texts:
"The knowledge about semi-permeable membranes is applied for various purposes. We know that semi-permeable membrane is capable of separating substances when a driving force is applied across it. Artificially synthesized semi-permeable membranes are used for separation of bacteria from viruses, because bacteria cannot cross a semi-permeable membrane."
My Question is Why Bacteria cannot cross a semi-permeable membrane? Reason?


texts: Alternative plant taxonomies to Linneaus

texts:
In addition to Linneaus-inspired taxonomies of the botanical world, I suppose there are some other proposals for different kinds of taxonomic accounts, perhaps for specific sub-domains of botany or perhaps historical. I'd be keen to learn about those.

Additionally, if any of you know there are some other alternative non-taxonomic approaches to botanic classification that are widely-used in sub-domains or in the early days of science, I'd be keen. I guess there are still some "common sense" classification to be made between use (ornamental/non-ornamental; medicinal/edible/poisonous), but perhaps there's more.


texts:
I am well aware of the phenomenon of neurogenesis induced by exercise, as well as the dopamine release that results from exercise. I am really interested in neuropsychology and the effects of exercise on personality. What are some other biological processes that are stimulated by exercise, does it activate our parasympathetic nervous system? Is there any cool research out there for me to read? I am grateful for any input. Any information about exercise and its effects on human biology is appreciated.

UPDATE
While this answer was appreciated, i'm interested in other biological processes... What happens to stress and anxiety? Do our adrenal glands stop secreting as much corticosteroids? What effect does exercise have on circadian rhythms? With exercise, can you circumvent the problem of not getting enough light in the winter? What effect does exercise have on memory? It should probably help, since it would lead to decreased damage to the hippocampus. How does exercise effect sleep, learning, memory, metabolic processes??? I'm searching for the comprehensive list of different primary and secondary effects of exercise from a biological standpoint. I'm really interested in what the short term and long term effects of exercise are on the brain.


texts:
Millions of lymphocytes pass through lymph nodes every hours (Hall, 1967). Anyone happen to know how many reside in a lymph node, roughly? Lymph nodes seem to have volume of around a ml, average (Ying, 2009). This is a rough estimate. The upper bound for how many lymphocytes can be crammed in can be calculated as rough estimate. With average lymphocytes diameter 10 µm, volume as squares 10^3 = 1000 µm^3, 1×10^-9 ml. 1/10^-9 = 10^9 fit in a ml, a billion, so upper bound.
How many are in a lymph node, millions, hundreds of thousands, or closer to a billion? Anyone know, or, know any "literature" that documents it? In humans or other animals work well too, was mostly thinking from human PoV but it overlaps.
References
Hall, J. G. (1967). QUANTITATIVE ASPECTS OF THE RECIRCULATION OF LYMPHOCYTES; AN ANALYSIS OF DATA FROM EXPERIMENTS ON SHEEP. Quarterly Journal of Experimental Physiology and Cognate Medical Sciences, 52(1), 76–85. https://doi.org/10.1113/expphysiol.1967.sp001887
YING, M., & PANG, B. S. F. (2009). Three-dimensional ultrasound measurement of cervical lymph node volume. The British Journal of Radiology, 82(980), 617–625. https://doi.org/10.1259/bjr/17611956


texts: How many strands of Myosin Head is in a Myosin filament?

texts:
I am doing a research about sacromere in striated muscles, I read a paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963759/
) and it states the follow:

"Rotational symmetry is defined by the number of strands present. Actin filament has two strands and hence has a 2-fold (C2) rotational symmetry; myosin filament has three strands and hence has a 3-fold (C3) rotational symmetry. Helical symmetry is defined by the integral number of sub-units contained in a given number of turns in a single strand. So for example actin filament strands have a 13/6 helix, i.e. thirteen subunits in six turns of a strand, whereas myosin strands have a 9/1 helix, i.e. nine subunits in one turn of its strand."

Now what does it mean by "myosin filament has three strands and hence has a 3-fold (C3) rotational symmetry" ?

How many strands of myosin heads is in myosin filament? I saw visualizations in different papers showing different numbers.


texts: Do animals exhibit handedness (paw-ness?) preference?

texts:
I have been observing my cat and found that when confronted with an unknown item, she will always use her front left paw to touch it.

This has me wondering if animals exhibit handedness like humans do? (and do I have a left handed cat?)

One note of importance is that with an unknown item, her approach is always identical, so possibly using the left paw means allowing a fast possible exit based on how she positions her body.

This question is related to Are there dextral/sinistral higher animals?. However, I question the "paw-ness" as a consequence of how the cat is approaching new items (to be ready to flee), whereas the other question remarks about the high number of "right-pawed" dogs and questions the influence of people for this preference.


texts: Polarized epithelium and localization of ion channels

texts: I'm trying to learn more about polarized epithelial cells of the gut. I am familiar with classic brush border transporters localized to the apical memebrane to facilitate nutrient absorption. I am wondering though, where are ion channels located? I would guess basolaterally since they would be exposed to the extracellular space. I would appreciate a primary reference showing the location of voltage-gated channels in particular as I could not find them myself.


texts: What disease does Saccharopolyspora erythraea cause?

texts: For an examination assignment I have to find a disease caused by the bacterial species Saccharopolyspora erythraea, but I have searched the internet and have found no report of patients being infected with Saccharopolyspora erythraea. The only information I found on this bacteria is about its production of erythromycin.


texts:
Why do we feel terribly cold on catching fever of any sort, however our body becomes hotter?
Why is it that a rise in temperature makes the sufferer feel colder? Also, sweating symbolises betterment of the conditions. Why?
{This question has been asked with reference to personal experiences}


texts: Can your immune system's cells destroy you? (Critical thinking and Fictional sense)

texts:
In an imaginary sense, If you alone were replicated into 2 so that there should now be 2 of "you" (meaning you both have the same DNA). Then let's say one of you shrunk to the size of a bacteria, and was placed inside the other you (normal human size. Let's call this the actual you).

The question is how would your immune system affect the bacterial sized you in your own body?

Would white blood/T cells try to get rid of the smaller you?
If so, how? And could the smaller you die from this?


texts: Do the light and dark reactions happen at the thylakoid?

texts:
My professor said that light reactions and dark reactions happen at the thylakoid. He did not choose the answer that "both reactions happen at chloroplast".

Isn't the thylakoid a part of the chloroplast?


texts:
What is an MHC restricted peptide?

I got this definition from wikipaedia, but cannot exactly extract what the phrase MHC restricted peptide means.

  MHC-restricted antigen recognition, or MHC restriction, refers to the fact that a given T cell will recognize a peptide antigen only when it is bound to a host body's own MHC molecule. Normally, as T cells are stimulated only in the presence of self-MHC molecules, antigen is recognized only as peptides bound to self-MHC molecules.

I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful.


texts: Is there any simple explanation as to why human bones are more curved than straight and are thicker at ends and thinner in the middle?


texts: What mechanisms do animals living in groups (herds, packs, swarms) have against spreading contagious diseases?

texts:
While for example a wolf pack provides protection to a sick wolf, increasing its chance of survival, there is a risk of infecting other members of the pack, decreasing their total chance of survival.

Do animals have mechanisms for preventing that? For example the sick member leaving its group temporarily?


texts: Is it possible to exclude article types in a PubMed search?

texts:
I have a question about searching PubMed. I want to search for original research papers while omitting reviews. Is this possible in PubMed?
Example
If I am interested in the relation between Acute Renal Failure and Salt, I could use the following search string:

("Acute Kidney Injury"[Mesh]) AND ("Sodium Chloride"[Mesh])

Using the column on the left of the article overview list, you can select which article types you are interested in.
Question
But I wondered if it was also possible to exclude a specific article type (e.g., reviews) from the search?


texts:
According to Tiefenbacher,

Egg white is naturally alkaline with an initial pH of 7.6–7.9 but in storage the loss of carbon dioxide by diffusion through the shell
increases the pH of the egg white up to about 9.7 with age.

The loss of $\ce{CO2}$ means loss of $\ce{H2CO3}$, an acid with pKa of 6.3. This reduces acid and in a neutral solution pH would approach 7. Since it goes up towards 9-10, what is the base? Albumin is a buffer in biological systems but I don't think it is that strong a base. What is the alkali causing pH of around 9-10?


texts: Why doesn't alum coagulate my cyanobacteria?

texts:
My collected rainwater has a pronounced blue-green tint which I believe to be due to the presence of cyanobacteria.
I have been trying to remove the cyanobacteria using aluminium sulphate, but it doesn't seem to work.
Would anyone like to suggest why?


texts: Why a repeat wasp sting cause an anaphylaxis shock?

texts: I understand that an anaphylaxis shock caused by a huge dose of histamine. But why the first sting does not cause an anaphylaxis shock like the second sting? As i think there may be a relevant between antibody and histamine because the victim already have antibody presence in the second sting, is that right and what is it?


texts: How much plant grow is required for a human's oxygen consumption?

texts:
I think Plants do:

6CO2 + 6H2O -> C6H12O + 6O2

I'm thinking that plants take 12 + 6 moles of oxygen and give back 12 mols of breathable oxygen and 1 mol of Cellulose.

I've read that a person needs about 550 liters pure oxygen (not air) per day, which I believe is about 785 g of oxygen (1L /22.4 L/g * 32 g/mol * 550 L).

I've read that grass is the most common plant, and is about 85% water.

Cellulose is about 162 g/mol, O2 is 16 g/mol, so for every cycle of photosynthesis, a plant's increase in sugar weight yields about ((6*16)/162) = 59% weight in oxygen. Since this sugar weight is only 15%, a plants total weight in growth will produce .59 * .15 = 8% weight in oxygen.

Does that mean that if a person needs 785 g of oxygen per day, there needs to be 9812.5 g (about 21.6 bl) of new plant growth that same day?


texts: Is protein production doubled if you have homozygous dominant genes as opposed to heterozygous genes?

texts:
At school we were taught in quite simplistic terms. We were told that there is a dominant and recessive type of every gene and that if the dominant gene was present, the protein is produced and if it isn't, then a protein is not produced. We were just told that dominance was just an intrinsic property of some genes.

