedia page for the vermiform appendix:

  This proposal is based on a new understanding of how the immune system supports the growth of beneficial intestinal bacteria, in combination with many well-known features of the appendix, including its architecture, its location just below the normal one-way flow of food and germs in the large intestine, and its association with copious amounts of immune tissue. Research...showed that individuals without an appendix were four times more likely to have a recurrence of Clostridium difficile.

This quote seems to be implying that the appendix can act as a breeding ground for certain gut flora that are slightly less common (like C. difficile) and not as ubiquitous as E. coli or Enterobacter sp. The appendix could be seen as an ideal spot for this growth of microbial populations in the gut.

Given that, to a first approximation, anatomically, the appendix and a common diverticulum of the colon are both outcroppings of the large intestine: to what extent would a diverticulum also be able to support less common or more diverse flora, and how likely is this to be due to a difference in extracellular environment (pH, ion concentration) and how likely is it simply due to shape?


texts: Trying to identify the species to which this vertebrae belongs

texts: Found vertebrae in the "graveyard of the Atlantic" (on account of the 5,000+ shipwrecks since the 1520's) off Frisco/Hatteras, North Carolina. Tried searching online but not finding any perfect patches (although some were close with some seemingly minor differences to the untrained eye). Any ideas would be much appreciated. I have images from every angle and can take specific images if instructed on exactly what is needed. This is new for me and I am unsure who to contact if this is fruitless. If (fairly certain) identification is not possible from the image(s) please comment with any suggestions on my next contact.


texts: What makes learning more difficult as we age?

texts:
Why is it harder to adapt yourself to different cultures, places, and languages as you age? What makes breaking up with emotional patterns or ideas after years of habit more difficult?

Is there a natural process in which the neuron's synapses are set, while later in life the plasticity of the brain is nearly lost?


texts: Why Isn't mineral transport in xylem multi-directional?

texts:
According to our textbook, Xylem transport is only unidirectional while transport through phloem is multi-directional.

But minerals are taken up by xylem from the surrounding tissues actively, and even though they flow along with the water column, they are actively unloaded near 'sink' sites. Sometimes, minerals are also taken up from aging parts and transported to growing areas of the plant. Then shouldn't mineral transport through xylem be multi directional?

Please Explain


texts: qPCR: Accounting for different sample mass when interpreting and comparing Ct

texts: I'm trying to use qPCR to quantify the amount of a specific bacteria species in patient sputum, but I don't really have the option to use consistent quantities of sputum to elute DNA from. The qPCR works fine, but once I have the Ct results, what is the best way to account for the fact that I'm using different masses of sputum?


texts: Papers where protein oligomerization has been engineered away

texts:
I have a protein that acts as a monomer, but appears to have a relatively high self-affinity in vivo (measured using transient transfection of a plasmid coding for the protein), which is annoying because I'm trying to engineer conditional self-association like with FRB-FKBP w/ rapamycin. Have there been any papers where self-clumping of a protein has been engineered away?

My current approach is to use threading to identify a protein structure and a docking program to identify sites of self-interaction and mutate those sites away.


texts: Pearson correlation of neural responses with it's linear estimation

texts:
I am trying to anderstand the following fact from this article (page 13):
How can single neurons predict behavior

Suppose I have a linear estimation of a stimulus:
$ \hat{s} = \mathbf{w}^T(\mathbf{r} - \mathbf{f}(s_0)) + s_0$

where $\mathbf{w}$ is a vector of weights, $\mathbf{r}$ is a vector of responses responses of two neurons to a stimulus, $\mathbf{f}$ is the vector of average neural responses to the stimulus, and the stimuli (angels between $-\pi$ to $\pi$) are symetric (amount and location) around $s_0 = 0$.

