texts: Using Jpred to predict secondary structure

texts: I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i use when using Swiss mod. How do i interpret these hits, do I just ignore them and force jpred to predict structure anyway?


texts: What makes a strong polyadenylation signal a strong signal?

texts: I was wondering why is it that "AAUAAA" is a strong Polyadenylation signal whereas the rest of the polyadenylation signals show reduced cleavage and polyadenylation efficiency?


texts: Why are there N's after Sanger sequencing?

texts: After sending a DNA sample for sequencing, the resulting sequence had N's in the beginning and end of the sequence.  I know the N's mean that the computer can't tell what the base pair is, but why is this?


texts: Could a prolonged amount of Antibiotics severely affect the digestion Gut Microbiota?

texts: Could taking antibiotics for a prolonged amount of time severely harm or even worse kill off a large proportion of Gut Microbiota responsible entirely for  digestion, Resulting in lifelong digestion problems similar to Crohn's Disease?


texts: Nerve/muscle fibre depolarizaitonand repolarization balance

texts: if continously sodium is pumped in during depolarization and pottasium is pumped out during repolarization, eventually there will more sodium and less sodium inside. How the does the fibre/cell return to the balance?


texts: Can simple bacterial culture be done at home using food agar as the medium (with some additives found in the store)?


texts: What causes the pain when a bone fracture is healing?

texts: Why does a fracture still hurts when it is healing? I understand the pain at the beginning - the bone is not in its place, there is a pressure against the nerves, also the swelling pushes the nerves etc. But why does it still hurt after several weeks, when the swelling is gone, the bone is more or less fixed? Is the cause of the pain mechanical, or chemical?


texts: Cellular respiration — How is the water expelled?

texts:
The equation of cellular respiration is as follows:
6 O2 (g)  +  C6H12O6 (aq)  $\rightarrow$ 6 CO2 (aq)  +  6 H2O (aq)  +  ATP

How is the water produced expelled from the body (of course, after some of it is used)? Is it expelled in urine? Or is the water vapour we breath out actually the by-product of respiration? Or, is it expelled in both methods/ways?


texts:
I’m looking for internationally applauded  textbooks on fundamental biology. Books that are a must for a pre-medicine student/high school advanced. Currently, I study Biology by Neil Campbell, Jane Reece(and team) and I really like it. What I’m looking for is 21st century pedagogy and a modern writing style(as opposed to a stiff, unfriendly writing style that reads like a fact presentation pamphlet); books so good you don’t need an amazing teacher(which I definitely do not have.) Thanks.
P.S.- If you have come across amazing books in branches of biology like say biochemistry or neuroscience or immunology, even those suggestions are welcome.
P.P.S- My question is distinct from the “Books for beginners” question asked by user31782 because: 1.cost is no bar 2.I am not a beginner in biology, I’m studying pre medicine; and 3.All the resources suggested in the answers, I already know about them/have used them.


texts: The detail about the exact time of heart attack

texts: Storage of cholesterol in coronary artery tends to heart attack. But in which phase heart attack occurs? Why only a definite time is called heart attack? Why this is the extreme point of coronary block?


texts: What is the purpose of Y-shaped adapters in Illumina sequencing?

texts:
Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library.

The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary.

What are the advantages of this?

My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that:

-Upon primer annealing, the primer in turn would bind to the start AND end of the DNA fragment, and thus not allow synthesis to continue to until the end. Therefore, the next primer would not have a template to bind at the start of the fragment...

Y-shaped adapters also allow for paired-end sequencing. Fragments have a unique sequence on either end, which allows for the first "run" to sequence one side of all molecules, then synthesize the reverse and sequence that.

Am I on the right track?


texts: Which was the last significant event in human evolution? What's next?

texts:
At 10.000 BC (12 ka), we became the last of the Homo species on Earth. In evolutionary terms this is a very little time range to something happen, but I'm wondering anyway, in this meantime which are the most significant changes in our species? Were there any?

Also, I've heard something about how our body hair and nails will be gone 'soon', there's any estimation of when such a thing could happen?!


texts: What would be a good plant to show the process of evolution to a small kid? Obviously it's a long term experiment, and preferably a fruit or a veg that is edible (like tomato?), and what characteristic would be (size, colour) good to select for?


texts: How does the original ionic distribution restore after synaptic transmission

texts: During synaptic transmission the calcium ions around the presynaptic membrane diffuse in due to the influx of Na+ ions and the resulting depolarization. This happens because the calcium channels are voltage regulated ones. At the same time on the other side of the membrane there is efflux of K+ ions in order to repolarize the membrane. My question is how does the original ionic distribution restore which is more K+ on the inside and more Ca2+ on the outside? What kind of pump does this job and what is the exact mechanism? As contrast to the nerve membrane where the Na+/K+ pump does this. I don't find a pump like K+/Ca2+ pump to do this.


texts:
It is widely know that each cell cycle during DNA replication some fraction of the telomeres is lost, and this phenomenon is called the end replication problem. Well this is due to the fact that the DNA polymerase only adds nucleotides in 5´--> 3´ direction, thus the synthesis of one of the two DNA strands will need some RNA primers for its polymerization (and DNA polymerase will replicate DNA in a "jumping" pattern). Then, in the very end of the synthesis of this strand (called lagging strand) one last fraction will not be copied from the template as even if the last primer is set in the very end of the chromosome, once this RNA is degraded a void space is going o remain invisible for DNA polymerase.

Well this is all well known, but my question is whether during each DNA replication it is ONLY the telomere of the chromatid whose origin was in the lagging strand  which will be shortened? (Thus chromosome shortening is happening in a truly asymmetrical and stochastic pattern)


texts: Is there a statistical analysis test I can perform that will give me a estimate of total population from my own smaller data sets?

texts: Doing my dissertation on the long term trends in moth populations. I am looking at the trends of specific species. Is there a method to obtain an estimate of total population from smaller samples?


texts: can anyone help me identify this ant queen, if it's an ant queen? I only assume it is because I caught another with wings which looks exactly the same. Thanks in advance..


texts: Why does something taste less sweet after eating something else that is sweet?

texts: Why does something taste less sweet after eating something else that is sweet, especially if you don't drink water in-between.


texts: Blood circulation - How to expand blood capillaries?

texts: Do blood capillaries expand? If yes, through what means can it be done? And can warm water also be used to expand blood capillaries?


texts: Is Protein-to-DNA ratio a good estimate of cell size?

texts:
I need help interpreting the result of an experiment. My class performed an experiment measuring protein concentration between heart, liver, and kidney tissue samples. The results were:

Heart: 4.714 mg/ml
Liver: 10.586 mg/ml
Kidney: 9.140 mg/ml

The DNA concentration was given to us and they were:

