texts: What is the use of shampoo; is it for the hair or for the scalp?

texts:
Apologies for the confusing question; I did not know how to better ask it.

I was doing a search on wikipedia when I found this statement.

Wikipedia's entry on hair states;

  "The hair that is visible is the hair shaft, which exhibits no
  biochemical activity and is considered "dead"."

With that being said, why does one use shampoo? Is it because of the scalp that requires nourishment and cleaning because skin is not of a "dead" nature? Or is it to maintain the silkiness and smoothness of hair? Because it seems really redundant to take care of and maintain something which is already "dead".


texts: How to search NCBI in bulk for a list of accession numbers?

texts:
I have a large ( >100 ) list of accession numbers I want to look up and match to searches in NCBI (nucleotide); mainly for getting a tentative organism to match to the accession number.

ex:

KJ841938.1 would match to  Setoptus koraiensis
...
FJ911852.1 would match to  Uncultured eukaryote
...

I googled for tools, and I found this site. However, it is not what I really want since it doesn't list my queries in the same order as my list, which means I cannot match.

I also attempted to write a script in biopython using Entrez E-tools, but was unsuccessful due to a lack of coding skill.

Does anyone have any way I can go about this?

EDIT:
Via this tutorial,
I attempted to use this code sample:

from Bio import Entrez
Entrez.email = "Your.Name.Here@example.org"
handle = Entrez.efetch(db="nucleotide", id="AY851612", rettype="gb", retmode="text")
print(handle.readline().strip())
# expected output : LOCUS       AY851612                 892 bp    DNA     linear   PLN 10-APR-2007
handle.close()

But modified to take any list instead of the variable id, as below:

import Bio
print (Bio.__version__)
from Bio import Entrez
import time

Entrez.email = "Your.Name.Here@example.org"
id_list = ["KJ841938.1", "FJ911852.1"] # real list is about 500 elements

x = 0
while  x < len(id_list):
    handle = Entrez.efetch(db="nucleotide", id=id_list[x], rettype= "uilist", retmode="text")
    #print(handle.readline().strip())
    print(handle.readline())
    handle.close()
    x = x + 1

Output is:

1.69
673539906

283462561

However, I do not believe I am using the right "rettype" parameter in the .efetch function as I keep on getting GI numbers, where as I was hoping to get something like a species name directly. Unless I can then search with these GI numbers in batch with more code or a tool to produce a ordered list?


texts: What is the best file format to store gel images?

texts:
I store many gel images which are included in my Latex notebooks. The geldoc software normally produces TIFF files, however, Latex only accepts PNG or JPEG.

If I am going to store only a single copy of my DNA agarose gel images, which format is a good idea? PNG, or JPEG? Is there a good reason to keep one copy in TIFF and one copy in another format for every gel?


texts: What is the effect of exendin on beta-cells?

texts: Do you know if exendin, an analog of GLP-1 (glucagon like peptide-1), can be toxic for beta-cells? For example, what is the effect on INS1 or Min6 cells at a certain concentration or after 90 mins of incubation. And what is the impact on insulin secretion?


texts: How do diving marine mammals avoid decompression sickness?

texts: How do marine mammals, whose very survival depends on regular diving, manage to avoid decompression sickness or "the bends?" Do they, indeed, avoid it?


texts: How do asexually reproductive organisms mutate?

texts: In accordance to my limited knowledge of biology, asexual organisms exactly copy their DNA as there is no "contaminant", which in sexual reproduction is the other organism's DNA.


texts: Is there a simple way to generate sets of sequences that re-capitulate the topology of pre-defined phylogenetic tree

texts:
I would like to generate ensembles of N sequences in such a way that the phylogenetic trees obtained from my ensembles (e.g., by neighbor joining) have the same (or nearly the same) topology as a specified "real" tree obtained from an alignment of N proteins.

My starting point would be an empirically determined amino acid substitution matrix. The matrix would be used to generate a "random" sequence representing the root of my simulated tree. The root sequence would then be evolved, "split", and its products evolved, iteratively until N sequences are generated. Somehow, the topology of the "real" tree would be used to guide the branching process.

This problem arises in determining the significance of correlations between mutations at different sites in a protein (specifically, the "mutual information" measure). One would like to determine the contribution of "pure phylogenetic" correlations to the mutual information for a given alignment of proteins.

The answer to my question seems connected to the "parametric bootstrap procedure" commonly used in phylogeny reconstruction. In fact, the reference below seems to use this procedure to generate the ensembles I describe above. However, their procedure is not explained in detail. This makes me think that there may be a simple answer to my question.

reference :

"Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap"
K. R. Wollenberg and W. R. Atchley (2000) PNAS 97, 3288–3291


texts: Why is LH level much higher than FSH level at ovulation?

texts:
My teacher showed us an elaborate collection of graphs with one of them showing FSH and LH plasma levels during the menstrual cycle. LH level was almost 3 times higher than FSH level. Why?

Does this have anything to do with their synthesis or cellular responses?


texts: Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles

texts:
First Question :
RNA interference - small-interference RNA
in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin
this Figure is Shown

my question is : if the foreign RNA is double stranded and the Dicer Cleaves it so it is still double stranded and Risc Forming with single stranded RNA ,i feel there is step missing here ? and how siRNA is finding those complementary RNA when they are in the cell in double-strand ? steps are missing or it is not essential or i myself miss somthing ?
Thank You


texts: How do AC magnetic fields affect tissues?

texts: AC magnetic field refers to an oscillating magnetic field. How do AC magnetic fields affect human tissues in vivo?


texts: Which lipoprotein has the highest protein content?

texts: I know that HDLs have the highest protein/lipid ratio but know that the HDLs are very small molecules too and I couldn’t find the exact answer for this question. I mean, by amounts which of these lipoproteins have the most protein?


texts: Function of ER in reviewing mutated proteins

texts:
At least in the case of Cystic Fibrosis it happens that a mutant protein (which could actually function!) is held in the ER because the ER detects it as misfolded. Does this happen in every type of mutant protein?

If so, should I conclude that such genetic disorders are caused because of the total absence of a protein rather than because of a misfolded protein? If not, why would the ER or anything else in the cell allow some mutated proteins to do any job (Like in the case of Sickle cell anaemia, where an amino acid substitution happens)?

How do scientists conclude that a misfolded protein could have done a good enough job (Like in the case of cystic fibrosis)?


texts:
I am slightly confused about the mechanisms that makes histone modifications associate with gene expression.

That is, H3K36me3 is believed to be present in actively transcribed genes, H3K27me3 in repressed regions, etc. What is the mechanism that makes the presence of H3K36me3 to be in active regions, etc.? Is it causal or just an association?


texts: List of genes across species (or just for humans)

texts:
Wondering if there is a place that has a list/table/database of all the genes in the human genome, and/or all the known genes in all the species we've studied so far. Something that contains any of this would be great.

I found this but not sure yet if that is just for humans and just for one chromosome. But I'd like something along those lines across species, or the closest thing to that that exists.


texts: Are gene variants at different loci also called alleles?

texts: I think the title says it. I always read that alleles are gene variants at a given locus, which confuses me. Thanks!


texts: How is the beginning of an episodic memory encoded in the brain?

texts:
before asking how information is stored, I need to understand

how does episode start and end are determined by the brain ?
how do i remember a movie ?

can you suggest a link to article addressing this issue

thanks


texts: Why is HIV so large compared to other viruses?

texts:
The HIV-1 virus is about 120-150 nm in size and has a genome only about 10,000 base pairs long.

Other viruses are far more efficient, for example lambda phage has something like a tenth the volume and a genome five times longer. In other words, while half the volume of a lambda phage is taken up with DNA, in HIV it's more like 1%. Why is HIV so space inefficient?


texts:
In the figure 1A of http://photobiology.info/Jones.html
the Mg is not belong to other structure.
Is that because something is omitted or is it indeed like a pearl in a mussel's mouth? In the later case could we replace the Mg by some other atoms (and the bacteriochlorophyll still live well)?


texts:
I am fairly new to phylogenetic analysis, so I'm guessing this is a basic question. If I have a bunch of aligned sequences, and I ultimately only care about pairwise distance (e.g. for calculating phylogenetic diversity) then is there any way to make sure these distances reflect an ultrametric tree without having to first calculate the tree itself? From what I can tell, to create an ultrametric distance matrix I have to first calculate an ultrametric tree and then use this tree to get distances. But this seems a bit backwards to me, since I can create a pairwise distance matrix without needing to create a tree, but I can't tell if there is a way to ensure that this matrix assumes some sort of underlying molecular clock so as to make sure the distances reflect an ultrametric tree.

I assume I'm just fundamentally failing to grasp something. Any help would be much appreciated.


texts:
According to NCBI, type I REases have a specific target sequence but randomly make cuts at sites far from the target sequence.

How does the restriction enzyme travel from the target sequence to the distant site of restriction, and what is the point of having a target sequence if the cuts are random and far away from the target sequence?


texts: How old would seashells be if I found them 9 ft deep 30 miles from the ocean while digging a pond in North Carolina

texts: This is a picture of some specimens that I found while digging a pond. I'm 30 miles from the coast in Wilmington, North Carolina and dug down about nine feet past the blue clay and hit a layer of seashells.


texts:
I noticed that since the 1970s the bearded vulture , which had disappeared from the Alps due to hunting, has been successfully reintroduced. I have searched for the modern habitats of vultures, but it appears (the wording on the site is a bit imprecise) none occur in Germany beyond the very mountainous regions.

I want to know whether at any point in the past vultures of any species where common across large parts of Germany other than the Alps. I am especially curious about the Middle Ages.

Edit:
This site in German claims that vultures in Medieval Germany followed sheep herds, eating dead, stillborn and afterbirth of cattle. It mentions, beside the Alps, the upper Danube Valley and the Moselle–Rhine region:

  Bis dahin hatte es vom Mittelalter ausgehend, auch in deutschen Ländern eine einträgliche Zusammenarbeit gegeben. Geier folgten den wandernden Schafherden, beseitigten verendete Alttiere, totgeborene Junge, die Nachgeburt oder die Knochenreste vom Essen der Schäfer. Geier nisteten im Mosel-Rheingebiet, den Alpen und im oberen Donautal.


texts:
Look, let's get something straight.  I am not the worlds biggest sissy when it comes to bugs, but I'm not David Attenborough either.

