texts: Does the arrangement of amino acids in a protein matter for nutrition?

texts:
Let's say there are two diets, consisting of entirely different proteins. If you split up all of the proteins from one day of each diet, you'll get the same set of amino acids and the same count of each. Assume everything else about the diets is the same.

Would these diets have the same effect on the protein composition in your body? Different polypeptides, but overall the monomers are identical. Does your body break down proteins entirely, or will it reuse some chains of amino acids?


texts: Can one become addicted to tea like coffee addicts or smokers? I heard there are some common substances in tea and coffee, do they cause addiction?


texts: Confusion regarding the Kir2.1 inward-rectifying potassium channel

texts:
I was trying to find out more about gustation and the transduction of sourness when I came across the supposed inward-rectifying potassium channel $\ce{K+_{ir} 2.1}$. Here's the thing, despite being inward rectifying, all the articles I read about it involves it sending potassium ions out of the cell. I thought that maybe there is a special mechanism that makes it outward-rectifying, or just switches off its mechanism for inward rectification but to no avail.
So here's the context: On taste buds that detect $\ce{H+}$ ions, when intracellular pH rises due to intake of protons, potassium channels will be closed which causes accumulation of $\ce{K+}$ and thus depolarisation. The article pinpoints $\ce{K+_{ir} 2.1}$ as one of the potassium channels involved, saying that its inhibition will allow for depolarisation. This doesn't make sense to me, if this channel is supposed to prefer intake of potassium ions and almost entirely prohibit outward flow. If we want to accumulate potassium in the cell, shouldn't this channel be left open?
The only thing I can think of is that this channel remains open at membrane potentials near that of resting potential. So maybe then there is no selectivity over which direction the ions travel, so there is a net outward flow?
I'll link some of the articles I mentioned below:
The K+ channel KIR2.1 functions in tandem with proton influx to mediate sour taste transduction
Inhibition of Kir2.1 channel-induced depolarization promotes cell biological activity and differentiation by modulating autophagy in late endothelial progenitor cells.


texts: How many consecutive cell divisions are required to form the adult human body from the single cell zygote?

texts: The preferred question would have been what is the total number of cells in a full term human foetus and how many cell divisions are required to reach that number. However estimates of total cell numbers in foetus could not be found. From the abstract of the July 5, 2013 article published in Annals of Human Biology, the adult human body consists of approximately $3.72 \times 10^{13}$ cells (37.2 Trillion). The question is: what would be the approximate number of cell divisions required to reach that number (Ignoring the fact that different tissues may reach full differentiation at different times)?


texts: Where can I find an image of the gut/anatomy of the mealworm?

texts: Specifically, I'm a student working on an experiment involving the dissection of the mealworm (Tenebrio molitor) but for the life of me, I can't seem to find an image anywhere on the internet. Speaking to Carolina.com also got me no results. We're looking to dissect the mealworm and extract its gut/GI tract. However, at the moment it seems like we're going in blind. Is there anyone out there who can provide some insight?


texts: Is there a difference between any of these terms for proteins: "crystal structure," "NMR structure," "solution structure," and "complex structure"?

texts: My homework wants me to plot all crystal structures determined per year, but when I search on PDB for all structures, many of the articles say "crystal structure," but some say "solution structure" or even "complex structure." Are all of these considered to be subsets of "crystal structure"?


texts:
If the "primordial soup" theory of abiogenesis is to be believed, self-reproducing organisms spontaneously arose on Earth at least 3.5 billion years ago, surprisingly soon after the Earth cooled down enough to potentially harbor life.

It may never have happened again, however, since all lifeforms on Earth today are similar on a molecular level (DNA), suggesting a common origin.

This appears to imply at least one of the following:

Immediately after the first spontaneous abiogenesis, environmental conditions on Earth changed dramatically, making a repeat impossible.
The first organisms that arose consumed any subsequent organisms that came into being. This was suggested by Alexander Oparin, but I find it very difficult to believe since it would have to happen everywhere on Earth. Also, most single-celled organisms found today do not consume other organisms, and even where they do that does not usually lead to their complete extinction.
The common origin theory is in fact false, despite the similarities between organisms, and abiogenesis did occur multiple times in the same way.
Abiogenesis happened more than once, but only the descendants of one occurrence survived till today.
Spontaneous abiogenesis never occurred on Earth after all because the conditions never allowed it; instead, a proto-organism arrived on Earth from a planet where the conditions do (Panspermia).
The standard theory of geological history is wrong (i.e. the Earth was in a "fertile" state for much longer before the eventual origin of life than commonly thought, due to some unknown mechanism causing radiometric dating to give wrong results).

None of these seem likely to me, yet even less likely I find the idea that life arose spontaneously almost immediately (within a few hundred million years, possibly even faster) after the Earth's crust solidified, and never again afterwards.

What are the currently held theories on that matter? Can poeple provide references to relevant publications.


texts: Why can't plasma proteins migrate from capillaries?

texts: Why can't plasma proteins shift from capillaries to connective tissue but WBCs can be very rich in connective tissue even though obviously the WBCs had to go through capillaries.  Another example: in alveolar sacs neutrophils are there in the lumen  despite the presence of epithelia of alveolar sacs,  and it can only reach there via capillaries. So, how can they get into lumen despite the epithelia lining? Histology textbooks say that no plasma proteins can enter or leave capillaries, but WBCs (which are much larger than proteins) can move to connective tissue via capillaries?


texts: Why are vegetations in Infective endocarditis common on the atrial side?

texts:
Robbin's Pathology says that vegetations of IE are more common on the atrial side in AV valves. In Liebmann Sack's Endocarditis, which is a sterile (non bacterial) type of endocarditis, the underside of the valve also has vegetations. Why is it so? If its just colonization of bacteria in IE, how does it matter where?

Does gravity matter in colonisation of bacteria!! ?


texts: I have tried reading about development of vitreous humor but it is all very confusing. When does it first developed ? Does it renew itself ? Please provide reliable sources..


texts:
I read in Tortora and Derrickson that goitre is associated with euthyrodism.

How is that possible?


texts: Insect Identification (badly damaged corpse)

texts:
The photo is of the insect in question in a strainer. The body of the insect is just over half an inch long. I see a separated wing cover and leg in the photo as well.

My location is New Hampshire, USA. Given that it is February (middle of winter), I don't think it was sourced locally.

I believe that this came from a packaged item that would have been sealed in San Diego, CA or possibly in Asheville, NC. The packaging likely occurred no earlier than June or July of last year. The packaging would have occurred indoors in a manufacturing-type setting.

After coming out of the packaging, this individual was submerged in liquid on a stir plate for 36 hours, so it took quite a beating.


texts: What would the resulting karyotype be if someone with Klinefelter syndrome fertilized an "empty" egg?

texts:
Endoreduplication: is a form of nuclear polyploidization that results in multiple, uniform copies of chromosomes. This process is common in plants and animals, especially in tissues with high metabolic activity, and it generally occurs in cells that are terminally differentiated.
  Investigating the hows and whys of DNA endoreduplication. - Larkins, et. al.

What would be the karyotype of the sex chromosomes of a complete hydatidiform mole that was the result of a sperm (monospermy) of someone with Klinefelter syndrome (47,XXY) fertilizing an "empty" female egg?

I know that in a situation without Klinefelter syndrome the sperm inside the egg would double all it's chromosomes by endoreduplication (since the mother's chromosomes are all missing), but in this situation there would not be a need to double the sex chromosomes if the sperm already contains "XX" or "XY" (Since Klinefelter syndrome has 4 possibilities for a sperm : Y, X, XY, XX).

Or would it be that the cell doubles every chromosome if there are too many missing?


texts: Nomenclature of enzymes involved in synthesis of glutamine

texts:
I am considering nitrogen fixation and in my lecture notes, there is the statement

  The glutamine synthetase- glutamate synthase system requires use of an ATP molecule as well as reducing power. Although it is energy intensive compared with glutamine synthase, the Km of glutamine synthetase is much lower than that of glutamate dehydrogenase. When NH3 is scarce, the additional ATP investment is worthwhile.

Try as I might, I can't find anything about glutamine synthase. Searches online seem to only return results for glutamine synthetase. I was wondering if this is a mistake in my notes? If so, I can only think that this should be 'glutamate dehydrogenase', in which case the statement is about comparing the method used by animals and fungi (which use glutamate dehydrogenase to fix nitrogen via a Schiff base) compared with plants and other microorganisms  (which use the glutamine synthetase glutamate synthase method).

This is my first exposure to learning about nitrogen fixation, so I would very much are coated any clarification.

Also, I was wondering what the general difference is between a 'synthase' enzyme and 'synthetase', if there is one.


texts: I'm trying to understand how does  DNA methylation and histone methylation status of promoters differs given their position in a gene? Does position affect whether they are repressive or activating?


texts: How are 23 chromosomes in human sperm chosen?

texts:
I'm not biologist and I have just a basic knowledge. I've been thinking for a long time about the following question: How does the body choose which 23 chromosomes should be active in human sperm and female eggs?

Thanks in advance for helping me with this!

Edit:
Each egg cell or sperm contains 23 chromosome whereas a normal cell has 46 chromosomes. So How is it that those specific 23 chromosomes are the chosen ones. Are a random collection of chromosomes selected at the end of meiosis or is it more specific than that?


texts: What is the difference between a human being, a Homo sapiens, and a Neanderthal?

texts: I know that the Neanderthals were part of the genus Homo. How do they relate to other members of the genus, such as Homo sapiens?


texts: Where do the phosphate units come from when EGF units dimerize?

texts: Upon EGF binding, EGFR units dimerize and cross-phosphorylate. The phosphate groups are transfered to intracellular c-terminal tyrosine rich regions. Where do the phosphate units come from in this cross-reaction? Is it from bound GTP units?


texts: Do telomeres appear at just one end of the chromosome?

texts:
I have just studied DNA Replication for my Biology Class and I have this question that leaves me stuck, though I have tried to figure it out myself.

