texts: Is it possible to convert nerve signals or electrical pulses into a readable format?

texts: Can we have the technology to recreate the informations (like images, sounds etc.)[as in the form of signals in our mind] from human mind to human understandable format? In short, can we read human mind?


texts: Are lymphocyte sizes clustered in two groups?

texts:
Tortora writes in Principles of Anatomy and Physiology:

  Lymphocytes may be as small as 6–9 μm in diameter or as large as 10–14 μm in diameter.

Those ranges are quite close to each others. Should the above be taken to mean that lymphocytes sizes are clustered in two groups, or is it just a way of saying that lymphocytes are 6-14 μm?


texts: What kinds of bacteria live in water bottles?

texts:
I've always heard not to re-use disposable plastic water bottles.

According to this Huffington Post article, the reason is because:

  everyday wear and tear from repeated washings and reuse can lead to physical breakdown of the plastic, such as visible thinning or cracks. Bacteria can harbor in the cracks, posing a health risk.

Also, a study from the Canadian Journal of Public Health found nearly two-thirds of bottles sampled had bacterial levels that exceeded drinking water guidelines. (See here).

So my question is: What kinds of bacteria (or other microorganisms) live in water bottles? In other words, which species should we worry about in these cases?

This Livestrong Article lists species found in the water itself, but I'm more curious about what organisms get introduced and grow through re-use of the bottle.

This is relevant because bottled water just became the most sold consumer beverage in the US.


texts: The evolution of poor eyesight: is there weaker selection in modern humans?

texts:
Short question:
Poor eyesight might have been a major impediment to survival and reproduction in early man (say, 100,000 years ago), but, with the advent of agriculture, major cultural changes, and modern medicine, one might imagine that genes for poor eyesight would persist more easily.
Is that true? Has selection on eyesight been relaxed, or changed significantly, in modern humans? If so, when? Do we know what might explain relaxed selection? If there are any genes associated with, for example, myopia, has their population frequency increased through human history, or has it remained constant?
This New York Times article discusses genetic changes 8 to 4 thousand years ago related to skin color, amino acid absorption, and eventually milk digestion, but it does not mention eyesight.
Background on why I find the question interesting:
A friend of mine speculated that human eyesight is worse today than it was only a few centuries ago, due to the invention and widespread adoption of glasses: a person with poor eyesight genes will now survive and have children, whereas in 1600 they might have died without reproducing.
I'm skeptical: first, glasses became widespread only a few generations ago; second, blurry vision plausibly has little effect on evolutionary fitness. I see no reason why someone with slight myopia would on average have significantly fewer offspring than someone with 20/20 vision, even in a tribe of hunter-gatherers. A short-sighted person could specialize in making hand-axes, for example, and trade them for food -- so I find it plausible that eyesight-related allele frequencies have not changed much over time.
However, I recently heard someone on the radio speculate that eyesight might have worsened significantly a few thousand years ago with the invention of agriculture; the story is that above-average eyesight is a major fitness advantage for a hunter, but not for a farmer.  What does the evidence say?
Side note: I realize that eyesight is affected by more than just genes -- for example, age as well as time spent reading books probably both affect eyesight. That's not what this question is about -- I'm interested in genetic selection.
Edit:  this question is indeed similar to Bad Eyesight and Evolution, but it isn't identical.  That question asks why poor eyesight can persist at all, while mine asks whether evolutionary pressures have changed over time.  In particular, do we know of any genes associated with, say, myopia?  Do we know whether their allele frequencies have changed over human history?


texts: Why isn't the ovum reabsorbed into the body (like sperms) if it is not fertilised?

texts: I have read that when sperms are not ejaculated out of the body, they are broken down and reabsorbed. Why can't the ovum be reabsorbed into the body instead of shedding it out during menstruation.


texts: What kind of spider is this? First time I have ever seen one

texts:
This was taken 07/06/19 in Cape Breton, NS, Canada.

I would say that it is about an inch (2.5 cm) in length and seemed to be pretty uniformly grey. The belly was the same colour as the legs, it had a few small brown spots but I couldn't tell if that was an actual marking or maybe just environmental.

It was just hanging out right beside the handle of the door exactly where you don't want a spider to be.

In usual spider fashion it has dipped and is now...somewhere :(


texts: Will the heart keep beating if it's separated from the body?

texts: The heart is a vital organ in our body, as it drives blood circulation. I was wondering if a heart keeps beating if it is separated from the body? If yes, then why?


texts: Bacterial 16S rRNA PCR amplification with universal primers

texts:
I am doing an experiment to amplify the 16S rRNA gene from bacteria present in gut contents of fish. After extracting DNA, I perform one-step PCR with universal bacterial primers (27F, 1492R) and I see a strong band of expected length (approx 1500bp). My DNA extraction readings range from 50ng/ul in some samples, to 150ng/ul in others, as measured with Nanodrop.

Does this band represent all of the 16S genes present in the sample? Thus, does this band represent 16S genes from all of the bacterial species present in the sample?

Do I need to perform a microbiome profiling PCR to differentiate and identify all of these species?

Thank you.


texts:
This question may sound silly.
How does it come that the DNA molecules are not totally entangled with time in the cell ? If I take long strings in a box and shake it, that would create knots, and I wouldn't be able to easily isolate each string apart.

But during mitoses, the chromosomes are totally isolated from each others while otherwise, the DNA is freely floating in the nucleus.


texts: Wearing sunglasses during a solar eclipse

texts:
Note: I had asked this on Physics, but it is off-topic there due to being about safety.

On the BBC's guide to eclipse-watching, Dr Lucie Green says:

  Watching an eclipse with normal sunglasses provides virtually no protection. In fact, they trick your eyes to let in more light, so they can cause even more damage.

This doesn't seem right, because proper sunglasses should block UV to a safer level. Surely wearing proper sunglasses at any time is safer than not? Whilst I can understand staring at the sun with sunglasses on still allows too much UV in, why couldn't someone just glance at the eclipse from time to time?


texts: Why do some foods do not taste good when eaten together that eaten separately would taste great

texts:
The way I understand it, 'good tasting food' is evolutionary concept e.g to be able to distinguish between high nutritional value foods and ones that have no nutritional value whatsoever.

So if well-prepared fish tastes well and so does some other food (birthday cake/[put food that would not go along]) on its own why then when mixed together they might taste bad. The mix has the same nutritional value, same proteins carbs, and fats, but they just don't go along.

Why do some foods do not taste good when eaten together?


texts: How can protein allergens be passed from mother to baby via breastmilk is proteins are broken down after ingestion?

texts:
All over the Internet new mothers are urged to avoid dairy products, a slew of vegetables and even beef if their child displays symptoms of reflux.
In the case of dairy, for instance, it is said that an allergic reaction can be caused by specific proteins that exist in cow's milk.
What I don't get is this: aren't ingested proteins broken up into their constituent amino acids, which are then recombined, presumably somewhere in the milk-producing glands, to create new proteins that are then passed on to the child through the mother's milk?
If that is the case, the original, allergy-inducing proteins should be long gone by then, right? If that is indeed the case, then what is causing the allergy and is there an allergy in the first place or could the cause be something else?


texts: What is the probablity that SARS-CoV-2 will mutate?

texts:
In many epidemic/pandemic situations, a lot of time the pathogen in question will mutate. For reference, this is the definition of mutation taken from Wiki:-

  A mutation is an alteration in the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA. Mutations result from errors during DNA replication, mitosis, and meiosis or other types of damage to DNA (such as pyrimidine dimers that may be caused by exposure to radiation or carcinogens), which then may undergo error-prone repair (especially microhomology-mediated end joining) or cause an error during other forms of repair or else may cause an error during replication

So my question is,

1》What is the probablity of SARS-CoV-2 mutating?

2》 How can we predict, in advance the mutation of the virus? (Maybe by studying the environmental factors of a specific place)

3》Lastly (something that makes the biologist cringe) is there any way to prevent mutation? Any way at all to somehow limit the mutations which can be used widely?

  BTW I am not a biologist, only a person among the millions out there, trying to find a way to help prevent the spread of the disease. My aim is to somehow use ML with Covid data to predict mutations (if possible...)


texts: Could mating/recombination be responsible for evolution of entirely novel features?

texts:
The diploid chromosomal architecture is rather interesting. For example, because of diploidy we Humans have to mate. Of course in that sense, because diploid organisms often have mate, this has led to emergence of sexual organs as novel features etc.

But, what I am interested in, is the prospect of recombination and mating being able to lead to drastically novel evolutionary traits.

For example, if a remote tribesman from the Pygmy peoples of Central Africa were to mate with an urban dweller, one theoretical example of a novel feature could emerge in the offspring are new inter-gene/protein interactions between these "never met before" sets of alleles. Recombination would then "seal the deal" by shuffling these allele sets between the maternal/paternal chromosomes, such an individual's offspring would now become a mosaic of their hybrid parent. Just imagine cross-over events occurring between two very divergent promoters of the same loci.

Questions:

Could the unison of such divergent sets of alleles theoretically lead to unique phenotype and features that bear little resemblance to any features belonging to the parents?
Are there any real examples of morphological/physiological features such as that I have tried to describe?


texts: According to the endosymbiont theory, mitochondria and chloroplasts originated as bacteria which were engulfed by larger cells. How many times is it estimated that this occurred in the past? Are there any examples of this process being observed directly?


texts:
I have a very basic question, but it seems the hardest to me.
So we have 46 chromosomes (23, 2 copies of each). Do all chromosomes have the same DNA? If so, does it mean that in different cells with different functions some genes are expressed and some aren't? Also, if each chromosome has different lets say "fragment" of the genome, how is the genome interconnected?


texts: Why are Chloride Anions necessary for gastric acid functioning?

texts: Why do parietal cells of the gastric mucosa release Chloride anions along the H+-ions, which are pumped into the lumen by the proton-pump. Wouldn't the presence of protons alone be enough to denature proteins?


texts: There are small parts between Genes in an Operon that does not encode for any amino acids. What is the purpose of these parts?

texts:
What is the purpose of these parts in the translation process ?
Picture to demonstrate below :


texts: How to engineer chromosomal duplications?

texts:
Specific genetic engineering of chromosomal aberrations like deletions, inversions and translocations are doable by using the CRISPR/Cas system or the other programmable nuclease systems. Insertions are also possible but mostly limited by the size of the insert.

