texts: Is there any evidence of blue jays preying on other birds?

texts:
Are blue jays known to prey on other birds?  I've found that they are known to raid nests of eggs and young, but have not found any evidence of them actually preying on other birds.

Background:  A few years ago while raking leaves this time of year (late Oct/early Nov) the head of a house sparrow fell on me.  I looked around in the spruce tree I was under and saw a blue jay eating the rest of the house sparrow.  This was approximately 10 feet from my bird feeders.  I can't say that it wasn't dead beforehand, but it's proximity to the feeders made me wonder.


texts: Staphylococcus (antibacterial soaps and Traditional Lathering soaps)

texts:
I have been working on a biology research assignment regarding the claim:

Antibacterial soaps are superior to traditional lathering soaps in
minimizing the transmission of disease

I have made a research question regarding the effectiveness of antibacterial soaps. However, information on antibacterial soaps is limited whereas traditional soaps appear to have more information.
My question is: does anyone have any information about the effectiveness of antibacterial soaps and plain soaps with respect to staphylococcus disease?


texts: Is there such thing as "meters per calorie" for living organisms?

texts:
I'm interested in learning if there's some way of quantifying the organism's metabolic efficiency associated with movement.

It seems to me that some organisms would be more efficient than others at using energy. For mechanical systems, there are clear metrics of efficiency, for example "miles per gallon" or "liters per 100km". Is there a similar metric that converts calories into how far an organism can go?

Thank you for your input!


texts: Is it theoretically possible to restore the Tiger population to 100,000?

texts: The current global Tiger population is roughly 5100 according to Wikipedia. With habitat destruction and poaching continuing and no effective improvement in conservation, most likely the Tiger population will continue to decrease. I'm wondering what is the theoretical maximum population to which the Tiger species could be restored. Suppose poaching and habitat destruction stopped today and conservation efforts were increased drastically, so the only factors limiting population growth are the natural dynamics between the species and its prey. Could we then restore the global population of tigers to its pre-20th century level of 100,000?


texts:
Can you explain (or direct me to a link) the process by which a photon of $8.10^{14}$ Hz is absorbed by the skin without damage, whilst a slightly more energetic one (UVB) makes damage?

What area of skin is necessary to absorb one single photon? How many photons of visibile light per $\mathrm{cm^2}$ are required in order to produce burns to the skin?


texts: What's the difference between germ line and germ cells?

texts:
I'm currently reading some introductory chapters about genetics (in Campbell's book, chapter 13) and I realized that I don't really understand what is the difference between the germ line and the germ cells.

From what I read so far, I understand that germ cells are specialized cells from which gametes are produced, and I suppose that the germ line is the "set" of all germ cells + gametes, but for some reason I couldn't find a good definition of what the germ line is and I was not satisfied with what I found in books and on the internet (because it was not as clear as I thought it could be)...

So, even if I'm ashamed to ask... Could someone explain to me the difference between those two concepts? Thanks in advance!


texts: Why do athletes see a dip in performance in their thirties?

texts:
I have noticed a lot of athletes hit their prime when they are in their 20s and that by the time they reach their 30s they are past it and start to decline. Great athletes tend to prolong their careers by adjusting their game strategy, but even so they can't do the things they used to do when they were younger. Examples of this are abundant in the NBA, NFL, MLB, NHL, football, etc.

Why do athletes suddenly have such a drop off in performance? What happens to their bodies,  muscles, etc that prevents them from doing what they once did? Can someone explain the biological/physiological reason for this?


texts: What should we do when someone is diagnosed with the methanol poisoning What harm does methanol cause on our body, such as the harm to some proteins? What first-aid measures should we take?


texts: How are nutrients absorbed by a pitcher plant?

texts:
I've read that pitcher plants thrive in nitrogen-poor soil, which is solved by dissolving insects and absorbing nitrogen that way.
I have a few plants, and when a pitcher start to rot, I cut it off and study the insects that've been trapped. I've never actually observed a dissolved insect. Both interior and exterior seems unharmed.

What digestive enzymes does the plant use?
What part of the insect gets dissolved?
What structures allows absorption and transport of nutrients into the plant? And how is it exploited?


texts: How long would it take for a change to the DNA would take effect?

texts:
I am not a Biology Student (sorry guys!) but I have thought about this question for a while and hope that maybe one of you can answer it. Lets say that I had my DNA changed so that I wouldn't be vulnerable to certain diseases or perhaps to make my body change so that I'd lose weight easier (Just a hypothetical here not sure if sci-fi have skewed my view on DNA).

From the change occurs to the DNA until the changes take effect, how long would that hypothetically be?


texts:
I found this caterpillar eating my parsley, around Austin, TX.

It looks very monarch-ish, but apparently monarchs don't eat parsley.  Plus it has knobs on its back.

But it also does not look like the Eastern Swallowtail since there is almost no hint of green in its color.

Hoping that this turns into some type of pretty butterfly I am letting it run amok on the parsley for the moment.

Any ideas?


texts: Difference between negative allosteric regulation and non-competitive inhibition

texts: Both connect to some site other than the active site which controls the shape of the active site and causes the enzyme to be less active. So what is the difference?


texts: I am thinking about this thought experiment: Suppose we have three taxa which are grouped into the following tree: {{A,B},C}, clearly {B,C} is a paraphyletic group. But if A go extinct in the near future, we are left with {B,C} only, then can the group be called monophyletic?


texts: What is this insect found in Western Arkansas?

texts:
I had my cup of water outside with me, went inside for a few minutes, came back outside and this insect almost found out what was unpleasant about being drunk.

It's 1-2cm long, mostly black, with some white spots on the back. The bottom of the abdomen was also white/gray & black striped.

What did I almost drink?

Update:
I saw another one of these at the park - it's rear legs were positioned like a stink bug, and before I could take any pictures of it, it flew off. It had a sustained flight, like a wasp, rather than say a grasshopper.


texts:
Occasionally on this site I’ve noticed the following definition of evolution being given:

  Evolution is a change of allele frequency through time in a population

( For example, from here)

Recently the following (From here):

  The statement "evolution is driven by mutations" is very misleading if not simply wrong. Just have a look at an intro course to evolutionary biology!

  In short, evolution is a change of allele frequency over time.

But mutations are important to evolution, and I feel must be included in the definition.

Here’s why that concerns me:  One group of evolution deniers, and others like them, use comments like these above to try and show a weakness in evolution.
See:
http://creation.com/don-t-fall-for-the-bait-and-switch

With comments like:

  “It is a bit of a trick played by using sloppy language. Evolutionists use adaptation, which is observed, to support evolution, which is an entirely different process. It is an example of bait and switch.”

Also:

  “Next time someone says that evolution is an observed scientific fact make sure you get them to clearly define what they are talking about.
  They will almost certainly be referring to adaptation but want you to believe they have proved evolution.
  Don’t be fooled. Sloppy language leads to sloppy thinking.”

Ok, I hate to give them ‘air-time’ by posting that, but perhaps it will cause us to clarify ourselves better.  Answers like "a change of allele frequency through time" just end up feeding right into this kind of evolution-denial.

SO, here’s my question  Since there’s a lot people here smarter than me:  Can someone please offer up a stronger definition of evolution than just ‘a change in allele frequency over time’?

In researching answers I found this on Berkeley’s site:

  “Biological evolution, simply put, is descent with modification. This definition encompasses small-scale evolution (changes in gene frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations).”

I like that it goes beyond small-scale (which these others would just call adaptation).  But this doesn't mention natural selection, and mutations; which I feel are important distinctions given the kind of comments these deniers make. Is there a reason Berkeley's definition didn't include those distinctions?

EDIT:  Can someone explain the down-vote?  I followed everything outlined under How to ask a good question


texts:
Wikipedia says:

  Furthermore, bone marrow performs a valve-like function to prevent the backflow of lymphatic fluid in the lymphatic system.

How can bone marrow act like a valve eventhough they neither have lymphvesseles nor contracting property?


texts: Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

texts:
I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in original Cymate paper (master sequence and clones - aligned in ClustalW, blunt ended).
My problem is that I got gaps in results (image is attached, it is from Cymate Result) on positions 27, 50, 58 etc.

When I looked back at my original alignment FASTA file and compared those positions, I noticed that those gaps are from C to A, or C to G transitions (and obviously Cymate outputs only C to C, and C to T cases).
Does anyone know why do I get those C to A, or C to G, are those some mismatches, should I manually remove it from alignment, or did I made some other mistake?
Any advice from you would be very useful for me!
My FASTA file alignment, which I uploaded to Cymate, is here (if anyone wants to check). First sequence is master sequence (non-treated, orifinal sequence) and the rest are clones (bisulphite treated sequences).

Consensus_cepa__(289_bp)
GAAAGCCAACCACCACATCCGCCATCCCTCACAGTATGCCAACGAGCAGCTGAATGACTCCGAACAACGCAAAGCATGACGCCCAAACCGACGAACACCCAACCGAAAGGCCACAAGCGCAACGTGCATTCCAAAACCCCATGAACCACCGAATCCTGCAATGCACACCACGCTCGACGCCATTCGCTACAGACCACATCGACACGAGCGCCAAGCCATCCATCACCCGAAGCCATCCACCCACTCACAAACATACCACGAAGCACAGCAAATATGAAGACAAACCCTC
MV_A_SP6_izrezani_s_primerima__(295_bp)
AAAAATCAATCTCCACATCCGCCATCACTCACAGTATATTTAC-AGTAGATAAATAA-TTAAAATAACGCAAAACATAACGCCCAAACAGACGTACTCTCAACCTAATAACCTCGAACGCAACTTACATTCAAAAACTCGATAATTCACGAAATTCTGCAATTCACACCAAA--TATTGCATTTCGCTACGTTCTTCATCGACACGAAAACCAAAATATCCATTGCCAAAAATCATTCAGACGCTCACTGAAATAACACAAAACACATCAAA-ATAATAACAAACTTTC
MV_B_SP6_izrezani_s_primerima__(295_bp)
AAAAATCAATCTCCACATCCGCCATCACTCACAGTATATTTAC-AGTAGATAAATAA-TTAAAATGACGCAAAACATAACGCCCAAACAGACGTACTCTCAACCTAATGACCTTGAACGCAACTTACATTCAAAAACTCGATGATTCACGGAATTCTGCAATTCACACCAAA--TATCACATTTCGCTACGTTCTTCATCAACACGAAAACCAAAATATCCATTACCAGAAATCATTCAGACGCTCACTGAAATAACACAAAACACATCAAA-ATAATAACAAACTTTC
MV_C_SP6_izrezani_s_primerima__(291_bp)
AAAAATCAATCTCCACATCCGCCATCACTCACAGTATATTTAC-AGTAAATAAATAA-TTAAAATAACGCAAAACATGACACCCAAACAGACATACTCTCAACCTAATAACCTCGAACGCAACTTACATTCAAAAACTCGATAATTCACGGAATTCTGCAATTCACACCAAA--TATCGCATTTCGCTACGTTCTTCATCGACACGAGAACCAAAATATCCATTGCCAGAAATCATTCAGACGCTCACTGAAATAACACAAAACACATCAAA-ATAATAACAAACTTTC


texts: Is there a downloadable list of all species along with their traditional classification?

