texts: Looking for book or article that derives formula for estimating the "average heterozygosity"

texts:
An online lecture I need to watch on population genetics describes a formula for the "average heterozygosity" as follows:

  ...we can theoretically predict that the average heterozygosity in the population will simply be four times N, the size of the population,
  multiplied by the mutation rate.

The formula that appears on the screen as the lecturer says this does not match what he says (but it's hard to say; the typesetting is terrible).  Furthermore, I find this description too vague (I have a million questions about each of the words in it).  Also, I would like to see how this estimate is derived.  Finally, judging by the number of egregious typos I've found in this series of lectures so far, I'd like to get a second independent rendition of these ideas.

I thought that Google would make quick work of this question, but to my surprise, when I search for "heterozygosity" or "average heterozygosity" none of the hits I get mention this formula.

I imagine that this is textbook-level stuff (i.e. not something that I'd have to go to the current research literature to find).  Can someone point to a textbook that derives this estimate?  (I am interested only in textbooks that discuss the formula alluded to in the quote above, as opposed to general textbooks on population genetics.  I've already consulted several of the latter, and not been able to locate the formula in question.)


texts: Importance of germline and somatic genomic mutations to the purpose of treatment in cancer

texts:
Is there a hierarchy in the sets of genomic mutations (somatic and germline) to the purpose of treatment in cancer?

Can they be considered at the same level in the context of targeted therapy or are there reasons to prioritise one set vs the other?


texts:
I was thinking about how alcohol is used to sterilize, and I was wondering if it would be possible to use alcohol as an antibiotic? if it kills bacteria, couldn't (conceivably) alcohol in the bloodstream kill any bacteria there, and the alcohol would be cleaned out by the liver later? Or would the concentration of alcohol necessary be too high and cause poisoning?

Sorry if this has an extremely obvious answer, but all of the results I found in Google were about drinking alcohol while on antibiotics.

Could, in theory, alcohol (delivered in any way) be used as an antibiotic? If so, how? If not, why?


texts: Are there enzymes found in nature or the man made world that can help break down metals?

texts:
The title says it all.

Do natural or human engineered enzymes exist that can speed up the break down kitchen utensils, aluminum cans, wires, etc. into small particles or powders?

To be clear I am not talking about chemical transformation (e.g. iron turning to rust).


texts: https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are submitting their data unannotated (WGS submissions are allowed to be unannotated assemblies)?


texts: General undergraduate zoology textbook recommendation?

texts:
I am very interested in zoology,and I want to study zoology in my spare time.
Any undergraduate level zoology text book recommendation?


texts: Diffusion approximation to genetic drift

texts:
I am reading from the classical textbook Principles of Population Genetics, Hartl and Clark (pdf here).

Introduction

Let $f(p,x,t)$ denote the distribution of allele frequency $x$ at time $t$ knowing that at time $t=0$ the frequency was $p$. One can model the change in this distribution with time using the Kolmogorov forward equation

$$\frac{\partial f(p,x,t)}{\partial t} = -\frac{\partial [M(x) \cdot f(p,x,t)]}{\partial x}+\frac12\,\frac{\partial^2[V(x) \cdot f(p,x,t)]}{\partial x^2}$$

where $M(x)$ is the "drift parameter", which represents natural selection (thus, in the absence of the selection $M(x)=0$), and $V(x)$ is the "diffusion parameter", which represents genetic drift. The diffusion parameter is $V(x) = \frac{x(1-x)}{2N}$, where $N$ is the population size.

Question

Why is it true that $V(x) = \frac{x(1-x)}{2N}$?

I welcome intuitive explanations and mathematical proof.

Thoughts

I would think it derivates from the Wright-Fisher model of genetic drift where the distribution of allele frequency at the next generation is given by a binomial distribution.


texts: How does boiling water release dyes from vegetables?

texts:
Why does boiling water always seem to release and become the colors of whatever vegetables I am boiling?

For example, beet root and red cabbage both vividly color hot water.

I'd assume it's something to do with collisions with water particles breaking down cell walls and releasing anthocyanin, but how would this work on a cellular level? I.e., how does boiling water succeed in breaking through (correct assumption?) cell walls?


texts: How does ubiquitin recognize misfolded proteins?

texts: Misfolded proteins are tagged by ubiquitin and then are destroyed by proteasomes. How does ubiquitin know which protein to tag?


texts:
I was hiking and saw this spider in the mouth of a cave in the Ozarks in Arkansas (USA). I believe it is some kind of wolf spider. I have never seen a spider in the wild this large, except for tarantulas in Texas (USA). The approximate size from the tip of back leg to front was 7-8 inches. It was bigger then my hand and I am 6'1" tall man. The spider did not have anything to reference size and did not want get too close, though I am sure it was harmless. I can go back to cave and take same picture holding a ruler to the rock if needed.

I believe my initial guess was off mark. I am thinking this may be a fishing spider. I only say this due to it being on a vertical surface and having banded/striped legs. I have never heard of one attaining this size before. Any info on this spider is greatly appreciated.


texts:
I would like to make a network with all the interactions of the alpha-synuclein protein (in homo sapiens), that is, I would like to visualize the pathways where this protein participates, I would also want to include in the network the genes that encode this protein.
I would like to make this network in cytoscape. Could someone tell me where I can find a guide to do this.
thanks in advance


texts:
In the Gram stain, is there any replacement for primary stain, secondary stain, decolourizer and mordant? What results will the replacements produce?
I found that crystal violet can be replaced with methylene blue but in that case, what will the secondary stain, mordant etc. be? Please also explain what result we might get.


texts: How do I tell whether a mass spectrum was made with ESI or MALDI?

texts:
I was working through a previous exam and came across the following question (with reference to the picture shown below):

  "What MS ionization method was employed (MALDI or ESI)?"

I cannot seem to find the answer, so I'm guessing it is not possible to tell, but if there is a way to see which one was used, please enlighten me.


texts: What the difference between an inverted and everted retina?

texts:
I'm looking specifically for examples and comparisons, because the definitions of inverted and everted are remarkably similar; e.g. from Dictionary.com/Reference.com:

  everted
  verb (used with object)
  to turn outward or inside out.

http://dictionary.reference.com/browse/everted

vs. (esp. #5)

  inverted
  verb (used with object)
  1. to turn upside down.
  2. to reverse in position, order, direction, or relationship.
  3. to turn or change to the opposite or contrary, as in nature, bearing, or effect: to invert a process.
  4. to turn inward or back upon itself.
  5. to turn inside out.

http://dictionary.reference.com/browse/inverted

I'm curious because of this:

  Structurally, the cephalopod eye differs from the vertebrate eye.
  Cephalopods do not have a cornea, and the retina is everted so that
  the distal end of photoreceptive cells lies directly behind the lens
  and points toward incoming light. As a result, photoreceptor cells
  connect to the optic nerve behind the retina (Packard 1972).

From: Evolution: Education and Outreach
October 2008, Volume 1, Issue 4, pp 439-447

http://link.springer.com/article/10.1007%2Fs12052-008-0084-1
http://link.springer.com/article/10.1007%2Fs12052-008-0084-1/fulltext.html

via

https://en.wikipedia.org/wiki/Cephalopod#cite_note-Serb2008-12

If you have the rep please tag this with cephalopod; the tag doesn't exist and I don't have enough rep to create it. Thanks.


texts: How to determine the most likely reading frame of a DNA sequence?

texts:
This question is from a past exam paper for an introductory bioinformatics module. I'm a computer scientist doing biology for the first time.

"A short bacterial gene has been sequenced, giving the following DNA sequence. Write out the 6 possible reading frames for this sequence and indicate which is the most likely protein translation of this sequence. Explain your reasoning for picking the given translation, and write all the translations in single letter amino acid code form.

5' - ttattcatccgccagcgccatgcgcgccat - 3'  "

I think I understand the 6 possible reading frames: three from the 5' end starting tta, tat and att; and three from the 3' end starting tac, acc and ccg.

I could also write out the translations for a given reading frame with a codon usage table.
It's the most probable reading frame part I don't get. I thought perhaps I was looking for the longest open reading frame. I can only see one start codon (atg). What is the correct way to recognize the most probable reading frame?

I can't find this problem exactly on Biology Stack Exchange. I did find:

Help reading chromatogram

It made me wonder if I'm getting confused between "reading frame" and "open reading frame", this question only asks or the former.

Thanks!


texts:
Which animals are known to not have pheromones besides humans?

I can't find any research on this. There are examples of every class that uses pheromones. However nobody seems to answer conclusively that any particular species is not likely to have pheromones.


texts: What is the effective relatedness of inbreeding?

texts: If a human inbreeds with a relative, how distant does the relative have to be before the homozygosity in the child is no higher than if the mate were randomly chosen from the global population?


texts: how can I get stronger staining for my lymph node sections

texts:
I am using the same protocol and same antibodies that the literature says but still I cannot get good staining for my lymph node sections, I tried to change the fixation method and I am using now acetone instead of PFA, I also tried with acetone plus ethanol, the antibody concentration used worked in previous sections.
How could I increase the signal and/or remove the noise?

It also happened to work in some sections before but not in others even I did exactly the same, why could that be if I am using the same tissue?

Thanks


texts: Are there any detrimental effects to long term electrical muscle stimulation?

texts:
I know that different types of electrical stimulation can be used in fields such as physical therapy to get muscles to contract. However, these electrical stimulation sessions are not prolonged and contiguous.

Does anybody know if stimulating muscles to contract and retract for an extended and continuous period of time has negative side effects? Does it damage the muscle? Nerve?


texts: Beetle (?) on Acacia (Senegalia) greggii?

texts: I was working on my botany skills and took a photo of Acacia (Senegalia) greggii.  When I reviewed the photos, I saw a beetle (I think it's a bettle) that I had not noticed in the field.  I'd say its body is about 2 cm long.  This plant was growing in a dry wash in Phoenix Arizona USA, and the flowers on the plant were just maturing.  Observed around 9 am and the temperature was about 75-80 F. What species is this insect?


texts: Does long term use of antibiotics in humans actually lead to a greater risk of infection?

texts: I've read about the overuse of antibiotics leading to antibiotic resistant strains of bacteria, so generally does long term use of antibiotics breed these strains in the bodies of antibiotic users and increase the risk of various bodily infections?


texts: Is it possible to express a mutant gene only in a specific tissue?

texts:
Imagine that someone tries to develop a knockout mouse for a gene, but this result in lethality for the homozygous.