Here two papers on the topic:

http://www.nature.com/nrg/journal/v15/n5/full/nrg3686.html

http://www.nature.com/ncomms/2014/140424/ncomms4728/full/ncomms4728.html

However these methods appear to be inadequate in case you want to insert a long DNA piece (>1Mb) into a chromosome (in case you want to engineer a duplication).
As far I have understood, problems arise when 1) you want to make such long DNA in the first place and 2) --suppose you have the DNA-- you need to transfect it into the cell...

Does anyone know how to tackle the genetic engineering of a large  chromosomal duplications? Is there any way to induce it without the need of supplementing the extra DNA?


texts: What is meant by “genes at the trunk of the evolutionary tree”?

texts:
Recently I went through a paper about hepatocellular carcinoma in which they talked about trunk genes (p. 26, second paragraph):

  Branching tumor evolution complicates efforts to implement
  personalized medicine and suggests that targeted therapies might be
  directed to genes that are mutated at the trunk of the evolutionary
  tree. Transposons provide powerful tools for identifying trunk genes,
  as insertions in trunk genes are more likely to be associated with a
  higher number of sequencing reads.

I really don’t understand what are the trunk genes. Can anyone please explain them clearly.

Thank you


texts:
Within a single species, how does the relative number of cells in the body relate to the relative size of the organism?

Let's say we take two humans, one of them is 6 feet tall and the other one is 5 feet tall.  They have similar BMI, age, physical condition, genetic background (aside from height) and are the same sex.

Does the tall one have more cells? Or does he have bigger cells?

PS: Ideally, answers should be backed up by appropriate sources.

PPS: While I'm grateful to everyone for the very nice answers I got, I should point out that I'm waiting for an answer which includes references to accept it.


texts:
The following paragraph on Wikipedia about the Hardy-Weinberg principle is bothering me.

It should be mentioned that the genotype frequencies after the first generation need not equal the genotype frequencies from the initial generation, e.g. f1(AA) ≠ f0(AA). However, the genotype frequencies for all future times will equal the Hardy–Weinberg frequencies, e.g. ft(AA) = f1(AA) for t > 1. This follows since the genotype frequencies of the next generation depend only on the allele frequencies of the current generation which, as calculated by equations (1) and (2), are preserved from the initial generation:

Why is it so that the genotype frequencies are dependant on the previous generation, but not in the case of the first as compared to the inital generation?
https://en.m.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle#math_1


texts: Is this adaption of the Gillespie algorithm using Michaelis constants justifiable?

texts:
I would like to run a discrete simulation of a biological system as it can be done, e.g., using the Gillespie algorithm. However, the Gillespie algorithm requires you to know the reaction rate constants of each involved reaction whereas I only know the Michaelis constant $K_M$ and the maximum rate $V_{max}$ of each reaction.

Since the Gillespie algorithm only uses the reaction rate constants to calculate the reaction rate $v$ (which, again, is used to determine the probability of a given reaction), I wonder wheter it is justifiable to simply replace this calculation of $v = k * [S]$ by $v = \frac{V_{max}\cdot[S]}{K_M + [S]}$ for each reaction $S \rightarrow P$ and, apart from that, use the Gillespie algorithm as is? If not, is there any better way to run a discrete simulation of the system with the given parameters?

Note: I've already asked in a different question whether it is possible to get (an estimation of) the reaction rates knowing only the parameters $K_M$ and $V_{max}$. I hope my both questions are sufficiently distinct to justify two different posts.


texts: Estimating diffusion constant of a protein based on number of amino acids

texts:
Is there a way to estimate the diffusion constant of a protein based on the number of amino acids it is comprised of. I know that the shape of the protein has an influence on the diffusion constant, but I didn't know if there was some estimate that could still be used to good approximation.

If this does not exist, is there still a way to approximate the diffusion constant of certain proteins. I am trying to make a rough model based on reaction-diffusion equations, and I wanted to estimate diffusion constants of certain species in the model.


texts: How does blue white screening work in selecting E coli that have taken up a plasmid vector?

texts:
The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of bacterial culture on them, one white and one blue.

I think that the blue cultures have accepted the plasmid as they are able to grow on ampicillin, so have the ampicillin resistance gene, and are able to convert the X-gal substrate to blue via the lac Z gene. What i'm confused about is the white colonies. If the colonies are able to grow on ampicillin, surely they have accepted the gene because they have the resistance, and surely they should to be able to convert the X-gal?

So why are these not expressing the lac Z gene? Is it that the lac Z gene and ampicillin resistance aren't on the same plasmid, or is it that the lac z gene didn't make it into the plasmid?


texts: Does the MS2 RNA binding protein have any translational repression effects?

texts:
Reposted from Quora: http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects

I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the interaction of the MS2 protein to the hairpin placed upstream of a ORF cause any translational repression?


texts: Could someone tell me a bit more about this fungus found growing in a nearly straight line in the lawn in a wooded area of Virginia, USA? It seems rather fragile, maybe a bit "dry"


texts: Do HIV particles die without host cells?

texts: When a person is on antiretroviral therapy (ART) which blocks HIV particles from infecting cells, where do those particles go? Do they die out while floating in the bloodstream? I particularly want to understand if this is the reason viral loads go down once a person starts ART.


texts: After how many hours water drunk is expelled from the body?

texts:
If one drinks a liter of water at 7 am when (in what span) will that water be eliminated through uresis?

Is that process influenced by any factors such as empty stomach, sleep or other?


texts: Drinking soda triggers tingling on a tiny spot on my upper back... but how?

texts:
The title pretty much says it all.  Yes, I know it doesn't make sense. That's why I'm baffled.

For the past week or two, I've noticed that drinking soda seems to cause a tingling/stinging sensation on a very tiny spot on the skin of my upper-left back. It happens within a second or two after I swallow. This has been happening pretty consistently since I first noticed it. (I've noticed it at least a dozen times; I'm pretty sure I'm not hallucinating...) I think it also happened once or twice when I was drinking plain water, but not enough for me to be sure whether or not I actually felt it or if I was just imagining things...

I've been otherwise healthy and there's nothing particularly special about that spot on my back, so I'm pretty baffled at the moment. How/why could this possibly be happening?


texts: What are the lower and upper hearing limits of the human ear?

texts:
I am looking for the loudness limits, expressed in decibels, for the human ear.

Google and Wikipedia is only giving me the frequency limit that the human ear can receive, but I cannot find mention about the decibel limits.

Related question on acoustic frequency: why-do-humans-hear-better-between-2khz-and-5khz


texts: Where are the ATP synthases synthesised?

texts: The nano-machinary of energy production ATP synthase is well known to exist on mitochondrial inner membrane and chloroplasts. But how and where are they formed or synthesised ?


texts: Are there any neurotransmitters that trigger all neurons?

texts: I'm reading into the basics of the nervous system, and am intrigued by neurotransmitters. I understand that certain neurotransmitters can trigger more than one neuron type, and may be used as inhibitors or regulators (antagonists). Conversely, are there any types of agonists that trigger excitation in all neurons, regardless of type? If so, what functions do these play?


texts: Why does the T7 RNA Polymerase require a reducing environment ie. DTT

texts: Every bloody protocol suggests adding in DTT when doing in vitro RNA transcription. Why? The rationale seems to be that the cytoplasm traditionally has a reducing environment but as the only protein we care about is the T7 polymerase, why is this necessary.


texts: How does an animal having toes create more friction than not?

texts: I was looking at the morphology of different animals when I found that apparently part of the reason vertebrate mammals have toes is that they grip the ground. But, why is that better than having a solid foot with no toes if friction increases with the surface area in contact with the ground?


texts: How does promoter sequence affect initiation?

texts:
I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear"

I'm wondering if anyone can suggest sources for more information, or perhaps has seen recent research papers highlighting the properties that cause such variation between strong promoters and the weakest?

I've tried researching but the older research is descriptive rather than mechanistic and the search terms involved are quite ubiquitous so it's hard to actually find more on this specific point.


texts: What kind of bird is this and what does it eat?

texts: My father found this little guy in one of the tractors of where he works (in the fields) i’m not sure what species of bird it is and what it eats. It just keeps chirping not stop and I have no clue what so ever to what it eats. If anyone knows please tell me, I don’t want to see him starve to death.


texts:
How do bats distinguish between day and night? Do they hunt at night - if yes, how they know that?

Are they afraid of sunlight?


texts: Regarding hydrolysis of ATP in ABC transporter

texts: So, I was going through this lecture about ABC transporter and one point about it confused me. ABC transporter is not the same as an ATPase but let's take an example of Cystic Fibrosis Transmembrane Regulator. In it 2 molecules of ATP bind with the channel and then they undergo hydrolysis in order for Chloride ion movement to occur. So,if hydrolysis is occurring when ATP was bound to the channel then shouldn't it also function as an ATPase or is it so that it is binding and the channel isn't doing the function of hydrolysis, some other molecule is and it is just using that energy.


texts: How to derive the Equilibrium value $\hat F$ equation

texts:
In population genetics, there is a relationship between $\hat F$ and $Nm$.

$\hat F=\frac{1}{1+4Nm}$

In population genetics textbook, (i.e. Hartl, D. L., and A. G. Clark. 2007. Principles of population genetics. Fourth edition. Sinauer Associates Incorporated, Sunderland, Massachusetts.) it reads that using the equation below:

$F_t= \bigg(\frac{1}{2N}\bigg)(1-m)^2+\bigg(1-\frac{1}{2N}\bigg)(1-m)^2F_{t-1}$

  Set $\hat F = F_t = F_{t-1}$. After expanding the squared terms on the right-hand side, and assuming
  that $m$ is small enough and $N$ large enough, and that terms  in
  $m^2$ and $m/N$ can be ignored, some rearrangement leads to:

  $\hat F=\frac{1}{1+4Nm}$

I tried redoing it algebraically, without success. So do you know how to get to "$\hat F=\frac{1}{1+4Nm}$"

$(1-m)^2 = 1-2m+m^2$

$F_t= \bigg(\frac{1}{2N}\bigg)(1-2m+m^2)+\bigg(1-\frac{1}{2N}\bigg)(1-2m+m^2)F_{t}$

$F_t-\bigg((1-2m+m^2)-\frac{(1-2m+m^2)}{2N}\bigg)F_{t}= \frac{(1-2m+m^2)}{2N}$

$F_t(1-(1-2m+m^2)-\frac{(1-2m+m^2)}{2N})= \frac{(1-2m+m^2)}{2N}$

$F_t(-2m+m^2-\frac{(1-2m+m^2)}{2N})= \frac{(1-2m+m^2)}{2N}$

$F_t(\frac{2N(-2m+m^2)}{2N}-\frac{(1-2m+m^2)}{2N})= \frac{(1-2m+m^2)}{2N}$

$F_t(\frac{2N(-2m+m^2)-(1-2m+m^2)}{2N})= \frac{(1-2m+m^2)}{2N}$

$F_t= \frac{(1-2m+m^2)}{2N} * (\frac{2N}{2N(-2m+m^2)-(1-2m+m^2)})$

$F_t= \frac{1-2m+m^2}{(-4Nm+2Nm^2)-1+2m-m^2}$

Then $m^2= 0$

$F_t= \frac{1-2m}{(-4Nm)-1+2m}$

$F_t= \frac{1}{(-4Nm)-1+2m} -\frac{2m}{(-4Nm)-1+2m}$

??