texts:
I'm looking for a downloadable list of all known (or better said, online documented) species in this straightforward format, as an example the European Frog:

Kingdom: Animalia
Division: Chordata
Class: Amphibia
Order: Anura
Family: Ranidae
Genus: Rana
Species: Rana temporaria

I'd like to have this list offline in a structured text or database format that I can parse. If such a list has other useful attributes (credits, distribution, common names), it is welcome, but the above is the absolute minimum I need. I know there are more taxonomy levels in the above system (Species 2000 & ITIS Catalogue of Life: April 2013 ), but I only need these basic 6.

I have been looking at several collections and am having difficulty getting the data that I need. Either the database is incomplete, not accessible as a database, has complicated data structures, or has poorly described and slow web APIs that I cannot rely on.

Conceptually, it seems to me that http://www.catalogueoflife.org comes closest to my needs, yet their download is a tool, not a database. I do see the download has a MySQL folder containing lots of files, but I don't know how to reconstruct it into a database. It seems also that they pulled the page to describe the database download.

As simple as my question seems (I'm not a biologist, so I assumed it was simple), I have wasted several hours coming up empty. I was wondering if anybody has done the work to provide basic species info in an understandable format as requested?

As for species completeness, the 1.3m of Catalogue of Life sounds really good, as I'm currently basing my system on Wikipedia, which only has 180k species.


texts: Heritability of trait stronger from one sex over another?

texts: Given a trait that can be expressed (and measured) in both parents (e.g weight, height, strength, speed), are there ever traits in the child that correlate better with one sex parent than the other? If so, can you give some examples. This could be in any species.


texts: Lab experiment: Enumeration of Leukocytes

texts:
The images below were obtained in an experiment to enumerate leukocytes in a blood sample using Neubauer counting chamber.

The following solution was prepared and added to the Neubauer chamber and viewed under a compound microscope:

100 microlitres of acetic acid (acidic reagent to haemolyze RBCs) + 50 microlitre of Leishman's stain + 1-2 drops of blood.

Are these granular transparent circular objects in the images the leukocytes? If yes, do these include the smaller ones too? I am unable to decide which ones to take into account.

Moreover is this count normal (for instance, I counted around 250 (excluding the very small ones and applying the margin rule) in the top left box of the grid (Image 3))?


texts: What does it mean to protect RNA polymerase?

texts:
From this paper

  However, based on the strong interaction between NusA and RNAP, we propose that the chaperone activity of NusA could provide more direct and concentrated protection for RNAP under stress, i.e., NusA could simultaneously act as a latent protector of RNAP during transcription elongation and termination.


texts:
I have seen lot of people sleep or say that they are feeling sleepy after taking some medicines. Why? I mean, if a medicine acts on some cell of the body because that cell has got its receptors and other cells have receptor for another part of that molecule, then too why do a large range of medicine induce sleep?

This also points to a doubt that there are only one kind of receptors for sleep inducing medicines (the real ones not the ones which have sleep as side effect) or many? If many are there, then it can be possible that a large range of medicines induce sleep.

Is it due to induction of sleep gives relaxation and thus give time for action of other medicines? Or is it just a natural process? If latter, why only some?

I don't want metabolism, just a reason.


texts:
To the exception of woodlice, Crustaceans live in aquatic (marine or freshwater) environments. Crustaceans are arthropods which is an immensely diverse taxon. Many arthropods live in terrestrial environments and many live in aquatic environments.

Pisani et al (2004) report evidence of fossil of terrestrial arthropods as old as ~450 million years ago. According to Wikipedia > Arthropoda citing Lin et al. (2007) (the paper is behind a paywall, I could not read it myself) report evidence of fossil of arthropods as old as ~550 million years ago.

Were there any terrestrial species in the ancestry of all crustaceans?


texts: Can you explain the behavior of this snake?

texts:
I just saw this video in which a snake is swallowing grapes.
 ("Whip snake eating grapes").
In the video, the snake just doesn't eat but goes on to swallow 2-3 grapes.
I did some research on the internet and in "bio stack exchange" but only to find that "snakes are obligate carnivores", which simply means they don't have the body mechanism to digest a vegetarian diet.
My guess is that it mistook the grapes for a prey due to the smell coming from the grapes, which may be left there by a rodent or any other organism the snake feeds on.
Can you provide a possible explanation for this snake's behavior? Regards


texts: When did bison exchange smartness for larger skeletal muscles or a digestive system that can ferment grass?

texts:
Patricia Churchland (2019) writes:

  From time to time, evolution favors a dumbing down; sacrifice some smartness in exchange for larger skeletal muscles, like bison, or for a digestive system that can ferment grass, again like bison.

Roughly when did these evolutionary changes occur?


texts: Does xylitol kill all kinds of bacteria?

texts:
Xylitol is known as a bad bacteria killer in human's mouth.
But I am curious about one thing.

Does xylitol kill all kinds of bacteria regardless of good or bad?

If so, Does xylitol kill bad bacteria more than good ones at least in human's mouth?


texts: Frequent urination caused by sound of running water

texts: I urinate at sound of running water when I brush my teeth or wash my hands . This only happens when I am home


texts: Why is metabolism of ethanol catabolism? Could it be also detoxification?

texts:
Detoxification is the physiological or medicinal removal of toxic substances from a living organism, including the human body, which is mainly carried out by the liver. Additionally, it can refer to the period of withdrawal during which an organism returns to homeostasis after long-term use of an addictive substance. (Source: https://en.wikipedia.org/wiki/Detoxification)

Ethanol is metabolised in liver with ADH, which oxidises ethanol to acetaldehyde. The latter is a toxic substance and can cause tissue damage, therfore, it must be further oxidised by ALDH to form a non-toxic product, acetate.
Ethanol can be an addictive substance.

Why is ethanol metabolism catagorized as catabolism? Could it also be detoxification (according to the assumptions above)? Why not?

Is ethanol metabolism a catabolic metabolic pathway because it provides NADH and acetate (which can be activated to acetyl-CoA) for anabolic reactions? Or is there another reason?


texts: What technique biologists use in order to determine the function of organs?

texts: How the biologists were able to determine the functions of body organs? Using a specific example organ for an answer would be ideal.


texts: Meaning of Phred score - probability of base calling error

texts:
I learned that Phred quality scores are logarithmically linked to error probabilities. For example, if Phred assigns a quality score of 10 to a base, the chances that this base is called incorrectly are 1 in 10.
How is it possible to have 10 possiblities when you can only have 4 bases (ACGT) ?
When assigning a base, there are only three ways to be wrong to me.


texts: Are the Fastq files content is truly random

texts:
I'm building a system to generate fastq files as they are being output from HiSeq 3000 and HiSeq 4000. This will serve us to test our internal systems with some gold standards.

As we are working with microbiome a standard sample may contain around 1500 different species, is there a a bias in the output regarding how 'close' each assembly record appear next to each other or is it truly random?

If record 1,1 is from assembly 2913, what are the odds that record 1,2 is of that assembly as well (assuming 1500 species with the same strain length) ?

I couldn't find any paper on that so any help from experience would be great.

Thank,
Eden


texts:
There is a, probably wounded, pigeon (common rock pigeon) in my balcony. It is dark right now and thus, I have very little idea about its condition. But it seems it is finding it difficult to fly/move its wings because when I approached the balcony door, it 'walked' towards the farther end of the balcony while flapping its wings very slowly.
What is the right way to handle the bird and what is the best thing I can do for him/her?


texts: In which reactions of glycolysis is magnesium involved?

texts:
I am currently studying the metabolic pathways for biochemistry and I am not quite clear in which reactions of glycolysis magnesium is involved.
So I have now found out that magnesium is present in the three ATP-dependent reactions (1st, 3rd and 10th reactions), but also in the 2nd, 7th, 8th and 9th steps.
According to this diagram:

In our university we have been tought, that Magnesium is present in all ATP reactions, but also in Step 2... this is what causes confusion for me:


texts: Do mutated c-sis oncogenes only affect cell growth?

texts:
Since c-sis regulates only cell growth, a mutation there should only lead to an out of control growth of the cell, but the cells would still be mature, since c-sis does not regulate the function or maturing of the cell.

However a mutation in c-sis leads to cancer, and cancer is not just cells that grow out of control, but also don't performe their function (are not mature). Can someone explain how a c-sis mutation still leads to cancer please?


texts: "Signal Advance": Unsure of meaning or contextual use

texts:
I am reading through Recombinant DNA; Genes and Genomes - A Short Course - Third Edition by James D. Watson, et. al. and I came across this paragraph in the discussion about discrete factors of inheritance in Mendelian genetics:

  The character shown by a plant depends on the pair of factors it receives from its parents. If both factors it receives are the same, that is, two dominant (yellow seed) or two recessive (green seed), then the plant exhibits those traits - yellow seeds for the former and green seeds for the latter. If one factor is dominant and the other recessive, then the dominant character is expressed; in this case, a plant with a factor for yellow seed and one for green seed will show the dominant trait, yellow seed. But the factor for green seed persists, even if the plant is yellow, and can reappear unchanged in later generations. This was a signal advance. In the 19th century it was believed that the traits of parents were blended in their offspring and, once mixed, the contributing traits could not be recovered. At the time, this was a severe problem for Charles Darwin's theory of evolution through natural selection. His critics pointed to that any favorable variation arising in an individual would have no long-term effect, because it would immediately be lost by blending.

