texts: Long-term efficacy and absence of side effects of anti-covid vaccines

texts:
The question is about the methodology/biostatistics of clinical trials (I state this beforehand to avoid accusations of being an anti-vaxxer).
As multiple anti-COVID vaccines are offered on the market, the question naturally arises about their long-term efficacy and possible side effects. As SARS-CoV-2 virus has been known for a bit more than a year, neither of these could be tested directly, so one probably has to rely on indirect knowledge due to the experience in developing other vaccines. Given that multiple vaccines have been approved for a wide use, there should exist well-established procedures to assure their efficacy and safety.
The question is: how does one prove the long-term efficacy and absence of side effects during a short period of time (short in comparison to the expected duration of immunity and absence of side effects).
Update
As @MattDMo have correctly pointed in their answer, the absence of long-term effects is established in the last phase of the clinical trials, while observing cohorts of vaccinated individuals during a long period of time. @MaximilianPress, in their comment, has also correctly brought up the fact that this is done within the framework of survival analysis. In particular, this means that it is sufficient to follow the vaccinated cohort during several years to evaluate the side effects that occur during their lifetime, as the survival analysis keeps track of the sensored data.
Here we are dealing with a situation where such a study could not be done - the best we can guarantee is the absence of the side effects in the next few months. We thus need to rely on a different method, which would account for the similarity between the established and the new vaccines.
I am less concerned about the vaccine efficacy, since the inefficacy of vaccines is usually against different strains of virus, as is in the case of influenza and Dengue.
Update 2
The accepted answer points out two important things:

The long-term side effects of a vaccine/medication can be truly understood only in the Phase IV of the clinical trials, i.e., after the vaccine is in widespread use.
The threshold for approving this specific vaccine is lower due to the emergency of the current health crisis.

This however still leaves open the question of the safeguards undertaken in the Phase III of the clinical trials, before the vaccine approval. I.e., the question is about ranking the candidate vaccines against the above-mentioned threshold.
Remarks:

I understand why this question irritates, but I believe that it is not the asking, but rather refusing to seek the answer that plays in the hands of anti-vaxxers.
I did follow the suggestions in the comments to pose this question in the medical and the statistics communities, but it seems to get there even less traction.

Update 3
Recent suspensions of Astrazeneca vaccine in 9 European countries demonstrate the importance of this issue.


texts: Wondering if there is a tree of life in Text format for open data sharing.


texts: Why do neurons have a negative resting potential?

texts:
Neurons expend the majority of their energy powering ion pumps to maintain the chemical gradients that power their electrical activity. To have a negative resting potential, neurons leak potassium across the membrane, which seems like a terrible waste of energy to me. I would like to know what benefit a neuron receives in exchange for this seemingly unnecessary metabolic load.

I am not asking how the resting potential is achieved. I am also not interested in the trivial answer: that the voltage-gated channels are configured to require a transition across the -40mV or so threshold in order to fire an action potential. It seems to me that this threshold is arbitrary; if there was no advantage to maintaining this gradient then neurons would have evolved to avoid it.

Any ideas? Or better yet, pointers to places where this has already been answered?

My best guess so far looks like this: The total range of available voltages is more-or-less fixed from -90 to +50mV. We want to avoid getting too close to either end, since the channels become less effective near their reversal potentials, so maybe the effective range is more like -70 to +30 (to go outside that range, we must sacrifice speed). Within that 100mV range, we leave the bottom 30mV or so for EPSP integration, and the other 60mV for action potentials.  Now, if the resting potential was 0mV, the available dynamic range for integration and spiking would be much smaller which probably translates to making the output noisier.


texts: Values of the blood tests pancreatic amylase and lipase

texts:
Anyone know what is considered slightly elevated, moderately elevated and strongly elevated values of pancreatic amylase and lipase?

Many different laboratories in my country divide between these categories for interpretation, but they don't specify which values qualify for each category.

Hope this is the right place for this kind of question.

Thanks in advance.


texts: Is there an example of a new species through mutation breeding?

texts:
Is there a demonstrable species that went through mutation breeding and through successive generations it drifted so far away from its initial parent species that it can't breed with them anymore? (I assume it would need to be able to breed with intermediate generations though). Also by "demonstrable" I mean a case where we can directly demonstrate this process by starting from a parent species to a new species and not establish this relationship by looking back (like observing the connection between corn and teosinte through genetic information).
Edit: I'm mainly curious about postmating/post- zygotic reproductive isolation. As I understand, the timescale of us is not enough to observe that kind of speciation (we can either directly observe the start of the isolation or the end of it but not both), that's why I'm curious about whether induced mutation could speed up the process enough to directly demonstrate speciation by the most difficult to achieve definition.
I have checked the thread Have we ever observed two drosophila lineages that evolved reproductive isolation in labs? but it seems to me that those results only shows premating isolation.
I have checked: Sexual and postmating reproductive isolation between allopatric Drosophila montana populations suggest speciation potential article which says, that postmating barriers observed may be due to postcopulatory-prezygotic mechanisms.
Thank you for the corrections, Im reading into Examples of creating a new animal species by humans


texts: Does the Petri dish lid orientation on workbench affect aseptic technique?

texts:
When examining an incubated plate, it is rather clear that holding the plate in one hand and the lid in another is best for aseptic technique, or simply resting the lid on the plate as shown below.

However, I can't seem to find an answer for what to do with your Petri dish lid when doing manipulations like plating. It's pretty obvious that the above practice is, well, practically impossible.

Thus, I always went under the assumption that when placing the Petri dish lid on the workspace, the orientation of the lid did not particularly affect risk of contamination, assuming that you're technique is indeed aseptic (ethanoled workbench, Bunsen burner, etc). However, discussing with collegues has resulted in mixed answers. Some say it doesn't matter, some say the lid should be facing up, some say down.

When doing manipulations like plating, is there a common practice for exactly how to place your Petri dish lid?


texts: Intrinsically disordered proteins as potential drug targets

texts: Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological functions. Many IDPs are implicated in cancer, neurodegenerative diseases, and diabetes, which makes them attractive drug targets. Are there any successful examples of that? Are there any drugs which disrupt protein-protein interactions (as one of the protein being IDP)?


texts: How to quantify the strength of social bonding between the individuals of a colony? How to compare the strength of social bonding across the species?

texts:
Consider two different species of honey bees. If I have to compare the strength of social bonding between the two species i.e. in which species, social bonding between the individuals is stronger than another.

Is there any methodology to do the comparison of the strength of social bonding across the species?


texts:
I'm doing some variant discovery in a human trio (affected child, non-affected mother, non-affected father) and I have found what looks like a homozygous novel mutation. All of the aligned reads in the child have the same nucleotide in that position, but neither of the parents do.

In looking at a small handful of variants, I've seen plenty of novel heterozygous SNVs. But on first blush a novel homozygous SNV seems extremely unlikely. Two independent germline mutations at the same position on both paternal chromosomes is all but impossible, right? Are there other mechanisms by which a novel mutation would become homozygous? Or am I right to be skeptical here?


texts: Microarray experiment validation meaning

texts:
I have a quick question: what does microarray experiment validation mean ?
I was reading a paper in which they say that the data of the experiment show that the 3 genes radB, dp1 and dp2 are co-regulated following gamma irradiation "validating our microarray experiment".
I tried to find something in Google but it is not yet clear.


texts: The dominance variance on a single locus

texts:
I was reading the book "Genetics and Analysis of Quantitative Traits", by Lynch and Walsh. I how the covariance between two individuals with IBD $\Theta$ gets divided into just the additive variance and dominance variance component, even in the simple $1$ locus case.

Here my understanding of the modelling (for the simple one allele case):

Given a genotypic value $G_{i,j}$ of mean $0$, $i,j \in \{0,1\}$ we find numbers $\alpha_0$ and $\alpha_1$ minimising the least squares of the following form $\mathbb{E}(G_{i,j}-\alpha_i-\alpha_j)^2$, where the expectation is over the population.

We next define the error terms in each case as $\delta_{i,j}=G_{i,j}-\alpha_i-\alpha_j$. From the properties, viewed as functions of the population $\alpha_i$ is independent of $\delta_{i,j}$, and both have
mean $0$.

The claim made in the book is that given two individuals, with IBD $\Theta$ and probability that the genotype is equal $\Delta$, the covariance of the genotypes $G_{i,j}$ and $G_{k,l}$ is given by,

$$\text{cov}(G_{i,j},G_{k,l}) = 2\Theta \sigma_A^2 +\Delta \sigma_D^2,$$

where $\sigma_A^2= \text{Var}(\alpha_i)$, and $\sigma_D^2 = \text{Var}(\delta_{i,j})$.

Expanding the LHS of the expression, showing that $\mathbb{E}[(\alpha_i +\alpha_j)(\alpha_k+\alpha_l)] =\Theta \sigma_A^2$ is quite easy. It also seems to follow from the  that the the terms $\mathbb{E}[(\alpha_i +\alpha_j)\delta_{k,l}]=0$ from independence of errors from the $\alpha$.

On analysing $\mathbb{E}[\delta_{i,j}\delta_{k,l}]$, we see that if both genotypes are equal, which occurs with probability $\Delta$, then this reduces to $\sigma_D^2$. This gives us a term $\Theta \sigma_D^2$. Further, if both $i,j$ and $k,l$ are not IBD then the covariance is $0$. However when one of the two alleles are IBD, then it is not clear to me that this the covariance will still be $0$.

The book seems to claim that unless both alleles are IBD,  $\delta_{i,j}$ and $\delta_{k,l}$ are independent. I do not see why this is the case. Am I missing anything here? I'd appreciate any help wrt this.


texts: Brain capacity of Cro-magnon man vs Modern man

texts:
Cranial capacity of Cromagnon man was about 1650cc whereas average cranial capacity in modern human is 1450cc.