Is it possible to express that mutant gene only in a specific tissue of interest to get a idea of which phenotype it produces? Does someone know an experiment which used this idea or something similar?


texts: How was Crisper Cas9 function discovered?

texts: What paper outlines the discovery of how the CRIPER DNA, CrRNA, and Cas9 interact?


texts: Resting membrane potential: K+ concentrations and charges on inside and outside of the neuron

texts:
According to this site, there is a greater concentration of K+ ions inside the cell than outside. The following screenshot, taken from this website, supports this statement.

However, I don't understand how the inside of the cell can have a net negative charge if there is a greater concentration of K+ inside the cell. This seems like a contradictory statement to me. (1) Why is the interior negative despite the fact that there are more K+ ions inside than outside, and (2) What exactly causes the net negative charge?


texts: Could someone Identify this Insect Hive on my Balcony Grill

texts:
A smallish insect hive has been forming on the grill of my balcony in the last month or two, and I wanted to know should I be worried or can I just let it be. Its 13th floor in Singapore, if the height helps in ID. So far they have not been very aggressive, and have not bothered us even if we get within few feet of it, but want to know if that can change in horror movie style..

You can find the pictures below, both are pretty much the same, but with some flash tweaking. For a size estimate, they appear to be between half and 1 cm long, and the distance between the bars of the grill is about 12 cm or so. Are they some kind of bees? Would they leave eventually or is this a long term thing. Also, the length of the hive appears to be growing at ~ 1-2 cm per week.

(crop of larger picture found below)


texts: Creatinine accumulates in blood if kidneys fail to excrete it.  Does this unexcreted creatinine ever get thrown out of body? What prevents creatinine from continuously rising in the blood?


texts: Trying to identify a beetle seen in Ontario, Canada...and its babies, or parasites?

texts:
I'm trying to identify a beetle I took video of in July (around 2010) in the Muskoka region of Ontario, Canada. Attached below is a still frame.
I've done some googling and was thinking this was a Milkweed Leaf Beetle because of the orange and black stripes. This beetle however has an interestingly marked green head, and Milkweed Leaf Beetles appear to only have a black head.
I'm especially curious to know if the smaller insects on this beetles back are its young, or some type of parasite.

I've just posted the original video to youtube. It's right here: Beetle Video


texts: The genetic and physiological origins of laughter?

texts:
This Wikipedia article  defines laughter in many terms, such as...

  "a visual expression of happiness, or an inward feeling of joy"

and

  "a part of human behavior regulated by the brain, helping humans clarify their intentions in social interaction and providing an emotional context to conversations".

Note: the emphasis was added by myself.

The article also states that laughter is "probably genetic", and that

  "Scientists have noted the similarity in forms of laughter induced by tickling among various primates, which suggests that laughter derives from a common origin among primate species."

According to this report which the Wikipedia referenced, the expression of laughter in general is present among other great apes. Phylogenetic trees were reconstructed to represent the evolution of this trait among primates (which concludes that the ability to laugh must have a genetic basis, at least to some degree).

Note: I also found this WikiAnswers post, but it clearly can't be that reliable.

A search on the OMIM database yielded this result, where children with Angelman syndrome were characterized with "excessive laughter", this result, in which Charles Bonnet syndrome was characterized with "inappropriate laughter", as well as many other genetic mutations which resulted in some sort of uncontrollable laughter.

I understand that laughter is a complex psychological expression of emotion likely associated with more abstract thought, and that there simply can't be "a laughter gene", but my question is:

Is there any known genetic or physiological origin of laughter? What is biologically different in great apes which allows for laughter, in comparison with a panoply of other animals? I'm looking for more of a molecular answer rather than an ecological or psychological one.


texts: Why do cucurbits produce so much fluid when their stems are cut?

texts: When carrying out some germination tests on species in the Cucurbitaceae, I notice that young plants of this family produce a lot of clear fluid when they are dissected. Most plants I dissect do not produce any fluid, even ones which appear to be turgid and have large cells. Why do cucurbits do this, and what's the fluid?


texts: Is Sda a protein, or is it a protein domain of DnaA?

texts:
I initially thought that a domain was a specific part of a protein, with it given tertiary structure, to which a given molecule is able to bind. (I think I recall phrases such as "the haem binding domain of protein X..." being used in lectures?)

Having consulted Wikipedia on protein domains, I see the definition is a bit more subtle:

  A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded.

I can understand this, however the reason why I started questioning what a 'domain' actually refers to was because if it's use in reference to Sda in control of endosporulation of bacteria. In my lecture notes, it is stated that "KinA is bound and destabilised by Sda, a DnaA target,"

From this I was under the impression that Sda is a protein (although to the best of my knowledge DnaA only binds DNA, so I do not know why Sda would be target of DnaA. Anyhow,) on the other hand Wikipedia states "the protein domain Sda is short for suppressor of dnaA or otherwise known as sporulation inhibitor A.", which seems to me to suggest that Sda is a part of DnaA whose modifications allow DnaA suppression?

Also, on Wikipedia, it is later written "Sda protein domain is a checkpoint which prevents the formation of spores." How can a protein, if Sda is one, be a checkpoint?

On the other hand my lecture notes later talk about the regulation of Sda levels, so it again is referred to as a separate protein!

I would very much appreciate if someone could explain what 'domain' means in this context.


texts: What are the advantages and disadvantages of using beta-galactosidase compared to luciferase as a reporter gene?

texts:
In the University labs, we have used Beta-galactosidase as a reporter gene to quantify the expression initiated by the stress-response promoter in yeast. This was done by exposing one of the two groups to osmotic stress (high salt concentration) whilst the other was unstressed. Then the levels of beta-galactosidase were compared.
A question given to us afterwards asked to give advantages & disadvantages of using Beta-galactosidase compared to Luciferase as a reporter gene in this experiment. And which one would be, overall, more suitable?


texts: Why do some macaques have redder faces than others?

texts:
I'm watching Monkey Kingdom, and I noticed some of the macaques have redder faces than others.

Specifically the females, and as the social ladder increases, so does the redness.

An alpha female:

Does the redness-hierarchy correlation have something to do with attractiveness or aggressiveness? (These seem to be leading factors in defining hierarchy otherwise.)


texts: Is there a correlation between brain size and amount of sleep?

texts:
As far as we know, sleep seems to be the part of the daily cycle when executive functions are resting and memories are fortifying. Many, but not all, of the functions that become dysfunctional upon sleep deprivation seem to be situated in the frontal lobe or associated with the neocortex.

My question is whether there is a correlation between percentage of the day spent sleeping and brain size (either the whole brain, or a part of the brain such as the neocortex or frontal lobe). How do other species correlate compared to us? Either in absolute brain size, or in brain size relative to body size.


texts: About the definition of ketogenic amino acid

texts:
I am studying biochemistry and have been looking at metabolic network diagrams showing the different intermediates of glycolysis and the citric acid cycle that amino acids can be converted to.
I have gone over a list of which amino acids are considered ketogenic and which are considered glucogenic. I was surprised that Serine, Glycine, Cysteine, and Alanine are not considered ketogenic as they can be converted to pyruvate and pyruvate can be turned to acetyl-CoA, so that these 4 amino acids seem like they can then be used for ketogenesis.
I then looked at the definition of ketogenic amino acids on Wikipedia and it says "A ketogenic amino acid is an amino acid that can be degraded directly into acetyl-CoA".

The question is if there's some reason this is the definition of ketogenic amino acids; it seems to make more sense to me to classify Serine, Glycine, Cysteine, and Alanine as ketogenic due to what I said.

Thank you.


texts: What is the scientific name of this butterfly?

texts: I have this  butterfly but I don't know its scientific name. I think that it's a common butterfly which can be seen everywhere (btw, I'm in Taiwan.) Thanks for your help :D


texts: Simulating substitution rate of neutral mutations

texts:
I am trying to computationally simulate a population based on the Wright-Fisher model I would like to get to the classic result of the neutral theory of molecular evolution that the rate of neutral substitution equals the rate of mutation. However, the results of my simulations never show that. I will briefly explain my simulation process and how I calculate the mutation and substitution rates. Please let me know if there is something wrong in my procedure.

I have a non-structured haploid population that grows in discrete time steps. I start with a population of N individuals in an environment with carrying capacity K. I use a K-allele model of mutation. At each generation, every individual will reproduce n offsprings and it will immediately die afterwards. A u fraction of offsprings will be chosen randomly to have a single mutation in each generation (u is mutation rate per gene per generation). At each generation, I record how many mutations have occurred and how many mutations have reached fixation in the population (reached frequency of more than 99% of individuals). Thus, mutation rate and substitution rate per generation is calculated as the number of mutations and number of substitutions divided by population size, respectively. With this set up, even with hundreds of repetitions, the rate of fixation will never be as big as mutation rate u.

Where do you think is the problem?
I have struggled with this a lot and I appreciate any help.

Edit:
My code is written in Python. This my pseudo-code:

Parameters: population size, genome_size, mutation_rate, generation_number, fixation_threshold.