Now that that's out of the way, down to business.  Living in Michigan as I do, I was quite surprised to find what looked like the spawn of Predator and a cicada living in my back yard.   Suffice to say it made me nervous.  In one of the pictures below, I have included a cigarette with about 3 drags smoked off of it for sizing.

Please offer insight into the true nature of this animal.


texts: Stabilizing forces between the protein sequences?

texts: we know that Protein structures from secondary to Quaternary are maintained by noncovalent or weak interactions including electrostatic interactions,van der Waals forces & hydrogen bonding. What is the significance of these weak interactions why they are preferred by nature rather then strong covalent interactions?


texts: Why does eating saturated fat increase blood cholesterol?

texts:
I am interested in the biochemistry of diet and the way we have been advised to eat for the past forty years.

In researching an explanation for the relationship between dietary fat and blood cholesterol I came across the following: "It is clear that eating too much saturated fat increases the levels of cholesterol in the blood, especially our "bad" cholesterol which doctors refer to as LDL". This is from heartuk.org.uk.

"It is clear ..." - really?

I am mystified! I understand that dietary fat, other than very short chain fatty acids, does not immediately enter the blood stream but is transported via the lymphatic system as triglycerides packaged in protein assemblies called chylomicrons, finally entering the blood via lymph nodes under the armpits. Once in the blood the triglycerides are hydrolysed into fatty acids and transported to appropriate cells in albumin complexes.

Where does LDL feature in this transportation? And, by the way, why just saturated fats? Surely the small intestine doesn't differentiate between saturated and unsaturated fats, or does it?


texts: How to Extract RNA and perform RT-qPCR from very few cells ( ~5,000)?

texts:
I am currently conducting an experiment which involves FACS-sorting a specific population of cells using an antibody of interest.

In order to validate the type of cells I have collected using this marker, I want to perform qPCR on their extracted RNA, using certain known cell-type marker primers.

My problem is that in each sorting session, I am only able to collect anywhere from 5,000 - 10,000 cells. Do you know if it is possible to perform RT-qPCR on such a small sample size?

I have collected the cells in 1mL of Trizol.

Would I maybe have to amplify the cDNA after reverse transcription in a general manner ( using random primers)?

Thanks for your help.


texts:
Carbohydrates are often defined as compounds with only C, H, and O and the H and usually the O atoms are in a 2:1 ratio.

Exceptions like deoxyribose exist, but why is it recognized as a carbohydrate?

What distinguishes a carbohydrate from other compounds?


texts: The antibiotic 'kanamycin' in the growing of culture E. coli

texts:
I'm a first year student and I'm not sure if I understand correctly the role played by the antibiotic 'kanamycin' in the growing of culture E. coli (Rosetta).

Can anybody explain me why we use 'kanamycin' antibiotic and kanamycin resistance gene during that process?


texts: How can some animals see ultraviolet or infrared light?

texts: I know that some animals like birds, bees, and fish can see ultraviolet and infrared light. Whether it to detect flowers that bare nectar, or the urine trails of prey. But what I don't understand is how they see these wave lengths. What is different about their eyes or brain that allows them to see different wavelengths than humans?


texts: Western cascade forest, definitely was planted. In a clearing in the forest along with some western red cedars. I couldn't find anything that would match it when looking for native Oregon trees.


texts:
Sometimes I get confused about why this or that enzyme was named in this or that particular way.

1) TCA: Why was not isocitrate dehydrogenase named isocitrate decarboxylase?

Wouldn't it have been at least as accurate to name the enzyme in question isocitrate decarboxylase as to call it isocitrate dehydrogenase? It does remove the -COOH, doesn't it?

2) Glycolysis: PEP (phosphoenolpyruvate) carboxykinase. Why isn't it oxaloacetate carboxykinase? Isn't it agreed upon that enzyme substrate be used in the name of enzyme?

3) Why name enzymes by reverse reactions (especially when the reaction is irreversible)? Pyruvatekinase makes pyruvate from PEP. Why not use another name, PEP phosphatase, for example?

I understand that this is the way the enzymes were named and I just have to accept it. But I would also like to understand the logic behind these names.


texts:
Pre-exposure prophylactic treatment (PrEP) for HIV is commonly said to reduce infection rates by more than 75%.

Similar treatments for already-infected patient treatments do not cure HIV, but reduce viral load to undetectable levels. If treatment of these patients is stopped, viral load will eventually rise.

Do we know that PrEP actually prevents infection, rather than masking it? Are there no cases of someone engaging in no risk behaviors, then going on PrEP and engaging in risk behaviors, then coming off it, not engaging in any further risk behaviors, and nevertheless testing positive for HIV?


texts: What does 'kinetically accessible' mean in protein folding?

texts: The hydrophobic collapse model discusses this term in the energetics section. What does this actually mean?


texts: Does freezer burn affect only the cells on the surface of food?

texts:
Suppose i submerge a banana halfway through in a tray with water. Part of the banana is submerged in water, part of it is on the outside. The water and banana in the tray is being put in the freezer and freeze. Since part of the banana is exposed to air freezer burn is going to take place. How deep does it affect the tissue?

Not a homework question.


texts: How does decreasing surface tension of lipids help to emulsify them?

texts: According to my chemistry book, water has higher surface tension than lipids. But in my biology book it is written that "the gall forms an emulsion of water and lipids by lowering the lipid's surface tension". This will increase the difference between the two substances even more. How can this be beneficial?


texts: Is the relationship between worm (C. elegans nematode or any worm) behavior and the worm brain understood? Is the learning technology within the worm brain understood? If so, what's a summary of the mathematical processes and biological implementations used? If not, what is the impediment to understanding?


texts: Can animals, like monkeys, be homosexual?

texts:
I heard that some monkeys can be homosexual? a friend of mine was saying that he saw a male monkey having sex with another male monkey in the zoo, I honestly didn't believe him, I think he just got confused or he made it up.

Could this be true? can monkeys become homosexuals? does homosexuality (other than human) exist in the animal kingdom?


texts: Does night sleep provide more energy-regain than sleep during the day?

texts:
After reading this, I know that sleeping is an universal function, and that basically everything with a brain has the need to sleep.

However, I am still confused to what extent it is necessary to sleep at night to regain energy, or if some rest during the day provides a sufficient energy-regain?


texts:
I read in New Scientist recently that microchimerism occurs between previously born siblings and grandparents, not just the mother.

Do we know which parts of the genome are likely to be transferred? Is it possible, given a genetic sample of relatives, to predict which genetic traits might be transferred by microchimerism?


texts: How does the cardiac cycle and electrical activity all relate to blood pressure in the heart?

texts: I know how the cardiac cycle works and understand the electrical activity in the heart such as the AV nodes, SA nodes and Bundles, but how do they work together in relation to blood pressure?


texts: In plant photosynthesis, in the light dependent reactions, why is 3 ATP produced per 2 H2O?

texts:
I've been looking at the light-dependent reactions on Wikipedia and Khan Academy.

This is the net reaction:

$$2H_2O + 2NADP^+ + 3ADP + 3P_i \to O_2 + 2NADPH + 3ATP$$

So for every $2H_2O$ I expect $2NADPH$ and $3ATP$. I tried to count:

These are my assumptions:

Cytochrome b6 complex pumps $1H^+$ for each $1e^-$.
FNR makes $1NADPH$ for each $2e^-$.
ATP synthase makes $1ATP$ for each $1H^+$.

If we want to end up with $3ATP$, then $3H^+$ need to diffuse through. The thing is, there's too many $H^+$. $4H^+$ is contributed by the cytochrome b6 complex pumping alone, and another potential $4H^+$ is contributed by the water splitting.

Clearly I'm missing something here that would lead to the correct count.


texts: I have a question about IBD. Please see the figure below. How many pairs of alleles are IBD for X and Y, or what is the IBD value for X and Y. Is it four (4)? I have seen it to be maximally 2, but then we assume that no inbreeding occurs, right?


texts: Experiments in vitro vs those with dead organisms and fixated tissue

texts:
Does the term in vitro necessarily imply that the organism/organs/cells of study are  dead?

If not, is there an alternative latin term to refer to studies of dead biological matter ? (e.g. in Connectomics where the tissue is biologically dead, and has been fixated and sectioned with a microtome)


texts: Would constant light or fading light be registered as more wakefulness promoting by the Supra Chiasmatic Nucleus?

texts:
During the fall and winter season, a number of people are experiencing Seasonal Affective Disorder. One of the way it has traditionally been treated is with a dedicated lightbox - a very high intensity light (5k-15k lux) that is positioned somewhere the user can see it.

One of the possible ways such light affect the brain is through being picked up by Melanopsin receptors in the eye and this info being transmitted to the Suprachiasmatic Nucleus (SCN). The SCN makes sleep/wake decisions by suppressing melatonin release.

It has been tested that melanopsin receptors in the human eye respond most strongly to the light at around 470nm wavelength.

My question is about the mechanism by which this light influences the brain - which would have a stronger influence on the brain:

A constant, high intensity source of light that is ignored by the conscious mind (fades into background)?

OR An alternating, moving or fading, less intense source of light that the eye is drawn to, such as dancing light, a moving lamp or some other form of light that the conscious mind might be drawn to watch?

To clarify my question, I know that brain has a number of self-attenuating circuits (for example dopaminergic system), where extended release of some hormone numbs the sensitivity to the hormone. I'm interested - are SCN, melanopsin receptors or melatonin suppressing process are also self attenuating, where prolonged exposure to constant light would attenuate these processes?


texts:
First of all, sorry if this is the wrong place to ask this question, please redirect me if it is so.

I have a project in mind involving and EEG, which is the following :

Using a "consumer-grade" EEG (see this one, for example) I would like to be able to control a binary system with my mind (for example, turning a led on and off). From what I've seen until now, this seems to be possible since the headset is able to detect eye blinks, for example. It also gives access to two variables "focus" and "relaxation", which you can learn to control somewhat accurately (accurately enough for a binary system, at least).