However, upon researching a little, I see that some genes are dominant because their corresponding allele simply doesn't make the protein but the dominant one does (please correct me if I'm wrong).

Does this mean that if someone is homozygous dominant for a particular gene, they produce double the amount of that certain protein as someone who has heterozgous genes or is there a mechanism that suppresses the expression of one of the dominant genes?


texts: If I were to do a blue/white selection of transformed E. coli on LB agar ampicillin plates at room temperature (23⁰C) for about 2 days and 18 hours, will I run into the issue of satellite colonies or any other issues?


texts:
I came across three terms in an article on pseudocopulation. However I don't quite understand what it means.

They are:

1) solitary and haplodiploid

2) social and haplodiploid

3) diploid

These are mentioned in reference to pollinator mating systems in orchids. Could anyone please explain the above mentioned terms?


texts: What are the response frequencies of sensory neurons?

texts:
Both visual and auditory stimuli are sent to the brain via ganglion cells (retinal resp. spiral). Both are the first cells along their resp. pathways that produce action potentials.

My question concerns typical frequencies of action potentials sent along the axons of the visual vs. auditory ganglion cells as a reaction to a "typical stimulus", i.e. a medium long, medium strong signal of some fixed frequency (e.g. light: red, sound: 440Hz) against a white resp. silent background.

Are these frequencies of comparable range, or does one type of ganglion cell (retinal vs. spiral) fire with a significantly higher or lower rate than the other?

(The question would not make sense, if the physical frequencies of light and sound - which trigger the receptor cells - would be coded by frequencies of action potentials. But I assume that this is not the case, is it?)


texts: What exactly does 'reverse use-dependence' mean?

texts:
I understand 'use-dependence' related to a drug, for instance, more angiotensin2 effects in a hypertensive more prominent is the action of angiotensin2 receptor blockers. But I do not get the term, 'Reverse use-dependence'.

https://en.m.wikipedia.org/wiki/Potassium_channel_blocker
In this site, in Medical Uses, the term is mentioned.


texts: Difference between null and recessive allele?

texts:
I get that in a single gene locus, an individual can have RR, Rr, or rr as the two alleles for that gene. R is "wild type" because it is the allele occurring most frequently. r is the allele that is not WT.

RR and Rr show dominant phenotypes, whereas rr shows the recessive phenotype.

But what's the difference between r and a null allele (allele generated by a loss of function mutation outputting the complete loss of the WT phenotype)? Where _ is a null allele, my questions are below:

R _ would produce the same as Rr, correct or not?
r _ would produce the same as rr, correct or not?
_ _ would produce the same as rr, correct or not?


texts: Can a color-blind person see color with filter glasses?

texts: Why does color vision improve in color-blind persons using these filter glasses from Enchroma? Will a color blind person be able to see the same colors on a television? I'm asking, because the colors for every point on a TV screen are combinations of red, blue and green.


texts: At what point in life's history was biodiversity at its greatest?

texts:
When considering plant & animal species throughout the entire Earth, at what point in life's history was biodiversity at its greatest?

The aforementioned question stems from this article about extinction rates, and me becoming curious of the period of time where there was the greatest difference between new/current species rates and extinction rates (while favoring new/current species rates).


texts: How can I get the coding region from gene sequences?

texts: So, I have a file with 600+ sequences of a gene, each one from a different population. This file was obtained after blasting the chromosome sequences against the gene sequence. However, I need the coding regions as well. Should I do the same and blast the chromosomes against the exons, or should I blast the gene sequences against the exons?


texts: Three foramen lying in one vertical plane

texts:
In the human skull we can see that 3 foramina named as supraorbital notch(foramen) , infraorbital foramen and mental foramen share a common vertical plane.

Is there any surgical significance of for such a geometry or its just a coincidence?


texts: Evolutionary uselessness of the male nipple

texts: The Male nipple serves no evolutionary function, yet it remains in the Genomic code. Is there only one Gene for the human nipple?


texts: What direction is a sequence in databases written?

texts:
In many databases, the DNA sequences for proteins are given as a string of a,t,g,c without specifying whether the starting is from 5' or from 3'.
Also it is not specified if it is the coding or non coding strand.

Is it because all the sequences are written from 5' to 3' of coding strand only?


texts: In the endomembrane system, after a protein leaves the rough ER, where does it go?

texts: It can either go to the smooth ER then to the Golgi or it can go directly to the Golgi, right? Also, the smooth ER gets all of its material to synthesize things from the rough ER, right? Sorry, I looked around but couldn't really find a direct answer to my question. Thanks!


texts: BLAST protein sequences from 2 different bacterial species

texts:
I am interested in finding a consensus sequence of a protein found in e.coli, in Pseudomonas aeruginosa. I am using pseudomonas.com to BLAST p the amino acid sequence of the protein that i have found with help of PDB. However i have seen that people do the BLAST N first and then BLAST P if they are interested to check whether they can find similarity of the protein sequence. Also in PDB the aa sequences are strange since they are not that specific.

Any advise on this issue or reliable links to databases when i can search and align sequences for similarities?

thanks


texts: Is this a moth? How might these wings unfold?

texts:
I'm having trouble understanding how these wings might work. Are they somehow folded or bent by 90 degrees so that part of the wing is vertical and part is horizontal to be more compact?

If so, how mechanically are they then made quickly more rigid and straight each time it enters flight, which should be fast to avoid being eaten?

Also, I'm guessing this is some kind of moth, but I have no idea. I don't really need an exact species ID, but some classification guidance would be appreciated!

This individual is about 2 cm long, and was seen recently (late July) in Taipei, on a hot, sunny day.


texts: What information do microarray image convey?

texts:
OK I have read that a cell generates 4 kinds of digital (to be precise discrete) data namely DNA, RNA, Protein (sequences that can be encoded as string sequences of nucleotides/ amino acids) and micro array image. I am not a biologist, but my interest is in the statistics and information theory of these data. I would like to know what information do DNA micro array image convey? For example after processing it with the aid of a suitable software, what sort of information we do obtain?

Sample micro array image:


texts: Around what time did dark skin disappear from Europe?

texts: As Europeans gradually became lighter skinned, there would have been people that still had dark skin. Around what time period did Europeans become completely light skinned?


texts: Why are bees attracted to Stag Hides in Lime bath

texts:
A friend has some stag hides in lime-water solution. He noticed the stag hides were covered in bees of several different species. He also noticed that the nearby sheep hides in a similar bath have no bees. What attracts the bees to the stag hides? Alternatively, what repels them from the sheep?

There are a lot more bees when the sun shines. The bees principle seemed interested in the hairy side of the hides. There is a small stream and a dried up pond nearby, so probably other places if they just wanted a drink. There is no noticeable scum on the water of either container.

Photos of the stag hides:

Photo of the sheep hides:


texts: Methods of nuclear transfection - nuclear transport

texts:
I am reading through the ENCODE papers, which is taking me well out of my comfort zone in terms of modern laboratory techniques. At the risk of asking a question which may well be thoroughly answered somewhere else on the internet, I was hoping for a brief explanation of nuclear transfection.

In Whiteld et all, they describe the direct assay of transcription factor binding site efficacy in human cells.  To do this, they transfect a luciferase plasmid, presumably into the nucleus of the cell (because they subsequently observe that the luciferase plasmid is transcribed).

Reading through Materials and Methods and getting to the supplementary file, they disclosed their transfection protocol. The relevant reagants appear to be:

FuGene 6

  a nonliposomal formulation designed to transfect plasmid DNA into a wide variety of cell lines with high efficiency and low toxicity.

(From Promega's website.)

Lipofectamine LTX

  efficient reagent for plasmid delivery and protein expression

(From Invitrogen's website.)

PLUS reagent

  PLUS™ Reagent is used in conjunction with transfection reagents, such as Lipofectamine™, to enhance transfection in adherent cell lines.

(From Invitrogen's website.)

Apparently, the protocol is to combine the DNA plasmid with transfection reagent, wait a few minutes, and then add in the cells, and incubate at 37ºC for 24 hours. That's all that is required to get the plasmid into the nucleus.

I have consulted Wikipedia and Strachan and Read's Human Molecular Genetics 4th edition, but been unable to answer my question about this technique.

I think I have a pretty clear understanding of how these reagents are able to get through the cell's lipid membrane, but I don't have a similar understanding of how the DNA then passes to the nucleus.

In Human Molecular Genetics 4th edition, I can find only one paragraph about plasmid transfer across a nuclear membrane, page 704: "Transport of plasmid DNA to the nucleus of non-dividing cells is very inefficient because the plasmid DNA often cannot enter nuclear membrane pores. Various methods can be used to faciliate nuclear entry such as conjugating specific DNA sequences or protein sequences (nuclear localization seuqences) that are known to facilitate nuclear entry, or compacting the DNA to a small enough size to pass through the nuclear pores."

But nothing in the materials and methods section of Whiteld et. all mentions any of these techniques. I'm sure they would have mentioned if their plasmid included a DNA conjugation sequence, so that can't be it. Perhaps these reagents implicitly include some sort of DNA compaction polycation, such as PEG-CK30?

Isn't the cytoplasm an extremely hostile place for DNA plasmids? Shouldn't they just flail around in the cytoplasm until they are digested?

Or perhaps these vectors sneak into the nucleus during mitosis? (This is a theory that just occurred to me when contemplating the "non-dividing" qualification in the Strachan quote.)

Since the question isn't addressed in the paper, I can only assume the answer is elementary and something that a professional cell biologist would be expected to know. I've run out of obvious next steps for finding the answer, so I beg pardon in advance for asking it.


texts: Is there a known efficiency rate for CO2 capture from ambient air in photosynthesising plants?

texts:
When humans take in air to their lungs, we capture about 5% of the total quantity of the air as oxygen (which in turn equals about 24% of the available oxygen in the air)
Is there an equivalent rate for plants when photosynthesising (or a rate for any one specific plant?). I.e. if a plant had a given amount of air pass through their stomata, what percentage of the available CO2 is used by the chloroplasts?


texts: Why do crocodiles have a high concentration of lactic acid in their blood?

texts:
Crocodilians have high concentration of lactic acid in their blood. This is the cause that prevents them from prolonged intense activity, since prolonged intense activity causes the muscles to secrete more and more lactic acids, up to the stage where the lactic acid level become lethal - even for the crocodile.