Heart: 8.6 ug/ml
Liver: 57.6 ug/ml
Kidney: 28 ug/ml

Computing the Protein:DNA ratio:

Heart: 0.548
Liver: 0.184
Kidney: 0.326

Doesn't this mean that the protein-to-DNA ratio has an inverse relationship with cell size as the results show that the liver tissue has the highest protein concentration and DNA concentration, yet has the lowest protein:DNA ratio. Also, why does DNA concentration differ so significantly between each tissue sample? My understanding is that genome remains the same between different cell types. So why does DNA size change?


texts: The wood wide web strengthening/expanding the heartwood of damaged pines

texts:
My grandfather told me about a practice: girdling/ring-barking (not sure which was employed) of pine trees in order to make the wood stronger. Now, he didn't give too many details, so I had to do some research. He said the resultant, strengthened wood is called adel, adl or al, which is Norwegian.
When I searched for it, I found that these terms mean the same as heartwood, but in the context of pines. I believe that this process he explained in essence just strengthen and/or expands the heartwood of the pine. Such pine wood, that contains higher amounts of heartwood, is called ore-pine, and this Wikipedia article states that this was achieved through the removal of branches, as opposed to girdling/ring-barking, which is what my grandfather said.
Now, whether the mechanism of expansion/strengthening of the heartwood is via branching or girdling/ring-barking is one question. However, the question I am most interested in, is the mechanism of how this process happens. I know it has something to do with the increase of resinous substances in the wood, but what I'm wondering about is if this strengthening is happening via the "wood wide web". When my grandfather started talking about this, I said that it probably happened via the wood wide web. The damaged tree sends out information of its damaged state, and the other trees in its vicinity divert more resources to it, leading to the strengthening and/or expansion of its heartwood. My grandfather however, said this process did not involve the wood wide web, and that this process happened completely locally at the tree.
Which is correct (if either)?


texts: I'm looking for data - maybe CHP^2 data that shows chromatin binding to a prokaryotic genome under some specific conditions.  Can anyone point me to a source?


texts:
I found the words "stretch of amino acids" in a newspaper article.

"This lipopeptide matches the stretch of amino acids in the spike protein of SARS-CoV-2 exactly."

What is the "stretch of amino acids"? Is this different from "amino acid sequence"?
I looked for a definition of the word but could not find it.
From the usage, I guess it means something similar to "sequence", am I right?


texts: Why are most of deleterious mutations recessive in nature? I understood that if it's recessive then one reason may be that the mutant gene doesn't code for a functional protein and so there is no  phenotype to express.  But why is it recessive in the first place?


texts:
What insect is this on these photos?
Found in Russia in the living room.


texts: Looking for a dichotomous key to identify primates

texts:
I'm looking for a dichotomous key to identify primates by physical and possibly geographical traits.  Any format is fine (print, web, mobile app, etc.).

Other than classroom activities and genetic classification references the best I have found is on WikiBooks: https://en.wikibooks.org/wiki/Dichotomous_Key/Primates


texts: Nucleotide frequencies in Kimura's two-parameter model

texts:
Here's an excerpt about Kimura's two-parameter model from Felsenstein's Inferring Phylogenies:

  "The model is symmetrical, and one can immediately see that, after
  enough time has elapsed, it will be equally likely for the base to be
  a purine or a pyrimidine."

I think I understand the assumptions of the model but it's not obvious to me why the equilibrium frequencies are equal. Why is that so?


texts: Metazoan branching: Placozoa or Porifera?

texts:
Of Placozoa and Porifera, which branched off first? (Conversely: which are closer cousins to us?)

I've heard both suggested as our most distant cousins with bodies, so was wondering which ordering is currently considered most likely. Of suggestions that Placozoa branched off later, I've heard some saying that the branching was even post-Cnidaria/Ctenophora. This seems very unlikely: is it?


texts: What is the proper way to dispose of a medicinal substance?

texts: Is there a protocol or a set of guidelines to safely dispose off a batch of expired drugs (as a manufacturer)? I guess the process may vary for different drugs. My specific question regarding the safe disposal of expired amlodipine; which is better — incineration or landfill or any other technique?


texts: Why is the neuraminidase used as a target for drugs against influenza virus instead of haemagglutinin? Is there some basic reason that this will make a more effective drug?


texts:
I'm equipping a lab room (~3x5 meters) that's supposed to be used for DNA and RNA extractions. I know  about the basic safety precautions when working with RNA and DNA extraction (fresh gloves, labcoat, separate workstations/pipettes, RNase-free workspace etc), but it is my first time seting up this sort of things
so I'm a bit unsure how strict I have to be about some of these things, so my question might seem a bit silly/stupid to some but here it goes anyways.

The question; I want to buy UV-lamps to clean out old DNA in the environment so I don't contaminate my fresh samples. I don't work in any hoods. I have a downdraft ventilation table and a bench that both stands along one wall on which I'll be Working on. I wonder if it is enough to just have one UV-lamp that covers my working area, or should I buy enough UV-lamps that cover the entire room (since I'm not working in any hood -> risk for airborne contamination)? Or is it over-kill to cover the entire room? I don't want to spend to much money.


texts:
You don't need to explain to me what the theory of evolution is, or how it works. This question is purely about what exact meaning the word "natural selection" is ascribed to.

There seem to be multiple meanings that are given to the term "natural selection":

The process by which, in a single generation of species, the most fit individuals tend to survive. The "things that are being selected", are the individual organisms, and the "moment that selection took place", is the moment that these individuals reproduced or failed to reproduce, or alternatively, the moment that they died or survived.
The process by which, over many generations, the genotypes that result in highest fitness tend to to be selected for. The "things that are being selected" are the genes, and the "moment that selection took place" is not a single instance in time or a single generation, but a long time-span. In fact, I sometimes hear the idea that natural selection is already selecting for genes even if those particular genes don't exist in any organism. For example, if natural selection is selecting for "height", and there is a gene X that would increase height, then it is said that X is being selected for even if X does not yet exist.

Are both of these interpretations generally accepted?


texts: Can a carnivorous animal consume plants with no adverse effects?

texts:
While I know that in nature, carnivorous animals are poorly suited to eat plants (largely due to having sharp teeth, not grinding teeth, as far as I know), I was wondering if, in an emergency situation such as imminent starvation, could a carnivorous animal such as a wolf survive solely on plant life, maybe requiring it to be ground up before hand? Could an herbivore survive on meat, if the meat was prepared in a manner that would allow the herbivore to eat it? Would a wild animal voluntarily consume food that it is not suited for if it would stave off certain death, or would it require force feeding or training?