During telomere replication, I am aware Telomerase elongates the 3' end of the template strand on both molecules and then DNA repair Polymerase comes in to fill in the gap that could not be previously synthesised after the last primer.
After this is complete, we would have the T-loop formation and Shelterin complex arrangement to protect these ends and form what we know as telomeres. However, if we take both DNA molecules, this only happens at one end of each of them, right? As the other end would correspond to the leading strand.

So I am confused: do telomeres just appear at one end of the chromosome?


texts: Electron Transport Chain in Mitochondria

texts: I was researching cellular respiration, and this is a rather confusing part. I need help understanding the purpose of Complex II and how the ATP Synthase generates the energy to turn ADP to ATP.


texts:
First off, my specific query: When depicting a spider - be it in a picture or in textual/verbal description - should the chelicerae be always be placed so that they project outwards from the ventral side of the cephalothorax's anteriormost part, like in this diagram? Or are there other possibilities (e.g. attached by their basal undersides to the front of the cephalothorax) that are still anatomically correct?

Second, a more general inquiry: Are there any common pitfalls in depiction of spider anatomy that I should be aware of?


texts: Is the start codon regarded as part of the UTR (untranslated region)?

texts:
The Wikipedia entry for Gene contains the statement:

  The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator and start and stop codons.

But the page on the Start codon says:

  The start codon is often preceded by a 5' untranslated region (5' UTR)

So is the start codon a part of the UTR?


texts:
Background

  Linking number: the linking number represents the number of times that
  each curve winds around the other.
  Twist, called "twist", refers to the number of Watson-Crick twists in the
  chromosome when it is not constrained to lie in a plane

 I read these explanations on Wikipedia and I understand the concept of this (supercoils have to form to compensate the "tension" etc..) however I'm not able to discriminate between these terms while looking at a picture.

   (source)

Based on the formula I can easily calculate the twists in the right image. But I'm searching for a way to see/count the twists.

Question
What is the difference between the linking number and the twists (not from a formula perspective)?


texts: Why does it take many sperm for one sperm to fertilize an egg?

texts:
Hundreds of acrosomes must undergo exocytosis to digest holes in the zona pellucida. This is one case that does not bear out the adage, “The early bird catches the worm.” A sperm that comes along later, after hundreds of sperm have undergone acrosomal reactions to expose the oocyte membrane, is in the best position to be the fertilizing sperm.

—Human Anatomy and Physiology, 9th edition (Marieb)

I’m having trouble understanding why this would be the case—the last sentence, that is. Perhaps it does take a lot of sperm to break through the zona pellucida, but why would any sperm that comes after have an advantage? Do the sperm cells die after the acrosomal reaction? If not, can’t the first few sperm cells be the ones in best position to attach to the oocyte’s receptors once the zona pellucida has been penetrated with the help of other acrosomes from other sperm?

Moreover, are the acrosomal enzymes degraded? Why would there be a need to have so many acrosomes if the enzymes can continue working through the zona pellucida? All you would need is time and soon the zona pellucida would be broken down, even just by a low number of enzymes, would it not?


texts: Why do ribosomes associate with rough endoplasmic reticulum but not other membranes?

texts: As far as I am aware, all eukaryotic membranes consist of a lipid bilayer. Smooth endoplasmic reticulum (ER) and rough ER are distinguished by the presence of ribosome on the rough ER surface, but are apparently otherwise similar. So what causes ribosomes to associate with the membrane of rough ER but not that of smooth ER. Or do ribosomes convert smooth ER to rough ER by binding to their membranes?


texts: What constitutes the determination of a normal blood glucose level?

texts:
Several on-line resources (e.g. MedlinePlus) suggest:

Normal range for non-diabetic people who are fasting should range between: 70 and 100 milligrams per deciliter (mg/dL)

Non-diabetic people who are not fasting should have a blood glucose level below 125 mg/dL

What I am interested in however, is the coverage interval of the population that was used to determine these 'normal' values.

Also are there differences based on age, sex or any other factors.


texts: Where do transamination and deamination take place?

texts:
The only information I know is about deamination is that it occurs in the liver and kidney. But in which part of the cell does deamination occur? To which tissues is transamination specific, and in which part of the cell does it occur?

I have searched Google and Google books and have come across some information like L-Glutamate dehydrogenase occurs in both cytoplasm and mitochondria and transamination occurs in the cytoplasm of all cells. But they were not from authentic sources, so I am asking it here.


texts: Identify this insect seen in a rural area in North India

texts:
During my stay at a village in Haryana, India, I noticed many of these grey-brown insects in my room. They spend most of their time crawling but occasionally fly too (for short distances—one metre to a few metres). Here are some photographs—the spacing between the ruled lines is about 7 mm:

I am curious to know what species they are. Any help would be appreciated.


texts:
I'm a physicist by training am looking to learn more about the biophysics of plants.

Can you give me your recommendation of good resources on plant biophysics? Books are preferred.


texts:
From wiki:

  Human accelerated region 1 (HAR1) is a segment of the human genome found on the long arm of chromosome 20. It is a Human accelerated region. [..] These 49 regions represent parts of the human genome that differ significantly from highly conserved regions of our closest [living relatives, the chimpanzees] in terms of evolution.

What could explain those differences?

A back of the envelope computation shows that in the course of 8mio years, at a rate of 64 mutations per generation, one can expect 1% of mutated basepairs. Indeed, the HAR1 of length 106 bp has 1.08 substitutions in the chimp. But humans have 13.93. (Data: see the table in this article.)


texts: Do people even notice when insects other than butterflies and beetles go extinct?

texts:
Lists of endangered animals only include beetles and butterflies if they bother to mention insects at all. Here is an example from where I live:

http://www.dec.ny.gov/animals/7494.html

All of the insects are beetles, dragonflies, moths, butterflies and there is a mayfly, but that is kind of similar to a butterfly when it comes to their "fanbases." Where are the ants, lice, silverfish and aphids? Is there a better list?


texts:
For how long can a human sustain a temperature of 180 degrees Fahrenheit (82oC) without damage in a confined place?

For instance, suppose a person is sitting in a steam-filled room, without external air flow (but with enough oxygen) - how long could one resist the heat before permanent physical damage would occur?


texts:
Does trp repressor form a tetramer or a dimer before it binds to its corepressor tryptophan?
I've been reading BIOS Molecular biology it says that it is a dimer

  The repressor is a dimer of two subunits that have structural similarity to the CAP protein and lac repressor.

but according to wikipedia it is tetramer. What is correct?


texts: neural genes expressed in nasopharyngeal specimens

texts: Is it possible in a nasopharyngeal specimen genes of neural system to be expressed? For example, genes about neural differentiation?


texts:
I was going through this webpage and I found the following lines:

  We hypothesised that despite unimodal distribution of CD4 co-receptor on naïve CD4 T cells they are not homogenous in their function.By testing naïve CD4 population from mice and humans expressing highest and lowest (~10%) levels of CD4 in a variety of functional assays we find that indeed naïve CD4 cells with high CD4 levels respond much better to activation and survive more easily post-activation.

Now what does "CD4 level" means? How is the CD4 receptors distribution obtained? With repect to the value of which feature is it obtained?(If you are not able to understand the last question, let me know, I will try to explain more in details)


texts: Effect of extremely hard water on marine life?

texts: When researching water quality standards, I found that a minimum and maximum was set for water hardness. Several sources also state that water can in fact be too hard. The question is how does hard water harm marine life? I understand that it is required to reduce the toxicity of Hydrogen ions and other trace metals, but cannot find anything concerning the effect of water that is too hard.


texts: Pyruvate as a final electron acceptor in the electron transport chain

texts:
During anaerobic respiration, why are electrons carried by NADH not transferred to the electron transport chain (ETC)? What happens is that lactate dehydrogenase reduces pyruvate to lactate, while removing H+ from NADH to form NAD+.

Why doesn’t pyruvate simply take the place of O2 as the final electron acceptor in the ETC during oxidative phosphorylation? Electrons would still be able to flow through the ETC and allow for the regeneration of NAD+, wouldn't they?


texts: How are the first mammary glands thought to have functioned?

texts:
I happened upon a book (not about biology) containing this text:

  A life-changing birth occurred on the planet about 190 million years ago [...] the first tiny shrew like creature brought forth an infant and began suckling her young. [...] this furry little mammal embodied a huge leap in biological evolution

The description is nicely dramatic, but it doesn't ring true for me. While I know that evolution likely wasn't as gradual as high school books represent it, the thought that a non-mammal bore a daughter with fully functional mammary glands who actively suckled her young is a bit too much for me to swallow. For other body systems, I have read stories how they emerged gradually, for example the oldest species having a few nerve cells, then new ones having a whole nervous "network" with a few ganglions, before actual brains emerged. Or similarly, worms having a patch of photosensitive cells on the skin evolved into animals with eyes. I know that platypuses have mammary glands without nipples, but presumably even they are already much more sophisticated than the first mammary glands.

So what are proto-mammary glands thought to have been like? Did they evolve de novo especially for feeding babies, or were they maybe repurposed sweat glands or something like that? What are they supposed to have functioned like?


texts:
Found this insect in São Paulo/Brazil. Its length is ~2cm

Any help to identify this insect would be appreciated.

Also see my video


texts: Infant tissues, organs, body parts or reflexes in an adult organism

texts: What is the phenomenon, when a normal useful tissue, organ, body part or an inborn reflex or instinct existed in the infant organism and normally should disappear or at least completely lose its function in the adult organism but it won't? Atavism and vestigiality don't seem the right terms. Is there a specific word that refers to the phenomenon?


texts: Hypothetically, what is the smallest functional form of human?

texts:
Since the my first encounter with doraemon manga, I've been wondering many things, one of them is the small light.

Assuming we had an instrument, such as small light, which enabled people to grow and shrink as they wanted to, what would be the smallest and the most compact functional form of a person?

First, I can rule out that we couldn't be as small as an atom because we couldn't be function as human being if we were compressed into 1 atom. So did 1 molecule. and so did 1 cell.

Second, you need more than 1 cell to construct organs, i.e. I couldn't imagine an eye which consists only several atoms or molecules.