$F_t= \frac{1}{(-4Nm)-1+2m}$

Magic

$\hat F=\frac{1}{1+4Nm}$


texts: Where can I find disease diagnosis datasets?

texts:
For an epidemiological study, I'm looking for datasets for any kind of vector-borne disease (i.e. West Nile Virus, Malaria, etc.), or any parasites that are dependent on intermediate hosts (i.e. Schistosoma spp., which have snails as intermediate hosts).

The data should include day or week and location of each diagnosis. I have been able to find diagnosis data for individual countries for each year, but I'm looking for daily or weekly data for city-wide resolution or at least smaller regions inside countries.

Additionally, it does not matter what country/continent the data is for, as long as there are many data points (i.e. at least 10,000). For example, if there is a lot of good data for Brazil, that's fine.

Does anyone know if such information exists, and if so, where I can find it? I've been searching for it for the past month but have had little luck with finding anything useful. Any help and guidance is appreciated!


texts: What is the relationship between stroke volume of blood and ventricular end-diastolic volume?

texts: I do know what each term means. That is, i know that stroke volume is: the volume of blood pumped by each contraction of a ventricle, while ventricular end-diastolic volume is: the volume of blood in the ventricle just before systole. However I can't relate the two in terms of, say, graphs or in the mode of action of the heart between this period(s).


texts: Recommendation for book about soil and their food webs

texts: Are there any de facto books for studying soil biology; specifically with details in the context of food webs? I am trying to teach myself about the subject and would like a good introductory book, although I will take any recommendations. Thanks


texts:
Gnathostomates are vertebrates having jaws. But when I search on the internet for Gnathostomates, I always find out that they are sharks and fish-like organisms.

But are humans not also Gnathostomates? Don't we have jaws?


texts: What fish (and/or shellfish) species with a multi-year life-cycle, besides salmon, die after spawning?

texts: Most species of salmon die after spawning. Are there any other types of fish that spawn once and then die after a multi-year life-cylce? Is this a rare life history strategy among our human exploited marine species? Googling this question only yields articles about Salmon.


texts: How to determine the number of parameters in a phylogenetic model?

texts: I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?


texts:
I need to splice a gene into a human cell genome, with highest rate possible. I mean, doesn't really matter where the gene enters, nor does it matter if some cells die as a result of this.

CRISPR know to knock-in genes with very high specifically, this reduce the success rate if we have a low amount of gRNA and/or of the protein.

I need to insert the gene, without the need of targeting some specific place.

Is this possible in some way with CRISPR?

I know that there may be better technique to do this, but I can only use CRISPR.


texts: Is there a name for the use of sunlight in metabolic processes?

texts: "Photosynthesis" is what is used to describe how plants use sunlight to synthesize sugars, but, I also heard some animals like humans use sunlight in the process of creating vitamin D. Is there a comparable name for when sunlight is used by animals in a metabolic process?


texts:
Amylase is an enzyme that breaks down starch in the form of amylopectin and amylose. Both amylose and amylopectin are formed by alpha glucose joined together by (1-4) and (1-6) glycosidic bonds. Glycogen is no exception, just that it has more branching. However, why is it that a google search shows that it is hydrolyzed by Glycogen Phosphorylase rather than amylase? Also, how can amylase digest both (1,6) and (1,4) glycosidic bonds?

Any help would be greatly appreciated.


texts: optimization of density gradient centrifugation

texts:
I'm trying to isolate a ~320kD protein (in oligomeric form) using density gradient ultra centrifugation technique.
Can any one tell me that what gradient (sucrose or glycerol or trehalose or etc) I should use and why ?
Any references regarding the optimization of gradient cutoff for macromolecules will be highly appreciated.


texts: Can a woman give birth to twins with different fathers?

texts: Is it possible for a woman to conceive from two different men and give birth to half-siblings?


texts: Incubation time of Antarctic Phosphatase in lab

texts: Antarctic Phosphatase is used to catalyze the removal of 5' phosphate from DNA. If I'm using it in the lab on a sample of 1-5 micrograms of digested DNA, how would I figure out how long to incubate the sample at 37 degrees Celsius?


texts: Can Mother-to-Child Transmission Occur in Relation to Mycotoxins or Mycoestrogens?

texts:
There are 17 officially noted cases in which leukemia or melanoma cancer cells crossed the placenta from mother to child. Other crossings include metals (or metalloid elements), such as mercury or arsenic (just as an example). There are also crossings of bacteria, viruses, and general foodborne illnesses.

With all this in mind, my question is: "Can a mother who is hosting a mold, transfer that to her unborn child?"

(Please don't supply an answer about how the child is at risk during the birthing process or caesarean section. Other than that, even opinions are welcome. Thanks in advance.)


texts: Complementation cloning: what, why and how?

texts:
I get that you're cloning a whole cDNA library, but why does E. coli need a complementary gene to allow the gene expression?
Why is that complementary gene considered to be a mutant?
AND how does one detect the gene of interest after cloning?

What is this kind of cloning used for?


texts: Why are siblings unidentical? (Which chromosome of the pair do gametes have?)

texts:
I know that a normal human cell has 23 pairs of chromosomes (total: 46).
On the other hand, a gamete has only 23 chromosomes.
Which chromosome does the gamete choose out of each pair?

And if "One of each pair of chromosomes comes from the mother, the other from the father.", then the chromosomes of a gamete could be an exact copy of the chromosomes in a grandfather's gamete?


texts: What are the visual, behavioral similarities and differences between Yellow Fever Mosquito (Aedes aegypti) and the Tiger Mosquito (Aedes albopictus)?

texts:
The Tiger and Yellow Fever Mosquito visually look very similar.

Recognizing the difference is important for tracking and controlling the spread of Yellow Fever, Dengue fever and other diseases. Especially important, now that the range of the two have overlapped in the United States.

I have some questions about the commonalities of these mosquitoes.

Evolutionarily, How can the similarities be explained?

Why do they both have the black body with white stripes?

What is the best way to tell them apart?

A. aegypti, the Yellow Fever Mosquito

A. albopictus, the Tiger Mosquito


texts: How does the DNA cross through bacterial cell wall during electroporation?

texts:
There exists a lot of literature on electroporation of Gram-positive and negative bacteria. Most of it gives an explanation that electroporation works by creating transient pores in cell membranes of bacteria for the DNA to pass through.
Both types of bacteria have a cell wall as well (differing in thickness). How does the DNA pass through the cell wall that it encounters on the way?


texts: Human's capacity to withstand extreme heat in dry air

texts: What is the maximum temperature a human can withstand for short periods of time in an environment with dry air (e.g. oven @+300F, other confined spaces) and what would be the immediate risk of being in such environment be (lung damage, core temperature, etc.).


texts: Are tergo-sternal muscles of cockroach involved in blood circulation?

texts: Tergosternal muscles help in the blood circulation in a cockroach as well as in movement of the wings for flying. I came across a question that claims that these muscles are used in blood circulation as well. I can't seem to see a relation between blood circulation and these muscles.


texts: In men, why do over 80% of sperm have abnormal form?

texts:
Here is the percentage of normal forms among fertile mens according to the centile (Source: Cooper et al. 2010):

2.5: 3%
5 (below this is Teratozoospermia): 4%
10: 5.5%
25: 9%
50 (median): 15%
75: 24.5%
90: 36%
95: 44%
97.5: 48%

Men who have less than 4% of their sperm that have normal morphology are diagnosticated with Teratozoospermia (also called Teratospermia) and are likely to be infertile, though technically 5% of fertile men have Teratozoospermia.

I read on the internet that abnormally-shaped sperms are bad and useless because their abnormal shape prevents transport through the cervix and/or prevents them from adhering to the ovum.

But I think that if they were really that bad, Mother Nature would not have engineered the average men with 85% of their sperm abnormally-shaped.

And I also heard that even animals have a big fraction of their sperm that are abnormally-shaped.

So, in men, why do over 80% of sperm have abnormal form?


texts: What does "oleracea", as appears in numerous plant species (scientific) names, mean? Examples: Euterpa oleracea, Brassica oleracea, Portulaca oleracea, Acmella oleracea, Spilanthes oleracea.


texts: Is this maritime plant a species of zostera?

texts: This photograph was taken on the intertidal mudflats at Lindisfarne, Northumberland, UK today. It was about 40m from the shoreline at low tide. Is the green plant a species of zostera? Can anyone help with the identification?


texts: Why isn't the phosphoglycerate kinase reaction of the glycolysis pathway irreversible?

texts:
Step 7 of the glycolysis pathway is the conversion of 1,3-bisphosphoglycerate into 3-phosphoglycerate by the action of the enzyme phosphoglycerate kinase, resulting in the production of 2 ATP molecules (per glucose).

This reaction has a large negative value of ΔG (-18.5 kJ/mol). If reactions having large negative value of ΔG are classed as being irreversible, then why is Step 7 of Glycolysis reversible?


texts: Berries ID - Can someone help us identify this plant?

texts:
Found it in the hilly areas of Meghalaya - a state of India.

Not sure if is edible or not, we haven't tried it but it gives a beautiful blue color when used for dying.

The seeds are big and there is not enough fruit except its like the skin covering the seeds.


texts: How do signal transduction pathways utilize transcription factors to express a specific gene?

texts:
I have an inquiry regarding the regulation of genes via extracellular signaling.