Also, I am interested in the other side of this question: if an animal cannot safely consume food outside of its normal diet (carnivore eating plants, herbivores consuming meat), what negative effects would this action have on the animal?

Just a note, this is purely a hypothetical question, and I am only asking out of curiosity. I am in no way planning on doing this, nor do I advise anyone else doing this if there is a high chance of it harming the animal.


texts:
In Cholinergic Urticaria, some people believe that the itching which is generally more in winters might be because that the diameter of sweat pores is less due to less activity(less sweat production) and in summers the diameter is usually more due to high activity (more sweat production).

Question: Hence the question in general, Do sweat pores change diameter?


texts:
I am reading about Inspiratory Reserve Volume and Expiratory Reserve Volume in my textbook. So my general question is aren't the two terms show the same amount of air ?
I would like to tell you why I think so. Like IRV tells us about the maximum amount of air we can intake other than normal intake. So this extra amount is what going inside our lungs and I think this is the part which comes out in the form of ERV .
So shouldn't the total capacity of lungs be equal to (Tidal volume + IRV + Reserved Volume) only ? Why do we need to include the term ERV in the above equation ?


texts: What is the least costly method to generate sequential amino acid deletions?

texts:
I'm looking to generation sequential deletions from a gene of interest. The total size of this region is 8 amino acids. I'm trying to determine which portion of this region is necessary within the gene.

For example, if this is my sequence:

ABCDEFGH

I want to generate:

BCDEFGH, CDEFGH, DEFGH, and so on.

What is the least expensive way to do this (by minimizing primer use, enzyme use, etc). I already have this gene sub-cloned into an expression vector.

Thanks!


texts: How do tumor cells 'gravitate' towards each other?

texts:
In a popular article it is mentioned that in centrifugal experiments with cancer cells that

  When subjected to microgravity-conditions, the cancer cells were unable to sense each other and therefore had a very hard time coming together.

which is because

  [...] the process through which cancer grows and spreads would seem to indicate that there is a means through which the cells are able to sense each other and gravitate together to form a tumor.

I would now be interested in the role of such fundamental forces in cell-signaling.

How does gravity interact with cell-signaling and lead to the 'gravitation' of tumor cells towards one another?

To my knowledge, cell signaling is a bunch of processes that involve the propagation of electrical signals by chemical means, so I am rather surprised that gravity would play any role in this.


texts:
Naïve question - feel free to shoot it down.

To the best of my knowledge an infant doesn't really 'shrink' from something without first trying it. Even the action of looking at the fierce expression is undertaken without qualm - squalling comes later (if at all!)

Are human infants inherently frightened by anything?


texts: What would be a reason for a tree to have flowers of different colors?

texts:
The spring is here and the cherry trees along my street are blooming again!  Some trees have white flowers, some dark pink. But then... there're these trees which are all white yet just a few flowers are pink, just like that:

Is there a layman explanation for this phenomenon?


texts: Is there an evolutionary advantage for coconut oils to be rich in saturated fats?

texts: I know that coconut oil is composed of multiple saturated fatty acids, but is there a reason why this would have increased the fitness of the coconut plant?


texts:
What do we mean when we say that: Haemophilus influenza genome is 85% genic.
How do we measure gene density in percentage, especially for the above-mentioned case?


texts: difference between neurotransmitters and hormones

texts: I have been reading a lot about neurotransmitters and hormones but what's the difference between them both or are they the same? It's been confusing for a while now. Also, why do some neurotransmitters act as hormones?


texts: Everybody seems to agree that endocytosis is an energy-using process, and as such requires ATP hydrolysis. However, which particular step requires it? More precisely, which 'molecular machine' involved in endocytosis requires ATP? I cannot seem to find a good answer in the literature.


texts: Is the resting state of the forearm in the pronated or supinated position?

texts: It seems to me that my forearm is naturally in a more pronated position than the anatomic (supinated) position and that it actually takes work to make it hold the supinated position. Anyone an expert in human anatomy/physiology here or know of any sources that could point towards a more scientific answer?


texts: What can the timing of human urination tell about the human's physical condition and circadian rhythms?

texts:
I've noticed a peculiar phenomenon. A subject drinks 400 ml of water, then observes time until the urge to urinate is felt. The time is 15 minutes. The subject releases water. 14 minutes later another urge to urinate is felt. The subject releases water again.

I'm particularly interested in what kinds of biological systems are involved in timing of such events.
Does the time depend on how full the subject's stomach is? Does caffeine and other diuretics play a part?
Is it time of day (circadian rhythm) sensitive?
Does that predict anything about the suppression/release of diuretic hormones?

What I'm trying to understand is if the timing between human urges to urinate after water consumption can be used to make predictions about the human biological clock and the state of various systems within the body (for example the digestive system).

I will be conducting this experiment at different times of the day. My hypothesis is that at night, when diuretic hormones are suppressed, the timing would be longer for the same amount of water consumed. This is based on my limited research in the area.
Update: I did perform the same experiment at night, the time was 75 minutes for the same amount of water. The experiment was performed at the end of one of sleep cycles, which makes me think that 75 minutes was the duration of the subsequent sleep cycle.

I appreciate your input on the subject, along with any keywords that can help me advance my research in this area.
Thank you!


texts:
I was just trying to understand how in insects, specifically mosquitoes does the process of emergency responding, stress regulation take place? Or in simpler words how are flight, fright and fight situations handled?

I understand that insects have a ganglion system and they do, suitably, respond to external stimuli, but I would like to know if there is any chemical coordination that works specifically in emergency situations just as adrenalin and nor-adrenalin do in our case.


texts: Identification of red, plum-like fruit (probably from Southern Russia)

texts:
My parents are currently on a holiday in St. Petersburg (Russia). They sent me this photo of plum-like fruits they bought on a market there (toilet paper for scale, I guess).

The fruits are 20-30mm long, have a big stone, taste sourly like red currant (based on my fathers opinion) and are supposed to come from Southern Russia (don't know where this information is coming from).

Can you please help to identify them?


texts: What are some examples of non-homologous sequences having similar functions?

texts: I am trying to find some proteins that are non-homologous but functionally similar. However, I cannot seem to find concrete examples. Can someone please point out any resources or provide examples?


texts: Specialist evaluation for people aged under 40 years with stage 1 hypertension

texts:
Reading the NICE clinical guideline for Hypertension it says...

For people aged under 40 years with stage 1 hypertension and no evidence of target organ damage, cardiovascular disease, renal disease or diabetes, consider seeking specialist evaluation of secondary causes of hypertension and a more detailed assessment of potential target organ damage.