Therefore, there should be a limit to the the size of human organs in order to fully retain their functions and thence, there should also be a limit to the minimum size of human organs.

What are the limits of size of each of human organs?

What are the limits of size of human then?


texts: What advantage does the pseudostratified epithelial structure type provide over squamous, cuboidal, and columnar?

texts:
I'm currently and have had difficulty receiving an answer about the role the pseudostratified columnar structure provides.

I understand that that the following have their respective advantages:

Cuboidal: Very tight cell junction
Columnar: Increased Surface Area relative to volume
Squamous: Allows easy passage for materials across

In the tissue we observed from a trachea, the ciliated pseudostratified columnar was responsible for the movement of material across its surface, however it seemed that the cilia provided that, not the structure.

Why not have ciliated columnar tissue? What does pseudostratified bring to the table?


texts: Identification of species found in fly lab

texts:
I just found this in my Drosophila lab (within a closed vial) - unfortunately it was dead having been frozen for two weeks. Can anyone help id what it is, and whether it poses a risk to my flies (like mites do)? My inclination is that it is some kind of (moth?) larvae. Note the awesome corkscrew tail...

Found in Uppsala, Sweden, May 2014 in a vial of Drosophila with food (a yeast, sugar, and agar mix). Length is about 3-4mm excl. tail.


texts: is there an easy way to remember taxonomy?

texts:
So I have trouble remembering the order of taxonomy for classification.
i.e domain>kingdom>phylum>class>order>family>genus>species

I can never remember it, is there an good mnemonic to remember them? How do you guys remember it?


texts: Is there a measurable variance in neuronal transmission speed and fidelity?

texts:
My understanding of how neurons transmit signals is pretty basic - dendrites receive signals (both excitatory and inhibitory), transmitting them to the cell body where, if a sufficient depolarization builds up, the axon fires an action potential, sending the signal along. This entire process is carried out by various ion channels, especially voltage gated ones. My question is this - do we know how sensitive the speed and reliability of the process are to genetic variations that control how these ion channels are built? Is it robust enough to permit small variations, or is any change catastrophic? If it permits small variations, do we know how variable the human population is for features like signal fidelity (low rate for failing to fire when the neuron should, and low rate for firing in the absence of stimulus) and transmission speed?

Considering the difficulty of studying humans, is this sort of information known for mice, rats, primates, or etc?


texts: I found it in my computer but I don't know what it is


texts: What are the key differences in giant and large unilamellar vesicle preparation processes?

texts:
I have to study my peptide's folding on membrane mimetic (model membrane) by circular dichroism spectra. Now I'm looking for suitable methods for preparation of vesicles: LUV, SUV, GUV- large, small and giant unilamellar vesicles.

I have studied several methods but I am having a hard time grasping the key factors that affect the resulting vesicle size (LUV, SUV, GUV, etc.)

Any pointers are greatly appreciated.


texts: Does using animal models for medical research also promote veterinary research on these animal types?

texts:
I have been reading about mouse models for studying inflammatory bowel diseases such as Crohn's disease and Ulverative Colitis. For example, according to this publication, a widely used mouse model for colitis is the Dextran Sulfate Sodium (DSS)-Induced Colitis.

This got me thinking: when we induce disease in mice (or monkeys, fish etc.), is that somehow beneficial for veterinary research of these animals when they get sick (unrelated to medical research focusing on humans)? Are the data from pre-clinical trials used for that purpose in any way?


texts: Does cataract condition cause red film when sun is shining?

texts:
Since two years ago I have a red film in my field of vision when the sunlight (or a white spot) is at the border (or even lightly behind) of the vision field, the red color is especially obvious at the shadows or dark places (it seems logical that the film color is more visible where there is less light).
My eye doctor recently diagnosed a little bit opalescence of my eyes, that is, a beginning cataract.

So my question is simple : does cataract condition cause a red film when sun is shining at the vision field border ?

I have an explanation for this : at the eye border the white sun light goes trough the skin and is colored red by the blood, then because of opalescence the red light propagates into the whole vision field, thus creating a red film. So if this explanation is correct then any people with a cataract condition should see a red film in such situation, that is what I want to check. Should be quite simple.

(Without strong spots there is still a mild gray film, making black appearing grayish and making shades differences less obvious to see than before this condition. Vision tests on green or red background doesn't make any differences)


texts: What Does Transcription Factor E25 Activate When a Cell is Transitioning from G1 to S

texts:
Cyclin D/ CDK4 phosphorylates Rb allowing for the activation of transcription factor E25 during the G1 phase of the cell cycle. Supposedly, this transcription factor then activates as set of genes helping the cell to enter the S phase.

My question is what genes do E25 exactly activate? Are there any associated pathways with these genes involved in transitioning the cell from G1 to S?


texts: Online multiple sequence alignment with constraints

texts:
This is probably a naive question.

I have accesssed the Clustal Omega online multiple sequence alignment tool at http://www.ebi.ac.uk/Tools/msa/clustalo/ for the first time, but I think I need to provide more input to get it to do what I want, by specifying more constraints.

Edited to clarify constraints:

The original sequence P sequence has four symbols, say A,B,C,D.

The algorithm has access to 4 derived sequences.

P1: all occurrences of A,B deleted, no other change

P2: all occurrences of A,D deleted, no other change

P3: all occurrences of C,D deleted, no other change

P4: all occurrences of B,C deleted, no other change

Goal: given P1,P2,P3,P4, recover P

Example

P:
ABACCADDACBBC

P1
CCDDCC

P2
BCCCBBC

P3
ABAAABB

P4
AAADDA

Note that I have removed the under bars by which I had tried to indicate deleted symbols but since the deletion processes for the Pi are deterministic they can be supplied to Clustal or whichever tool is appropriate.

End of edit

Toy madeup example illustrating my input, the output, and the problem.

The actual sequence from which these sequences came after deletions, followed by the resulting sequences is as below:

p  ABACBAC

p1 A_AC_A_

p2 _BA__AC

p3 __ACBA_

so I input

>p1
AACA
>p2
BAAC
>p3
ACBA

and got the output

p1 _AACA_
p2 BAAC__
p3 __ACBA
      **

Which is entirely reasonable, but I have constraints.

I want to align with the constraints that

for certain symbols matches between certain sequence pairs should be maximized, and
for certain symbols mismatches between certain sequence pairs are allowed

In fact given p1,p2,p3,p4, which all arose from p after deletions, there are the pairwise constraints

A should be a match between p3 and p4 (it never appears in p1 or p2)
B should be a match between p2 and p3 (it never appears in p1 or p4)
C should be a match between p1 and p2 (it never appears in p3 or p4)
D should be a match between p1 and p4 (it never appears in p2 or p3)

This means that p1 has only C,D; p2 has only B,C; p3 has only A,B; and p4 has only A,D characters after deletion.

I want to obtain the most likely alignment or a few most likely alignments of p1,p2,p3,p4 under these constraints.

I have looked to see if I could figure out how to input the constraints but no luck.

Should I have used another tool? In general I will have much longer sequences, typically 4 of them, with pairwise agree/disagree constraints, as stated above.


texts:
Hormone levels in humans decrease with age. The effects are especially detrimental for women after menopause.
Biologists state that turtles do not exhibit most of the phenomena related to aging. For example telemore shortening does not happen in certain turtle species.
Here is my question:
Do turtle hormone levels decrease with age as in humans?


texts: What exactly is the time constant of an ion channel gating?

texts:
Let's take a channel that does not get inactivated, but is only in open and closed states. I understand what m (activation variable) represents. It's the fraction of the gates open.

But what does $\tau$ (tau) , the time constant represent? Does it mean the time taken to open the gate? If tau is higher then it mean more time taken to open the gate?

I'm slightly confused.


texts: Trying to understand the big picture behind DNA sequencing, alignment and searching

texts:
I'm about to start a bioinformatics research project but I haven't any biological background.

I know my project is in regards to a performance analysis of DNA sequencing and searching "weapons" like Hadoop, Apache Spark and Apache Flink - so I've spent the last couple of days trying to put together the "DNA picture" before I get started with the programming stuff.

My understanding of the situation is that:

Next-generation sequencing (NGS) techniques are used to efficiently provide reads of DNA (conversions from real, physical DNA to something that can be read and analysed), however today's most practical methods provide reads that are short and in disorder.
Reads tell us which nucleotides, labeled one of ACGT, occur in sequence. Different nucleotides or values to take their place may exist, like N or X. Reads could range from 50 to 1000s of nucleotides in length depending on the method of sequencing.
You can find historical raw read data in various places online, including the Sequence Read Archive (SRA). The same website contains lots of other DNA/bio related information. Reads are commonly stored in .fasta files which follow a simple and practical standard. A single file could contain a very small or very large read or sequence.
Reads are then provided to DNA alignment programs like bowtie which will place them back in the correct order. The algorithms could use a template sequence to align them, or run "de novo" (without a template). The result of these alignments have also been indexed online however for the purpose of my studies I'll probably be aligning them myself.
Once aligned (or maybe during alignment), nucleotide differences from a template sequence can be programmatically found or searched for, with crossbow for instance. Note that many other tasks can too be performed - not only this search. If a particular substitution occurs in more than 1% of a what I think is called a "genome's" population, then it is called a Single-nucleotide Polymorphism (SNP or snip). Most SNPs have two alleles, or two different recorded nucleotides (like either G or C), but more than two is possible.
SNPs can be studied and mapped to various conditions or characteristics. A particular nucleotide could be responsible for part of one's emotional tendencies, reaction to particular medicines, or maybe anything, so a particular SNP could make a big difference.

What am I missing/what did I get wrong?


texts: Do the left half and right halves of the diaphragm undergo the same displacement during breathing?

texts: Do the left half and right halves of the diaphragm of a normal person move exactly the same distance between inhaling and exhaling?


texts:
What is the composition of the liquid that comes out of a raw mango when you break it off from its stem? It oozes out some sort of juicy liquid. Any idea what that is?