My question is, why during the course of evolution, a reduction in cranial capacity is seen ?


texts: I found this queen ant on the pavement (in Adelaide) its about 1 cm long and I am not sure what species it is, is someone able to help me?


texts: What are the methods for infering genetic interactions?

texts: Is there a classification of methods for inferring genetic interactions? I mean some work published, utilizes genetical genomics data.  Is this possible with expression data alone? And how about perturbation screens? I guess they all need information about mutants/genetic variations?


texts:
Is it possible that an insect poisons itself while eating "wrong" plants/fruits/... and have symptoms like pain (may hard to measure or detect) or orientation disorder?

Background:
I observed a physically apparently healthy caterpillar moving in circles (or rather changing its direction constantly and end up at the same point again) on the street and falling over in middle of moving or standing. My first and a bit naive thought was, that it may have eaten something wrong...


texts: Are there nerve endings on or inside the corpus cavernosum/spongiosum?

texts:
The penile skin has many nerve endings, but what about the inner structure of the penis?

There are two dorsal nerves on either cavernosum. But it is unknown whether these nerves provide sensitivity to the corpus cavernosum/spongiosum externally or internal.


texts: Effect and functional role of voltage-gated channels on dendrites

texts:
I'd like to understand better the effect and functional role of voltage-gated channels on dendrites.

What I believe to have understood:

It is important that a more distal post-synaptical potential (PSP) arrives at roughly the same time and with roughly the same strength at the soma than a more proximal PSP generated at the same time (to give them comparable weights and to detect that they were synchronous). Let me call this the goal of adjustment.
Achieving this goal is the main function of (properly distributed) voltage-independent channels on dendrites (→ Rall model)
The main function of voltage-gated channels on axons is unattenuated signal transport.
Voltage-gated channels on the dendrite lead to non-linearities.

The immediate physical effect of voltage-gated channels on the dendrite is hard for me to imagine and understand. But even harder to understand are the (specific) functional advantages and disadvantages of those channels.

Some possibilities come to mind:

They allow to achieve adjustment better (more precisely) or in some other way more efficiently.
They allow to achieve other goals better or more efficiently (which are only poorly achieved without them).
They allow to achieve completely new goals which are not achievable at all without them (by having some magic computational powers due to non-linearities).
They may have disadvantages (which should not exceed there advantages, otherwise they would not exist), e.g. by distorting PSPs in an unwanted way.

I know that there is a lot of literature on the topic of dendritic processing, but not so many gentle introductions. A gentle introduction - answering some of the following question  - would be welcome. And of course immediate answers!

Do voltage-gated channels on dendrites (distributed as they are) allow to achieve adjustment better or in some other way more efficiently?
Which other goals do they allow to achieve better or more efficiently?
Which new goals do they allow to achieve?
Can their extra computational powers be pinned down?
Which disadvantages do they have (possibly)?

[I believe it wouldn't make sense to split this question into five: they are too strongly related, aren't they?]


texts: Inexpensive way to determine mass of tiny seeds?

texts:
My niece is doing a science project and she wants to weigh various seeds, determine their volume and density. She tried using my kitchen scale, but it is not sensitive enough.

I've suggested weighing 100 seeds then dividing to get an average weight, but she (she's 11) wants to weigh each one. I don't want to get in the way too much. I don't mind buying a scale, or other simple equipment as long as it isn't expensive.  Is there any way to do this inexpensively?


texts: I have some RNA-Seq data and I'd like to align it to the physical genome and see which sections of chromatin are geometrically open and being transcribed.  The data are already sequence-aligned, and every Google search I do for tools that might help ends up sending me down a rabbit hole.  What computational tools have helped you?


texts: What is the mechanism of regulation of PER /CRY genes?

texts:
I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate each other. Do these genes encode proteins that once created bind to the DNA and cover the transcription sites for other genes(like PER protein covering the binding site of CRY)?

A lot of diagrams and descriptions of the process are very complex, and I would appreciate a simple answer (if it exists).


texts:
Do humans exhibit territorial behavior like other primates? I have seen people sometimes stare at others -- notably males -- and then physical fights spontaneously turn up. Is this territorial? It seems it either goes two ways: One person looks at another; the other looks back and either looks away or both look away; or they both hold a stare until one or both erupt in to physical blows and try to dominate the other or fight/assault them. Is this a display of human territorial behavior? I know some chicks do it too.

I've also read that in males more so that staring can be an "alpha" or "dominating" gesture to others -- especially if a stare is held at one in response to them either turning away or provoking a fight.

This can be seen in every area, but possibly more so in clubs, bars, or certain social settings.


texts: How fast does activity affect synaptogenesis?

texts:
How long does it take for the increased activity due to a novel stimulus to cause an increase in synapse generation?

There are many studies which show that the number of synapses in the brain increases within 24 hours of doing a novel task, so I know the number is less than 24 hours. I'm interested in questions like "If I do yoga for an hour, will the later part of the hour benefit from synapse creation caused from earlier in the hour?" Obviously I don't know if yoga in particular would benefit from said synapses, but if synaptogenesis is not up-regulated in less than an hour, then I can certainly rule such an effect out.


texts:
I am just a beginner of BIOLOGY as a Grade 7 student!
But the information which I got from my textbook and Internet has got me confused as MY TEXTBOOK SAID:-

  Viruses are part of "Akaryote"

And 'Acaryote' (or 'Akaryote' or however 'Akaryocyte') is just a Smaller group of ORGANISM than Prokaryote. Example:- Blood (As said in Wikipedia)

Pic-1:- A VIRUS DECRIPTION BY BBC

(END OF PICTURE 1)


texts:
In animals temporary anaerobic respiration leads to the breakdown of the pyruvate formed by glycolysis into lactate.  The buildup of lactate in the bloodstream is accompanied by a large number of protons causing lactic acidosis, which is detrimental to the health of the organism.  This is one of the main suggestions I have come across for why a lack of oxygen is fatal to cells, however the LD50 for lactic acid as referenced by the COSHH MSDS seem awfully high (even if the route is by ingestion rather than directly into the bloodstream) for this to be a cause of cell death:

  Toxicological Data on Ingredients:
  ORAL (LD50): Acute:

  3543 mg/kg [Rat (Lactic Acid (CAS no. 50-21-5))].

  4875 mg/kg [Mouse (Lactic Acid (CAS no. 50-21-5))].

I also wonder if this is a larger problem for an organism as a whole rather than on a cellular level.

The alternative, I suppose, is that glycolysis alone does not provide sufficient ATP for vital cellular processes to occur.  If this is the case, which ATP requiring processes are most vital for the short term survival for a cell?


texts:
Many trees first reproduce decades after germination.  Many pests of trees reproduce in under a year.  It would seem that the pests have an advantage in the evolutionary arms-race, as they can evolve a means of attack far faster than the tree can evolve a defense (cf. Does an increased reproduction/mortality rate provide an evolutionary advantage?).
I once read a speculation that trees might mitigate this by varying the genetics (or perhaps only epigenetics?) of different branches within an individual.  The branches that do better produce more seeds.  The seeds produced by a branch carry information specific to the branch.  This means evolution (or the epigenetic equivalent) happens at the level of the organ, not the individual.
Is there any research supporting this speculation?  If it has been refuted, how do trees compete effectively in the arms-race?


texts:
I have read in biology text-books that one of the most important constraints on the size of an insect happens to be the importance of the surface-volume ratio. It simply states that
if we assume constant oxygen levels and increase the size of an insect there would be a point where the insect's exoskeleton would no longer be able to support its weight.

Some textbooks go on to say that this is why we don't have insects the size of elephants. But, if this is true...is there a least upper-bound on the maximal body mass of an insect?


texts: Guide RNAs and SNPs for nanopore enrichment

texts: In which part of the gRNA sequence is it most important to not get SNPs? I know the PAM site cannot have any SNPs but what about other ones? And secondly, are there any positions in the gRNA sequence where it is acceptable to have SNPs?


texts: Why does wood become darker when it ages?

texts:
I have lots of pieces of pine furniture which have different colours depending on how old they are. So, I just wondered why that is. I guess it has something to do with structures and chemical compounds that were already in the wood when it was still alive, so I hope this is not off-topic here.

What processes take place in dead wood when it ages?

What determines the colour it will have? For example, pine and spruce wood looks very similar when freshly cut, but will develop very distinct colours afterwards.

Is there also wood that does not become darker?

Is it something to do with the processing of wood, or will that happen to any stick you leave lying around in your room (so it doesn't rot)?


texts: What is the lifespan of Skeletal Muscle Cells?

texts: I have read that skeletal muscle cells cannot multiply and are generally not created after early development. However, I have also read that they have a "lifespan" of 10-15 years. Could this lifespan actually be referring to the turnover rate of the majority of material in the cell, and that the literal lifespan of the cell (if we count all of its components, including the nucleus) would be the same as that of the owner?


texts:
According to Wikipedia, muscle cramps are caused by the inability of myosin fibers to break free from the actin filaments during contraction, resulting in a prolonged contraction.

A lack of ATP would obviously produce cramping, as myosin requires ATP to become free from actin.

However, I have heard that potassium and sodium are useful for treating cramps and that their deficiencies can lead to cramping.

So, how does a deficiency in sodium or potassium result in the inability of myosin fibers to break free from the actin filaments during contraction?


texts: Isn't it possible to reverse tomography methods to create means to deliver heat or radiation precisely in 3D? This would be "3D scalpel" i.e. device which would be able to eradicate tumor cells precisely in otherwise unreachable areas?


texts: Can breathing in helium (from balloons for example) cause damage to the throat in the long term?

texts: Often an activity to do at a party, breath in helium and speak like one of the chipmunks. But, I am wondering, would infrequent inhalation of helium cause long term harm to the throat? in particular, the vocal cords?


texts: What is the difference between chloride shift and Bohr shift?

texts:
Does anyone know the difference between chloride shift and Bohr shift?

Is it that Bohr shift happens in respiring tissues when CO2 concentration is low, and that Chloride shift happens in the blood as a buffer?