However it is not clear in the guidelines exactly what "specialist evaluation of secondary causes of hypertension and a more detailed assessment of potential target organ damage" would entail.
I understand that it is typical to carry out blood tests to look at kidney function, thyroid function, cholesterol and glucose levels; and that further tests such as a 12-lead ECG, echocardiography and renal ultrasound scan may be ordered if necessary to test for organ damage.
My question is what further tests would be performed by a specialist on a patient aged under 40 years with stage 1 hypertension and no evidence of target organ damage, cardiovascular disease, renal disease or diabetes? I have done several searches on Google but most of the papers I've read relate to patients who already have signs of organ damage or existing disease.


texts: Do animals have social status as humans in our society?

texts: As our society and it's functioning is closely related to the ones of animals, one question arises: Do animals in nature have social status as humans? People often display it publicly, by buying nice cars, searching for women and partners and so on, accumulating wealth and so on. Does similar things happens in nature? How our behavior is similar to animals?


texts: Suppose you want to stand on one leg. Doing it eyes open is not that difficult, but doing it eyes closed seems to be difficult. Why?


texts: Why does the slope of parent-offspring regression equals the heritability in the narrow sense?

texts:
Background

---- Notations and assumptions ----

let $W_{ij}$ be the fitness associated to the genotype $AiAj$. $x$ is the frequency of the allele $A1$ in the population. The frequency of the allele $A2$ is $1-x$ because we'll consider only the case of a bi-allelic locus. Also, we consider that only one locus influence the random variable $W$ (the fitness). We will assume that the environment does not influence the fitness. We also assume random mating in order to use hardy-Weinberg equilibrium.

---- calculations ----

The mean fitness is:

$$\bar W = x^2W_{11} + 2x(1-x)W_{12} + (1-x)^2W_{22}$$

The variance of fitness is:

$$\sigma^2 = x^2(W_{11}-\bar W)^2 + 2x(1-x)(W_{12}-\bar W)^2 + (1-x)^2(W_{22}-\bar W)^2$$

We then want to calculate the covariance between father and son with respect to fitness.

Suppose first that the father is $A_1A_1$ Then the son will be $A_1A_1$ if the mother transmits an $A_1$ gene to him, an event with probability x. Similarly the son will be $A_1A_2$ with probability $1-x$. The father himself will be $A_1A_1$ with probability $x^2$. Continuing this wa it is possible to draw up a table of the probabilities of the various father-son combinations in genotype and hence fitness.

Therefore, assuming no change in frequency of $A1$ between the two generations, the covariance father-son is:

$$cov = x^3W_{11}^2 + 2x^2(1-x)W_{11}W_{12} + x(1-x)W_{12}^2 + 2x(1-x)^2W_{12}W_{22} + (1-x)^3W_{22}^2-\bar W^2$$

which also equals

$$cov = x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2$$

The correlation between the two fitnesses is found by dividing the co-variance by the variance (since the variance of sons is the same as that for fathers):

$$cor = \frac{x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2}{\sigma ^2}$$

We then define dominance and additive variance:

$$\sigma_D^2 = x^2(1-x)^2(2*W_{12} - W_{11} - W_{22})^2$$

$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$

such as

$$\sigma_D^2 + \sigma_A^2  = \sigma$$

My question

The slope of a parent-offspring regression equals the heritability in the narrow sense $h^2_N$.

Heritability in the narrow sense is defined as $h_N^2 = \frac{\sigma_A^2}{\sigma}$ (see Why is a heritability coefficient not an index of how “genetic” something is?).

We defined above that the correlation between parents and offspring is $cor = \frac{cov}{\sigma}$. So I'd expect the slope of the parent-offsprings regression to equal $cor = \frac{cov}{\sigma}$ and not $h_N^2 = \frac{\sigma_A^2}{\sigma}$

What am I missing? Is there a mistake in my background calculations? Is there a mistake in the way I defined some concepts? The answer might be much simpler than it looks like!


texts: Assembly of polypeptides expressed from different chromosomes to make a fully functional protein

texts: In case of human beings, the whole genome is divided in 23 pairs of chromosomes in somatic cells. It has been observed that in case of many proteins (e.g. immunoglobulins, hemoglobin) different polypeptides are assembled together which are expressed from different chromosomes. My question is- what guides them to assemble them for the making of a fully functional protein??


texts: Since nature highly favors the pyranose forme of Ribose, what explains the fact we find it in the form of furanose in DNA and RNA?

texts:
I read in my notes that relative abundance of ribopyranose represents about 80% of all ribose in solution (including the alpha and beta anomeres).

I'm curious as to why evolution favored the use of the least abundant conformation for DNA and RNA.

Do we have enzymes that convert pyranose to furanose in order to achieve this? or are we just using the furanose?

Thank you,

Pierre-Eric


texts: Population Dynamics problem concerning Allee Effect

texts:
I am reading Nonlinear Dynamics and Chaos with Applications to Physics, Biology, Chemistry, and Engineering, 2nd Ed. (Strogatz 2015).  I came across a problem involving the Allee Effect which I have not been able to solve.
Problem:

I tried comparing terms with the Allee effect as stated on Wikipedia,  but it is still not clear to me how to solve this.  Can someone please help?

Since my last post, I have tried plotting several values for the parameters, and I solved for the zeros of this equation.  My guess, is that I am supposed to qualitatively analyze this plot and see that it is maximized for intermediate values of N.  I am including a picture from Mathematica of my work.  Please let me know if I am on the wrong track.


texts:
What is the fate of first and second polar bodies formed during the menstrual cycle in human females?

Do they degenerate?

Does any other mammal also produce polar bodies?


texts:
Found it on the floor of my basement laundry room in a mostly wooden house in the woods in Westchester County, NY. However I had done a mountain hike (same general area) and I may have brought it from there on my pants or something, but I'm not sure.

When it noticed me it stopped moving, but it was still alive because when I put it in this cup for a pic I accidentally flipped it upside down and it started squirming to get itself upright.


texts: Why warfarin is given as racemic mixture?

texts:
Warfarin is administered as a racemic mixture of S- and R- warfarin.
S- warfarin is 3 to 5 times more potent than R- warfarin.

So, what's the logic behind giving a mixture of it? Isn't administration of only one form gives more predictable results?


texts: What are these little leaves growing on these other leaves? (plant growing near the ocean)

texts:
I saw many of these plants while hiking on a hill facing the ocean in northern Taiwan. I've included a snapshot of a nearby part of the same trail to show it's rugged, wet, green, and rocky, and another photo of some what looks to be the same kind of plant without these things, and one that has a reddish coloring.

Any idea what these little (~10 mm long) "leaf-shaped" brown/orangish things are, growing from points along two regular rows of bumps that are repeated everywhere? Is this reproduction, if so how does it work?