Can anyone see why the following is true for the Pearson correlation (where $\Sigma$ is the covariance matrix of $\mathbf{r}$):

$$ Corr(\hat{s},r_k) = \frac{\langle \hat{s}r_k \rangle - \langle \hat{s} \rangle \langle r_k \rangle}{\sqrt{( \langle \hat{s}^2 \rangle - \langle \hat{s} \rangle^2) }\sqrt{( \langle r_k^2 \rangle - \langle r_k \rangle^2) }} = \frac{(\Sigma \mathbf{w})_k}{\sqrt{(\Sigma_{kk}\mathbf{w}^T \Sigma \mathbf{w})}} $$

Thanks!!


texts: Do lizards expand in the summer and contract in the winter?

texts:
We all know that objects expand on heating and contract on cooling.

Lizards are cold-blooded animals, i.e. they become hotter and cooler depending on their outside temperature. Warm blooded animals like us however maintain a constant body temperature.

This must mean that lizards are cooler in the winters and hotter in the summers, which should mean that they expand in the summers and contract in the winters, although by a very unnoticeable amount.

Does this really happen? How does the lizard or other cold blooded animals accommodate this expansion and contraction?


texts: Do common terms for animals such as amphibian or reptile fall somewhere in taxonomy levels?

texts: Where in the "ranks" of taxonomy (domain, kingdom, phylum etc.) do common words used to describe animals such as amphibian and reptile fall?


texts:
I hope this is the appropiate place for this question, asked from a math/physics perspective with little to no training in biology.

Bacteria are very small and live in huge colonies, ants are bigger (but also very small) and live in smaller colonies (but also very big). Ignoring the human species, I can't think of any big animal living in big colonies

Is there any name for this relation? I want to study it from two perspectives: first, why? (this may be easy to explain in terms of resource supply or energy available) and second, what is the precise relation? (clearly inverse, but linear, logarithmic...?)

Thanks!


texts: What is the length and number of the parts of a conformational epitope?

texts:
I am interested in the question whether exposure to protein A might create antibodies that also bind to protein B.

I am wondering whether, if the antigen of protein A is a conformational epitope, it would still be possible to predict (or at least guess at) the reaction against protein B with only a sequence comparison.

This might be possible if the subunits are long enough and if there are enough of them, which is why I ask about their length and number.


texts: Which organism has undergone the least evolutionary change?

texts:
A favorite documentary of mine is Encounters at the End of the World, in where, "Film-maker Werner Herzog travels to the McMurdo Station in Antarctica, looking to capture the continent's beauty and investigate the characters living there."

During his time there, he films under-ice divers who risk their lives to explore the depths of antartica's ocean waters to study organisms that are believed to have not evolved for millions (if not billions) of years.

  I noticed that the divers, in their routine, were not speaking at all. To me,
  they were like priests preparing for mass. Under the ice, the divers find themselves in a separate reality, where space and time acquire a strange new dimension.

  One of the foremost scholars in the world in his field, Dr. Pawlowski, studies the DNA sequences of foraminifera. What looks esoteric is in fact one of the fundamental questions about life on Earth. In the same way that cosmologists search for the origins of the universe, the scientists here are tracing back the evolution of life to its earliest stages.

While watching this part of the documentary, it always makes me wonder: Which form of live (lineage of organism) has undergone the least evolutionary change? And how exactly is this quantified - just differences in DNA/RNA?


texts: Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, mutation contribution and data dimensionality reduction. I could find Expander, MeV, Genesis software for the microarray experiments, however, could not find similar tools for the whole genome sequence analysis of mycobacteria. Sorry, that my question has no code.


texts: How much does a biological experiment to validate a gene function cost?

texts:
I am computer scientist working on machine learning methods applied to predicting missing Gene Ontology annotations.
In many papers, I wrote that my computational methods are very useful to suggest to the biologists  on which gene functions they should address their research, because my software need less resources (a simple laptop connected to a database) and less time (e.g. with a dataset of all the Homo sapiens Gene Ontology annotations: about 3 hours) than their biological experiments.

Now a reviewer asked me to be more precise. Truly, how much does an in vitro experiment to biologically validate a human Gene Ontology annotation run by biologists cost?

How much money, broadly?

How much time?


texts: Can connections between neurons be weakened?

texts:
Connections between neurons are said (by Wikipedia) to be strengthened as part of learning - can they also be weakened (below the original level)?