So the shortcomings of high level of lactic acid are clear, it restricts activity and endangers the croc to death.

So why in the first place crocodiles have high level of lactic acid? What is the advantage of this?


texts: Do all monarch caterpillars have two pairs of needle-shaped protrusions(or they can have three pairs)?

texts:
I found this here:

Is this a monarch caterpillar?
Do all monarch caterpillars have two pairs of needle-shaped protrusions?


texts:
It is common practice to use ice packs on injuries that cause bruising and swelling. It seems to be  an effective method to assist in reducing swelling.

Why does ice reduce welling?


texts: Do humans secrete and detect pheremones?

texts:
Many animal species are capapble of secreting and also detecting pheremones from members of the same species, which relay messages and signals such as indicating sexual readiness.

Do humans do the same thing? Are humans capable of communicating in this subconscious fashion?


texts: When it comes to hyperthyroxinemia, how is it possible for TSH to be normal when there is an elevated thyroxine concentration? What I know so far is that it is caused by a mutation in the Human serum albumin (P02768)that carries normally around 10% of the thyroxine.The mutation apparently makes it have a higher affinity for thyroxine, but how does it allow the TSH levels to remain normal?


texts: Prostate, seminal vesicles or testis which one is bigger(by volume and size)?

texts:
I can't understand this by looking at these photos, especially the last picture makes me more doubtful.

Do you know which of them is the biggest one by volume?

Another question is, what is the biggest organ in the male reproductive system? (Note that the bladder is not a part of it.)


texts: I am designing a researching proposal for the class. Because it uses microinjection to up-regulate the gene in C. elegans, the plasmid pCFJ104 - Pmyo-3::mCherry::unc-54 sequences has been chosen. But because the plasmid already has a unc-54, I wonder if there a way that to cut the unc-54 out of the plasmid?


texts: What makes the cytoplasm a reducing environment?

texts:
It is known that the cytoplasm is a "reducing" environment, where disulfide bonds cannot form (will soon be reduced to 2 cysteines) [I'm not putting a link as this is a fact in many biology textbooks].

The NAD+:NADH ratio is high in the cytoplasm (around 1000 (725 in this paper)), which should make the cytoplasm an oxidising environment. The NADP+:NADPH ratio is low, making a reducing environment. Also, there is Glutatione Reductase, which should also make the cytoplasm a reducing environment. Which one of these is the underlying cause of this reducing environment? Or is FAD also involved in this?

As an additional question, what does reduce disulfide bonds? Is it using the NADPH or the FADH2 or the glutathione reductase?


texts:
It's easy to find information about the biggest animals at land / at sea / in the air. But what was the biggest underground-living animal that ever existed?

No animals that were forced to live underground (e.g. pit ponies)
The animal should live at least 95% of its life under the earth (e.g. foxes)

There are two possible answers:

By length
By mass

My first guess was a mole


texts:
I am a graduate student looking to incorporate some protein engineering into my training. I have been reading a lot about E coli lysate based systems, but they still require 3rd party additives like amino acids etc.. ($$$).  I need this to be ultra cheap as this will be a side show until I can show something for my efforts. I prefer a cell free workflow because of the quick turnaround from template to protein and ease of purification. My backup plan is just to add a tag at the end of my constructs but I would prefer to avoid this.

Any suggestions would be much appreciated.

Thanks


texts: Backbone hydrogen bonds between adjacent amino acids in a protein?

texts:
Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO?

Are there any examples of such situations in proteins and how common are they?

If such bonds are rare, why is this so?


texts: Is there a difference between Luria Broth and Lysogeny Broth?

texts: Is there a difference between Luria Bertani and Luria Broth? Or are they both the same thing? Is it necessary to autoclave LB medium after it has been made?


texts:
As part of a data analysis project, I encountered two kinds of single-cell assays
for transposase-accessible chromatin using sequencing (single-cell ATAC seq) methods. The first uses combinatorial indexing (also called sci-ATAC seq  [link]), whereas the other counts the number of Tn5 cuts in peaks (called sc-ATAC seq  [link]). I'm not a trained cell biologist or biotechnologist so I am possibly overlooking subtle similarities between the two methods here.

To my knowledge, sci-ATAC seq generates a binarised array, whereas sc-ATAC seq generates a counts matrix. (I'm also aware that there are post-processing tricks to convert binarised arrays to other array types, eg, normalised counts arrays.)

My question is, what about combinatorial indexing results in the array being binary rather than integer-valued? I'm looking for an explanation that relates the data collection method and combinatorial indexing with the resulting array type.

Thanks in advance!


texts: Calculating Rate of Growth without a Population

texts:
Lets say that by studying individuals of a rare species, you have determined that species gestation period, age of sexual maturity, average time between pregnancies, maximum lifespan, and average number of individuals born per pregnancy. However, you have never had enough specimens at the same time to establish a breeding population.

How can you calculate the maximum rate of growth of a population from just the information already gathered? If not, what other information would be needed?


texts: Hiding identical sequences in NCBI web interface

texts:
Sometimes there are identical sequences in Genbank/Genpept, most often coming from the same species but different strains. Ie if I look up "bacteria chitin synthase", the 624-aa protein from Dickeya dadantii shows up three times. There even is an "identical proteins" link.

Is there any filter that I can use to get only one sequence from every group of identical ones? I mean, other than parse downloaded file on my own computer.


texts:
Often, a smooth response to a hormone means that some processes must be sped up and others must be slowed down.

How can a single hormone have opposite effects like this?


texts: How do catalase and other antioxidants neutralize free radicals?

texts:
In learning about how cofactors are essential to proper enzyme function, my textbook mentioned catalase and its relation to the human body. According to my textbook, catalase is similar to hemoglobin in that it has 4 hemes which cradle an Fe (iron) atom; the iron atom is used to neutralize free radicals when it "pulls on the substrate's electrons, which brings on the transition state" after catalase is holding a substrate in its active site. I already know that free radicals have one or more unpaired electrons which make them dangerous as they "seek out" an electron to complete its pair on any molecule, atom, or ion it can find, perhaps causing significant tissue damage in the process. I also know that the transition state is a key point in a reaction in which the activation energy required has been met and the reaction will continue spontaneously until it ends.

My question is, what exactly is happening here that helps to neutralize a free radical, and what is the part after the transition state doing?

If I had to guess, based on that cofactors generally can be affected during a reaction, perhaps Iron somehow binds with the free radical and share its electrons, effectively neutralizing the unpaired electron as well as using up the Iron atom? I imagine the "pulling" in the book could fit a description of a weak chemical bond/attraction, but I'm still unsure.


texts:
Kwashiorkor is characterised by decreased serum protein (including serum albumin) due to poor dietary protein intake.

What is the effect of this lowered serum protein on highly-protein-bound drugs? Is it substantial enough that administering such drugs (such as warfarin, though it's hard to imagine a situation in which a patient with kwashiorkor would need anticoagulant therapy) is potentially dangerous, and if so, can this be compensated for?


texts:
I have a phobia of bugs (or other small creatures) living inside my pillow and crawling into my ear in the night. It might seem silly, but bare with me.

Recently I got wondering, what organisms could actually live inside a casual foam pillow?
I machine-wash it every now and then to keep it clean.


texts:
I know we defecate or/and urinate to rid ourselves of toxins and excess undigested food. If I was somehow able to get exactly what my body needed to function.

Let's say that I create a pill (or something) that provides the body with literally and exactly the nutrients and hydration it needs, would there still be a reason to carry out excretion?

Do humans or any animal, absolutely have to excrete?


texts: Is it ok for Chili pepper plant's fruits to fall into its soil?

texts: I wonder if Chili pepper's fruits which fall into the soil near the plant will harm it, since the peppers are so spicy for people.


texts:
I am working on my bachelors thesis, where one part of it is to find width of vein in fingertip. I use database images and extract vein patterns from it, but i have to calculate the width of vein and I have no comparison of how many pixels in pic refers to how many milimeters in real.

I would like to ask how wide is the vein approximately in fingertip or in finger.

Thanks a lot, it would be really helpful.


texts: Can the shoulder bones grow after the growth plates have fused?

texts:
Body builders have broad shoulders. If one start lifting weights after one's growth plates have fused, can one still increase the width of one's shoulders? If yes, does that mean shoulder bones can grown longer?
Which bones, (if any) can grow longer after growth plates have fused without causing an abnormal condition like acromegaly?


texts: Is there any virus that contains both DNA and RNA in its genome?

texts:
It is known that viruses contain DNA or RNA- either one and not both.

I came across a question: Which virus contains both DNA and RNA?


texts: Does an increase in cancer cell traction forces increase metastasis of the cancer cells?

texts:
I am not very familiar with biology, but I have read some articles about cell traction forces lately, where the cells are cancer cells. I found this very interesting, so I thought it might be nice to read about the relationship between cell traction forces and metastasis for cancer cells. I thought that an increase in cancer cell traction force should indicate that there would be more metastasis. I have looked at two references, but one of the articles says that increasing the cell traction force increases metastasis [Kraning-Rush et al. (2012)], while the other says the opposite [Indra et al. (2011)]. Both are experimental articles.

My question is therefore:

Is it correct that most often, an increase in cancer cell traction forces would increase metastasis, or should it most often decrease metastasis?


texts: Can undigested food proteins enter the bloodstream?

texts:
I know that food proteins in our digestive system are denaturated and broken down into amino acids or very small peptides that are then absorbed in the small intestine. If some proteins stay undigested they move to the large intestine and either gut flora eats them or they are excreted.

But lately, I've been hearing a lot of stuff like "if you eat a lot of eggs there will be egg proteins in your blood" or "drink liquid collagen and it will travel to your skin through the blood". It seems really stupid to me. I imagine if all sorts of food proteins entered our blood they would wreak havoc there catalyzing random reactions, triggering immune responses, etc. So it cannot be a very frequent event. But I've been wondering if some of the food proteins can on occasion end up in the blood of relatively healthy people. Does this ever happen? With food allergens maybe?


texts: Can oral baking soda effect tumor cells in mice

texts:
Could anyone explain me please, how exactly (according to research article in Cell journal) adding the baking soda in drinking water can influence the acidity of tumor cells? What about homeostasis and ph buffer systems?