To my knowledge, in autocrine, paracrine, and endocrine cellular communication, large protein ligands that cannot directly diffuse through the plasma membrane of the target cell(s) use surface receptors to perform their desired action on the target cell(s).

I have learned that some of these ligands activate signal transduction pathways such as the MAPK/ERK and JAK/STAT pathway and drive the expression of specific genes by utilizing transcription factors (of course, in eukaryots). A simple example of this would be the action of epinephrine (adrenaline) on hepatocytes (liver cells), where the amino acid-based hormone uses the transcription factor CREB to express the gene coding for Glycogen Phosphorylase to engage in glycogenolysis.

Here I have two questions:

How does the transcription factor chemically indicate which gene to express? (Is there a gene indexing system like a computer filesystem?)
How does the transcription factor locate and bind to the promoter of the gene it is trying to express?

Thank you.


texts: How would our circadian rhythm change over time if we had no sunlight whatsoever?

texts: Of course, over the span of a couple days, our circadian rhythms would lengthen a few hours. But what would happen to the circadian rhythms of humans overall if we had no daylight ever? Say we can live for 10,000 years, how would our circadian rhythm be different 10,000 years from now after zero exposure to sunlight? Would it still be slightly more than 24 hours?


texts: Troubleshooting for Agarose Gel Electrophoresis

texts:
SI ran my 2% agarose gel on constant voltage (100 V). For a few times it worked at CV but, after a week or so the machine would automatically switch to constant current by itself. And this only happens when I try to increase the voltage to 100 V. It works fine between 50-80 V. Beyond 80 V it keeps fluctuating between CV and CC.

Is there a problem in my power supply (GENEI electrophoresis power supply) or is the TE buffer that I am using? Although I checked its pH and it's fine.


texts:
with respect to the paper:

Adaptive reconfiguration of the human NK-cell compartment in response to cytomegalovirus: A different perspective of the host-pathogen interaction

What is meant by NK-cells compartment? I searched Google but couldn't find a proper text that would help me understand what it means.. Google search shows papers which has this term, but I need to understand what it means before reading the paper. Please help.


texts: Why does the apex of the human heart usually point to the left?

texts:
In the majority of human beings, the apex of the heart (left ventricle) points towards the left side of the body.  Sometimes however (approx. 1/12000 births), a person is born with a condition known as "Dextrocardia", in which the apex of the heart points to the right side of the body instead.

Is there an evolutionary reason as to why the human heart usually points to the left side as opposed to the right side of the body?

(Note:  Please don't answer with, "because there is a notch in the left lung", because I will simply reply with, "is there an evolutionary reason for the apex of the heart AND the cardiac notch being on the left as opposed to the right side of the body").


texts: If a zygote has all the cytoplasmic determinants and all the specific transcription factors, does that mean that all genes in the genome are expressed?


texts: How thick is the neural tube at Stage 10 in a chick embryo?

texts:
As the question states - I am really struggling to find ANY website/paper/article which states this. I want to know if the neural tube is still one cell thick and stage 10 of development. Any evidence that can be supplied to show this would be useful.

Thanks


texts: Is there any reason to use an upright microscope over an inverted microscope?

texts:
I've never actually owned an inverted microscope, but it seems it has only advantages compared to an upright microscope: taller, heavier samples; no crashing the objective into the glass slide; easier to operate, etc.
Why then do people still use regular, upright microscopes? Is there a disadvantage I'm missing?


texts: Why do people use anti-inflammatory drugs?

texts: Why people should take anti-inflammatory drugs, when inflammation is a physiological way to defend our organism?


texts: How to produce correct epithet of a species named in the honor of a person?

texts: I want to name a new diatom species in the honor of Prof. Vodyanitskiy. What will be the species epithet: "vodyanitskiya", or other? Are there any rules that regulates how the end of such epithets is changed?


texts: Creating expression template from PCR: What annealing temperature to use?

texts:
I am creating a transcription template for expression in PURExpress and was confused about the annealing temperature to use.

I have two primers with the T7 promoter and an RBS on the forward primer and a termination sequence on the reverse primer.  The melting temperature of these primers are 84.4 and 83.8 degrees C.  The melting temperature of the regions that are complementary to the gene of interest I want to amplify by PCR are both about 65 degrees C.

What annealing temperature should I use a h?  Since at the beginning of the PCR reaction I will have mostly template that will have the complementary sequences of the primers binding to the GOI and not the 5' and 3' extensions.


texts:
Found in my saliva
(Optical microscope 40x)


texts: Is there a model perennial plant species?

texts:
Most of plant science is conducted on small annual species with short life cycles; predominantly Arabidopsis thaliana, but also a handful of others like Oryza sativa and Medicago truncatula etc.

Is there a model perennial species? And, if not, is there a good candidate that is relatively small but fast growing and able to be grown in lab/glass house environments that someone could recommend?


texts: How to choose the most appropriate measure of genetic distance

texts:
I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures of genetic distance, such as Nei's DA, DS, and Edwards Chord distance. The answers I get between these measures are conflicting, but each explained by a sound hypothesis, and so I must carefully and objectively choose which measure of genetic distance is to be most trusted given my data.
So my question to the community is not, "which should I choose?" but "how should I choose?" I am interested in an answer or (ideally) resource that describes what factors I should take into account and that may bias my result.


texts: Why does our body regulate metabolic processes using the thyroid hormone?

texts: People with hypothyroidism do fine when taking medication containing their daily dose of thyroid hormone. This means that the signaling function of the thyroid hormones is, in principle, unnecessary. If a constant signal would do, then there is no need for that signal in the first place, as you could just by default switch on whatever process is now switched on by the thyroid hormone. So, what's the whole point of regulating metabolism via the thyroid hormone, especially considering that it predisposes us to thyroid disease?


texts: How do alcohols and aldehydes destroy the plasma membranes of bacteria?

texts:
I am interested in knowing why a 60-80% solution of alcohol (usually ethanol or 2-propanol) can effectively kill vegetative bacteria and fungi. I know that it can coagulate essential proteins like enzymes but the process has never been explained to me.

I'm also interested in knowing how aldehydes like the polymerized form of glutaraldehyde inactivates proteins and nucleic acids. Could someone with any insight / knowledge share what they know?


texts: Is there any biological limit on muscle growth in human body, one can keep pushing body and keep growing more and more muscle but somewhere it must become diffcult for body to sustain those cells right?


texts: Providing small molecules to cells on a filter plate

texts:
Lets imagine that I have mammalian cells that I've immobilized on a filter. Now I want to keep providing small molecules to these immobilized cells without resolubilizing the cells.

The caveat is that I would like to do so without fixing the cells or waiting for them to adhere to the filter. The small molecules are small enough to diffuse through the filter.


texts:
Lamarckism is a pre-darwinian theory according to which an organism's traits acquired to adapt to the environment are passed onto its offspring. A couple of years ago, I attended an event with Richard Dawkins and Jerry Coyne, both preeminent evolutionary biologists, in which I remember them agreeing that it is basically B.S. and that acquired traits don't get passed but instead propagate themselves through natural selection. As a non expert in biology, it does not make sense to me that acquired traits would make their way into the genotype and then get passed on, which coincides with what Dawkins was saying. But I am a non expert.

I also have read a few things about epigenetics and it sounds strangely similar to lamarckism. Steven Pinker also discusses all these things in The Blank Slate and he gives a notion that thare is some idealistic ideology behind promoting ideas that we can radically change an organism by environmental conditioning and "save" those changes into the genotype. He says that ideology is to justify government programs aimed at rapidly enhancing mankind whereas natural selection, which proponents of such ideas may deem reactionary, simply is not so optimistic.

My questions are:

Is lamarckism, or inheritance of acquired traits, been conclusively discredited?
What does lamarckism relate to epigenetics


texts: In humans, are diseases inevitable during old age?

texts: Considering that dying "from old age" actually means that one dies from an illness related with aging, is it inevitable to eventually acquire diseases in old age?


texts: In submitting sequences using tbl2asn to NCBI/GenBank, the documentation states that there is a controlled vocabulary for the key "moltype", but no where on the Internet can I find a full list of that vocabulary.  "mRNA" and "genomic" are given as examples on several pages, and I can see from Sequin documentation what the GUI descriptors of all the vocabulary terms are (e.g., "genomic DNA"), but I can't find the terms themselves.  Any ideas where I can find this list?


texts: How can I accurately measure glucose concentration in culture media?

texts:
I am trying to identify the best way to measure glucose concentration in culture media with E. coli. Now, I imagine I can use those glucose meters that diabetic people use, but unfortunately can't find any papers as background.
Any ideas would be appreciated.


texts: Role of calcium chloride during competent cell preparation

texts: I am aware of the fact that $CaCl_2$ settles down on the cell wall making it less negative may be by forming bond with Teichoic acid. Also due to the positive charge it attracts DNA (DNA is negatively charged due to phosphate group). But is there anything else the $CaCl_2$ does? Also if its the work of $CaCl_2$ why we are adding $MgCl_2$ first in the standard protocol of the making competent cell preparation chemically?


texts: can recessive alleles produce codominance?

texts:
Maybe I'm confused by the term "codominance", but I wondering if codominance only occurs with two dominant alleles.

Can two recessive alleles produce codominance in an individual?

Likewise, can two recessive alleles produce incomplete dominance?


texts: Are there lifeforms that have more than 2 sexes?

texts:
Are there any lifeforms on earth that have more than male and female biological sexes?

If so, are all three mates required for reproduction or is there something else going on?

If not, why not? There are species that have one sex and there are species with 2 sexes. I get some of the basics of why there are two instead of one, but would those benefits not be even greater if there were three sexes?

  NOTE: I am of course only talking about sexual reproduction. I have no intention or desire to talk about transgender or LGBT issues nor am I wanting to make any points on the issue. This is solely a question about sexes in biology and not human social constructs.

Also, I am a computer programmer, not a biologist. Please forgive me for not knowing any of the terminology.


texts: Can two different species in the same genus generally succeed in the same habitat?

texts:
This plant-care website writes

  In the context of plant care, usually most plants within the same genus need the same environmental conditions suitable for plant growth. If the genus of a plant is known, the information can be used to apply the appropriate levels of plant care.

I'm wondering if this is true in general. A more general question would be, if I know that two species are in the same genus, what phenotypical similarities will they have?