Sorry for asking such a trivial question and thank you in advance. And sorry for any wrong tags or title (new to the community and is seeking to improve)


texts:
I taught in elementary school for 20 years and noticed that males were far more likely to be classified as handicapped than females.
More males than females die at birth and are more likely to have birth defects. Why?


texts: Male-Male competition limited to breeding season?

texts:
I'm currently reading about sexual selection in the context of evolution. Unfortunately, the focus is always on animal behavior during the breeding season. What is 'normal' behavior outside of breeding season?

For instance: Red deer compete with their antlers. Are they doing that throughout the whole year, or just specifically during breeding season?

More general: Does male-male competition exist outside of breeding season?


texts: Did John Hopkins let people outside of the university use the Hela cell-line that was isolated from an immortalised cervical cancer?


texts:
It's pre-monsoon season here in India. The temperatures in the Northwest of the country really take a spike around mid April. Apparently the heatwave-like conditions seem to have announced themselves quite early this year. The mercury is at 42°C for most of this past week.

I'm new to this region and even though the relative humidity is quite low, such weather conditions prove unbearable to me. A few minutes walk down the Avenue and I start to sweat in bucket loads.  However, I find locals here don't sweat too much even in this hell of a weather. They say this weather is still bearable and that the monsoon phase proves to be the worst.

Having witnessed monsoon in other parts of the country I find favorable weather conditions prevailing at that time. The rain brings down the temperature and the air seems to get cooler. Most people here and elsewhere in the world would disagree with me on that. They say humidity is the worst and than dry heat can be combated by drinking enough fluids. I also see people sweating more in humid conditions compared to in temperatures of 42°C. The opposite applies to me. I barely break a sweat in temperatures of mid 30s despite there being high humidity.

What is this anomaly? Is there evidence that some bodies are just meant to excel in certain weather conditions while finding life difficult in others? Kindly help me understand the science behind it all.


texts:
What is the smallest oligocelluar organism?

How many cells does it have?

EDIT

The question is motivated by this comment@Philosophy.SE

EDIT as recommended in comments

I'm looking for an example of an organism made of very few (the fewer, the better) sister cells (obtained by mitosis or aggregation) that are morphologically and functionally different. I would accept examples of species that exist in different "conformation" (unicellular and multicellular).


texts: Why does migration distance depend on log of molecular weight in SDS-PAGE?

texts: I really want to know why in the result of SDS PAGE, log of molecular weight(MW) and migration distance (distance from the loading well) have a linear relationship. Why is it log(MW) instead of MW? Thank you!


texts: Can you use a cell in meiosis to create a karyotype?

texts: Why might it be problematic to use a cell undergoing meiosis to create a karyotype?


texts: What is the justification of Chargaff's second parity rule?

texts:
First parity rule
The first rule holds that a double-stranded DNA molecule globally has percentage base pair equality: %A = %T and %G = %C. The rigorous validation of the rule constitutes the basis of Watson-Crick pairs in the DNA double helix model.
Second parity rule
The second rule holds that both %A ~ %T and %G ~ %C are valid for each of the two DNA strands. This describes only a global feature of the base composition in a single DNA strand.

[source]
It makes sense that in the context of dsDNA, that A = T and C = G, but I don't see an obvious reason why in a single strand of DNA, A ~ T and C ~ G.


texts: I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help?


texts:
So this is derived from a lesson at Khan Academy.

The mind activity assumes that the one ventricle heart pumps blood to the lungs for oxygenation then rest of the body. However, the problem is that there is too much pressure at the lungs leading to bleeding.

This problem, however, can be solved if the lungs come before the one ventricle heart. This way, most of the pressure is used going through the body and pressure would not become a problem.

Thus, is a one ventricle heart that connects to body tissues first then lung feasible? If so, why have organisms not developed this way?


texts:
Before going to the details of the question let me post a few other details-
(I posted something similar and got no useful answers-probably because I didn't explain things properly or something else)-
1. My background is not genetics.
2.I am not interested in knowing how dna sequencing or genotyping is done.
3. I am interested just in the nature of the results as in-https://en.wikipedia.org/wiki/DNA_sequencing#/media/File:Radioactive_Fluorescent_Seq.jpg
Now coming to the question- Humans have two sets of chromosome in each cell. So if I say sequencing chromosome1,what does that actually mean? Which of the two chromosome's gets sequenced?
Of genotyping-do comparison take place between two+two=four chromosome1's?
Or is my entire undertanding flawed?


texts: Organisms using thermal energy as their sole energy source

texts: After seeing this question I remembered that in secondary school we watched a documentary stating something along the lines of "all organisms derive their energy directly or indirectly from the sun. *pause* Well, except a couple of organisms in the deep sea cultures that get their energy from small undersea volcanoes" . Now, after doing a lot of searching I was able to find the 'giant tube worm', however that still indirectly relies on energy from the sun as well as it relies on free Oxygen being available that in the end comes from photosynthesis (if my understanding is correct). So my question is two fold, am I correct in my understanding of the giant tube worm and if so, are there any organisms that function in a way that does not require any energy source beyond geothermal energy?


texts: What is the difference between an alpha subunit and a non-alpha subunit in ACh receptors?

texts: When reading about ACh receptors, it is frequently the case that a protein is described as (alpha) or (non-alpha).  However, I haven't really been able to find out what that means.  What is the difference, and why would it matter if a subunit is alpha or not?


texts: Correct migration rate expression in infinite island model

texts:
In Sewall Wright's infinite island model, where all demes exchange migrants each generation, I have seen the migration rate stated variously as $m$ or $\frac{m}{d - 1}$ (as in Matthew B. Hamilton's Population Genetics textbook, chapter 4, p. 132, figure 4.12), where d is the number of demes.

My question is, which expression for the migration rate is the correct one?

If it's the latter, then where does the "-1" come from?


texts: What happens with the nitrogen in blood in membrane oxygenators?

texts:
The air we breathe consists of about 80% nitrogen and 20% oxygen. The oxygen gets diffused into the blood and CO2 out of it, the nitrogen does mostly nothing, as there isn't a partial pressure of nitrogen between the air and your blood.

In membrane oxygenators the blood flows arround small tubes which contain pure oxygen. The oxygen diffuses in your blood en the CO2 diffuses in the tubes, basically doing the same thing lungs does. However, since it's pure oxygen that flows through those tubes, the nitrogen in your blood should get diffused into the tubes.

So is this what happens? Does the nitrogen simply diffuse untill there's nothing left? Isn't that then bad for your body if all the nitrogen is out? Or can't nitrogen pass through the membrane the tubes are made of? Or does it differ wether you use 'true' membrane of microporous membrane?


texts: If I stop consuming protein, will I still excrete urea?

texts: Will an animal that is not eating any aminoacids stop excreting urea (or whichever other form of excreting nitrogen)? If the body is not in a position to lose nitrogenated compounds, in which processes is nitrogen inevitably turned into waste products like amonia/urea?


texts:
I am a bioinformatician working with plant data. Therefore my formation on plant biology and botany is "ok" but not very strong.

When people talk about sections, I know that they talk about a phylogenetic rank that is lower than the genus but higher than the species. It groups subsets of species belonging to a genus together.

What is the thing that puts them together? Morphology, origin, geography, metabolism, genome identity, ...?


texts: Transmembrane protein: does signal peptide always form a loop?

texts:
So I have read a few times that

b. SP probably forms loop not arrow. Loop enters channel (translocon) in membrane. SP loop is probably what opens (gates) the channel on the cytoplasmic side.

Source
And I was wondering why this would be the case? It seems much more complicated to me for the protein to loop around than fior the signal peptide to just embed itself in the translocator pore and the rest of the polypeptide chain be synthesised in the cytoplasmic side.
Then if the protein was meant to pass through the membrane again, there wold be another start-transfer signal sequence (so the two first signal sequences would be two start-transfer sequences rather than a start transfer and a stop transfer).


texts: What is a set of chromosome and what is a pair of chromosome

texts: What is the definition of set of chromosomes? Does it differ from pair of chromosomes?


texts:
The viceroy butterfly generates a toxin compound which make it distasteful to predators.  Biologists agree that the viceroy must have developed this trait as a passive defence mechanism to prevent being eaten.

Let’s look at it from an information point of view.

For this to work, information about the bad taste of the viceroy must be known to the predators.  This can happen by a predator eating one viceroy, discovering the bad taste, learning and never doing it again.  Unfortunately, the unpalatable butterfly had to die in the process.

The second, and most important, information path is the genetic one.  One way, evolution work is by the survival of the fittests. In this case the important trait of “tasting bad” dies with the butterfly and is less likely to have been transmitted to a new generation, unless (and this might be part of the answer) we consider the local population of butterfly as the evolving organism.

The question:
If a successful gene is only proven successful when removed from the gene pool, how does the species evolve a trait involving this gene?


texts: How do humans detect temperature differentials on the skin?

texts:
I just read this question on Physics SE about how the body detects cold or warm surfaces. As someone who already understands how heat flux devices like thin film gauges and thermocouples work (by exploiting the known relationship between temperature gradients and electrical/thermal properties of the relevant materials), I was actually more interested in how the nerve endings in my body actually implement this.
When I touch something warm or cold, what is the nervous mechanism that causes the correct signal to be sent to my brain, causing me to perceive a hot or cold surface?
How is the "thermocouple", which tells me whether a surface is hotter or colder than my finger, implemented?


texts: Which proteins are part of the most different protein complexes?

texts:
Let n be the number of different protein complexes (as defined here) that a protein may be a stable part of for a considerable amount of time (and not only transiently). Which proteins have the largest n?

An answer should include the number of different protein complexes  the protein is part of.

Or where should I start doing my own research? I have no clue.


texts: What is the difference between RFLP and DNA fingerprinting?

texts: Is RFLP (restriction fragment length polymorphism) analysis the same as DNA fingerprinting? I looked for information online and I don't understand the difference.


texts: Thin layers or laminae that make up a single summer band in tree ring, what are they?

texts:
I took the photograph below of some tree rings. Each division on the ruler is 1 millimeter:

Each tree ring (the areas between the pizza crusts) represents one seasons worth of growth. The growing season is from about March to October. My question is about the small lamellae or dark bands that make up each ring. I have placed a green box around one set of these bands. What are they?