In this article in Cell, discussed in this news source, in addition to a number of experiments with cell lines, a live mouse model with xenograft tumors was used to show the effect of oral bicarbonate on tumor acidification, and support the in vitro results re: the effect of tumor associated acidification on the circadian clock.

How is it possible that oral bicarbonate could make tumors in these mice less acidic? Wouldn't the physiological buffer system prevent any changes to the pH in tissues?


texts: How do trees use Adhesion and Cohesion to move water against gravity?

texts: I have an AP Bio class where I have to name 3 properties of water and I chose adhesion and cohesion for one of them. I'm having trouble finding out how exactly trees use adhesion and cohesion to move water. There is a lot of different answers out there on the net. How do trees use adhesion and cohesion to move water against gravity?


texts: I've seen men starting to lose hair in almost all ages. Why is the onset of hair loss in men different? Is there a normal distribution?


texts: Why can cats interpret things on a monitor/tv, but dogs cannot?

texts:
E.g. you can see a lot of videos where cats are smashing some mouse or spider on an ipad, but I have never seen it with a dog. I have a dog myself and I know that he sometimes responds to the sounds from the TV, but not to the images.

Why is that?


texts: Correlation seen with low billirubin levels but not the gene that causes Gilbert's syndrome

texts:
I was reading the following study on associations between bilirubin and CAD (coronary artery disease). They looked at the bilirubin association, and the genes that cause Gilbert's syndrome, which increases bilirubin concentrations. Study here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648823/

The study states in the abstract:

  "Both polymorphisms showed a strong association with bilirubin levels with higher levels for homozygote carriers of the minor allele."

But then goes on to say, a few sentences later:

  "Logistic regression analysis revealed low bilirubin levels but not the UGT1A1 polymorphisms to be significantly associated with CAD: OR (95%CI) 0.90 (0.86–0.94), p=2.6×10−6 for men and 0.77 (0.68–0.87), p=3.2×10−5 for women, respectively for each 0.1 mg/dl increase of bilirubin."

How can we see a "strong association" between the gene that causes gilberts sydrome and bilirubin levels but not see an associatoin between the gene and CAD risk? If the study is stating bilirubin is significantly associated with CAD risk, and the polymorphism is strongly associated with the level of bilirubin, shouldn't it follow that we would see an association between the polymorphism and CAD?

My guess is that polymorphism correlation to bilirubin levels isnt actually all that strong, or that the association between bilirubin and CAD isnt all that strong, or both. Hoping someone could offer some thoughts on what they think is going on.

Thanks!


texts: How to preprocess htseq counts for gene expression (TCGA)

texts:
I want to prepare a matrix of gene expression to analyse TCGA LAML data.

The required data is available at TCGA LAML - Gene expression quantification.

The following is an example of the kind of data retrieved from the TCGA data portal:

ENSG00000000003.13  9
ENSG00000000005.5   1
ENSG00000000419.11  661
ENSG00000000457.12  1434
ENSG00000000460.15  1211
ENSG00000000938.11  405
ENSG00000000971.14  251
ENSG00000001036.12  786
ENSG00000001084.9   4423
ENSG00000001167.13  5038
ENSG00000001460.16  246
ENSG00000001461.15  2773
ENSG00000001497.15  1932
ENSG00000001561.6   1693
ENSG00000001617.10  55
ENSG00000001626.13  8
ENSG00000001629.8   4629

Each row displays, for each gene, the quantification of read counts by the htseq tool.

My question is, how do I have to preprocess the data (e.g. regarding gene length) before using data for subsequent analysis?

In this case I will not consider normalisation (such as loess) and batch effects removal (e.g. with combat).


texts: How does vasoconstriction increase the pressure of blood?

texts: Is the increase of pressure due to the decrease in volume? Wouldn't the decrease in volume push the components of blood closer to one another resulting in an increase of repulsive forces, thus increasing pressure? Or is the increase in pressure due to the heart pumping the blood with more force in order to maintain blood flow?


texts: How to get the average number of pairwise differences among populations?

texts:
I have genetic data in .structure and .vcf format (and can easily reach other formats with PGDSpider). The population of interest is structured and I would like to calculate the average number of pairwise differences (over a given window) between any pair of populations.

Is there an existing tool that would do it?


texts: What's the transposon difference between chimps and humans?

texts:
I was reading that humans and chimps share 98-99% of the same DNA sequence but I also read humans and chimps only share around 20% of the same proteins. Also, 45% of the human genome is transposable elements, It's 42% reverse transposons and 3% DNA transposons.

So, I wanted to know the difference between humans and chimps when it comes to transposable elements, especially reverse transposons.

Sources added:

Eighty percent of proteins are different between humans and chimpanzees. ncbi.nlm.nih.gov/pubmed/15716009 and Retrotransposons - In mammals, almost half the genome (45% to 48%) is transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons, while DNA transposons account for about 2–3%.[3] [en.wikipedia.org/wiki/Retrotransposon]2


texts: Balanced vs Maximized Codon Optimization

texts:
I have worked with the optimization of several viral proteins, from different viruses/families, with different results.

When Menzella, 2011 was published I tried that method.  I found quite the contrary result, in that randomization did far poorer than straight maximization of codon usage.  I chucked this up to working within the context of viral infection (though it was also true in transient expression from plasmid transfection under CMV promotion).

I was quite excited by Pechmann and Frydman's Nature article which highlighted the importance of the location of the codon within the protein when regarding optimal vs suboptimal codon selection. Oddly enough we were able to deploy this information most successfully with the purposeful deoptimization of a protein.

Pairing a locational awareness, screening for secondary structure, and then maximizing codon optimization has had the best results for more than a year.  By maximization, I mean choosing the most optimal codon in every instance that doesn't violate:

Needed restriction sites
Predicated Secondary Structure
Location gradient to a lesser extent (ibid.)

This is all well and good, but we've been having problems with my institutions preferred vendor for gene synthesis.  A post-doc that just joined my lab recommended a company I had never heard of before, and they posed an optimization strategy I had never considered before.  Instead of maximizing codon optimization, they propose a "balanced" codon optimization that matches the normal distribution of codons in the target organism.

For example, the codon bias for alanine in humans breaks down (roughly) as follows:

GCC 65%
GCT 20%
GCA 11%
GCG 4%

As opposed to a maximization strategy which would seek to use "GCC" when ever possible and only when there was an issue switch to "GCT," the balanced stratgy would seek to replicate the above distribution as closely as possible.

Has anyone tried a balanced codon approach, especially when compared to a maximization technique?  My overall goal is to maximize expression of naturally poorly expressing protein.  I know that straight maximization can occasionally lead to poor expression for a variety of reasons (often fatal secondary structure), but this seems like it would hardly increase expression at all.

I would be further interested if anyone else had experience within a viral context.

I know that there have been a few related questions, mostly in the context of E. Coli.  I don't think this is a duplicate, but would be willing to remove if it is seen as such.  If I run into some extra funds I may test this empirically, but often when I'm trying such a test it's only in relation to 2-3 proteins, which might not be representative.


texts:
Rubbing the leaves between your fingers feel strong, pleasant aroma of citrus.

The leaves are not fuzzy and are about 2 cm long.

In Germany.


texts: Why does anxiety cause diarrhea or constipation?

texts: Anxiety sometimes cause diarrhea, sometimes constipation, and sometimes both. It's interesting because it seems their underlying neurophysiology is somehow different. What are underlying physiological processes that lead to these two symptoms in anxious people? Particularly in terms of the activity of sympathetic and parasympathetic nervous system?


texts: How do viroids propagate to other hosts?

texts:
As viroids are simply non-encapsidated non-coding RNA molecules, it is difficult to imagine a mechanism for their continual infection, other than horizontal transfer which doesn't seem to be the case.

Is there a working theory on how viroids propagate and continually infect hosts?


texts: Can methionine peptidase liberate selenomethionine?

texts: Can methionine peptidase liberate selenomethionine from proteins? I'd be happy to know if any can that are active in humans, but am also especially curious about METAP2.


texts: What is the physiological difference between snorting/swallowing cocaine

texts:
I know that mucosa inside the nose absorbs cocaine molecules when snorting cocaine, but what difference is there compared to swallowing?

Also more cocaine administration equals more cocaine molecules in the brain equals more inhibition of repute equals more serotonin–norepinephrine–dopamine in the synaptic clefts equals more work for receptors equals more intense effect, right?  What about the duration of a particular molecule which inhibits reuptake? How long this particular molecule stands there?


texts: Restriction Mapping of Plasmid Assignment

texts:
pUWL22 is a circular, double stranded, 10.5 kb plasmid. It contains a
  gene encoding an enzyme that confers ampicillin resistance in the host
  bacterium. Cloning into the kpn I and Sst I sites abolishes ampicillin
  resistance, whereas cloning into other sites on the plasmid does not.
  Digestion with the following restriction enzymes singly and
  combination results in the following data:

Enzyme Digest     ()()()()()()   Fragments Produced (kb)

Hind III  ___________________________10.5

Kpn I  _______________________________10.5

Not I  _______________________________10.5

Pvu II  ______________________________10.5

Sst I  _______________________________10.5

Stu I  _______________________________10.5

Hind III + Kpn II  ___________________8.5  _______________2.0

Hind III + Not I _________________8.0  __________________2.5

Hind III + Pvu II ________________6.0  __________________4.5

Hind III + Sst I _________________7.5  __________________3.0

Hind III + Stu I _________________7.5  __________________3.0

Stu I + Not I  ____________________10.0  __________________0.5

Stu I + Pvu II  ____________________7.5  __________________3.0

Now the actual questions:

  A) Create a circular map of pUWL22, designating the Hind III site as
  the position 0 on the map. Once you have completed the map, indicate
  the relative position of the ampicillin gene.