So far I've only found that genus classification is based on genetic similarity, but that doesn't say anything about what phenotypical similarities there may be between different species in the same genus.


texts:
I have recently switched from electronics to computational biology. So having some hard time with my homeworks. Can someone guide me on this problem?

  Consider 6 genes A,  B, C, D, E, F, G. Some recombination rates are
  given between these genes AB = 0.2, BC = 0.1, AC = 0.25, AD = 0.5, BD
  = 0.5, DE = .1, AE = 0.5 ,EF = 0.1 ,DF = 0.15.

  a) Find the number of linkage groups? b) Construct possible genetic
  map showing relative positions of these genes?


texts: What causes weight loss and fatigue in Addison's disease?

texts: Why would a lack of cortisol cause fatigue? In terms of normal functioning of the gland.


texts: What are the chances that the contraceptive pill will cause death of human zygote?

texts:
The preventative pill, as I understand it, can cause zygotes to fail to attach to the uterine wall, or pry them off of it.

Ignoring any and all ethical implications, what are the chances that this will occur, provided the woman in question has taken the pill regularly preceding sexual intercourse, comparing with and without barrier method as well, the latter taking into account if it fails.


texts: What are the differences between a liposome and simple cell membrane

texts:
I'm learning about chemical evolution and the transition from RNA to protocells to cells.  I understand that the protocells have a phospholipid structure called a liposome.

I recently saw a video showing CG animations of the workings of a cell and it seemed that the cell wall was much more complex than what it seems a liposome is.

I'm looking for information about the differences between a liposome and a basic cell wall (not sure of the difference for different types of cells -
 but I guess for prokaryote since that would have been first.)


texts: Is there a tool to find the action of an enzyme in a metabolic pathway?

texts: Is there any tool to search the biochemical action of a particular enzyme in a metabolic pathway of an organism? In other words, how can I find if enzyme "E"  is involved in the metabolic pathway for organism "X".


texts: Can cats use ketone bodies as only source of energy?

texts: I recall reading that much of the energy a cat produces from its food comes from proteins which I assume would produce energy via being catabolised into amino acids which in turn, if glucogenic, would undergo gluconeogenesis and then, by means of being metabolised into glucose, enter glycolysis and the resulting pyruvate would be converted to acetyl-CoA and enter the TCA cycle to produce energy. I'm wondering whether this recollection is accurate and whether cats could, like humans, use ketone bodies for their sole fuel source if need be.


texts:
Oysters have been thought of as aphrodisiacs for millennia.

Is this a case of the bark of a willow tree as a precursor to modern paracetamol, or some sort of marketing ploy.

Is there any biological evidence that foodstuffs such as lobsters, oysters and other sea delicacies boost our sexual health and desire? If so, what biological mechanism underlies this property?


texts: Why do classic psychedelics not cause withdrawal, despite high tolerance?

texts:
"Classical" psychedelics, such as LSD, DMT, and Mescaline, are serotonin agonists that cause hallucinogenic effects. They are notorious for having rapid tolerance, such that after consuming such substances, one would need to (at least) double the dose to feel the same effect if taken daily. No other substance, not even opiates, have such a high tolerance curve.  While this tolerance contributes to the less-addictiveness nature of psychedelics, there is no observed withdrawal. Furthermore, because of the high Therapeutic Index, some users may consume large doses.

Wouldn't such tolerance result from 5HT downregulation, and therefore cause withdrawal? Is it something with serotonin, or is the mechanism different?

There is evidence that 5HT downregulation is what actually causes the effects of anti-depressants. This explains why it takes a few weeks for SSRIs to kick in. Perhaps, this explains why psychedelics can have an antidepressant effect? Perhaps, unlike other neurotransmitters, activation and downregulation of 5HT is not harmful?

https://www.ncbi.nlm.nih.gov/pubmed/7972628


texts: Is it possible to condition the body to reduce bruising?

texts:
I do combat sports, and in these sports there are a lot of hits that can cause bruising.

I've found that, over time, physical conditioning can reduce and/or eliminate the bruising to the point where even after hard impacts, there is no residual bruising.

However, I was under the impression that it is not possible to "condition" for reduced bruising since bruising is the result of ruptured capillaries, and you can't condition to not rupture blood vessels.

Can someone offer an explanation to why, with conditioning, it is possible to reduce/eliminate bruising?


texts:
Why do you retch when you see something disgusting?

I imagine it is some sort of evolutionary response, although I can't see the connection between receiving a signal that unhealthy conditions are in the current environment and wanting to empty the contents of one's stomach, which likely were eaten elsewhere. The response I would have expected to have developed would have been one of fleeing, rather than vomiting.

As a subquestion, why does the same reaction sometimes occur when imagining something disgusting, even if it is not real?

(I know "disgusting" is subjective; I'm referring to things humans may want to not be around for health reasons, e.g. rotting flesh, infestations of traditionally disease-carrying insects, etc.)


texts: How does toluene inhalation damage the brain?

texts:
We just had a discussion about toluene abuse. It is known, that people inhaling toluene for a long time have significant brain damage, including  decreased intelligence.

I found that toluene is a lipid solvent, and that it can damage the myelin. However, myelin is only present in the white matter, but intelligence is related to the grey matter which does not contain myelin.

Is there any indirect damage, or did we miss some important point in this case? Second, how does toluene get to the brain? Is it able to infiltrate from the nose through the mucous membrane, or is it carried in the blood? I am just curious.


texts: What stops myosin during muscle relaxation?

texts:
I understand that when the muscle is relaxed tropomyosin blocks myosin binding sites on actin filaments thereby preventing muscle contraction. What I am concerned with however, is whether myosin filaments - given that ATP is found in the muscle fiber- continue trying to bind to actin, and hydrolyzing ATP...
So how are mysoin filaments stopped from trying to bind to actin when the muscle is relaxed, to stop the hydrolysis of ATP?


texts: What is the strand specificity of a reference genome?

texts:
It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue.

So here's to putting all those questions to rest.

Is the reference genome a positive or a negative strand? And why so.


texts: How do organoarsenics improve digestion efficiency in poultry?

texts:
It struck me as very surprising that these organoarsenic compound with structure looking not very compatible with living system is widely used as food additive to increase weight gain and improve food efficiency in poultry. I wonder what is the mechanism of action that causes the effects in these animals?

For instance, here is the structure of one particular additive - Roxarsone:


texts: What does "optimal balance of biological control" mean in nematodes?

texts: I have been reading several articles on nematode life-history for my insects class. Several articles say that Entomopathogenic nematodes(EPNs) are the only nematodes possessing an "optimal balance of biological control attributes". What does this mean?


texts:
I know humans can cook and prepare almost anything, but are humans specifically adapted to eat meat?

One of my doubts humans are not particularly well adapted to eat meat because they lack canine teeth. I read more reasons for this here.

What does an evolutionary biologist have to say on this matter? Perhaps evolutionary biology is the field related to this?

Some links supporting my doubt:

http://www.peta2.com/blog/humans-supposed-eat-meat/
http://mindfullybliss.com/humans-are-designed-to-eat-meat/


texts: What does chromosome CHR_Un, CHR_MT in the ftp site of NCBI mean?

texts:
I am not a biologist. But need some genetic data. So I searched internet and reached NCBI's website. I came to know from the FAQ page that I can the complete genome data of organisms from ftp://ftp.ncbi.nih.gov/genomes/. So I went to the FTP site and opened the homosapien section ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/. I found folders CHR_1 to CHR_22, CHR_MT,CHR_Un, CHR_X and CHR_Y.

My doubt is this : Normally there are only 23 pair chromosomes right? 1 to 22 pairs OK. XY make another pair. Then what are MT and Un ?

And the folder which I am looking is a genome of male right?


texts: How far into a pregnancy is it before visible signs of it is apparent and risk of physical trauma increases

texts:
I'm doing research for a series I'm writing. in it the main character is pregnant however goes off to fight a criminal organization who have been killing her friends and i want her appearance to show that she may not be pregnant however she fights and defends as if she is mindful of heavy impacts could cause a miscarriage

I am wondering how far into a pregnancy is it before visible signs of it is apparent and risk of physical trauma causing miscarriage increases, if there is also a point during the pregnancy where the fetus could mutate via outside interference then that would be good to know too however I can go without that information.

NOTE: I want to know this information so that even though the world in this series I'm writing is totally fictional, one can begin to question how fictional it really is when some parts are based off actual science and logic of real life.


texts: Are cell biology and cytology the same science?

texts: According to Wikipedia, the terms can be used interchangeably, but according to my college professors, cytology is exclusively the study of chromosomes and identification of their abnormalities.


texts: Experiment to show that carbon dioxide is needed for photosynthesis

texts:
In my school test, the question is as follows:

Will the experiment work satisfactorily?
What alterations can you make to obtain expected result?

What I wrote:

Yes, it will work satisfactorily. Lime water absorbs carbon dioxide and hence there is no carbon dioxide for the leaf and hence photosynthesis does not take place and no starch is prepared. Hence on iodine test, the presence of starch is negative and thus proves that carbon dioxide is required for photosynthesis.
We can put half of the leaf inside the flask and half of it outside. So, the inside part will not show presence of starch and the outside part will show presence of starch.

[Note]: It was marked incorrect by my biology teacher. It got it reviewed by another biology teacher and HE SAID WHAT I WROTE IS CORRECT and the teacher who marked it wrong gave the opinion as follows:

It will not work satisfactorily because lime water does not absorb carbon dioxide. [which to me, seems incorrect as lime water ABSORBS carbon dioxide]
The alteration is that you have to use Potassium Hydroxide instead of lime water. [which to me, seems incorrect too since both lime water and potassium hydroxide absorbs carbon dioxide and then there is no need to use potassium hydroxide when lime water works!]

Now I am confused what is correct and what should I write in my final examination??  Please help. Any help will be appreciated, Thank you.


texts: What is it about the housekeeping genes that makes them almost immune to gene regulation?

texts:
When it comes to eukaryotes, including ourselves, we have all different kinds of specialized cells and tissues that are so different, yet originally all came from the same single cell. And apparently the reason for that is differential gene expression, where different genes get to be expressed in different cells. But there are, however, a set of genes that gets to be expressed in almost all of the cells.