'''
Population_size: Here it is 1500
Genome_size: the number of loci that can be mutated. Each locus can be mutated to any of ACTG. Here 10^4
Mutation_rate: number of mutations per genome per generation. Here 0.05
Generation_number: The number of generations that the population grows. Here 1000
Fixation_threshold: The fraction of individuals having an allele in the population so that the allele is considered fixed. Here 0.99
'''

The initial population is created. All individuals are the same without any mutations
A vector to hold the number of mutations and a vector to hold the number of fixations is created

For each generation:
    I determine how many individuals in each generation should be mutated. Here 8.
    I randomly choose  (uniform with replacement) the individuals to be mutated
    For each individual in the population:
        It will produce an offspring. The offspring inherits the genome of its parent, i.e. the mutations of the parent.
        If the individual is among the ones to be mutated, the offspring will receive a mutation that is randomly picked.
            The mutation can be a back mutation
        The individual will die
    I record the number of mutations that occurred (it will always be 8 in this case)
    I record any mutation that has a frequency in the population of more than 0.99 of individuals. This is the number of fixations

I run this code for at least 100 times. I expect that the average number of fixations to be equal to the average number of mutations in each generation, or they converge over generations. Because the neutral theory of Evolution by Kimura predicts that for neutral sites in the genome, substitution rate is equal to the mutation rate.


texts:
From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese:

  More recently, concerns have been raised that HGT from genetically modified organisms (GMOs) could have adverse effects (Pontiroli et al., 2007). HGT of an introduced gene in a GMO may confer a novel trait in another organism, which could be a source of potential harm to the health of people or the environment. For example, the transfer of antibiotic resistance genes to a pathogen has the potential to compromise human or animal therapy (Bennett et al., 2004), transfer of a viral gene to a non-homologous virus may result in an emerging disease (Falk and Bruening, 1994) or gene transfer to humans has been controversially proposed as a potential trigger for oncogenesis (Ho et al., 2000).

What is a "non-homologous virus"? A virus whose species is the same but the strain is different from the virus taken as the donor for the GMO? Or just any virus (including viruses from different species) whose DNA or RNA sequence is different from the GMO donor virus?

Excuse me if the question seems too simple.


texts: I have never obtain an Electroporator for my home-lab. Because it's very expensive, I'm trying to create a diy cheap version for myself. In all commercial design, I see that we need to put the sample to a 0.1cm-0.2cm cuvette to doing an electroporation, can I just replace it with an eppendorf plastic tube and put my 0.1->0.2cm alumium electrode inside?


texts: Can I use a basic compound microscope to analyze the ploidy of plant chromosomes?

texts:
So, I'm not really any kind of trained botanist. But I do have two things: some dandelion seeds from France, and, collecting dust in my garage along with related accessories, this thing.

Normally, the dandelions growing in an American yard are apomictic triploids, but in Europe there's both triploids and sexual diploids, the latter getting even more common the further south. I'm assuming that, because these French seeds are a specific common cultivar (Vert de Montmagny), that regular sexual selection was used in breeding it, making it a diploid. But I don't know who to ask to confirm this so I may as well do some testing. If it's a diploid, maybe I can do some breeding of my own?

But I don't even know the first step. Are there some parts of a plant that I'll have an easier time finding chromosomes in? What do I put them in to express their DNA and what do they best stain in? Would I even be able to discern the different chromosome shapes without training? I've heard the standard science project way to extract DNA (dish soap, salt, alcohol) damages the chromosomes so that you wouldn't really find them in a microscope; if true I hope there's another way.


texts:
Can anyone identify this succulent plant?
Location: Tamil Nadu,India


texts: Why are certain types of clams prevalent in certain areas?

texts:
I live near a large tidal estuary and according to one person the only kind of clams to be found there are razor clams. Why would there only be one kind of clam? I mean mud is mud right? What makes it different?
I guess one issue might be salinity. It's an estuary where a river meets the sea, so the water is brackish, not fully saline like the ocean.


texts: Could Wobble Base Pairing ultimately yield an amino acid that was originally uncalled for or not expected?

texts:
How does the cell choose which amino acid to attach to tRNA when there is wobble base pairing involved (not the other way around)? Consider the example below.

For the purpose of this question I'm picking UGC, UGA and UGG codons (Cys, Stop and Trp aa's) so that the 3rd position of the codon really makes a difference (if it does).

I know there are other pairings out there but to keep it really simple for myself I derived the following tRNA anticodons to match the codons using these rules:
G pairs with C or U,
C pairs with G,
U pairs with A or G,
A pairs with U,
I pairs with A, U or C.

UGC: ACG or ACI anticodons

UGA: ACU or ACI anticodons

UGG: ACU or ACC anticodons

My question is (assuming I did my work correctly) if there are multiple possibilities for anticodons to match with each codon how would we know which amino acid will attach to which anticodon? Take for example the ACU anticodon that could potentially match with UGA or UGG codons which codes for STOP or Trp. Wouldn't there be a discrepancy/confusion on which to code for by the cell? Ultimately wouldn't this affect the peptide/protein synthesized?

NB I have edited the original question to clarify my problem, which I do not think is answered elsewhere.


texts: E. Coli growth inhibited in Powdered Honey

texts:
I ran into problem with my method validation since the E. Coli that I've spiked into my Honey Powder sample can't grow in the media. The media I've used is Merck CCA (Chromogenic Coliform Agar). I've also used the MPN method (3 tubes) using LST Broth with the same result.

Really appreciate if someone Can  lead me into why would this happen and give any suggestion on how to troubleshoot this?

Regards.


texts: Ammonia smell after physical exercise? What is the explanation?

texts:
After exercising vigorously one can sometimes smell ammonia and it feels like it's coming from within the nose actually. There is no indication that others can smell it when I do (i.e. seems to be internal rather than external). I know I'm not the only one experiencing this, but I was wondering what the physiological processes are that are responsible for that?

Also: is this merely a perceived smell or is there actually ammonia in/on my body after the exercise.


texts: Are insects really strong or just small?

texts:
It's a common statement that insects are stronger, faster and jump higher than almost anything by mass.

However, this leaves out that compared to their mass, all large creatures are actually pretty weak and small creatures are usually strong.

Have there been any studies where the strength of insects and mammals, for instance, is compared directly rather than by this ridiculous "per mass" method? I'd like to have comparisons between creatures that are similarly heavy.

My goal is to figure out the differences in strength between insects, reptiles, amphibians, mammals, fish, etc while actually considering that strength doesn't scale as easily as mass.


texts: Why are disaccharides less reducing than monosaccharides?

texts: My teacher told me the statement, but if both monosaccharide and disaccharides have a single free active group, how is this possible?


texts: I wanted to buy black tea at a pharmacy and the pharmacist told me that russian tea is actually black tea so I bought it instead.It's made out of theae folium leaves and for some reason I can't find anything about that plant on the internet and I know that black tea is made out of camelia sinensis leaves, not theae folium.Can anyone tell me what is this plant and is it really russian tea (i found somewhere that russian tea is made from a different plant) and what is this "Russian" tea good for?


texts: I am trying to design primers for sanger sequencing snp detection. In the past I have used Primer-BLAST, but I'm trying to pick up KRAS codon 12 mutations. The problem is that in Primer-BLAST you specify refseq gene ID and so it doesn't seem to design primers outside of the gene locus. This means that my primers will sit on the SNP. Is there a way to tell Primer-BLAST the exact locus I am trying to sequence? Or is there a better way of doing this? Thanks.


texts: Molecular cause of cramps, spasms and strengthening in muscles? (incl. intro to muscle contraction)

texts:
When motor neurons are stimulated to trigger an action potential, this potential propagates down the spine, eventually reaching a neuromuscular junction, causing the release of acetylcholine (ACh).

ACh binds to nicotinic ACh receptors (nAChR) on the muscle fibers, leading to an action potential. The nAChR is a non-selective, ligand-gated ion channel, permeable to sodium-, potassium- and calcium ions. This means sodium ions will flow in, leading to depolarization, but potassium will flow out, working towards hyperpolarization.

If enough of these channels are opened, the post-synaptic membrane potential will be drawn towards $E_{Na}$ enough to reach a threshold, so that voltage-gated sodium channels open on the post-synaptic membrane, causing a post-synaptic action potential.

This action potential travels down inward extrusions of the plasma membrane, called transverse (T) tubules. Is the membrane continuous along these tubules, or does the tubule just end somewhere inside the muscle fiber? Anyway, the action potential comes in contact with the muscle fiber version of an endoplasmic reticulum: The sarcoplasmic reticulum (SR).

Upon contact with the action potential, the calcium ion channels in the SR open, causing calcium ions to flow into the cytosol. Here they bind to troponin complexes on the tropomyosin protein - a regulatory protein, that twists around the thin filaments of the muscle fiber. In short, when calcium ions bind to troponin, it reveals binding sites for myosin on the thin filaments, letting the muscle contraction cycle of the myosin heads proceed, and the muscle contracts!

When the stimulus goes away, calcium ions are transported back into the SR, and myosin has nowhere to bind, thus the cycle is halted, and the muscle relaxes.

When the muscle is twitching... is this neurological of nature, or is it related to a molecular cause in the muscle itself?

When the muscle is cramping... I'm almost certain this arises in the muscle. What causes it? A malfunction with regard to the calcium ions?

Lastly, and on a slightly different subject, what are the microlesions in the muscles that occur during strength training, and what is the overcompensation that happens? The basis of this might not be entirely on the molecular level I feel.


texts:
This may be anecdotal...

The Indian sub-continent is in the rainy part of summer. It follows the mosquito population goes up.

So when I sliced my palm, I expected the mosquitoes to collect there in force. Yet whilst they continued to go about their business on the forearms, face and elsewhere - the blood flowing out of my palm held no attraction for them. This even after I deliberately stood still for nearly a minute! Perhaps the clotting process/platelets/etc were a repellent.

Why do mosquitoes not collect blood after platelets activate?


texts: What is the insight of Frank Starling law of the heart?

texts:
The Frank Starling law appears to be a trivial observation:

stroke volume is directly related to the end diastolic volume

In everyday language, as more blood fills the heart, the heart pumps more blood out.

Can someone point out whether there are some inaccuracies in the above description because I don't understand why every article on FS law requires upward 20 pages. Even youtube video on this topic is 8 minutes long.

What is the big idea here that I am missing?


texts: Is Behe's experiment (evolving the bacterial flagellum) plausible in the lab?

texts:
[Warning: this question is motivated by a prominent proponent of "intelligent design": Prof. Michael Behe.  I'm not interested in debating creationism.]

