texts: How does the inactivation process of vaccines work on a cellular level? e.g. how does an inactivated virus look really?

texts:
it's very easy to find information what is an inactivated or dead virus, more or less.
But I want the full detail.
If you heat treat a virus, what is left of it? like chopping the virus into pieces? destroy the dna / rna but keep the membrane in tact?
how can you imagine a dead/killed virus if it didn't live in the first place?
it cannot reproduce - why not? like, what happens exactly


texts: Is there a difference between macroevolution and group selection?

texts:
I encountered two different attitudes towards macroevolution:

The first one included long-term microevolution such as the evolution of Cetacea.
The second one included only macroevolution in terms of group-selection - that is for example the evolution of altruistic behaviour (the groups - families or tribes survived more likely if they were altruistic and shared the resources).

What about for example evolution of the parental instinct? Would it be considered a macroevolutionary (because it is about the evolution of families) or a microevolutionary trait?

And in general, am I getting macroevolution right with the second attitude?


texts: If plants benefit from carbon dioxide, why is car traffic something bad?

texts:
This is going to sound really stupid or as a joke, but... Ever since I was a little kid, I have been confused about the following:

Humans need air/oxygen to breathe in order to live.
Plants/trees/bushes/flowers produce this oxygen, and are thus crucial for humans to survive.
Plants/trees/bushes/flowers need "carbon dioxide" to survive, just like humans need oxygen.
Plants/trees/bushes/flowers MAY also need some oxygen/air? (I assume so.)
Cars (traditional ones) output "carbon dioxide"... yet they are... not good for nature?

I don't understand how this fits together. It seems as if nature should absolutely thrive in the middle of highways and nearby, if they get so much nice carbon dioxide from the cars! Yet cars are instinctively seen (also by me) as "evil nature-polluting machines of death". Car exhaust seems to be the opposite of what a plant or tree wants, yet it's full of carbon dioxide, so... why?

Can somebody explain this once and for all?


texts: Why do some drugs require you to take them in an "upright position"?

texts: A friend of mine was taking the supplement Metamucil and on the container it says to take in an "upright position." Why would this be necessary? Doesn't your digestive system push food/liquid downwards anyways?


texts: Was Dr. Livesey's treatment a valid one in the Treasure Islands?

texts:
Here is that incident from Treasure Island by Robert Louis Stevenson, where Billy Bones had a 'minor' heart attack or a stroke (according to R.L. Stevenson).

To give a little background about Billy Bones, he was a pirate, a toughened and hardened person who has gone through the deadly and unethical ordeals of life. He was an alcoholic and used to drink rum a lot. Dr. Livesey had previously warned him of taking any rum at all. But its quite a daunting task to let go a life long bad habit. Another thing worthy to be mentioned is that (to me it felt) Billy Bones had a very short temper which is indicative that he is a very likely candidate of high blood pressure.

In one incident, Billy Bones had a fight with an old foe of him. His foe escaped after collecting some major injuries caused by Billy Bones namely known as the Captain in Admiral Benbow inn. As the fugitive left the vicinity, Billy Bones gasping called out for rum and immediately he fainted.

  I heard a loud fall in the parlour, and running in, beheld the captain lying full length upon the floor. ...He was breathing very loud and hard, but his eyes were closed and his face a horrible colour.

Jim called in Dr. Livesey downstairs who was treating Jim's father upstairs.

  “Oh, doctor,” we cried, “what shall we do? Where is he wounded?”

  “Wounded? A fiddle-stick's end!” said Dr. Livesey. “No more wounded
  than you or I. The man has had a stroke, as I warned him... I must do my best to save this fellow's terribly worthless life; Jim, you get me a basin.”

  When I got back with the basin, the doctor had already ripped up the captain's sleeve and exposed his great sinewy arm. It was tattooed in several places...

  “Prophetic,” said the doctor, touching this picture with his finger.
  “And now, Master Billy Bones, if that be your name, we'll have a look
  at the colour of your blood. Jim,” he said, “are you afraid of blood?”

  “No, sir,” said I.

  “Well, then,” said he, “you hold the basin”; and with that he took his lancet and opened a vein.

My question is about Dr. Livesey's little surgery. R.L. Stevenson writes after this 'surgery',

  A great deal of blood was taken before the captain opened his eyes and looked mistily about him.

It almost had an immediate positive effect on the patient. My question is about Dr. Livesey's little surgery. What did he do here? Was it any form of valid treatment?


texts: What are the highest and lowest possible pH, paCO2 and HCO3 in the blood of living human?

texts: What are the highest and lowest possible values of pH, $paCO_2$, and $HCO_3$ in the (arterial or venous) blood of a living human being?


texts: Why is the current Ebola outbreak different from previous outbreaks?

texts: I don't know if this question has an answer at this time, but I would like to know if there is some biological reason why the current Ebola outbreak is so much more complicated and widespread than in the past. Traditionally it has been initially very virulent and has then has rapidly waned. I hope what I am saying is accurate, and if so why dont we see the same pattern now ?


texts: This was found in my home in Mojave county Arizona. It was about 1/8 inch long. I have a cat. Hoping not a flea.


texts: At what level of relation does inbreeding become dangerous?

texts:
Inbreeding within first cousins appears to have an established history of dangers, and anything closer than that relationship also.

However, how distantly related do two individuals have to be for the risks of inbreeding to be in line with having a child with an unrelated person?

Are second cousin children more likely to have children with defects? 3rd cousins? 4th?


texts: Why is CLL B-Cell leukemia t(12;21) more responsive to chemotherapy?

texts: Chronic Lympoid Leukemia targeting B-Cell (with the particular translocation mutation on chromosome 12 and 21) is known to be more responsive to chemotherapy. Is there a known molecular mechanism for why?


texts: What effect does the Barr body have, in relation to female Turner syndrome?

texts: Why do persons with Turner syndrome have  developmental abnormalities, when normal XX-females do not, even though they only have 1 active X chromosome? From what I know, one X-chromosome is inactivated into a Barr body in normal XX-females, but these obviously don't show the symptoms of Turner syndrome. What function does the inactive chromosome have?


texts: Difference in length of Okazaki fragments

texts:
The length of Okazaki fragments in the lagging strand is about 100-200 nucleotides in eukaryotes and about 1000-2000 nucleotides in prokaryotes.

  What (molecular mechanism, enzyme type ) determines the length of
  these Okazaki fragments?

  Moreover, which, longer or shorter, fragments would be more
  advantageous (energetically and considering accuracy)?

Longer fragments means less use of DNA ligase, DNA polymerase-I (prokaryotes) and other enzymes required to convert the okazaki fragments with dispersed RNA primers into a normal strand, and hence lesser scope of mistakes during replication in the lagging strand. Shorter Okazaki fragments improve telomere longevity, by reducing the capped-off portion after every division. Which of these views is correct?


texts: Can DNA test of my grandparent's brother reveal my heritage from that branch of the family?

texts:
I'm thinking about doing that DNA test on all my grandparents to know where their genes come from. They are getting very old and I don't want to let the opportunity pass to gather more knowledge about my heritage, something I find very interesting.

One of my grandparents died long ago, but he still has a brother and I was wondering if DNA testing him would reveal relevant information about my heritage from that branch of my family tree. Obviously all of his genes come from family of mine(his parents) but not all of his genes are the same as my grandparent's. Just how should I look at his tests to find information about my heritage?

By the way can I really trust these sort of tests?


texts: How are negligibly senescent animals dealing with senescent cell buildup?

texts: Well known animals like the rougheye rockfish, which can be bought from the fish market, appear to be negligily senecent. Senecent cell buildup appears to play a key role in senecence, in mice at least (http://www.nature.com/nature/journal/v530/n7589/abs/nature16932.html). Is there no buildup of senecent cells in such negligible senescent animals over livetime?


texts: Vigorous shaking for HFR interrupted mating

texts:
I am trying to reproduce E. coli interrupted mating using an HFR strain, and I read that the cultures should be vigorously shaken  at times to interrupt the DNA transfer from the F+(HFR) donors to the F- cells.

How vigorously(I'm OK with a qualitative answer) should I shake the culture for optimal results?


texts: I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606 and on ftp://ftp.ncbi.nlm.nih.gov/snp/database/shared_data/. I tried to use the search on this webpage : http://www.ncbi.nlm.nih.gov/SNP/snp_db_list_table.cgi which is supposed to be a data dictionary for all tables and columns, but I think it is outdated. There are many tables which do not have any definition. Also, there are tables in this dictionary that are not in the ftp site at all. Does anyone know of any better dictionary for the dbSNP database tables?


texts: What causes the variable/conserved structure in the 16S rRNA gene?

texts:
See the image below for a visual representation of the 16S rRNA gene. It is composed of conserved and variable regions however I can't see to find a reasoning for why this is the case

Thanks


texts: Why is the administration of exogenous Anti-D not harmful to the foetus?

texts:
Haemolytic disease of the newborn can result from Rhesus incompatibility in utero.  In this disease an Rh- mother becomes exposed to the antigens of an Rh+ foetus by fetomaternal haemorrhage causing her to mount an immune response against the D antigen.  In her second pregnancy, repeat exposure to the D antigen activates memory cells causing a large production of IgG Anti-D antibodies that cross the placenta adhering to foetal red blood cells, which are then destroyed.
To prevent this, Rh- mothers are normally given exogenous Anti-D at 28 and 34 weeks gestation or after any sensitising event.  The aim of this treatment as I understand it is to 'mop up' any D antigen in the maternal bloodstream, covering it in exogenous antigen so the mother's immune system does not mount its own response.
I had previously assumed that these exogenous antibodies would be IgM to avoid them crossing the placenta, however looking at the summaries of product characteristics for some of the common preparations I see that "at least 95%" of protein content other than albumin is IgG.  I then wondered if the exogenous antibodies had a much reduced half life, however the half life is "about 3-4 weeks."
Why does the exogenous IgG not cause haemolytic disease of the newborn in the exact same way that endogenous IgG would in a previously exposed woman who had not had prophylaxis?  Is it dose-dependent or am I missing something entirely?


texts: New infectious diseases appear mainly as a result of chance mutations in pathogen genomes?

texts: I am reading the book 'Homo Deus: A breief History of Humankid' by Harari. He mentions the following statement highlighted in the picture below (picture provided for context). I would be appreciated if someone could (1) explain the meaning of it (I have very little background in Biology) and (2) the reason behind it.


texts: In the below picture I believe  bird in the foreground is a female. The one that opens the wings is the male.


texts: Can a drug induce specific mechanism of resistance in tumors?

texts:
For example, can a drug that targets a given protein induce overexpression of that protein or increase the copy number of the gene coding that protein?