My question is not why, but what is it about these genes that in a way makes them above the laws of regulation? Is it in their sequence? Or are they located on a single chromosome or perhaps regions that are somehow non-regulatable?


texts: Is there a correlation between Animal Intelligence x Playing time?

texts:
I'm writing a small text for a blog about playing time and I wish to have more resources about the correlation between Intelligence and Playing time in animals. If not exactly that, maybe some indications leading to this conclusion or even going against it. Correlations between playing time and animals sociability are welcome too.

Thank you very much in advance.


texts: What type of spider is this that just decided to stop my plans of sleeping

texts: This tiny little spider decided to stop my plans of sleep at 1am, since I have no plans of getting to sleep any time soon may someone tell me what type of spider could be this monsterous!


texts: I am researching the complement system, and have ran into something I'm not really sure about. In the past, the C1r2s2 complex was thought to be an 8-like structure tucked inside C1q's collagenous strands. However, this article says that the serine proteases actually protrude away from the core. Originally, it is said the C1s SP cleaves the C4 and C2 proteins because the C1r proteins are hidden in the core. If this new structure is true, however, then the C1s and C1r proteins are close to each other outside the C1q core. If this is the case, what is preventing C4 from being cleaved by C1r instead of C1s? Their serine protease domains should be largely identical.


texts: What is the oxidation state of iron at the photosynthetic reaction center?

texts:
Is the iron at the reaction centre  in the $3^+$ or $2^+$ oxidation state?

For instance, 1AIG is $2^+$ or, perhaps it will depend upon charge separation state? I checked the PDB: some are $3^+$ while some are $2^+$.


texts: Production of $CO_2$ basal metabolism test

texts:
Can the production of $CO_2$ be used as a type of basal metabolism test? Explain.

The answer to this is obviously yes, but I don't know how to explain it. Would the following be a good explanation?

  The faster your metabolism the more cellular respiration your cells do, and you produce more $CO_2$, so $CO_2$ output can be used as a type of basal metabolism test.


texts: What is the fluid clearance rate inside the retina?

texts:
I'm attempting to model the chemical concentration between several compartments of the eye, including the retina. Does anyone have any idea what the rate of fluid removal is in the retina, or could direct me to a study of this?

EDIT: It appears that Müller cells play a crucial role in this, dehydrating the retinal tissue. I am attempting to find the rate at which they achieve this. (see link)
http://retinatoday.com/2008/11/1108_07.php/


texts: What are the differences between Trachinotus and Bramidae species?

texts:
What are the differences between Trachinotus(Pompanos) and Bramidae(Pomfrets) ?

...like the difference between where they live/can be found, bone structure, etc.


texts: Albinism inheritance problem: what are the father's alleles if he got an albino kid?

texts:
Albinism is caused by a recessive gen "c". A normal man marries an
  albino woman. The first son happened to be albino. What are the
  possible phenotypes of the parents? What is the chance that their
  other kids will be albino?

Alright, since "c" is recessive and the woman is albino, then the woman must be "c c" right? And since the son is albino, he must be "c c" too. Hence the father must have at least one "c". But since he is normal, then the other allele must NOT be "c" too (otherwise he would be albino).

My question is, when writing the Mendel table, how do I express that allele of the father (the one that is not "c")?

$$\begin{bmatrix} & c & c\\
? & ?c & ?c\\
c & cc & cc\end{bmatrix}$$

I marked it with $?$ because I'm not sure what to put there. My first thought was "well, it could be a capital C I guess..." - but that doesn't sound right to me. A capital C would mean there is a dominant albinism allele (but I am told that albinism is recessive only...)

I can see clearly that there is a 50-50 chance of having albino kids. I just don't know how to draw that inheritance table.


texts: Does a large effective population size result in faster decay of linkage disequilibrium (LD)?

texts: I am thinking about an invasive species that was introduced into North America just a few (<20) generations ago. Using microsatellite genotypes (105 loci), I have identified almost no significant linkage across the genome. I'm tempted to speculate that this has something to do with rapid population expansion that has caused LD to decay that quickly, but I'm not sure whether this is a reasonable train of thought. Can anybody think of why this might or might not be the case?


texts: Incomplete dominance with gain-of-function allele

texts: Can somebody site an example of incomplete dominance with gain-of-function mutation?


texts: How does one maintain balance sleepwalking?

texts:
Anectodal. Feel free to shoot it down.

Walking is an acquired skill; As far as I'm concerned exhaustion causes disorientation. Even after waking up it sometimes takes a second or so to get balanced.

How is it sleepwalkers don't stumble around when walking?


texts: Can someone please identify this fish. Someone had asked me to rehome this fish but they were unsure what type of fish it is. Right now I have it in a quarantine tank until I find out what type of fish it is. I know it is some sort of clown but I cannot find the specific type after that. The fish is the one in the foreground of the image being black and white. It is a saltwater fish.


texts:
Are they podoplanin positive cells (cells that tested positive for podoplanin)?

"...though it has been shown that podoplanin (PDPN+) cells analogous to mouse FRCs are found in human secondary lymphoid organs..." (https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005046)

"Although rare, the few SFTPB+ observed in HLOs resemble AECII cells seen in the adult human lung, and PDPN+ cells resembled the elongated AECI cells in the human lung" "Few PDPN+ cells also showed elongated, squamous morphology seen in the adult lung." (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370217/).

Thank you.


texts: Approximately how long do bacteria live for?

texts: I would like to know how many days or years do the bacteria live approximately.


texts: Insects are attracted to light, what if the light is too bright?

texts:
Insects are known to approach light sources. I know that they use it as navigation tools, by maintaining a constant angle between their path and the light beam. However, if a light source is exceedingly bright, I mean like "blinding" bright, would an insect still use that as navigation tool?
What I have been thinking is, the insect wouldn't use it, and try to escape from the light source. I believe this because the extreme blindness may cause the insect to damage it's eyes, although I am neither knowledgeable nor capable of confirming this.
Such a thing usually doesn't happen in nature, so I'm unsure if such a test has been made before. Nontheless any help would be great. I also understand that my definition of "bright" isn't well defined, since I don't know the maximum intensity an insect can handle. I also haven't mentioned the insect, so for consistency sake, assume it to be a Black Witch moth (Ascalapha odorata)
tl;dr
Would an insect use a light source that's exceedingly bright to navigate?


texts:
I've read that Russians have been performing selective breeding on Red Foxes for about fifty years, aiming to make them tame. The wikipedia article says

  The experiment was initiated by scientists who were interested in the
  topic of domestication and the process by which wolves became tame
  domesticated dogs. They saw some retention of juvenile traits by adult
  dogs, both morphological ones, such as skulls that were unusually
  broad for their length, and behavioral ones, such as whining, barking,
  and submission.

I wonder, since dingoes are completely wild dogs that have only relatively recently split off from domesticated dogs, do they show more 'wolf-like' characteristics? That is, has their life in the wild selected against domestication genes?


texts: Is survival probability the same thing as relative fitness?

texts:
I created a model where I calculate the survival probabilities from a Mark-recapture design.

I'm wondering if I can call the survival probabilities as "relative fitness".

  Phenotype or genotype: $X$
  Absolute fitness: $W(X)$
  Relative fitness: $w(X)=\frac{W(X)}{\bar W}$

Since relative fitness is a ratio, I would have the tendency to say that it's the same thing as survival probability (keeping in mind that survival is only one component of fitness, so conceptually not exactly the same thing).

If I refer to this article, since I'm computing survival probabilities per individual, I would just need to call it "individual fitness".

It seems that "relative fitness" is more appropriate with a certain categorical phenotype: the relative fitness of tall vs short plants. If you have a continuous trait, how is the relative fitness interpreted?


texts: Do birds require cilia for left/right symmetry during their embryological stages?

texts: I know that in humans ciliary dyskenisia can lead to a Situs inversus, is this also the case for birds and reptilians?


texts: Is it really detrimental to humans as a species to reproduce with one's own first cousin?

texts:
Tired of hearing of these urban legends and popular opinions, I ask this question here to see if there really is scientific merit to this belief. My questions is, is it really "harmful" for a person to reproduce with his/her own first cousin? Everyone, at least in America, seems to think that this is incest which I completely dismiss because incest is purely a religious concept. The next argument I get is that we want more genetic diversity and having offspring with a first cousin is detrimental to our survival as a species. If you have any genetic weaknesses then your cousin is likely to be carrying them as well and then the chances of your offspring carrying them increase and so on.

I don't really believe any of this. It is rather well known (or may be not so well known) that only a very small percentage of a human individual is different from another human individual's genome. Differences due to skin color, race, ethnicity, and such are literally skin deep. So one reproducing with her cousin or someone half way across the globe is only negligibly different.

Forgetting about religion, has this been scientifically systematically tested and/or proven? Has any research been done on this? Is it true one way or the other? I don't mean to spark any debates here. Opinions are of course welcome. But if anyone can point me to any reputable sources or published results/references, that would be ideal.


texts: Why all particles have same influence on osmosis

texts:
When people talk about osmosis, they say that when we add a mole of NaCl, then each its molecule gets dissolved into 2 separate particles and therefore we have 2osM/L solution.

But both Na & Cl are attached to molecules of water which means that those water molecules are not water anymore and they can't penetrate the membrane. Thus not only the presence of Na & Cl itself changes the concentration of water in solution, but also the number of water molecules taken by those particles.

Therefore if we put 1 particle that binds to 1 water molecule and 1 particle that binds to 5 water molecules - they change the water concentration differently.

Please somebody tell me where I'm wrong.


texts: True anatomical/physiological explanation for "metaphysis" etymology

texts:
The anatomy textbook1 I use for my students states that the prefix meta- means "between:"

  The metaphyses (me-TAF-i-sez; meta = between; singular is metaphysis) are the regions between the diaphysis and the epiphysis.   [my emphasis added]

This sounds reasonable given the explanation. However, I have never seen meta- applied in this manner; more generally, the suffix meta- usually seems to refer to "after."

In fact, Dr. Toby Arnold's Glossary of Anatomy provides the following etymology of the word metaphysis:

  metaphysis: Greek meta = after, and physis = growth; hence, the end of the shaft of a bone alongside the epiphysial or growth cartilage  [again, my emphasis added]

The latter explanation is somewhat underwhelming, but the etymological usage fits more with my prior experience with meta-.

So, which is it?

Can someone find a reputable source definitively indicating a clear anatomical/physiological explanation for why meta- was used in the case of "metaphysis"?