Also curious, any thoughts on what kind of plant to call this? I don't need a species identification necessarily, but is it a kind of fern?

below: Additional photos, click for full size.


texts: What is the biological/evolutionary advantage to baldness?

texts:
Male pattern baldness is a common genetic trait. With a distinctive pattern/ density gradent (as apposed to general old age thinning as the body ages)

Hair has an advantage of protection from the sun/weather. So to lose it in a distinctive pattern (and lose that advantage) appears to have a reason*; and as it is a genetic trait, it seems like it would have been something that was selected for (or it would be more likely to be selected out).
So why is it better to develop pattern baldness as someone gets older?

So what might be the biological/evolutionary advantage to developing baldness?

Traits get selected for good and bad reasons(in retrospect), however I am interested in the reason why this particular trait has been selected.

* Lets assume that there is a specific cause (causes) and it is not just a leftover evolutionary artifact.

The related question: Why do some bad traits evolve, and good ones don't? provides some interesting background, but doesn't specifically address the What causes in this question.


texts: Why is Botulinum toxin the most potent poison known?

texts: Botulinum toxin (trade name Botox) inhibits acetylcholine release in neurons and causes botulism, an acute paralytic disease which leads to nerve degeneration and takes a long time to recover. I've read the statement that Botox is the most potent poison we know a few times now and was wondering why exactly it is. All sources I've found only claim that it is, without explanation.


texts: What is the difference between the neural tube and the dorsal ventral cord?

texts:
I was wondering what the difference is between the neural tube and the dorsal ventral cord.
I know that the neural tube forms during embryonic development from the ectoderm layer that folds inwards.
I thought that the neural tube gave rise to the central nervous system, however sometimes I see the following:

  "the central nervous system develops from the hollow dorsal nerve
  cord"
   for example: https://en.wikipedia.org/wiki/Dorsal_nerve_cord

question
What is the difference between the neural tube and the dorsal ventral cord or are they both the same?
(talking about humans)


texts: What is it that creates that wonderful smell after a fresh rain?

texts:
I've heard that the wonderful smell of a fresh rain is actually chemicals  released from the trees and grass and other plants.

What is the process that allows these chemicals to be released?
What are the chemicals that create that smell?
How is it advantageous for the plant to release the chemicals rather than hold onto them?


texts:
Due to the advent of social networking and dating sites, it is now possible for almost anyone to find a potential mate. Therefore, there is not as much of a pressure based on physical characteristics or even intelligence anymore. Society does not present the same pressures as was historically present in nature to find food and avoid being killed by predators and potential mating rivals. Almost all alleles regardless of their characteristics are passed on to the next generation through someone or another and attractive traits are no longer chosen above deficient ones. The only exception often being conditions such as dwarfism, Down Syndrome or Parkinson's Disease where the recipients of disadvantageous alleles choose to remove themselves from the gene pool.

Therefore, does this mean that human evolution has been halted due to an absence of natural selection?

My question differs from "Has human medicine stopped humans evolving?" because my post focuses on societal and cultural changes as opposed to medical changes.


texts: What is this plant in the Butler, Pennsylvania area?

texts: This is growing in the woods near my house in the Butler, Pennsylvania (USA) area. I have not seen it around before, and I have no idea what is it. What is it? Is it poisonous to pets (or little kids)?


texts: Difference between Fulminant and Acute Meningococcemias

texts:
Fulminant seems to mead rapid.
There is however some articles with both phrases: "fulminant meningococcecemia" (about 5000 Google matches) and "acute meningococcecemia" (about 3000 Google matches).

I am thinking Neisseria meningitidis and its pathogenesis

  Portal entry nasopharynx (pili)-> attach epithelium cells -> bloodstream (bacteremia); upper respiratory tract infection -symptoms; may be asymptomatic in transient flora; fulminant meningocococcemia (regardless of meningitis)

What is the difference between the two diseases?


texts:
How does fungi network transfer substances between plants?

I recently read a short article about fungi network. And I am wondering  about how fungi network works (Mechanism).

  Plants have fungi network. And a plant which lost it gets prone to insects.

Wikipedia link


texts: What if target DNA doesn’t have restriction sites

texts: All the examples on DNA cloning I have encountered have assumed that the target gene and vector both have compatible restriction sites at just the right locations (probably for ease of explanation). Instead suppose I have a vector that has restriction sites for multiple restriction enzymes, but my target DNA sequence doesn’t have a restriction site for any of them, how would I go about creating a recombinant DNA from these?


texts:
I'm investigating HIV-RT 3KLF and 1LWF trying to find a perfect pose of thymine. Which residues on HIV-RT is Thymine supposed to contact on 3KLF and 1LWF? Where exactly is the nucleotide binding domain on 3KLF and 1LWF?

Please provide a journal article as proof.


texts:
So 5'-AUG-3' is the start codon on an mRNA transcript

Does that mean that the tRNA anticodon is 5'-CAU-3'?

Here, I see that the tRNA anticodon for methionine is UAC, and the chart doesn't specify which end is 5' and which end is 3', but I'm guessing it's 3'-UAC-5'. I thought nucleotides are supposed to be written 5' to 3', and that's a norm, but apparently it isn't the case here? Am I missing something?


texts: What is this bizarre in-growth in this red bell pepper?

texts:
I just chanced upon a rather strange red bell pepper (or capsicum?):

The green formation is bulbous to touch, just the like the outside of the bellpepper, and it has the same smell as one. I'm no biology expert, but I have a feeling that's a tiny ingrown bellpepper in there. My mom thinks it's a strange genetic experiment and wants me to throw it away!

What is that strange growth, and what might have caused it? Is this safe to consume?


texts: What is the mechanism by which Melatonin increases dream vividness and intensity in humans?

texts:
I'm looking at the wikipedia article on Melatonin and noticed that it mentions vivid dreaming caused by melatonin. I have the "Melatonin and the Biological clock" pamphlet referenced in the article, and it does not go into too much detail of how vivid dreaming is happening.

I've personally experienced vivid dreaming side effects of melatonin today - dream after dream of profound intensity, but completely unrelated content. This makes me interested - how does melatonin influence the intensity of dreaming in humans? Is it by interaction with Serotonin? Or does it get metabolized into something psychoactive?


texts: Should I consider one or two DNA chains to find how many nucleotides are in a gene?

texts:
I am trying to solve an exercise.

How many nucleotides does a gene contain if information about 287 amino acids is encoded in it? What is the molecular mass and length of this gene?