Now here's my problem. While the methods that I described above do work, they would also continuously activate even when I don't want them to. Everytime I blink, my led would turn on, even though my intention wasn't to turn the led on. Everytime the "focus" level goes over 50/100, the led would turn on, even though I'm just focusing on my physics problem.

Having said that, I was wondering if it is possible to pick up more subtle and "controlled" information on the EEG. One thing I was thinking about is, if I think and visualise the color red, maybe that could cause a signal that can be picked up ?(Of course the led would activate when I look at something red, but that's still an improvement) Or even looking at the led I want to turn on, would that have any discernable effect on the EEG ? My guess is that those "thoughts" are way to subtle to be picked up by an EEG, which is just an average of the brain activity, but I'm not an expert on the subject !

So I guess my question is : what are the "kind" of thoughts that I can somewhat reliably see on the EEG data ? For example, I know I can reliably pick up a eye-blink. Are there any thoughts that are not related to muscle movement that can also be reliably read on a EEG ?


texts:
Don't rush to conclusions. This is a serious question.

The most widespread depiction of intelligent, "human-like" aliens are that of a species with considerably larger eyes in proportion to body size vis-a-vis human beings (just google alien and select images and you will see what I mean). Example:

Now, say we were to find a race of alien with such characteristic. Assuming their form of life is based on evolution as we know it, what could we deduce about their needs and environment based solely on such information? (i.e. that their eyes are larger than ours, ceteris paribus).

In other words, according to our scientific knowledge of life on Earth, why might alien have relatively large eyes?

This article suggests animals have big eyes because of their primarily night activity, being in places with little light (e.g. deep under the ocean), or because of better 3D range. But I would like something more scientific. The article is a bit "pop".


texts: Is complete dominance actually a genotypic process?

texts:
An example often stated for codominance is blood groups, where both alleles version of the protein is expressed and can be found in the cell membrane.

An example of incomplete dominance often given is of red and white flowered snapdragons giving pink flowered offspring because enzymes for both pigments are transcribed and translated and the mixing of these pigments gives the intermediate phenotype.

In both these examples both alleles are transcribed and translated.

In the text-book mendelian situation of a dominant and recessive allele are there actually a cellular mechanisms by which a 'dominant' allele silences the 'recessive' allele and inhibits it's translation, transcription or both? If so are there any well characterised examples?

Or are all alleles actually codominant at the transcription/protein level? e.g like in many recessive gentic diseases where both the mutant and the normal protein are present (cystic fibrosis, sickle cell anemia etc) but the activity of the normal protein gives the 'healthy' phenotype.


texts: Why doesn't blood remain on a mosquito's proboscis in quantities that could spread blood-borne diseases?

texts:
We know that HIV can't be transmitted by mosquitos, and nor can other highly virulent viruses that are transmitted through blood and bodily fluid exchanges, such as Ebola (thankfully!).

Marcus Junius Brutus asked an interesting question in a comment on that above-linked question's answer:

  [Why can't] tiny droplets of blood remain on the proboscis of the mosquito long enough for said mosquito to inject its proboscis into the bloodstream of another person? In particular, in what physical aspects is the proboscis different than a needle or razor? I am not talking about blood sucked into the gut of the mosquito, I am talking about blood remaining on the proboscis

There's no doubt that dirty mosquito proboscises aren't a vector for blood-based viruses (if they were, Ebola would be completely uncontainable in West Africa), and I understand the explanation on the above linked answer that there's no route from the mosquito's stomach to its proboscis other than via saliva production, but given how tiny the amounts of blood are that are required for transmission of such highly virulent viruses, why does it never happen in a similar way to transmission from a dirty needle or razor?

I've never seen a mosquito put its proboscis in sterilising fluid or an autoclave between feedings...

My best guess would be that mosquitoes are very efficient at taking up all available fluid, and that surface tension means that at this scale it is possible to take up every last droplet - but that's just a guess.


texts: How can I tell if regulation is at the transcriptional or translational level?

texts:
I was reading a paper, http://www.pnas.org/content/109/8/E471.short, where the authors claim that (e475)

  Translation of the TfR (Transferrin Receptor) is regulated through sequences in the 3′ and 5′
  UTRs (untranslated regions) of its mRNA. To study the regulation of TfR levels independently
  of translational control, we measured the levels of TfR-EGFP expressed
  from a plasmid lacking the regulatory sequences present in the
  endogenous TfR mRNA (Fig. 6A).
  Endogenous and GFP-tagged expressed TfR levels were reduced equally in
  response to Rabenosyn-5 depletion, ruling out an effect of this
  protein on transcriptional or translational control of TfR expression.

I believe I understand that the effect can not be post-translational, since TfR-GFP has no region for translational regulation and so it cannot be regulated by any translationally active regulating factor.

My question is: Wouldn't the statement above, that Rabenosyn-5 has no effect on protein transcription, require a proof that mRNA levels are not affected by this protein?

Fig. 6A, http://www.pnas.org/content/109/8/E471.figures-only


texts: Why is ATP produced in photosynthesis used to synthesize glucose?

texts:
In photosynthesis ATP is produced in light-dependent reactions only to go to the Calvin cycle to be turned into glucose to make ATP during respiration:

Why isn't this ATP just directly released into the cell? Is there a benefit to using the ATP to make glucose? Also, ATP can be made in the chloroplasts with cellular respiration? What happens to this ATP?


texts: Why do drugs which are hormones have long half-life?

texts:
Hormones normally have short half-life.

How is it possible that they have long-life in drugs?


texts:
Hi, can u please help to identify what kind of scorpion is this? A friend of mine found it at home, in urban area in Ohrid, Macedonia. It is aroun 5 cm long.
Thank you.


texts: Chemical methods to detect cell division

texts:
So I have been working on a project for a while, and there is one mechanism that I need a little bit of advice about.

The project is chemical-biology based, so don't be deterred :)

Theoretically, by this point in the experiment:

I put cells (let's say lymphatic or endometrial) into stasis, through means of lyopreservation, and now, I have brought them out of stasis, through exposure to a sucrose (trehalose)-based medium.

Now I am attempting to chemically detect mitotic growth within the cells, how can I do this?

This is where the chemistry comes in: My first thought was to use a chromatic indicator that would fluoresce or irradiate in response to mitotic acceleration, but I have not yet found a suitable chemical. In research, I found that a similar experiment had been done in bacteria, and the chemical dimyristoylphosphatidylcholine (1,2-Dimyristoyl-sn-glycero-3-phosphocholine) had been used. Would this work in mammalian cells? Another idea was to use a chemical that detects the unnatural growth from the spindle fiber and centriole point of view, reacting when the centrioles entered the phase to replicate. I have been unable to find any chemicals that make use of the replication of centrioles, or the spindle fibers, so I need ideas.

To summarize: Does anybody know of any biochromatic indicators that react through detection of rapid, mammalian, mitotic growth? Not necessarily cancerous and uninhibited, but rapid meaning 'a speed of mitosis that is faster than the norm.' Preferrably, the indicator would be able to stay in stasis for extended periods of time.

If such an indicator is not available (or you do not believe so) then does there exist a biochromatic indicator that reacts in the presence of any sort of cell division?

Is there a way to chemically detect cell division?

I am welcome to all ideas.


texts:
I have a follow up question to this question: Does freezing microorganisms such as probiotics kill them?

If freezing bacteria kills some of them, then you are effectively putting selective pressure on bacteria when you freeze them (the bacteria more resistant to low temperatures survive, bacteria less resistant die). Why then is it a good idea to freeze bacteria?


texts:
It consist approximately 7 percent of body weight.

By definition organ is composed of multiple tissues. Blood is a fluid, a circulating tissue.

Therefore can we call this fluid system a liquid organ?


texts: What predates on cactus in the Atacama desert?

texts:
Introduction

Last week, I was in the Atacama desert where I've seen many cacti. Some / many of them were seemingly suffering from predation. Most of predation seemed to be on cardón, often restricted (but not only) at the interface between the woody bottom part and the green spiny part. It looks like a big piece (maybe over 300 $\text{cm}^2$) of the flesh was bitten away. Unfortunately, I do not have a picture.

These cacti have very long spines and it was unclear to me what predator could maintain selection for cactus lineages to produce that many large spines.

In the desert, I have seen rabbits, guanacos, small birds, vultures, large black coleoptera and butterflies.

Question

In the Atacama region,

What species predate on cacti?
Is there a single species that causes most of the predation on cacti?


texts: How does the muscle return to its resting state after muscle contraction?

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I know that when ADP binds to the myosin head, it moves along and as it does so, it releases the ADP. The ATP attaches to the myosin head and releases the myosin head from the actin filament. Then the enzyme ATPase hydrolises the ATP to ADP, causing the myosin head to move to the original position.

My question is:

How does the actin filament (troponin) move to its original
position? Does it use a mechanism similar to a spring?
Is there a limit to how much the myosin head can pull the actin filament?


texts: E. coli has two oxygen sensors: FNR (fumarate-nitrate reductase) and ArcBA (Anoxic Redox Control, two component control systems). FNR directly senses the oxygen, while the interaction of ArcB with oxygen is indirect one via quinone pool. Out of theree quionones in E. coli, which one (oxidized and reduced forms of all three types)  play roles to what extent in what direction (inhibiting/activating) is much debatable. I would like to see some intuitive level arguments for why a cell, even in principle, need to have two sensors for oxygen?


texts: Does "eating less" stimulate cell starvation?

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2016 Nobel Prize in physiology or medicine was given for the study of autophagy.
Judging from the description, a healthy cell responds to starvation (and other types of stress) with autophagy.
Does starving of the organism for short amount of time (around a day) cause cell starvation? And, can we say that starving for short amount of time stimulates autophagy?


texts: Why do I see the world in blue when I open my eyes?

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So I was standing outside, waiting for the train. I was tired so I closed my eyes for a while. Then when I opened them, the world was a lot more blue than it normally is - why is this? I tried it a couple more times to be sure that it wasn't just a mistake, which confirmed it, as the world kept being blue (of course, not permanent, it slowly gets back to the "normal" colors).