I strongly suspect that antineoplastic resistance happens due to natural selection alone but I was wondering if there are examples that suggest otherwise.


texts: what is this bug ? i found it on bed 2 times

texts:
What is this 1mm long bug I found on my bed in Egypt?

Here is its back photo


texts: What are preparation mistakes that could make red blood cells appear crenate in isotonic solution?

texts:
Thank you for your time. I separated red blood cells from a whole blood sample purchased from a blood bank. In isotonic solution, the red cells appear crenate. I would like to know if there is anything wrong with my procedure. I used the following controls:

I purchased two samples which came from two different donors. Both samples are more than 48 hours old.
I used three different solutions to spin the blood including RMPI 1640, saline solution, and phosphate buffered saline. I used multiple solutions because the RMPI is past the expiration date.
I spun one sample at high speed and the other sample at low speed.
The first sample was delivered at room temperature, it was not on ice. The second sample was on ice. I believe the buffers and the blood sample were roughly the same temperature when I spun them.
I mixed the buffer solution with the RBCs by gently rocking the test tubes back and forth.
Thinking that the problem may be when I preparing slides, I cut the tip of the pipette in case pressure was disturbing them.
I used both refrigerator and room temperature isotonic solution when preparing the slides.
I use a spacer in the slides with double sided tape and I seal it with nail polish. I'm not sure if that should matter.

If you have any ideas as to why the RBCs look like burr cells in isotonic solution, I'd greatly appreciate it if you'd share them with me. Thank you!


texts: Lateral corticospinal tract and termination

texts:
I'm studying the motor pathways of the brain and I'm a bit confused about how the lateral corticospinal tract descends.

From Neuroanatomy: Text and Atlas by Martin, J. H., 4th edition, right before Figure 10-4:

  Some of these [terminating] axons descend ipsilaterally; many descend
  contra-laterally and re-cross midline within the gray matter in lamina 10.
  The function of these ipsilateral axons is not well understood.

I understand that the axons cross over at the Pyramidal decussation, but this paragraph is really confusing me. What descent is being referenced here? Is it descending in the spinal chord? Alternatively, is the paragraph implying that some axons don't decussate in the pyramidal decussation?


texts: Do brain cells regenerate in the adult brain?

texts:
I know that most cells in the body regenerate, dying and being replaced with new cells. For example, in bone special enzymes move radially outward from the marrow in a narrow tunnel, destroying the old bone as they go and replacing it with new bone cells. In this way, our bones are slowly regrowing and being replaced constantly.

Is a similar process at work in the adult brain? Do neurons in the adult brain die and become replaced with new neurons? If so, how are the connections re-established? Each neuron is connected to other neurons by a complex network. If cells are regenerated, how do they re-connect to existing cells?


texts: Can acetylcholine leak away from the synapse and cause spasms?

texts: I am currently studying Pharmacology and a question came to mind. We know that Acetylcholine is used as a neurotransmitter in the neuromuscular junction, both Sympathetic as Parasympathetic, but as I understand, correct me if I am wrong, they don't interfere with each other because of their locations being physically separated. My question is, could somehow occur the incomplete absorption of Acetylcholine in the receptor of the organ, let's say for a Parasympathetic response and it "leaked" to a nearby muscle or even into a Sympathetic receptor and create a involuntary movement for example?


texts: Which classes of drugs (filed by their pharmacology) induce a release of β-endorphin?

texts:
Which classes of drugs (filed by their binding sites) induce a release of β-endorphin? I know of agonists of the nAChRs and 5-HT1A and ethanol. Are there any others?

Please cite journal articles with links to the respective articles


texts:
I was watching a lecture by Richard Dawkins earlier today and he mentioned that “Your 185th million grandfather was a fish.” I started wondering about the following question,

Is it true that my 185th million grandfather is the same as your 185th million grandfather?

Now, I fully recognize that there are more generations in my family tree than in yours or vice-versa so the 185 million may not match up exactly. This is not the point of the question. Do Humans share a common ancestor substantially after the origin of life?


texts:
Why do men produce so much spermatozoa, that will get discarded, but women, just one ovulum, which is a good one.
Couldn't men produce good spermatozoa as a limited edition?
Where is the evolutionary advantage of things being like they are?


texts:
I have 4 RNA-seq samples (1st is control and the other 3 are treatments) and 5 spikes. I used different concentrations for 5 spikes but over different samples, I used similar concentration. for example I used similar concentration for spike1 in 4 samples. and this is the case for the rest of spikes. I am trying to normalize the read counts for the spike. do you guys know how to do that?

this is what I have done so far:
I counted the spikes in different samples and and got the ration of them (treatments compared to the control for all spikes). the ratio is as expected (looking at the concentration of spikes).
one thing that I can do to correct the read counts for spikes is to multiply by the ratio between samples. but I am not sure if that is the right way.


texts: How can toddlers expend seemingly boundless energy when they eat so little?

texts: A toddler's food intake seems very little: only milk and water and some solid food. Therefore, from where does this energy come?


texts: Why are bed bugs attracted to Carbon Dioxide?

texts: All over the Internet it says bed bugs are attracted to Carbon Dioxide. This is why they congregate around beds. Your bed is the only place you are stationary for long enough periods of the day to exhale enough Carbon Dioxide. So, I grant that there seems to be a consensus that they are in fact attracted to Carbon Dioxide. But, why? Certainly they're not breathing it. (Are they?) I was under the assumption that all animals are aerobic.


texts: Why did life on Earth develop with two sexes?

texts: If evolution gives us the best adapted organisms for survival of the fittest, why does so many of Earth's organisms require two sexes for reproduction?  Shouldn't this have been bred out of our populations millennia ago?


texts: What actually kills a plant that requires winter dormancy if it is kept indoors all year?

texts:
In bonsai practice, beginners will commonly purchase a juniper (often Juniperus procumbens 'Nana'), which is an outdoor tree, and keep it inside all year.  The tree invariably dies.  It is commonly explained to the beginners that this is because junipers are outdoor trees and require a winter dormancy.
My question is what exactly goes wrong that leads to the death of the plant?  Let's assume that the person gives the tree appropriate care, e.g. assume that desiccation or root rot or other more direct causes of death are not the reason.  (Of course, a valid answer is that it is impossible to give "appropriate care" for some specific reason.)
I have two strong hypotheses, in more detail but not in a rigorously scientifically biological detail.

The first is that the warmth and low humidity of the indoor environment cause the plant to continue to transpire water and attempt to grow or maintain foliar mass, while the reduced daylight hours signal the plant to "do something" (what, though?) that results in lower metabolic action.  And so the tree expends its stored energy (starches and sugars?).  Then in spring, the when the tree tries to put on a strong flush of growth, it has nothing left to build on.  So it struggles and eventually dies.

The second is that there is a daily metabolic cycle that is disrupted when the tree is kept in the more or less constant indoor environment.  That is, there is a cycle that depends on the daily differences in temperature and humidity the tree experiences during daytime and nighttime.  Through my own measurements, I have found, for example, that the vapor pressure deficit (VPD) reduces to near zero outdoors during the night in springtime as temperatures drop and relative humidity rises.  This, I think, means the respiration demands on the tree are near zero.  That is not the case indoors, where the VPD is more or less constant.

Is either of those at all consistent with what really happens?  And what does really happen from a biological perspective?  That is, what part of the plant's metabolism fails?  Is there something that happens during dormancy that doesn't happen when it doesn't get a cold dormant period?  Is there something detrimental that happens when it should be dormant but isn't?
If anyone has any pointers to resources where I could do further research on this question, that would be much appreciated, too, and I will update here with any further information I can find.


texts:
I need a ppi network for cancer or Alzheimer .
I'm using BioGrid , In the search field I can specify the gene id only ,
I want to know how can I make an interaction network for one of the disease ? the only condition is the network ought to be huge , 3k 2k proteins .
I had used IntAct , String but none seem to give me what I'm looking for

If not could anyone give me a direct download link of such network


texts: I have performed PCR with 50 μL, which showed a clear band in the gel electrophoresis. I then performed large-scale PCR with 3650 μL, which showed an unclear band in the gel electrophoresis. What can be reason for this? Could it be plasmid loss even though there is a band, just a very unclear one? It should be mentioned that the single PCR was performed in the summer, and the large-scale was performed now


texts: Do all parts of a plant contain the same type of cell?

texts:
I have only learned about the plant cell which is shown below. But plant stems alone are made up of different parts like xylem, phloem, parenchymatous cells, sclerenchymatous cells etc.

Are all the parts of a plant made up of cells like the one in this diagram or is the cell diagram changed for different parts of a plant?


texts: Which theory has more evidence, humans appeared in Africa 200,000 years ago, or there were already humans in Europe at least 210,000 years ago?

texts:
This theory

Modern humans originated from a woman who lived in modern day Botswana

says

  Every person alive today descended from a woman who lived in
  modern-day Botswana about 200,000 years ago

And this finding states

Piece of skull found in Greece ‘is oldest human fossil outside Africa’

  A broken skull chiselled from a lump of rock in a cave in Greece is
  the oldest modern human fossil ever found outside Africa, researchers
  claim.

  The partial skull was discovered in the Apidima cave on the Mani
  peninsula of the southern Peloponnese and has been dated to be at
  least 210,000 years old.

Which certainty these findings have? Which one are we supposed to believe?

The question of the topic is, which theory has more evidence, humans appeared in Africa 200,000 years ago, or there were already humans in Europe at least 210,000 years ago?


texts: Is there a free alternative to Gelcompar for comparing banding patterns across multiple gels?

texts:
In order to run my microbial community samples from my experiments through DGGE, I was required to use multiple gels.