Note: Added emphasis is mine.

I have done both Google and Google Scholar searches for

Signal Advance
Signal Advance Biology
Signal Advance Genetics
Signal Advance Science

and I have not had much success finding a definition for the use in this context.

One article, Plant biology: Signal advance for abscisic acid was one of the only relevant references I could find that used the words in combination, however they were only used in the title.

I am not sure of the context that it is being used in Recombinant DNA or in the plant biology article.

Are they saying that the signal advance marked a change in thinking on the subject, the way we would use the terms paradigm shift or quantum leap?

Or are they instead using the term in the sense of the recessive gene being maintained in the genome and was able to be expressed in future generations?

I have not come across the use of the term signal advance before, and it is difficult to work out from the context as the first half of the paragraph speaks about the genetics and then the second paragraph discusses how it provided evidence to change the hypothesis of the day.

There is a similar problem with the plant biology news and views as it talks about six new papers on a topic that had been elusive, but as it happens to be about a signaling pathway; I am left wondering the context here as well.

If anyone has come across this before and can help to clarify it for me, I would appreciate it. Thank you.


texts:
What are the evolutionary explanations for why women are physically weaker than men (on average), and is this difference adaptive? See figure one here.

I suppose that something puts pressure on men to be physically stronger than women, but I don't see what it can be. Why the discrepancy between the sexes?


texts:
What are the mistakes in here?

The image below shows a part of the energy flow diagram in an ecosystem.

1. Part P of the biomass of the primary producers does not get consumed. Give a concrete example of how this energy can get to the decomposers.

I think this energy can get to the decomposers, because the biomass simply dies. E.g. dead animals, dead trees, etc.

2. The amount of energy that is represented by R may end up with the decomposers in different ways. Name three ways.

I can come up with natural cell dead (dissimilation after assimilation).

3. The energy that is released through dissimilation, is not only released in the form of heat. What can this energy 'Q' be used for by the organism?

I think this energy (e.g. dissimilation of glucose) could be used for movements by the organism.


texts:
Like mosquito eggs are important for fish, what’s our role in balancing the life on earth or its ecosystem.
Please suggest if this question doesn't fit in this community.
I am a mechanical engineer with interest in knowing biology and biochemistry.


texts: What is happening physically when I get sleepy and when I wake up?

texts:
After a week of too little sleep, I slept about 12 hours last night to "catch up". It made me wonder: what is happening physically that signals that I'm done sleeping,  or conversely,  that I need to sleep. I read this question and its answers, which explain how brain waves indicate different sleep stages: Why sleep? No, actually, why wake?

But what causes the changes in these brain waves? I'm curious about the mechanism by which my body determines that it needs sleep, and not just a set amount,  but a specific amount based on my previous week's lack of sleep. is it something in my brain or is it a hormone or something else?


texts:
I'm a 12th-grade student and I have an entrance exam this year.

I have a question in biology. I would appreciate you if you help me <3

as we thoroughly know platelets are multiple pieces of a big cell which is called megacaryocyte so they do not have any nucleus. so I wanna know if they cytoplasm contains any type of DNA or not? I'm sure that without the nucleus there can't be any linear DNA but I doubt on the cycle DNA.

thank you


texts: Can you detect if a mutation is spontaneous or induced?

texts: Is it possible to determine if a certain specific mutation had a spontaneous origin (for example from a mistake of the DNA polymerase) as opposed to an induced origin (for example, from some genotoxic agent)?


texts: Why glycosylation of a protein increases its non-specific binding properties?

texts: This doubt arose while reading this website: https://www.thermofisher.com/cn/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/avidin-biotin-complex-method-ihc-detection.html


texts:
Terrestrial animals face two common sources of heat extreme enough to pose a danger to them: Sunlight and fire.

It therefore stands to reason that they would evolve systems for sensing heat and behavior making them averse to extreme levels of heat, and most terrestrial animals have indeed done so.

Fish, on the other hand, live in an environment where neither of the above heat sources have a profound impact, and the one source of high temperatures underwater (geothermal activity, such as underwater volcanoes) does not exist within the habitat of many species of fish.

In summary, there does not appear to be any pressure for fish to evolve or retain an aversion to heat like terrestrial animals have.

Are fish averse to extreme heat?


texts: How are CheY, CheA, CheW, CheZ pronounced in speech?

texts:
This is a quick followup question to this question about proteins that play important roles in chemotaxis:

How does one pronounce the protein names "CheY", "CheW", etc., in English?  My guess would be that they're pronounced like "key why", "key double-u", etc.

(I want to refer to these proteins in a philosophy of science presentation, but don't have much background in molecular biology. I know about chemotaxis only from reading.)


texts: Why don't all organisms reproduce asexually?

texts:
According to a comment at Why are not all species hermaphrodites?, asexually reproducing species go extinct more easily. However, I don't think sexual reproduction is a true evolutionary stable strategy. Since humans reproduce sexually, somebody with resistance to malaria and no sickle cell anemia can produce a kid with sickle cell anemia. For any sexually reproducing species, if a mutant asexually reproducing individual that happened to have the right genome arose, her clones would outcompete the rest of the species because almost none of them would produce an offspring with a bad trait, because they have weaker genetic drift against advantageous traits and so have a larger amount of some of them, and because they would be so slow to evolve by genetic drift to be unadapted to all those future sudden changes in the environment that they're already adapted to. Wouldn't an asexually reproducing snail from a species that snakes eat with the mirror image form from most of its species have the advantage of being harder to be eaten without having trouble finding a mate. Maybe just like humans could evolve to have resistance to malaria without the risk sickle cell anemia if they reproduce asexually, maybe if a mutant asexually reproducing cheetah with the genome that would make its clones spread arose, its clones would evolve to be furless poikilotherms that can thrive the low night temperatures because that would enable them to chase their prey longer before they became too hot to continue the chase because they would start at a lower body temperature, and individuals with that trait would never produce an offspring with any costly trait that comes with it except for a tiny costly trait.

In addition to that, if a mutant female asexually reproducing individual arose in a sexually reproducing species with the right genome and the species currently was in an evolutionary stable strategy with monogamy with each couple just able to get food fast enough to rear two children, the mutant female would also get a mate and with his help still be able to get food fast enough to rear two children both of which have entirely her genome, and then her asexually reproduced clones would spread very quickly. Once the species reaches a new evolutionary stable strategy where each individual can only get food fast enough to rear one child because there are so many females taking the available food, they may still have a slight evolutionary advantage over other species that's not nearly as high as the evolutionary advantage of asexually reproducing individuals was over sexually reproducing individuals of the same species earlier.

Source: https://www.ncbi.nlm.nih.gov/pubmed/16217668


texts: Regulation of the replication of mtDNA at embryonic level

texts:
While reading an article on mitochondrial inheritance I came across this link.

The results state that mitochondrial DNA replication is regulated in different cells of an embryo at different levels. How is this regulated?


texts: Factors for sensitivity to electric shock

texts:
I'm frequently getting electric shocks in my office when touching things. I basically know why this happens and how to avoid it.

Still I started to wonder what would be the best way to touch something if you knew you will be shocked. I know that fingertips have more nerve endings but I guess they also have more callus. What are factors for sensitivity to electric shock and what part of the hand is therefore the least unpleasant to be shocked?


texts: Are viruses technically organisms, or not?

texts:
Are viruses technically organisms or not?

A quick Google search query for the term; are viruses organisms?, reveals various conflicting and somewhat inconclusive arguments & opinions from a range of sources. (Examples provided below).

Note: These answers are mostly opinion-based and inconclusive; falling short of the Stack Exchange community's quality control standards.

Let me be clear: I am not seeking opinions, or debate; but rather definitive answers supported by facts.

  Wikipedia | Organism.
  The most common argument in support of viruses as living organisms is their ability to undergo evolution and replicate through self-assembly...
  Some scientists argue that viruses neither evolve, nor self- reproduce.
  ~ https://en.m.wikipedia.org/wiki/Organism

  Encyclopedia of Life | What is a Virus?
  A virus is a microscopic organism that can replicate only inside the cells of a host organism...
  Viruses infect all types of organisms, including animals and plants, as well as bacteria and archaea.
  ~ http://eol.org/info/458

  Virology Blog | Are Viruses Living?
  Therefore, viruses are not living things...
  So technically speaking they are non- living organisms.
  ~ http://www.virology.ws/2004/06/09/are-viruses-living/

  Popular Science | Are Viruses Alive? New Evidence Says Yes.
  Viruses seem to carry out only one life process, reproduction, but even then, individual viruses don't carry translational machinery, namely, the proteins needed to read their DNA and RNA and build new viruses. They invade a cell and hijack its genetic tools to do it for them...
  But within the last decade, developments in virology have started to reveal more and more that viruses might in fact be alive...

  One was the discovery of mimiviruses; giant viruses with large genomic libraries that are even bigger than some bacteria. (To put this in perspective, some viruses, like the Ebola virus, have as few as seven genes.) Some of these giants have genes for the proteins that are required for translation—those readers of DNA and RNA that in turn build new viruses...
  This throws the lack of translational machinery argument for classifying them as nonliving on its head.
  ~ http://www.popsci.com.au/science/medicine/are-viruses-alive-new-evidence-says-yes,409690

  Science Daily | Virus.
  A virus is a microscopic particle that can infect the cells of a biological organism...
  At the most basic level, viruses consist of genetic material contained within a protective protein coat called a capsid; the existence of both genetic material and protein distinguishes them from other virus-like particles such as prions and viroids...
  It has been argued extensively whether viruses are living organisms...

  Most virologists consider them non-living, as they do not meet all the criteria of the generally accepted definition of life...
  They are similar to obligate intracellular parasites as they lack the means for self-reproduction outside a host cell, but unlike parasites, viruses are generally not considered to be true living organisms...
  A primary reason is that viruses do not possess a cell membrane or metabolise on their own - characteristics of all living organisms.
  ~ https://www.sciencedaily.com/terms/virus.htm


texts:
How much do crocodiles eat? The closest I found to an answer was on German wikipedia, where it says that adult nile crocodiles eat "only about 50 full meals a year." While interesting, without knowing what a full meal is this is meaningless. So how much does an adult crocodile actually eat?