These small bands all seem to be the same width, so tree rings that are wider (good years) have more of them, and rings that are narrow (drought years) have fewer.

What are these bands?


texts: How is respiration an unbalanced equation

texts: The equation for respiration is C6H12O6+6O2→6CO2+6H2O+36ATP. The chemical formula for ATP is C10H16N5O13P3. How is this possible, since it violates the law of conservation of mass because it is unbalanced?


texts: Is there animal other than human that can recognize distal causes?

texts: We know animals can recognize proximate causes. For example, if animal A hits animal B and injures it then usually animal B is able to associate animal A with his injury. From our everyday experience with pets and other animals we know that. What about distal causes? Proximate causes are not always the most appropriate causes, sometimes distal causes are more appropriate to identify the responsible agents. Let's modify the previous hypothetical example by bringing another animal, animal C: Animal C pushes animal B so that animal A hits animal B and injures it. If animal B is capable of recognizing distal causes, it'll associate animal C with his  injury (not animal B which is the proximate cause of the injury).


texts: What confuses me about "homologous gene"

texts:
When I first encountered homologous genes I thought those genes are identical because the text book said so, and "homologous" meant the same knowledge.

But as I studied along, it comes out that diploid is a two sets of haploid, each from mom and dad.

This means they are not identical, doesn't it? How could they be "identical" since they are from mom and dad seperately?

If they were identical, crossing over during meiosis loses a point(mixing chromatids is meaningless if they are "same").

Then, when the text book says homologous genes are identical, what identical trait is the text book referring to?


texts: Prolactin and Dopamine throughout orgasm?

texts:
Dopamine is also known as a prolactin-inhibiting hormone, which keeps prolactin levels in the body in check. However, during orgasm, dopamine is released to make the experience pleasurable. I know that prolactin is released as well. Don't they counteract each other? The prolactin also has a meditative effect, which from what I know causes a refractory period where another orgasm can't be achieved.
Does prolactin inhibit dopamine release too?


texts: How to increase the shelf life of yogurt without refrigeration?

texts:
When we make yogurt at home and do not refrigerate it, it will become sour because of conversion of lactose into lactic acid by Lactobacillus bacteria, but this does not happen in case of Nestle's yogurt or any other brand until it remains air tight.

I wonder though bacteria is still present in it and continue to convert lactose into lactic acid then why does not packed yogurt becomes sour? How these companies increase the shelf life of yogurt..?


texts: How much does a human brain's metabolic rate vary?

texts:
Possible Duplicate:
  How does brain energy consumption depend on mental activity?

Our brains consume about 20% of our energy when we're at rest. How variable is a human brain's energy consumption? Will thinking harder consume more energy? Does this change significantly when we sleep?


texts:
Why does olfactory sensation need lateral inhibition? If it's not helping in spatial discrimination then why is it needed? Don't we just smell the odour which is more concentrated?

My attempt: It is said that lateral inhibition is an important part of olfaction as it aids in odour discrimination by decreasing firing in response to background odours and differentiating the responses of olfactory nerve inputs in the mitral cell layer. But we also know that sensory perception is based on the pattern of receptors activated by the stimulus. So following questions arise:

Why don't background odours laterally inhibit the target odour? Isn't there more chance of inhibition of target odour being inhibited since its concentration is less?


texts: Can some colours be processed faster/more accurately than others?

texts:
Is the human visual / motor system able to track, and move in response to, objects of certain colours more quickly and reliably than for others?  By more reliably, I mean with greater accuracy in judging position and velocity, and with greater accuracy when moving in response.

Which colours are "most visible" in that sense, as a function of background and illumination?

This interests me specifically in the context of juggling: I like to juggle, and I wonder whether there's a difference in my response time and accuracy with different colours of balls/clubs.  Usually I'm indoors, and ceilings are usually white, sometimes black or brown, with strip lighting.  My only personal observations are rather obvious: dark colours can be hard to see against dark backgrounds, and white can be hard to see against white.


texts:
Last night I came across a question that goes as follows:-

Cells cannot exist without
a) cell wall
b) cell membrane
c) mitochondria
d) ribosomes

I am getting confused with option B and option D

If RBC is lacking ribosomes then where the antigen proteins on RBC are coming from ?


texts:
Which types of blood vessels can regenerate in humans/mammals?
From what I understand, arteries and arterioles can be created later in life, while this is not necessarily the case with veins. However I don't understand why damaged blood vessels in an eye recover, while this is not the case for other body parts. Also, I don't understand how angiogenic agents work.

The types of blood vessels I've been thinking about include:

Arteries
Arterioles
Capillaries
Venules
Veins

Also, does the capability vary in different organs (e.g. blood vessels in a hand vs blood vessels in an eye)?


texts: Collective name for the X- and Z-chromosomes

texts:
Chromosomes are grouped as sex chromosomes or autosomes, with the X, Y, Z and W all falling in to the former category. The Z and X are present both in the homogametic and heterogametic sexes, and the Y and W only in the heterogametic sex.

Is there a collective name for the chromosomes in such groupings (X/Z & Y/W)?

I want to talk about Z- and X- (and analagous) chromosomes in general. Rather than having to write "The X-chromosome, and analagous chromosomes such as the Z-, are present in both sexes...." I'd like to say "The blank chromosomes are present in both sexes...."


texts: Would it be correct to say that viruses are genotoxic?

texts: I know it is an unconventional way to describe viruses, but would it still be technically correct?


texts:
Most of the cells in multicellular organism undergoes cell division through Mitosis.

While most of the single celled organism reproduces through binary fission by mitosis.

In both cases,the offspring are very genetically similar to the mother cell.

But one is defined as Cell division and other is defined as Reproduction.

Why?


texts: What makes/breaks the hydrogen bonds between DNA and RNA during transcription?

texts:
So I know that RNA polymerase catalyzes the phosphodiester bonds that hold the sugar backbones of a growing mRNA molecule together during transcription. However, I'm less sure about the hydrogen bonds between the nitrogenous bases of the forming RNA and the template DNA strands.

I do assume that hydrogen bonds are forming, but they must be short-lived.
Their existence are confirmed here:

  ribonucleotides containing 3 phosphate groups hydrogen bond through the process of complementary base pairing with the exposed deoxyribonucleotides on the unwound strand that is to be transcribed

and represented in this gif:

Is RNA polymerase responsible for creating the hydrogen bonds between DNA and RNA? Is it, then -- I assume -- also responsible for breaking these bonds? Are the breaking bonds driven by chemical reactions or more due to the physical movement of the polymerase along the DNA template?

This site mentions the transient H-bonds formed by holoenzyme at promoter sites, but I haven't been ale to fnd a reputable source discussing the transient H-bonds between nucleic acid strands.

I'd appreciate if someone can provide a clearer molecular description of what's going on here. Pictures/animations are a plus!


texts: What does a hornet nest foundress feed on?

texts:
After wintering, hornet queens will build a new nest from scratch. Once the new workers have hatched, they will fly out and collect carbohydrates to feed themselves and the queen and will also hunt for protein to feed the larvae.

I’m interested in knowing how food collection for both larvae and queen are taking place before the role is taken over by the workers (as none have hatched yet).

Does the queen collect both carbohydrates and protein?
Does the queen leave the nest to collect food when there’s already larvae (as opposed to having stored enough food before starting to breed)?
How long (in terms of weeks) after the queen started building a new nest until she can fully rely on her workers for food supply?

While I assume the answers to the first two questions to be ‘yes’, I have failed to find a source confirming this. My questions primarily refer to the Vespa Velutina (invasive in Europe), but I’m also interested to hear about differences in other wasps/hornets present in Europe.


texts: Genomic library preparation: Why does the restriction enzyme not cut into the gene?

texts:
I am currently trying to understand creating a genomic library more profoundly. In most textbooks I read (as well as wikipedia), they mentioned that the genomic library is created by isolating the DNA and fragment it with a specific restriction enzyme that cuts approximately as many times as there are genes. However, that cannot really work, can it?
Let's say E. coli has 4000 genes with a 4,600,000 bps genome. That means I must generate fragments of more than 1150 bps in theory (if each gene is the same length and no other sequences are present). That would mean I need a restriction enzyme that cuts about 4000 times creating over 1150bps fragments. So I would either use a restriction enzyme with a recognition site of 5bps (cuts every 1024bps) or with 6bps (cuts every 4096), of course just if the base-pairs are random.
Now you already see, with the first restriction enzyme I will (even in theory) cut through many genes, while with the second I might get genes of the appropriate size but I will also fragment others.
Furthermore the genes, especially in more complex organisms are not spaced out equally, but may be concentrated in some areas, while in others just repetitive sequences are located.
So why does every textbook mention that I can create a full genomic library with one restriction enzyme? Wouldn't it make more sense to shear many copies of DNA randomly, just as it is done for shotgun sequencing, to get a higher coverage?
So my question is, how is a genomic library REALLY prepared without knowing anything about the sequence? Do you just take into account that much genes will be cut in the middle and hope for the best? It seems like a very weird strategy to amplify complete genes.
Thank you! :)


texts: Why aren't the brains of most advanced life forms in the middle of their bodies?

texts:
This question is designed to be the successor to Why don't most animals have "heads" in the middle of their bodies?

The previous question was flawed as it fails to accurately define what constitutes a "head".

Keeping on topic, the question here is largely focused on placement of brains and brain-like structures.

Intuitively, common sense would dictate keeping the brain roughly equidistant from everything it controls, decreasing the number of potential failure points between the brain and peripherals.