I understand the concept of the connections strengthening. After reading the article Ants Swarm Like Brains Think, my understanding is that positive feedback (I forget the words that I should use for positive vs negative action potentials) should strengthen the connection, and negative feedback should weaken it.

I'm interested to know whether neural connections can weaken below their original connection strength.

I'm curious about this so as to grasp the way that the human brain (or even simply the ant brain) learns good and bad. If I'm not completely wrong about what I'm asking, then I think I get it pretty well: The things that are good (like finding food) trigger positive feedback among the associated neuron groups, and the things that are bad (like pain or danger) trigger negative feedback in the associated neurons, and that's basically how brains learn good from bad.


texts: We have lots of lily flowers inside our garden. Their flowers are open in day and closed in night. How do lilies sense day and night and open and close their flowers?


texts: Would a clone of myself have exactly the same development (character, appearance) as me?

texts: If I'd have a clone of myself (with my DNA) and I would record the development of that person, would I be able see exactly the same development as myself (same personality, appearance)? For example that at a certain time, that clone would look how I looked like when I was 8?


texts: Plating 96-well bacterial transformations

texts:
I need to clone 96 different inserts into the same backbone in arrayed format. I am planning to perform Gibson assembly reactions in a 96 well plate, and then do chemical transformations in a 96 well format.
However, I am not sure how to plate 96 well transformations in the most efficient way. I could just plate them one by one onto petri dishes, dividing each petri dish into 4 sectors. However, I suppose there could be a better way of doing it. Any suggestions?


texts: How does receptor downregulation/upregulation work?

texts:
My understanding is that if a cell is flooded with a certain neurotransmitter, it may decrease the density of that neurotransmitter. What I don't understand is how.

Is it a direct physical result of the receptor-ligand complex being internalized? I.e., the receptors simply aren't there anymore, because they've been internalized?

Or, does the internalization of specific receptor-ligand complexes actually get sensed by the cell somehow, causing it to produce fewer receptors in the future?


texts: How good is the reproducibility of preclinical models?

texts:
Unofficially, biology researchers always complain how frequently fail to replicate results others have achieved. But of course, such failed experiments are underreported.

Is there data, or at least well-reasoned guesses, on what is the success rate of experiment replication in preclinical models? I don't mean translational research and the impossibility to replicate a mouse result in a human. My question is about failing to reproduce the results within the same model system, replicated at the detail level available in the original publication (e.g. same animal strain, same drug dosages, etc.)


texts:
This wikipedia page says that mesosomes are artifacts produced by chemical fixing techniques. Most of my textbooks still show a mesosome and describes it as having functions like - respiration, helping in DNA replication, etc.

Has the idea that it is an artifact been widely accepted by the scientific community ?


texts:
Let me explain... A friend and I read some articles, part of a Biology book, and watched a video on evolution. We then tried to explain what Evolution is to each other.

My friend said that Natural Selection is a mechanism inside the organism that mutates the DNA to make its offspring survive in an environment; that natural selection mutates the DNA beneficially and that random mutations are not useful (like blue eyes). But I disagree and think that it is closer to Lamarkian theory.

I told him that DNA from male and female recombines and randomly mutates making a new "recipe" for the offspring (adding a new characteristic(s)). If the offspring is well suited for the environment, then it survives and passes on its characteristics to its offspring. If it does not have fitness for its environment, it dies. So, Natural Selection is were nature "selects" who survives and reproduces a lot.

So is the DNA mutation process random or is mutation directed to make an organism that is suited to survive its environment?

None of my friends are Biology students, so I can't ask then which explanation is correct (or at least more valid).