I'd appreciate a simple explanation, as I'm not a biology or physics student. I only have a very basic understanding of both subjects. Thanks in advance!


texts: What is a secretion target family protein?

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I came across this link: https://www.genome.jp/dbget-bin/www_bget?btw:BF38_3398
What is this protein, is it a secreted effector protein or is it something else?

What is the difference between type VII secretion protein (https://www.genome.jp/dbget-bin/www_bget?sams:NI36_12950) and type VII secretion effector (https://www.genome.jp/dbget-bin/www_bget?bmyo:BG05_3891)?


texts: How do Benzodiazepines induce Rewarding (Euphoric) effects?

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Benzodiazepines are a class of drugs that serve as positive allosteric modulators of the GABAA receptor by binding to their own "site" on the aforementioned receptor. By doing this they produce euphoria and a wide range of effects characteristic of Central Nervous System (CNS) depression (e.g. anxiolysis, sedation, amnesia, mental confusion, muscle relaxant effects).

I know that an interaction with the mesolimbic dopamine ("reward") pathway would have to come in somewhere but where? I also know that GABAergic neurons downregulate activity in the mesolimbic dopamine pathway and that this is how opioids and cannabinoids induce euphoria -- they inhibit the release of GABA from presynaptic neurons in the mesolimbic dopamine pathway. I just find that this would be confusing in the case of benzodiazepines since they increase GABA activity, presumably also in the mesolimbic dopamine pathway thus producing dysphoria and not euphoria.

I just would like to know how they manage to induce euphoria in full (what they do to increase activity in the mesolimbic dopamine pathway that thus leads to euphoria)

Please cite journal articles to substantiate your claims.


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When I was moving to another house, I found this plastic bag on the top of the cabinet of my old house. It looks like someone cut it all with a scissor, but no one have access to my bedroom, and it was not me.

I don't thing it could be rats. That bedroom was very tiny and closed, there's no way for a rat to enter.

The house is very near a university with a little "forest", there are many types of mosquito and little flying animals, but I can't imagine which could do this.

I'm just curious. (and not sure if "zoology" is the correct tag here, but I had to choose one)


texts: Are cerebellar basket and stellate neurons actually different cell types?

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The title more or less says it all, but to contextualise a bit:

Cerebellar molecular layer interneurons have been classified, probably since Cajal, into the basket cells, which synapse onto the soma and axon initial segment of Purkinje cells, and stellate cells, which synapse onto the dendrites. The types are distinguishable in tissue slices by positional and morphological differences, but it is at least arguable that the variation is continuous and the boundary somewhat arbitrary. Both types take basically the same inputs and deliver the same outputs, albeit in marginally different cellular locations.

As far as I'm aware -- and I would be incredibly happy to be told otherwise -- there is no known difference in protein expression that can be used to distinguish between these interneuron types, for instance in dissociated culture.

So, is there in fact some identifying marker? And if not, is it still useful to classify them as separate types?


texts: Can a brain process auditory signals at 18 weeks of human development?

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According to When a fetus hear , When a baby can hear in the womb and several other similar articles, a baby starts to hear sounds at week 18. And according to How hearing works. Hearing involves

  nerves communicate to the brain. The hearing nerve then sends the
  information to the brain with electrical impulses, where they are
  interpreted as sound.

Does this actually mean a brain is actually processing auditory signals at 18 weeks of human development, or is the brain at 18 weeks only processing sounds by a process that doesn't involve the brain? Perhaps the conclusion might seem obvious for some, but not for me considering the supposed inability of the brain to process several others (or any other?) kind of signals at that stage, such as pain At what stage is the nervous system developed enough to interpret neuronal signals as 'pain'? and being the hearing experience directly connected to pain sometimes.


texts: In a sugar such as a disaccharide are both ends of the sugar known as reducing ends?

texts: For example, in maltose (a disaccharide of glucose monomers) are both of the ends either side able to be opened to form an aldehyde group?


texts: Detecting cancer or a genetic predisposition based on DNA sequencing

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I am not by any means a biologist - so go easy.

What would be a method for determining whether or not a patient has cancer based only on a genomic sequence?

Update Thanks for the help in revising the questions.

What information is extractable once a genome has been sequenced?
Is it possible to derive whether or not a person has cancer based only on the genome which was sequenced? i.e. Are there anomalies to look out for to detect the cancer.


texts: Plants that are siblings: How does this impact pollination?

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A friend has two cherry bushes (prunus tomentosa). Prunus tomentosa is said to be partially self-fertile, but benefits from cross-pollination.

The two cherry bushes set fruit, and so my friend saves me two seeds. I plant the seeds at my house, which is miles away from his, and now have two bushes of my own. They are in bloom.

My cherry bushes are siblings. How will this impact their ability to pollinate?


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Result of genetic testing indicated: c.341del, p.Thr114Lysfs*37.
The c.341del probably means:deletion at the cDNA 341 nucleotide.
Buy what does the second part:p.Thr114Lysfs*37 ?


texts: Isn't heritability more important to genic capture than just genetic variance?

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Rowe & Houle (1996) give two criteria for the selection of costly female choice:

Condition dependence of sexually selected traits
High genetic variance in condition

Regarding heritability, they wrote,

  comparisons based on heritability are misleading, as Fisher's fundamental theorem of natural selection shows that the response of fitness to selection depends only on the additive genetic variance, and not on other components of variance.

However, the magnitude of environmental variance should matter for the selection of female choice for sexually selected traits, since the more environmental variance means the less likely offspring of fitter males will be fitter themselves and the less likely females should be to incur costs to mate with fitter males.  Am I not correct?  Is this an oversight on their part?


texts: Does pre-operational exercise affect recovery from surgery? Statistical Analysis

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https://www.medicaljournals.se/jrm/content/html/10.2340/16501977-2210

I understand the difference between statistical significance and effect size, but I am having trouble interpreting the data on Table III in the article linked above. I am evaluating the WOMAC scores. My first question is can effect size confidence intervals cross zero and still be valid? My second question is about the negative and positive values of the Hedges'g. The first study scores the WOMAC in a way where the higher the score, the better the outcome. The second two studies score the WOMAC in a way where the lower the score, the better the outcome. Does this mean that in the first study a positive Hedges'g indicate larger effect for the treatment group and a negative Hedges' g for the other two studies indicate larger effect for the treatment group?


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and the lung cancer has not spreaded to other parts of A, does transplant help to remove cancer?

If someone B transplants a lung 'contaminated' by cancer, does B necessarily get cancer too? His body may kill cancer?


texts: What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

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If there is a need to align structurally different parts of distant homologs, which program one should use?
Since distant homologs often have significant structural changes, does that means the assumption of a similar physico-chemical environment for aligned residues would be violated?
Any program/tools or suggested reference will be a great help.
Thanks.


texts: Selective breeding of organisms to survive on Mars

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It seems that there may have been life on Mars, and it's also tempting to terraform and colonize the planet. This question is about testing the hypothesis "Can primitive life survive on Mars?". This is closely linked to the lithopanspermia hypothesis, that life can be seeded from bacteria on meteorites.
The hypothetical experimental setup is as follows:

Take microorganisms that live in the upper atmosphere and can survive high radiation
Recreate their natural environment in a lab, and let them live there
Slowly change the environment to be more similar to Mars: pressure, temperature swings, radiation, relative gas concentration
See if they are able to adjust

My question is: Is this possible? Has anyone done it, or is doing it currently? I know tardigrades are being sent to the moon, but they're hardly thriving there.
My apologies if the non-expert question is off topic. If you can suggest a more appropriate place to ask, I'll keenly do so.


texts: What happens to our umbilical cord internally as we age?

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I was always curious as to if or how much of the internal structure or workings of the umbilical cord are still in existence as we age.  What happens to it over time?

The wikipedia article naval almost exclusively describes physical appearance and only touches on some disorders that affect physical appearance.

Then the wikipedia article on umbilical cord explains what happens briefly after birth, and only touches on it becoming part of the circulatory system.  What does it actually do in later life, as part of that system?


texts: What does basipetal succession (of flowers/leaves) mean?

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The definition says that basipetal succession is the arrangement of flowers such that the older ones are present at upper side and the young flowers are arranged towards base. But in this diagram:

the oldest flower is at the base and the youngest is towards the upper side. Can anyone help me understand this?


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Pilobolus is a fungal genus whose fruiting bodies consist of a stalk ending in a spore mass that is launched via turgor pressure to disperse the spores.  The fruiting bodies grow towards light, which ultimately influences the direction in which the spores are launched.

It seems that gravity-directed growth would be sufficient to ensure an upward trajectory, so I'm wondering what the value is of phototropism.  Has this been studied at all?


texts: Career progression through biosafety levels?

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Does a career in infectious disease typically progress through biosafety levels, or do people select one and specialize their training in procedures specific to those hazards?

That is, say Dr. Kliener wants to work on TB (BSL3). Does he first on have to work on MRSA (BSL2), which he has no interest in, just to build up experience? Or could he simply learn everything there is to know about TB and BSL3 lab procedure, don hairnet and gown, and get to work with someone who has experience under those conditions?


texts: Identify function of cluster with high identity of genes

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Let's say there is a secondary metabolites biosynthesis cluster in fungi A.
and I just found out a gene B(identitiy>=50% with nrps gene located in the cluster) from fungi B and also found that gene B is located in some gene cluster in fungi B genome. My question is, with these two proofs can I say the gene cluster including gene B is doing same function with a secondary metabolites biosynthesis cluster in fungi A?


texts: Part of a fish outside the intestinal sac on the back?

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I saw an expert Japanese chef fillet a mackerel (Scomber scombrus). He cut off the head and the whole intestinal sac came out with it as a single unit. Then he took the knife and scraped something from inside on the back. The object(s) were dark and bloody. Would those have been the kidneys?