The standard argument in favor of putting the brain in the head rather than in the middle is for dedicated specialized visual processing. This argument is easily debunked seeing that there's no reason why you couldn't have a brain in the middle of the body and a smaller dedicated optical co-processor in the head. (similar to how a certain premium laptop design 7 years ago had only integrated video built-in but comes with a dock that supplies a high-end external video card). The smaller head-brain would run all of the intensive processing and send a compact representation to the central brain, adding a modest amount of extra reaction time lag. Extra credit if the central brain can partially offload high-level or heavily spatial thought processes to the smaller head-brain (think of it as using a CPU and GPU working together to solve a problem more quickly than the CPU could on its own).


texts: I2D vs STRING for protein-protein interactions

texts: Can someone clearly explain me the differences between STRING and I2D(Interlogous interaction database) ? What does each database do best ? Which database is better for what kinds of studies etc ?


texts: I hope this is a good place to ask such question. I have to do some data analysis on RNA-seq data from human cells. I am currently searching for tools to help me with that. Specifically, I would need some tools to analyze the gene expression from the data. Something to help me plot the expression of selected genes in each fastq file and compare the differences in the expression with the possibility to export the results or some command line interface for scripting. Basically I need something where I can put a fastq file and perhaps also a human genome annotation file as input and get gene expression as output. I have looked at bioconductor and it's packages and on Wikipedia's List of RNA-Seq bioinformatics tools. I suppose some of these tools have to be able to do what I need, but I have been unable to find out which one and how should they be used to achieve that. Could someone please give me some advice?


texts: Limitations of the Self-Incompatibility Mechanism in Plants

texts: For a given plant species, how many types of S-loci exists to prevent self-pollination? I would like to know how often a plant stops fertilization process by other plants, thinking the pollens belong to itself due to limitations of SSI/GSI.


texts: What kind of spider is this? Brown with white spots

texts: It was found in Houston, Texas, but I've never seen one before. Does anyone know what it is?


texts: Why are goosebumps so ineffective at keeping us warm?

texts: If the purpose of "goosebumps" is to keep us warm, why is it so ineffective? Or are the changes subtle, but important?


texts: How to determine the direction of regulation of a gene by comparing gene expressions?

texts:
I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a specific disease.

I am confused about how people can determine whether a gene is down-regulated or up-regulated by its gene expression.

Assume we have a few samples of a gene: some of the samples are normal patients samples and rest of them are disease-infected samples. Do we determine the direction of regulation of a gene by the ratio of gene expression of normal/disease-infected samples?

For example, if the ratio of expressions is a negative value, do we say that the gene is a down-regulated gene, otherwise, it is a up-regulated gene ?


texts: What is the term for a given interpretation of a fossil record?

texts:
There exists a term, that I have heard and forgotten it appears, for taking a described species in paleontology and creating a version of what it was like in life.

For example, a prior [insert this term here] for T Rex had it upright and dragging it's tail, while a more recent [insert term again] has shown a much more horizontal and rigid body plan.

I know you 'describe' it formally when you identify it from remains, and 'mount' when you set up a specific set of remains. But what is it when you interpret those remains to a specific form?


texts: Are high sounds worse for your hearing than low sounds?

texts:
From about 80 dB it is possible to suffer loss hearing after a couple of hours. But does it make a difference what frequencies those sound waves are or is it just the volume of the sound in dB that matters?

In your ear the first sounds you lose in case of hearing loss are the high sounds because they are at the beginning of your ear. So are high sounds also more dangerous?


texts:
I have heard and read about Peter's rule informally in the past, but never saw a formal definition or description.

Informally I have learned to understand Peter's rule as the assumed correlation between the amount of overlap between axons and dendrites and the post synaptic density in the synapse. Here is a sample of the search results in Google.

Is my interpretation correct? Is there a more rigorous, perhaps quantitative,  definition of Peter's rule?


texts: In sandwich ELISA the Fc region of primary antibody bind to the polystyrene coated well. But what are the specific interactions (like 'hydrophobic interaction' or 'van der waals force') happen between well and Fc region?


texts:
We sequenced RNA using RNA-seq from biofilm (attached to bottom) and planktonic growing bacteria (supernatant) in 3 mL microtiter plates.

I'm not sure how is possible to obtain planktonic cells since they may have precipitated. For bacteria growing on the bottom I'm convinced these were derived from initial attached cells and then formed biofilms growing anaerobically (this is a facultative bacteria). However, since this bacteria is not motile, how is possible I obtained planktonic bacterial cells RNA? Maybe was a suttle layer on the surface growing aerobically. Wouldn't them have precipitated after the 36h of the assay?

Specie: Haemophilus parasuis. A facultative anaerobe.


texts: Why do large, aromatic residues prefer beta-pleated sheets?

texts:
I read in many journals that amino acids with branched and large aromatic R-groups have higher beta pleated sheet propensities. However, none really go in depth into the significance or reasoning behind this finding. I have made an educated guess based on my findings on alpha helix propensities:
In alpha helices, branched and aromatic R-groups are not favored as the g+ and g- isomers can extend into the helix and interfere with the hydrogen bonding. In beta pleated sheets, however, the R-groups are pointed perpendicular to the hydrogen bonds, and even large R-groups like that of phenylalanine or tryptophan will not able to reach the site of hydrogen bonding. Coupled with the fact that smaller amino acids will rather be more tightly bound to each other (so they prefer helices, e.g. collagen helix, alpha helix, save space, amide hydrogens and carbonyl oxygens closer together), larger amino acids therefore favor formation of beta pleated sheets.
I need a few key pieces of info to really accept my own explanation (if it is correct) as factual. First, I will need proof that beta pleated sheets are more structurally rigid than alpha helices (or else, smaller R-groups like that of alanine and cysteine will also prefer beta pleated sheets). I also kinda want to see the structure of beta pleated sheets with large R-groups to further ground the thought in my head, as I can't really see how R-groups like valine (heavily branched) will not affect hydrogen bonding. As an example, I attach one that I found for alpha helices.


texts: How would I represent this on a cladogram?

texts:
So, right now I am making a cladogram (More of a dendrogram) for a kingdom of fictional species, and I'm not exactly sure how to represent a certain relationship.

Let's say that the oldest class in the kingdom is Clade A. And, while it is a clade in itself, it also evolved into two other classes. The first class it evolved into was Clade B, but Clade A still persists. Then, later on, Clade A evolves into Clade C - but still persists.

If I was to represent this on a dendogram, how would it be done?


texts:
I was reading some articles about CRISPR and the world of gene editing, but then a lot of questions for which I couldn't find any answer online came into my mind. Those are all about how far can we edit an organism. So here is the general question, followed by some other to narrow down a little bit this broad subject:
What are the limits of gene edition?

Can one edit the genes in its entire body? (as a human, or a multicellular organism)
What are the risks? I heard that some people who did try gene therapy ended up having some of their modified cells turned into cancer. Was is because of gene incompatibility  or because of error during the gene editing process?
Can we go as far as adding some chromosomes or changing an entire chromosome? For example, if a male human would like to change their sex, could they switch all their Y to an X?

EDIT: I decided to accept the answer from @MattDMo. However, I'm still interested in some development (clues with other technologies...)


texts:
Can anyone please offer a suggestion of what the insect below is?  It is about 3mm in length, and I saw it on my kitchen counter.  I live in an apartment, 9th floor of a highrise.  It is January 5 (winter), 2021, in Ottawa (-3C outside).
I suspect that is might not be relevant, but last month, I saw what might be Dermestid lavae.  The beetle below, however, doesn't look like a Dermestid beetle
Thanks.


texts: Why is free ribose not reduced to deoxyribose rather than the reduction occuring on ribonucleotides

texts: I cannot understand why deoxyribonucleotides are not synthesized directly from deoxyribose, but ribonucleotides have to be synthesized first, and only then can deoxyribonucleotides be synthesized.


texts: How well does the radius of a tree correlate with its age?

texts:
I'm looking for a cheap non-invasive ways to approximate the age of a tree (a birch). Measuring the radius pops up in the mind as the first alternative. How would one do that? Measure at multiple defined heights?

I'm hoping that I could get some kind of confidence interval for the approximation, so that the data could be used in a scientific publication.

Or is there any reliable DIY radiocarbon dating technique?


texts: Transmission of disease from mother to fetus

texts:
Can  parasite, microbes be passed from mother to fetus through the placenta ?

I know some like HIV can be.


texts: Metabolic efficiency for fats and sugars

texts:
I am making an exercise for physics students about the first law of thermodynamics, burning heat and evaporation heat. So my idea is to use cycler which runs on fats and sugars where proportion determined by respiration quotient. The amount of evaporated sweats would be determined from inefficiency of using the fuel. Unfortunately I am unable to find efficiency data to form the exercise.

So what are typical efficiencies to run skeletal muscles on either fat or sugar molecules?

EDIT

Assuming respiratory quotient measured at the time of cycling is 0.7 so all energy is obtained from oxidizing fats:
$$ C_{16}H_{32}O_2 + 23 O_2 -> 16CO_2 + 16 H_2O + \Delta G$$
what part of the $\Delta G$ can do mechanical work $A$ or simply what is typical value of efficiency coefficient:
$$\mu = \frac{A}{\Delta G}$$


texts: Physiologically, how can stress/anxiety cause neuropathy?

texts:
According to the Mayo Clinic, stress/anxiety can cause "pins and needles" (neuropathy) sensations all over the body.

But how can this be? My understanding of the sensory pathway is that sensory receptors (nerves) fire "pins and needles" signals to the brain whenever there is a lack of blood flow to them.

So does stress reduce blood flow to nerves? Is it a chemical reaction, perhaps where stress releases hormones that prevent the nerves from functioning correctly? Something else?

I'm looking for a biological/physiological/scientific explanation of what stress does to make nerves misbehave.


texts: Is there an absolute minimum intensity level to the stimuli we can perceive?

texts:
By stimuli that we can perceive, I mean what our five senses can perceive.

Is there an absolute minimum for humans, or can we "train" ourselves to perceive stimuli at lower intensity?