I'd prefer you don't answer: "None of these explanations are correct," but to say which one is more valid and correct misconceptions or add more that is missing (of course these are only summaries of our discussion). But of course, you can answer that neither of our explanations is correct...


texts: Is there a way to identify a species of tree?

texts: My family has been passing down  seeds from a lemon tree for about 3 generations now, There is some controversy about its origin or species. The lemons look like tangerines and when cut the pulp is very orange but are sour just like lemons. People always think we dye the lemonade. We have asked family members where our family got the original seed from and some say it was from Vera Cruz, Mexico but other family members say it might have came from Hawaii. Regardless it appears to have been from a tropical region. Is there a way a seed or part of a tree can be tested? If so, how much can I expect it to cost and where could I get it done?


texts: How fast do different organs turn over cells?

texts:
It is said that the human body turns over all cells or molecules in 7 year cycles. This is not quite correct, because there are different organs changing at different speeds. My interest is what is the scale of change and especially, is it possible to measure and how fast do:

1) cells change

2) molecules change

3) atoms change

High, medium and max rate organ examples would be appreciated.


texts: Identify a lone bone (jaw including teeth) found on a beach at Trouville-sur-Mer (France) in 2018

texts:
Found this on the beach at Trouville-sur-Mer in France, on 11 May 2018. It was laying in the sand, close to a trash can. Considering the strong smell of sand within the skeleton, it must have been near the sea for a very long time.

What species is this from?

Also posted on other identification websites and fora:

https://www.inaturalist.org/observations/14323892
https://observation.org/waarneming/view/160056539
https://forum.waarneming.nl/smf/index.php?topic=431852.0
http://www.nhm.ac.uk/natureplus/message/115302/

The length of the bone (the piece remaining) is under 12 centimeter.

The height of the only easily removable tooth (the smallest remaining one) is under 25 milimeter.

Old pictures in sunlight (all in low resolution & without measure bar):

Click the images for enlargement.

Update of 22 July 2018 (most in higher resolution & with measure bar):

This new set of pictures is archived at Wikimedia Commons.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side A, photographed on 22 July 2018 - Image 1 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side A, photographed on 22 July 2018 - Image 2 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side A, photographed on 22 July 2018 - Image 3 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side B, photographed on 22 July 2018 - Image 1 of 2

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, side B, photographed on 22 July 2018 - Image 2 of 2

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, top side, photographed on 22 July 2018 - Image 1 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, top side, photographed on 22 July 2018 - Image 2 of 3

See Wikimedia Commons for a higher resolution.

Jaw with teeth (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, length smaller than 12cm, top side, photographed on 22 July 2018 - Image 3 of 3

See Wikimedia Commons for a higher resolution.

Smallest remaining tooth from jaw (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, height smaller than 25mm, side B, photographed on 22 July 2018 - Image 1 of 2

See Wikimedia Commons for a higher resolution.

Smallest remaining tooth from jaw (lone animal bone) found on beach of Trouville-sur-Mer in France on 11 May 2018, height smaller than 25mm, side B, photographed on 22 July 2018 - Image 2 of 2

See Wikimedia Commons for a higher resolution.


texts: Quantification of various amino acids from bacteria?

texts:
I would like to characterise how much of various (uncommon) cytosolic amino acids  are produced in bacteria, and was wondering if there are good suggestions of how to go about doing this. I know that chromatography is a good end-point analysis once I have isolated a fraction of what I suspect contains the amino acids; however, I am unsure about the smartest way to do the 'rough' initial purification prior to chromatography.
I know that you in general lyse the cells, pellet cell debris and then start some form of purification. I have also heard of certain resins that can bind natural products (e.g. Diaion® HP20, synthetic adsorbent resin) had thus aid the first purification step of the amino acids. Do people have experience with this? Are there also good solvents for separation of amino acids from lysate, that could be used in the first step (phase separation)? Does someone have any experiences with this? Any alternative suggestions would be appreciated.


texts: Can you recognize this larvae that came from a human nose? (probable nasal myiasis?

texts: Those larvae came at least four different times from the nose (inside - from the mucosal) of a 60 year old man from a tropical area in South America. He lives and works in a city with a tropical climate. On another occasion a living insect came out of his nose, the picture is also attached.


texts:
I'm sorry if "gene markers" is not the correct word. An edit could be appreciated but I don't study in an English speaking country unfortunately.

Question overview:

In a family, there is a genetic, dominant disease. The father and a son is sick.
A gene marker analysis is performed with markers close to the assumed mutated gene on chromosome 11.

Marker D11S4088

Marker D11S1344

How do I read these and "What sort of markers are these"? I'm not sure what is going on here and I'm not sure what to search either due to language problems.