Thus it is necessary to compare banding patterns across more than one gel.  This means that I need some way of assessing whether the 4th band on gel #1 is the same OTU as the 4th band on gel #2.

The industry standard for this procedure seems to be the Gelcompar software.  Unfortunately this software is greater than $10,000 and is proprietary (thus, not open science friendly).

Does there exist a free (ideally as in speech and beer) alternative to Gelcompar?


texts: Do chromosomes line up as pairs in mitosis or meiosis?

texts:
Here is a question from the book SAT II Success Biology E/M (where the SAT is the exam taken by the American high school students):

  Homologous chromosomes line up in pairs in
  (A) metaphase of mitosis.
  (B) metaphase I.
  (C) metaphase II.
  (D) interphase.
  (E) prophase of
  mitosis.

In my opinion, we can definitely eliminate D and E since in both mitosis and meiosis, chromosomes line up during the metaphase.
Then, I would choose the answer choice B because as far as I know, after prophase I -- when the chromosomes are in pairs during crossing-over -- the chromosomes are still in pairs and become separated into the different ends of the cell during anaphase. In mitosis and metaphase II, however, they align along the "equator" of the cell, forming a line of single chromosomes.
However, I am confused here because of my book. Here is its explanation for this question:

  The correct answer is (B). In meiosis, the homologous pairs line up as
  individuals in meiosis I in preparation for final segregation in
  meiosis II. Meiosis simply needs to ensure the pairs end up in
  opposite daughter cells in meiosis I. It is in mitosis that the
  homologous pairs line up as pairs, and interphase, of course, is not a
  phase where the chromosomes even appear.

You can see that even though the first line indicates that the answer actually is B, the phrase that's in the cursive contradicts that statement.
I suspect there is a mistake either in the bold or the cursive statement. Could you help me here?


texts: Butterflies, like many other insects, understand that I am getting near from behind. How do they feel this - through vision, hearing, or some other sense?


texts:
Reposting from the stats stackexchange.
John Cook, in his blog https://www.johndcook.com/blog/2015/03/09/why-isnt-everything-normally-distributed/, writes that many aren't:

Adult heights follow a Gaussian, a.k.a. normal, distribution [1]. The usual explanation is that many factors go into determining one’s height, and the net effect of many separate causes is approximately normal because of the central limit theorem.
If that’s the case, why aren’t more phenomena normally distributed? Someone asked me this morning specifically about phenotypes with many genetic inputs.
The central limit theorem says that the sum of many independent, additive effects is approximately normally distributed [2]. Genes are more digital than analog, and do not produce independent, additive effects. For example, the effects of dominant and recessive genes act more like max and min than addition. Genes do not appear independently—if you have some genes, you’re more likely to have certain other genes—nor do they act independently—some genes determine how other genes are expressed.
Height is influenced by environmental effects as well as genetic effects, such as nutrition, and these environmental effects may be more additive or independent than genetic effects.

I have two questions regarding this. First, I can't come up with any obvious example of phenotypes that don't follow a normal distribution. Could anyone help me? And second, his claims seem to contradict this other paper: https://www.uvm.edu/~dstratto/bcor102/readings/4_Evol_of_Phenotypes.pdf

To understand the genetic basis of quantitative traits, it is important
to think about the effect of a particular allele, not simply its
presence or absence. A single locus can produce three discrete
phenotypes, but as more and more loci contribute to a trait the
phenotypic distribution comes closer and closer to a normal (bell
shaped) distribution

Who is right here? Does the fact that genes are digital rather than analog really make a difference? And what about the second argument that they aren't independent. Is that really necessary (second paper seems to indicate otherwise if I am understanding properly).


texts: Is ampicillin a good choice of drug to treat a urinary tract infection caused by E.coli

texts:
Is ampicillin a good choice of drug to treat a urinary tract infection (cystitis) caused by E.coli? How does the environment of the urinary tract effect its ability to treat the bacteria.
When cultured on a CLED agar plate and an ampicillin disk is placed in the centre it appears to work well, but will it work this well in the human body?


texts: Is recognizing one's own mirror reflection a valid test of animal intelligence/self awareness?

texts:
I've been looking at this Ted talk on interspecies internet, and it appears that they have selected a small number of species of animals (dolphin, elephant, and some ape(?)) and are intent on developing interfaces for these animals to be able to connect with other animals over the internet.

From the talk, it appeared as if one of the criteria for animal selection was whether or not an animal recognizes itself in the mirror. This got me thinking - there are many more cats that have access to technology like the internet or TV or cats that have been interacting with touch screen displays. Yet apparently cats cant recognize their own reflection as themselves.

What is so special about being able to recognize one's own reflection? Is it a true measure of self awareness? Does it only appear in animals with larger brains?


texts: What are these tiny, almost transparent, dots in my vision?

texts: Sometimes when I stare at a very bright thing such as the sky I see little dots. It's actually more of a circle with a little dot inside it. They are half-transparent and they move around a lot. When I first see them they tend to appear in a group out of nowhere. I have seen one that is gray and almost black. What is this?


texts: How much energy does a small spider expend per day just waiting for its web to vibrate?

texts:
Roughly speaking, a small, complex electronic circuit or IC might sit in "sleep mode" using a current of roughly 1 µA (e.g. 1, 2), thereby using roughly $3\times 10^{-6}$ Watts, and that converts to roundly $2.5\times 10^{-6}$ kcal/hour or $62\times 10^{-6}$ kcal/day.

I suppose you could call that 62 micro-kcal/day or 62 milliCalories/day.

One day I noticed a small spider in my home, sitting in its small web, and kept an eye on it. After several weeks of watching I hadn't seen it catch anything. I slightly perturbed the web and it reacted. It was still alive.

Question: I'm curious to know roughly how much energy a small spider needs to sit and wait. Might this be termed roughly the spiders Basal metabolic rate? It could be for any small spider that spends much of its time waiting for prey. As long as an approximate size or mass is available then it could be expressed as kcal/day/kg or some similar unit.

I have read about Kleiber's law in this answer, but I don't think it is meant to extend down to small spiders.

note: I'm just asking for the energy expended during resting periods. Of course during a day the spider may do web maintenance, catch or eat prey, but it's the resting rate of energy consumption, on a daily basis, that I'm asking about.


texts: Potential homogeneity across cell membrane

texts:
During respiration, individual bacteria (and mitocondria)  produce a relatively large potential difference (∼100 mV) between the inside and outside, using energy to pump $H^+$ out of the cell to the liquid environment (a proton motive force is created). Together with proton pumps, or sources, also sinks of protons are present, channels which reuse the voltage difference for other goals.

Imagine a cell like a bag, with only very few and sparse sources and sinks of protons. At the limit, take only 1 source and 1 sink, diametrically opposed, which continuously work. Is it reasonable to assume that the voltage difference created is homogeneous in space (it has same value everywhere along the surface)? How would this depend on the size of the cell?

My guess is that the homogeneity of the voltage should depend on the speed of diffusion of protons in water, which I imagine is extremely fast (but how fast?). So all variations around the mean value would be washed out on very short time scales (shorter than the shortest times of μs−ms
which are biologically relevant). But I may miss something. Any insight will be appreciated.


texts: Why doesn't chloride cause high blood pressure?

texts:
Assuming osmotic pressure is the (main?) culprit, why isn't the chlorine ion loose in your body after eating salt considered equally responsible for hypertension?

I have searched Google and Wikipedia, and cannot find an answer.

I have looked here at Stack Exchange, too.

Why is it that you always hear about how bad 'sodium' is for your diet, but every sodium cation comes with a chloride....

Could someone point me to an article, at least?


texts:
For instance, when pressure is applied to the skin, what determines how much pressure results in nociceptor stimulation. And when a sharp object pierces the skin, why is pain, rather than simply touch, perceived? Also, what causes nociceptors to sometimes be stimulated when there is no painful stimulus present, such as during a migraine when the skin feels painful to touch and in chronic pain?

Thank you in advance :)


texts: Help with designing the analysis of radio telemetry study

texts:
I was wondering if there are any spatial ecologists out there who can provide some insight on the trouble I'm having with my Masters research.

I am looking at the association a bat species to high density aggregations of a flowering plant. The bats were tracked throughout the night with a point taken at approximately 10 minute intervals. The bats were tracked over consecutive nights until an asymptote in their space use was reached. So now I have point patterns for each bat that pretty much covers the entirety of their space use at that period.

When the data is displayed visually there is a clear pattern of the bats that were tracked during the flowering period moving into the aggregations of the plant however they also spend a lot of time foraging around their roost sites.

I have simulated the point pattern of each bat 999 times by randomly shifting and rotating the points within the study window (the internal structure of the observed pattern was maintained in the simulations to account for autocorrelation). I then did randomisation tests to see if the average distance to the nearest plant aggregation for the observed data is within the lower 5% of the distribution of the averages for the simulated point patterns. However because the majority of the points collected are highly associated with the roosts the average distance is primarily effected by the position of the roost in relation to any of the plant aggregations.

I've been thinking of ways to disentangle the association with roosts and the association with the plant.

First I was thought about putting a buffer around the roosts and removing the points falling within these buffers from the analysis. The problem is deciding on a buffer. In the other areas I have been using a buffer equal to the circular error probable of the radio tracking error but placing this around the roost will only incorporate the points where the bat was actually inside the roost not foraging around it. All the bats have different foraging patterns around their roosts and I can't see how to assign a buffer distance that is not completely arbitrary.

The second method we have been looking into is taking out the points that are more closely associated (closer in distance) with the roost than the nearest plant aggregation and then running the randomisation to look at the association of the remaining points to the plant. I want to get an idea of whether or not removing the association with the roosts in this way will potentially bias the analysis.

Any thoughts or further suggestions?!

Thanks in advance!


texts:
Eating animal brains is considered a delicacy in parts of China. We know that eating animal brains can lead to prion related diseases.

Prions are misfolded proteins that are potentially infectious. But the whole body of an animal is full of proteins. What makes the brain special? (or specially infectious?)

My question is: Why do you get prion diseases from eating animal brains but not other parts of the animal?


texts: What is the genetic difference between two cone branches?

texts:
As we can see on this larch, male and female cones are sometimes directed to grow on the opposite side of the branch. We were told in school that this mechanism works against self-fertilization. Also they flower in different times, so they are mostly fertilized from the other conifers.