And if there is an absolute minimum intensity, do we know what its value is?


texts: Is there any kind of immortality in plants?

texts: I asked a question about immortality of hydra and learned good things about senescence. Now I would like to know about immortality in plants, if there is some kind of immortality in plants and how this occurs - how does it protect itself from senescence?


texts:
I ran a PCR product of ~300 bp on a 2% TAE-agarose gel for 30 minutes. I used Sybr-safe as a DNA stain. Voltage was 80V.

When I imaged the gel, the DNA on the bottom half of the gel, including the ladder had disappeared (it showed no bands). The DNA in the top half looked-clear and well-separated, but the bands on the bottom were somehow missing.

What could be the reason? I've never encountered this before.

I know it's not due to gel overheating - I ran the gel in the cold room and when it was done it was cold to the touch.


texts: What is the difference between Warburg effect and Crabtree effect in metabolism?

texts: In addition to answering my question, please suggest a good review article that provides comparison of the above effects. Which pathways affect central carbon metabolism to produce these effects? Also, how many unique metabolic effects are known for metabolism in general? Is there a good article which covers such unique aspects of metabolism?


texts:
Do all the arthropods molt ? Which ones do not molt ? Why don't they need to molt ?

I tried googling this - but did not get satisfactory answers.


texts: Why do nerve gas victims have chronic neurological issues?

texts:
The article on Wikipedia says the following:

  The effects of nerve agents are long lasting and increase with continued exposure. Survivors of nerve agent poisoning almost invariably suffer chronic neurological damage and related psychiatric effects.

Unfortunately, the original paper seems to be paywalled. Why does this happen? Is it because it takes a long time to replenish the acetylcholinesterase inhibited by the nerve agent?

Here is the link to the original paper.


texts: How to calculate the LOB, LOD and LOQ of an enzyme assay

texts:
I understand how to calculate limit of blank (LOB), limit of detection (LOD), and limit of quantitation (LOQ) in the traditional way i.e., average and SD of raw analytical signal of blanks and low concentration samples. But the enzyme assay makes things unclear. I am not sure what measure to use in my calculations.

The enzyme assay with seven calibrators produces a very nice dose-response that I fit with a nonlinear regression model (4-parameter aka. Hill equation). Running blank samples gives three relevant measures that I could use to calculate LOB, LOD, LOQ:

Raw absorbance at 405 nm

Problem here is absorbance increases over time as the enzyme goes to town on substrate. Results across multiple experiments are not comparable. Not a good candidate.

Normalized enzyme activity (as a % of uninhibited control)

I like this option the best because it's not time-dependent. Blanks run on various days are comparable.

Concentration (ng/mL)

Concentration is interpolated on calibration curve using % activity as the input. Problem here is sometimes the nonlinear model cannot calculate results that are beyond the upper asymptote (parameter A for those familiar with the Hill equation). So roughly half of my blanks don't get a concentration.

I feel like I want to proceed using % activity as my measure for calculating LOB, LOD and LOQ but it just doesn't feel right.

For example, my 20 blanks run over 8 experiments have an average enzyme activity of 99.4% and standard deviation is 2.2%. If I calculate LOB the traditional way LOB = mean of blank + 1.645*SD of blank, I get 103% which doesn't make sense (it should be mean - 1.645*SD instead, which gives 95.7%). First red flag.

I need to report my LOB, LOD and LOQ to external stakeholders. No one is going to understand what it means when I say my LOB is 95.7% activity, LOD is 92.1% activity, and LOQ is 77.2% activity. They'll want the limits expressed in terms of analyte concentration.

But... to go from % activity to ng/mL, I have to interpolate on my calibration curve. But I got the data from 8 separate experiments. Am I supposed to average out the curves for the 8 experiments and use that to turn % activity into concentration?

I would really appreciate some help on this one. Everyone in my lab is pure analytical chemistry and they don't get the whole enzyme thing.


texts: How should I put a large phylogeny into a scientific paper?

texts: I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is crucial to show the whole tree on which the among-species distribution of a characteristic is indicated. I have looked up some journal issues but so far haven't found any similarly large phylogeny in one article. How do people usually treat this kind of situation in scientific papers? Could anybody tell me how to do it, or show me examples? Thank you so much.


texts:
The little amount of body hair humans have don't seem to be of much use for keeping warm.
Our Simian cousins on the other hand sport thick furs.

At which point during the species evolution and why did humans lose their fur?


texts: Why does crying lead to a running nose and reddened nose tip?

texts: Why do we have a running nose for quite some time after crying? It persists even after we stop crying. Why is it so? I have faced this always. Also, why does our nose redden on crying for long?


texts: When was the first exception to Mendelian genetics discovered?

texts: In addition to the the question in the title I'd like to know , how scientists reacted to the exceptions?


texts: What is the minimum population size that Hardy-Weinberg calculations can be applied to?

texts:
I'm trying to find out if a particular allele is in Hardy-Weinberg disequilibrium, but the data is poor. What's the minimum population number that you can use to get any sort of respectable conclusion?

I've heard it's 5 individuals minimum for each genotype but can't find a source on that.


texts: I conducted an experiment involving a fluorescent F-actin stain called sir-actin which is removed by an efflux pump. After increased time and removal of the medium containing sir-actin, the cell actively removed the sir-actin using the efflux pump but an increase in cell area was reported when the images were processed in matlab. I was wondering if anyone can propose a possible cause for the increase in cell area with the removal of sir-actin by the efflux pumps. The f-actin of the cytoskeleton was also found to have a reduced length with increased time. Thanks in advance. I also used MSCs and the cells were alive until fixed at each time point and then imaged.


texts: Why do some people have a fear of depths?

texts: I'm asking this question on this website because I want an evolutionary reason rather than a reason of how the human brain works. In one episode of "The Nature of Things," I heard David Suzuki say he was terrified when he went in a deep mine because he's afraid of depths rather than because of the higher temperature there, so I assume other people feel the same way. I'm also scared to go into a submarine that will go really deep into the ocean because I know the laws of Physics and realize that there might be a mistake and it's not as strong as the designers thought and it might implode under the extreme outside pressure. Maybe for some people, it's a fear for a good reason like me and for other people, it's a fear for no reason. I want to know a reasonable theory on what the evolutionary reason for it is. Is it similar to the reason why the human selection of nonaggressive dogs led to dogs with floppy ears? I think it was so rare for somebody to be able to kill themselves with depths by implosion that the fear of depths wasn't selected against directly. For example, in our evolutionary history, by the time somebody swam deep enough that they could not swim back up to the surface without drowning first, the pressure still wasn't extreme enough to implode their lungs. I think that instead, there were many ways people could kill themselves but there was also a pattern between the different ways they could kill themselves so it was easier for them to evolve  a simpler way to avoid killing themselves in any of those ways, and although death by being crushed under extreme pressure at great depths wasn't one of the ways, it fit into the pattern of the other ways people could kill themselves so the natural selection for people who don't kill themselves those other ways came with the trait of fear of depths automatically. Could the fear have actually been selected for directly after all because people could not think ahead and by the time they've swum to the deepest depth they can and still make it back to the surface, they're like "I still don't yet have the desperate urge to breathe so I can swim even deeper" so instead, natural selection selected for people who were afraid of swimming that deep below the surface of the water?


texts: Do mitochondrial DNA have repair enzymes?

texts: Mitochondria are considered endosymbionts originated from a prokaryote. So, do they have a DNA repair mechanism ?


texts: Is there any non-pathogenic gram negative bacteria?

texts: In the category of Gram-negative bacteria, is there any non-pathogenic species? Is such a list of non-pathogenic gram-negative bacteria's available? Can you give maximum 5 examples of such bacteria which has been proved to be non-pathogenic and is gram-negative?


texts:
What I understand of these two terms is that:

Paratope is a portion of antibody that recognises and binds to specific antigen.

Idiotype is an antigenic determinant of antibody formed of CDRs that have specificity for a particular epitope. Some authors call the antibodies recognising a particular epitope an idiotype.

Well the CDRs, they actually form the paratope so is it right to say the CDR that acts as an paratope also forms the idiotypic determinant/ idiotype ?


texts: Investigating rare variants in ethnically different populations (European ancestry & African ancestry)

texts: If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) especially considering that the populations have different allele frequencies. Is the main object to see if they're could possibly be novel rare variants in each population at different allele frequencies?


texts: Do bees from different continents have different "taste"?

texts:
This question was already asked by me at Gardening Stack Exchange, but I was advised to ask it here instead. I see there is already a closely related question: Do animals have different taste preferences within the same species? . However, I would like some bee-specific clarification or study material, if possible.
I live in Europe, and planted several supposedly bee-attracting, but non-native (originate from Americas) perennials, most notably:

echinaceas
hellenuims
rudbeckias

For all species, I chose several cultivars, for the sake of experimenting.
Although all three species are listed as bee-attractive, bees at my place like only echinaceas and hellenuims. They totally ignore rudbeckias! Is there any plausible explanation for this?
Can it be that european bees are just not used to rudbekias, or simply don't like it, while american bees do?


texts: Could light/occasional smoking strengthen the lungs?

texts:
Here's my thought process, correct me where I'm wrong.  It seems the human body has thresholds.

Examples: You lift too much weight, and the muscles and tendons risk serious injury, but otherwise they tend to rebuild stronger to handle more weight.  Too much sun can lead to sunburn or worse, but moderate UVB exposure can lead to melanogenesis and increase protection to UV damage.

Do the lungs behave in a similar manner where a small amount of smoking might actually strengthen your lungs before reaching the threshold where you're causing severe damage?  My guess is the answer is "probably/somewhat" but that there haven't been any studies since it'd be difficult to analyze and quantify, but maybe somebody has an answer based on theory.


texts: What are the movement mechanisms of thrombus?

texts:
I am thinking how thrombus (veins, arteries and heart) can move.

Secondary mechanisms come to my mind only:

some enzyme which lyses it, probably adhesion mechanism.
Blood circulation (flow rate) is one secondary measure, I think.

I am not sure if there exist any primary mechanisms:

In veins, there are valves which probably can help thrombus go forward by pushing.
Veins can also dilate so dilation of vessel can help.