A webpage on EnglishLearner.com reports that our earliest usage of the term "metaphysis" came from an obstetrician named William Dorland (1864–1956) in the early 20th century. I couldn;t find additional info.

1. Tortora, G. J. and B. Derrickson. 2014. Principles of Anatomy & Physiology, 14th edition. John Wiley & Sons, Inc., USA.


texts: What is possibly wrong in my gel electrophoresis when I didn't see bands of DNA ladder on gel?

texts:
What was possibly wrong in my gel electrophoresis when I didn't see bands of DNA ladder, and genomic DNA sample on gel ? I could see bands of genomic PCR and RNA solution.

Edit

Thank you all of guys for sharing your opinions. From some opinions, I found out the possible error that my genomic DNA didn't show up because it was not pure (I forgot the detail that our group used a sample of DNA which was extracted from a previous lab and we didn't obtain an expected ratio for the purity of DNA. Then, we also used the impure DNA sample to do PCR, and finally used the amplified DNA for gel electrophoresis lab). However, the reason for DNA ladder didn't show up I'm not sure. I just can suppose that my groupmate who handled with DNA ladder solution possibly contaminated it.


texts: How to attain a deep conceptual grasp of key atomic/molecular/genetic/ notions?

texts:
It's a total noob question, I know.

I'm a layperson trying to come to grips with basic scientific terminology. I always face a conceptual hurdle in trying to understand micro-talk. The way I'm using the expression 'micro-talk', I take it to refer to any kind of discourse that relies extensively on concepts that refer to unobservables like DNA, adenosine triphosphate, other molecules/compounds, chemical elements, atoms, etc. i.e. the kind of quasi-tangible entities that we can never perceive directly owing to our particular evolutionary history that prioritized engagement with mesoscopic objects.

Whenever I read anything in an introductory textbook, the talk of such entities is always presented as a given to me. It's not explained on how on earth we know about them (or even if such explanation is given, it's usually quite shallow and circular i.e. it makes references to the entities in question). I can recite, or rather parrot facts about them just fine. If you ask me why a second magnesium ion is important for ATP, I retort that that's because of its functional role in regulating kinase activity. I might be able to successfully make certain inferences between sentences that involve such concepts. So I might even successfully pass a scientist's Turing test, but that's all there is to it. I don't really have an understanding of what I'm talking about. I feel like I'm a robot or a medieval scribe.

How can I get over this conceptual chasm? Learning about a historical development of a particular discipline might help, but I need to find a way to systematize my study and I can't have a recourse to university right now (even if I did, I'll face the same conceptual hurdle). I have library loans and will to study, but I haven't internalized a good number of micro-talk related concepts and they feel so foreign to me.

This is quite maundering, but I couldn't put it any more succinctly. If there's anyone who experienced a similar frustrating feeling to the one I've described, I'd be very grateful if they could offer me some tips. Thanks a lot.


texts: Why would I see no bands in DNA gel electrophoresis of red blood cells?

texts:
For forensic inspection, you only obtained red blood cells from an individual and amplified for the D1S80 locus in chromosome 1. Twenty nine different alleles of D1S80 have been identified, and 435 allelic combinations are theoretically possible. Approximately 86% of the population is heterozygous at this locus. You set up a PCR reaction for this locus and ran a DNA gel electrophoresis. What would your expected results be based on the described protocol?

A) You would most likely see no bands

B) You would see more than two bands

C) You would see two bands for the heterozygous while one band for the homozygous

D) You would see two bands for the homozygous while two bands for the heterozygous

I thought the answer was C given that heterozygous people would have two bands, one for each allele, and homozygous people would have one band for their one allele. The answer points to choice A for some reason...


texts: Vitamins — how did they get their names?

texts: There are several types of vitamins. A,B,C,D,E,H,K,P, etc. How did they get their names?


texts: Why can't certain nucleoside analogs be used to label bacterial RNA?

texts:
A 2020 publication in Nucleic Acids Research 1 includes the following passage:

A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among them, 4-thiouridine (4SU) and 5-ethynyluridine (EU) are two most widely used noncanonical nucleosides that can be conjugated via thiol coupling chemistry and click chemistry, respectively (9,10). Although the metabolic RNA labeling technique has been instrumental for studying RNA dynamics in eukaryotes, it is not applicable to bacteria.

The authors give no citations or further explanations for the bolded claim.  Indeed, I have found at least one publication that contradicts this statement,2 showing 4SU labeling in E. coli:

We have defined conditions allowing the substitution of 13 +/- 2% of the uridine residues in bulk RNA by 4-thiouridine.

One explanation is that 4SU is a natural RNA modification in bacteria, as Rogers et al. 3 states that most bacterial tRNAs contain 4SU. So, while bacterial RNA can be labeled with exogenous 4SU, naturally occurring 4SU confounds analysis. Concerning EU, Blenkiron et al. 4 used this analog to label nascent RNAs from uropathogenic E. coli in order to track the fate of bacterial RNAs in membrane vesicles:

We then looked at whether we could track uptake of MV RNA cargo into treated host cells by labelling UPEC nascent RNA in the bacteria before it was packaged with MVs. This was achieved by adding an excess of a modified uracil, 5EU (5-ethynyl uridine), which was incorporated into the newly synthesised and MV associated RNA.

Additionally, the text of this research grant award abstract 5 suggests that EU is suitable for labeling both E. coli and B. subtilis:

We have been investigating whether bacteria can incorporate the “clickable” RNA analog 5-ethynyl uridine (EU) for subsequent attachment of fluorescent label (Alexa Fluor) for microscopic detection or a chemical tag (desthiobiotin) for streptavidin-mediated RNA capture. The results for both aspects so far are a qualified “yes”. Both Escherichia coli and Bacillus subtilis grown with EU can subsequently be detected by fluorescence microscopy, but E. coli becomes considerably more brightly labeled.

I can find no research stating EU / 5EU naturally occurs in bacterial RNA.
My question, in short: What aspects of bacterial metabolism or RNA composition justify the claim that 4SU and EU are "not applicable" for bacterial RNA labeling?

Edit, 1 March 2021 -- I'm adding a bounty to garner more attention. From further reading, I suspect the answer to be one of 3 possibilities.

Per David's comment, the bacterial cell wall may be impermeable to certain formulations of nucleoside analogs or the reagents subsequently used in thiol coupling / click chemistry.
Certain nucleoside analogs are toxic in bacteria to an extent not seen in eukaryotic cells, perhaps by a mechanism that causes the elongating RNA polymerase to stall.
4SU and EU labeling are applicable to bacteria, and the claims of the authors are unsubstantiated.

References

Meng L, Guo Y, Tang Q, Huang R, Xie Y, Chen X. Metabolic RNA labeling for probing RNA dynamics in bacteria. Nucleic Acids Res. 2020 Dec 16;48(22):12566-12576.
Favre A, Bezerra R, Hajnsdorf E, Lemaigre Dubreuil Y, Expert-Bezançon A. Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis. Eur J Biochem. 1986 Nov 3;160(3):441-9.
Rogers KC, Crescenzo AT, Söll D. Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon. Biochimie. 1995;77(1-2):66-74.
Blenkiron C, Simonov D, Muthukaruppan A, Tsai P, Dauros P, Green S, Hong J, Print CG, Swift S, Phillips AR. Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA. PLoS One. 2016 Aug 8;11(8):e0160440.
Click-chemistry labeling of RNA: A new tool for microbial ecology?


texts: How can i confirm that the given pedigree chart is of an autosomal dominant trait?

texts: This image is from the NCERT textbook. In diagram A, which represents an autosomal dominant trait, I found out that autosomal recessive inheritance also satisfies the pedigree. Yet, the NCERT text book states that it is a dominant trait. How can that be? Is it because the dominant trait is more probable here? If so, how is that it is more probable in this case?


texts: Are tendons and ligaments classified under the muscular or bone system?

texts:
Are tendons and ligaments classified under the muscular system or the bone system?

Basically they are not bones or muscles and that's why I have doubt.


texts: Origin of term ‘confluency’ in cell culture

texts: Since as long as I have been doing cell culture, the word confluency has been used to describe the percentage growth of cells or area covered by them. However, no dictionary that I have found uses this word. I was wondering if anyone could reliably state where the meaning comes from or how the association began, and truly what it means. I don't believe I can post this on another Stack Exchange  because the word doesn't have even a resembling meaning in the dictionary. Cell culture is such an integral part of cell biology, medical research and biological manufacturing. And this term is an integral part of cell culture. I was surprised to be unable to reliably verify its meaning.


texts: Can Cas13 be used with multiple crRNAs in the same reaction?

texts:
CRISPR-Cas13 equipped with crRNA (complementary to transcripts of interest) can be designed to target ssRNA transcripts in cells.

Upon successful crRNA and ssRNA binding, a fluorescent domain on Cas13 generates a signal, indicating that target has been found.

As far as I know, this method has been used to find one ssRNA target at a time. If we use different wavelength fluorophores for distinct Cas13-crRNA targets, is it theoretically possible to mix them all in the same reaction and distinguish the presence of different targets based on the different fluorescence wavelengths generated during target binding?

In this paper one fluorescently labeled crRNA is used to detect cleavage of one RNA target through complimentary binding. So is it theoretically possible to use several crRNA, each labeled with a different fluorophore, to cleave and detect several target RNAs?


texts: Can a cell receive multiple copies of an insert when using different MOIs?

texts:
I want to transduce a cell line with virus that carries a specific insert.
When using different Multiplicity of Infection (MOI), I expect to get different percentage of transduced cells, but is it possible to get more than one insert integrated in the cell genome?
I use high MOI and I always get 1 copy per cell, so I am not sure if increasing it a lot may also affect the number of in integrated inserts.


texts: Where would vegetarians/vegans get a substitute of hemo/myoglobin from?

texts:
As far as I understand, there is a difference in the iron absorbed from meat than from other sources like grains and vegetables.

If this is the case, is it possible that not ingesting the hemoglobin and myoglobin found in meat leads to some kind of deficiency in a protein or iron itself that creates some symptoms similar to anemia, like fatigue or headaches? Or, is the iron found in non-meat products just as viable as that found in meat-based products?


texts:
I have to classify them either as transported in vesicles or without vesicles.