When I saw this picture, I got that idea, that maybe they face the branches on above by design: To decrease the genetic uniformity at least a little.

But how important this effect actually is? And how big is the genetical difference between two branches? Are there any other factors taking effect in the tilt of the cones?


texts: Wasp using plant fibers in old carpenter bee hole (Indiana USA)

texts:
Location: Indiana, USA

Every spring, carpenter bees make a few holes in our exposed porch wood.  This year, we observed a woodpecker removing three 1+ cm white grubs from one of the holes after a week or two (this hole is on the underside of a porch rail).  Interesting enough.  But now, I observed some kind of wasp carrying plant fibers into the same hole, so I guess it is using it as a nest.  Here's a picture of the wasp, and also of the wasp disappearing into the hole with large green piece of grass (at least it looks like grass - definitely a strong flyer).  The hole is about 8 mm across, and the wasp body about 1.5 cm.  Anyone know the species of this wasp?

Update: Here is the apparently completed nest:


texts:
I found this diagram in my textbook regarding the process of spermatogenesis. But, I doubt if the labelling done is correct or not. Especially, I can't figure out any difference between the cells labelled as spermatids and those as spermatozoa. Also, I doubt the labelling of Sertoli cells.
Please help me clarify my doubt.

As per my textbook,

  The spermatids are transformed into spermatozoa (sperms) by the process called spermiogenesis. After spermiogenesis, sperm heads become embedded in the Sertoli cells, and are finally released from the seminiferous tubules by the process called spermiation.


texts: Why might you NOT observe a tradeoff between two life-history traits?

texts:
I have traditionally thought of and heard about life-history traits (e.g., size at first reproduction, number of offspring, size of offspring, survival, etc., etc.) as drawing from a finite pool of resources that an organism has, and therefore exhibiting tradeoffs. So, for instance, an organism that invests in a lot of offspring would experience a decreased probability of survival.

It has recently come to my attention that this is not always the case, and I'm not sure why. I have been directed to the work of David Houle, who wrote extensively on the topic of life-history traits, but some of his work is inaccessible to me intellectually. I was hoping that somebody had a more digestible explanation or was maybe more familiar with Houle's work.


texts: Why is ATP the preferred choice for energy carriers?

texts: Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?


texts: In insects, does the Alanine repeat occur on the homeodomain sequence of the abdomen or does it occur on a different sequence?

texts: By "Alanine repeat", I am referring to the suppression of the formation of extra insect legs due to Ubx gene suppression through Distal-less repression.


texts: Color perception vs shade perception demo

texts:
I can't seem to find one of the best demos I've seen of color vs brightness perception.

It consisted of a rotating animation of earth made of red of bright red points on a dark green background. As the animation plays, the red points slowly get darker while the green background gets brighter. At some point they are of the same brightness (but different colors), which is where something very cool happens; your brain no longer perceives the red points as a 3D object, and they just look like a jumble of points bouncing around the screen. When the red points are darker than the background, the 3D object appears again.

Does anyone know what is this animation called, or where to find it? It's hard to find on google without knowing what to call it.


texts: Excess protein consumption effect on kidney

texts:
How does excess protein consumption through food as well as through supplements affect body especially kidneys?
Why it is advice to consume low protein diet during summer ?


texts: How can sodium and potassium from burned organic matter (ashes) reenter the ecosystem?

texts:
If you thoroughly burn something you end up with bunch of oxides and hydroxides, as far as I know.

Sodium and potassium hydroxides are plentiful in ashes, which is why lye was created by soaking ashes in water. Lye is not exactly nice to organisms.

So the question is, how can caustic lye ever reenter the ecosystem as potassium. If it cannot, does that mean that nature cannot renew it's potassium content?


texts: What advantages do birds gain when they mimic other bird species calls in the wild?

texts: I've read that birds such as crows and blue jays often mimic other bird species calls.  There seems to be evidence that birds do learn and react to other bird species calls, specifically when they relate to danger.  What I'm curious about is what advantages do birds gain when they imitate other species calls?


texts: High frequency human genetic oscillators?

texts: The most well studied genetic oscillators in human genomes are involved in regulating the circadian clock (which operates on an approximately 24-hour cycle) and cell cycle activity (with single cycles usually lasting several hours to many days). Are there any known genetic oscillators in humans (or other mammals) that operate on shorter timescales?


texts:
What species of centipede is this?
Found it 3 miles from San Ramón, Costa Rica


texts: Gestation period of African savanna elephants?

texts: I found out it is 22 months for African bush elephants, but is this also true for African savanna elephants?


texts: During the process of correcting mutations via gene therapy, is the defective gene removed?

texts:
Just recently started learning about gene therapy, many websites explain that the corrected DNA can be added to the genome using a vector and all that. I just don't understand what happens to the other sequence of nitrogenous bases that codes for the incorrect protein.
Thanks in advance for any answers :)


texts: Examples of humans intentionally introducing non-native species where everything went well?

texts:
It's easy to find examples of humans introducing non-native species to solve some problem (e.g. for food, to control the population of a pest), but later regretting it as the introduced species upsets the ecosystem.

Rabbits in Australia
Mongooses in Hawaii

Are there any examples of this going as expected?

I guess, since I'm really interested in how well humans can predict this sort of thing, what I'm looking for is examples of a situation where there were no unintended consequences. (Rather than beneficial, but unintended, consequences).


texts: Why does crossing over take place at all?

texts: I already know that crossing over causes genetic variation. My question is that since DNA is a stable molecule, why would it undergo process like crossing over during which it becomes so unstable and develop a chance of mutation?


texts: Voluntary actions of Autonomic Nervous System

texts:
Somatic motor activity is always voluntary, while ANS motor activity is usually involuntary. pgno:762

This indicates the possibility of voluntary activity by ANS.
So, what are the voluntary actions by ANS?

My Attempt:
Wikipidea says:

Most autonomous functions are involuntary but they can often work in conjunction with the somatic nervous system which provides voluntary control.

So, is right to say that Flight or Fight response is the voluntary activity of ANS?


texts:
Is there a model of how the B-cell-antibody pool in the lymphoid organ evolves during the first two weeks of infection by a new virus ? With a model I mean something like this

  At first we have $10^6$ different antibodies binding weakly to 4-5 amino acid  motives and through somatic hypermutation and selection the pool converges to a few dozen of antibodies binding strongly and specifically to some 8-10 amino acid  motives in the most numerous antigens presented by T cells (mostly motives found in the viral protein sequence since they must be in the peptide presented by antigen presenting cells).

This is what would make sense from the algorithmic point of view, which is often valid in biology, but not always. I have a few refs 1 2 3 but they stay elusive on that point.

If there is no such model then please make a few expert guesses.


texts:
I need help to see exactly what is going on here. According to the textbook here is shown a synapse, but I cannot quite see the things the textbook says are there.

From what I understand: (1) At1 and At2 are axons?, (2), The black thing on the bottom left is a dendrite?, (3) s1 and s2 are post-synaptic densities?

Is there more to see here that I am missing?


texts: Looking for a biological/physiological mechanism ... effect of diet on those who exercise vs those who don't

texts:
I'm researching the effect of adherence to Mediterranean diet on levels of inflammation in the body (C-reactive protein & a couple of other markers).  I want to stratify participants over levels of exercise (which I believe is an effect modifier) and need to come up with a biological/physiological mechanism whereby the Mediterranean diet would have a different effect on CRP in people who exercise versus those who don't?
Would really appreciate any pointers here.


texts: How could pharmaceutical metabolizing bacteria be used to synthesize them?

texts:
Lets say I have a pharmaceutical "P". It can be broken down by enzymes of one strain of bacteria into two molecules one of which can be further metabolized enzymatically by a different strain of bacteria. Both strains as a result can decompose "P" to the simplest metabolites.

Could one hope to reverse the reaction using the same enzymes and have the two bacteria produce "P" from basic nutrients and if so, how would the conditions have to be altered? Or perhaps would it be possible ex vivo?


texts: Fate of antigen-presenting cells after antigen presentation to Helper T cells

texts:
In many texts, the Antigen-presenting cells (APCs) that initiate helper T cell responses are often "forgotten" after their antigen presentation function is discussed.
I have been wondering how the antigens in these cells are destroyed since they are complexed to MHC II protein (not MHC I).
Yes, the macrophages can receive additional signals from already activated helper T cells to destroy the pathogens harboured in their cytosol, but what about B cells and Dendritic cells which lack such abilities?


texts: The pectoral fins of a whale and a shark. Are they analogous organs?

texts:
Analogous organs: Different origin, same functions,
Homologous organs: Same origin, different functions but same main structure//  right?
So, what is the case for the pectoral fins of a shark and a whale?

Are they analogous organs, because the two animals have different ancestors(shark-Some Chondrichthyes fish, Whale-some mammal) but have organs that do the same thing?

Or are they homologous organs, because the two animals have the same ancestor(A vertebrate animal) and have organs that have a similar structure?(I learned that it is alright for homologous organs to do the same function, for example the wings of a bat and a bird are homologous organs, although they do the same thing)


texts: Species identification. Is this a leech?

texts:
The pictured creature, shown at the bottom of a glass, was attached to a friend’s child after he was swimming in the Ottawa River today. It stretches out to roughly an inch in length but in this “resting pose” was around half that length. Below is a shot of the mark left behind:

It looks like a leech to me, but I thought I’d ask the Internet.


texts: Whole gene sequence analysis to determine source infection

texts: Is it possible to use whole gene sequence analysis to distinguish between a common source infection and a person-person disease transmission?


texts: Biology Experiment Data (Hodgkin-Huxley)

texts:
I'm doing research into the Hodgkin-Huxley Model from an electronics/mathematics perspective and I'm looking to find actual numerical results from experiments on squid axons. I want to compare the results of the experiments to the curves produced by modelling the equations in MATLAB.

My problem is, that while there are an abundance of resources discussing the equations and methodology of the experiments, I am having great difficulty finding tabulated experimental data (not just numbers generated from modelling the equations).