Arteries do net dilate their diameter.
So aim would be there to maximise laminar flow, and decrease turbulence.

So probably the question is related somehow to the laminar flow which could help thrombus to move.

How can thrombus move in veins, arteries and heart?


texts: Feffects of frequent & sudden variation in room/surrounding tempratues

texts:
If out door temprature is like 40°c with 100% humidity and indoors temperature is around 35°c. Whereas an air conditioned room in the house has  a temperature maintained at 20°c with very less humidity.
A person doing household chores moves in & out of all three temperature zones very frequently, like 3 to 5 times every ten minutes, for a total duration of say half hour.
In such a situation, what could be the physical effects on ones body?
Can it cause dizziness, sleep onset, fatigue, headache & muscular cramps, palpitations, breathing problems etc?


texts: Involuntary twitches and apnoea during early phases of sleep

texts:
I assume most people either experienced or have seen people with the following phenomenon: in the early phases of sleep sometimes involuntary twitches occur that usually accompany the pause of breathing (I'm aware that there's a  chronic sleeping disorder called sleeping apnea but I think it's different because what I'm asking about now is acute). I wonder if the twitching is some sort of emergency signal, so that the person would wake up (to some level not necessarily full awake) and start breathing. Is there any data that these (the pause in breathing and the twitches) are connected or they are independent? Also I'm also interested why this acute pause of breathing occurs?

Edit:

I've researched myself on this topic and it seems that what I've described is more likely a form of Obstructive sleep apnea.


texts: Consumption of different type of energy when one is inactive

texts:
I'm wonder if there is any study done on this and what are the results?
how much of each type of energy one's body(healthy normal person) uses when inactive(seating down)

I know there are alot of dependencies, but any kind of ball park answer will be great.

ps: when I say type of energy, I mean: fat, carb, protein.


texts: Why we utilize dextro glucose and levo amino acids?

texts:
Our body only digest dextro(Right handed) glucose and levo(Left handed) proteins and can't digest Levo glucose and dextro proteins. Why?

Our body synthesis levo proteins. What is the reason?


texts: Are there any multicellular forms of life which exist without consuming other forms of life in some manner?

texts:
The title is the question. If additional specificity is needed I will add clarification here.

Are there any multicellular forms of life which exist without requiring the consumption (destruction) of other forms of life in some manner? Thus purely on inorganic material.

I do understand that the definition of life is a semantic distinction, so for this discussion I will assume the one Wikipedia provides:

"Life is a characteristic distinguishing physical entities having signaling and self-sustaining processes from those that do not, either because such functions have ceased (death), or because they lack such functions and are classified as inanimate. Biology is a science concerned with the study of life."

I am open to considering alternative suggestions.

Thank you.


texts: How can cancer preventing genes from animals be transferred to humans?

texts:
I recently read this non-peer reviewed article that states that the prevalence of cancer in crocodiles or elephants is really low, much lower than humans.  It is said below

A team of researchers in the US looked closer, and found an abundance of a gene called TP53. This gene is known for its ability to repair damaged DNA and thus halt the spread of cancer, and it's some 20 times more common in elephants than it is in human beings. It appears elephants have developed more of these genes as they've evolved, in part to protect calves born to older mothers
"These findings, if replicated, could represent an evolutionary-based approach for understanding mechanisms related to cancer suppression," says the report, published in the Journal of the American Medical Association.
Naked mole rats are even more miraculous - they never develop cancer, even when scientists try and induce it artificially. What appears to be happening, at least according to a recent study, is that the mole rats are using natural mechanisms to clamp down on the spread of cancer and fight back against the mutation.

Question
So why is it that these genes cannot be transferred from animals to humans? Maybe when the baby is at fetus stage?  What are the current problems/limitations and if possible, how would scientists transfer these genes?
My logic is that since mice and elephants are both mammals,  it should not be too hard to achieve this.


texts: Does Sirtuin protein family Sir2 work in low-calorie diet mostly?

texts:
I am reading about the protein family in relation to the prolongation of cell life.
It is known that

  Sirtuins have been implicated in influencing a wide range of cellular
  processes like ageing, transcription, apoptosis, inflammation and
  stress resistance, as well as energy efficiency and alertness during
  low-calorie situations.

However, I am not sure if these physiologic processes are only during low-calorie situations.
Alertness is at least.

It says in the original paper only that

  Our results suggest that in the hypothalamus, SIRT1 functions as a key
  mediator of the central response to low nutritional availability,
  providing insight into the role of the hypothalamus in the regulation
  of metabolism and aging in mammals.

However, it does not specify how the Sir2 works to high-calorie diet.
Therefore, I asked mostly.
When is the protein family active?

Does the Sirtuin protein family work mostly during low-calorie diet?


texts: Is there is difference between "homozygosity" and "homozygosis"?

texts: Are these just two terms for the same phenomenon, i.e., the state of being homozygous? Merriam-Webster says so, but I know dictionaries sometimes miss the nuance of scientific terms. If they are indeed synonyms, it seems homozygosity has won out, according to Ngrams


texts: How can rhodobacter possess a single 'PS-II' like reaction center?

texts: I recently came across an information in my book Trueman's Elementary Biology ,  a popular text in India, that photosynthetic bacteria like Rhodobacter, Rhodopseudomonas etc. possess a single photosystem where the reaction center is PS-II like. Now how can PS-II work as a single unit? As far as I know, PS-I can operate singly in cyclic mode generating ATP only. But PS-II works in conjunction with PS-I to generate ATP, $\ce{O2} $ and $\ce{NADPH} + \ce{H^+} $. So how can PS-II work as a single unit in this case?


texts: is having more copies of gene better then having it less? if it's why is it ?

texts:
I was learning about elephants rarely getting cancer and learn that elephants have 40 copies of genes while human only has 2 copies of genes each from parents.

so I wonder if it's better to have more copies of the gene then having 2


texts:
I found some bees or wasps, in my garden.

Auckland, New Zealand
13mm long head to abdomen, fluffy on thorax and head. Abdomen is orange brown with black stripes.

The nest or hive is underground (otherwise I'd suspect honey bee, though they seem a little smaller even than honey bee workers).

I managed to catch one eventually, but then I realised the container had oxide powder, so the bee in the attached picture is a lot blacker than it was in life. It is also dead ( just in case that's not obvious)

They don't seem to be aggressive - there is a new fence being built right past their nest, they don't seem to be bothered by it.

I am a beekeeper but only beginning, so I do have honeybee workers to compare it to, but not a whole lot of experience.

NOTE: it is autumn (fall) here - high temperature was 23° c (73° f)


texts: What is the minimum caloric intake for a truly starving adult

texts:
What is the minimum caloric intake for an adult?  I'm not talking about a healthy diet.  There's plenty of advice on that.  I'm wondering what the absolute limits of H. sapiens are.  When there's a multi-year famine, and the body is willing to shut down as much of its capacity as possible without actually failing to function for years at a time, how much energy is it consuming?

I know the Basal Metabolic Rate is a key factor to this, but the numbers I have seen for it are all "healthy" BMRs.  I'm interested in the unhealthy numbers.  For example, I'd consider maintenance of temperature optional for these circumstances (assume we have a temperate enough climate), and I presume heart rate and breathing will go down, decreasing those loads.  Obviously there's limits as to how many environmental constraints can be addressed (if I knew what environments this was studied in, I'd likely know which studies to look for!).  And obviously not everyone is the same, but that's an issue in every human study ever completed.


texts: How could one calculate the gene flow between two populations?

texts:
Imagine there are two populations X and Y, and for each population you have the genotypes of each individual in that population (e.g. Aa, AA, aa, etc.), but for multiple loci (e.g. AABb).

How could one calculate the gene flow between population X and population Y?

An answer would ideally recommend either or:

An R/Python/C++ library, or any other software tool
the breakdown of the maths, for which I would be much obliged, but not entirely necessary in the answer

Background reading

Indirect measures of gene flow and migration: FST≠$\frac{1}{4Nm+1}$

Related questions

Variance in Fst in the infinite island model (by Remi.b)


texts:
Why do these circles form around the eyes if somebody is tired? And why does fatigue express itself around the eyes this way? Can I get eye bags very quickly in another way?

http://www.todayifoundout.com/index.php/2014/06/causes-dark-circles-eyes-sleeping-people-really-tired/

http://www.top10homeremedies.com/how-to/how-to-get-rid-of-dark-circles-fast.html


texts: Does eating hard food really cause wisdom teeth to erupt properly?

texts:
According to the article Bad molars? The origins of wisdom teeth, in our evolutionary history, people were eating harder food like nuts and had unimpacted wisdom teeth. Later, that article appears to have jumped to the conclusion that if you eat hard food, that can actually cause your wisdom teeth to erupt properly. I don't see any reason for that conclusion. Maybe they made that mistake because it's a reasonable mistake to make but it's actually not true. I think that in our evolutionary history, people reproduced at the age of about 14. Although at the age of 28, I started getting an infection from an impacted wisdom tooth and had to have it removed, that was probably already nearly grandparent age according to our evolutionary history and that explains why the natural selection against that type of problem at that age was weak. Maybe after we started eating soft food, we had an evolutionary advantage in having a smaller jaw but the evoluionary cost in having a smaller jaw was smaller because we could just evolve to slow down the growth of the wisdom teeth to delay the potential problems it causes to grandparent age. Just because a change in diet affected the way we evolved doesn't mean a person's actions affects the way their own body grows at the individual level. I do realize that it some cases, ones own actions affects the way their body grows.