You can see the video here: https://www.youtube.com/watch?v=udTHiRg34KI. The moment is at 2:20.


texts: Can Taq polymerase be stored with PCR primers?

texts: I don't think it's possible for TAQ to be stored with the primers, but I'm not sure. This storage wouldn't be long-term (a few days, or a week at most). Thoughts?


texts: What do phagocytes release after interacting with a pathogen? I know that this is a broad topic but I only need a general and concise answer.


texts: Trying to identify an Ontario bird photographed in Spring in the Don Valley

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Any help is appreciated! I think this may be a juvenile bird? I thought it might be a brown-headed cowbird, but the plumage and head markings don't seem quite right (compared to examples on the internet)? Any assistance is greatly appreciated.!

Rob aka orbitrob


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What if Staphylococcus Aureus are extinct?

Can it be good for human or bad for human?

Thanks for your answer in advance.


texts: Electrode locations for neuron study in stereo EEG?

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I am thinking where to put optimally depth electrodes in stereo EEG outside sulci in studying the functioning of neural transmission of N neurons over one perivascular space in rodents, mice or rat, where I would like to know how small N can be. The theoretical minimum is one neuron but I would like to understand the Physics how small current you can measure by EEG reliably with not too high Signal Noise Ratio (SNR).
I did not find any meta-analysis about EEG electrode locations in DynaMed Plus.

I am not sure about the anatomic therminology of Neurology so I use the terms cerebral cortex, sagittal and coronal planes in describing directions.

Definition of electrode's location somehow in cerebral cortex

The further the electrode is away from the source, the lower SNR.
This proposes me that there has has to be at least 20 neurons to minimize the variance.
What is the average distance between two neurons?

Here my conjunctures about location of electrodes where the picture is from Virginia's university Nature publication here:

where the electrode is surrounding N neurons and one blood vessel such that one electrode is below the neuron and one above.
It is contraindicated to put the electrode too close to the blood vessel.

Definition of electrode's Coronal-Sagital locations

I am interested in

how close perivascular space can the electrode be? Stereoelectroencephalography (SEEG) implantation method has a safety distance minimally 2 mm but practically more than 5 mm of depth electrodes. [TODO cite]
how superficial can the electrode #2 be? 1.0 - 1.5 mm in microelectrode EEG here i.e. mostly in superficial layers.
how deep can the electrode #1 be? I think mostly in superficial layer i.e. 1.0 - 1.5 mm with microelectrodes. SEEG with depth electrodes - minimally 2 mm but practically more than 5 mm.

Stability of electrodes

The stability is affected by many processes discussed here.
The array of electrodes is allowed to float with the motions of the cortex due

heartbeat
respiration
...

Sources

Talairach J, Bancaud J, Szikla G, et al. Approche nouvelle de la neurochirugie de l’epilepsie. Méthodologie stérérotaxique et résultats thérapeutiques. Neurochirurgie (1974) 20 (Suppl. 1): 1-240.
Cossu M, Cardinale F, Castana L, et al. Stereo-EEG in the presurgical evaluation of focal epilepsy: a retrospective analysis of 215 procedures. Neurosurgery (2005) 57: 706-718.

How can you define evidence-based locations of stereo EEG electrodes?


texts: How does a plant decide when to grow a branch?

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As a plant grows, at some point the first branch forms. As it continues, branches grow new branches, and so on, in a seemingly random way. Is it random, or is it driven by the environment (heat or cold, sunshine, wind)? Or is it somehow defined in the plant's DNA, that each branch will grow at in such and such a direction, at such and such a time?

Does this generalize down to successively smaller branches, and eventually leaves?


texts: Does dreaming have any physiological impact on our body?

texts: Personally speaking, when I wake up after a really good dream, I feel really happy, similar to how I would feel if something good has happened in reality. This makes me wonder if we are actually going through stress when we are having a nightmare. Is there an increase of epinephrine in our body when we dream about being in trouble or running away from a scary situation? Similarly, are endorphins released when we are experience a happy moment in our dreams?


texts: I was pulling weeds in my backyard in Southern California, when I saw a spider over a white area on the underside of one of the leaves. It's staying right near the white spot. Are those spider eggs? Also, what kind of spider is this?


texts: Why do some bacteria have an asymmetric replication?

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Our teacher said that Bacillus subtilis has an asymmetrical replication fork.

I know that this happens only in some strain of the bacteria . She asked us to find an explication for this mechanism , but all that I was able to find is that the chromosome is more compacted in some areas, therefore it slows the replication .

Are there other reasons?


texts: I've been reading some research papers about p53 and associated tumour suppressor proteins, such as p21. I see them referred to and associated with cyclin-dependent kinases. Is p53,p63 et cetera part of the CDK family?


texts: Do the phage repressors CI and Mnt exhibit crosstalk?

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I am interested in using the CI and Mnt proteins as well as their respective promoters (pR and Pmnt) within the same synthetic system, but am concerned as to their similarity and potential crosstalk. A quick search of the literature yielded no results and a Multalin did show some significant sequence homology (although Mnt forms a homodimer while CI does not).

Sequences: CI and pR, Mnt repressor and Mnt promoter

Has it ever been reported that the CI or Mnt repressor exhibit crosstalk on the pR and Pmnt promoters?


texts: Which books give data on how humans grow physically from birth till death?

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I am searching books on how humans grow physically from the birth till death. I am not a biology student, and don't know any technical terms. I searched amazon but didn't find any such books. I need book to be precise. Even if the book is a textbook, it would be helpful.

If it is not possible to get all the data in one book, is there any other alternative reading to be made via multiple source reading.


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A phenotype such as hair color
like blonde hair.
I am curious because mutations cause new alleles but does that mean that there always has to be a dominant or reccessive allele?


texts: Recombination frequency, linked genes, and independent assortment

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Gene R is genetically linked to gene T with a recombination frequency of 0.3. Gene T and gene X assort independently from each other. Your colleague tells you that gene T and gene X reside on the same chromosome. How is this possible?

So I know that R and T are on the same chromosome. T and X assort independently, so they should be on different chromosome. And then due to recombination, X gene crosses over so that it's also on the same chromosome as T and R? Can someone please help me?


texts: How do I deal with sticky and viscous samples from cell lysates?

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To check a protein expression I pelleted a small amount of E. coli before and after induction and lysed them by redissolving them in SDS-PAGE loading buffer and heating them to 95 °C for 1 minute.

This lead to a solution with some very sticky and viscous parts in it, that make pipetting the sample into the gel wells extremely annoying. As far as I heard, this is probably genomic DNA, and my usual way to deal with this is to centrifuge the samples and only pipet a small part out from the top. This does seem to help sometimes, but not always.

How can I avoid the formation of that sticky and viscious stuff or how can I avoid pipetting that stuff into my wells?


texts: If I inject a dose of GFP or some other types of protein into a long-living human cell like brain neuron cell. Will these proteins being degenerated or excreted over time?


texts: How can ionized amino acid form be important for the catalytic activity?

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I can imagine that protonated amino acid form, particularly at the active site, is important for the catalytic activity so hydrogen bonds can be created between the substrate and the enzyme. However, I cannot imagine how the ionized form can be important for the activity?

Both forms are important for the activity as stated in this study:

https://www.ncbi.nlm.nih.gov/pubmed/7306491

  The pH dependence of log V/K for dihydrofolate showed that a group with a pK value of 4.7 must be ionized and that a group with a pK value of 6.6 must be protonated for activity

I cannot understand how the ionized form is important for the activity, could some one help me to understand that?


texts: Why do I have 95% of chimpanzee's DNA, and only 2% of Neanderthal's DNA?

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Excuse me if it is a question with a simply answer, but I don't understand these discoveries, looking a discrepancy from my unknowledge of genetics:

I have 95% of Chimapanzee's DNA,

and,

I have [only] 2% of Neanderthal's DNA.

Neanderthals should had also chimapnzee genes, so what does that 2% of  correspondency between Neanderthal and actual Homo sapiens genome exactly means?


texts: What is the name of this strange white caterpillar?

texts: My friend found this caterpillar in south-central Tennessee in August. No identification guides or databases I've searched had a similar picture. Does anyone know the name of this species?


texts: How are cardiac cells connected by intercalated discs?

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I understand that intercalated discs run transversely across the longitudinal axis of the muscle. But what I don't understand is how this same disc binds the cardiac cells together.
Are the cells joined end-to-end (in series) or side-to-side (in parallel) by the disc?


texts:
In the amino acid sequence X-Hyp-Gly (where X can be any amino acid) of the triple helix can the Hyp residue be both hydroxyproline and hydroxylysine? In our textbook it says that the Hyp residue is hydroxyproline but "hydroxylysine also occurs in the collagen".

Thank you!


texts: A trivial question on the meaning of "relatives" in an article on horizontal gene transfer

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Am I right in suggesting that by close relatives the author meant closely related species, or did he have individual organisms in mind?

  DETECTION OF HORIZONTAL GENE TRANSFER

  There are several approaches to identify genetic changes due to HGT,
  including:

  (1) experimental evidence, whereby a genetic marker is monitored for
  gene transfer to a recipient organism;

  (2) phylogenetic analysisof gene sequences to identify topological
  inconsistencies between different gene families;

  (3) nucleotide compositional analysis to identify any gene that has a
  nucleotide pattern that differs significantly from the overall genome;
  and

  (4) evolutionary scenarios to explain the patchy appearance of a
  genetic signature, sequence or function that is not shared by close
  relatives.

(From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese)


texts: If a hemophiliac patient injects his factor 8 through the veins directly into the bloodstream to provide the body with clotting factor... Why don't they just make the drug as a pill and have the liver do its job with extracting protein and dumping it into the bloodstream?


texts: Can oxygen diffuse out through the lungs?

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Let's say you accidentally walk into a room pressurized with pure nitrogen (or you're jettisoned into space). Within a couple of seconds, the partial pressure of oxygen within your lungs drops to 0. But there's still a (small?) reserve within your bloodstream.

Now, will the oxygenated blood travel to your lungs? If so, will the usual gas exchange reverse, with oxygen going from your blood to the oxygen-poor environment?


texts: Does body fat percentage effect storage of fat soluble compounds?

texts: Would a person with a higher body fat percentage store more of a fat soluble compound, or store for a longer time, than a person with a lower body fat percentage if they both consumed the same amount in the same time frame?


texts:
Why does ear wax taste sour?