As I am coming from outside the field of biology I would like to know are there sources of quality numerical data for these types of experiments? In particular I am looking for the data for Potassium Conductance vs Time, here is the plot from the 5th paper in their series of publications that earned them a Nobel prize:

Hodgkin AL, Huxley AF. A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of Physiology. 1952;117(4):500–544.


texts: What is the cause that angina pectoris is felt in your left arm?

texts: When someone has heart problems sometimes they feel pain in their left arm. But why is the left arm painful?


texts: What conditions are necessary for HPL (human pancreatic lipase) to activate?

texts: What conditions are necessary for human pancreatic lipase to activate? Is there an optimal temperature or pH? How quickly does it take effect?


texts: What kind of Caiman is this and what is on it's nose?

texts:
I was able to snap a good picture in the Manù Parque Nacional in Peru. When I reviewed the pictures in more details I noticed something on it's nose, that resemble insects. What are those? Is it a known symbiosis? What do they gain?
Also our guide called it a "white river caiman", is this accurate?
And lastly: It seems one teeth is sticking out on top of it's mouth. By looking at the shape of the jaw it looks pretty natural. Is this common for caimans?
Picture for reference:

I took the picture around here:

Nose only:

Photo taken around May 2018.


texts: Biological terminology: "codes for" vs. "codes a"

texts:
Maybe this is answered already before, but I cannot find it:

Most authors say/write "a gene codes for a protein", some use "a gene codes a protein". The latter seems to me the grammatically correct use of the verb "code".

What's the reason for saying "code for"? Is it because of RNA processing (e.g. splicing)? What about the coding of single amino acid: "AAA codes Lysin" or "AAA codes for Lysin"?
I would also like to know some history of the use of these (and may be other) terminologies.

Tia Udo


texts: Possible complications due to gene-therapy?

texts:
Edward Lanphier, CEO of Sangamo BioSciences mentions here(https://youtu.be/dJ1B8XnyEnM?t=1215) that scientists can now specifically target cells, change the genome within a cell. Say you want to cure a type of disease, which can be linked to your genome. You have successfully removed the faulty gene in your genome (GenomeA), replaced it with a correct gene resulting in a improved genome (GenomeB) in a single cell. The next step will probably be to put it back into the human body. However, as I understand it every human cell contains your faulty human genome (GenomeA).

Question:

Even if you put a few cells with the correct genome sequence (GenomeB) into your human body, it is probably going to be overwhelmed by the other cells that contain your faulty genome (GenomeA). Cells containing the correct genome (GenomeB) will divide and multiply but so will cells containing the faulty genome (GenomeA). In this “genomic war” will the fewer cells containing the correct Genome (genomeB) ever win? Or will you need period infusions of cells with the correct genome "forever"?

How would you guys think about this?

Optional questions:

Even if it wins, it will probably take a very long time to completely replace all the cells with the faulty genomes. How much time is required before you can completely replace all the cells with the incorrect genomeA, with cells containing the correct genomeB?
Say you realize that you have a faulty genome (GenomeA), and you attempt to replace your genome with a correct genome (GenomeB). After 2 years, you have another disease and realize that you have to again correct your genome with GenomeC. However, 2 years is not enough to replace all your cells with the incorrect GenomeA, with the correct GenomeB. If you attempt to undergo genetherapy, now you will have to introduce another group of cells with GenomeC. Now you have cells with multiple different types of genomes floating around: genomeA, genomeB and genomeC. Are there any complications that happen due to the presence of multiple types of cells with different genomes in your body?


texts: How do mosquitoes maintain telomere length?

texts:
While the vast majority of eukaryotic organisms maintain their chromosome ends (telomeres) via telomerase, an enzyme system that generates short, tandem repeats on the ends of chromosomes, other mechanisms such as the transposition of retrotransposons (e.g. Drosophila) or recombination (e.g. Yeast) can also be used in some species.

I would like to know of your thoughts on the possible mechanisms that regulate telomere lengths in mosquitoes.


texts: Did the chromosomal fusion within humans affect phenotypical change compared to the separated chromosomes in the other apes?

texts: I just read this article on the evolutionary divergence between humans and chimps, and how the most significant event was when the 24 number of chromosomes in chimps was reduced to 23 in humans due to chromosomal fusion. However, while this even significantly supports the theory of evolution, how does this affect natural selection? What phenotypical changes may have occured between these two groups because of the chromosomal fusion? And what if chromosomal fusion did not occur? Would speciation still occur by other means, e.g. geographic isolation?


texts: What is this rather large insect in northwestern USA?

texts:
As you can see from the ants in the first picture, this insect is peculiarly large - over an inch long. I thought it was dead in the first picture, but it started moving around the next day. A couple of days later I found it again, dead. I have two dead specimens and other pictures if desired.

I think I've seen a shedded exoskeleton of one on a forest trail and another dead one from months earlier.

What species is it?

Location: Oregon, USA.


texts:
I was reading Cellular and Molecular Immunology
By Abul K. Abbas, Andrew H. H. Lichtman, Shiv Pillai and stumbled upon the following excerpt $-$

  In every individual there are millions of different clones of B-cells,each producing antibody molecules with the same antigen binding site and different in this site from the antibodies produced by other clones.

What are these clones of B-cells, one producing monoclonal antibodies and the other polyclonal antibodies?


texts: I was dissecting a sheep's brain for my students and one of them asked a question about the corpora quadrigemina he asked why did two of them(the superior colliculus) look more red than the other two and I have no idea why was that. also I read several topics about it but in the photos there was no such thing as I saw. can you help me with that?can it be due to any wrong doing in dissection procced? any help is appericiated


texts: Cardiac Excitation Threshold - in C++ modelling

texts:
So I am trying to write a code in C++ about the cardiac excitation threshold.

I know that this excitation threshold is the shortest stimulus2 value at which it can conduct an action potential (known as the effective refractory period) at that stimulus1 value.

So my question is: In my code should I have: apply_stimulus1 for basic_cycle_length = 1000 and while you are applying this stimulus1 apply and a stimulus2 and print out the shortest value of s2 where I can have a potential? -> the way I am thinking this is apllying both stimulus simultaneously. If we say .... this is stimulus 1 and this is ,,,, stimulus2 at the end I will have ;;;;.

Or should I say when you finish applying that stimulus1 apply a stimulu2 and give me the shortest time where I get action potential? But here I will have stimulu1 .... || (meaning ends applying stimulus1) ,,,, apply stimulus2.

Is this how I am thinking it correct or I just got lost in my own thoughts and it is easier than I make it look?

My question is:

How do I get the cardiac excitation threshold using stimulus1 and stimulus2 and how can I incorporate the theory in my C++ code.


texts: Is sexual reproduction outside the same biological family possible? Has it ever occured successfully?

texts:
Are there any examples of two species taxonomically classified in different biological families that have successfully hybridized and produced viable offspring? If not, is there an example of where reproduction occured with non-viable offspring?

To be clear, I mean regular sexual reproduction that could occur in the natural world outside a lab. Even so, I'd be curious to know if it could even occur in a lab without direct genetic manipulation.

For example, grolar bears which are ursid hybrids between different species in the Ursus genus are known to exist. Also ursid hybrids between bear species in different genuses have been produced in captivity (sloth bear Melursus ursinus x Malayan sun bear Ursus malayanus and sloth bear x Asiatic black bear Ursus thibetanus). Would an extra-familial hybridisation be possible? Would this be more likely in the plant kingdom?

This question is inspired by a separate question on the Gardening SE which hints at a general lack of understanding of the genetic similarity required for cross-pollination in plants. It made me wonder whether there are any exceptions to the general assumption that extra-familial hybridisation is impossible.


texts: Do genetic modifications exist to enhance the taste of tomatoes?

texts:
GM tomatoes seem less tasty. Has there been any research on GMOs with regard to taste?

Can scientists introduce a gene to, let's say, tomatoes, which would enhance the flavour? If not, why?


texts: Why does M1 RNA together with C5 protein in 100mM Mg(II) fail to cleave tRNA?

texts:
Sidney Altman discovered that RNA moeity of RNAse P (M1 RNA) alone is able to perform enzymatic cleavage of ptRNA, which won him the Nobel Prize of Chemistry in 1989.

However, when I read the Nobel Lecture on Bioscience Report, Vol. 10, 1990, the figure on page 325 (the image below) confused me.

I listed the relevant parts of the figure legend as follows:

(R: M1 RNA was added, P: [C5]=2x10^(-8) M, 20P: [C5]=4x10^(-7) M)

Lane 3: R+P,   [Mg(II)]=10  mM.  ptRNA cleaved.
Lane 5: R,     [Mg(II)]=100 mM.  ptRNA cleaved.
Lane 6: R+P,   [Mg(II)]=100 mM.  ptRNA NOT cleaved.
Lane 8: R+20P, [Mg(II)]=100 mM.  ptRNA cleaved.

In Lane 3, RNAse P was formed and was able to catalyze cleavage; Lane 5 showed that M1 RNA with higher concentration of magnesium could function as enzyme.

But how did the addition of C5 protein, compared to Lane 5, inhibit the cleavage of ptRNA, as shown in Lane 6? (Or, how did raising [Mg(II)] to 100 mM compared to Lane 3 inhibit the reaction?)

And how come by increasing the concentration of C5 protein by a factor of 20 compared to Lane 6, M1 RNA was able to function again, as shown in Lane 8?

I would appreciate any kind of help, and sorry for my poor formatting.

Thanks.


texts: Which matched normal(s) to use when computing CNAs from exome data with a Read-Depth approach

texts:
I want to use a Read-Depth algorithm to call copy number alterations (CNAs) from Whole Exome Sequencing data (WES) of a specific tumor.

I have a set of WES tumor samples, some of which also have the matched normal sample. My question is: would be more effective, to call CNAs for each tumor, the whole set of matched normals or, if available, only the corresponding matched normal sample?

I thought that using only the single matched normal could spot only somatic variations, while using the whole set of normals would also add germline variations into account. Is that right?