According to Wikipedia[1]:

  In Darwin’s Black Box (Behe 1996) I claimed that the bacterial
  flagellum was irreducibly complex and so required deliberate
  intelligent design. The flip side of this claim is that the flagellum
  can’t be produced by natural selection acting on random mutation, or
  any other unintelligent process. To falsify such a claim, a scientist
  could go into the laboratory, place a bacterial species lacking a
  flagellum under some selective pressure (for mobility, say), grow it
  for ten thousand generations, and see if a flagellum--or any equally
  complex system--was produced. If that happened, my claims would be
  neatly disproven.

[emphasis mine.]

As far as I can tell, nobody has actually performed this experiment (although, my literature search was not comprehensive, so it is possible I simply haven't found the appropriate publications).  [However, there are arguments that the flagellum could have (or likely has) evolved from the type III secretory system, which shows similarity[2].]  This state of affairs strikes me as peculiar -- Behe's proposal sounds like an interesting experiment to perform (even disregarding any external debate).

  Question: Is the experiment proposed by Behe (or another experiment in the same spirit) plausible to implement in a laboratory experiment?

Experiments reproducing steps in evolution seem to turn out much easier than I would have expected a priori, e.g. reproductive isolation of fruit flies[3], experimental evolution of multicellularity[4], so perhaps Behe's experiment would also be surprisingly easy to implement.

References:

Wikipedia: Michael Behe
 Blocker A, Komoriya K, Aizawa S-I. 2003. Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proceedings of the National Academy of Sciences of the United States of America 100: 3027–30.
 Dodd DMB. 1989. Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila pseudoobscura. Evolution 43: 1308.
 Ratcliff WC, Denison RF, Borrello M, Travisano M. 2012. Experimental evolution of multicellularity. Proceedings of the National Academy of Sciences of the United States of America 109: 1595–600.


texts: Amino Acid requirement + intake in relation to diet + meat type

texts:
I was arguing with a friend:

I said: The Yulin festivals cannot be condemned by western culture, as we also kill animals in equally cruel ways.

She said: It isn't just that the killing is cruel, but it doesn't help us, as humans do not derive the same essential amino acids from consuming these less traditional meats (e.g. dogs, cats, etc) like they would from consuming more traditional meats (e.g. cow, pig, goat, etc) She cites her father, a geneticist, as her source.

Question one:
Are my friend and her father correct? Does the consumption of a less traditional meat (e.g. cats, dogs, etc) provide fewer essential amino acids than the consumption of traditional meats (e.g. cows, pigs, chickens, etc)?

Question two:
My friend also made a comment about veganism and vegetarianism (I am a vegetarian), stating that for the same reason as her and her father's above comment, people who exclude meat from their diet need to use supplements. Is this correct, or would it also be possible to just vary diet to obtain these essential amino acids?


texts: When is Pheophytin used in electron transfer to the q cycle in plants?

texts:
If I understand it correctly:
(short version)
The Q cycle starts with PQH2 it removes the 2H(+) and gives one electron to Plastocyanin and the other to a stored Plastoquinone to charge it to Plastoquinone (-). This process is repeated and adds the electron to the stored Plastoquinone(-) to create a Plastoquinone (-2). This then gets 2H(+) to form PQH2. And the cycle begins anew.

But in a lot of pictures is shown that the excited P680 gives the electron to Pheophytin and that gives it to the Q cycle.

Please let me know when and where the Pheophytin interacts to give the electron.


texts: Neurological response to food cravings caused by bacteria

texts:
Our microbiome (Kurzgesagt video) is thought to send our brain information to chose certain foods to eat over others and it's our increase in a certain type of bacteria that will form a stronger craving for whatever that bacteria happens to appreciate the most. I'd like to know more about how the brain makes those choices in relation to the bacteria, than in relation to a general reward (The brain receives dopamine for things that are achieved, how does bacteria affect that?). Do the bacteria affect the amount of dopamine released- if so then how are the neurons that appreciate that bacteria award, broken or less interested when another type of bacteria now wants a different type of food?

NOTE Neurons are formed when the brain "achieves something" like when bacteria are given the food they thrive on I suppose, so when another type of bacteria receives more food and takes over in your gut, how is it that your neurons are broken and seemingly replaced? I understand this is a stretch but bare with me I just spoke to a neuroscientist about a month back who informed me about the basics of this process.


texts:
I live in Europe and found this interesting longhorn beetle I think and I was curious what species it is or what's it's name!
Thanks to anyone who identifies it!


texts:
I learned the citric acid cycle in biotechnology school and how cells work; about ADP and ATP and how the Cellular respiration (C6H12O6 + 6O2 -> 6CO2+6H2O) works.

I am interested in understanding why exactly too much glucose is harmful, e.g. when having diabetes.

What happens inside the cells so that the organs get damaged over time? Why can't the cells not simply "ignore" the needless glucose or convert it into energy?


texts: How are signalling pathways specific when secondary messengers are not?

texts:
I'm a biochemistry and physiology student and am aware that secondary messengers like cAMP and IP3 are used in specific signaling cascades.
However, they and other molecules can innervate a variety of effector molecules which makes me wonder how specificity is maintained.

For example, if GPCRa/Gsa activation leads to the activation of PkAa, why doesn't it lead to the activation of PkAb?


texts: Why doesn't Sanger (fluorescent) DNA sequencing double count nucleotides?

texts:
My understanding is that PCR is carried out until a fluorescent nucleotide halts replication. The segments of DNA are fed through the capillary tube based on size, sifting through the segments from smallest to largest; subsequently, the sequence is read from one end to the other.

I'm confused as to how we know that each nucleotide in the sequence has been accounted for, or if a nucleotide has been counted twice. If two fragments of the same size, ending with the same ddNTP, pass through the capillary tube at slightly different times, how do we know if that specific nucleotide hasn't been double-counted?


texts: And another insect from SE Brazil Oct 2017

texts: Photographed in the low areas of the Brazilian Atlantic Rainforest - Oct 2017 and about 2cm in length.


texts: Definition of species - location of gene

texts:
I know that species have been classified on basis of reproduction , DNA similarity , niche, etc.

Has there been a classification based on locus of genes ? What are the drawbacks/shortcomings of classifying this way ?

Isn't it simple to classify on this basis as - a species can have variation at a locus but the position of that locus with respect to a chromosome is fixed in every individual of that species. This fact can eliminate the subjective criteria of DNA similarity.

But I think this isn't valid for bacteria as there is so much recombination going on.


texts: How do scientists kill the bacteria they themselves made resistant?

texts:
I was reading this article on researching bacteria resistance to silver by removing some of their genes.

  Researchers then used "colony-scoring" software to measure the differences in growth and size of each plate's bacterial colony. E. coli strains with genes deleted involved in producing sensitivity, or toxicity, to silver grew larger colonies. Strains with genes deleted involved with resistance grew smaller colonies.

Once you end up with some resistant bacteria and you're done researching it, you can't just flush it down the toilet. How do you safely dispose those colony plates in a way that ensures those bacteria don't get out into the wild and reproduce?


texts: Why isn't the DNA in bacteria always split up and replicating?

texts: Isn't helicase always free floating in bacterial cells, and the DNA without a nuclear membrane and uncoiled and freefloating and so why doesn't the helicase keep breaking the double helix of DNA? Also, since other DNA synthesizing enzymes like polymerase and RNA primer and other replication enzymes also free floating, so why doesn't the DNA in bacterial cells keep replicating at all times?


texts: Do people who have been blind all their lives dream?

texts: Do the people who have been blind all their lives dream and do they experience or report "imagery" in the dreams?


texts: Gene expression for mouse feeder cells (inactivated MEFs)

texts:
I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there is.

I've spent quite a while looking (in GEO, Google Scholar, PubMed, etc) with no luck. Any leads would be appreciated.


texts:
Type I topoisomerase changes the linking number by ±1 by changing the number of twist present in a DNA, breaking only one strand.

Type II topoisomerase changes the linking number by ±2 by changing the configuration of the writhe,breaking both the strands.

Am I right?


texts: From what I can tell, it is not well defined, but at least in the US it has to do with cessation of cardiopulmonary functionality. Any reliable sources that give a definition of when a human being is considered to be no longer living?


texts: How can heart disease cause dizziness after eating?

texts:
I have been reading several articles explaining dizziness after eating (see here and here), and both articles gloss over something that I found pretty remarkable.

Both articles claim that "heart disease" can cause one to experience dizziness after eating. For instance, as one article merely generalizes:

  A healthy heart is needed to pump blood faster during digestion. Certain heart conditions can lead to its inability to send enough blood to the abdominal organs, which may lead to a drop in blood pressure, resulting in dizziness and sometimes, nausea.

To me, this is pretty vague and uninformative. Making a blanket statement like "certain heart conditions can...lead to a drop in blood pressure" is like saying "not eating or drinking water can cause death."

I'm interested in are the hows and the whats: How does/can heart disease cause dizziness after eating, what are the reasons why this happens, and what are some examples of heart disease ("certain conditions") that cause this (as I'm sure there are many similarly-related diseases)?


texts:
I follow a protocol to get protein from E.coli cells after sonication.

I used to grow 6 litres of large cultures and add IPTG to express the protein. I centrifuge for 10 mins at 8,000 rpm and get the pellets.
Then I do sonication and centrifuge again at 20,000 for 1 hr.

My question is: can I do the last step of centrifugation at 4000 rpm for 2 hr? The centrifuge is no longer working at high speed (20,000rpm)

Thanks


texts: Modern reference for Kropotkin's lazy bees

texts:
I have been reading through Peter Kropotkin's Mutual Aid: A Factor of Evolution and he mentions a curious fact about bees (bolding by me for emphasis):

  predatory instincts and laziness continue to exist among the bees as well, and reappear each. time that their growth is favoured by some circumstances. It is well known that there always are a number of bees which prefer a life of robbery to the laborious life of a worker; and that both periods of scarcity and periods of an unusually rich
  supply of food lead to an increase of the robbing class. When our crops are in and there remains but little to gather in our meadows and fields, robbing bees become of more frequent occurrence; while, on the other side, about the sugar plantations of the West Indies and the sugar refineries of Europe, robbery, laziness, and very often drunkenness become quite usual with the bees. We thus see that anti-social instincts continue to exist amidst the bees as well;

He does not provide a citation for this (and even if he did, it would be something from the late 1800s). Is there a good modern reference for the above behavior?