My plasmid mapping:

What I need help with in indicating the relative position of the ampicillin gene. In the statement above it said "Cloning into the Kpn I and Sst I sites abolishes ampicillin resistance." Does that mean its inbetween Sst 7.5 and Kpn 8.5? Please tell me where it is and why its there.

P.S. I made a mistake on the on the Sst I enzyme, it's suppose to be @ 7.5 not 7.8.

The question after that is:

  B) Propose 2 other double digests that could be done to confirm your
  analysis. Predict the sizes of the fragments that would be generated
  from these digests.

Please answer this and explain why.


texts: What would happen if we place denatured DNA in acidic medium?

texts: DNA can be denatured at high temperatures or in alkaline solutions. But DNA can be annealed at low temperatures. I want to ask, could it be annealed in acidic medium?


texts:
I understand that HKA test tests for neutrality. And under neutrality we say that "ratio of segregating sites with species (S1) and fixed differences between locus (F1)" (S1/F2) at one locus is equal to S2/F2 of another locus.

But what will S1/F1 > S2/F2 signify? And what will S1/F1 < S2/F2 mean?


texts: What is the chemical structure of myosin? Specfically, what functional groups or monomers are they made of?


texts: Which secondary structures of RNA are symmetric?

texts:
I'm trying to understand what is the meaning of this statement.

  A088518       Symmetric secondary structures of RNA molecules with n
  nucleotides.      4

  %I

  %S 1,1,1,2,2,4,5,9,12,21,29,50,71,121,175,296,434,730,1082,1812,2709,

  %T
  4521,6807,11328,17157,28485,43359,71844,109830,181674,278769,460443,

  %U
  708840,1169283,1805291,2974574,4604363,7578937,11758552,19337489,30064037

  %N Symmetric secondary structures of RNA molecules with n nucleotides.

  %C Diagonal sums of triangle in A088855. [From Philippe Deléham, Jan
  04 2009]

  %C Number of prime symmetric Dyck (n+2)-paths with no ascent of length
  1. E.g. the a(3) = 2 5-paths are

  UUUUUDDDDD and UUUDDUUDDD. - David Scambler, Aug 27 2012


texts: Temperature Tolerance In Relationship To Body Temperature

texts:
A humans body temperature averages at around 98.6°F
A dog's body temperature averages at around 101.5°F

If the temperature outside is 45°F who would feel colder?

The dog's temperature is higher than the human. So you would assume since its temperature is higher it would feel warmer than the human.

However, the temperature difference between the body and the external temperature is the following:

Difference in humans internal and ambient temperate: 52.6°F
Difference in dog's internal and ambient temperate: 56.5°F

I'd like to know as I keep telling my mom that the dogs feel hot when she puts on doggy sweaters for them when its slightly cold for us humans.


texts: Computer Models of E Coli / Saccharomyces cerevisiae metabolite pathways

texts:
Are there mathematical models one can use to predict the expression levels of a foreign gene inserted into a well studied host organism like  E Coli or S cerevisiae?

I'm not, obviously, looking for some magical, accurate in silicio model; but even an approximate heuristic. e.g. Before starting a cloning experiment to estimate levels of a secondary metabolite expression in different organisms that both contain the substrate natively but may have it in different levels.

Alternatively, can the math models help in estimating which other competing pathways may be draining away a precursor of interest so that a rational attempt can be made to block such pathways to promote selective expression of the metabolite of interest.

Of course, the cloning experiment is the gold standard but are there ways to simulate a part of this and reduce the dead ends of experiments. Is there standard software I ought to be looking at?


texts:
In total how many blood types are there?

And why do people normally know only 8 of them? (A+, B+ , AB+ and O+ and Rh- counterparts)


texts: Are brassica oleracea cultivars the same species?

texts:
I used to think Brassica oleracea cultivars (e.g., kale, cabbage) were different species originating from the same species Brassica oleracea.
But it seems I were wrong, right?

If so can we breed two different cultivars with each other, e.g., cabbage + cauliflower?


texts: Does translation have a way of preventing mismatching between mRNA codons and tRNA anti-codons?

texts:
What happens in translation if a tRNA with an inappropriate (non-cognate) anti-codon binds to the A-site of the ribosome carrying mRNA?

For example, what would happen if an ile tRNA with the anti-codon 3'-UAG-5' occupied the A-site when juxtaposed to a met codon: 5'-AUG-3'? This would seem possible to some extent as two of the three  bases pair correctly.

Does something prevent this occuring or are incorrect amino acids removed or the protein degraded?


texts: How do I determine an acceptable $F_0$ value in sterilization?

texts:
Here's a sample question:

  The sterilization process using moist heat is used to kill B.stearothermophilus by heating to 115 degrees C and holding it for 30 mins.

  For B.stearthermophilus, it is given that $D_{115} = 11$minutes and z=10 degrees C.
  Determine the sterilization process equivalent time at 121 degrees C. Is this an acceptable $F_0$ value ?

By using formula $F_0 = \Delta(t) \cdot L$

I found $F_0 = 7.5$minutes.

How do I know what is the acceptable $F_0$ value? I've been told it's 15minutes. Is it 15 mins for ALL sterilization methods or is there a method to calculate this regulatory requirement of $F_0 = 15$ ?


texts: What are limiting factors for intron length?

texts: For predicting genes from a sequenced genome, you need to set a maximum intron length. How long can introns get in animals? Is there some limit?


texts: Predicting DNA nucleotide bases sequence from fully formed protein

texts: I know there are many algorithms (and a lot of different implementations) that allow predicting the outcome of protein synthesis given a set of nucleotide bases present in the DNA. In other words, given a sequence of such bases, produce a final protein (going through a simulation of the various processes that end up in a protein). However, are there any algorithms that allow to predict the opposite, i.e. the sequence of nucleotide bases that were the basis for the synthesis into a given protein?


texts: What are genome wide functional linkages?

texts:
There are two types of interaction classifications used to describe Protein-protein interactions, namely physical and functional. Whilst physical interactions are obvious in nature and methodological determination, I was wondering what a functional interaction/linkage refers to, such as the one cited in the below paper, and is it purely inferred from genomic data?

"Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps."


texts: meaning of the "reads" keyword in terms of RNA-seq or next generation sequencing

texts: I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs can be found here and I've seen a word RNA-seq read. Altough I searched a lot to learn about, I can not find the definition of it, the thingsI found was about performance issues of techniques rather than explanation of the word. So, is there anyone who can simply explain me what is the meaning of this word as well as RNA-seq technique?


texts:
There are four alleles of Adh which are Adh-1, Adh-2, Adh-3 and Adh-4.  Their respective frequencies are 0.11, 0.84, 0.01 and 0.04.  What are the Hardy-Weinberg frequencies of the possible 10 genotypes?

My Attempt:  First I thought that there were more than 10 genotypes (4*3*2*1) = 24.  I've never done HWE with 4 genotypes so im not sure how to use $p+q=1$ or $p^2+2pq+q^2=1$.


texts: Which area of neuroscience\biology deals with the effects of genetics and drug discovery based on brain microcircuits?

texts:
So the title I chose might be a bit too broad or even misleading compared to the specific example I have in mind, but I couldn't choose something longer or more specific than that, so I apologize if that's the case!

Due to its close connection to Autism Spectrum Disorders (ASD) and even some personality dimensions in psychology and my interest in these topics, I was reading an article about the reward circuit (cortico-basal ganglia reward network: microcircuitry, Susan R Sesack and Anthony A. Grace, 2010) which in my opinion is a pretty nice article and as the title suggests talks about the different parts of the cortico-basal ganglia network mostly at a fairly high level of detail (e.g. nucleus accumbens, ventral tegmental area, prefrontal cortex, etc), their interconnections, some physical characteristics of those interconnections, the associated neurotransmitters for the different parts and connections, and some of the functional implications of these topics, and also presents a couple of nice diagrams depicting the afferents and efferents of this circuit. as far as I understand and perhaps obviously, most of this data comes from primate and mouse data, however I would imagine there could be a lot of similarity in humans, and we also approximately know from cognitive neuroscience or other disciplines the general function of some (if not most) parts of this circuit.

The question that came to my mind is, which area of neuroscience or biology deals with modeling and simulating this circuit at this level (not necessarily at the neuron to neuron level) to understand it better, and also understand the effects that genetics or environment could have on it, so that ultimately we might for example come up with a treatment for ASD? is it more related to systems neuroscience, computational neuroscience, systems biology, or even bioinformatics and computational genomics?

Thanks in advance!


texts: A significant amount of research has gone into the fauna of the deep oceans, but not so much that I can find on the deep great lakes (specifically the North American Great Lakes).  I'm interested in seeing pictures and learning more about the types of fauna in these lakes.  Can anyone provide a reference to get me going?


texts:
I have a large amount of protein sequences in the .fasta format and I would like to extract only the amino acid mutations from these sequences, so that, in the end, I want to have a list that looks something like this:
I456L, W675T, etc
Is there a program or way to do this?
Thankful


texts: Can I use fluorophore conjugated antibody as neutralizing antibody?

texts:
I need to order a neutralizing antibody to block a protein of interest.
The pure grade functioning antibody (no conjugates) is substantially more expensive than the fluorophore conjugatated ones.
Can I achieve the same by using let's say Ab conjugated with APC/PE as a neutralizing antibody compared to the pure functioning grade ones?
Any insight would be great.


texts:
I'm studying microbiology in Iran
The university that I'm studying in doesn't provide that much help in research areas and we don't get to research or write essays that much ,while I'm trying to write an ISI essay and communicate with universities abroad in order to get admission for my masters degree and be able to study abroad
But the problem is , I don't know how to start and find ideas for writing papers and research
Like, what is the first step you take as a scientist when you want to start research?


texts: What are Some Classical Examples of Local Adaptation?

texts:
Question

Can you please give a list of classical (textbook) examples of local adaptations?

How to answer

Examples don't necessarily need to include what evidence supports this specific example of local adaptation. A simple description of the local adaptation (e.g. coat colour changes from black on dark soil to white on light soil) and an brief explanation of the reason (e.g. because being nicely camouflaged prevents from predation from hawks) is enough.