Which best strategy do you suggest?


texts: Why does Anti-A antibodies make type-A blood type clump?

texts: A-type blood has B-antibodies; it also clumps anti-A antibodies are inserted. Why is that? The blood has no antibodies against the A-antibodies to make clump in this way.


texts: Can animals train to be noticeably stronger, faster, more agile... than other animals of the same species?

texts: Humans have a huge variation in physical ability because of exercise differences. Olympic athletes are a number of times stronger than average people on the street. It seems that variation in animals is very small, but I am wondering if one could force an animal to follow a specific program and eat specific food to get a lot stronger, agile, etc. than an average animal of the same species.


texts: Is an animal's body height dependent on its environment?

texts:
Imagine the follwing situation: a newly born animal is brought into a small room. This room has no windows, but artifical light to imitate the sunlight. Furthermore, this light behaves like the sun, so that there are artificial nights and days in the room. The animal will be provided with food and water, too, so that it has enough nutrients to develop in a normal way. What will happen with the animal, when the room is so small, that it would limit the body height of the animal?
(One extreme example: an elephant, living in a normal sized room)

Would the growth of the animal be limited by some biological/biochemical mechanism? Or would the animal grow in a more or less normal way?

In summary, my question is: does the body height of an animal depent on its environment? If yes: how strong is this dependence?


texts: From the total water absorbed by the root system, how much water does the plant use for transpiration and how much water does the plant use for photosynthesis?


texts: Are RNA cleavage sites always polyadenylated?

texts:
During RNA processing (including both mRNA and non-coding RNAs), is the end of 3'UTR always polyadenylated after cleavage?

I could not find the answer to my question in the Wikipedia entry for polyadenylation.

If a recent reference could be provided, that will be great. I've done quite a bit search and hasn't found a good source yet.

Some background to this question: we are developing bioinformatics tools to predict potential cleavage sites, we need to understand this problem better in order to design a suitable algorithm


texts: Can you name this plant that likes shade on Asturias?

texts: This was located in the Turón valley on Mieres, Asturias, Spain. Usually, I find this plant in shadowy, not too illuminated spots, although I'm not sure if that's important or simply coincidence. This picture is from yesterday 16th February 2019. The plant is lower than knee high, so let's say a maximum of 30cm tall maybe.


texts:
Does the DNA of a tadpole change after it becomes a frog? In other words what changes take place as a tadpole becomes a frog, and does this metamorphosis affect the DNA in any way?

I would appreciate your help. I am doing research for a book I'm in the process of writing. If you can refer me to research material, I would appreciate that also.


texts: Why are two forward and reverse priming sites depicted here? what do they do?

texts:
This question is in regard to the baculovirus expression system.

(source: amsbio.com)

Why do we need to generate primers for the polyhedrin promoter and the baculovirus?
Primers are needed to amplify DNA regions of interest.Here, why exactly do we need to amplify these regions? and at which steps?

PS : I am not asking about the need for forward and reverse primers.


texts: Do archaea undergo the same horizontal gene transfer processes as bacteria?

texts: Do archaea also undergo processes like conjugation, trasformation, etc.? If not, do they have their own horizontal gene transfer methods? Can bacteria conjugate with archaea?


texts: What is the name of this plant with many purple blooms with orange inner parts?

texts:
I have photographed the following plant in Pittsburgh, PA. It has many blooms and every bloom is very small (about 5mm diameter), purple on the outer and orange in the inner. You can see it here:

What is the name of that plant?


texts:
Just out of curiosity (I am completely strange to biology), as I have been unable to find this info on the internet:
How long does the whole DNA replication process take? (say, the replication of a whole chromosome)
Approximately, how long does the DNA spend in a single helix structure during replication?

I am curious about the time scales of these processes, from the moment the polymerase starts cutting the double helix till the moment there are two double helices perfectly formed (one of them a copy of the other). How long can this take? miliseconds? seconds?


texts: Lengthening muscles not good from evolutional perspective? Why do we do it with explicit stretching?

texts:
Stretching has many advantages, among other things it helps us to be flexible in our movement (which is an advantage?!).

But why do we need to actively stretch, it seems that the body wants to shorten the muscles by evolution (e.g. when training often in fitness studio). This is the opposite of what we do when stretching.

It seems to be that there are advantages of being not stretched. So what are these advantages / what is the evolutional rationale?

Edit: Why this question is different from this question:

That question asks, why we automatically stretch sometimes after e.g. sleep. The answer is that we stretch the soft tissues because of transitions of high and low activities (especially after sleep, in which we ease the tension in our muscles [muscular antonia]).

This question asks something different. It asks about explicit stretching in sports and not about automatically stretching behavior. The aim is different. In sports we stretch because, we want to lengthen our muscular. The question is why lengthening doesn't seem to be a good thing from an evolutional perspective.

Edit 2: I'm not sure, if it is clear for everybody, what I mean, so I add a succinct example: Why would it be bad (evolutional rationale), if everybody could do a split (gymnastics) by nature (disadvantages?)? In our reality, the ability to do this is almost always an result of stretching. This is only one extreme example, mostly people don't strech to such extremes. Maybe this now  helps to understand, for what this question heads.


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


texts: How to determine which allele GRCh37 has?

texts:
is there a website where I can search GRCh37 by location or rs IDs, to determine which allele it has at a specific location?

I think http://grch37.ensembl.org/ might be the answer to my question, but I'm not sure if when it says the "ancestral" allele on the results page, if that allele is the one in GRCh37. Or if it'll tell me which one GRCh37 has somewhere else on the page.

Also as a side note: I assume GRCh37 only has one copy of each chromosome (i.e. it can't be heterozygous for something?).


texts: Why do soil bacteria produce nitrous oxide as a result of anhydrous ammonia fertilizer application?

texts:
The NPR article and 4 minute audio news item Can Anyone, Even Walmart, Stem The Heat-Trapping Flood Of Nitrogen On Farms? discusses unexpected contributions of greenhouse gasses from the manufacture of consumer goods. One example is bread, or agricultural products in general, and part of this is the anhydrous ammonia used in fertilizer.
Carbon dioxide seems to be a bi-product of the manufacture, but nitrous oxide a more potent greenhouse gas is produced by bacteria in the soil as a result of application of ammonia.

Manufacturing nitrogen fertilizer is energy-intensive, burning lots of fossil fuels and releasing carbon dioxide. What's just as damaging, and perhaps even more so, is what happens when it's spread on a field. Bacteria feed on it and release a super-powerful greenhouse gas called nitrous oxide.
These bacteria are naturally present in the soil, says Philip Robertson, a researcher at Michigan State University, "but once they get exposed to nitrogen fertilizer, they really light up" and pump out nitrous oxide.

Question: Is it common for most soil bacteria to make significant quantities of nitrous oxide after ammonia is added, or is there only a small subset of bacteria present in soil that might do this? Also, what is the metabolic pathway in this case? Is this a waste product from "eating" ammonia, or something more complicated/subtle?

below: Anhydrous ammonia tanks in a newly planted wheat field. Walmart has promised big cuts in emissions of greenhouse gases. To meet that goal, though, the giant retailer may have to persuade farmers to use less fertilizer. It won't be easy. TheBusman/Getty Images. From here.


texts: Hoverfly Identification Wing Resting Position

texts:
I've found an interesting insect which I believe to be a hoverfly:

length: approximately 1/2 inch.

However when compared to the Wikipedia poster on Syrphidae or the InsectIdentification.org Hoverfly entry (as well as the flower fly entries) the resting state of the wings differ. In my photographs the wings are resting above the back while hoverflies appear to keep their wings extended.

I know wing position is important in identification, i.e. dragonfly vs damselfly, moth vs butterfly. Does it matter with true flies?


texts: Is there any conclusive study relating the food consumed and the occurrence of acne?

texts:
The internet says a million things about what to eat and what not to eat in regards to impacts on acne. For instance:

Refrain from dairy products.
Refrain from food heavy in unsaturated fat.
Refrain from too much sweet.
Consume fresh food (raw fruits & vegetables) but no cabbage and cauliflower.
No Alcohol
Etc.

My question is:

Is there really any relation between food consumed and the occurrence of acne?


texts:
Jellyfish use jet propulsion to move forward, according to http://earthsky.org/earth/how-do-jellyfish-swim. Otherwise, they drift with the ocean currents.

Does this mean that, without the presence of water currents, jellyfish cannot swim backwards?

(This question was inspired by watching countless SpongeBob episodes and seeing the efficiency in which SB catches jellyfish).


texts:
I'm come across this question and I'm somewhat confused:

In the test for staphylococci, the clumping factor detects:

staphylothrombin
DNase
mannitol fermentation
Fimbriae
fibrinogen-binding protein

I know that bound coagulase can convert prothrombin into staphylothrombin and eventually fibrinogen into fibrin.

I'm thinking it's staphylothrombin, but when it says ''detects'' does it mean that the test concludes whether staphylothrombin is produced or does it mean that the clumping factor actually ''detects'' a substance?


texts: Clarification of the brightness of bioluminescent proteins

texts: One basic thing I'm not too clear on, which I would like to be clear on, is the brightness per mass unit of GFP or luciferase.  I was having trouble finding a resource that would state the brightness at least for standard GFP or luciferase per gram, for example.  Is there a basic rule for the maximum brightness for either of them?  I'm aware this might end up being a vague question, but I could use help clarifying this.  I found brightness as a product of the extinction coefficient and quantum yield but I wasn't sure how to translate that to watts.


texts: Identification: Is this really a case of Progeria?

texts:
There are some news about a boy being born in Bangladesh that looks very aged and presumably has Progeria: http://metro.co.uk/2016/09/29/newborn-baby-who-looks-like-an-80-year-old-after-being-born-with-rare-ageing-condition-6159215/

To my knowledge, humans born with Progeria looks quite normal at first, and it's not until after birth that the associated symptoms start to develop.

Is it plausible that this actually is a case of Progeria? Is there any other syndrome that would better match the appearance of the boy?


texts: Databases for metabolic pathways of human disease

texts:
Which databases contain the metabolic pathway of human diseases?
I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.


texts:
Generally, EMT, Epithelial to Mesenchymal Transition is thought to be involved in the mechanism in which cancer cells metastasize in the early stage. EMT is an process in which epithelial cells depolarize and lose their cell-to-cell contacts, and gain mesenchymal morphology. The mesenchymal cells is capable of reaching distant sites through the blood vessels. So, EMT is thought to be a necessary mechanism for metastasis.