I think relevant other questions in this context are:

Do all adult crocodiles (or even all crocodilia) eat roughly the same (corrected for body mass)?
Some crocodiles apparantly eat fruit and seeds on a regular basis*, is this is a relevant part of their caloric intake or just a "vitamin supplement"?

*paywalled article, I only read the abstract


texts:
DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two molecules differ in the hydroxy group in the ribose which is only a single proton in the deoxyribose. This part of the sugar molecule is not directly involved in binding reactions, nevertheless it causes the whole difference in RNA and DNA.

I wonder: could a dNTP be used in an RNA strand (or vice versa)? Is it chemically possible that we have a RNA molecule that contains a dNTP next to its NTPs?


texts: Why do both the mango and the bee have "Indica" in their binomial name?

texts: In my textbook, it is written that the binomial name of mango is Mangifera indica and the binomial name of a bee is Apis indica. Now in the name the second part is the name of species. But mango and bee are not the same species. One is a tree and the o,ther is an animal. Then why is their second name the same?


texts: Can anyone identify this insect larvae please?

texts: I found thus tiny creature in my shower its about 19mm in length with a see through body and moves much like a caterpillar.


texts: How does an axon "know" it's not connecting to its own neuron?

texts:
I recently read about an experiment where they removed the dendrites and axons from rat neurons and placed them on a grid. After a while they started reconnecting and were able to learn things.

Since I'm trying to create a model simulating this, I'd like to know (as much as is needed to make it look at least a little bit realistic) how they reconnected. As far as I know some molecules are secreted attracting or repelling axon growth cones.

I think I can model that part, but the problem is that the axons can easily grow back to where they came from, so how do the axons in a brain 'know' they are not growing back to the neuron they originated from.


texts: Examples of heterologous expression in human cell beside viral expression

texts: Usually, people are interested in expressing human proteins in fast-growing organisms like bacteria to yield a maximum of protein within a short time lapse. Codon usage harmonization/optimization have been used to increase the protein production. The role of codon usage have been studied in the context of viral protein expression, but outside this viral context, is there any example of using human cell lines for heterologous expression?


texts: How can I describe running a solution four times through a chromatography unit (in an instruction)?

texts:
I'm translating a document from Russian:

  The mean retention time for the first four injections of RNase should be (40.8± 2) min. If the mean RT is beyond this range, adjust the gradient system (change the content of acetonitrile within the 20% - 32% range) and chromatograph the RNase solution four times.

I'm aware that we don't use chromatograph as a verb in English usually, but we do use it in Russian this way. What would be the generic English expression for this, usable in a procedure description? I know that we have the word run but this might be too colloquial for an official paper.


texts: For humans, why is red the color of distinction rather than green?

texts: The human eye is most sensitive to the color green. However, for some reason red is often selected as the color of distinction or alert. For example, in Renaissance times, painters would outline their figures in a thin red line. In manuscripts, a "red letter" (or "rubric") was used to emphasize an initial capital. Today, we routinely use red for emergency lights or whenever we want to call attention to something. Considering that red is the color our eyes are least sensitive to -- and green the most --  it seems counter-intuitive that we would use red when we want to draw attention to something. Why is this?


texts:
I know you can purchase dog and cat breeds that are hypoallergenic so those who are prone to pet allergies will have reduced allergies or none at all. These breeds are specifically bred for that trait, and as a result are typically pricey compared to another breed. These breeds are not necessarily hairless or short-haired, so I do not think it has to do with the amount of fur shed.

What makes these animals different from other breeds in their inability to cause allergies?


texts: Why does our visible range not include infrared or UV radiation?

texts:
As the radiation peak of the sun is in the UV region and since at around room temperature materials emit radiation at IR, I wonder why our eyes are not capable of using these wavelengths.
I guess there is a reason why we exactly only see the region between these intensity peaks?


texts: Experimental evidence for the selfish gene vs. the selfish individual

texts:
In the Selfish Gene, Dawkins makes the argument that a better  view of evolution (i.e. more in accordance with experiment) is obtained if you view the basic unit of evolution to be the gene rather than the group. Having read the book, I am convinced (inasmuch as a layperson can be convinced) that group selection comes up with incorrect predictions about evolution, so is a fallacious interpretation of evolution (is this a correct interpretation of the book and is this conclusion common opinion among biologists?).

I have heard that historically, his book was part of a backlash against the then prevalent viw of group selection.

TL;DR

However, is there an experimental way to prove whether the gene-selection or individual-selection interpretation of evolution is more correct?

I hope my question is not ill-defined whilst leaving 'unit of evolution' vaguely defined.


texts:
I saw a news story about someone who had participated in a COVID vaccine trial, and he said that he had taken an antibody test that came back positive, and he had concluded that he had not gotten the placebo, but the vaccine, and it had made him immune.
Isn't that problematic behavior? The trial is supposed to be double-blind. Are there ethical guidelines about trial participants getting tested?


texts:
DNA supercoiling refers to the over- or under-winding of a DNA strand.

Source : DNA supercoil

  When a relaxed DNA is subjected to bends, or openings of DNA, over winding or unwinding, its base pairs per turn changes, and the DNA is subjected to stress and strain.  In order to overcome such distortion, which has rendered the DNA unstable, the DNA twist around itself, like a circular rubber band undergoing twisting, such a twists on its own thread is called Super coiling; it is also referred to as tertiary structure.

Source : DNA Super Coiling

What they mean by over winding and under winding of a DNA ?


texts: In our 23 chromosome pairs, do the 2 members of the pair have distinct or virtually identical sequences?

texts:
I understand that we have 46 DNA molecules in the nucleus of our cells, arranged in 23 pairs: 22 autosomal and 1 sex chromosome pairs.
I have read in different sources that the pairs contain nearly identical members, excluding any mutations. I have also read that the pairs contain 1 member we inherited from our mothers and 1 we inherited from our fathers, which are different due to inheritance.
This seems contradictory, given that genealogical companies match up on the differences on these chromosomes.
My understanding was that meiosis creates sperm and egg cells that each carry 23 chromosomes - they are haploids. During the first steps of meiosis that creates the reproductive cells we have a combining of the parent's chromosome pair from their parents to create 4 daughter cells, each independently viable, where the recombination of the chromosome pair has occurred at somewhat predictable spots (for you perhaps :-) ) and that these spots can be related to genes. It is this step that give us our genetic variation between siblings for example. A new person's DNA is partially formed from any one of these highly varied daughter cell possibilities.
Fertilization combines the reproductive cells to produce the 46 chromosome zygote with is again diploid.
I think this understanding supports the second interpretation that our chromosome pairs are not 2 nearly identical DNA molecules but are distinct.
Have I got this right? Is there a missing process or a misunderstanding in my interpretation?


texts: What is a substance that is safe to eat, not absorbed and not metabolized?

texts:
I would like to know whether there are substances that are safe for humans to consume, are not absorbed and do not interact with any digestive process.

So, food is disqualified because although it may be safe, it is processed by the digestive system and is metabolized. I'm looking for things that go entirely unprocessed (other than passage).

One such material, or a discrete class of materials is sufficient.


texts:
I mean it seems first step is rennin or pepsin digestion in stomach - then what happens with remaining peptides?
I am interested in the whole process from casein to amino acids.
Is there brush border enzymes involved in the small intestine or all process is in the stomach?


texts: Is there a good explanation for this swarming pattern?

texts:
A film clip would be helpful here. A few days ago I noticed a swarm of newly hatched flying bugs about 20 feet away from me with the sun behind them so the shape of swarming (such as it was) was easy to make out. Several times, after creating various spiral shapes or chaotic masses they returned to a sort of 'holding pattern' which I either never noticed or never saw before. To a pretty good approximation the bugs arranged themselves in what seemed like an "oscillating drum head" pattern that is well approximated by a rotated sinc function. The peak at zero is a little exaggerated here but the bugs were more or less dispersed on a shape like:

subject to a light breeze and continuous adjustment. I know that people have studied swarming behavior and made models but are there any that account for this one? It has a lot of significance in ODEs and engineering but I never associated it with swarming behavior.

Thanks!


texts:
On holiday in southern France and we found this small plant growing out of some rocky soil:

It smells quite strongly like anise but seems to be a different plant?


texts: Do we posses technology to rebuild sequenced DNA?

texts:
Is there existing technology that would allow to rebuild DNA molecule from a digital file storing sequenced DNA?

If not, does there at least exist theory explaining how such device could be built?


texts: Re-establishment of Hardy Weinberg Equilibrium After Selection

texts:
I have been given this question:

In a population of 2500 mice, light-colored fur is dominant to dark-colored fur. 2400 mice originally have light-colored fur. However, an owl species moves into their environment, preying mainly upon the light-colored mice as they are easier to spot when hunting at night. When the owls finally leave, 80% of the dark-colored mice are left, and only 10% of the light-colored mice. After many generations, Hardy-Weinberg equilibrium is re-established. Approximately what percentage of mice now have dark-colored fur?

Answer choices are:

A) 10%
B) 15%
C) 20%
D) 25%
E) 30%
F) 35%

My thought process goes as such:
When the owls leave, the groups are 240 light mice and 80 dark mice.
$q^2 + 2pq + p^2 = 1$
q is recessive allele, p is dominant allele.
$0.5^2 + 2*0.5*0.5 + 0.5^2 = 1$
Apply fitness:
$0.8*(0.5^2) + 0.1*(2*0.5*0.5) + 0.1*(0.5^2) = 0.275$
(0.8 and 0.1 correlate to the fitness of dark and light mice, respectively)
Now divide everything by 0.275 to figure out new allele frequencies:
$0.727 + 0.182 + 0.091 = 1$
This means that 0.727 = 73% is the new frequency for homozygous recessive (dark) mice.
However, the correct answer is B) 15%
Any idea what I did wrong/how the correct answer is achieved?


texts: How exactly are game theoretical evolutionary models described during implementation for computer simulations?

texts:
When a biologist or a layman tries to reason the evolutionary explanation for something, they would simply use English with some math thrown in (for a random example, pick any explanation out of "The Selfish Gene" -- for example, the reasoning why "discriminate in favor of one's own eggs" strategy is employed by Guillemots, in "Genesmanship" chapter, page 103. I won't quote it in full since it's a page worth of text).