Also, is it edible?


texts: Does natural selection still increase biological complexity?

texts:
I recently read The Selfish Gene by Richard Dawkins, which I found very interesting. In one of the last chapters, he gives multiple possible explanations to the question "Why did natural selection give rise to complicated lifeforms?".

Since complex (say: multi celled) life exists, that means natural selection at some point did increase complexity, as we went from the primal soup to multi celled organisms (with many steps in between). My question is whether this trend of increasing complexity is still going on? Is natural selection a never-ending arms race, tending towards increasingly complicated genomes? Or did natural selection reach some plateau, local optimum, of biological complexity, after which the only evolution taking place is "on the same level".

I have thought a bit about a metric for complexity, but since I have no background in biology I am not at all certain. At first thought, the length of the genome sounds like a promising candidate, but the phenomenon of freeloading, not-functioning DNA (conveniently described in The Selfish Gene too) undermines this. I hope it is clear what I mean by "complexity".

Thanks for answers in advance, it has been fun speculating.


texts:
I found several of these worms falling from the upper part of a mosquito net framed in a window while opening/closing it after several months of inactivity. Location: big city in Southern Europe.
Any idea what they are?
I'll add better pictures, should any more of them fall down.


texts:
What is the difference between narrow sense heritability and broad sense heritability?
Does heritability in the broad sense refer to the degree of genetic determination?
Heritability in the narrow sense refers to additive effect of alleles , what does it actually mean?


texts: Can someone help me identify this spider? Saw it in Malawi; aprox. 5 to 6 cm. Seems like a Solifugae but I cannot go any further... I thank you in advance!


texts: Is there a method to isolate half of the chromosomes of a cell?

texts: Each cell has 2N number of chromosomes, I wonder if currently there is a technique allows isolation of N number of chromosomes out ?


texts: What is a Mitochondrial Eve and Y-chromosomal Adam

texts:
I've read this question:
What kind of event would cause the current Mitochondrial Eve to be replaced by a new one?

And the values in Wikipedia about Mitochondrial Eve and Y-chromosomal Adam and I am not sure I understand the concept behind them.

When talking about a maternal unbroken linage and a paternal unbroken linage, is the meaning that Mitochondrial Eve had a linage of only women reaching every person today, and the same with Y-chromosomal Adam and men? So that other humans that lived in their age, didn't have an unbroken line of linage consisting of only same sex descendants?

How is the specific "identity" or time period of those persons is known, assuming that researchers didn't check the Mitochondrial DNA or Y-chromosome of every single living human being today, how can they know for sure that there aren't some tribes in the Amazons, which have a direct female linage to Mitochondrial Eve's sister?


texts:
Saw this equation in the conext of epidemiological genetics:

I have never seen it before and I don't know what variable it represents. Help?


texts: What is the advantage of having multiple pathways to activate complement?

texts: We all know there are three pathways to activate complement: classical pathway, lectin pathway and alternative pathway. What is the advantage of having multiple pathways?


texts:
What's the distinction between a tetrad and a synaptonemal complex in meiosis?  Are they synonyms?

I ask because the concepts seem very closely related, but it seems like there may be a subtle distinction.  Unfortunately, none of the sources I've been consulting use both terms.


texts: To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)

texts:
I have to answer a question about a sub-task of my thesis: Can the bacteria X produce the protein Y?

I searched of course Google and BLAST. There is no data supporting that this specific bacteria ever produced this protein sequence.

However, my thesis supervisor wants me to go deeper[1], but I don't know how to do it in silico in a way to offer a proper answer.

What I'm thinking of doing with the data at hand is to create a DB on localhost with all the versions of the protein listed in BLAST (I'm using ruby, not sure how can I fetch all this data in FASTA format yet, but I'll figure it out), and all the strains of the bacteria listed in BLAST and perform a fuzzy string matching.

That's like brute-forcing. After I have a possible score I can get the closest score of them all, study it a bit and then submit my answer.

Is there any other way to attack this problem in order to submit a proper, at least partially polished answer?

NOTE: I don't have access to any lab, any experiment must be performed in silico.

[1] My supervisor believes that IF this bacteria needed this protein it WOULD be able to to produce it at will without undergoing mutations. And since his level of dedication and knowledge revolving molecular biology is scary, it's kind of hard to believe that he is wrong.


texts: How does it make thermodynamic sense for photosynthesizers to turn CO₂ into O₂?

texts:
My understanding is that animal metabolism consists of exothermic reactions like

$$\ce{C6H12O6 + 6 O2  ->6 CO2 + 6 H2O + energy}$$

This makes thermodynamic sense to me. Animals need an exothermic reaction to produce the energy we need to move around, etc. However, the other half of the picture, plants and other photosynthesizers producing oxygen, has never made complete sense to me. Are plants consuming $\ce{CO2}$, a "low energy" (I think) substance, and producing higher energy $\ce{O2}$ as a waste product? Is there so much energy available for photosynthesis that plants can afford to waste some of it producing $\ce{O2}$ simply to have enough carbon atoms to store energy via sugars?


texts: Why is a butterfly actively looking for cool, dark spot, long before dark?

texts:
Here in Croatia, the Woodland grayling Hipparchia fagi flies constantly in the garden of my holiday home.
Yesterday, I observed that one of these bufferflies was actively looking for a cool/dark spot around 6 pm. First it hid at a wall in a shaded corner behind a bush. During the day these butterflies are very alert, but this specimen could be approached to a few cm. Finally it flew away, to take refuge inside the house, even more cool and dark. Again, it didn't move until I blew it away (couldn't lock it in, could I).

Now, my question is why this butterfly behaved like this.

I am convinced it did not seek shelter from the heat, because they keep flying during the hottest part of the day.

Was it already looking for a place to spend the night? That seems rather early. At 6 pm, the sun is going down a bit, but temperature is still around 30 degrees and it won't be dark for 3 or 4 hours. Other butterflies like Iphiclides podalirius are still active. Or has H. fagi a higher heat demand than other species? That seems inconsistent with its habitat (woodland). Any thoughts?


texts: How does a change in the potential across a neuron's membrane get turned into a signal that is sent down the axon?

texts:
I understand

How a signal is propagated down the axon.
How the membrane potential of a neuron changes during the course of it's "firing".

But I don't understand how physically the change in the membrane potential actual starts the signal down the axon.

A stimulus causes the voltage gated sodium channels to open and sodium ions rush in. This creates a positive charge density inside the cell and negative charge density outside. This difference is by definition a potential difference.  Potassium gates sensitive to this difference then open, the potassium ions to rush out, which again flips the polarity of the inside and outside such that positive charge density outside the cell and negative charge density inside.

But how does that actually lead to the signal that is propagated down the axon? Can someone explain?


texts: Empirical Measurements of Barr Body Ratio

texts: 'Both X-chromosomes in a female have an equal chance of becomes a Barr body in each cell.' Every source I can find on Barr bodies claims this and I can think of no reason for why it may be wrong. What I want to know is if anyone has empirically tested this. Has anyone ever taken a model organism, measured the distribution of Barr bodies, and calculated exactly how far the result is from the 1:1 ratio that the theory predicts? Has anyone ever tested the Null Hypothesis of this statement, or has it just been accepted based on the theory alone?


texts: In genomic DNA extraction, is it possible that too much CTAB hinders subsequent DNA precipitation with isopropanol?

texts:
I'm trying a genomic DNA extraction protocol that uses 4% CTAB, 3M NaCl, 2.5% PVP-40, 20mM EDTA (pH 8), 100mM Tris-HCl (pH 8) and 3% beta-mercaptoethanol as lysis buffer. I incubate at 65oC for 60 - 80 min. Then, precipitate complexed cell debris with chloroform:isoamylalcohol (24:1). Collect the upper fase and precipitate DNA with isopropanol.

I tried this procedure in 51 samples of cotton leaves. In most samples I obtain a nice DNA precipitate after adding isopropanol. However, in 12 of them, I obtain 2-phases, with no DNA precipitate at all. The lower phase looks yellowish and sometimes a bit dark. Why would this happen? Any thoughts?
Thanks!


texts: Agarose gel electrophoresis - wrong running conditions?

texts:
Please have a look at the electrophoregram.
The DNA ladder used is GeneRuler 50bp (loaded according to the instructions), size of the gel is 6*7cm, lane width is 4mm, agarose percentage is 1%, TBE buffer. The power supply is Consort EV243. Running conditions were: 120V, 200mA, 45W, 40'.

What went wrong? The ladder is very far from the lane, and the sample bands look fuzzy. During run voltage remained constant (120 W), while current and power were  slightly changing (56mA and 7W ~in the middle of the run). Should I change running conditions? And/or make a fresh TBE running buffer?


texts: What is the copy number of a given gene in GRCh37?

texts: sorry for the naive question, but how do I determine what the copy number is in GRCh37 for a gene with multiple CNVs? (e.g. DRD4).


texts:
After experiencing things like stress, intense exercise, or using drugs such as caffeine and amphetamine, subjects often assume a depressive and lethargic state afterwards, known as a "crash." What is the neuroscience behind it? Could it have to do with the depletion of neurotransmitters such as the catecholamines, or a downregulation of certain receptors in response to the overproduction of such neurotransmitters?

(This question is a remix of a previous question I posted, which was not focused enough)


texts: Why are superantigens not "MHC-restricted", and what's the significance?

texts:
MHC restriction is the requirement to recognize an antigen in association with a self-MHC molecule; CD4+ cells can only respond to an antigen if it's presented with a self-MHC II molecule, and the same goes for CD8+ cells and self-MHC I.

Various sources say that super antigens require an MHCII+ antigen presenting cell to activate a T-cell, but they're not MHC-restricted. I've found one "clarification" on what this could mean, and it's that various MHC II molecules can present a superantigen. Does this mean that MHC II from different hosts can activate a clone of T-cells if a superantigen is involved? What's the significance of that in a single host, e.g., someone infected by a microbe that produces one of these things?


texts: Which human cell lines do not express the GLP-1 receptor?

texts:
I need a human cell line that does not express the GLP-1 (glucagon like peptide-1) receptor.