However, I found a surprising report from Nature article indicating that EMT isn't required for metastasis:

Fischer, Kari R. et al. "EMT Is Not Required for Lung Metastasis but Contributes to Chemoresistance." Nature 527.7579 (2015): 472–476.

They established an EMT lineage-tracing system in mice with the mammary tumors to monitor metastasis of the epithelial cancer cells to lung through EMT using epithelial-specific and mesenchymal-specific markers. This report showed that a small proportion of cancer cells underwent EMT and lung metastasis mainly consisted of epithelial cells which didn't undergo EMT.

I think this report is innovative and overthrows the commonly accepted thought that EMT is necessary for metastasis,
However, some questions come to me.

How the epithelial cancer cells gain the motility and metastasize without undergoing EMT？


texts:
It appears to be a kind of fig tree (perhaps similar to the fiddle leaf fig tree but without the fiddle?), although the leaf shape doesn't match. It didn't seem very appealing to eat (!), it was oozing white sap from the stem and from the fruit itself when i broke it apart.

The fruit felt like a hard sponge.

I found the tree in Israel, although, in this location there are a number of non-indigenous trees.

Here are some pictures:

(NOTE: photo of full tree was taken in March, not at the same time as the first two photos)


texts: For catheter purpose, femoral and subclavian arteries are mostly used as starting point. Why? Are there other arteries which are used for the purpose?


texts:
I read that

  [SARS-CoV-2 has] a nonstructural protein called NSP3, a component of which blocks the host’s efforts to fight off the virus. In particular, this protein shuts down host enzymes called PARPs, which prevent viruses from replicating, and interferes with cellular calls for the release of virus-fighting immune proteins called interferons.

I'm somewhat acquainted with interferons, but I'm trying to better understand the part about PARPs. Alas the Wikipedia page on these does not mention an anti-viral-[replication] function. So, how do PARPs stop viruses from replicating? (Is it by triggering cell death?)


texts:
I have been watching some bow hunting videos on youtube. When hunting with a bow, the hunter needs to get really close to the animal, sometimes less than 10 meters.

It seems to me implicitly, and some hunters even say explicitly, that the animals (deer/elk/moose/buffalo) only see the hunters when they move. As long as the hunter has reasonably camouflaged clothes and is not smelled by the animal, they can stand in plain sight and the animal does notice them.

Do these game animals (deer/elk/moose/buffalo) really have such poor eyesight?

here are some videos as examples:

https://youtu.be/OqGSaGXHXgY?t=654

https://youtu.be/9tx_l9Jco_M?t=213

https://youtu.be/bP38tYhyhW0?t=303

https://youtu.be/xP9L885noEI?t=58


texts: Do benign tumours have no functioning apoptosis mechanisms ? If so what stops benign tumours from excessive growth? Also can a benign tumour have a functioning apoptosis mechanism?


texts: Is MHC1 knockout sufficient to prevent transplant rejection?

texts:
A few days ago I read about MHC1 knockout pigs for organ transplantation research.
I was just wondering, is it enough to knock out MHC1 in the donor (lets say from same species, pig to pig) for successful transplantation?

I understand that someone without MHC1 is more sensitive to  viruses, cancer, to NK and more. But the study pigs lived fine, so in theory it is possible to have knockout MHC1 and survive.
But is it enough for successful  transplantation from one pig (donor with knockout) to another (fully healthy, normal pig) ?


texts: Should hydrogen peroxide be applied on a bloody nose?

texts:
When I was a kid, my parents taught me to apply hydrogen peroxide on my nose whenever it bled. It's a rare event, but my nose bleeds from time to time, and when it does, I always go through the same procedure of dipping a cotton bud in hydrogen peroxide, and applying it to the inside of the bleeding nostril. It always stops the bleeding immediately and I get on with my day.

It happened right now, and since I always just go through the motions without thinking about it, today I was curious about the principles at stake here. In looking for an answer about why it does what it does, I found only references to the effects of drinking hydrogen peroxide, which looks like a controversial subject whose benefits may be non-existent; but I didn't find a single mention about the application of hydrogen peroxide directly on a bleeding nose, which made me worried if what I'm doing is even recommended or if I'm doing something potentially dangerous.

So my question is: is this practice beneficial, and why?

Update: This question mentioned oxygenated water, which is the literal translation of "água oxigenada" (PT), but apparently that's only the commercial name for "peróxido de hidrogénio" where I live, which translates to hydrogen peroxide (H2O2); and since that returns many more hits on google, I've renamed all instances of oxygenated water to hydrogen peroxide in this question.


texts: Do micro-organisms survive and live normally in a zero-g environment?

texts:
Have there been any experiments in space regarding micro-organism behavior? Are they able to move around in a drop of water like they do on Earth? Are they able to eat and reproduce normally?

Edit: by zero-g, I mean an environment where you feel zero acceleration. Orbiting the Earth would be this since you're constantly in free fall. A rotating environment is not zero-g as the things inside will feel a "centrifugal" force pushing them into the wall (though it's actually a centripetal acceleration coming up against your intertia).


texts: Behavioral change in dolphins during different hemispheres activity periods?

texts: It is known that dolphins never sleep in the sense that we do, instead they have one hemisphere of the brain sleeping while the other one is awake. I wonder, do they show observable changes in behavior in regard to this, depending on which hemisphere is active? Do their hemispheres even have a specification similar to ours (logic and emotion)?


texts: Regulation of Glycolysis and other pathways at ‘irreversible’ reaction steps

texts:
The hexokinase, phosphofructokinase and pyruvate kinase steps of glycolysis (1,3 and 10, below) are the only ones that are irreversible, and are also the steps where glycolysis is regulated.

Is it necessary for a regulatory step in glycolysis to be irreversible, and if so does this apply to metabolic pathways generally?


texts: Is the poly(A) tail added while transcription is still underway?

texts:
I read in Campbell that

  ....splicing and poly A tail addition may also occur while transcription is still under way.

How can the poly(A) tail be added while transcription is still going on?


texts: Is there an antidote for caffeine, e.g. as a supplicant for caffeine-intolerant persons?

texts:
First, let me state I'm not talking about a medical emergency. No one is in a serious condition.
My girlfriend is, we think, caffeine-intolerant. She loves the smell of coffee and the habit of coffee drinking, so naturally she risks drinking caffeinated beverages every now and then, even knowing she'll suffer. She experiences the regular effects of coffee, but they are uncomfortably strong and last much more time than usual. We've read that it's because her body metabolizes caffeine slowly, likely due to a gene mutation. We think it's not caffeine allergy.
We were wondering if there's kind of an antidote, a molecule which metabolizes or deactivates caffeine specifically. Then one example use could be

drink regular coffee;
wait some time (e.g. half an hour);
take a pill to take care of the excess caffeine in your bloodstream.

We're asking mostly out of curiosity - she's not that addicted to coffee as to actually take pills just to be able to drink it. The real (bio-chemical) question is - can an antidote, which targets a this very specific molecule, be actually manufactured? Or is it that it's not researched purely because of market size reasons?


texts: What is the contribution of the cockroach to the ecological environment?

texts: I've read a lot about cockroaches but was unable to find how they contribute to the ecological environment. Does anyone know?


texts: What is the role of hippo signalling in oral squamous cells

texts: What role do hippo signalling have on squamous cells in oral health & diseases


texts:
If we have humans A, B and C who are different:

A is thin (skinny) without significant muscle or fat mass.
B is muscular
C is fat

Which one of them has the best body for survival in accidents like car crash, aircraft crash, fall from the ladder, fall down the stairs, being hit by a car, slip in the bathroom, etc?

What are the effects of muscle and fat mass on survivability?


texts:
Short summary

I'm having a glass surfaces and I want to adsorb proteins onto them. I have no problem, when I first adsorb fibronectin (human) onto some areas and afterwards any other protein. The second protein will only adsorb onto the remaining "free" areas.

But as soon as I apply fibronectin in the second place, it just adsorbs everywhere. And I want to avoid this.

More detailed Protocol

(direct microcontact printing):

Incubate a pdms-stamp with Protein-Solution #1 for some time and concentration
Dry pdms stamp and press onto coverslip for some time
Remove stamp and put a drop of Protein-Solution #2 for some time and concentration onto the coverslip

I varried already concentrations and times without noticeable success. I also tried adding some BSA to Fibronectin - also without success. All solutions are within PBS.

Further steps I anticipate:

Varying pH around the protein's isolectric point (Fibronectin: around 5.2)
Adding some detergens to fn-solution (e.g. Tween)
Variation of salt-content in fn-protein-buffer

My question

I'm wondering what the exact reason for the stickiness of Fibronectin is and which parameter is the best to vary? Did I miss something? Does Fibronectin stick to the other proteins or rather to "free areas" of the surface?

Please note: surface modification techniques (e.g. using epoxys) are no option.

I'm not sure, whether this topic perhaps suits the chemistry-community better. Feel free to move.


texts: What is the heritability of brain gyrification?

texts:
Brains of mammals with a folded neocortex do not have identical patterns of folding in the same species.

Do two genetically identical individuals of a species have the same pattern of brain gyrification (i.e., folds/wrinkles)? Or are there other causes?


texts: List of non-native terrestrial molluscs in California?

texts: I'm looking for a list of non-native terrestrial molluscs in California. Ideally, I also need the date each taxon was introduced into California. Can anyone help?


texts: Need help interpreting Western blot data

texts:
So the paper I am reading (here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094582/) uses densitometric units to quantify the western blots.
The authors mentioned that the unphosphorylated proteins were used as loading controls, and their quantities are represented by the densitometric graphs for each corresponding figure, but protein activity is measured by their phosphorylated counterparts which I believe is represented by the densitometric graph on the right of each corresponding figure.
Questions:

Did I interpret that correctly?
What exactly are loading controls?
I am trying to use these data for parameter estimation purposes. Is it possible to find the basal mass quantity of a particular protein?


texts: I found this spider on my balcony in Sunnyvale, CA. It sat in a irregular net. The body was approx. 6mm long. Which species does it belong to?


texts:
I have read an answer to a question about dna repair during and after replication.