What I think -

Non-vesicular

2.vesicular

3.vesicular

4.vesicular

5.non-vesicular

6.vesicular

7.vesicular

8.vesicular

9.vesicular

Am I right ? Is it true that a  protein transported by vesicles is made on ER ribosomes ?
How are proteins transported non-vesicular transport ?


texts: What industry job am I qualified for with a PhD in virology?

texts:
I'm considering applying for a PhD studying innate resistance to HCV. I enjoy research but I would prefer to have a stable job, instead of moving from contract to contract and writing grants to ensure that I get more funding.

Would such a PhD enable me to transition into industry? What roles would I be eligible for?


texts: How do spiders get silk from their spinnerettes?

texts:
I'm 13 and writing a report on spiders. How do they use the silk protein gel from the spinnerets? How does it get from the spinnerets to the web? P.S. I know how silk is created, all the way up until the tapering duct

As I currently understand it, the silk proteins are created, then dissolved into a liquid/gel, and stored. Then it is put through a funnel into the tapering duct, liquid is removed. I'm missing an understanding between the removal of the liquid and formation of the silk. Could someone fill in the gap?


texts: What would happen if brain neurons did not reduce their sensitivity to neurotransmitters after prolonged exposure?

texts:
From my understanding, neurons decrease their sensitivity to neurotransmitters by reducing the amount of receptors on the cell membrane in response to sustained neurotransmitter activity. One explanation I heard is that cells do that to protect themselves from damage.

This makes me ask - what kind of damage could be caused by sustained neurotransmitter activity in the brain, if cells did not reduce their sensitivity? Can a brain survive/thrive if neurons always had the same number of neurotransmitter receptors?


texts: Is the problem of cryonics only the pressure?

texts:
According to the pop-sci sources which I drew on from, the only problem with freezing whole bodies its that you can't conserve it without freeze-damage.

If you were keeping a cold-blooded animal in a cold surrounding (well, before that removed the parasites somehow) and optimized the pressure in there so to make the cells not to collapse, could you stop all its functions and bring it back to life again later?


texts: Why is ATP the main nucleoside triphosphate used to exchange energy?

texts: Out of all of the nucleoside triphosphates what makes ATP the most used? Is it its structure? The amount of energy it contains? Why is GTP not used as much? What is the deal with the other nucleoside triphosphates (dATP, dGTP, dTTP, dCTP, UTP, CTP)? Are there any artificial NTPs that can substitute for ATP? (like something that could cure Cyanide poisoning or a disease/illness that somehow de-functionalizes the Electron Transport Chain)


texts: Where do biologists get information about mouse genes?

texts:
From this article https://ui.adsabs.harvard.edu/abs/2005Sci...308.1909S/abstract

“We created transgenic mice that overexpress human catalase localized in the peroxisome, nucleus, or mitochondria (MCAT).”

How exactly do such changes occur step by step? Those. how did they find which genes needed to be changed in order to get the result in overexpression of catalase and in mitochondria?

I am new to biology, and although I understand, for example, how CRISPR works, it’s not clear where people get such data "this gene in the mouse is responsible for the expression of catalase in mitochondria. "Where to find such data?


texts: How long does it take the neurotransmitters to diffuse accross the synaptic cleft?

texts:
Neurotransmitters get from the pre-synaptic neuron to the receptors on the post-synaptic neuron by diffusion across the gap between these two (the synaptic cleft). My question is, how much time does it take the neurotransmitters to diffuse from the edge of the pre-synaptic neuron to the receptors on the other side?

I have seen different values online, ranging from 0.05 ms to 1 ms. Which one is true?


texts: What exactly are genes, DNA and chromosomes. How do they relate to each other and what is their function?

texts:
So I am new to biology and I have been reading, and searching the web, but I couldn't understand the whole framework of a cell. So as I understood:

A DNA, is a double chain of Nucleotides (A,T,G,C and a sugar) and a phosphate residue. Some parts of a DNA code a gene and some do not, exons and introns accordingly. As I understand it these the sequences of exons hold genes and the whole sequence is called genome. Now I read in the book Introduction to Computational Molecular Biology by J. C. Setubal and J. Meidanis. that I cite Each cell of an organism has a few very long DNA molecules. Each such molecule is called a chromosome. So each X shaped thing called a chromosome holds one DNA molecule?

Or is each "hand" of the chromosome one complete double helix of DNA so we have 23 pairs of such chromosomes? or is it that each we 23 pairs Xs?

Shouldn't we have just one uniquely identifiable DNA sequence? I am asking this, because I have also read that each chromosome encodes a different part of one's genome. Does this mean we have several DNA sequences?

This is really bothering me, since I can't figure out the correct structure of a cell.

EDIT:
Now if each chromosome contains a pair of DNA helices. We have 46 chromosomes so overall within the cell there are 92 DNA sequences? All of which are the same? Or are they different? If they are different how do they code for different aspects of one's genome?


texts:
I recently stumbled upon the Biological Dark Matter wiki page. Its pretty light on details, but it appears to be genetic material found in humans that doesn't fall into currently classifications.

But what do we know about it? Is it really a big black box that we know nothing about? The article claims that it can make 40% of the genetic material in our gut, and I find it hard to believe that we really know nothing about it.


texts:
What is the difference between "hamstring tendon" and "common hamstring tendon"?  I have seen both terms being used but I don't know whether they referred to the same tendon.

For example,
Johnson, Anthony E., Robert R. Granville, and Thomas M. DeBerardino. "Avulsion of the common hamstring tendon origin in an active duty airman." Military medicine 168, no. 1 (2003): 40-42. (https://doi.org/10.1093/milmed/168.1.40) uses the term "common hamstring tendon" but I don't see any difference with the "hamstring tendon" when reading the article.

Since there are more than one hamstring tendons, I would have guessed that  "common hamstring tendon" specifies which hamstring tendon is being referred to, but I haven't seen the term of any anatomy diagram yet.

The hamstring tendons that I am aware of are:

Lateral hamstring tendon of the biceps femoris (long head) (2 tendons: distal+proximal)
Lateral hamstring tendon of the biceps femoris (short head) (2 tendons: distal+proximal)
Medial hamstring tendon of the semitendinosus (2 tendons: distal+proximal)
Medial hamstring tendon of the semimembranosus (2 tendons: distal+proximal)

(image source)

(image source)


texts: Does one need to perform two Chi-square tests?

texts:
A question from my University's Question paper 2016:

  A newly identified fruitfly mutant, cyclope eye –large and single in the middle of the head is hypothesised to be autosomal dominant. The experiment started with homozygous wild type females and heterozygous cyclopes males. The data from the F2 generation was 44 wild type males males, 60 wild type females, 110 cyclops males and 150 cyclops females. Does this support or reject the hypothesis$^1$? Use chi square to prove.

I think the following should be a proper approach at solving it:

H0= The proportion of cyclope eyed male and female is not that same,i.e. the gene responsible is not autosomal. $or$ There is an association between the sex of fruitfly and the phenotype.$^2$

H1= The proportion of cyclope eyed male and female is the same, the gene is present on autosome $or$ There is no association between the sex and the phenotype.$^2$

Chi square contingency test with Male and Female (in the columns) and Wildtype and Mutant phenotype (in rows).

Once the H0 is proved wrong (if it is proved wrong), we consider a next Chi-square test, goodness-of fit, where :

H0= The proportion of mutant phenotype is the same as the wildtype i.e. 1:1 ratio is followed

H1=The proportion and the mutant phenotype is greater i.e. the allele responsible is dominant.

When the final H1 is accepted the $^1$hypothesis is correct or else wrong.

$^2$ I'm not sure which one is better / proper.

Is it alright?


texts: Do scouting bees get to pass their genes to offspring?

texts:
Let's say the food-scouting behavior of scouting bees are enhanced when some particular alleles are expressed. By natural selection, the allele frequency for that "good" allele should increase because more of the scouting bees with that allele get to pass the allele to offspring generations, as more of them survive in the ecosystem.

But considering that only male bees get to produce offspring with the queen bee, do scouting bees (I assume to be females) ever get a chance to pass their genes to future generations? Or are they males? If they are males, do they get to produce offspring?


texts: Why does walking mitigate the urge to urinate?

texts: When feeling a strong urge to urinate humans tend to walk around when e.g. waiting for the current bathroom occupant to get out. Why is that?


texts: identification request - tiny flies invasion

texts:
Since they are tiny, this is the best photo I can do:

We are in Berlin, Germany. It has become very hot outside and the flies have invaded us for the last couple days.
The insect is about 1mm long, 0.2mm wide, they are absolutely tiny. They fly but seems to like camping on the ceiling.
The have come in massive numbers, probably over a thousand, but they're so small we barely see them. They don't seem to be interested by our food, nor water, etc but rather just stay in cool and darker areas.
Since we have a newborn, I don't want to use insecticide to get rid of them, so I'm trying to figure out what they are and then.. what to do next :) Right now I am welcoming spiders!


texts: Are there any effects of elevated Cysteine levels on cognitive function?

texts:
I'm looking at this diagram of homocysteine metabolism and see two distinct pathways that the amino acid may get metabolized to: with vitamin B12 it gets converted back into methionine, while with B6 it gets converted to cysteine.

I've followed the links for the products that Cysteine gets metabolized to and could not find any references to cognitive effects. Are there any cognitive effects of Cysteine or other amino acids that it gets metabolized to?

I'm interested in learning what are the possible effects of pharmacological (50mg - 100mg) doses of vitamin B6 on this metabolic cycle, while folate and B12 levels stay at the baseline levels. It seems to me that if vitamin B6 is more readily available, there will be a higher chance of homocysteine metabolized into Cysteine. Is this assumption correct? What are the implications to this metabolic cycle that may be caused  by elevated levels of vitamin B6, while keeping folate and B12 at baseline levels?

I'm particularly interested in the implications of this process on dreaming. There has been numerous reports among dreamers that 50-100mg of vitamin B6, taken in the 3rd-5th sleep cycle produces very intense and vivid dreams, sometimes featuring spontaneous awareness (lucid dreams), while B-complex vitamins (B6, B12, Folate, Niacin, etc) appear to produce the opposite effect - very vague dream recall.

I'm trying to understand if there is indeed a connection between the metabolic pathway that homocysteine may take and the vividness of dreams, capacity to recall them clearly and the phenomenon of being able to spontaneously realize the fact that the person is dreaming while still asleep.

Thank you for your input!

Diagram obtained from here