I'm working with HeLa cells, do those express the GLP-1 receptor? Which other cell lines exist that don't express this specific receptor?

Are there any general resources where I could find this kind of information?


texts: Do adult mosquitoes have color preferences?

texts: Do adult mosquitoes get particularly attracted or repelled by any colour, or darkness or light? If so, what are they?


texts: What is the healing process of mouth wounds?

texts:
When we have an external wound, blood generally tends to clot there, forming a layer of solid scab.

Yesterday, while brushing my teeth, I somehow hurt my gums and it got all bloody. However, it did not clot, neither did it hurt just after the incident.

After maybe like 12 or 15 hrs I had trouble opening my lips and when I looked at the spot in the mirror the gum tissue around and on the wound had colored white/yellowish.

Our mouths are supposed to be the among the most contaminated parts of the human body, so why do mouth wounds heal in just about a week and don't get infected?

What is the healing mechanism found in the mouth tissue, because I figure it is completely different from the processes in wounds occurring in the external skin.


texts: what causes epigenetic dysregulation in cancer?

texts: Do mutations in regulatory gene sequences lead to changes in epigenetic alterations   in cancer, and if so which ones? I know abnormal hypermethylation of GCP islands occurs in promoters of tumour supressors, but what drives the abnormal methylation? Thanks


texts: What negative effects does cannabalism have in other species (like prion diseases) and how are they mitigated?

texts:
It is well known that human cannibals are likely to suffer from a variety of ailments, particularly prion diseases.

However a great many other species, from insect to ape practice cannibalism at much higher rates.

Do they suffer from similar diseases as a result of their cannibalism? If not why not? and do they have evolved mechanisms for dealing with these negative effects?


texts: What is the significance of the amplitude of brain waves?

texts:
What does the amplitude of brain waves represent and to what neuronal activities is this amplitude related to?

For example, in a hypothetical situation, the frequency of brain waves is kept the same, but the wave amplitude is increased or decreased by some means. What would be the effect on human brain and its activities?

Can resonance related to waves effect human brain waves?


texts: The Mystery of The Cretaceous' Songbirds

texts:
Before Passeriformes perched on the branches of our trees and sang their sweet, inspirational tunes, there was Enantiornithes, the "Opposite Birds".  So far, we have discovered at least 80 species from five different families.  (However, some of those names come from just one bone, so the nomenclature may not be valid.)

The really odd thing is that despite their diversity, they had become extinct during the Mesozoic-Cenozoic extinction event 66 million years ago, even though their rivals, the forefliers of today's waterfowl, shorebirds, tube-noses, rails and ratites, did not.

The question is:  How come?  Was there any paleobiology saying that this particular order of birds was too specialized to withstand an impact winter?


texts:
When a pine cone is wet, it remains closed. However, when it's dry it opens again.

From the perspective of physics or biomechanics, what is the mechanism that allows a pine cone to open and close as I've described?


texts: Would expression of GroEL and GroES in erythrocytes be a potentially effective therapy for sickle cell disease?

texts: Would expression of GroEL and GroES in erythrocytes be a potentially effective therapeutic strategy for sickle cell disease? Why or why not?


texts:
Parthenogenesis is defined as:

"A type of asexual reproduction in which egg develops without fertilization to form a new individual."

If parthenogenesis takes place in bees, a drone or male bee is produced.

My question is that parthenogenesis is the development of EGG into new individual so, how can egg be developed into male because egg won't have that "Y" chromosome required for male offspring?


texts: What would happen if a cell is poked by a fine needle?

texts:
I had seen this question in an exam:

A living cell has a protoplasm which is water based and demarcated by a lipid bilayer membrane. If a cell is pierced to 1/5th of its diameter with a very sharp needle, after taking the needle out
(a) no effect will be observed.
(b) protoplasm will leak out from the hole made by the needle for a few minutes until the cell heals the wound.
(c) protoplasm will keep on leaking out till the cell is dead
(d) the cell will burst like a balloon.

I understand that the answer is option (a) as the cell membrane will reseal itself after getting pierced.
But my doubt is that if in the question 1/5th was replaced by 1/2 or by any number greater than 1/2, will the answer be different.
Or in other words, I want to know whether the number 1/5 significant in this question.


texts: Could transfusion of a different blood type cure blood-based cancers?

texts: Different antigen detection triggers an immune system response that could perhaps stimulate mitochondria and such in killing cancer cells - something like chemo without the hair-loss?


texts: When consuming carbohydrates and fats together, why are the fats caloric?

texts:
If I understand things, and I most likely don't: mammals primarily use carbohydrates to produce metabolic energy when there are sufficient carbohydrates to do so.  The use of fats for fuel requires the organism to break down the fat into constituent parts and from there produce either glucose (right?) or ketone bodies.  Presuming that the organism is not in ketosis, it seems that its body would preferentially use carbohydrates for fuel.

This is where my confusion comes in: why would the mammal's body use fats for fuel if its diet contain sufficient carbohydrates?  The real underlying layman's question is: why is that when I eat fat, I have to count those calories, if my body preferentially uses carbohydrates for fuel?


texts:
What is the order in which this DNA samples would would reassociate ?

e.coli DNA

plasmid DNA

viral DNA

satellite DNA

DNA-RNA hybrid

This is a homework question and I have not been given any information about the condition in which they are reassociated.


texts:
Sterile hybrid with genome AB undergoes doubling of chromosome set to form fertile tetraploid with genome AABB.
But since A and B is not homologous, synapsis cannot occur at prophase I, so there is no meiosis.
So how does the chromosomes double? If through non-disjunction in mitosis, where did it occur? Did it occur in one cell only or all of the cells in the organism?
Did non-disjunction occurs at gonad to produce AABB cell, then it undergo meiosis to form AB gametes, and then self fertilise with AB gamete to form AABB offspring?


texts: What genes are required to make E. coli photosynthetic?

texts: "All" of the genes for bacterial photosynthesis were discovered in a gene cluster almost 40 years ago. Marrs, J.Bact.  What more is needed to make E. coli photosynthetic?


texts: Is there anything that is completely non-toxic to humans at any dose?

texts:
Lately I have seen a number of unrelated "scientific" debates over whether certain substances should be outlawed because they are toxic to humans. My initial, informal reaction is usually to respond that anything is toxic to humans if you give them a sufficiently large dose.

However, formally I don't know if that's really true for everything a human being could ingest in some way. I started to wonder if there were some substances that our body could handle unlimited amounts of without any negative consequences.

As this question has been (correctly) identified as a bit vague, I'll try to explain what i'm looking for. For the purposes of this question, I'm willing to ignore the limitations of actually ingesting a given substance in "the usual way". For example, if you can't physically drink enough of some liquid fast enough to kill you without your stomach filling up and vomiting, but that same liquid injected intravenously could be lethal, I could consider that toxic. I also recognize that the body can only physically contain a certain volume of stuff, after which sheer pressure would cause it to fail; I'm more interested in "biochemical toxicity" as opposed to any physical damage (I just don't know the term for what I'm looking for.)

In other words, one of my goals is to learn if, under laboratory conditions, a properly motivated researcher could always find a dose that would be toxic, regardless of the impracticality of a real person ingesting that dose under normal circumstances.

So, with that qualification, my ultimate question is:

Is there any substance we know of that is completely non-toxic to humans at arbitrarily large doses ingested over an arbitrarily short period of time?


texts: Why does PCR use heat as opposed to helicase like in semi-conservative replication in order to separate the double DNA strand?


texts: Why do raw prawns turn red after sitting in vinegar?

texts:
Yesterday morning I put some raw prawns (shell removed) into vinegar (more specific this one), and put them in fridge. When I came back at night all of them turned red, which looks cooked, except those not covered by vinegar.

Why do the raw prawns change colour?


texts: I know how to solve these equations, but I'm not sure what t' represents?

texts: I am investigating the Wilson Cowan neuron population model, and I can follow most of it, but I'm not sure what is meant by t' in the equation for proportion of neurons in the refractory period. The equation of interest is below.


texts: Why would deer continue to cross a river full of crocodiles even though some of them have been killed?

texts:
I recently watched a clip on Discovery Channel, where I saw deer crossing a river full of crocodiles, ignoring the fact that some of them would have been killed doing so.

Is there a possible evolutionary reason for this behaviour?


texts: Are there any natural cases of direct translation of DNA to protein?

texts:
I'm aware direct translation of DNA to protein (without the need for RNA) has been observed in test-tubes using e-coli. (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC219759/)
I wanted to know whether there have been any natural cases for this that have been observed. And suppose there aren't, would it be theoretically possible in a cellular environment?


texts:
I have a question that probably is to obvious, or just bad wording..

The terms endorthermy, ectothermy, and heterothermy, are used to describe:
A) cold and warm individuals
B) the three layers of the skin
C) different types of body cavities
D) the source of an animals heat
E) none of the above

I think it's E) or D). My thinking process is B and C completely irrelevant.  A) i think it is very ambiguous as an answer as those three terms refer to a type of classification rather than the characteristic itself (like if their skin is cold or warm). On the other hand D) the source of an animals heat, doesn't seem very right to me. The 3 terms refer to the source of the heat that predominatly determines the body temperature, meaning that it is not THE SOURCE, but the way they exchange and regulate their temperature... That means that probably it is E?!

Thanks


texts: Has the acronym DNA ever been widely understood to stand for deoxyribose nucleic acid?

texts: I have a friend familiar with evolutionary biology who was recently bragging about how much he knows.  I asked him what DNA stood for, and he answered it stood for 'deoxyribose nucleic acid'.  When I claimed it stood for deoxyribonucleic acid, he said it depends on the source you go by.  I was curious and decided to look into it, but the only source I could find using his answer was the paper "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" published in the 1950s, and no explanation regarding if and when the term was officially changed.  Can anyone shed light on the history of the term and explain if deoxyribose nucleic acid is still acceptable?


texts: What causes the sound of climaxing bees?

texts:
I just saw the funniest video of bumblebees(?) having sex. (mirror) As they were getting it on, there seemed to be an almost audible 'moaning' coming from the pair. From what I presume it was a sexual climax we heard!
Bees have neither vocal chords nor lungs, so I wonder: what is that sound?