AFAIK, I have to consider two DNA chains to find molecular mass, and one DNA chain to find the length of the gene (am I right here?).
But I am stuck trying to find how many nucleotides are there in a gene. Should I consider both or only one DNA chain? I suppose that both (as for the molecular mass of the gene) but I am not totally sure.


texts: I've a Begonia species. Somehow it started to grow new leaves on top and right in the center of an existing leaf which you can see in the center of the image. Why is it doing this? Apparently it is not a disease because the Begonia itself is growing fast. Will the new leaves eventually become a new Begonia which can survive on its own?


texts: Gene expression: which allele is considered?

texts: For human beings, we have two copies of each gene inherited from the parents. The question is, when referring to gene expression, which copy (or allele) is considered?


texts:
Why doesn't $k_\text{cat}$ change in uncompetitive inhibition, given the fact that uncompetitive inhibition lowers the enzyme–substrate complex efficiency (which is the reason for lowering of $V_\text{max}$ as well)?
Source of information: https://youtu.be/0ZiCqwtFMTs


texts: In cell division, are daughter cells "newer" than the parent cell?

texts:
I learned that cells go through cell division to generate new cells to replace dead or damaged cells.

Are the daughter cells "newer" than the parent cells? For example, the parent cell has an "age" of 9 days and the daughter cells will have an "age" of 2 days.  Because if they are not "newer" than the parent cells and all have an "age" of 9 days, they will all still die  together at the same time in the end.

For a real world example, skin cells only live a few weeks. But not all skin cells on our body die after a few weeks. So the only logical way I can think of to get around this is that daughter cells are "newer" or "younger" than parent cells. Or perhaps my notion about the "age" of cells is wrong.

And if the daughter cells are "newer", why is that possible?


texts: Neurons with thousands of connections: where are the extra connections coming from?

texts:
If every neuron has only one Axon but can can have thousands of (or let's say, even just ten) incoming Axon connections via its dendrites, where are the extra connections coming from?

It seems to me that since neurons dont act as initiators (that is, decide to initiate signals) but rather act more as repeaters (that is, sending incoming signals forward to the neuron that their axon is connect to), then for every neuron, there must be at least one neuron whose axon is connected to it, and at least one neuron that its axon connects to (because without those two things, the neuron does basically nothing, right?), but since each neuron can only have one axon, I'm confused about where all of these extra axons are coming from.

Based on that understanding: 1 billion neurons means exactly 1 billion axons and one billion required inputs (axon -> dendrite connections), eliminating the possibility of any one neuron having more than one dendrite connection, since there can only be one billion axons to connect to those dendrites (and each neuron would require at least one input to function, right?).

But regardless, I've been hearing people talk about neurons having thousands of connections. And based on my understood model, the brain would have to be just one long linear chain of neurons, which makes no sense at all.

So clearly I've got something wrong in my understanding of neural structure. What is it?


texts: Why does mint oil feel cold on the skin?

texts:
When putting (japanese) mintoil on the skin it produces a cool feeling.

You can experience this, when adding it to your bath or using a spray with mint oil on your skin. The cool feeling occures even if the actual temperature of the spray or bath is quite warm.

Where does this sensoric impression come from?


texts:
I would like to know the origin of the term Monilophyta. I know it's from Kenrick and Crane, but where did they get monilo-? It's not in my enormous Liddell and Scott Greek dictionary, nor is there any word starting with ilo- or hilo- that seems at all likely. Is it from the Latin word "monile" meaning necklace?

This is driving me crazy.


texts: Do foraging ants carry dead ants back to colony for disposal or leave them where they died?  I would think they would leave them behind just based on the energy expended that would be needed to transport them.  If they brought the dead back to the nest that might indicate 'feeling' or 'emotion' which everybody seems to say is impossible.


texts: When I go to NCBI & Select nucleotide option there and in search box write For Example CNGA3 gene the page shows that there are 553 items.I know the method of downloading or retrieving the One item's or record's FASTA format but "if I have to download the FASTA Format of all the 553 items simultaneously without opening each link then what options should I use..?" If you know it then please help me.. ?


texts: Different names in paired-end sequence files

texts: I am aligning paired end sequence reads using bwa mem and I get an error saying that paired reads have different names: "M01814:86:000000000-A6MU9:1:1101:15545:1335", "M01814:86:000000000-A6MU9:1:1101:16059:1338" So it looks like the locations for some of the reads don't quite match up. Is there a way to ignore these reads? Or to use them but not treat them as pairs?


texts: Perception of artificial light - flickering

texts:
I noticed something strange a couple of years ago. I was walking down the street at night, when it struck me that the street lights were flickering. But, when I turned to take a direct look at the light source it did not flicker any more. In other words, when the light is not the main focus of your eye, it can flicker.

From then on, I started to focus on these flickerings and they are everywhere. Street lights, lights in a house, but also computer monitors or even projections on a screen. Again, the flickering only happens when you do not look directly at the source.

Does anyone have an explanation for that? Is it the brain's fault, or the eye's?


texts:
I stumbled upon this word in a webpage by bio.libretexts.org:

  The dam-methylase of E. coli recognizes the tetranucleotide GATC in DNA and transfers a methyl group (from S‑adenosyl methionine) to the amino group at position 6 of the adenine in that sequence. Note that GATC is a pseudopalindrome, so both strands read the same for these four nucletides in DNA.

What does it mean? How is it different from palindromic sequence?

I've searched google,ncbi and google.books but couldn't find anything.


texts:
I'm interested to analyse hemolymph cells from a marine mollusc. I wanna count only "alive" cells so my strategy was the following: DRAQ5+ (nucleated cells) and PI- (alive cells) and identify population in FSC vs SSC.

Staining independently with DRAQ5 and PI I found positive and negative populations for each one but, in the fully staining I lost DRAQ5+/PI+ population... (https://ibb.co/VpgcCTN)

Does anyone know if DRAQ5 and PI are incompatible?

Note:

DRAQ5: excitation with 640nm and emission filter 675/25.
PI: excitation with 488nm and emission filter 585/40


texts: What class of histone deacetylase (HDAC) inhibitor is sodium valproate (VPA)?

texts:
VPA is a known HDAC inhibitor. But I cannot find what class it is.

What class is it?

And is there any method of finding an answer better than floundering with Google?


texts: Dragonish caterpillar from North Vietnam

texts:
I encountered this caterpillar in North Vietnam (Hanoi) and could not find any reliable web site for this kind of search. I am not an entomologist, so I don't even know how to describe it, except that it has hairy head stalks. I hope my pictures will help.
Thanks to anyone who can help me here.


texts: A balanced diet with the minimum carbon footprint

texts:
Many studies shows that 1 kg of non-vegetarian food as 3-4 times more carbon footprint than 1 kg of vegetarian food. I think that does not represent the complete picture food from animal sources are rich in some nutrients. For example pound for pound fish will be much richer in protein than normal vegetables to so get the same amount of protein as from fish, we will have to eat lot more vegetables. So at the end of the day, the net carbon footprint of our protein requirement might be much closer between veg and non-veg food. Similarly for carbohydrates, cereals may be the most carbon efficient than any animal source.