I think a list of 10 or more such examples would be great.

Definition of local adaptation

Note that I define here local adaptation as differentially adapted subpopulation of a single species (with existing gene flow between subpopulations especially for sexually reproducing species).

Justification for the question

I found surprisingly complicated to find such list online. I think it could be a valuable post for many.

Examples

Examples of local adaptation (that you are free to add in your answer with a description) include beach mice camouflage, altitude adaptation in tibetans and peppered-moth camouflage.


texts: Effects of HRT on transgender(M to F) physiology and athleticism.

texts:
I often heard of athletes in the Olympics who would be accussed of having an advantage because they were intersexed.

Now I know transgenderism and being intersexed are not the same thing, but they can both involve Hormone replacement therapy.

Therefore would a transgender women (ie: a person assigned male at birth, who transitioned to female) have advantage over cisgendered(not transgender or intersexed) women in sporting events due to anatomy or physiology from previously having a male form?

To add detail, I guess it would depend on the state of their transition, so one could use MMA competator Fallon Fox, as an example, or any other transgender women.

My thoughts on the effects of HRT on athleticism for transgender people is that if they were more advantageous, then they should be dominating their respective fields.

As for the biology, I know that bone growth stops at around 20, but how would the HRT affect their muscles, and would muscles even matter without the corresponding frame?

.


texts: Power consumption of a ATP synthase in Watts

texts: Considering the ATP synthase to be a rotating machine, does anybody know its power consumption and/or power production in Watts? At least roughly, e.g. based on the average chemical energy produced per time unit?


texts: I was wondering if you would be able to help me with discovering what the main regulatory feature of a phosphatase is. I understand many have separate catalytic and regulatory subunits, however, so do kinases so I feel that there is a different answer that I am not understanding. Thank you,


texts: Determining net charge of amino acid at given pH

texts:
I am trying to calculate the net charge on an amino acid, but I seem to be doing it wrong. The question I am trying to answer is "In a pH 7.0 buffer, what will be the charge of Methionine?" We are referred to a table that gives us the following information:
$$\pu{p}K{_\pu{a\mathrm{1},\ce{COO-}}}=2.28$$
$$\pu{p}K{_\pu{a\mathrm{2},\ce{NH3+}}} = 9.21$$
$$\pu{pI = 5.74}$$
From what I understand, if pH > pI, (which it is here), the amino acid should have a negative charge because even though the pH is high enough to deprotonate all the carboxyl ends and not enough to deprotonate all the amino ends, since it is higher than the pI some of the amino ends have been deprotonated (in addition to all the carboxyl ends).
Yet my answer book says that the net charge would be zero! Are 5.74 and 7.0 "close enough" that we can consider net charge to be zero still? If so, what is the standard permissible 'fuzzy' range? If not, then what is going on here?


texts: Which requirements are needed for 2 different species to be able to have offsprings?

texts: Sometimes different species mate and they are able to have offsprings, usually with anomalies. Are there known requirements for 2 different species to produce offsprings? Why species like the lion and the tiger, which seems to have many differences are able to produce offsprings, when others which supposedly share 99% of the DNA can't?


texts: What is the percentage of food that goes to a lamb fetus?

texts:
Does any one know the percentage of food eaten by a pregnant ewe that goes to the lamb fetus?

Specifically how much does the mother take for her body from every one kilo of food
and how much does the fetus take?


texts:
I know that colonial Cnidaria enlarge their colony by the means of asexual reproduction and sexual and asexual reproduction can originate individuals that will be part of other colonies.

Nevertheless, I cannot find any precise information about whether the individuals of a certain colony are all descendants of one founder or not. I thank you anybody for any answer!


texts: Why don't we hear all the processes in our body and what prevents us from doing so?

texts:
Why don't we hear all the processes in our body (like the rushing of our bloodcells through our arteries, the pumping of our heart, the electricity of neurotransmitters or our brain cells, etc.)

Is it only because the sound is too low for us to hear?


texts: why didn't natives of south america evolve darker skin?

texts:
I understand that darker skin tone is caused by melanin which helps to protect against the extra UV radiation that comes from more direct sunlight. It evolved in Africa before we migrated away from Africa and as I understand it was later evolved away from in areas further from the equator, where less sun meant less need for UV protection, because less sun also made it harder to get sufficient Vitamin D. Thus those near the equator tend to have darker skin and the further from the equator one goes the lighter the skin.

There are parts of South America which reside right on the equator, where melanin would provide important UV protection and where vitamin D deficiency was not a concern. I would expect them to have black skin, as dark as someone from Northern Africa or the Indonesians has, due to the extra UV exposure associated with the equator.

However, natives of Brazil and other equatorial parts of South America don't seem to have the same skin pigmentation as I see in the other equatorial areas.  They have skin darker then Europeans and other northern natives sure, but not to nearly the degree of other equatorial natives.  They clearly have the mutation for melanin, since that existed before we left Africa and they do have partial dark skin, which suggests that for some reason there was an evolutionary advantage to having skin as dark as theirs, but not darker.

Can anyone explain to me why South Americans wouldn't have evolved (or not evolved away from, depending on what part of the world they originated from) the almost-black level of dark skin the other equatorial natives possess?


texts: Is there a standard definition for plant "maturity"?

texts:
Is there a species-agnostic metric for identifying plant maturity?

There seems to be plenty of literature defining life-history stages for specific crops, but it is not clear if there is a generic definition.

In the context of crops, I would like to be able to identify the stage at which plants are no longer exhibiting juvenile traits.


texts: Is the amount of phosphoric acid added to colas enough to disrupt the function of the kidney over the long term?

texts:
Both Coca-Cola and Pepsi add phosphoric acid $H_3PO_4$ to their colas to give them a signature "bite".

The kidneys use a phosphoric acid/dihydrogen phosphate/hydrogen phosphate homeostasis as one mechanism to eliminate/excrete excess acid from the body.

The issue of whether sodas containing phosphoric acid can exacerbate osteoporosis and related conditions has been explored here and in some detail on Wikipedia, but I'm more interested in direct effects on the kidney.

I'm interested to know if the overall renal physiology is adversely affected by extra phosphoric acid that long-term moderate consumption (say a single 2L bottle per week for a year) of soda would introduce (including interrupting or saturating the Na-Pi transporter)?


texts: Effect of zero selection (pressure) on the population health

texts:
Evolution naturally produces better features: stronger muscles, teeth and minds. Killing the weakest, evolution wipes defective genes out of populations.

The mutations are necessary for advance. However, they are random and, thus, mostly negative. Right? How does the nature eliminate them from the population?

I see that one mechanism is polygamy: male have higher mutation rates. They tend to reproduce as much as possible. Female have lower mutation rates, they couple with only with best men and contribute much more to their offsprings. So, men generate as much random solutions as possible, whereas the role of female is to conserve the best of them. This means that the most of the male (bad mutations) die unreproduced. This eliminates the bad mutations and favours the progress of good qualities. The higher animals started to form harems and tournaments over their ownership. This further fosters the elimination of weak men and profileration of strong genes. However, human monogamy has disabled this selection mechanism. Best men are dedicated to only one woman. Other women cannot mix their genes with other good genes from previous generations. They are forced to look at the low quality men, who carry degenerate mutations. Might be it is monogamy that makes us human but it implies that all genes reproduce.

Yet 100 years ago it was not a big deal since we still had another filter: our grandfathers were born in families that had normally 10 children (I am speaking about Russia) and only 2-3 survived until reproduction (the population increased really slowly). I bet that those who survived had really good health: thanks to the bad health and immense selection pressure, the negative mutants are eliminated immediately and population maintains a perfect genome (aka biologic health). Killing more weakest in the current generation improves the health of next generations.

However everything has changed during the 20th century. The advances in economy and medicine have almost eliminated the selection. The selection pressure has relaxed to essentially zero so that everybody survives and leaves the same amount of offspring (and some scientists are even concerned that degradatory individuals leave more offsprings than the prosperous ones). We have even eliminated the infant mortality. We use baby incubators so that the people with the weakest health could survive and reproduce as normal and we are proud of it. It may sound strange but the mutation rate has not changed at all. Does it mean that the human genome is in danger?

I see the situation like you have inherited a perfect mechanism and decided not recovering it from the inevitably adverse action of entropy, that degrades it constantly. There is a constant chance, d, that every good gene is affected by a mutation. It is a fraction of healthy genes that will fail passing to the next generation. This will leave only (1-d) genes healthy in the next generation. The fraction of healthy genes will melt like 1, (1-d), (1-d)², (1-d)³, an so on, with every generation.

You see the fraction that stays healthy over generations. It decays exponentially. Any utility turns into entropy (aka garbage) exponentially, if not protected. Is this model correct? How quickly does this dissipation go? What is d? Let's assume absolute survival and equality in the reproduction rate among all groups people. How many generations is needed to lose 50% of good qualities?


texts:
I read in Bruce Alberts Molecular Biology of the cell :

  Normal mice,for example, cannot make an immune response against one of their own protein components of the complement system called C5.
  Mutant mice, however, lack the gene encoding C5(but are otherwise
  genetically identical to the normal mice) can make a strong immune
  response to this blood protein when immunized with it. Natural
  immunological tolerance for a particular self molecule persists only
  for as long the molecule remains present in the body. If a self
  molecule such as C5 is removed, an animal gains the ability to respond
  to it after a few weeks or months. Thus, the immune system is
  genetically capable of responding to self molecules but learns not to
  do so.

So, why does an immune reaction not happen when a new protein is introduced to patients lacking it ? For example if you give clotting factor to hemophilic patient.


texts:
Reading the articles it seems that for several human virus strains, synthesizing the full-length genome then electroporating into vero cells and incubating a few days gave birth to living viruses that can infect people as well as the original do (thus offering an easy way to add some mutation and make chimeric virus)

Am I correct and what are the few facts to know about this ? For example influenza would need more efforts, transfecting either seven separated plasmids, or the full genome plus infecting with a living virus producing the influenza RNA polymerase.


texts: Cell growth conditions for preparing electrocompetent cells

texts: Usually the protocol for preparing electrocompetent E. coli cells calls for growing the cells at 37deg and 225rpms until they reach OD of 0.3. I was wondering, is there any reason they should grow at optimal conditions for growth, instead of at suboptimal, for example at 30 degrees? Also, what is the physiological/epigenetic difference between a culture of OD 0.2 vs 03. vs 0.3?


texts: Why doesn't Poison Ivy cause a reaction under one's fingernails?

texts: Okay, so I pulled up a bunch of Poison Ivy last week and I got itchy up and down my arms. I scratch and I think that causes the oil to spread causing more misery. However I notice that I don't get a reaction under my nails where I would think the oil might accumulate. Why not? The skin under the nail seems relatively delicate and yet it doesn't react. ?


texts: Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?

texts:
Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions.