You may be thinking "Why didn't you ask the question 'Why did we evolve to have impacted wisdom teeth when it sometimes causes a severe infection?' before asking this one? You could have used its answer to help you ask this one better." I could do that but then I would just end up explaining that I Google searched "why did we evolve to have crowded wisdom teeth if it can lead to infection" and then got the article Bad molars? The origins of wisdom teeth as the first search result. That's the very article I linked earlier in this question that I explained why I suspect is inaccurate. I don't think it would have been better to ask that question first and then explain how the first search result didn't answer my question when that search result is in fact inaccurate. If the question I have can be answered, some way of asking a sequence of questions and picking which Stack Exchange website to ask each of them on that will get me an answer to the question I have has to be accepted.


texts: How many allele for one gene are found inside our cell?

texts:
I know it depends on phase. So i am talking of -

1) in human (diploid organism) with cells before prophase (before replication, when 23 pair of homologous chromosomes are present ). I think answer is 2 if we not consider male XY sex chromosome because they are not homologous in which case the answer should be 1. But then i get confuse why genotype is shown like Tt (doesnt this means two alleles per chromosome).

2) in gamete cell. I think the answer should be 1.

Please tell if i'm correct.


texts: How diverse are dogs in their traits other than appearance?

texts:
I've asked this question about dogs not so long ago, and the short answer was - dogs are the most diverse looking species of mammals because they got a small number of genes that have a big impact on appearance.

I would like to ask a follow up question- differences in appearance are easy to notice, and I would like to learn about other traits that might be genetically based.

Are there other major differences between dog breeds, like longevity, cognitive performance, friendliness, etc? Or are all dogs more or less the same in traits other than appearance?

Are there plots of traits like these among different dog breeds that identify outliers?


texts: How is bad garlic breath eliminated by swalllowing a bit of raw garlic?

texts:
Please bear with me, as I am just a poor physicist.

I have learned how to make traditional pastourma  from a recipe given by my late aunt Dora, which is like pastrami except with a very strong garlic contribution and a lot of other spices. This leads, after eating, to strong garlic breath. My daughter complained of the "stink" when she was near me.

I somewhere heard that if one swallows a bit of raw garlic before eating food with strong garlic content, the breath stays fresh. I have tried it several times, and it works (my daughter the detector). It seems magical, or homoeopathic!

As a physicist, I would like to know how is this possible?


texts:
I read on http://www.spine-health.com/glossary/muscle-tension:

  Muscle tension refers to the condition in which muscles of the body remain semi-contracted for an extended period.

What is the difference between a "semi-contracted" muscle and a "contracted" muscle?


texts: What phosphorylates tau protein & and what causes tau to be phosphorylated?

texts:
I want to know what phosphorylates tau protein and its 6 isoforms.
I know kinases cause phosphorylation events, and in tau it can be phosphorylated in a healthy neuron in the trans conformation, but when it is hyperphosphorylated it becomes the cis conformation of tau.

Do the same or different kinases cause the normal phosphorylation / abnormal hyperphosphorylation of tau? Is it completed by a single kinase or multiple kinases?

----Edit---

So I've done a lot of reading of many different papers and have uncovered that there two types of broad spectrum kinases classified as:
Proline-directed kinases, such as CDK5 and GSK-3beta
Non-proline directed kinases

Source: https://www.hindawi.com/journals/omcl/2015/151979/

But I read in this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601591/

that Cdc2 can also phosphorylate tau

My new question is a follow up to my existing previous question, I guess why is tau phosphorylated at all? What causes tau to be phosphorylated at in the first place?
Thanks.


texts: What physical traits are derived from the Neanderthal DNA in human DNA?

texts:
Some researches had found that Human DNA has a bit of Neanderthal DNA. So they suggested there would have been crossing between Homo sapiens and Neanderthals.

Now the Neanderthal looked a bit different from Homo sapiens, so is there something in human that has some neanderthal looks?

And is it only found in European people or also in Asian or African people. Could it be be possible that a larger hairiness of European man is due to Neanderthal DNA?


texts: Last night I came across this spider outside my house (costal Southern California). It was bigger than any I'd seen before, about 2.5 or maybe 3 inch legspan, maybe just under an inch for the body length. It is a brown-gray color, the cephalothorax has two dark brown stripes, and some mean looking fangs. Can anyone identify it?


texts: Why spider's web don't burn when electricity touches it?

texts:
I saw and spider on it's web at an electrical cable and thinked: If the web is made of proteins, why dont burn.

Sorry, the photo is dark because is night in Ecuador


texts: What bird is this (found at Alice Springs Desert Park in Australia)?

texts:
I was reviewing photographs of the animals we found on our trip to Australia during the past September and I cannot find what is the bird in the picture. It was found inside Alice Springs Desert Park, so it has to be a native bird, same as all the others.

Could anyone please help me?


texts: How does strength of a pulse related to EKG(ECG)?

texts:
There are variabilities in the heart rate as well as strength of heartbeats. I want to know if one can predict which heartbeat will be strong or weak based on the corresponding EKG/ECG signal. I am interested in the displacement of brain due to the heartbeat, which probably correlates with the peak pressure, and total volume caused by the beat.

If there is such a correlation, which part of EKG would be related? The interval between P and R? The amplitude of QRS?

Human or primate information is preferred.

image from wikipedia


texts:
I'm using Cytoscape to visualise a ppi network having 2000 proteins ... I m trying to export it but the supported format are only cytoscype formats not a usable ones
and for the table format the network is separatted , I don't find it explorable .

How to I export that network in format convertable to csv . or csv so that I can use it in a tool supporting only csv  file format format


texts: I know that human body contains FA some of which are essential and the other is not depending on the ability of the body to synthesize them in a sufficient amount, but I need a reference of the lipids types that are found at animals, plants, insects, microorganisms,....etc but not in the human body.


texts: What does 'virus prototype strain' mean?

texts: Does the term 'prototype virus strain' mean the first virus isolated and without mutations?


texts: I just do not understand how myelination speeds up action potentials

texts:
first off, I've watched like 7 youtube videos, read a bunch of articles, and the explanations for why myelination actually increases action potential propagation differ each time are very vague. I've read and heard that because action potentials only occur on the nodes of Ranvier, that it simply takes less time for them to travel down an axon. I get that, but I was under the impression that increased +ve charge = further generation of action potentials. if that is the case, wouldn't that mean that myelination should slow it down as there is less +ve charge influx? I understand that it takes time for action potentials to be generated, but is the variable affecting the rate at which they occur not the influx of +ve charge, and wouldn't this positive charge be less if there are fewer action potentials generated? it's not like myelination decreases the time taken for particular na+ channels to open, right? ftr, I'm not doubting that myelination speeds up action potential propagation, I just don't get it and the explanations are contradictory (nothing that I've mentioned here is contradictory to my knowledge FYI, I just mean that I have heard other contradictory explanations). I understand that it insulates the neuron, thus preventing k+ leakage. Does the insulation possibly increase the rate of propagation by decreasing the ability of extracellular ions from interacting with intracellular neurons? I would understand that I suppose since then there wouldn't be positively charged particles on the exterior exerting electric force upon the intracellular +vely charged particles, thus making it easier for +ve charge to spread throughout the negatively charged axon. even if there is any truth in that, could that possibly compensate for the decrease in intracellular sodium that the decreased amount of na+ influx channels would imply?
thanks to anyone who responds! a long one for sure, lol.


texts:
This is a follow up to this previous question:

In biosynthesis of cysteine and methionine, where does the sulfur come from?

Can animals use gaesous H2S in the atmosphere, say for instance from a sulfur rich hot springs, to aquire sulfur?


texts: Can bioluminescence be used for cancer or tumor detection?

texts: What diagnostic applications, if any, are there in using bioluminescence to detect cancer or tumors (in vivo)?


texts: Are there functional examples of parallel DNA double helices?

texts:
The anti-parallel structure of the DNA double helix is well studied, but I am curious if there are any examples of parallel DNA double helices. There are reports of synthetic such structures; see this paper, for example. However, my question is: are there functional examples of parallel DNA double helices? Here are some implicit/additional/guiding criteria:

It should be double stranded. This excludes structures such as G-quadraplexes, which do have some parallel strands.
It does not have to be an extended helix. I don't have any specific length restrictions, but don't assume it needs to be hundreds or even tens of base pairs long.
The structure need not be solely composed of DNA. If a parallel helix is induced by, say, protein or small molecule binding, so be it.
By "functional examples", I mean that the parallel structure should have some effect on cellular processes. The structure can be studied in vitro, even using synthetic constructs, but it should have some functional significance in vivo (or, at least a proposed significance).

Note that although I only mention DNA above, papers discussing parallel RNA double helices in the same spirit would also be welcome.

Related question: why is DNA antiparallel? Can it be parallel?


texts: Understanding presynaptic and postsynaptic inhibition

texts:
One way to classify neural inhibition is based on the inhibition being "presynaptic" or "postsynaptic".

As far as I understand, the two different types of inhibition refer to the following:

Presynaptic inhibition: A neuron N1 is inhibited "indirectly" insofar as the presynaptic excitatory neuron's action on it are dampened. This is typically achieved by neurotransmitter's impact on the presynaptic excitatory neuron which inhibit Ca2+ channels, and consequently prohibit vesicle release of neurotransmitter's into the synaptic cleft - hence the excitatory impact on neuron N1 is reduced.
Postsynaptic inhibition: A neurotransmitter acts directly on  neuron N1's receptors, leading to hyperpolarization of the membrane potential and hence a reduced probability of firing.

My questions:

(1) When we speak of "inhibitory post-synaptic potentials" (IPSPs), is this hence
always in the context of post-synaptic inhibition?

(2) I often read of "interneurons" (and it seems that this concept is used typically to refer to inhibitory neurons). Is inhibition by interneurons also always post-synaptic?


texts:
Scientists have found mammoth blood, and are planning to clone a mammoth.

How does one go from having its blood to a full blown living mammoth? Is it possible?

Why does it matter if the blood is frozen or not? Suppose one found dinosaur blood, could one clone a dinsosaur (as in say 'Jurassic Park')?


texts: What are the naming conventions for mutations of proteins?

texts:
I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50.

Please can someone explain the naming convention for this? i.e. what does the 'E' stand for? Does the number refer to the amino acid that has changed?


texts: The plant was photographed in spring in Morocco. It's an angiosperm. It is about 2 metres high and has feathered fruits. What species is it?