Thanks!


texts: Is it possible to get (an estimation of) reaction rates from the Michaelis constant?

texts: I want to apply the Gillespie Algorithm to a biological system so I need to know the reaction rates for the relevant reactions. However, for all those reactions, I only know the Michaelis constant $K_M$ and the maximum rate $V_{max}$ (see Wikipedia). Is it possible to derive (an estimation of) the reaction rates $k_f$, $k_r$ and $k_{cat}$ (see image below) given $K_M$ and $V_{max}$? If so, how can it be done?


texts: Why do stem cells injected into muscle become muscle cells?

texts:
In this article published in Science Daily, researchers injected teratoma-derived stem cells into mice with muscular dystrophy, and the stem cells regenerated 80% of the lost muscle. But what is the mechanism that results in their becoming muscle cells, rather than any other type of cell?

I'd have to assume some sort of cell signaling is responsible for this directed differentiation into muscle cells, so what is it? Can it be reproduced in vitro?


texts: Shot in Brasil.  Anybody know what it is called!!?


texts: DNA Longevity in Keratin, Ivory and other Bioplastics

texts: For how long is DNA viable for extraction and/or sequencing in bioplastics created by the human body? I checked out a few links online, and this article gives a record of about 7000 years for frozen mitochondrial DNA, and Ötzi's DNA remined viable for 5000 years. However, I suspect that the samples used to analyze both were not taken from anything that was like keratin or ivory, with their limited cellular matrix. What is the longest record of sequence-viable DNA being stored that way?


texts: I was reading an article on Hydra where they mentioned Nematocyst Battery. I know that Hydra and other Cnidarians have nematocyst but why are they called Nematocyst 'Battery'?


texts:
Kombucha can be brewed even with tiny amounts of inocculate, such as the little bit of sediment at the bottom of store-bought kombuchas. Over 1-2 weeks, this can grow into an inch thick film covering the entire surface of the brew; a very striking accumulation of biomass. Where is the material for this biomass coming from?

It seems like most recipes for kombucha brew consist of:

5.7% sugar
0.7% black tea
10-30% of a previous, "finished" kombucha
SCOBY (optional, the kombucha in the previous step is sufficient)

I can see how the sugar provides carbon, oxygen, hydrogen and energy. Of course, merely providing the elements is not necessarily sufficient, since often enough cells require specific compounds as well. But I'll assume the SCOBY community, in aggregate, is able to transform the sugar into every CHO compound it needs. However, what about nitrogen? The amount of tea seems minute, and tea seems like not a very rich source of protein/amino acids. Sugar doesn't contain nitrogen, and while dead SCOBY constituents from the initial kombucha can conceivably be cannibalized, the cannibalism cannot account for dramatic increase of SCOBY biomass because of conservation of mass.


texts: Cyanobacteria: Gram negative or Gram positive?

texts:
My (school) textbook states that cyanobacteria ("blue-green algae") are Gram positive (no references provided). They mention this at several points over the chapter we're doing so it doesn't look like a typo.

However, this Wikipedia article on "Gram staining" (under "Gram negative bacteria") states:

  Gram-negative bacteria generally possess a thin layer of peptidoglycan between two membranes (diderms). Most bacterial phyla are gram-negative, including the cyanobacteria, spirochaetes, and green sulfur bacteria, and most Proteobacteria (exceptions being some members of the Rickettsiales and the insect-endosymbionts of the Enterobacteriales).

   Emphasis, mine.

There is no mention of cyanobacteria under the section "Gram positive bacteria".

I understand that there is a possibility that some cyanobacteria stain positive, and other stain negative (owing to the lack of a very sharp definition for "cyanobacteria", as well as the limitations of Gram-staining).

So what I want to know:

1) Are cyanobacteria generally Gram positive or Gram negative?

2) Are there exceptions to that general trend? If so, what are they?


texts:
Raynaud's phenomenon can be a serious health issue, as the blood flow to the extremities, mainly the fingers is compromised, causing fingers to blanche, and then turn blue. Severe Raynaud's can cause gangrene in illnesses like progressive/ diffuse scleroderma.