I am interested in both the physiochemical mechanisms and the evolutionary reasons behind the sour taste of earwax.


texts: Why can fish breathe under water but land mammals can't? How can fish extract oxygen straight from water but humans can't?


texts: Why does carbon dioxide diffuse easier through the bilipid layer than oxygen?

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When gas exchange occurs during respiration, the pressure of oxygen in alveoli is around 105 mmHg, whereas in the blood vessels in close contact with alveoli is 40 mmHg. For carbon dioxide the values are 40mmHg in alveoli, and 45mmHg in vessels. So the difference in pressure for oxygen is 65 and for carbon dioxide 5.
The fact that the pressure difference required for oxygen diffusion to occur is greater than that of carbon would mean that is diffuses with more difficulty. But how is that possible since the oxygen molecule is smaller and non-polar, so would technically pass easier through a hydrophobic membrane?


texts: Confused at what is happening with these action potentials

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Ok so for a bit of a background, I am doing a science project looking at the action potentials of the earthworm. I anaesthatized the worms then hooked them up to a spiker box (http://backyardbrains.com/products/spikerbox) and stimulated them.
This is an average result:

What I am confused about is why the action potential goes negative first before then going back up. From my readings online, I thought that the action potentials were meant to go up first then travel down and then continue on its course. If it helps I used a program called audacity to record the action potentials.

Thanks very much guys. Sorry if I'm not being clear. Just ask anything if you need more information!


texts: Common Metrics of Assessing DNA Sequence Quality

texts: What are commonly accepted metrics for assessing DNA sequence quality (platform-specific answers are fine)? I am relatively new to this topic, and I want to either find or code (in Python or C++) algorithms for checking sequencing data quality before getting into analysis.


texts: Does blood carry metallic nanoparticles?

texts: I find this particular chart about constituents of blood very informative and interesting. Looking through the different components, I see metals such as copper, zinc, etc. Are these only carried as ions or conjugated to proteins, or does blood carry nanoparticles of these elements as well?


texts: Persistency of botulinum toxin in environment

texts: There is information about decontamination times here on pages 6 and 7. My specific question is how persistent botulinum toxin is in a natural environment, or alternatively, what is the half life of this toxin?


texts: What is the molecule responsible of the yellow color of the Agave americana?

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Does anybody know what is the molecule responsible of the yellow color at the edges of this plant?
I noticed also that the new forming yellow part at the begging stage is soft green until it is exposed to light. After the exposition to sun light it change from soft green to yellow(like that of the image bellow).
Does anybody have any explanation?


texts:
When I searched carpenter ant in Google, this looks kind of like some of the images. Some other images show reddish or winged ants and I have not seen any of those.

I've seen 3 or 4 of these big black ants in the last month we've been in our new house, wondering if I should be concerned.


texts: Reason for the source of fetal bovine serum

texts: What is the reason that perhaps the most commonly used serum in labs is fetal bovine derived? Is there something about fetal serum that is particularly useful over say serum just harvested periodically from adult cows, or cows going to slaughter?


texts: Why is it advised that infants are fed mother's milk?

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I have heard that mother's milk is preferred over other baby foods, because it contains immunoglobulins (secretory IgA), and other essential nutrients.

But why is mother's milk so special? Any mammalian milk, such as the widely available cow's milk, should presumably have a similar composition as human milk? What makes mother's milk in specific so healthy?

Could the mere act of breastfeeding, in itself, lend to some beneficial outcome?


texts: After doing some statistical analysis of the raw math involved in DNA contributions, I would like to understand the scale of the biological factors.  I know that 99% of the human genome is identical in all human beings, so genetic recombination and gene conversion should be irrelevant in those areas.  I know that recombination occurs at different rates depending on the chromosomes and loci.  But what is the average order of magnitude?  That is, if I know that a chromosome mainly came from Grandma, how much of it is likely to be from Grandpa?  .1%, 1%, 10% ?  And, does the age of the male affect the rate of recombination to a measurable degree (in spermatozoa only, as body cells would not affect inheritance).


texts: Why upper surface of leaves is more green and shiny than the lower one?

texts: I have properly googled this and got various answers. However, those answers do not provide an answer to the "Why" part of my question. Why is it that the upper surface of leaves is more green than the lower one? Some sites suggest that it is because of the thick cuticle. Yet, that sounds weird and doesn't fully convince me. What other reasons to why the upper surface of leaves is more green and shiny than the lower one, could there be?


texts: Is the amount of blood same in the pulmonary and systemic foetal circulation?

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We learn that the stroke volume is the same for the right and left side of the heart. So the amount of blood in either circulations should also be the same. (is it? I myself doubt this statement. As in, does it need to?)There's also a list of adaptations in the pulmonary vasculature that accommodates the huge volume of blood. But that's the adult. What about the foetus?

My doubt is that, in the presence of a patent ductus arteriosus in the foetal circulation, doesn't this distribution change? This shunting of blood into the systemic circulation would result in a low pulmonary venous return and hence, a low left ventricular stroke volume. So in the foetus, both blood distribution (in the two circulations) and also the stroke volumes (of either side of the foetal heart) should be differrent. Is this so?

This actually concerns me because the DA joins after the initial three branches (left brachiocephalic and the carotids). So, wouldn't such a shunting drastically reduce blood flow/perfusion to the brain? As in there would be decreased flow to the carotids when compared to the adults.

Finally, what are the consequences of the differential blood volumes in the two circulations and differential stroke volumes of the two ventricles due to a patent ductus arteriosus in a foetus? (If happens)


texts: Is there life on other planets and if so how frequent?

texts:
Some shed tears of joy as the news about the successful landing of the Mars Rover Curiosity came in. Then the most comprehensive 3D map of our observable universe was published. 2012 is literally an astronomical year.

As an layman I would like to know about scientists current understanding about the frequency models that life forms on other planets?

See also:

Drake equation


texts: Rushed publications based on flawed data

texts:
In 2014 BICEP2 made a very controversial press release. It was rushed, given before any papers where published, because they feared they would be scooped by another similar experiment. In the end it turned out that their analysis of their data was flawed. It was particularly dramatic because if they had been correct it would have been a significant development.

Are there any similar cases in biology? Not necessary an identical situation, but a high profile result that was released in a hurry that later turned out to be incorrect.


texts: How does "be altruist to those who are similar to you" evolve?

texts:
There are many cases when people commit altruism. One is relationship. I am willing to die for 2 of my children or 8 nieces, say an evolutionary psychologist. Another is reciprocal altruism, which is just a selfish cooperation rather than true altruism.

  In the 1930s J.B.S. Haldane had full grasp of the basic quantities and
  considerations that play a role in kin selection. He famously said
  that, "I would lay down my life for two brothers or eight cousins".[8]
  Kin altruism is the term for altruistic behaviour whose evolution is
  supposed to have been driven by kin selection.

Is it possible that humans may be altruists not for their 2 children or 8 nieces but to say, 1000 people that are similar to them.

If so, how does "Be altruist to 1000 of people similar to you" evolve?

Note: If the answer is negative, then we will have a hard time understanding voting. Why sacrifice your time. However, if the answer is positive that humans do love other humans "a little bit" then voting, or even suicide bombing make sense. Those humans sacrifice their little time to improve reproductive success of those who are similar to them.

Answer DOES NOT have to be about humans. If you can show me why strong/weak chimps tend to help each other or whether alpha males like one another, that'll do. Of course, naturally we would expect that leaders need followers and followers need leaders. But sometimes there are behavior that defy even this complementary nature.

Similarity does not have to be genetic. For example, fellow programmers and fellow engineers tend to be gang up.... Or does it have to be genetic?


texts: Is missing Q wave characteristic for Wolff-Parkinson-White Syndrome?

texts:
No my study books says about that no Q waves in WPW syndrome.
They are about wide QRS complex often however.
I heard today that the characteristic property of WPW is often a missing Q wave, like here

This is caused by the presence of an abnormal accessory electrical conduction pathway between the atria and the ventricles.
However, some books are about delta waves which is characteristic in the above picture.
However, it is many times very difficult to see.
These missing Q waves are however much easier when PRS complexes.

How much false positives do you get if you categorize all missing Q waves and PRS complexes as WPW syndrome?

How characteristic is the missing Q wave for WPW syndrome?


texts: Why do some bacteria have most genes on the leading strand of the genome?

texts:
Genes in the (+) strand are black and genes in the (-)strand are red.
The gene distribution in E. coli genome is somewhat expected: transcribed regions would tend to alternate with non transcribed regions, as a consequence of (random) evolutionary process. Also, genes don't overlap (it would be highly  unlikely that two complementary strands both carried useful information).
In B. subtilis, on the other hand, there seems to be a preference for one of the strands in each side of the chromosome. What sort of evolutionary pressure could give raise to such a pattern?
I have a guess, but I'm not sure, that this may be related to bacterial transformation.


texts:
Homozygous DYT1 mutation carriers have not been reported in humans.

Does this mean that the mode of inheritance for dystonia (DYT1) is autosomal dominant? This to me implies that if one has both alleles for dystonia, then one must also have the phenotype, as people with both alleles cannot be carriers.


texts: So how can mesosomes (found in prokaryotes only) participate in cellular respiration, if a prokaryotic cell doesn't have mitochondria?


texts: What is the essence of difference of how different chemicals affect the same receptor?

texts:
It is known that various chemicals can bind to the same receptor type, producing different effects. Be these chemicals agonists or antagonists, there are more variations in how they influence the receptor than just sending an activation or inhibition signal. There seem to be various flavours of activation (not sure about inhibition), where, for example, a psychedelic drug binding to a serotonin receptor produces a different result than serotonin itself.

For a more clear representation, I have split the question into logical parts:

What is the essense of this difference? Does it come from the chemicals molecule properties like shape and electron configurations of the atoms?
If we were to draw two comparative pictures of how two such different chemicals affect a receptor, how would we picture that? What would we chose to be the characteristic figure(s) on our pictures? What qualities of the connection (probably changing over time) would we consider to display on the picture?

Does this question make sense or are there any false assumptions?

UPDATE:

Response to the comment by WYSIWYG: I cannot cite any source saying so. It is that I got this question at some point: is ligand-receptor activation a binary function, which can only give either 0 (no interaction or inhibition) or 1 (activation) values, or it is something more varied?