Another example of such a wall of English is (Dawkins-inspired) Bio.SE question: " Why is 'Grudger' an evolutionary stable strategy? "

When a biologist tries to actually model evolutionary development to see which traits would win, they would need to somehow teach the computer to implement that model: what the environmental factors are, what the genotype involved is, how exactly it's expressed in different phenotypal and extended phenotypal traits, and how environment would affect an individual with that phenotype.

My question is: is there some sort of standard way to build such a model? A domain specific language (in computer science terminology) that is used by many different biologists or some standard modeling packages/software? E.g. some sort of special XML format, etc...

Or is it always just hand-built custom implementation by individual researchers for their current model?

Just to clarify:

I'm NOT asking what the models look like theoretically. I'm asking what language/format (if any standard one exists) is used to encode them to run simulations.
If there are discrepancies between the type/purposes of models, the ones I'm most interested in are game theoretical ones.


texts: Questions concerning synaptic input and dendritic processing

texts:
In the article How Spike Generation Mechanisms Determine the Neuronal
Response to Fluctuating Inputs, I read (p.11629)

I have four questions concerning some formulations:

What is "the membrane time constant" if this depends on the membrane resistance and capacitance which varies over the membrane? Maybe "local membrane time constant"? Or "mean membrane time constant"?
What do the authors probably mean with "instantaneous postsynaptic currents"? Occurring at the same time all over the dendritic tree?
What do they probably mean with "exponentially decaying synaptic currents"? The decaying of the PSPs while travelling down the dendritic tree?
What's the relation between "synaptic decay time constant" and "membrane time constant"?

(Having digested the paragraph a bit more, another - probably more accurate - reading of "instantaneous" came to my mind: "starting and ending abruptly with the abrupt opening and closing of the ion channel".)


texts: Difference in reptile inner ear and otosclerosis

texts:
In reptiles, the sound is conducted from the tympanic membrane to the inner ear by a single bone.

In the disease otosclerosis the stapes of humans become fused to the other middle ear bones( or to the oval window ). This disease leads to the loss of hearing.

My question is - From what seems like superficial resemblance between otosclerosis and having one bone in reptiles, what is the difference between the two that leads to loss of hearing in one case but not in another ?


texts: Is it fine to leave pulverized plant tissue in CTAB buffer at -80 degrees over night? will the buffer remain effective to generate good quality nucleic acids?


texts: What is the difference between the basal membrane and the basal lamina?

texts:
I'm researching about the basal lamina in lung tissue and I'm not sure if the basal membrane is the same.

What is the difference between them?


texts: Discrete vs Continuous Replicator Dynamics

texts:
The replicator eqn in the case of discrete non-overlapping generations and asexual reproduction is given by the discrete replicator eqn:
$$x_i(t+1) = x_i (t)\frac{f_i(t)}{\bar f (t)}$$
where $x_i$ is the frequency of the strategy $i$ and each individual playing strategy $i$ produces $f_i$ copies of itself in the next generation. $\bar f$ is the average fitness. Thus
\begin{equation}
\Delta x_i = x_i(t) \frac{(f_i(t) - \bar f (t))}{\bar f (t)}
\end{equation}
In the case in which $x_i$ is a continuous variable, we have the continuous replicator eqn given by
$$\dot x_i = x_i (f_i - \bar f)$$

Question: I suppose we should be able to derive the continuous replicator eqn from the discrete replicator eqn by evaluating the discrete replicator eqn for $\lim_{\Delta t \to 0}$. How can I do this derivation?


texts: I have found two species of this strange looking animal on the Eastern shore of the Adriatic Sea and I was simply unable to recognise them.


texts: Why not replace the human genome with it's decoy genome version?

texts:
https://www.biostars.org/p/73100/
http://www.cureffi.org/2013/02/01/the-decoy-genome/

The decoy genome is an improved human genome from the regular reference. It's faster for mapping and it reduces false positive rate.
In this case, there shouldn't be any reason to use the regular human reference, because the decoy genome is simply better and faster. For instance, it has DNA sequence for common virus genomes presented in humans. It has everything in the regular reference.
Q: What's the point of the regular human reference (e.g. hg38) if the decoy version is more accurate and is a better representation for the human variation.


texts:
So, I've noticed a pattern in water fowl (here meaning birds who can take off and land on water, who float in the intervening time) tend to be larger birds.

The smallest I know of are gulls.

Are there any smaller water fowl? Anything the size of a partridge? Or a wren?

If it is only large birds, why is this?


texts: Is there a superterm combining "animal line" and "cell line" in disease models?

texts:
Biologists researching diseases will frequently use animal models. The way I understand it, there are species of animals, such as "mouse", and lines of mice, such as Black six, NMRI or also genetically engineered lines like B6.Cg-Tg(CAG-cre/Esr1*)5Amc/J. But they also sometimes take cell lines such as HeLa and transplant them into animals, or treat them in vitro.

Is there a word which covers both "animal line" and "cell line" and is in widespread use? I thought that "model organism" would be a good way to express it, but a biologist working in disease models told me that when she hears that, she only thinks of animals, never of cell lines. She wasn't able to come up with a term which covers both. Her best try was "experimental system", but she conceded that, if used out of context, no biologist would recognize that it is about animal and cell lines.


texts:
I'm having a hard time understanding why my slides in my biology course have two different representations of the "basic structure" of the amino acid:

1:

2:

The top one seem like what I would expect.  The bottom one, it looks like the amine group gained a Hydrogen ion and the Carboxyl group lost one.  Also, the center carbon gained an H.  I honestly don't know if this description is even correct or not.

I'm extremely new to this level of biology, so very simple explanations are much appreciated.  I just don't totally understand why there are two versions of the basic structure.

Also, I apologize if the tag is wrong, again, this isn't my major, so I'm very new to this material.


texts: Does the 1:1 sex ratio at birth apply to every human pregnancy or is it a statistical average?

texts: Are there genetic factors that biase the sex ratio of offsprings for each person but average to 1:1 for the entire human population, or does the 1:1 ratio apply to every single fertile person?


texts:
I would like to know were to download a table file with all reported bacteria and its corresponding PHYLUM, CLASS, ORDER and FAMILY.

Basically, its the same table than this one from GOLD genomes but containing the non-sequenced bacteria too:

Thanks for you help, Bernardo


texts:
At the beginning of the superb documentary film “Un jardin d’Eden sous les mers” (“A garden of Eden under the seas”) [1], we see a group of curious cetaceans. At about 1 min.

What are these cetaceans?

I think that they are odontocetes. But what species are they? This is a mystery.

[1] Documentary film “Un jardin d’Eden sous les mers” (“A garden of Eden under the seas”). It will be rebroadcasted on Arte on 2016‑04‑01 at 7:45 Paris time. You can watch it on-line here.

Thank you.


texts: Do trees really get a large share of their mass from the carbon in the air?

texts: I remember hearing that trees and other plants actually obtain a large amount of their mass from the carbon floating in the air, not the ground beneath them. Does the makeup of air actually contain enough carbon to support this theory, and is a tree's surface area actually large enough to obtain the amount of carbon it needs directly from the air?


texts: What are microRNA, siRNA and antisense RNA?

texts:
From what I understand, microRNA binds to proteins which can cut certain mRNA strands do that this protein is not synthesised. This seems like gene silencing to me, however I have also come across the term siRNA and antisense RNA...

Would be grateful if someone could explain what these are and how they work, and perhaps how they can be applied to treating diseases... Thank you in advance :)


texts: Relationship between body size and damage done by electricity

texts:
We all know that if a person gets stunned by a 2000 volt stun gun, he/she may be knocked unconscious, but he/she is still alive and apparently no damage done on his/her body.

But what could happen if that 2000 volt is applied to a snail whose body is way smaller than that of a human being?
Will it create a lot of damage into the snail's body?
Or the same effect as that of humans.


texts: Carrying or packaging capacity of SAD B19 dG rabies virus

texts:
I'm wondering about the carrying capacity also referred to packaging capacity or loading capacity (how many base pairs can be packed efficiently into virions) of the pseudotyped rabies virus SAD-dG as described in the Wickersham, Callaway publications.

Wickersham, I. R., Finke, S., Conzelmann, K.-K., & Callaway, E. M.
(2006). Retrograde neuronal tracing with a deletion-mutant rabies
virus. Nature methods, 4(1), 47–49. doi:10.1038/nmeth999
Wickersham, I. R., Lyon, D. C., Barnard, R. J. O., Mori, T., Finke,
S., Conzelmann, K.-K., et al. (2007). Monosynaptic Restriction of
Transsynaptic Tracing from Single, Genetically Targeted Neurons.
Neuron, 53(5), 639–647. doi:10.1016/j.neuron.2007.01.033


texts: How many proteins are synthesized in human body throughout life?

texts:
My idea to calculate this is:

Define up to what age will do the calculation. (for instance 60)
Determine how many cells born and died up to that point in life. (by type of cell)
Determine how many proteins are synthesized in the cells life. (by type of cell)

Points 2 and 3 are not constant throughout the life of the human body. To calculate this data I need a function.

After obtaining all the data: complete calculations of addition and multiplication.

The question is not about mathematics, but about useful data to make these calculations. Another approach would be welcome too.


texts: Are there any studies on the solar latitude limits of different plant species, beyond which they wouldn't thrive even with suitable weather?

texts:
Not sure whether this belongs here or in the Gardening & Landscaping StackExchange, but here goes...

According to maps provided in the paper Present and future Köppen-Geiger climate classification maps at 1-km resolution which assumes no reduction in greenhouse gas emissions, by the end of the century climates (for example) suitable for Theobroma cacao (with rigorous irrigation) and Cocos nucifera may extend at least to Porto Santo Island (33.08(3)°), the latter possibly to the Azores (38°) given that they are more tolerant of anemic winter heat than frost, for Carnegiea gigantea Northeast Kazakhstan (43.208(3)°), for Olea europaea North-Central Iceland (66.525°), for Malus domesticus Knivskjellodden (71.18(5)°), for Trachycarpus takil Knivskjellodden (71.18(5)°) or potentially even Southwestern Svalbard (77.5(3)°), and for trees in general the Eureka area on Ellesmere Island (79.48(3)°).