Question: I am interested in a balanced diet with the minimum overall carbon footprint. Any reference or studies on what is the minimum carbon footprint with which we can get say 100 g of all the essential nutrients such as carbohydrates, proteins, vitamins, omega acids, saturated fats etc.


texts: What is the effective population size of a simple two deme metapopulation?

texts:
I am confused as to how to compute the effective population size $N_e$ of a theoretical structured population. Let's consider here a simple case study.

Imagine a 2-deme metapopulation. Each deme is of constant size $N$ with a (forward and backward) migration rate $m$. Mating is random within each deme.

What is the effective population size of such population? In other words, how fast does the population loses heterozygosity through time?


texts: Effect of single nucleotide deletion or insertion on primer annealing

texts:
How is primer annealing, and, consequently, PCR amplification affected by single nucleotide deletion or insertion inside the primer ?

Imagine a primer like this:  GCGTCATAAAGGGGACGTG (primer)   and the corresponding part of template DNA has one G missing, so it looks like this:  GCGTCATAAAGGGACGTG (template).

The possible pairing could be
GCGTCATAAAGGGGACGTG primer
GCGTCATAAA_GGGACGTG template
or
GCGTCATAAAGGGGACGTG primer
GCGTCATAAAGGG_ACGTG template
 or anything in between.

Is it possible that amplification with such primer would be completely disrupted in normal real time PCR at 60°C annealing? Could this completely disrupt the amplification?

If the mismatch was substitution-like, I would be pretty confident, the primer would be still functional and amplification would occur. In the extreme case, it would be at least residual amplification at late Ct. There are a lot of data, how substitution mismatches affect primers and I also have a lot of personal experience with that.

Unfortunately, the deletion mismatches are less studied plus googleproof. The only indication I have found is this work:
Lipsky RH, Mazzanti CM, Rudolph JG, Xu K, Vyas G, Bozak D, et al. DNA melting analysis for detection of single nucleotide polymorphisms. Clin Chem. 2001;47:635-44.
In that work, single nucleotide deletion had similar or lower affect on melting temperature than substitution mismatch. But it was about longer oligos.  Examples:
Effect of deletion:
133 bp fragment, 67 % GC, deletion SNP at position 43, delta Tm (homo-hetero duplex) = 1.2°C
Effects of substitutions:
152 bp fragment, 43 % GC, substitution T to C at position 68, delta Tm (homo-hetero duplex) = 0.9°C
100 bp fragment, 41 % GC, substitution T to C at position 42, delta Tm (homo-hetero duplex) = 1.4°C
163 bp fragment, 60 % GC, substitution C to T at position 86, delta Tm (homo-hetero duplex) = 2.2°C
110 bp fragment, 59 % GC, substitution G to A at position 66, delta Tm (homo-hetero duplex) = 3.8°C

Questions:
1. Can you recommend me literature about how deletion mismatches inside (not at the very end of !!!) primers affect annealing and PCR ?
2. Would You guess the primer in my example would be still functional , at least partly, or would You expect no amplification at all ?

EDIT after your inputs:
This online application " mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting " thinks, deletion mismatches are more destabilising than substitutions, at least for short primers. For my own example, it calculated delta Tm (homo-hetero duplex) = 12.9°C .
If I try substitution mismatches instead, delta Tm (homo-hetero duplex) is in interval 3,8°C to 5,7°C.

New question   If you have experience as similar as possible to my case, which is 19 nt long primer with single nucleotide deletion in the comlementary template at position cca 6 - 9 from 3' primer end, annealing temperature used at 60°C, please let me know if You achieved amplification or not.  Please, give me a respective reference, if you have it, so I will quote it in my review :-) .

Also, I am still interested in general info, as long as the topic is narrow enough to be about single nucleotide deletions or insertions in primers. (Not substitution mismatches).


texts: Does breath-holding cause permanent brain damage?

texts:
My question is: Does voluntarily holding your breath at atmospheric pressure for a few minutes can cause brain damage? I'm talking about periods of time around 3 minutes.

I've read there are some studies showing brain damage in deep-water divers. However, it seems to me as insufficient evidence for breath-holding in general: it could be that frequent changes in pressure are the cause for damage, for example. Or the fact that the person cannot resurface immediately after feeling the need to breathe, which might cause them to hold their breath for a longer period of time than their body allows.

So are there any studies showing results for the effect on the brain in (healthy) humans holding their breath?


texts:
My question I have to answer is: A runner picks up pace on a warm day and starts sweating profusely. What property of water explains how sweating helps the runner continue running?
The following are four options I have to choose from to answer this question, and below that is the uncertain answer I chose.
A. Since water molecules are polar, they adhere to the surface of the skin, which allows cooling. The skin’s outer layer of dead cells enables the adhesion.
B. At elevated body temperature, the hydrogen bonds in water break, which allows water to escape as vapor. This causes heat loss in the body, which lowers body temperature.
C. Hydrogen bonds rearrange at higher temperatures and form a lattice structure that requires energy. This energy use lowers the heat in the body.
D. Sweating is due to the high heat capacity of water. When sweating increases, heat is released and the body temperature is lowered.
I chose (B), as (A) and (C) do not make sense and that (D) I think requires too much amount of time since water has a high heat capacity. Sweating, especially during running, is more immediate than (D). Would (B) be the correct answer?


texts:
My uncle was helping us spray the garage for ants, and he stumbled across a huge batch of some type of larvae. According to him...

  "It looked like a long, narrow clump of mud. When I broke it open, all of these larvae fell out. Whatever bugs were inside scattered pretty quickly!"

Geography: We're in Los Angeles, CA (southwestern USA)
Season: It's late summer here (early September)

Exhibit A: The pile of larvae...

Exhibit B: A similar husk of "mud" found in our garage. When it was shattered, nothing fell out...

My uncle thinks it's termites... I'm certainly hoping it isn't.


texts: Simulating Migration in SimBit Software Program

texts:
How is migration incorporated into the SimBit program of Remi Matthey-Doret and Michael Whitlock?

Is an island model or stepping stone model assumed?


texts: Why does catalase still produce oxygen when mixed with 1 mL of 0.1M NaOH (pH 13), but not when mixed with 1 mL of 0.1M HCl (pH 1)? Catalase's ideal from what ive researched is 7. In other words, since both are on opposite side of the pH scale and equally distant from catalase's ideal, why does the acid mixture stop working, but the base still function, even if a little slower? Why did the catalase denature after the acid, but not the base? Thanks for any help, I'm pretty curious


texts: How long does Lentivirus take to express in vivo mouse neurons?

texts:
Does anyone know how long it takes for a standard Lentivirus vector to express its genes (under a strong promoter such as CAG, CB7, etc.), after injection into the brain of a mouse?