Taking into account that ligand-receptor interaction is molecule-molecule, it is logical to assume that the resulting complex can put the receptor molecule in a variety of states, depending on the ligand molecule structure. Here the Ionic Bonds and Hydrogen Bonds sections shed some light on this - the described interaction patterns seem like they can produce quite different results. Like, for example, they put receptors molecules electron cloud configurations in different states. But does in reality such interaction always result in either 0 or 1 state of the receptor?

The pdf paper refered from this question leaves the reader to guess: are the varying effects of the chemicals produced solely by their profile of different affinity to different groups of receptors, or do they also interact with each receptor type differently. In other words, is the drug effect produced by a certain amount of 1s being fired by the receptors, or is it changing the quality of their firing signal itself, i.e. making the receptor to initiate different, non-typical processes inside the cells?

Or, in the cited Wikipedia article, under section The specificity of drugs it is said that muscarine and nicotine can selectively activate specific subtypes of acetylcholine receptors. Is the result of these chemicals activating these receptors exactly the same as of acetylcholine? If we deliver both muscarine and nicotine to their sites, will they produce the same effect as if we deliver acetylcholine to both of them?

Also, I cannot really find much information on what lies beyond the receptor, namely - how does it send the signal somewhere else.. but I guess that's molecule-molecule again, so here we get the chance of varying result too. Or don't we?


texts: functionality of protein based on amino acid covalently linked to something

texts:
This question is directly taken off from "challenge question" as part of my bio-engineering class.

The functionality of any individual protein covalently linked to a device is dependent on the specific amino acid through which it is chemically linked to the device.

Is this a true statement? I believe that different amino acid has different chemistry and orientation so it would affect the functionality but is it enough to say dependent on them. Also could you please provide an example if possible? I cannot think of an example. I would really appreciate your insight as well.


texts: Did some senses evolve from other senses or are they considered independent?

texts: Are there evolutionary connections between different senses, in such a way that one sense is evolved from the other or from a common root, e.g. the possibility that hearing and touch are derived from a common root? If there are such evolutionary paths, are there any attempts to draw a map between different senses?


texts:
These bumblebees live on my balcony, in ventilation holes in doors and windows. I'm trying to find the exact name of the species, but I can't find any that look exactly like this. Their top segment is completely black and the bottom one is completely orange. I'm not 100% sure that these are bumblebees, but they behave like bumblebees, I mean, they fly horizontally and like nectar.
The location is in the southern part of Germany (Bavaria). The insects are ~20mm long, similar to the size of a honey bee.

The closest match is probably Bombus lapidarius, but Bombus lapidarius only have orange "tails", most of their bottom half is black.
It looks very similar or even identical to Bombus alpinus, but the problem here is that Bombus alpinus usually live in the mountains (and I'm in 300km from the closest mountains) and they are considered to be almost extinct in Germany.
Do you have any idea what they are called?


texts:
Lyonization or X-chromosome inactivation is the conversion of all but one, X-chromosomes in Females into non-coding heterochromatin (i.e. deactivated) leading to the formation of one or more Barr bodies. The selection of the X-chromosome to be inactivated is different in different animals. In female Marsupials, the inactivation is always of the Paternal X-chromosome while in placental mammals, the selection is random. (Although the extent of lyonization is not completely random and varies directionally with age).

My question is

  If the X-chromosome to be inactivated is randomly selected in
  placental mammals (including humans), then why don't the females
  heterozygous for a X-linked recessive disorder do not show the
  phenotype of the disease though the functional gene is equally likely
  (as compared to the defective) to be the one to be lyonized?

There are some evidences of genes escaping inactivation and managing to exhibit themselves but I don't think they can account for all the recessive x-linked disorders.


texts:
Do animals get sick with hemorrhoids ?

And why Humans are most affected of it ?

Is it because the gravity center of Humans is sittuated in the anal ?


texts: Protein Design - Target Structure Specification

texts:
I'm curious about how protein structures are defined in general, but in particular, I'm wondering how a target structure can be specified without knowing the amino acid sequence.

For example, in protein design (or from what I gather on the wikipedia page http://en.wikipedia.org/wiki/Protein_designs), scientists design a 3D structure that will perform a particular function.  They then try to come up with an amino acid sequence that will fold properly into that structure.

How can a 3D structure be defined if no amino acid sequence (and hence no molecular geometry) has been determined?


texts: Microarray has various uses, and to analyse the data a main function classification is used. There are many methods used to classify the data but what are the best and most frequently used methods? Are there any well-known, web-based tools for microarray analysis?  Where can I find datasets of gene expression profiles, where I can find and understand the matrix of the dataset?


texts:
So I was reading on linker DNA, and the textbook only describes it in terms of structure. I was wondering if linker DNA can ever contain genes, and if it can, whether it will always be expressed or not. Since it is never wrapped around a histone, how is it regulated?

Thanks.


texts: What causes cells to inactivate one X-chromosome?

texts:
Normally, when a cell has two X-chromosomes (female genome), one is randomly inactivated. How does the cell detect that there are two X-chromosomes in the first place?

Is there some kind of protein that's coded in the X-chromosome, such that having two X's increases the protein concentration and a dosage effect causes one to become inactivated? I can't find any information about it in my textbook, nor on Google. A citation would be appreciated - especially for peer-reviewed research.


texts:
This is a question from an exam in my biology course.

Bacterial cells and human red blood cells were inserted into one solution. Upon testing one hour later the blood cells exploded, while the bacterial cells stayed intact. What answer explains the findings:

A. The bacteria cell walls prevented their explosion.

B. The blood cell walls didn't prevent their explosion.

C. solute concentration in the solution is equal to the blood cells and bacteria solute concentration.

D. solute concentration in the solution is higher than the blood cells solute concentration.

My lecturer said the right answer is B. I thought the right answer is A.
What would be the correct answer and why?

To my understanding, red blood cells don't have a cell wall, but rather a membrane, which is why in my opinion you can't say that it prevented the explosion if it doesn't exist. On the other hand, bacteria does have cell wall, that's why I thought this answer is the correct one.


texts:
I am no biologist, but I have this question buzzing in my mind. It's a matter of curiosity

What happens when two nuclei occupy the same cell? Would we expect the embryo (if it lives) to have complex cells (assuming the nuclei are from different species, i.e., genetically incompatible with each other)?


texts: Where does Taq polymerase migrate during electrophoresis?

texts:
Assuming a 1% Agarose gel with TAE.

Follow up questions:

Is there a way to stain for it?
Could the polymerase be captured and reused?


texts: Can a Turner syndrome patient develop male characteristics artificially?

texts:
From an answer to the question Can stem cells from male convert to cells of female-only organs, and vice versa?

  Y chromosome is the sex determining chromosome with SRY gene that determines testes development. Absence of the Y chromosome leads to female development by default. That is why XX forms women and there are people with only one X chromosome which are women. (Turner's syndrome)

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

  The Y has only a few genes (less than all other chromosomes), but it has genes that occur only on the Y. One of these in particular, the one called SRY, is the main gene that causes the individual to develop male characteristics. It mostly does its job indirectly, by making a protein that affects many other genes on other chromosomes that in turn do the work of building and maintaining the male form... they managed to cause mice without a Y chromosome to develop many male characteristics. They did this by faking one or two of the actions of SRY. One of the many actions of SRY is to turn on a gene called Sox9 (which is on a non-Y chromosome), and it turns out Sox9 causes most of the things that make the male mouse form.

My question: Is it possible to make a Turner syndrome patient develop male characteristics by artificial stimulation? Has it ever been tried?


texts: Can Down syndrome occur without trisomy 21 in the karyotype of an individual? Or vice versa can a person have trisomy 21 while unaffected by Down syndrome?


texts: Would ovoviparous to viviparous mutation have been gradual? How would that work?

texts: It seems unlikely that an ovoviparous ancestor of mammals long ago could have had a viviparous offspring in a sharp one-generation dividing line, but what would be the gradual steps between egg birth and live birth? Are there any examples of answers to the first question today? It seems that marsupials are a different thing altogether, not something in between egg laying and live birth (no modern mammal's ancestors aren't believed to have marsupial-style birth in their evolutionary history, right?)?


texts:
I recently took a picture of this bird flying around Geneva, Switzerland:

In the beginning, and because it was bright and the subject was against the light, I though it was simply another Buteo buteo as there are many around here. Now by tweaking the brightness and contrast a bit in Lightroom, I can be 99% sure that it is not a Buteo buteo and my mind goes more to a Pernis apivorus, which is another bird of prey present in the region in summertime (May-Sep).

Can anyone tell me if I am correct and what field marks can be deduced from my picture to be sure that it is the right bird?


texts: How does the Golgi Apparatus perform its function?

texts: The Golgi Apparatus is an organelle with a great number of functions, I am particularly intrigued in the role it plays in packaging macromolecules and sending them to their target organelle or to leave the cell in exocytosis.  I would love to know more about how this process works.  How does the Golgi Apparatus recognise which molecules are which and how does the vesicle it places the molecule into navigate to where it is needed?


texts: In what forms do plants and animals excrete sulfur?

texts:
Sulfur is part of the amino acids cystein and methionin, plants take up sulfur in the form of $H_2S$. These organisms will also need a way to get rid of excess sulfur, how? In what compounds?
Judging by the smell of some farts, I guess $H_2SO_4$ plays a role, but I can't imagine that one get'S rid of all the sulfur this way.


texts:
Originally I was pondering about why we have the ability to breathe manually. I couldn't think of any tangible advantage, given that the body can develop mechanisms to regulate the rate of breathing when needed.

An uncited source (on reddit) said "any animal that can vocalise 'can' breathe manually." Is that true?

Secondly, do non vocal animals, for eg., some arthropods, not have any conscious control over their rate of breathing?


texts: The above is an insect I found while visiting Peru. I’m no biology expert, and I was just curious to know what species of insect this was. I found it on a rock while exploring the ruins near Pisac, if that helps.


texts: Non-nucleated cell-like population with RNA

texts:
We're working on invertebrate hemolymph (blood) and we have found with flow cytometry (staining with DRAQ5) a cell-like population without nucleus but it has RNA production.