I would in particular be interested in something like a graph of %-robber-bees vs. plentiness-of-food (in some abstract measure of the latter) so that I could intuitively see the increase in lazy/robber bees as the environment is low on food, or as it is overly abundant and compare it to 'typical levels'.

Theories that explain this behavior are of interest, as well, but I am primarily after experimental measures/observations to support and quantify the above quote.


texts: What biproducts do vinegar eels produce?

texts:
What chemicals, acids, gases or other biproducts do vinegar eels (Turbatrix aceti) produce (in raw vinegar and/or in the vinegar-creation process, which process may have them in environments including such as fruit scraps and fermented fruit scraps, sugar, alcohol, or water)? I know they're said to feed on acetic acid bacteria and apples.

I'm particularly curious if they produce acetic acid, carbon dioxide, enzymes, and/or vitamins, but I'm generally curious about everything they produce. I'm not sure exactly how many chemicals a single nematode species can produce (so, if it's a lot, you can narrow your answer down to what might be particularly useful to a nutritionist and/or someone making vinegar).

I thought this might be a better place to ask than Seasoned Advice, seeing as it's about biological processes, and as far as I know, little is publicly known in the culinary world about what they produce (I couldn't find any information on it).


texts: Why doesn't yearly screening for lung cancer decrease mortality rates?

texts: In a large trial, screening yearly for lung cancer hasn't reduced mortality rates. Why is this? Isn't cancer best treatable when caught early? Is this because lung cancer is hard to treat anyway, because yearly is not frequent enough, or why?


texts: DNA Topology of two circular chromosomes

texts:
I'm reading DNA Topology: Fundamentals from where I quote :

  Topological aspects of DNA structure arise primarily from the fact that the two DNA strands are repeatedly intertwined. Untangling these two strands, which occurs in all major genetic processes may prove rather difficult. In the simplest case of a linear DNA in solution, untangling is possible due to the free rotation of the ends of the DNA. However, for all natural DNAs, free end rotation is either restricted or forbidden altogether. Consequently, untangling the two DNA strands becomes topologically impossible.

And from Wikipedia:

  However, a circular chromosome can provide other challenges for cells. After replication, the two progeny circular chromosomes can sometimes remain interlinked or tangled, and they must be resolved so that each cell inherits one complete copy of the chromosome during cell division.

Is there any evidence that proves the idea represented in the figure?


texts: I would like to manually movement some b-sheets from a 3D structure of my PDF protein to represent a change in its structure.There some tool i can do that?


texts: What is the Cordil that Edward Topsell describes?

texts:
In his "History of four-footed beasts and serpents", Edward Topsell describes a "serpent" called Cordil. Since he lists everything that crawls on the ground as a serpent, regardless of being a reptile, amphibian or even insect, there seems to be a wide array of possibilities.

So far, I couldn't find anything about what the cordil described here seems to be. Does anybody know more?


texts: Are there completely self-sufficient autotrophs?

texts: Are there completely self-sufficient autotrophs which can survive and reproduce indefinitely by consuming exclusively non-organic matter (plus energy from sunlight or thermal vents etc.)? I'm asking specifically.


texts: What is the best test for SNV clustering?

texts:
I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy variables as long as I want to examine minor allele presence or absence;

Principal Component Analysis
A priori (association rules)

Do you know of any papers supporting the abovementioned methods, or maybe suggest an alternative one?


texts: What metabolic activities are performed by a developing human fetus's liver?

texts:
I understand that organ function varies with the stages of development. Does a fetal liver EVER perform lipogenesis, gluconeogenesis, make bile, etc? Or does it only begin performing these actions postnatally?

I have heard that a fetus delivered between 24-26 weeks can potentially be "okay" with proper care and monitoring in a hospital. I would assume (please correct me if I'm wrong) that this implies the fetus's liver has developed at this time. So in the case of a fetus that was not delivered at 24-26 weeks, does it spend the remainder of the pregnancy in a fully functioning state? Or at least, which functions does it begin to perform?

I've been trying to find an answer on Google, but one walks a fine line when searching for human development information -- either the results are oversimplified "expecting mothers" websites, or journal articles speculating about the effect of X on the development of Y in the mouse/chick/zebrafish/giraffe/et cetera other nonhuman model.


texts:
Fisher's geometric model is still today one of the most important and fundamental model in evolutionary biology but it seems to me that most student in evolutionary biology don't really understand it (and I am one of these students). Such standard models are often found on wikipedia but in this case the wikipedia article (here) offers nothing more than a simple analogy.

According to Orr 2005:

  Fisher's geometric model shows that the probability $P_a(x)$ that a random mutation of a given phenotypic size, $r$, is favorable is $1-\Phi(x)$, where $\Phi$ is the cumulative distribution function of a standard normal random variable is a standardized mutational size, $x=r\frac{\sqrt{n}}{2z}$, where $n$ is the number of characters and $z$ the distance to the optimum.

Can you please explain what the Fisher's geometric model and the math behind it (how are these functions calculated)?


texts:
I have read the following {1}:

According to their envelope, tendons can be divided into tendons within a synovial sheath (i.e., sheathed tendons) and paratenon-covered tendons.

This means that all tendons have either a synovial sheath (a.k.a. true sheath) or a paratenon (a.k.a. false sheath). However, {2} seems to say that true (synovial) sheaths isn't that common:

However, not all tendons possess true synovial sheaths; these are in fact found only in areas where a sudden change in direction and an increase in friction require very efficient lubrication.

and {3} seems to say that false  (paratenon) sheaths isn't that common either:

In addition, some tendons have a ‘paratenon’ that is separate from the tendon itself, but nevertheless surrounds it. It is also known as a false tendon sheath and the best example is that around the Achilles tendon.

This confuses me. Do all tendons have either a synovial sheath (a.k.a. true sheath) or a paratenon (a.k.a. false sheath)?
Synovial sheath (image source):

Paratenon  (mirror):

References:

{1} Boris A. Zelle, Freddie H. Fu, in Rehabilitation for the Postsurgical Orthopedic Patient (Third Edition), 2013
{2} Bordoni B, Varacallo M. Anatomy, Tendons. [Updated 2020 Jul 31]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2020 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK513237/
{3} Benjamin, M., Kaiser, E., & Milz, S. (2008). Structure-function relationships in tendons: a review. Journal of anatomy, 212(3), 211–228. https://doi.org/10.1111/j.1469-7580.2008.00864.x https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408985


texts: We think that it's a type of alligator lizard. It was found in the open space area near my home in Moss Beach California (about 10 miles south of San Francisco). Thank you!


texts:
If one parent is nearsighted and the other is farsighted.
One parent developed nearsightedness later in life, while the other was born farsighted and they are both the first ones in their family to have any sort of eye problems.
Is there a possibility of their children having a perfect vision since both their conditions are the result of a recessive gene and can the probability of inheriting one over the other be assessed?


texts: What is the difference between these two depictions of chromosome?

texts:
I understand that this is a single chromatid, but would this be considered a chromosome? Also before mitosis, the chromosomes appear as single chromatids but during interphase they replicate to form sister chromatids which are attached by a centromere and are also collectively known as a chromosome.
I do not understand the difference between the two of them. Are they both to be termed chromosomes?


texts: Difference between Premature Atrial Contraction and Atrial Fibrillation

texts:
what is the difference between Premature Atrial Contraction and Atrial Fibrillation. I know that both have irregular heart beat but have normal QRS complex. Both have abnormal or absence P waves but a normal T waves.

Can PAC be considered as an isolated event? and AFib be considered as chronic event?


texts:
In relation to my work, I'm looking at ornithology as a field, and it would be interesting for me to know which areas in biology relate to ornithology.

Any help is much appreciated!


texts: Animals with substantial five-fold symmetry besides starfish? Any land animals?

texts:
Animals with four, six and eight legs are widespread while the concept of seven legs (fictitious Heptapods) are the makings of amazing scifi short stories and blockbuster movies.

Are starfish the only types of animals currently (or ever) with five mostly equal sized appendages and substantial five-fold symmetry? Are there theories why five is unusual on land but common in the sea?

update: There is an interesting subtlety here. This answer points out that a sea star's legs are the little things under the five appendages, so I've adjusted the question to address instead five-fold symmetry and five appendages.

below: "Ophiopetra lithographica from the Lower Hienheim Beds (Lower Tithonian,Upper Jurassic) near Regensburg, Germany" from here.

below: "A green brittle star - Ophiarachna incrassata" from here.

below: "Une ophiure superbe (Ophiolepis superba) à la Réunion." from here.


texts: How to calculate the percentage of heterozygous cells based on a gene map

texts:
I've encountered the following question and am quite stumped by it.

A female with genotype AABBCC has been hybridized with a male that has the genotype aabbcc. The first generation (F1) has been hybridized again (backcross) with offsprings that have the genotype aabbcc. Given the following genetic map, what would be the percentage of F2 offsprings that are heterozygous to all three genes:

A------- 20 MU ------- B -- 10 MU --- C

How should I approach the following question, the brute force approach is too difficult, I keep getting things wrong.


texts: What kind of skull is this-I found it on the beach in Cape May

texts: I am hoping someone can help identify this skull! We found it on the beach in Cape May. The skull size is about 4 inch in length. Thank you.


texts: This tree was found in the rainforest on subtropical Japanese islands. At first I thought that it was a camphor tree, which are indeed common in Japan. However, the leaves are slightly different and elongated, and the fruit  has a sharp tip and is much larger than that of camphor trees. The bark is very aromatic and smells like good cinnamon, perhaps a bit peppery. Any ideas?


texts: I would like to understand how (if possible) the measles virus could start to infect a population that was theoretically isolated from any other population group. Put another way, can the measles virus develop within a person without external influence/inputs?


texts:
I can find a great deal of information about how muscles contract, and how we divide them up into fast twitch and slow twitch and so forth.  However, I can't seem to find anything on how fast a muscle fiber can relax.