However, even though poleward areas may become suitable for species previously restricted to areas closer to the equator in terms of their thermal and precipitation profile, they may not in terms of their solar profile. I mean, while a Windmill palm would be able to accept the mid-10s °C summers and slightly-above-freezing winters of future Finnmark, would it accept the month of darkness and low solar angle except in mid-summer? Would olives tolerate the midnight sun? Would coconuts withstand the sub-30° zenith angles of the mid-latitude winter? This question could also apply to the extreme low latitude limits of species; for example, could hemiboreal Hol/Nearctic winter-deciduous trees live in the modern Southern Altiplano where average monthly temperatures are vaguely similar but the latitude is inside the tropics?

So... Have there been any studies on the potential latitudinal limits for different plant species? They don't have to be for the species I've mentioned, those were just examples.


texts: How are there alternative initiation codons?

texts: According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the mechanism of translation initiation in the absence of the canonical tRNAfMet.


texts: What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?


texts: Is the enteric nervous system found only in vertebrates?

texts:
The enteric nervous system is distinguished by being autonomous from the central nervous system and capable of independent action, such as the peristaltic reflex. For this reason the the intestines can be removed from the body of a vertebrate creature and they will still function.

Is this type of nervous system unique to vertebrates, or is it found in invertebrates and insects as well?


texts:
This site says:

  VIP [vasoactive intestinal peptide] nerves are absent in severely asthmatic subjects. Mice with targeted deletion of the VIP gene exhibit histopathologic features of airway inflammation (Said et al., 2010).

So can we consider asthma as a neurodegenerative  disorder?

What will be the mechanism of destruction of nerves if the above statement is true? If the above statement is not correct then how there is reduction in VIP ? I think of two possibilities either VIP is not synthesised in the neurons (Gene is down regulated, if so, by what?) or it is readily destroyed after its synthesis?

Could anyone please correct me?


texts: Why the tongue (like structure) in cockroach (or other insects) is called hypopharynx? In humans I know it's the lower part of pharynx, not a structure. Isn't this anatomical name misleading? Are there other ambiguous terms like this?


texts: Bacteriophages and their role in genetic editing?

texts: I know how plasmids and restriction enzymes work to change the dna of a bacteria cell, but I do not really understand how a bacteriophage works to edit the genome of a cell. Is it related to crispr since its a virus which inserted genetics in bacteria? Also, is it during the lysogenic or lytic stage that the bacteriophage alters the DNA?


texts: Reason for variation in the site of onset of edema

texts:
What is the reason for the observed clinical difference in the earliest site of onset of edema in cases of different etiologies?

For example, in Congestive Heart Failure, it appears initially as pedal edema (edema of the dependent portions, in general) but in nephrotic syndrome (or other kidney causes) appears first as periorbital edema?

In both these cases, since the onset of edema is distal to the organ of the original pathology, it must be a systemic hematological effect caused secondary to the pathology that causes this specific pattern (as opposed to a localized portal hypertension in liver disorders initially appearing as ascites). Although all of these may progress to anasarca, what determines the specific pattern observed?


texts: Is it mostly true that predators or parasites traverse wider spatial areas than their prey or hosts?

texts: Does it tend to be true that as you go up the food chain, the species tend to cover wider areas?  I am basically asking whether a population's prey varies spatially more than a population's predators and parasites, which would vary more temporally: the predators and parasites to which a population is exposed tends to be the same across the population but the prey vary more spatially because the prey tend to traverse smaller areas.  I would think this were true, since predators have larger body sizes and my thinking is that species with larger body sizes tend to travel farther and parasites may locate on multiple hosts, which collectively carry them farther than any single host.  This is my inference, but I do not even know what to type into Google Scholar in order to check this.


texts:
Is there a test method of proving a person being color-blind, without letting the test subject know, that he/she is being tested?

E.g. showing the person cards with colored dots like depicted here is not a valid answer.


texts: Can any glider incapable of powered flight strike its prey by descending on it?

texts:
TLDR
I was not able to find the precise definitions of “true flight“, “sustained flight“ and “gliding“, that are often used on Wikipedia.  My layman’s understanding is that true flight is the same as “powered flight” and means the animal can utilise muscles to generate life force that exceeds its weight under a wide range of air flow conditions. That is, it does not need upward air currents such as thermals
By contrast, gliding is defined here as:

falling at an angle less than 45° from the horizontal with lift from adapted aerofoil membranes

You are welcome to suggest more correct definitions.
Question
Can any animal that glides but is incapable of true flight (of course hawks may glide) descend upon its prey?
I am aware of this question not being very well defined, since animals such as sugar gliders can jump on their prey and  perhaps utilise a tiny amount of lift to prolong their jump. It is difficult to rigorously separate this from gliding. Let’s require that the animal glides a distance more than 10 times its length from a height more than 10 times its height.
Inconclusive information
Bats
Don’t count because they are capable of powered flight. But they can do it.
Sugar gliders
Can “leap out to catch flying insects“ (source), but that’s all I found.
Flying squirrels
“harvest fruits, nuts, fungi, and birds' eggs”(source), so they may not even prey.
Colugos
Appear to be strictly vegetarian (source).


texts: Is there human Anatomy software that provides great detail?

texts:
Is there Anatomy software that is exact representation of human body, like let's say virtual reality tour inside human body from head to foot, detailing all organs even small, covering all systems, nervous, blood vessels, muscular, skeleton systems, could be zoomed even to deepest skin layers, neurons,  that can be applied unapplied like layers in Photoshop?
If this does not exist, then which is the most advanced human Anatomy software?


texts: Can LSD in very small amounts increase mental ability?

texts: Can one take a small amount of LSD(acid) and not trip but still benefit from the intended purpose? It was said the military invented it for extra sensory abilities. It has also been said it could increase your hearing or sight?


texts: What determines when a virus becomes a "new strain"?

texts: The reason we cannot find a cure for the common cold is because viruses mutate rapidly. Where do the mutations occur in the DNA/mRNA of viruses and does this have any effect on the protein level? what has to change for the virus to be considered a new strain?


texts: What is the germ layer origin of human lung fibroblasts?

texts: What is the germ layer origin of human lung-derived fibroblasts?


texts: Are epigenetic changes involved in evolution?

texts:
Evolution leads to phenotypic changes through changes in DNA such as mutations. Mutations are transmitted to offspring. Cumulative mutational changes across many generations may cause evolution and speciation.

As far as I know, epigenetic changes causes an individual to change in how it appears (phenotypic changes). In turn, epigenetic changes may be transmitted to offspring, just as DNA mutations can be.

Is epigenetics a factor in evolution?


texts:
The general understanding is that when I touch an object, I perceive its (relative) temperature.

A metal object at room temperature, however, will often feel cool to the touch.

This leads me to believe that the skin senses heat flux in addition to, or instead of temperature.
(The metal conducts heat well, and therefore creates a greater flux when touched than a more insulative material.)

I am unfamiliar with the chemical process by which temperature or flux is converted into meaningful signals.

Do humans perceive temperature or heat-flux? (or both?)


texts: What are possible reasons for a DNA template not giving amplification?

texts: I am trying to amplify ~10kb length fragments using NEB LongAmp Master Mix. I had been using one particular aliquot of DNA (template amount in each PCR reaction of 10ul being around 60ng) and getting amplification results as desired. However, when I switched to a different aliquot of similar concentration, I am not getting amplification all of a sudden. I tried a different DNA sample and different primers and got results. So the problem lies with either the template or the primers. I have tried increasing amount of template, increasing Mg2+ by 1mM in the final reaction etc. but to no avail. The DNA templates/100x primer stocks are stored at -20⁰C and the DNA had been phenol-chloroform extracted. What could possibly be wrong here ?


texts: How do coyotes remove cactus needles from their paws?

texts:
Here, in Arizona, coyotes roam and hunt in the desert.

While hiking with dogs, I often see spiny bits of Teddy bear cholla cactus on the ground.

Dogs often step on these and get stung by the needles. Trying to remove them from dog paws with hands usually results in hands getting pricked too. A pair of stones, sticks, or tweezers usually works. I imagine letting the dogs chew off the needles would result in having needles in their lips/mouth.

Q: What do coyotes do with stuck cactus needles? Do they remove them, if so how? Do coyotes and perhaps other desert animals have special adaptations for removing/avoiding cactus needles?


texts: Why do my tomatoes start to rot on the same fruit part?

texts:
I observe a phenomenon for many years now. I observe it on a wide diversity of tomatoes produced all over Europe and Northern Africa that are sold at my local supermarket.

When I keep my tomatoes at ambient temperature around 20 to 25 degrees celsius, they deteriorate after a variable time, usually starting a five to fifteen days after I bought them. Nothing abnormal so far.

However, I observed that the mold pattern of virtually all these tomatoes is the same. It almost always starts a few millimeters from the junction where the tomato was attached to its branch, forming a ring on the top of the fruit.

I have thought why this could happen and my main hypothesis is that when they are grown the sun hits the top of the tomatoes (except where it is attached to the branch, obviously) and some ultraviolet radiation might weaken the tomato resistance in some way. The other reasonable hypothesis, although I cannot think of a definite mechanism, is that gravity would favor this polarized degradation. I have other hypotheses but they are too far a stretch, I believe.

So what is really happening?

I am a biologist, just not into botany or agriculture, so feel free to go technical and not just oversimplify.


texts: Meaning of "auto" in trans autophosphorylation?

texts:
Why this process called "auto"?
Is it because each tyrosine kinase receptor subunit of the RTK dimer has the ability to phosphorylate tyrosine or other amino acid residue present in other subunit of the RTK dimer's cytoplasmic tail? Is it because no new set of kinase enzyme is needed to phosphorylate them?


texts: Is global life expectancy normally distributed?

texts: I am trying to find out what the world distribution of life expectancy looks like.


texts: Why is there an extended delay before G.M. liver cells are attacked by the immune system?

texts:
In this BBC article a trial is described where patients with B-Haemophillia are infected with modified Adeno-associated Virus 8 which contained the genes for Factor IX clotting protein.  Trials seemed to be successful, however the article later mentions

  There was an immune response against the infected liver cells around seven to nine weeks after the virus was injected.