On a slide, it said that expression might be increased by mRNA injection or "VP16 fusion to binding domain of TF" and decreased by antisense morpholinos or "engrailed fusion to binding domain of TF".

I understand mRNA injection and antisense morpholinos, but I am unclear about the roles of VP16 and engrailed in this context. Can anyone clarify?


texts: Where do mushrooms get their energy from?

texts:
I'm wondering where field mushrooms get their energy from.
I've heard that they can easily grow on soil in a dark room. So, it seems to me that there wouldn't be any photosynthesizing plants from which they could get energy. Also, as far as I know, they don't have seeds from which they could directly get energy initially.

So, I have two questions:

Where do mushrooms get their initial energy from? (The spores, if that is the right term)
Where do they get their energy from in later stages? (If there is a difference at all)


texts: Why is peripheral vision not bleached by daylight?

texts:
In daylight, rods are known to be bleached: we have to wait some time after going into darkness before scotopic vision becomes effective. But, as I understand, peripheral vision is also mostly due to rods, since away from the fovea, cone density rapidly declines.

But I wonder then: if rods normally saturate in bright light, why does peripheral vision still work in daylight?


texts: Why do Major and Minor grooves exist in dna strands?

texts: I've been trying to find what causes the periodic appearance of major and minor grooves in DNA but have not yet been successful. Geometrical explanations would also be appreciated as I cannot understand any of the geometrical explanations I have come across so far. As far as my knowledge of DNA is concerned I know of all the high school basics (e.g complimentarity, bonding between the individual components of a nucleotide etc.)


texts: Does reversion of resistant strains to wild-type only occur when no more drug pressure is exerted

texts:
We always read that wild-type reversion of a resistant strain occurs when no more drug pressure is exerted. Could resistance reversion also occur under drug pressure, but from a drug other  than the one to which the virus is resistant.

To illustrate my question, let’s assume an HIV strain resistant to a specific anti-retroviral drug class (e.g. NNRTI drugs). Would NNRTI-resistance reversion to wild-type HIV occur under the pressure of another drug regimen (e.g. PI drugs) or does resistance reversion only occur when no more drug pressure at all is exerted?


texts: What is this insect wing, based on its vein pattern?

texts:
I've heard that it's possible to identify insect species uniquely based only on the vein patterns of their wings.  Is this true?  If so, what is this?

The image is taken from an unsolved Internet puzzle game from a few years ago.  (The creators of the puzzle are no longer to be found, so I can't ask them).  I believe the wing is probably from some species of cicada, but I couldn't be sure, and if possible I'd like to know what particular species of cicada.
Also, is there any kind of formal classification/notation for insects' wing venation?  Might shed some light on what the puzzle makers actually meant by the dratted thing!  (You can remove this bit, or I can, if it's considered to be asking two questions at once.)


texts: When searching for a plasmid on Addgene what does it mean if it is said to be an "empty backbone"? Why would one want an empty backbone?


texts:
I am searching for image and information, like distribution etc of the genus Acesina. The Taxonomic tree is:

Kingdom:        Animalia
Phylum:         Arthropoda
Class:          Insecta
Order:          Lepidoptera
Superfamily:    Papilionoidea
Family:         Lycaenidae
Genus:          Acesina

According to Catalogue of Life this genus has the 4 species. I haven't found any information by searching web, even the species are extinct or not! Any pointer would be appreciated.


texts: Why extract DNA from certain white blood cells instead of whole blood?

texts:
In my lab, human DNA is extracted from whole-blood samples.

I don't actually do the extractions and I am not familiar with the specific protocol but I understand that platelets and red blood cells do not have nuclei and therefore do not have DNA so I presume that isolating the sample's white blood cells is part of the procedure.

I also understand that different types of white blood cells have multi-lobed nuclei but I do not know how that affects the DNA which can be extracted from them.

I've seen a few papers, such as this one: http://www.ncbi.nlm.nih.gov/pubmed/15113441, state that they extracted DNA from specific types of white blood cells; lymphocytes in this case. These papers to not focus on, or even address, immune function.

Why extract DNA from only one type of white blood cell?

Do lymphocytes contain DNA that is more representative of the patient's genome than other types of white blood cells?

Are certain types of white blood cells easier to isolate than others?

Is this just the standard DNA-from-blood extraction procedure or are there multiple options to choose between depending on your research goals?


texts: I am studying animal science and I have been learning about reproductive theories however i cant seem to understand the theory of optimality


texts: Why should we preceed neostigmine by atropine in tubocurarine toxicity?

texts:
Why should we precede neostigmine by atropine in tubocurarine toxicity ?

I know that neostigmine act as anticholinesterase thus increasing the number of Ach molecules rendering them able to displace the tubocurarine, but I don't get the idea of atropine I know it's muscarinic inhibitor but we are speaking about nicotinergic receptors?


texts: How does glucose uptake happen in the various tissues of the body?

texts:
I know that the GLUT4 transporter allows for insulin-dependent uptake of glucose in skeletal muscle, liver and adipocytes. I also know that GLUT2 transporters are present in the liver and allow it to absorb glucose in the absence of insulin, and GLUT1/GLUT3 allow glucose to cross the blood-brain barrier and enter neurons.
However in my research I could not find the mechanism for glucose uptake in the remaining tissues of the body (Ex. epithelial tissue, connective tissue). Are there other types of transporters for glucose in these tissues? Surely these other cells also need glucose to survive.


texts: What can we infer from Warburg's Flashing Light experiment?

texts: The 'Dark Phase' in photosynthesis as I know is not dependent on darkness, but is just 'Light Independent'. But the Warburg Flashing light experiment, makes me think again. Warburg obtained higher rates of photosynthesis in Chlorella, when he exposed it to rapid alternate periods of light and darkness, instead of illuminating it constantly. But if the so called dark phase is just 'Light Independent', then why did Warburg get higher photosynthesis rate in the setup? I think if continuous illumination was provided ATP and $\ce{NADPH}+ \ce{H+}$ would be present more, and thus should give higher rates of photosynthesis. Can anyone point where I'm mistaken?


texts: Does our heart have to work harder in hot or cold weather?

texts:
In hot weather our perspiration is higher and often old people get tired faster when it is hot. But is there a relation between hot weather (sweating) and our heart if so what makes it have to work harder?

And does our heart have to work less (compared to hot) in cold weather where capillaries and vessels constrict, making it harder for the heart to pump blood.


texts: Why repolarization in ventricles start in last area which is depolarized "epicardium " rather than first area "endocardium"

texts:
About ventricular repolarization , l know it start in the last area which is depolarized ( that is why it has positive deflection on ECG ) but the question is why it start in that area ( epicardium ) although l think it can begain in first area depolarized "septum and endocardium" ?
- I heard answer about blood supply is differ because period of contraction is more in the "endocardium" than in"epicardium" which will generate high pressure inside ventricles that decrease coronary blood flow then slow repolarization phase ! If this true So how blood flow can effect repolarization ?


texts: Is there a link between digestion and nightmares?

texts:
A common belief is that eating too much before going to sleep can cause to have nightmares. In fact, I often experience it: I systematically have nightmares after eating too much in the evening.

Then I was wondering: is there really a link between digestive system's activity and unconscious brain's activity?

If it actually exists,
- is the influence linked to the neurons we have in out gut?
- or is it linked to the augmentation of the concentration of a nutrient in our bloodstream (which can then reach our brain and)?
- or is the neuronal activity which control digestion that interferes with the process of dreaming?

If the influence is linked to the augmentation of the concentration of a nutrient in our bloodstream, does this mean what we eat actually controls our mood or level of anxiety, or any subconscious process? (regardless of compounds known for having a particular effect, like theobromine, etc...)


texts: Decreasing Solubility as Solvent Moves Higher in Paper Chromatography

texts: In paper chromatography, as the mobile phase (I used 1:9 acetone/petroleum ether) climbs higher and higher, will the solubility of the solutes decrease as the solvent moves higher? I speak mostly about the beginning, when the solvent just begins to climb up the paper. Will the solutes travel right at the solvent front at the beginning, and then start to lag behind (and separate) as the solvent front moves higher?


texts:
From a general google search I have come to know that golgi 'blobs'(also referred to as "golgi haze") are tubular vesicles formed during the interphase of mitosis.
I would like to be reassured and also learn more about this topic. If possible please include a diagram in your answer.


texts: How to best conserve a beetle inside a jar?

texts:
Few days ago a giant beetle appeared on my house. Well, it's dead now. Since it attracted some attention from my little girl, I'd like to preserve it inside some jar. What's the best way to do it? What products should I use?

I've researched a bit in the internet, and it's said not to use formaldehyde because the specimen would become too hard (that's not a problem to me, but I don't like using such strong products considering that a child will probably handle the jar).


texts: What are the basic skills required to pursue future studies in theoretical ecology?

texts: I am a student and just about to choose a project for my Master's thesis in biology. I want to pursue studies in theoretical ecology in the future. Between field ecology and computational biology (as my two possible choices) what would be the best option to go for? Suggestions are needed as soon as possible .


texts: Which cell type cannot process and present antigen peptide in association with MHC-I when it is infected?


texts: If you have a constant pain in your body, why does a greater pain or pleasure make you not feel the original pain?


texts: small RNA bioanalyzer traces showing miRNA enrichment for sRNA-seq

texts:
I am bioinformatician trying to support some small RNA-seq experiments. All bioanalyzer traces that I have seen for RNA at the small RNA range show at peak at 22. But probably it depends on the protocol for the RNA purification (in this case only experience with RNeasy Qiagen).