But how is dna repaired if a deamination of of 5-methylcytosine happens? How does a repair mechanism identify which base was mutated (on '3 or on '5 strand, a C to T, or on the complementary strand an A to G)?


texts: Visualizing secondary RNA structure binding to target

texts:
I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but these only allow from prediction of secondary structure of the ribozyme folding on itself (which is thermodynamically less stable that 20-40 perfectly complementary nucleotides along the arms).

Is there any software that will allow for simultaneous prediction of secondary structure of two RNA molecules?


texts: If two definitive ovums are fused will they form an organism?

texts:
Pretend that somehow in a laboratory two definitive ovums (finished 2nd miotic divisions) are
are fused together. Will they form a new species?


texts: Measuring luminescence in a fluorescence plate reader

texts:
We're considering organizing some interlaboratory work on calibrating luminescence reporters (e.g., luciferase), and one of the key questions I don't know the answer to is whether most plate readers can measure luminescence or not.
From a first principles perspective, any fluorescence plate reader ought to be able to measure luminescence as well - just don't turn on the excitation light source. Thus, I would expect that a typical fluorescence reader should also be able to measure luminescence.
On the other hand, searching online, I am swamped by manufacturers eager to sell me specialized luminescence readers that emphasize their sensitivity, which leads me to think that maybe typical fluorescence plate readers can't measure luminescence.
My question, then, is this: should I expect that a typical current fluorescence plate reader will also be able to measure luminescence, or is this a much more specialized capability?


texts: What species represents the largest biomass on earth, ie, how much does the entire population weigh? Also, what species has the most members?


texts: Is there an example of a species wherein the female lays eggs in the male?

texts:
There are of course many species which lay eggs in the bodies of another species and also many species where either the male is eaten after mating or the male dies soon thereafter. So it seems possible that a species might exist where the female lays fertilized eggs in the body of the male with whom she mated or even a different male. I could see however the problem being that there is a significant time gap between mating and the eggs being ready to be laid, so perhaps there are no cases of the former but perhaps there are cases of the latter?

Note: Looking for a form of egg-laying that is destructive to the "host" -- where the developing larvae eat the host, like in the cross-species case.


texts: Is there a maximum amount of antibodies your body can keep?

texts:
I am wondering if you were theoretically able to get vaccinations or antibodies for any and every diseases and/or illness, would there be a limit to how many you can get and keep in your body at one time? If so, what is the limiting factor?

What would be the possible effects of this on the body and immune system? Thanks.


texts: To which SCOP Class corresponds the following secondary structure?

texts:
I need to classify this protein into one of the SCOP class (all $\alpha$, all $\beta$, $\alpha +\beta$, $\alpha/\beta$, or small protein).

I'm having difficulties understanding the difference between $\alpha +\beta$ and $\alpha/\beta$. I would have said, that it belongs to the group $\alpha/\beta$, due to the fact that presents an alternated combination of $\alpha$-helices and $\beta$-sheets, where the $\beta$-sheets are mainly parallel, but I do not know if I'm understanding the concept right.

Has anyone a tip to identify the differences quicker?


texts: Trouble understanding overlapping genes.

texts:
I read the wikipedia passage on overlapping genes.

https://en.wikipedia.org/wiki/Overlapping_gene

The Tandem overlaps they speak of make sense to me, as I understand that their are different reading frames(3 in total if I understand correctly) for genes to be read in the 3' to 5' direction and that this causes an out of phase overlap.

This out of phase tandem overlap for genes was shown by the picture below:

I am having trouble understanding the other scenarios spoken about in the passage, the in-phase tandem overlap and the Anti-parallel strand overlaps.
Maybe I just lack a good enough background in genetics.

I do not understand how you can have an in-phase tandem overlap. If the genes were in phase, how could they ever overlap and be different genes? Wouldn't they both respectively have a stop codon, and then one stop codon would "stop" the translation?

I picture it like this: pardon the crude drawing

The anti-parallel strand overlaps also confuse me as well, for I do not understand how genes can overlap when on opposite strands. If the genes are on opposite strands wont that mean they wont have any overlap in the first place? Am I missing something basic? Thanks.


texts: Sound volume drop when falling asleep in an airplane

texts:
Note: This question has nothing to do with pressure change.

When I'm flying in an aircraft at cruising altitude, the monotonous sound often lulls me to sleep. I've noticed that just as I am on the verge of drifting off, the perceived sound volume drops significantly. I then notice what is going on and the thought awakens me a bit and the volume snaps back to normal. I verified that the actual noise in the airplane stays constant while this happens.

I always try to hold on to the state where the sound is quieter, but it is very difficult to do while at least a bit conscious. That's why I suspect that it could be part of the process human brain goes through normally when falling asleep. Perhaps it happens every time, but I do not notice because I only ever sleep in such a noisy environment when flying.

I asked a bunch of friends and some of them experience the same phenomenon. I was unable to find any relevant scientific literature mentioning it, though.

What causes this fascinating phenomenon? Does it have a name? Has it been studied?


texts: What coronaviruses have been identified in racoon dogs?

texts:
Christian Dorsten says in an (Apr 26) interview in the Guardian that racoon dogs as [intermediate] source of coronavirues have been overlooked (in China):

Q: What do we know about that intermediate host – is it the “poor pangolin”, as it’s come to be known?
A: I don’t see any reason to assume that the virus passed through pangolins on its way to humans. There is an interesting piece of information from the old Sars literature. That virus was found in civet cats, but also in raccoon dogs – something the media overlooked. Raccoon dogs are a massive industry in China, where they are bred on farms and caught in the wild for their fur. If somebody gave me a few hundred thousand bucks and free access to China to find the source of the virus, I would look in places where raccoon dogs are bred.

So what studies are there on coronavirues in racoon dogs up to now? (A quick search found a 1992 US paper that some coronavirus [unsurprisingly] infects racoons too. But I can't find much else. Is there more up-to-date survey? Also, duh, racoon dogs aren't even the same family [Canidae vs Procyonidae].)


texts: According to a guy in a Facebook group I belong to, this fish was caught in the Missouri River near Omaha, NE, US. I have never seen one like it in my life, not in person or photo or anywhere. What on earth is this fish?! Is it even real? I've not seen it in person, only the photo below, but he says its real.


texts:
I have to perform an RNA extraction that should start with 900 uL of 2%SDS bacterial solution. The problem is that the sample is in 900 uL of PBS.

I thought about centrifugation of the sample at 5ºC, remove PBS and then add the 2%SDS.

DO you think bacterial RNA quantities will vary?

Thanks!


texts: How does noradrenaline result in rise of systolic blood pressure even when the cardiac output is decreasing?

texts: Systolic blood pressure[SBP] depends on the cardiac output. When Nor adrenaline is given there is vasoconstriction due to alpha-1 action on blood vessel, vasoconstriction results in increased total peripheral resistance and thus increases the diastolic blood pressure. The beta-1 action [increase in cardiac output] on heart by Nor adrenaline is counteracted by the reflex bradycardia  resulting in decreased cardiac output. Given the fact that SBP depends on cardiac output and the cardiac output is decreasing, why is there a rise in SBP on administering nor adrenaline?


texts: How much shorter is the short arm of a chromosome? And why?

texts: I keep reading that the p arm is shorter than the q arm. But I cannot find an explanation of how much shorter nor an explanation for the difference.


texts: What's the recommended maximum passage number for mammalian cells (NCI-H441)?

texts: Is there a generally accepted maximum number of times you should split and reseed mammalian culture cells before restarting cultures from new stock?


texts: What does FETCO2(end-tidal fraction CO2 concentration) represent?

texts: What is end-tidal fractional CO2 concentration? I have searched online and found little actually explaining what this measurement is. Thanks again.


texts: !Saw this bug/insect/spider? on a ranch in Santa Ynez, CA. Pretty fast moving-this was the only photo I could get. The creature is the thing in the photo that looks like two puff balls on a very black body. (The smaller puff is the front of the body.) Maybe a bumble bee? Did not appear to have wings.


texts: Is Nerve Growth Factor (NGF) commercially available?

texts: I'm curious if NGF, or Neurotrophins in general is available commercially. Can I order it online? If not, what are the medical/biological reasons. Does it breakdown quickly after synthesis/capture? Is it a regulated protein?


texts: Can dogs and cats recognize human sneezing?

texts: I recently noticed that my kitten gets startled by all manor of loud noises, with the only exception I've noticed being the sound of me sneezing. My sneezes are by no means quiet, so I began wondering if it wasn't fazed by the sound of me sneezing because it instinctually recognized it for what it was? I've seen dogs and cats sneezing before so I was curios if it simply made the connection and wasn't fazed by it, Googling didn't turn up anything useful on the subject.


texts: How it is possible that blood group shows that a person is not the son or daughter of their parents?

texts:
I see a family in which it has only one daughter. The blood group of the mother is AB positive and the father is B positive, but the blood group of the daughter is O negative.

When she was young, they apply to shift abroad permanently. When the Embassy test their blood group, the doctor said "She is not your daughter because of her blood group".

How is it possible? Why is she not the daughter of their parents?


texts:
From my experience humans can detect UV - not by seeing it but by pain in their eyes. Many people (me too) feel pain when looking at UV lamps. When looking at sun through clouds I still can feel pain very often even if the after -all-image is not very bright (because of the clouds) but when I look at a light bulb or when I look at sun through sun-watching lenses (which cut all UV) I don't feel that pain despite of them being much brighter than the cloudy sun. I also have read about it once or two.

So, can this be true (I mean humans can detect UV with their eyes) or that's just a coincidence? And if it's true, how it happens?


texts: It is similar to a kinkajou but it isn't for sure. I would include it into carnivora, and then maybe canifornia but I really don't have a clue.


texts: What is the difference between monoecious and homothallic?

texts:
In my plant reproduction book there are two distinct definitions for these two terms, but when I read them I found out that they are very much alike that I was confused and couldn't catch the difference between them. I searched on Google and found this on wikidiff:

  As adjectives the difference between homothallic and monoecious is
  that homothallic is (of some algae and fungi) producing male and
  female reproductive structures in the same plant while monoecious is
  (botany) that has male and female reproductive organs on the same
  individual plant (rather than on separate individuals).

But, still, isn't this the same sentence using another words?
Thanks for answering.