Does anyone any experience with something similar? May anyone recommend any publication with something like that?

More information:

1) We don't know the real population size because we have identified it by flow cytometry, future experiments we wish to use TEM to characterize it better.

2) We know that this "population" produces RNA because we have extracted total RNA using low input RNA kit and run the result in Bioanalyzer.

3) We "know"/suspected this population doesn't have cell-nucleus because DRAQ5 is a DNA staining and this population is DRAQ5-. We wish study that by confocal microscopy ASAP.


texts:
Lately, lots of these little bugs have been lurking in my house in Italy. Should I worry?

I'm curious to know what they are.
For reference, the 2 cent Euro is 18.75 mm in diameter.


texts:
A couple of days ago, I answered this question over on worldbuilding.SE with some information about volvoxes, and commenter Liam Proven pointed out that one of the claims I made was dubious.

I had first read about the volvox in a book that described their basic biology and life cycle (the book may have been Flatterland by Ian Stewart, but I no longer have a copy to verify). One detail I vaguely remembered was that since volvoxes are essentially colonial organisms, individual cells do not immediately die when the volvox disintegrates, but rather some of these cells can rejoin the cytoplasmic matrix of other colonies, similar to sponges.

Now, I read this a long time ago, and my memory is admittedly foggy, and I never had any university-level training in biology. It's entirely possible I'm conflating this with something completely different I read elsewhere, so Liam's comment sent me searching for more info.  And even if I am remembering correctly what I had read, it's possible the original author was mistaken.

The best article I could find on the topic was Cytoplasmic Bridges in Volvox and Its Relatives by Hoops, Nishii, and Kirk, but it doesn't appear to support my recollection (it talks mostly about the inversion process in embryos).

So I thought I'd bring the question to a wider audience. Do individual volvox cells reintegrate after disintegration, or do the mother's cells simply die?


texts: Energy transfer from P680 to oxygen-evolving complex

texts:
This topic is confusing me.

As I understand it, in the PS2, photons are used to split water into molecular oxygen + protons and electrons in the oxygen-evolving complex. To do this, a photon is used to excite an electron in the P680, this electron is then released to go through the electron transport chain and somehow the oxygen-evolving complex gets energy from it to make water endure a "photochemical reaction" as described in my biology book.

But how the electron can transfer its energy to the oxygen-evolving complex if it went directly to the electron transport chain? how the energy produced in the P680 transported to the Oxygen-evolving complex?

I would appreciate simple terms as I'm still a college student.


texts: BLAST(Basic Local Alignment Search Tool) is heuristic?

texts: How can we say that BLAST is based on a heuristic algorithm, as after finding one common word in the query sequence and a database sequence it performs pairwise alignment by dynamic programming - which is an exhaustive algorithm? Also, BLAST provides quantitative analysis by giving bit scores and E-values. As it gives quantitative results, why do we say it is based on a "heuristic algorithm", such as 'word algorithm'?


texts: Solubility of thromboxane A2 agonist U-46619 in H2O

texts:
First of all, I'm not sure I can dissolve U-46619 in water so that's also part of the question.

If it is soluble in water, how much can I dissolve before saturation?

If not, what's the right solvent to dissolve this agonist?


texts:
I built a script to detect microsatellites in a FASTA file. However, there are thousands of possibilities.
So, my question is:

what are the markers of a "good" or "useful" microsatellite?
- How many base pairs, how many repetitions?

And, are there any other heuristics that can be run to further detect usefulness of the microsatellite?

thanks.


texts: Is there already discovered non-carbon form of life?

texts:
I have heard of some rumors going around about a living organism based on non-carbon. Is Has research been done with real form of life based on non-carbon? Or carbon-based life is only type of life what humans know of?

Carbon chauvinism


texts: What changes do ants make to the soil they use for building ant hills

texts:
I live in South India ,and among the many species of ants in and around our house, some of them except the weaver ants build the typical small ant hills in the garden.

I have examined the coarse sand like grains on the top of the ant hill. They are somehow modified and don't mix with normal soil or disintegrate in water.The region I live in has red soil.
A quick search on ant hills brings up information from here

The ant hill is a byproduct of ants building their colony. As ants dig their long and winding tunnels beneath the ground, the excess dirt and debris is carried out and placed near the colony entrance, creating the ant hill. At the top of the hill, there will be a small hole that serves as the entrance and exit to the colony.
Typically, an ant hill will be made from a combination of dirt, small rocks, pine needles, and whatever other materials were left over after the ants have dug their colony.

Other sites also state same facts on the composition of ant hills, but nowhere I can find any secretion or something which changes the properties of the ant hill soil.

So do they secrete enzymes or something or mix the soil with plant
debris to change the size of grains?
Does doing this confer some added protection to the ant colony living underground ?


texts: Does apoptosis occur more at a particular time of day?

texts:
I am interested to know if apoptosis (programmed cell death) occurs more frequently during daytime or nighttime hours, e.g. if apoptosis is associated with a circadian rhythm.

A simple search turned up a couple of articles:

Diurnal variations in the expression of radiation-induced apoptosis

The Circadian Clock Controls Sunburn Apoptosis and Erythema in Mouse Skin

However, I'm not sure how to interpret these and would appreciate the help of a biologist. I don't have a very good idea of the limitations of our investigative tools, or indeed whether my question is well-formed. Thank you!


texts: What type of epithelium are the pancreatic Islets of Langerhans?

texts: The human pancreas contains exocrine acinus cells (simple cuboidal epithelium) and Islets of Langerhans. Despite looking online I cannot identify what type of epithelium the Islets of Langerhans conform to (e.g., cuboidal, columnar, squamous). I'm confident it is not squamous due to the shape of the cells, but the distinction between cuboidal and columnar seems equivocal here.


texts: How can insects survive without an adaptive immune system?

texts: How can insects survive in a world full of pathogens that are able to defeat the innate immune system?


texts: What is the smallest number of amino acids required for life?

texts: Is there any hypothesis on the minimum number of amino acids required for life?


texts:
"Each gamete is genetically unique because the DNA of the parent cell is shuffled before the cell divides. This helps ensure that the new organisms formed as a result of sexual reproduction are also unique."

Then why do we say that the DNA of the parent influences the characteristics of the child while the DNA of the child is formed as a combination of shuffled up nitrogenous and phosphate bases?


texts: Why do viruses last longer on hard surfaces, like glass, than porous ones

texts:
All the papers I've read about survival of viruses outside of the host refer to longer survival times on hard surfaces without explaination. As a layman I would have thought that a virus (who's main environmental dangers are things like UV would survive better on rough or porous surfaces, where they are protected and can hide from the light and weather, not the other way round.

For example, one paper I read recently (although it's an old paper) showed Ebola virus surviving for 50 days on glass but not even 2 on rough materials. Can anyone enlighten me as to what it is about glass that makes such an ideal home for viruses to extend its lifespan by over 25 times?

More scientific papers would be helpful, but the medical community does seem to think that hard surfaces in general preserve viruses better than soft ones. The Mayo Clinic and UK NHS web sites both make that claim, without explanation.


texts: How related do life forms need to be to produce hybrids?

texts: Specifically, I'm asking about infertile hybrids like ligers, mules, camas, etc. How closely related do animals need to be?


texts:
What is the use of the spermaceti organ of the sperm whale?

One possible theory considered is that it was used for floating and going underwater by heating/cooling the oil. However, it is a lot easier for this to be done mechanically.

Another possibility is that it is comparable to a helmet to safeguard it when it collides with another whale. However, other animals have much simpler structures to deal with this problem.

A third possibility is that it uses it to stun its prey like squid. However, research in inconclusive on whether squids can hear or not. The link below, says that it is probable that squids can only hear upto 500 Hz which is not the frequency used by whales, thus this theory is probably false as well.

https://www.treehugger.com/natural-sciences/what-can-squid-hear-and-why-does-it-matter.html


texts: (Bioinformatics) Protein-Protein Software Prediction

texts: I'm trying to figure out Protein-Protein interaction of two proteins without known crystallography structures. Any way software can predict this without the known structure? The problem is most software that does it is just textmining through articles, I was seeing if they can do some sort of prediction based off of just known sequences and other trivial things?


texts: It is said that only about 1-5% of water used by plants is used in photosynthesis while the rest is transpired. Suppose that a plant grows in an environment where the temperature is not too high but humidity is very high, e.g. in the shadow of a forest. Would the plant grow faster if the humidity was lower? To what extent is the photosynthesis limited by reduced transpiration?


texts: Did I understand the definition of "gross primary production" correctly?

texts:
According to wikipedia

  Gross primary production (GPP) is the amount of chemical energy as biomass that primary producers create in a given amount of time.

So if a plant creates 6g of biomass in 1 second for example, then the amount of chemical energy stored in the 6g increase in weight is the GPP?


texts: Is carbohydrate an important part of phospholipid?

texts:
My professor tells us that carbohydrate is an important part of phospholipid, but phospholipid is composed of Choline, Phosphate, Glycerol and two Fattyacid, and I don't think even one of them is carbohydrate.

What's wrong with my statements?


texts: Possible combinations in the Meiosis' Telophase 1

texts:
As you might already know

  Meiosis is the process in eukaryotic, sexually-reproducing animals that reduces the number of chromosomes in a cell before reproduction $^{[1]}$

One of the reasons why meiosis has been so important in evolution is variation.

As my teacher used to say: Nature rolls the dice... - It's the magic of genetics; two completely different persons might share the same parents.

So here the question:

Suppose we have a cell with four chromosomes (two couples of homologous chromosomes) in the Prophase 1. I've drawn all possible combinations that could happen - these are chosen randomly - in the Telophase 1.

  Is there a genetic disorder (not only regarding humans), in which the four initial chromosomes are split, in the Telophase, into two parts, each of them containing a couple of homologous chromosomes. I.e. (referring to the image) is the combination $(\color{red}{red}+\color{blue}{blue})(\color{green}{green}+black)$ in the Telophase 1 possible?

$$$$
$^{[1]}$ Quote from https://biologydictionary.net/meiosis/