I would like to know if some of you have some examples/experience of good bioanalyzer results after RNA purification that have been sequenced and got a big percentage of miRNA detected.

Currently I have a example where there is a broad peak at 25 and in some cases a small peak at 22. After sequencing there is almost not data. So at some point we lost the data. Trying to figure out if the bioanalyzer was good at that point, or already was something wrong.

thanks.


texts:
First, my exposure to biology is high-school. Should the answer to the question be obvious - please take a moment to laugh, and then point me in the right direction.
A quick google search (or perhaps my search parameters were wrong) didn't give me what I seek.

Animals usually exhibit some form of reflex. What I'm curious about is this -
Do all animals exhibit comparable reflex velocity? Here I use 'reflex velocity' to mean the amount of time elapsed between stimulus, and initiation of the reflex action.


texts: Is it possible to detect whether an organism has been gene edited (by humans)?

texts: Is it possible to detect whether an organism has been gene edited? For example, if someone gene-edits a human embryo (e.g., as He Jiankui did last year), can one later detect whether the human has been gene-edited?


texts: Why are there no known photosynthetic archaea?

texts: I'm taking a microbial physiology course and we noted that, while some archaea are phototrophic, there are no known photosynethetic archaea.  Are there any physiological characteristics that make archaea less suited for photosynthesis?  Or is it simply a matter of there likely being photosynthetic archaea, but they have not yet been found (which seems like it could easily be the case, given that there are many extremophilic archaea)?


texts: Why do we think chronic inflammation can cause cancer? I know the pathway is not fully understood, but what makes scientists believe that inflammation causes cancer?


texts: Why do people sleep with their eyes open?

texts: It's a fact that some people sleep with their eyes open, but why does that happen? Is it normal behavior, not a symptom of any sort of disorder? Are there any (dis)advantages to sleeping with eyes open?


texts: What is this insect? Seems to be in Indonesia

texts:
https://www.facebook.com/gadik63/videos/707361412787259/

This video has me completely baffled.


texts: Is it possible for a person to eat so many carrots that one turns orange?

texts:
I once read that Jerry Rubin (a famous 1960s activist) ate so many carrots that he turned orange. (This was in the East Bay Express, around twenty years ago.) I assumed it could be true, though he would have to eat hundreds or thousands of carrots; while a close family member thinks it's ridiculous. Is it medically/biologically plausible?

(I hope this question is appropriate to ask here--I'm new to this forum.)


texts: What is the specific role of the cerebellum when it comes to 'coordinating movement'?

texts:
In elementary biology (high school level in the UK - A levels), we are told that the cerebellum is the part of the brain that 'coordinates movement'. Literally nobody takes the time to explain what the word 'coordinates' encompasses. Hence, I do not know the specific role of the cerebellum in coordinating movement.

For example, one very daunting thing that we are told is that the frontal lobe contains the 'primary motor cortex', which supposedly contains motor neurons that connect to the spinal cord and brain stem and can send nerve impulses that enable movement in the body. Where is the distinction between such a role and the role of the cerebellum in 'coordinating movement'?


texts:
I read this wikipedia article on SNP genotyping and wasn't able to understand this part :

  In examining the results, if a genomic sample is homozygous, then the
  PCR products that result will be from the primer which matches the SNP
  location to the outer, opposite strand primer as well from the two
  opposite, outer primers. If the genomic sample is heterozygous, then
  products will result from the primer of each allele to their
  respective outer primer counterparts as well as from the two opposite,
  outer primers.

Can anyone explain this ?


texts:
I have been thinking about some alternative CO₂ fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of the pathway in databases (ecocyc,kegg). Does any of you know if the biochemical pathway and the genes involved in synthesis are known?

Thanks,Martin


texts: What is an efficient way to spike 10-50 cells to a culture

texts:
I'm trying to add on the order of 10-50 mammalian cells to a mixture of other cells (order of 1e6 cells). What is the best way to do this?

(edit) I guess this wasn't clear. I would really like to emphasize how to sort 10-50 cells to give me an precise (not necessarily accurate but that would be nice too) method of getting a desired number of cells.


texts: How does chest wall compliance affect functional residual capacity (FRC)?

texts:
The functional residual capacity is made up of expiratory reserve volume (ERV) plus the residual volume (RV) - i.e. the volume of air remaining in the lungs after passive expiration.

Compliance of the lungs is said to affect FRC. For example, if compliance of the lung increases (e.g. in emphysema), there is less elastic recoil and less air is passively expired, resulting in increased FRC. Could one explain this as increased compliance (where compliance = ∆V/∆P) meaning that the same intrapleural pressure at end of passive expiration results in a greater lung volume (FRC) at that time? This seems to explain instantaneous volumes rather than the actual expiration of less air.

How does this translate to compliance of the chest wall? As recoil of the chest wall tends to be outwards, would reduced compliance mean that there is greater tendency to recoil outwards, making intrapleural pressure more negative and reducing expiration of air, leaving greater FRC?


texts: Why do some animals try to imitate other animals?

texts:
There is a tendency of some animals (including people!) to be "copy-cats" and try to imitate members of their own, and sometimes other, species.

The most obvious example is a parrot copying human speech. Humans also try to copy the speech of their parents when they are little. "ma-ma, da-da"

The less obvious examples, I'm not even really sure are occurring. Like when a gorilla at the zoo assumes the same posture as a person sitting on just the other side of the glass. Like my cat, who tries to chew on bones similar to the two dogs we have.

I'm sure there are more/better examples I'm not aware of.

What is it that creates this behavior? Is it something that was learned, or is it some natural tendency? Is there such a thing as behaviors that are "encoded in the dna"?


texts: Can the brain influence gene expression?

texts:
A neuroscientist told me (according to my hazy memory) that the brain/nervous system can have an epigenetic function, ie directly regulate gene expression.

I'm not a biologist, but she talked me through how it worked, and I know enough of the basics to follow along and think it sounded reasonable.  I think the conversation was based on some post-doc research she was doing.

A quick google search (Maybe I don't know enough jargon to get a productive answer) brings up a chap called Bruce Lipton, who completely agrees, but who also, according to wikipedia "remains on the sidelines of conventional discussions of epigenetics, basically ignored by mainstream science".

So what gives?

Are there (a possible chain of) mechanisms by which the subconscious mind can affect gene expression?


texts: Does opening of ion channels alter the membrane potential directly?

texts:
Does the opening of a voltage-gated ion channel (i.e. the change of configuration of the protein) by an appropriate local change of the membrane potential directly and significantly alter the membrane potential in turn? Like the influx of ions that was caused by the opening of the channel does directly alter the local membrane potential?

(Assume there were no ions going through the channel: would there nevertheless be a significant change of the membrane potential by the mere opening of the channel?)


texts: Difference between 'Orbit' and 'Globe' in eye anatomy?

texts:
What's the difference between 'Orbit' and 'Globe' in eye's anatomy. Do they refer to the same ? I encountered this in this text:

  ... ciliary ganglion, which is approximately 3 mm in size, and located
  2-3 mm posterior to the globe and lateral to the optic nerve,...


texts: How was the guided daily amount (GDA) calculated?

texts: We are constantly shown nutritional information on food packaging stating this food contains "x" amount of your guided daily amount. A linked to the values is here. How were these values calculated? How do we know that men as a recommendation must not consume more than 2500 calories, 55g of protein 300g of carbohydrate etc...


texts: I'm not sure if this is a biology or chemistry question, maybe both? Some fruits, such as quince and quondong, taste of nothing when raw but have an extremely strong flavour when cooked. Why?


texts: Brood Parasitism - Parasitism/Ammensalism/Commensalism?

texts:
Parasitism has the parasite benefitting while the host is harmed. In brood parasitism, the cuckoo lays its eggs in a crow's nest for incubation. How does this harm the host? Why is it not considered ammensalism?
If I see the fact, while laying its eggs, the cuckoo might break some of the crow's eggs, and in this way the crow gets harmed. Parasitism from here fits.
But, as the chicks grow, the cuckoo chicks protect the crow chicks from other birds or predators. Seeing this, yet commensalism fits.
So, if I have to finalise which species interaction brood parasitism comes under, what should I select?
And why is that interaction preferred over the other?


texts: Saturation vapor pressure effect on human body

texts:
I found this calculator:
http://www.decatur.de/javascript/dew/
It calculates the dew point based on temperature and humidity.
In the result it is mentioned the saturation vapor pressure.

I barely understand the notions of vapor pressure, but I read somewhere that divers are rising back to water surface slowly, because the vapor pressure has negative effects on blood vessels, which can pop.

My goal is to find if a similar situation  (like divers' one) can be encountered by runners who are exercising when the vapor pressure is very high.

Thoughts?

Edit:
Is it possible to experience the effects of diving 10 meters in water, at surface with the contribution of climate factors (humidity, temperature and atmospheric pressure)?


texts: How RNA primer on leading strand is removed during DNA replication and how the gap is filled?

texts: Please can you explain me how the gap created by the removal of primer on 5'-3' leading strand is filled.


texts: Does it make sense to make my own DNA copy (kind of backup) while I am young?

texts:
As I understand, when I am getting older DNA becomes more and more damaged in my body.

Does it make sense to make my own DNA copy (kind of backup) while I am young (38 years old or for my kids) in case that in future there will be the technology which will make possible to restore damaged DNA from this copy and make me younger?

Or it does not make sense, because original not damaged DNA always can be found in some places of my body?

If it makes sense, what is the best way to do this DNA backup? Cut a piece of hair or nails or freeze a piece of saliva?


texts: Can radiation equilevant to 1 CT (computer tomography) scan causes significant changes in human body?

texts: I've read that CT scan causes radiation equivalent to few hundreds of ordinary X ray scan. It sound scary at the first look of it but I wonder is it the amount considered significant? Can dosage equal to the 1 CT scan significantly increase chance of developing cancer or other adverse effects?


texts: What is difference between breed, variant, subspecies and species?

texts: What is the difference between breed, variant, sub-species and species? Are there any similarities between sub-species and sub-population of a region?