As the pair is mating on a newspaper, I'm almost certain we're hearing transduced vibrations from the bees made audible through the paper and not the bees themselves. (Nonetheless, what a beautifully humorous anthropomorphism! Moaning bees certainly give vivid color to the birds and the bees!)
I have multiple theories:

The ejaculation of sperm by the drone is known to be 'explosive', even rupturing the endophallus and making a 'popping' sound. I wouldn't call the sound in the video 'popping' by any means, though.
(Un)controlled movements of legs or wings by either of the pair. This seems very likely considering the subjective frequency of the sound, but that's just speculation on my part.
Perhaps it's the queen piping? I'm really grasping with this one. I don't even know if that species' queens pipe or even have the ability to pipe.

Any excited entomologists wanna fill me in?


texts: Given that mitochondria have their own DNA and can replicate independently, can they ever become cancerous? For example, could a mutation in their DNA cause them to rapidly replicate, ultimately killing the cell it's in?


texts:
My friend heard that tea is worse for drinking than water because "cells have a special membrane and tea has special supplements and membrane doesn't let tea pass and this is why skin is dry even when you hydrate with tea a lot", something about "lipid bilayer".

Is there is some nice scientific article on water andd tea difference to human organism?


texts: Birth control hormones in the water? Or not?

texts:
This prior question talks about natural estrogen (TL;DR: Months to years):
How quickly do estrogens break down in the environment?

Ref:
http://dx.doi.org/10.1038/485441a

A lot of media has said, "birth control hormones in the water!!!!"
Ethinyl estradiol (EE2), is a synthetic hormone

eg: www.livescience.com/20532-birth-control-water-pollution.html

Conversely, a birth control advocacy group, says, "Naw, it's a very small part of the total estrogen load in the environment."
eg: www.arhp.org/publications-and-resources/contraception-journal/august-2011

(can't post more than two links) :P

What I recall reading was that one of the types of birth control hormones got processed by the human body, looked like it was changed (in the urine, etc), and so they were fine with it not causing an issue - but when it got into the environment, it rapidly got changed back into the (estrogen?) it was originally - and thus caused problems.

I'd like a nice summary of what's thought to be going on, preferably from a more neutral source.


texts: Has anyone yet figured out how sensory signals for eyes and ears are encoded by our organ into electrical signals?

texts: The most obvious way to give sight to blind and hearing to deaf is to give them a replacement organ for these. In order to do that we would need to understand how our eyes and ears encode sensory information into electrical signals which then go into the brain. My question is, how close are to understand this mechanism at this time?


texts:
Sir the protocol I followed where it has been written... 1st using lactobacillus in Mrs media (50 ml in 250 ml conical)..we allowed to incubate for 24 hrs then added 0.1M znSO4 (50ml) and 0.4 M NaOH(50ml)...followed by a vigorous mixture heating it for 15 mints at 40°C ...white portion observed at the bottom of conical..(.which I also showed)...followed by centrifugation washing it with deionised water again again ...finally pelleted portion collected which allowed to dry to make it powdery form..then it observed under UV spectroscopy by mixture the powdery with  deionise water...
But sir I don't get any pick in UV spectroscopy.. Is  there any method synthesis Zn Nanoparticles using lactobacillus culture?


texts: Is “Oxygen-Starvation” during exercise a real phenomen?

texts:
Cross-Posted from Physical Exercise, as I suspect this Q is a bit more bio-science focussed than is appropriate for that StackExchange

I play hockey (field hockey) at a slightly-below-elite level. I train (but don't play) with players who play in the UK National Prem.

I, and other players I play with, and coaches I've trained under, have always talked about us and our brains being "oxygen-starved", when you're playing beyond your fitness level. (Especially common during pre-season when everyone's unusually un-fit :D )

What we mean by this in terms of external observable actions is that, when we get very tired we stop making good decisions, and our fine motor control drops - we chose bad passes, we take people on when we wouldn't normally do so when not tired, our hand-eye cooridnation drops so that we can no longer execute skills as well, etc. etc. etc.

Certainly the effect exist - those actions are clearly observable.

But is there truly a physiological effect behind it, and if so, is that effect truly about oxygen levels in the brain?

If one were able to install an O2 sensor in one of major arteries leading to the brain, would you be able to see actual drops in O2 levels, when someone is reaching a point of combined aerobic and anaerobic exhaustion (hockey is a heavy mix of both forms of activity, like many team sports)


texts: Why does the liver produce ketone bodies instead of exporting acetyl-CoA from beta-oxidation for use elsewhere?

texts:
Under conditions of low oxaloacetate in the liver, acetyl-CoA that cannot be oxidised in the TCA cycle is converted to ketone bodies, which can then be exported for use as fuel in non-gluconeogenetic tissues (e.g. heart, brain).

To avoid this pathway, and the additional enzymes it requires, as well as the enzymes in the receptive tissues which are needed to reverse the pathway and re-produce acetyl-CoA, why does the liver not just export acetyl-CoA directly?

One consideration is an inability to transport acetyl-CoA across membranes, but fatty acyl-CoAs deal with this using a carnitine shuttle across the mitochondrial membrane. Would developing a transport system not, evolutionarily, be a more efficient solution?


texts: At what age are mice considered too old for their thymus to stop being functional and produce T cells?

texts: I am studying the effects of radiation on the immune system of mice. After exposing them to radiation, we will be harvesting their spleen, lymph nodes and blood to investigate immune cells such as T cells, B cells, etc. If our mice are 16-18 weeks old, would their thymus be beneficial to study as well? I’m not sure if this is considered Too old and their thymus would no longer be functional. Thanks!


texts: I am wondering why to use a kinase assay, since we can extract the proteins from cells and then do a Western with the specific antibodies we want to use.


texts: How are neural networks encoded in the DNA?

texts:
The central nervous systems as well as the brain->muscles and sensory cells->brain nervous pathways, need to be precisely wired for life to be possible. Moreover they are wired almost exactly the same way for the individuals of a same species (animal, man, insects, etc.).

This information, must therefore be somehow encoded in the DNA.

I have never heard of any study or theory on how this would be possible - only about how proteins are encoded, and I couldn't find any bit of information on this topic (I am not a biologist though).

I would like to have a broad idea of what is currently know about the construction of such networks, i.e. not detailed explanation but rather takeaways facts and references.

How is information about neural connections encoded in the DNA?

e.g. are there any genes linked with neurons (e.g. coding for neurotransmitters)? Do the DNA code for precise neural connections? Can development of specific parts of the brain be linked to specific parts of the DNA? How does a neuron knows from the DNA to which neurotransmitter be sensitive?

How are connections between specific neurons established?

e.g. how an axon does know where to establish deliver a potential? How can the end of an axon move to the correct place?


texts: Why only honey bee collects & store honey?

texts: In Insects, most of flying insects like butterfly etc, diet is sucking honey from flowers. none of them store honey except honey bee. Why so ?


texts: What determines whether a regulatory T cell suppresses a naive T cell binding the same antigen-presenting cell?

texts:
Here's what I learned about how regulatory T cells work:

There is a self-recognising naive T cell around.

A regulatory T cell that recognises the same self-antigen binds the same antigen-presenting cell as one of these T cells.

It suppresses activation of the naive T cell.

However, let's say the antigen-presenting cell is presenting foreign antigen on some of its MHC molecules. The naive T cell binds the  antigen and there happens to be a regulatory T cell nearby binding a self-antigen on the same antigen-presenting cell.

Does the regulatory T cell suppress the naive T cell? Is it just do with proximity, or do both cells have to bind the exact same antigen?


texts: Is it possible to breed neanderthals through selective breeding?

texts:
I've heard most non-subsaharan africans have neanderthal DNA with it being more prevalent in northern regions, that sometimes 1-4% of the DNA has neanderthal origins.

Speaking strictly scientifically, would it be possible through selective breeding to breed an individual where the majority of the DNA is neanderthal?


texts: Why does maintaining contraction of muscles require ATP?

texts: So from my understanding, if I maintain the contraction of my muscle, the myosin head will be bonded to the actin. Why is ATP needed to maintain this bond?


texts:
I am searching for an example in the nature, where a layer of something (skin, coat, film etc) can allow fluid to flow trough (not absorb) from one direction and prevent/repel from other direction. I am not talking about vein valves, prefer more like a nano-structure of valves as a layer on/around something.

Update:
I found something similar what i am searching for, but its not clear:

  Gap Junctions (animals)

  Directly connects the cytoplasm of two cells, allowing various ions
  and molecules to pass freely between the cells.

And there is a reason why this channel is hydrophilic, someone can explain this?

About me I have no deep knowledge about biology, please be patient and help me to understand things on basic level. Thank You!


texts: I am reading about a paper about inferencing pathway information in cancer cells. Authors refer to ERBB2 as a gene and a pathway. I don't have solid biology background. What exactly means when we refer to ERBB2 as a pathway? Does it refer to activity of a protein encoded by ERBB2?


texts: RAD sequencing: choosing the appropriate enzyme?

texts:
I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC and TTAA), the two enzymes similar and used in Peterson, B. K., J. N. Weber, E. H. Kay, H. S. Fisher, and H. E. Hoekstra. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135. (they are using EcoRI and MspI (GAATTC and CCGG).

Considering the huge list of restriction enzymes how to choose the appropriate enzyme? Is it a complete guess? The size of the genome of finches is about 1.07Gb. Do I have to take this in consideration?