I am not asking about connective tissue disease per se, but what occurs during an actual Raynaud event (for a better way of putting it), not what precipitates the condition to occur within a particular person and not another.

what are the underlying biological processes that cause the blood flow to be compromised like this?


texts:
How do gory images lead to nausea?

Yesterday my friend visited shock sites (a website). He said that he got nauseous sensation within seconds after viewing the gory images. However, I don't understand how seeing such sights can lead to nausea? Eyes are present at the top of the head and the digestive tract is present below the mouth. They aren't physically connected.


texts: Has medical progress stopped human evolution?

texts:
We can cure many diseases nowadays, and thus the natural selection is very limited.
Plus, mankind spent the whole beginning of its existence in almost the same hostile environment, and that's where he evolved the most, whereas our environment is changing very quickly. So, can we say that mankind froze, if not stopped, its own evolution ?


texts: What is the direction of the processing of light by the (human) retina and how does it happen?

texts:
Quoting Textbook of Medical Physiology by Guyton and Hall, 2016, page 647,

  ...the functional components of the retina, which are arranged in layers from the outside to the inside as follows:

  (1) pigmented layer, (2) layer of rods and cones projecting to the pigment, (3) outer nuclear layer containing the cell bodies of
   the rods and cones, (4) outer plexiform layer, (5) inner nuclear layer, (6) inner plexiform layer, (7) ganglionic layer, (8) layer of optic nerve fibers, and (9) inner limiting membrane.

  After light passes through the lens system of the eye and then through the vitreous humor, it enters the retina from the inside of the eye (see Figure 51-1); that is, it passes first through the ganglion cells and then through the plexiform and nuclear layers before it finally reaches the layer of rods and cones located all the way on the outer edge of the retina. This distance is a thickness of several hundred micrometers; visual acuity is decreased by this passage through such nonhomogeneous tissue. However, in the central foveal region of the retina, as discussed subsequently, the inside layers are pulled aside to decrease this loss of acuity.

I have attached Figure 51-1 for people who would like to see it.

My questions are: How does light travel to the inner parts of the retina first even when there are so many impeding layers preceding it? Why does it not stimulate the photoreceptors first? What is the pathway of the light after it travels to the the innermost retinal layer? Are the photoreceptors the first to be stimulated by the light?

As can be understood, I am quite confused, so if the framing of any question is reflective of erroneous understanding, kindly let me know. All help appreciated.


texts: How does an octopus eye react in free fall?

texts:
according to Wikipedia:

  Attached to the brain are two special organs, called statocysts, that allow the octopus to sense the orientation of its body relative to horizontal. An autonomic response keeps the octopus's eyes oriented so the pupil slit is always horizontal.

so how would an octopus' eye react on the ISS (assuming the octopus has an aquarium or something it can live in)? In which direction would the eye be parallel to?


texts: Are these Gram stain substitutions acceptable?

texts:
In the context of a Gram stain on a blood smear:

Are the following acceptable substitutions and/or what differences could arise by substituting them?

Using methylene blue instead of crystal violet
Using carbol fuchsin instead of safranine

I've seen text implying they are OK substitutes, but didn't find anything saying the if, why, or problems associated with replacement.


texts: Can somebody identify this species of spider?

texts: I ran into this cool looking spider in my yard in Banjaluka, Bosnia and Herzegovina.  It's about the size of a fingernail and unusually shaped (spherical). Could it be poisonous?


texts: In my textbook, it is written that atheromatous plaques block the artery. This leads to heart attack and and heart failure. But my question is why do the plaques only block arteries and not the veins? Do the plaques also block the veins?


texts:
One interesting thing I recently learned is that venom has medical uses that can actually save lives! But from what I see so far this either applies to venoms from creatures that are not fatal to humans or that only proteins or enzymes from these venoms are what is being used medically.

Are these proteins or enzymes themselves fatal to humans or is this just a misrepresentation of the fact that venoms can save human lives?

EDIT: To clarfiy, while I realize venom is harmless in lower doses, I also read the following :
Enzymes from cobra venom may be instrumental to finding cures for Parkinson's disease and Alzheimer's disease.
An enzyme derived from copperhead venom could be used to treatment for breast cancer.