How fast can a contracted muscle fiber stop providing force when the motor neuron stops innervating it?


texts: Text/resource with information on all skeletal muscles and their motor units

texts:
Something analogous to an encyclopedia on baseball players with a list of all thier stats would be ideal.

I'm not looking for just generic muscle names, locations and illustrations.

Good answers would include links to resources, textbooks etc. which include stats for most or all of the following of every skeletal muscle in the human anatomy:

Language of origin/LOO definition
Labeled by ? shape, location, size etc.
Type of Shape (i.e., fusiform, pennate, bipennate, multipennate, convergent, parrellel etc)
Angle(s) of pennation (if applicable)
# of motor neuron innervations
# of proprioceptors in muscle
# of fibers
Length of muscle
Length of fibers
Typical fuel system reliance (determined off of biomechanical placement and architecture..CPr, oxidative, etc.)
Biomechanical function (structure of corresponding bone/tendon anchors and corresponding movement manipulation)


texts: Can certain jellyfish photosynthesize in the medusa stage?

texts: Can jellyfish (at least some of them) do photosynthesis in the symbiosis with zooxanthellae in their medusa form as well? I've heard that only Cassiopea andromeda can but I wasn't able to find a credible source upholding such claim. (Wikipedia would be enough)


texts: Can food swallowed when a person is upside down reach the stomach?

texts: If a person positions him/herself upside down and swallows food, will it reach the stomach against gravity? If so how?


texts: How to seek information on the duration of biological entrainment processes in mammals?

texts:
This is a question that is a little bit hard to define for me. I'm interested in learning more about times of "attractor/entrainment" processes that may take place in the body/brain of mammals, and particularly humans. I want to get a general idea of how long it takes for a mammal to switch into a new mode of operation, be it behavior or physiological change? Is it days, weeks or more?

For example, a polar circle animals may change the color of their fur in response to photoperiod changes. How quickly does the change get registered and take place? Is it days, weeks or months?

Another example might be a mating season of siberian hamster, where their testes weight changes in response to photoperiod duration. How long does it take for a behavior change like that to fully manifest?

I've read that it takes ~21 days for a human to create a habit or break one. Is there any biological basis for this observation?

I'm not sure how to search for information like that, as it seems to me such things might only be incidentally mentioned in scientific articles. Are there some keywords that may help me improve the search results?

Thank you for any input.


texts: How does transpiration help in sucking water up?

texts: How can transpiration help in sucking water up as the amount of water that is sucked up by the evaporation of water equals to the amount of water evaporated. (Correct me if I am wrong). Then how it helps?


texts: What is the title of Darwin's paper on cellular structure?

texts:
I read somewhere that Darwin wrote a paper that dealt with cellular structure, but I've been unable to find the title or contents of the paper because Darwin wrote such a volume of material. What is the title of this paper or papers?

A google search does not turn up any helpful results, and a similar search in google scholar yields equally ambiguous results (at least to me, since I do not have a background in biology).


texts: Why does regular exercise increase brain volume?

texts:
It has been shown in several studies that regular aerobic exercise increases brain volume in aging humans. The changes were observed in hippocampus and were correlated with dramatic reduction of age-related dementia. Interestingly, the intensity of training had little influence on the results: walking, climbing stairs, gardening were just as effective at reducing dementia as more strenuous exercise.

What is the biological mechanism behind this phenomena?

Fig. The aerobic exercise group showed an increase in the anterior hippocampus and no change in the posterior hippocampus.[1]

Erickson et al. Exercise training increases size of hippocampus and improves memory. PNAS. 2011.
Colcombe et al. Aerobic exercise training increases brain volume in aging humans. J Gerontology. 2006
Ravaglia, et al. Physical activity and dementia risk in the elderly. Neurology. 2008


texts: Species that murder their own counterparts when put in captivity

texts:
Mary Midgley writes in her book, Beast and Man (p. 54 in this eBook: https://goo.gl/3NnhtP):

  Lorenz gives chilling examples from roe deer and doves, in both of which species stronger members will slowly murder weaker ones if kept in captivity with them[...]

I find this fascinating but I was not successful in finding any more info on this phenomena on the internet.

Can any biologists point me into a good direction? I do not have the work of Konrad Lorenz at hand, and would not know where to exactly look for in them.

Thanks a lot!


texts: Possible to cause the cells to produce less/no chemicals?

texts: I have a question regarding cells producing chemicals, e.g. some metabolite, inside the body. Is it possible to inject something (at least theoretically possible, and maybe practically possible in the future) into the body to inactivate these chemicals (e.g. enzymatically), or inject something which makes the cells produce less/none of the chemicals?


texts: Is it possible to grow any kind of plant soilless (hydroponics)?

texts:
Hydroponics is a subset of hydroculture and is a method of growing plants using mineral nutrient solutions, in water, without soil. [wikipedia]
My question is if is it possible to grow any kind of plant soilless (hydroponics)?


texts: Why does freshly cut grass smell like a watermelon?

texts: I found that, when I smell watermelon aroma outdoors, someone nearby has mowed  the grass. Is there an underlying basis?


texts:
We had in class following question which I had no idea how to get to the correct answer:

  The carrion crow and the hooded crow are fertile together,  but their
  reproductive success is reduced by 50%. In a certain region exist
  two populations of both species of roughly the same size. Thus,
  mixed couples occur in about 10% of all cases. What is the percentage of
  hybrids in the F1-generation?

(Translated from German.)

I thought it would be something like 5/95 = 5,3% but apparently the answer is 1%. Why?


texts: When I look up information related to the identification of disease genes, texts will often refer to the gene being "first cloned." What does "clone" mean in this context? Is it simply a synonym for discovery?


texts: Is there some branch of biology that deals with the entire organism?

texts:
I'm reading about various parts of the human body and brain and started to wander if there's a branch of biology that deals with the entire human? I know that there are branches various -biologies, from neurobiology to something like heliobiology or chronobiology. All of them look at different organ systems or parts of an organism, but from different points of view.

Then there are sciences that deal with behavior and cognition of humans.

As I read about these, I notice that there's quite a lot of overlap, particularly when neurotransmitters and hormones are involved. For example Melatonin, a hormone has functions in both the brain and the gut.

I'm wandering if there's some form of biology or science that deals with the entire organism, its behavior , as well as its parts? Am I thinking about Biology or Medicine or something else?


texts: What is the attachment after this gene name, following the comma: SULF1,hCG18956?

texts:
What is this part mean: hCG18956? Is it an alternate naming convention for genes? I am trying to read in a list of gene names using R, but I don't have an extensive biology background.

There are some rows where gene names is not listed. Only something like this: hCG1809003. Does that mean there is no appropriate gene name?


texts: Did the first cell self-replicate or was it multiple first cells?

texts:
We're almost sure by now that the first cell was born in a some kind of underwater vents environment which harvested all the necessary conditions for it to exist.

However, did the first cell self-replicate to have other cells or did the same process lead to the birth of others as well? If the latter is true, doesn't this make the evolution of cells more common once the primitive conditions exist?


texts: The majority of animals have two genders, and both are needed in reproduction. It seems like it would be more advantageous for creatures to be hermaphrodites, since they could mate with any member of their species instead of needing to find a partner of the opposite gender. Why did animals evolve to have genders instead of being hermaphrodites?


texts: Here is the second part of my question about how we sneeze. How are the sneeze droplets propelled at such a fast speed? I have heard sneeze travels at 100 mph. How is this possible?


texts: Is a double-yolk egg capable of producing two viable chicks?

texts:
As per title: If fertilized, is a double-yolk egg capable of producing two viable chicks (that could survive to adulthood)?

Have there been any reported cases of such (presumably) fraternal twins?


texts: Is it possible to consciously increase or decrease your own heart beat?

texts: By doing yoga, can we manipulate our own heart beat? Is that possible for humans?


texts:
I often buy baby spinach from the store, and sometimes, in a few bags of spinach I also find these leaves:

They have a different shape than the spinach leaves, they are a lighter green, and they taste differently. The bag doesn't say that "it may contain traces of" other plants, so are these some part of the spinach plant? Or are they something different? Why do they often come together with the spinach leaves? I haven't found any other kind of leaves (besides spinach) in the bags except those in the picture.


texts: Seen today on a hot summer day in Stockholm, Sweden. Length around 25 mm.


texts: Which concentration of BSA is recommended for dynamic light scattering experiments?

texts:
What is the recommended concentration of BSA to be mixed with water so as to prepare a very dilute solution in order to clearly study the intensity-intensity correlation with single scattering ?

I want to plot the intensity vs time correlation curve/graph, and eventually calculate the hydrodynamic radius in each case. I've seen different journals and texts provide varied concentrations ranging from 0.001 g/L to 3 g/L.


texts: In glycogenesis (i.e. the synthesis of glycogen), are sugar phosphates the direct substrates for glycogen polymerization? I would certainly think so since glucose is phosphorylated and then stuck onto a glycogen chain, but my textbook seems to think no.


texts:
How can we estimate what portion of a genome is repeating sequences without sequencing it?

Thank you


texts: Who were "Dawson and Wilson" (mentioned as authors of an embryonic postmortem examination method)?

texts:
A sentence from a Russian text I'm translating:

  Following the drug administration period, the pregnant animals were euthanized in order to examine the embryos using the method developed by Dawson and Wilson.

That made me curious. Who were they? Google fails to bring up both these surnames at once in response to queries like "Dawson Wilson embryo necropsy" etc. Maybe one of them developed an embryo examination technique, and the other perfected it?


texts:
Is trans-complementation a complementation of transgenes?

The crystal structure reveals a trans-complementation mechanism whereby an incomplete immunoglobulin-like domain assimilates an isoform-specific myomesin interdomain sequence.
https://www.ncbi.nlm.nih.gov/pubmed/27989621


texts: Why do naked mole rats live in colonies with a queen?

texts: What was the evolutionary advantage in having queens? Is it because the ones that had queen like tendencies in the new environment had kids that cooperated better giving higher chance of survival of the colony? Do the worker naked mole rats have an evolutionary advantage in not reproducing because it allows them to devote more energy to the long journey to make one of their siblings the new queen?


texts: When a kidney is transplanted from a donor to a recepient does the surgery occur keeping the donor's adrenal gland intact over the kidney or is the kidney minus the adrenal gland over it transplanted to the recepient?


texts: Which of the two chromosomes in a pair is expressed?

texts:
I have completely dummy question.