The reference genome is available Zhang, G., P. Parker, B. Li, H. Li, and J. Wang. 2012. The genome of Darwin’s Finch (Geospiza fortis). GigaScience.


texts: Do organic veggies contain more pesticides than regular food?

texts: Since organic farms can only use "natural" organic approved pesticides rather than frequently more effective "synthetic" pesticides in use by other farms, does it mean that, on average per kg of veggies harvested, a higher amount of pesticide is applied at organic farms in comparison to regular farms? And does it imply that organic veggies sold in stores have more pesticide inside them than regular veggies?


texts: What causes the line patterns in the palm of the hand?

texts: The line patterns on the hand are unique to each individual, but what causes these lines and re they advantageous in anyway?


texts: In a skeletal muscle contraction, what happens after ACh binds to the nicotinic iontropic receptors on sarcolemma?

texts: Does the bound ACh becomes unbound and then gets hydrolysed by acetylcholinerase?


texts: Out of all our sensory organs, we need to stop taking signals explicitly only from eyes in order to sleep. Even interestingly, those who are not able to receive signals from eyes (i.e., the visually challenged people) also need to close their eyes in order to sleep. I wonder what is the relation of closing eyes with sleeping. I think the reason might be related to the state of the muscles related to the eyes. Of course, even if it were the case that one could keep her eyes open while sleeping, the brain would stop paying attention to the signals received by the eyes -- just like the brain stops paying much attention to the signals received by the nose or the ears while sleeping even if these organs are not physically closed or prevented from receiving signals. But in the case of the eyes, they are physically closed while sleeping,  which makes me curious.


texts: How many chemical species are on average in a typical plant and animal cell?

texts:
I want to know what sort of range there is on the number of different chemical species in a typical plant and animal cell. Failing that, some specific examples (with sources please).

Thanks


texts: How non-invasive blood glucose concentration measurement work?

texts:
Diabetes patients need to conduct the “fingerstick” a few times a day. One of the mechanisms of "fingerstick" is to take small amount of blood sample and put it onto a test strip. The enzyme on the test strip reduces the glucose and the electronics of the glucose meter detect the redox species produced. However, this method is painful and increase the risk of infection.

Photonic sensing technology opens up a new method for non-invasive blood glucose concentration. According to an article of medGadget in 2013 (The link follows http://www.medgadget.com/2013/10/non-invasive-measurement-of-blood-glucose-levels-using-glucotrack-interview.html ), the non-invasive kind was invented. By simply clipping the earlobe (without puncturing the skin), the blood glucose concentration could be measured. Does anybody knows the working principle for that? Or, suggest a paper describing that?


texts: I have a friend who told me that anti-aging cream cannot work to reduce wrinkles as it only penetrates x amount of skin layers and can never make a long term effect. Me not knowing much about how penetrative skin actually is, I was wondering if anyone knows if this is true and if anti-aging products are only working like a temporary moisturiser?


texts: What are limitations on the number of objects the eye determine at a glance?

texts:
Take two people Sam (average human) and Jack.

Jack says to Sam "I'm going to show you some skittles (or other object) and I want you to tell me as quick as you can how many I'm holding." He opens his hands and there are three. Sam can instantly tell there are three. Then Jack shows five to Sam, who takes a little longer, as he knows there are around 4/5 but can't tell so has to count.

As the number of skittles increases, Sam takes longer and longer to answer to the point where he needs to count the skittles one at a time to be sure, and sometimes to even recount them.

Why is it that we can instantly if we are looking at three maybe four objects but any more than this we cant? It gets harder and harder to estimate?


texts:
I live at Vancouver, BC, Canada and I often find this kind of white stuff inside the apples I buy

I used to live in Europe (Switzerland) and never saw that before. It very much look like a fungus. Is it? What species is it? What is the geographical range of this species?

When I cut my apples open, I just remove it and assume it did not lay too many mycotoxins in the rest of the apple but when I directly bite into the apple, it has happened to me to eat some of this white stuff. What are the health consequences of it?


texts: I just had my genome sequenced. Can someone tell me what these different file formats are?

texts:
I just had my whole genome sequenced and now I want to play a bit with bio-informatics. However, the documentation is quite scarce on the file standards used.

These are the files I have been given (the "raw" data):

Can someone explain me with some detail what is each file format, and for what are they used?

Transcribed list of file-formats from the picture:

  Indel (TBI)
  Indel (VCF)
  SNP (VCF)
  SNP (TBI)
  CNV (TBI)
  CNV (VCF)
  BAM (BAI)
  BAM
  FASTQ R2
  FASTQ R1


texts:
US companies that sell rabies vaccines routinely recommend that they be given annually. Obviously, these companies have a financial incentive to recommend that their vaccines be given as frequently as possible.

No human vaccine that I know of requires annual booster shots. The standard recommendation to veterinarians that they receive a single primary course of vaccinations and no boosters at all. It seems inconsistent that the CDC recommends that vets that work with sick animals on a daily basis get a one-time vaccination, but the USDA "recommends" house pets get vaccinations every year. My understanding is that this USDA "recommendation" is based on no scientific evidence whatsoever.

Is there any scientific evidence indicating the effectiveness of vaccines as a function of the frequency of their application?


texts: Where occurs diamine oxidase in kidneys - in cells or in extracellular space?

texts: I would be interested in where the enzyme diamine oxidase in kidneys of human/animals mainly occurs? In cells or in extracellular space? A literature reference if available would be great. Thanks!


texts: is ventricular depolarisation same as depolarisation during nerve impulse conduction?

texts: Does the change in membrane charge accumulation occur in a similar way in heart and nerves cells?


texts:
Firstly, I don't know if this is the best site to ask this question. Please guide if its not.

Now my question:

If we take out a tissue out of its box, a new tissue comes out partially so we can easily take it next time. Now that tissue can easily collect germs from sneezes and coughing of other people around us.

Can that cause problems/infections? Why doesn't tissue box have a better design?


texts: Has a primate species ever weighed the average mass of a tonne (1000 kg)?

texts: If so, why can't primates weight a metric ton?


texts: Are there any websites offering graphs for the light absorption of different enzymes?

texts:
I have found graphs for the light absorption of water, haemoglobin, lipids, melanin, etc., but I am having a hard time finding graphs about enzymes.

Are there any websites or other reference sources for this type of information?


texts: Why do viruses cause different symptoms?

texts:
If the sole purpose of a virus is to hijack the nucleus of a cell to replicate, why do we have different symptoms for different viruses?

I can think of the following comming into play:

immune response of the body
destroying tissue of type A is different than destroying tissue of type B
the rate of the destruction --- some (virus, cell) combination are causing more harm than others

Reference:

Why Do Viruses Cause Different Symptoms In Different People? --- talks about how we can have different symptoms for the same virus.


texts: Might a previously administered MPSV4 vaccine react with a newly administered MCV-4 vaccine?

texts:
This is a hypothetical situation.

Meningococcal polysaccharide vaccine (MPSV4) is a vaccine against Neisseria meningitidis.
MCV4 is a conjugate vaccine.

I would like to know if the polysaccharide base could interact with the conjugate base.
I think they would not act like booster doses and that the efficacy of the conjugate vaccine would be decreased, due to the lifelong effects of MPSV4.

Might MPSV4's polysaccharide base interact with MCV4's conjugate base, and if so, what might be the mechanism?


texts: A question about cancer antigens and their mechanism

texts: Can you name the most common antigen that cancer cells in general can't live without?


texts: What determines the amount of data you would get from a sequencing experiment?

texts: When someone performs a sequencing experiment, what determines how much sequencing data you get from the machine (Illumina, PacBio, Nanopore, etc). Or maybe, put differently, how does the machine know that it is done?


texts:
I was reading up on CRISPR-cas9 and how it works and I am having trouble wrapping my head around how NHEJ to repair the DSB can cause indels to occur. Shouldn't the NHEJ just stick the two strands of DNA back together?

I believe I read somewhere that if other agents cause a DSB, such as certain chemicals, they can also damage / cleave nucleotides ; the damaged nucleotides would have to be removed and overhangs filled in by polymerase before the ligation, which could result in the errors that NHEJ is famous for.

Since cas9 does not cause such damage, how can it result in an indel?

Thanks.


texts:
It is commonly believed that vitamins can help our memory.

Is this really true? What is the biological basis of this?

Is there any specific research paper on the subject?


texts:
The recent news about a new supermassive virus being discovered got me thinking about how we define viruses as non-living organisms whilst they are bigger than bacteria, and much more complex than we first gave them credit for.

What biological differences between viruses and cellular organisms have made viruses be deemed non-living?


texts: What would happen if you "rewired" your eyes with your nose?

texts:
The nose sends sensory input through transduction of chemicals in the air via the olfactory nerves/tracts to the primary olfactory cortex.
The eyes send sensory input through transduction of light via the optic nerve/tract to the visual cortex of the occipital lobe of the brain.
Although both senses receive different stimuli, they (like all of our senses) convert external stimuli to a nerve signal. Given that, it seems possible that one could "rewire" the brain so that sensory organs sent sensory signals to different parts of the brain.

For example, it seems possible that we could splice olfactory tracts to the optic chiasm to send signals to the visual cortex.

My question: If we rewired the cranial nerves so that our nose was connected to our visual cortex, what would we see??

(or what would happen if we rewired any of our major senses with a different processing center of the brain?)


texts:
Today I saw an ant question biology and was reminded of a picture I had clicked 2 years ago.

Here, you can see these black guys cannibalizing this other black guy.

To reiterate, these guys had their nest inside a tree. I had cornered one of them.

If I remember correctly the ant was walking fine and the only fault might have been that I lead the guy astray a bit (not further than the farthest guy in the colony) and near the colony I turned it on its back which lead to a lot of difficulty for getting up again (as any ant knows). I mean I waited maybe a few minutes but it just kept waving it's legs in the air.

So later on as soon as these other ants got sight of their lost friend when it was able to hobble back near the nest, they came over and just pulled him apart.

In the picture you can see the first guy just got to him and the others started aggregating as soon as this guy came over. Within five minutes some 10 or 15 ants were all over the place.

Which ant species is this?

Why did they murder/cannibalize a member of their own colony?

Is this a common behaviour among ants?


texts:
Part of what we eat are proteins,
and our body is in part build of proteins.

Are the proteins of the body build based on proteins in food at all?

Are proteins in food directly reused in the body,
or are proteins first disassembled?

How far are they disassembled, randomly in various pieces, or systematically to keep what can optimally be used to build new proteins, while nothing is wasted for energy?