I am interested to know why there was a delay period of such length?  Would this be true of all cells and is it due to a long duration of clonal selection in the humoral immune response or is something else at play?  Also, I'm presuming that the Adeno Virus would be attacked long before the cells it has infected?


texts:
I have seen fake wasp nests sold as a deterrent against wasps and similar insects. Do they really work? Is there some scientific evidence for it?

A related link: http://www.scienceworld.ca/do-fake-wasp-nests-fool-wasps


texts: A question about a succession study by Chapin et al. (1994)

texts:
The succession study in Glacier Bay, Alaska (Chapin et al., 1994) is an example that is used in almost all introductory texts on ecological succession. In the study, the effect of each succession stage on the germination and development of spruce seedling was examined, and complex results were found (see Figure 4b in here). For example, In Dryas stage (one of successional stages), spruce seedlings had weak germination and survival rates due to increase in seed predators. Likewise, the results show the effect of each successional stage on the various attributes of seedling germination and survival.

My question here is what is the control/reference of this study? For example, Dryas stage decreased the survival of seedlings compared to what condition? The results show "increase" and "decrease", but the reference is not clear. Is the control same for all successional stages?


texts: In what stage of bacterial growth can penicillin inhibit the growth of the cellular wall?

texts:
The bacterial growth has 3 main stages: lag-phase, log-phase and stationary phase. I was wondering in which one of them penicillin can inhibit the growth of the cellular wall of bacteria and why.
I was thinking that the respons would be lag and log phase, because at these points bacteria multiply the most, while in stationary phase most of the bacteria are in adult form with a well formed bacterial wall already, but I'm not quite sure.


texts:
I looked up haplotype blocks in Google Scholar, and the results returned seemed to show that almost all the relevant articles were published between 2001 and 2009, with almost nothing since 2010.
Why has interest in haplotype blocks apparently waned over the last decade? Has the concept been discredited?


texts: Scientific name of a certain plant from Philippines

texts:
Can someone tell me what is the possible scientific name of this plant? The seller told me it was sun rise plant but I can't seem to find it in the internet.

Location: Santa Rosa Laguna, Philippines


texts:
Nando's chain of restaurants (UK) refers to chili peppers as just "chilies". My friend and I had a discussion with regard to whether chilies can be called "peppers" or if they do not belong to the pepper family at all. In fact, my friend added that there are 2 types of this specimen - "chilies" and "chili peppers."
To what extent is this all true, and what exactly are chilies?


texts:
I saw this harrowing video on how barnacle goslings have to jump off very high cliffs because the parent's can't feed them. The death rate seems high. Why did natural selection come to favor jumping rather than the parents bringing food to the nest like most bird species?

From Wikipedia:

  Like all geese, the goslings are not fed by the adults. Instead of
  bringing food to the newly hatched goslings, the goslings are brought
  to the ground. Unable to fly, the three-day-old goslings jump off the
  cliff and fall; their small size, feathery down, and very light weight
  helps to protect some of them from serious injury when they hit the
  rocks below, but many die from the impact.


texts: Can someone help me identify this queen ant?

texts: I found this queen ant near a river on the 14 july in Braga-Portugal, it was on a river bank, and it measures around 8 mm. Can someone help me identifying the species? thank you for your time :)


texts: Server for protein structure prediction for multiple sequences

texts: Does anybody have any idea about any online server that takes in multiple amino acid sequences in fasta format and outputs the 3D structure of the input amino acid sequences in the form of helix, sheet and coil? I searched but could not find any. There are servers that take in 1 sequence. I want to get the structure of multiple sequences together...


texts:
Can a human eat grass and digest it?
Could it be possible to use it as food just like other plants such as wheat or beans?


texts: How is "firing together" detected in Hebbian learning?

texts:
I assume, that the signal that forces a synaptic receptor/ion channel complex to change its behaviour (i.e. strengthening in the course of upregulation) must be the combination of the state of the complex ("occupied" or "open" or any other state except the ground or rest state) and an extraordinarily high membrane potential at the complex (caused by a retrograded action potential).

The not-ground state indicates that the presynaptic neuron recently has fired, the potential indicates that the postsynaptic neuron recently has fired. According to the rule "fire together, wire together", both conditions must be fulfilled for Hebb-like strengthening to occur.

I assume further that the membrane potential that triggers the upregulation of the complex must be significantly higher than the typical post-synaptic potential generated by the synapse, otherwise activation of the synapse alone would suffice for strengthening to occur, which violates Hebb's rule.

Is this way of thinking essentially correct? Or is strengthening triggered by other signals than the ones mentioned above?


texts: Are there medical treatments that were so effective they were never subjected to a randomized control trial?

texts:
I'm thinking of things like antibiotics for meningitis or tuberculosis, or thiamine for Wernicke-Korsakoff syndrome. In those cases the magnitude of the treatment effect might have been so great that it would have been unethical to assign subjects to a placebo group. However, I couldn't find any sources to attest that randomized control trials were never done in relation to those treatments.

I'm referring to treatments trialled in a time and place in which randomized control trials were an option.


texts: How does Reissner's membrane rupture cause Ménière's disease symptoms?

texts:
In Ménière's disease, an ednolymphatic hydrops (EH) in scala media leads to a distention and, eventually, rupture of Reissner's membrane. This results in an influx of K+-rich endolymph into the Na+-rich perilymph of scala vestibuli.

Supposedly, this causes an "injury to the sensory and neural elements of the inner ear, which manifests clinically as sudden hearing loss, tinnitus, and vertigo."

What is the pathophysiological mechanism? Aren't these elements part of the Organ of Corti, not in the perilymphatic space?


texts: How would one determine if an up regulation of one protein leads to an over expression of another?

texts:
Again, I'm new to biology and have a bunch of questions.
Does it depend on the proteins involved? OR are there basic co expression procedures one could implement to determine exactly how much one protein upregulation leads to overexpression of another protein ?


texts: When does histone synthesis occur in relation to DNA replication?

texts: Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones?


texts: Have some humans evolved to be less attractive to mosquitoes?

texts:
https://www.youtube.com/watch?v=38gVZgE39K8 at 10:10 minutes in the video.

It has been found out that single letter differences in people's genomes at specific locations have affected their attractiveness towards mosquitoes. This means there might be a possibility that some humans might have evolved to be less attractive to mosquitoes. Does any proof exist regarding that?


texts: What is the name of the condition where no pacemaker cells are active in the heart for a short-time?

texts:
Assume that the heart is beating, but no pacemaker cells are working for at least 15 seconds.
This would be a very long compensatory pause if extrasystole started it.
There may be some low frequent cells working at lower frequency (less than 10 Hz) but I do not understand what.

What is the name of condition where main pacemaker cells are not beating?
Main pacemakers are SA-node, AV-node and Purkinje-fibers/His-bundle.

Raoul is correct.
This is called asystole.
It is temporal in the above case.

My definition in research but note the difference to current Clinics so you do not get confused: Asystole is a state of no cardiac electrical activity from pacemaker cells when the conduction system and cardiomyocytes can be still functioning (so the case in my thread). The conduction system and cardiomyocytes of the ventricles are responsible for the bradycardia in my case for short-term.

What do you think about this case?
Some bradycardia?
Can you suspect asystole there between?

Please, do not make diagnoses based on just this picture (which is often the current standard).
Assume case where you see Time-Frequency of the heart perfectly and where you can see exactly the functioning of pacemaker cells at different frequency levels.


texts: tissue-specific expression of homolog genes

texts:
Two or more genes are homolog if thay have similar sequences. homolog sequences between species are called orthologs (caused by speciation events) and homolog sequences in an species are called paralogs (caused by duplication events).

I would like to know what is expression pattern of paralogs or orthologs in an specific tissue. Are paralog (or ortholog) genes have same expression in a tissue or they express different?

I hope my question is clear, but if it has mistakes I appreciate your corrections.


texts:
With a lack of mitochondria, can red blood cells perform intrinsic apoptosis and do they have another way of generating cytochrome c to attach to a CARD domain and assemble the apoptosome?

Or are they dependent on killer lymphocytes to bind via the fas ligand and activate procaspase 8 or 10 in extrinsic apoptosis? Do red blood cells even have fas ligand receptors for this process?

Or is there an entirely different method for red blood cells?


texts: How do our eyes detect light at different frequencies?

texts:
Here is my confusion: we can see colored light of different wavelengths: form red to violet. To my understanding, these stimuli cause a confirmational change in the photoreceptors in our eyes and results in a STP that eventually leads to an "all or nothing" action potential that sends another signal, again an all or nothing action potential through the optic chiasm to the occipital lobe and we perceive the colors as we see them.

My question is *how does this signaling work? *; How can a minor stimulus, resulting in an "all or nothing" chain of action potentials be converted into something as specific as the vision of color?

Asked another way, how does variation in a confirmational change at a receptor that results in "all or nothing" signaling lead to specific signals being sent such as colored vision ?

PS: I dont know jack about sensory physiology


texts: Drake's Law. What is the genome-wide mutation rate and what are the estimates?

texts:
Drake's rule

Drake's rule states that the genome-wide mutation rate is more or less constant across all species — from E.coli to the house sparrow.

Data

From what I think being Drake's original paper (table 1, page 4) on the subject (see here) is at the order of $3\times 10^{-3}$. When I look at this paper, I see that the genome-wide mutation rate is roughly around 30 for human. When I look at this paper, they cite some other papers suggesting a genome-wide mutation rate in the order of 0.1 to 1 in multicellular eukaryotes and typically at the order of 1 for vertebrates. Finally, when I look at this speech (at the 60th minute), it seems however that the genome-wide mutation rate in human is 2.2.

What is going wrong?