I have 23 pairs of chromosomes in the cells 23 single coming from my mother and 23 single from my father. So how my cell choose which chromosome, mother's or father's to use to synthesize peptides?


texts: qPCR (weird ntc curve, amplifies before templates and reaches plateau quickly)

texts: I'm new to qPCR, and I’ve been testing the AR expression on canine tissues. I’m currently using a pair of primers that have been tested in other article for canines.The issue I’m having is  that I have very early amplification of ntc AR (before the amplification of cDNA templates) but also this amplification curve looks weird since it reaches quickly the plateau phase (flattened). This problem persisted even after changing to a much more specific cycling. If anyone has any tips, or ideas on how I may be able to explain this, I’ll be very gratefull.


texts:
While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance):

CLNSIG=2|2|2|2|2|2|2

This is actually reported in this example, so I think the usage of the pipe is quite common for genomic annotations of this kind.

Which is the use of the pipe (|) character? I looked for it in the VCF file format specification; however, only the meaning of the comma (,) is specified (i.e., presence of multiple alternate value for that field). I am wondering, instead, what the pipe represents.

Thank you.


texts: I want to cast flowers in resin. The problem is that everyone is casting dried flowers in order to prevent the moisture from fresh flowers evaporating while the resin is curing and I need to cast fresh flower. I tought of freeze dried flowers but could not find any company that could do it in my country nor online shop where to buy in europe. I am thinking of castin stabilized roses which are dehydrated first and the soaked with glycerin, propyl glycol and som dyes for colors. I wonder  if the glycerin with propyl glycol will evaporate with the higher temperature during the resin curing process.


texts: I'm still not sure about the mechanics that lead to rabies being incurable. I know that it can be treated before any symptoms show up, but why is it that once symptoms show the person is a dead man walking?


texts: What factors affect the rate of siderophore production by microbes?

texts: Microbes produce siderophores which are chelators and bind to iron. This is how microbes absorb iron from soil or rock. What causes microbes to increase or decrease the rate of production of siderophores?


texts: Antibodies combine with antigens in the presence or abscence of macrophages?

texts: There was a mcq in book that antibodies combine with antigens when.... And the correct answer was if macrophages are absent. As far as I know macrophages release interleukin 1 which stimulates T helper cells to release interleukin 2 which further activates b cells. Plasma clone b cells then produce antibodies.  With respect to that macrophages presence is important.   Kindly clear my confusion.


texts: How does the digestive system determine what to absorb [as nutrients] into the bloodstream?

texts: If you put an egg into a sausage machine it will try to make sausages out of it because that's its job. Does the digestive system attempt to digest everything it receives? Furthermore, does it attempt to derive nutrients from everything it receives? How does the digestive system determine what is nutritious? Can "particles" (e.g., microscopic dirt) pass through to the bloodstream if they are small enough to be absorbed?


texts: Why does a blood test show ethanol when no alcohol was consumed?

texts: Why would ethanol show up in a blood test if a person had not been drinking alcohol in many years. What are other reasons for showing ethanol?


texts: Why is it important to have a restriction point? (G1-S phase control)

texts:
Why have eukaryotes evolved to control G1-S phase?
Surely if you could control G2-M phase very well, you will not get an excessive proliferation?
Thanks for your help.


texts: What does the immune system do to stop pathogens that aren't killed by macrophages?

texts: For instance, say a host is infected with salmonella where the pathogen can enter into a macrophage without the macrophage destroying it. How does the body then fight off an infection that is capable of surviving the mechanism by which pathogens are destroyed?


texts: NCBI EUtils. Get Homolog infromation using Gene ID

texts:
How to retrieve homologs information in xml or json format from NCBI using gene ID?

I tried one URL:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=homologene&geneid=9&WebEnv=???&query_key=???

I dont know what to add in question mark regions


texts: Why are red blood cells considered to be cells?

texts:
Wikipedia states that a cell is

  the basic structural, functional and biological unit of all known living organisms. Cells are the smallest unit of life that can replicate independently.

It then goes on to state that

  All cells (except red blood cells which lack a cell nucleus and most organelles to accommodate maximum space for hemoglobin) possess DNA.

Then why are red blood cells still considered cells, while they can't replicate? Is the definition on Wikipedia just a bad definition? Or are red blood cells wrongly considered cells, but remain so for historical reasons? Or are they considered cells for some other reason, such as this answer which states that red blood cells do contain a nucleus at some point?


texts: How does garlic preparation affect its active compounds or medicinal properties?

texts:
I read the following claims about how to consume garlic:

Consume immediately after crushing since the active compounds (allicin) is volatile and gets oxidized as soon as it's crushed
Allow to sit 10 minutes after crushing to allow time for allicin to form
Do not change the PH of garlic (i.e. mix with acid/lemon) in order not to disrupt the formation of allicin, during those 10 minutes
Allicin is completely lost within 20 minutes after crushing

If so:

Which of those claims is true? Is the wait-10-minutes practice is only recommended before heating the garlic? i.e. should you wait at all after crushing, when you consume it raw? (e.g. in a salad)
Given this is how I prepare a salad:

Cut vegetables and herbs

Crush garlic and mix in (no waiting)

Add lemon juice and vinegar and mix right away

Season with salt and pepper

Pour olive oil and mix right away

Let sit refrigerated in air-tight container 5-10 minutes

The salad is consumed at least 15 minutes after garlic is crushed, and it takes me another 15 minutes to finish eating the salad

By that time (30 min after crushing) are the active compounds in the garlic (particularly allicin) preserved or completely lost?
Will it make any difference if I mix the garlic in the oil first (to merely prevent oxidation), wait 10 minutes, mix in the acid, and pour everything over the salad right before serving?


texts:
Background:It is said that during the phase of isovolumetric contraction , due to sharp rise in the ventricular pressure, there occurs bulging of AV valves into the atria producing a small but sharp rise in the intra-atrial pressure called c-wave.( in the second cycle of diagram).

Question: I am unable to understand why is then pressure in atria falling after the end of isovolumetric phase, even though the pressure in the ventricles is rising, so this should further bulge the AV valve or atleast( due to action of papillary muscles) have same pressure, So why is pressure falling?


texts: Are we more attracted to people of the same ethnicity?

texts: Are humans more attracted to people from their own ethnic groups? I ask this because most of the time people have relationships with people of their own ethnicity, and I wonder if it's purely social, or if there's more behind it.


texts: Confusion about resting membrane potential and the Na/K pump

texts:
To this day, very few people and sources have been able to clear up my confusion about resting membrane potential and how it is maintained. It seems like this is one of those topics that few people are able to explain very well...

Here is what I do understand:

Chemical Gradients:

at rest, the inside of a neuron is negative and comprised mostly of Potassium (+) and negatively charged proteins (-)
at rest, the outside of a neuron is positive and comprised mostly of Sodium (+) and Chloride (-)

Electrical Gradients:

at rest, the sodium ions are attracted to the negative charge on the inside of the cell and tend to move inwards
at rest, the Potassium ions on the inside of the cell are attracted to the negatively charged chloride ions on the outside of the cell and thus move outwards

So overall, there is a net inflow of Sodium and a net outflow of Potassium. Got it, pretty simple.

However, the sodium/potassium pump is where I get lost. Why does it reverse all that just happened, and why doesn't it cancel out the resting potential if it moves K+ back inside and Na+ back outside? Isn't the voltage fluctuating because of this back and forth movement of K+ out, K+ back in, Na+ in, Na+ back out, etc.? I would imagine this would completely negate the positive/negative charge distribution, but it doesn't. Why?

Clarification: there is a net outflow of Potassium and a net inflow of Sodium. Why does the Sodium/Potassium pump intentionally reverse this by pumping out Sodium and pumping in Potassium? How does that contribute to resting potential?


texts: The phylogenetic definition of the clade Dinosauria

texts:
Up until two years ago the clade of Dinosauria was defined as all the descendants of the most recent common ancestor of Triceratops and birds. From Wikipedia:

  Under phylogenetic nomenclature, dinosaurs are usually defined as the group consisting of the most recent common ancestor (MRCA) of Triceratops and Neornithes, and all its descendants. It has also been suggested that Dinosauria be defined with respect to the MRCA of Megalosaurus and Iguanodon, because these were two of the three genera cited by Richard Owen when he recognized the Dinosauria.

However, after the resurrection of the clade Ornithoscelida by Baron et al in 2017 (see here), as the clade consisting Ornithschia and Theropoda, the MRCA of Triceratops and birds is defining Ornithoscelida and not the whole Dinosauria, assuming we still define Sauropodomorphs as dinosaurs.

So if dinosaurs include Sauropodomorpha, Herrerasaurs, Ornithoschia and Theropoda,  what is the most updated phylogenetic definition of the clade Dinosauria?


texts: Which types of hydrogen bonds are known to exist in RNA secondary structures?

texts:
I'm programming an implementation of an algorithm for pattern matching in RNA structures.
The algorithm assumes the following types of base pairs:

Plain: No base pairs (just the primary structure of the RNA)
Single: Each base can be connected to at most one other base
Multiple: Each base can be maximally connected to a number of other bases (where 'number' can be constant or infinite)

Although there is no problem with the implementation of the above types of base pairs (apart from the probable high computation complexity), I wonder if all of them were observed in real RNAs?

In particular, I'm interested in the following cases:

A base pair between two adjacent bases i,j.
One base (i) which connected to two different bases (j,k) (i is not adjacent to j or/and k).
One base (i) which connected to more than two different bases, all of them not adjacent to i.