What I was not sure of was whether the enzyme by itself was toxic or they were just extracting a non-lethal element of the venom to use medically. Can this enzyme alone of venom administered in large enough doses be fatal?


texts: I found this strange star-like thing while observing a slide of onion root somatic cells. I don't know that it is; I even doubt if it is an organism. It has conical arms directed  radially outwards all over it's body. It wasn't moving. If it was indeed living,  maybe I had killed it while flaming the slide. Anyway, I am interested in knowing more about this  unexpected guest of mine. Can anyone tell me what it is ?


texts: What are possible health risks to women having large numbers of children?

texts:
What is the possible health issue the women would face in this record?

  The record for most children born to a single couple belongs to the
  first wife of Feodor Vassilyev of Russia. In 27 pregnancies between
  1725 and 1765 she gave birth to 16 pairs of twins, 7 sets of triplets,
  and 4 sets of quadruplets for a grand total of 69 children.


texts: What does ophthalmologist see in your eye?

texts: I always wondered what ophthalmologists see inside someone's eye and what they're looking for. The whole thing is a mystery to me. Are there any photos of what the eye of a patient looks like from the doctor's point of view?


texts: What makes us all different and similar to some extent?

texts:
It is said that genes define how we look physically and psychologically; so for example if a male human sperm carries a certain number of genes, say x, and a female carries y, then mathematically there would be m genes from the male and n from the female, and a finite total available. Could there be people identical in appearance if the same genetic combinations recur?

Also we find similar-looking people with perhaps similar behaviour accross diferent geographic locations; does this means that they have similar genetic make-up, up to some percentage?

Please correct my biology and share the possiblity of having genetically identical people across different geographic locations.


texts: What is meant by "50% related to sibling" versus "95% related to chimpanzee"?

texts:
Obviously I am more related to my sister than to a chimpanzee, so what do these different percentages actually refer to?

Here is my preliminary research:

https://genetics.thetech.org/ask-a-geneticist/siblings-are-around-fifty-percent-related/

https://genetics.thetech.org/ask/ask395/


texts: Please identify this tree in the Netherlands

texts: Please identify this tree for me. It was found in a park in Eindhoven, Netherlands.


texts:
We learned that Cytotoxic T cells are MHC dependent, and if CMH matchup doesn't occur between the T cell and the cancer cell for example, the former won't attack the latter.
If this is the case then how are T cells given through vaccines and transfers?


texts: How is transport of glucose into prokaryotic cells different from transport into eukaryotic cells?

texts:
I was reading page 92 of Fundamentals of Microbiology, 4th edition, which states

  In facilitated diffusion, the substance (glucose, for example) to be transported combines with a plasma membrane protein called a transporter.

The section of text that says this is in a section describing prokaryotic cell anatomy. As far as I understand human biology, (just to use one example) that facilitated diffusion is regulated by insulin, which, to use less than perfect language simply to streamline my question, uses insulin to "unlock" the plasma membrane proteins.

What's the difference when prokaryotic cells aren't dependent upon insulin to get glucose in?


texts:
Processing bodies (P-bodies) are distinct foci within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover (ref). They play a fundamental role in RNA silencing/interference, particularly as an antiviral response, since they are the key site for siRNA-bound RISCs (small interfering RNA-bound RNA-induced silencing complexes) to degrade mRNA with an exogenous origin. Some mRNAs entering P-bodies then leave and re-initiate translation, and the switching mechanism for this is currently poorly understood.

However, I'm not clear on whether all mRNAs pass through P-bodies at some point, when not actively involved in translation. Is there is a separate step by which mRNAs of exogenous origin are specifically (or more rapidly) recruited to P-bodies - and, if this happens, how are they specifically targeted for this uptake?

It seems rather odd if RNAi has evolved to give viruses two independent targets for evasion, but if the only requirement for recruitment to a P-body (and potentially degraded via RNAi) is to not be currently involved in translation, wouldn't that select for viral proteins to be more highly translated (and therefore postpone movement to the P-body)? I don't really understand why mRNA processing doesn't simply occur in the cytoplasm.