Do I mix-up different concepts or are there some very contradicting estimates depending on the article we look at? Isn't the genome-wide mutation rate, $U$, which is just the number of de novo mutations transmitted to one offspring on average? What is a correct estimate of $U$ for human for example (1, 2.2 or 30)?


texts: What is the effect of reduced gravity on human height?

texts: There has been talk recently of building a base on either the Moon or Mars. What I'm wondering is, if you are born and grow to adulthood on the Moon, where the gravity is a tenth of the Earth's, would you be taller than if you had been born and grown up on Earth?


texts:
hello ,

I want to know if this is a bed bug nymph or it's just an another insect? I got an issue with bed bugs few days ago in a hotel during a travel to Prague. Once home (in Germany), I washed all I had taken with me (a backpack with some clothes) under high temperature > 150 Fahrenheit. So I was confused when I found this bug on my arm today. I'll point out that I was under a tree and there were many tiny insects just a few minutes before I found this one.  This specimen was ~1 mm in length.

Thank you in advance for your help.


texts: Why does opening of the Ca-channels trigger the release of neurotransmitters?

texts: I understand that the opening of the Calcium channels trigger the release of stored neurotransmitter in granules, but what is it about the flow of positive ions that makes the vesicles fuse with the cell membrane? Does the vesicle itself carry a charge or concentration gradient?


texts: What is the Baculovirus and how does it help in research?

texts:
I was reading up about Biotechnology and the use of insects, and came across an interesting article about Insect Cell culture Techniques that specifically talked about the usage of the Baculovirus. If I understand correctly does this virus help express certain genes when inserted into a cell?

Sorry if I am way off or did not use proper terminology, I am a high school IB Biology student who still has a a lot to learn

Thanks!


texts:
Dogs shed their fur twice a year, so I assume this is the same with cats.

What is the mechanism whereby the change in temperature (assuming this is what causes the shedding) leads to the falling off of fur? Is it the same mechanism as balding?


texts: What would happen if you slowly crushed a live brain?

texts:
In a hypothetical scenario, if you cut open a person's skull to show the live brain, and then you slowly start to crush it..

At what point would the person loose consciousness?

What would the person be feeling all this time?

Would it cause pain?


texts: Where is the line between Anaerobic and Aerobic?

texts:
I am well aware of traditional anaerobic respiration (lactic acid or alcohol produced - no Krebs cycle) and traditional aerobic respiration (O2 is used at the end of the Citric acid cycle).

I am wondering how to classify respiration that uses the Citric acid cycle, but consumes a nitrite/ate or sulfite/ate instead of O2. Is that anaerobic or aerobic?

I could only find this image on Google image search catch but it said it was from http://lecturer.ukdw.ac.id/dhira/Metabolism/RespAnaer.html


texts: How much does the Vitamin D3 concentration of the blood of a human change over the course of a day?

texts: Are there studies that measured how much the blood concentration of Vitamin D3 changes over the course of a day? If so, how strongly does it change? Does it change in predictable patterns?


texts: What is the use of futile reaction cycling such as Fruc-P to Fruc-BP?

texts:
One rate-limiting step of glycolysis is the conversion of Fructose-6-Phosphate (Fruc-6-P) to Fructose-1,6-Bisphosphate (Fruc-1,6-BP), catalysed by Phosphofructokinase 1 (PFK 1). The reaction involves hydrolysing one ATP to ADP.

The reverse reaction of gluconeogenesis is catalysed by Fructose-Bisphosphatase (FBP). This reaction uses 1 H2O for hydrolysis and yields 1 phosphate (Pi).

One would expect the cell to be utilising only one of the two reactions at any one time, either to break down glucose or to generate it. However, the case is commonly that both reactions are taking place simultaneously in an equilibrium [ref 'Biochemistry', Voet & Voet, 4th ed., 628-629 (Section 17-4-F-f,g,h,(i))], cycling Fruc-1,6-BP to no apparent benefit, at the expense of valuable ATP.

What is the purpose of such futile cycles?


texts: Recording policies in functional magnetic resonance imaging

texts:
Assume that the areas in a single-subject's brain that are involved in solving a task are supposed to be visualized with fMRI. The dynamics of the task solving process shall not matter (which areas are active first, which second?).

  How, i.e. by which policy, are the data collected to give the final image?

I believe to have understood that data are collected per slices (of some millimeters thickness) and later postprocessed to give the final image.

For the sake of definiteness, let $T$ be the overall time it takes to complete the task (e.g. 10 seconds). Let $t$ be the time it takes to simultaneously take the BOLD data of one slice (e.g. 100 milliseconds). Let $N$ be the number of slices to be recorded (e.g. 20). Let $n$ be the minimal number of recordings of one slice that is necessary for statistical analysis ($n=?$). So there are $N n$ recordings of slices necessary which takes $N n t$ milliseconds, if only one slice could be recorded at once. If $T$ is too short, the experiment would have to be repeated $N n t/T$ times to get all of the required $N n$ slice recordings.

If $m$ slices could be recorded simultaneously, a single run of the experiment would suffice, when $m > N n t/T$.

  In any case: In which order are the slices to be recorded chosen (in
  case they cannot be recorded all at once)?

Possible policies:

always from top to bottom (along the z-axis) in time $T$?
repeatedly from top to bottom in some time $T'=T/k < T$?
alternating between top-bottom and bottom-up in repeated experiments?
in a random order?
in an order informed by knowledge of the stages of the task (when different slices are primarly active at different times during the task)

Or is my picture of the recording process all too naive? Or is the question somehow meaningless (for reasons I do not see, but would like to learn about)?


texts: Can electricity be harvested from the soil around plants?

texts:
This is a rehash of a question I originally wrote on Skeptics which got moved to Physics, but I'm really after an answer from a biological perspective.

A device called the E-Kaia is making news by claiming to harvest enough electricity from the soil of a pot plant to charge a phone. They claim they can draw 600mA from the soil, which actually wouldn't charge most smartphones in the 1.5 hours they claim in the article (thanks Physics.SE!).

Is there really electricity in the soil around a plant? I can't imagine there being 600mA there for the taking in the soil of a huge tree let alone a pot plant. Maybe it isn't electricity in the soil but some other kind of energy or chemical that can be extracted to generate electricity - it sounds like the lemon battery experiment, which relies on a chemical reaction.

And surely, even if there was electricity there, extracting all of it would damage the plant?


texts:
I'm planning to order oligo, polymerase, nucleotide, buffer for my first diy PCR experiment (now I have nothing), so I have some questions.

How and how long I can storage them?  I have only a fridge that can freeze to -10 -> -20C.
I see the size/concentration of polymerase is 400 units and 25 nmole of oligo. So what can I do with 25 nmole oligo and 400 units of polymerase? How many PCR experiment I can do with 400 units of polymerase, and how many PCR experiment I can do with 25 nmole of oligo?
If I have a HPLC machine, can I reuse the polymerase by purify it after reaction?


texts:
I have been reading this article and they refer to this thing called 'slurries' that can be made from soil samples. This is in the context of being some sort of microbiological method.

"slurries can be made from these soil samples"

Does anyone know what this is? When googling it, I can not find a clear answer to what the method does.


texts: Why are there both stop and start codons?

texts:
Based on my understanding from wikipedia, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG.  AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA sequence.

But is there a chemical reason there are both start and stop codons?  Eg, if I only had a stop codon, would that also imply the next codon was start? Are there cases where there is a stop codon and the next codon isn't start?


texts:
I found it in Washington state, in a city south of Seattle. I found it next to a bush after it rained on someone's driveway. Here are two pictures of it:

( originally posted in instagram )

If anyone can identify this species, kudos to you.


texts: Are chromosomal microdeletions passed on?

texts: I've been looking around but can't find a clear answer: are chromosomal micro-deletions passed on (hereditary) or not?


texts:
I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've been looking at Chip Seq data. But to make sense of the Chip Seq data I wish to understand how the experiment is first performed.

Basically my question relates to step 1 of the following diagram:

Now my main question is how come the reads are overlapped? Where did we get so many of the (almost the) same reads?

My "understanding" is that:

1) They take a DNA sequence and crosslink the protien of interest. Then they get rid of the DNA sequence surrounding this area of interest so now we have a "small" sequence of DNA and in this small DNA is somewhere where our TF binds. Now we make copies of this small DNA seq and run it through a sequencing machine. Is this correct?

2) They take a bunch of cells = bunch of DNA sequences. Then they do the same procedure above (by crosslinking and getting a "smaller" DNA sequence of interest). Since they had many cells to begin with, this means they had many DNA seq to begin with. Now they shear the DNA seq and we have fragments. Then we align these up with the reference genome.


texts: Why are there 2 copies of RNA in the HIV virion?

texts:
There are two copies of the RNA in the HIV virion. These are retroviruses. So, they can make cDNA from even just one copy using reverse transcriptase.

What is the use of the other? Are both integrated into host chromosomes?

My guesses are:

To ensure increased chance of getting integrated. But, if one gets in, the other also should be able to.
To increase the amount of protein translated (if both get integrated).
Two for two sets of chromosomes. (Seems juvenile but still a possibility. although, I do not think there are specific sites of preference for the viral DNA. Are there?)


texts: Do any plants exhibit hormonal changes similar to puberty?

texts:
Just what the title states.

Are there any plants/trees that exhibit a growth spurt at a definite interval after the shoot appears?


texts: What modern insects are not (flying OR descended from flying ancestors)?

texts:
What modern insects are not flying or descended from flying ancestors?

(I read somewhere that 99% are, so of course I instantly became curious which aren't. xD )

EDIT:  Sorry, I should have been clearer: I meant examples of modern insects with no flying ancestors.


texts: Choosing the best assay for my experiment?

texts:
Which of the following assays can be used to determine whether cell death specifically due to apoptosis has occurred in a given cell sample? Choose all that apply.

WST-1 Assay
Caspase Colorimetric Assay
Trypan Blue Staining

Which of the following assays can provide direct information about the plasma membrane integrity and/or morphological features of apoptotic cells? Choose all that apply

Annexin V-FITC / Propidium Iodide staining.
WST-1 Assay
Caspase Colorimetric Assay
Trypan Blue Staining
Wright Staining

My knowledge is very limited with these assays. I know Trypan Blue is used to measure a cell's viability, with dead cells stained blue. Wright Staining is used to study the cell's morphology and makes fragmentation visible. Caspase color and the WST assay seem very similar to me. Both measure cell viability with spectrophotometry.