(The question Can proteins/peptides pass through the intestine? and it's answers are related, and provide some context and relevant parts, but is not a duplicate.)


texts: What is the suitable terminology to describe this study approach?

texts:
I need to know the correct term(s) which are usually used in the parlance of both biology and bioinformatics for this study approach:

About 11 transcripts were investigated using qPCR for a number of samples (about 200) and then  the gene expression data were subjected to data mining tools: principal component analysis (PCA), cluster analysis (CA) and the results were interpreted using other supportive data that were not included in PCA in order to reveal the nature of acquired clusters.
Clusters obtained were then predicted from the gene expression data using machine learning classifiers. In short, it is a blend of molecular biology, data mining tools, and machine learning classification (predictive modeling).

Please if you have ever done this kind of data analysis, what should be the appropriate term to describe this approach?

Likely candidates

Gene expression profiling study

Transcript profiling study

Transcript Wide Analysis Study or TWAS for short


texts: How can fruit flies and mice share the same gene that says to build an eye if they evolved separately?

texts: I saw a documentary where they inserted the gene of a mouse that basically is the starting "build an eye" command into a fruit fly, and a fruit fly eye grew. My question is, if eyes of different types of animal had different evolutionary beginnings (I don't know much about arthropod eye evolution, but for a different example, as I understand it, cephalopod eyes evolved from skin cells while vertebrate eyes evolved from brain cells), then how is it that the same gene controls the growth of two such evolutionary different eyes?


texts: What is the name of this plant? (found in a rock)

texts: I found it in Western Turkey.It was growing on a rock so what's it?


texts: What's the difference between life expectancy of cigarette smoker and general population?

texts: Some say that smoking cigarettes will shorten lifespan. By how many years is the lifespan of a typical smoker shortened? What are the common cause(s) of death among smokers? Are there any known statistics for cigarette smoking and life expectancy?


texts:
I found a beautiful scarce-swallowtail butterfly in my storeroom, but it was kind of frozen and couldn't fly away. So, I put it on my terrace in the sun. After a little bit, it flew a few meters away and fell. I was wondering what could these beings eat, so that I can help it...
Any answers would be great appreciated!
Thanks in advance


texts: Is most of the human genome functionless “junk DNA”?

texts:
In January 2012, David Icke published a book (ISBN: 9780955997334) entitled “Remember where you are and where you come from” in which he challenged what he claimed to be the view of mainstream science that 90–97% of the human genome was “junk DNA”, serving no function. He implied, instead, that it must have a function, but that this was unknown.

Is it still true that we do not know what all this DNA does? I see that we consider this DNA to be non-coding, but does that mean it is “junk”? I find it hard to believe that it can serve no function, otherwise why would the DNA be there? Is it possible that it is used for things we don't yet understand?


texts:
In the biochemistry book I'm reading (Box 10-1, Lehninger Principles of Biochemistry), an example is given in whales of how spermaceti (a wax located in the whale head), when at sea level is a liquid, and allows the whale to float due to its buoyancy.

As the whale dives deeper, the wax turns into a solid (due to the colder temperatures), and hence this more dense wax is less buoyant and prevents the whale from floating back up due to the greater density of the seawater at these depths.

My limited understanding is that density effects buoyancy in so far as that the weight of the object displaces an equivalent weight of water. If the quantity of the water displaced is small enough that the surface area of the object isn't completely submerged, it can float.

Now with the whale example, considering the wax is fully enclosed by the head, how would this change in local density effect the buoyancy of the whale as a whole? The weight of the wax still remains the same (in so far as the example used in the book), the only thing that changes is its density inside the whale.

So with a constant weight, and only a variable local density enclosed by an object (the head) and limited to these conditions only (as this is all the example in the book uses), how is this possible?


texts: Blosum matrix with probabilities instead of the positive and negative scores

texts: I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like to know the probability of LEU replaced by ASP.


texts: Why eyebrow growth stopped after it has specific length?

texts: When comparing with hair that grow forever after we cut it, why eyebrow not. what gene measure current length of eyebrow so it stop to grow after specific length.


texts: Why are some scorpion species fluorescent under UV light?

texts:
It's known for some scorpion species such as Pandinus imperator, Heterometrus Petersii etc. to be shining under UV light. That makes them easier to capture and collect by humans.

Is there any evolutionary advantage for this property?
Usually, in articles you stumble upon the phrase "It is not known" for this matter (example). Maybe someone knows of recent discoveries.


texts: Generate mesh surface from protein structure

texts:
What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated.

I'd prefer the output to be a watertight triangle mesh of the protein surface.
Also, I'd like the tool to be scriptable (i.e. no need to open a GUI).

So far, I've been playing with MSMS and EDTSurf. But I was wondering what was standard in research, as well as if there was anything in the standard bioinformatics libraries.


texts: In what animal species is the sex ratio skewed in favour of the fertile female?

texts: Ants have something like a single fertile female to several males. The same applies to bees, and larger animals - elephants too. Is the sex ratio universally skewed in favour of the female? What animal species exhibit this ?


texts:
Why do Valerian pills make us calmer? What is the mechanism behind it?

I understand how artificial tranquilizers work. Do valerian pill have similar chemical components?


texts: This is the bone of which animal? And which bone?

texts: so this bone was found on a construction site in Paris and I was wondering from which animal does it come from?


texts: What are the limiting factors of human stamina?

texts:
What are the limiting factors of (human) stamina? Let's define stamina as the capacity to continue doing a physical activity. We clearly have our limits, so what aspects of physiology impose a limit on human physical exertion? How do these aspects work together and interact?

Great detail isn't necessary, but a concise overview is what I am looking for.


texts:
I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to make a Russian doll analogy. I know about epigenetic markings but I am really looking at an example of a DNA region directly acting on a enhancer similar to an enhancer acting directly onto a promoter.

I am asking that because I couldn't find any examples and was wondering if I missed such a report/paper.


texts: Why does the seed of the coconut tree have a liquid in it?

texts:
What is the purpose of water in the coconut seed?  The reason I ask this is that I was reading about coconut water and all the benefits it has for us Humans.  But why does the tree put a liquid in the seed?  I read a lot more and learned that the liquid becomes a solid and is called endosperm, which is food for the coconut tree.  I'm still not happy with that answer because all seeds are food for the plant they become.  They are also a lot more.

I have come up with a very good explanation for the existence of coconut water and I want see if anyone else has any ideas.  Remember, I am not trying to find out why there is food in the shell.  That's obvious.


texts:
Amyotrophic lateral sclerosis (ALS) often starts at middle age, but I didn't find any suggestion why. Something seems to trigger the symptoms in middle age.

If I am not mistaken, the sporadic ALS is not genetic, but there are genetic variants. So these genes are with the person all his life. But why do the disease symptoms often start only in middle age?


texts: In the video, "Inner Life of a Cell", what's the empty space between the molecules?

texts:
In the video, "Inner Life of a Cell" there's a lot of empty space between the proteins. Is it just a simplification (i.e. they omit smaller molecules)? If so, what are the smaller molecules supposed to be? Or is it just a vacuum small enough to be ignored?

I've done some reading up on it, and found that it's called cytosol which is a complicated mixture of random proteins and molecules.


texts: what is the biggest known functional distance between an enhancer and its target gene (TSS) in cis?

texts:
since the title seems self explanatory;
It would be nice if anybody could provide a reference. I'm looking for a paper that I belive stated around 1.5 Mb but anything above will be cordialy welcomed.
thanks a lot


texts: How to find sequencing data of a specific drosophila strain

texts:
I'm trying to correct low coverage parts of an assembly of these PacBio reads with Illumina data. According to PacBio they "have sequenced adult males from a subline of the ISO1 (y; cn, bw, sp) strain of D. melanogaster.  This is the same stock used in the official BDGP reference assemblies since the first genome sequence release in 2000."

Unfortunately the Illumina data sequenced by the same guys (also  ISO1 (y; cn, bw, sp) but 2057) "revealed significant differences" to the official reference strain. Something I found out as well.

Now I'm trying to find Illumina data for the reference strain at NCBI, but I'm pretty lost. There seem to be dozens of different strains and I can't figure out which one is the reference strain, mostly because I'm completely unfamiliar with the biological nomenclature like ISO1, (y; cn, bw, sp) and 2057 or D8, D20-C2, mbn2 and so on.

So I guess my question is: What strain exactly is the drosophila melanogaster reference strain used in BDGP and how do I find SRA data of this strain on NCBI?


texts: Red transcriptional reporter in Psudomonas putida

texts:
I need to build a transcriptional reporter in P. putida with high excitation wavelength,in order to decrease phototoxicity (I have been using mNeonGreen until now,  and I would like to try something red).

My colleagues reported to me that previous tries with mCherry and mKate2 failed because:

mCherry seems to have a very long maturation time, not suitable for
my experiments
mKate2 did not show any expression at all

Does anybody have experience with transcriptional reporters in P. putida?
Any ideas? (DsRed? re-try with mKate?)

I am measuring the expression of a PsrI (sigma factor for siderophore production) regulated gene.


texts: We know that RNA polymerase produces mRNA by reading DNA strand. Which enzyme produces the first RNA polymerase if other RNA polymerases are synthesized in the same way like other enzymes(proteins) ?


texts:
Practical motivation: I have equipped part of my windows with mosquito nets. Despite not opening the unequipped ones at night, I still have mosquitoes entering my flat. To decide whether I equip all windows with nets, I am wondering whether mosquitoes are likely to take advantage of other ways to enter the place: it is a 3-century old building, and in no way air tight. There is likely to remain gaps of about 2 mm width in many places, both at some edges of mosquito nets (although I could improve on these) but also around front door, etc.

Zoology questions :

Given the strategy I observe for mosquitoes who fly upfront to the net and explore randomly while hitting the net repeatedly, I am not sure they may detect a small opening away from larger ones, or will they?

I am also unsure whether they would squeeze for a distance longer than a few mm, since they do not appear to ever walk or crawl but only fly?