The paper cited above says "The available evidence indicates that P bodies are sites where mRNAs that are not being translated accumulate, the information carried by associated proteins and regulatory RNAs is integrated, and their fate — either translation, silencing or decay — is decided", but this is from 2007 and I'm aware RNAi is a very fast-moving field.


texts: Spider found in Richmond, VA. Can anyone identify?


texts: What happens if a circulating naive B cell is met with a polysaccharide/lipid antigen?

texts:
These antigens should provoke a T-independent response, so will they differentiate then and there to form short-lived plasma cells?
Or do they have to go to lymphoid tissue, enter a B follicle, and then differentiate?
and can they differentiate into short-lived memory cells and short-lived plasma cells? Or only the latter?


texts: How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in FASTA format?

texts: The file size is really big (26.7 MB). So, I am unable to use the online web tools, as they cannot handle such large input data.


texts: Why is second pKa value of phosphoric acid different across different sources?

texts:
Am I missing something very fundamental here for phosphoric acid's second pKa value?

I check the Wikipedia page and these are the values: (1) 2.148, (2) 7.198, (3) 12.377
Then I check Sigma-Aldrich website and it says: (1) 2.15, (2) 6.82, (3) 12.38

Why is the second pKa value different? Any ideas?

I need to prepare potassium phosphate buffer for my proteins and got stuck with this simple problem.


texts:
I saw the following passage in the NPR 13.7 Cosmos & Culture commentary post The Big Idea Behind Big Data.

Using the Internet's first generation of Big Data, researchers like physicist Albert-László Barabási of Northeastern discovered hubs controlling the behavior of all large networks from protein regulation to webpages.
"Nature evolved the metabolic network for cells over 4 billion years," says Barabasi, "but that same architecture emerged in the World Wide Web after just a decade."
Different networks, same laws.

In a complex multicellular organism there is plenty of signaling between cells types and organs, and this can be viewed as a network.
But does network theory also apply to protein regulation within a cell? I should really ask; Has network theory been successfully applied to protein expression within a cell?
I ask this because it seems according to this clickable timeline template that 4 billion years ago, life was single-celled.
edit: There is a single link in the Wikipedia article that points to this paper, but the abstract is over my head, and I'm not sure if this is a one-off attempt, or if network theory is an established method that has useful success in explaining/understanding/predicting protein expression within cells.


texts: Why would mutation rates increase in a tumour?

texts:
This article describes a tumour:

Swanton found that even the primary tumour was surprisingly varied. He found 128 mutations among the various samples, but only a third of these were common to all of them. A quarter of the mutations were “private” ones – unique to a single sample.
The tumour had also split down two evolutionary lines. One area – part of R4 in the picture – had doubled its usual tally of chromosomes and seeded all the secondary tumours in the patient’s chest. The other branch had spawned the rest of the primary tumour. Even though this tumour looks like a single mass, whose cells all descended from a common ancestor, its different parts arehave all  evolved independently of one another.

My understanding is that if non-cancerous cells normally had such a rate of mutation it would be lethal to the cell if not the organism.

What about tumour cells would lead to a higher incidence of mutation?
How are these cells able to survive when non-cancerous cells would perish?


texts: The white blood cells' function is mainly to fight off external antigens. However, another one of its traits is its ability to bind to vascular endothelial cells with the help of L-selectin. What is the purpose of this, and how does this help us？


texts: Which diagram correctly describe an effect of tar entering lungs?

texts:
Which flow diagram correctly describes the effect of tar entering lungs?

Tar is a cause of Chronic obstructive pulmonary disease (COPD) which includes both chronic bronchitis and emphysema and it is also a carcinogen, too. So, I think that A, B, and C would be correct answers, but the solution is A. Why B and C are incorrect?

Thank you very much!


texts: (how) is it possible to choose the biological sex of a child?

texts: I recently read of a study that investigated the ethics of child's biological sex choice in humans, and now I want to find out how this can/could be done. Does anyone know of scientific papers or journals that describe the methods in some detail? The answers I was finding in my own search were not as specific as I would like.