Can these exist? Some of them?
If they can, how common is their existence?


texts: Is this a Tabebuia impetiginosa – Pink Trumpet Tree Flower? From Panama.


texts: What causes headaches (biologically)? What does it mean directly?

texts:
Even though your brain can't feel pain, thingies in your head are installed to compensate for that.
Once I thought your head starts to hurt when your brain is tired. I can't believe this any more. Several times I happened to skip sleep completely - while intellectually working (not just watching TV or something like that). The next day I didn't go to sleep to prevent breaking the day/night biorhythm. Yet I don't remember any headaches from not sleeping enough - and working instead.
However, when I was worrying about something deeply I often got a headache to the top. Also, you get headache when you're ill. You get them after drinking too much alcohol (or getting poisoned by some other things too as I've heard).
As non-biologist I believe that pain receptors are triggered when whatever they're guarding is damaged. Also I thought that they're installed so that you can do something about the cause of the pain - that doesn't seem possible in case of headaches.
But I do hope that headache doesn't mean that my brain is sustaining damage.
So what's triggering pain sensors? Is it a chemical/hormone that is released when the organism feels endangered (by illness or something else)?


texts: What is the mechanism of chiasmata terminalisation in meiotic prophase I?

texts:
There's barely any fresh literature available about how the chiasmata between the non sister cromatids of homologous chromosomes separate.
I'm curious to know about the forces responsible for pulling the cromatids apart to end the chiasma.
Most of the available sources state something like "The disjunction of homologues is accounted for by repulsion of the sister chromatids." Now why is that repulsion taking place and how is it responsible for the whole terminalisation process ? What other factors are playing here ?


texts: This question is regarding the conversation that took place here: Why don't mammals have more than 4 limbs?. I'm not sure if someone mentioned this and I just missed it, but everyone is talking about two pairs of limbs for all terrestrial vertebrates; what about the case of kangaroos? If we are analyzing this from a locomotion point of view, and tails are being considered limbs, then wouldn't the kangaroo be considered to have five? They use their tail for balance and to push forward in "walking" (not exactly a walk, but I am lacking the proper term at the moment), resting only on the tail and forelimbs as the hind limbs swing forward. Does anyone have thoughts on this?


texts: Is it a medical condition to not able to recall the word in a language while having a conversation

texts:
While having a conversation it happens to some peopl that clearly they know there exists a perfect word to be used but can not recall it during the conversation in real time and hence forced to use some other word which may not be so perfect.

But after the conversation is done they will be able to recall it. This happens very frequently to some people. Is this some kind of medical condition. If yes what is the name of this condition called as. ?


texts: Are brown eyes healthier than blue eyes?

texts: I have read somewhere brown eyes have more melanin than blue eyes and as melanin protects our body from cancers, I thought that brown eyes are more healthier.


texts: What is the difference between tonic and phasic firing?

texts: I am reading about dopamine, and I have realized that dopaminergic neurons can fire phasically or tonically. What is the difference between these two modes of firing?


texts: What is the creature with the lowest neuron count that demonstrates cognition beyond reflexes?

texts:
I'm under the impression that nematode worms just perform the same scripted actions over and over again in response to specific stimuli. They have 302 neurons. Chimpanzees display problem solving capabilities, as do other mammals with smaller brains (cats, for instance with ~ 1 billion neurons). You might say that bees demonstrate something more than reflexes when they communicate the location of nectar sources to the hive (~ 960,000 neurons).

What's the creature with the lowest number of neurons to demonstrate something more than mere scripted actions? I would imagine its somewhere between a bee and a nematode worm...


texts: Do acetic acid bacteria use the electron transport chain when converting ethanol to acetic acid?

texts:
Do acetic bacteria use the electron transport chain when converting ethanol to acetic acid?

And is wikipedia inconsistent here in its definition of fermentation. It says fermentation

  Fermentation takes place when the electron transport chain is unusable

(and this is consistent with (academic) microbiology books searchable on google books).
Wikipedia defines acetic acid bacteria as

  produce acetic acid during fermentation.

also

  Some genera, such as Acetobacter, can oxidize ethanol to carbon dioxide and water using Krebs cycle enzymes. Other genera, such as Gluconobacter, do not oxidize ethanol, as they do not have a full set of Krebs cycle enzymes.

I read in microbiology books on google books, that acetic acid bacteria use oxygen as the terminal electron acceptor, and have a respiratory mechanism.

Brewing Microbiology edited by Fergus Priest p165

  Acetobactor spp. possess a respiratory mechanism...Acetobactor spp. are obligately aerobic with a respiratory metabolism (O2 as the terminal electron acceptor)

So is wikipedia wrong to describe acetic acid bacteria as using fermentation?

I see mention of krebs cycle though, which I understand to be associated with respiration rather than fermentation. Also in this reaction/process :

$C_2H_6O\hspace{1mm}(ethanol) + O_2 \rightarrow C_2H_4O_2\hspace{1mm}(acetic\hspace{1mm}acid) + H_2O$

I see water mentioned but not carbon dioxide(if it had both I'd say that really looks like respiration, though it's being called oxidative fermentation).  So I still can't really see whether it's respiration or fermentation, though it's being called fermentation (oxidative fermentation), yet there is the mention of krebs cycle enzymes (krebs cycle being associated with respiration), so it makes me unsure whether the electron transport chain is used or not.


texts: Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.


texts: How exactly does DNA polymerase III detect a mismatched base? I know how it removes it, via exonuclease activity, but how does it 'detect' it molecularly in the first place?


texts: Need help identifying multi-colored grasshopper

texts: I was out hiking with my friend when we ran across what I presume to be a grasshopper. It didn't seem very startled by our presence, and we were able to get some pretty cool pictures. I've been having trouble finding out what species it is. I was hiking near Albuquerque, New Mexico, and the grasshopper was about 1 - 1.5 inches in size. It was about midday when I saw it.


texts:
I live in Oxford, in the United Kingdom, in a part of the city with a vibrant multicultural community. My local corner shop has an excellent selection of spices, pulses, and obscure and vegetables fruit that mostly tends to be from the region of Pakistan and India, and only labelled (illegibly) in a language that I do not speak.

I've just bought a fruit I thought at first inspection was an unripe mango -- previously they have had excellent, cheap, small alphonso mangos for sale that I'm rather partial to. I'm completely wrong, however, for I've bought something about the size of my fist with striking white seeds that taste very peppery, a green coat, and somewhat sour flesh. It floats in water, and the skin exuded a slightly sticky, partially white gummy substance when I removed it from the bag. It's not particularly soft to touch. The seeds look a bit wrinkly, and are not hard at all to touch. The flesh has a consistency of an apple.

I can't for the life of me identify it! I'd love to know any suggestions! Thank you!


texts: coverage calculations approach for clipped reads

texts:
Experiment: deep sequencing for mutants in 700nt fragment.
the fragment of dna was preamplified by primers flanking the fragment followed by hiseq.
per base coverage was calculated by coverageBed -d -abam in.bam -b ref.bed > out.cov

Observation: two distinct peaks in coverage at the ends as below plot.. coverage vs positions

the peaks are made from reads having part of primers..thus also show soft clipping at ends..
there is a huge difference in the calculations if i include such reads And if I exclude them.

Question: is there anyone who knows how to handle such a situation?


texts: Why do we see a different color when we mix two colors?

texts:
The compounds responsible for a color do not change when they are mixed with another material. The same compounds are there after mixing. However, when we mix colors such as blue and yellow we see green.

BUT we are able to tell where a color starts and ends in pictures. For example, if we hold a yellow piece of paper up to the sky, we can tell that the paper is yellow and the sky is blue. We can distinguish where the paper ends. And where the sky starts. We do not see a green outline near the paper.

I believe that  how we perceive colors may explain this. But I am not sure how. Is it because how the brain integrates information. Or is it because of how the cones cannot register two signals at the same time. Why do we see green instead of a blue and yellow?


texts:
When taking some pictures I accidentally captured two fruit flies doing this:

The photos are unfortunately blurry, but from what I can tell, one fly approaches the other from behind, and something is then retracted/pulled into the front fly's body. I'm guessing it has to do with reproduction, but it doesn't look like the fruit fly mating I've seen before.

Here are some stills from the sequence:


texts: What is the term for "technical extinction" of yet alive animals?

texts:
What is the term for an event in which a species is still alive, but has no chance of future reproduction and the species will be considered extinct once the current generation dies out?

For example a species of a tiger that has the last 5 surviving members left and which are all related and all male. Hence, even though they are still alive, there is no chance that the species will be able continue their bloodline and hence are already "technically" extinct.


texts: Multiple clones Sanger sequencing analysis

texts:
I am doing a 96-well arrayed cloning. I have done Gibson, transformations and minipreps in a 96-well format, then sent out the plate for sequencing. Normally, I sequence 3-4 clones and check if the sequencing looks good manually with Benchling cause it has nice visualization tool that highlights mismatches but also displays sequence quality. Now I have to check the sequences of 96 individual clones. Obviously I can write a simple script that would do alignments and report the alignment quality. However, I am guessing there should be already tools available that work with Sanger clonal sequences and provide nice visualization for many alignments at once. Any recommendations for specific tools I should use?
Thank you!


texts: Why doesn't cellular, replicative senescence (or the hayflick limit) constrain the normal development of an organism?

texts:
The wikipedia article on cellular senescence states:

  Cellular senescence is the phenomenon by which normal diploid cells cease to divide. In culture, fibroblasts can reach a maximum of 50 cell divisions before becoming senescent. This phenomenon is known as "replicative senescence", or the Hayflick limit.

My question is, if many cells in diploid organisms (e.g. humans) have an inbuilt limit of the number of cell divisions, how is it that a human can develop from a single celled zygote to a organism comprised of many 10's of trillions of cells - if many cells can only divide 50 or 60 times?

Wouldn't the cells "use up" their available telemeres during development? or is it a simple mathematical relationship, that whilst yes, existing cells are "burning up" their telemeres as they divide during development, but because the number of cells are increasing exponentially they develop all the tissue mass the organism needs before hitting the hayflick limit?
e.g. if cell numbers are doubling during each division phase, it only takes 30 doublings to achieve a billion cells, after 40 doublings you have a trillion cells.
i.e. after 40 or 45 doublings it has developed all the tissue mass of a mature organism, and still has some telemeres left over for additional tissue generation during the organisms lifetime?