By hearsay I think it's 2 weeks for full expression, is that true?


texts: What is the name of a gene whose effect comes from the dominant and recessive alleles

texts: The p53 gene has a mutation which results in the cell having a cancerous phenotype.  This effect is dominant as one allele being mutated is enough to result in this effect.  However when both alleles are mutated then the phenotype changes / become more pronounced so it's not a simple dominant mutation.  What is this kind of mutation called?  Is it hemi-dominant or something?


texts:
I often hear Japan has a declining/ageing population.
It seems to be the prime example for this kind of thought.
Yet after moving to Japan and after having been there for travel several times already. And in comparison with my native country Germany as well as Europe in general, I think this concept seems questionable.
While I hardly see any children outside in Germany and it's mainly parents with one child.
Everywhere I go in Japan I meet a lot of children. Especially in the greater Tokyo area, if I go to restaurants there's always a bunch of kids. And usually you see at least two children per parents, if not three.
I can understand that in general this concept might be true but might not be applicable for bigger cities.

Where does the concept come from? Is there any proof it's actually true?


texts:
I am not sure if this question is better suited CogSci.SE so please tell me.

My question is why are we satisfied when we get things that aren't useful in any important way? For example, relating to Stack exchange, why are we satisfied and happy when we get badges because badges don't increase reputation or help you get privileges in Stack Exchange. Similar with Winter Bash. Why are we happy when we get hats? They are just for decorations. Is there a biological explanation for this?

What chemical leads to us getting that feeling of satisfaction?


texts: I am trying to make sense of this diagram.  Can Ras activate RAF or MAPKKK, or is RAF a MAPKKK, making MEK a MAPKK, and ERK a MAPK?


texts:
The genetic code is redundant, there are 20 amino acids for 64 possible nucleotide combinations (triplet codons). Therefore some amino acid are coded by several different codons. While leucine is coded by 6 codons, tryptophan is coded only by one codon.

[I am aware that the set of codons that code for one given amino acid tend to look alike each other more than random. Usually it is only the last base that does not affect the amino-acid that is encoded.]

I therefore do not think that the genetic code can be entirely be explained by “it happened to occur that way the first time” (at the origin of life or in the last universal common ancestor) “and it never changed”.

So, my questions are:

Why are some amino acids coded by a several codons while others are coded only by one or two?
Specifically, why is methionine coded by only one codon — AUG — which has also to serve as a start signal?
In general, how (by what mechanisms, selective pressures) has the genetic code evolved to give this pattern of redundancies?


texts: Neisseria meningitidis transformation into a pathogen

texts:
I read the wikipedia article about Neisseria meningitidis, and it says that

  N. meningitidis is a part of the normal nonpathogenic flora in the nasopharynx of up to 5–15% of adults

In some cases however, it infects the bloodstream, creating a Meningococcemia disease which is highly lethal. It may also create a meningococcal meningitis.

The article also says that this disease is somewhat infectious. Not as infectious as common cold, but it is known to cause epidemics in Africa and Asia.

My question is: How can it be so abundant in its non-pathogenic form (up to 15% of adults) yet cause epidemics? It seems that it's transmitted from nose to nose somehow and doesn't cause a disease, yet when it does cause a disease it also causes a disease upon transmission.

It's not like a strain of E. coli that may cause disease in immunosuppressed individuals yet is a part of normal microbiota for other people. Because then it wouldn't cause epidemics, since the majority of the population is immune to it as evidenced by the fact that it's part of their microbiota.

Does N. meningitidis mutate to become pathogenic? Do the nasal strain and the pathogenic strain have different genotypes?

I tried searching for an answer but didn't find any.

Thank you very much.


texts: About what percent of mutations are not adaptive?

texts:
Many popular texts that discuss evolution and natural selection often mention that many (or most) mutations are bad (not adaptive).

Have there been any studies on what the rough percentages are? (E.g. Is it 90%? 99%? 99.9%? If this number varies by species, an answer could just focus on one particular species.)


texts:
If the conductance of a single ion channel is 1pS and its capacitance per cm2 is 1uF and the time constant for a human neuron is 1ms

How many ion channels on average must there be in one µm2 of neuronal membranes?

How is it possible to know how many ion channels with only these information? would you be able to explain it?

Thank you


texts: How did giraffes develop their rete mirabile failsafe?

texts:
Giraffes, being one of the tallest mammals in the world, have a failsafe called rete mirabile to prevent them from dying from excessive blood pressure while lowering their head.[1]

Due to their long necks, a formidable amount of blood pressure is needed (quoted from animals.about.com):

  A giraffe's heart has special adaptations to enable it to pump blood up the animal's long neck to its head.
  A giraffe's heart has the formidable task of pumping blood at high enough pressure so that it can flow up the giraffe's neck to the brain.
  To accomplish this, a giraffe's heart is specially adapted.
  It can weigh up to 10 kg (22 lb) and generates twice the blood pressure of other large mammals.
  Having enough blood pressure to pump blood to the brain when the giraffe's neck is extended upward is one challenge, but when the animal lowers its head it risks injury due to excessive blood pressure.
  To counter this, giraffes have a pressure-regulating system known as the rete mirabile which restricts the amount of blood that rushes towards the brain when the giraffe lowers its head.

How did this evolve? I believe in evolution but I can't wrap my head around this. If an "overload" of blood would reach the giraffe's brain while it is, for instance, drinking water and either instantly killing the animal or severely wounding the animals mental and physical capabilities by rupturing the brain, how could a failsafe like this evolve?


texts: How can I set micropipette volume with decimal separators, for example 109.5 in p200?


texts: How do tardigrades defend themselves from predators?

texts:
Tardigrades or water bears are well known for their ability to enter into a cryptobiotic state which allows them to survive extreme environmental conditions such as extreme temperatures or radiation. However, something I've noticed is that while it has been extensively discussed how tardigrades survive abiotic dangers, it is almost never discussed how they protect themselves from biotic threats such as predators.

This is a picture of a tardigrade. As you can see, tardigrades are soft-bodied and thin-skinned, with no obvious means of defending themselves and no real hard parts aside from the tips of their claws. Given that they are a soft-bodied, slow-moving organism with little ability to escape or defend themselves from predators, how do tardigrades avoid being eaten when they are otherwise an ideal prey item?
It doesn't appear as though tardigrades survive predators by living in extreme environments where nothing else lives. Although they are famous for surviving extreme conditions, tardigrades are also common in  biodiverse environments such as mosses and soils where there are a variety of other animals such as mites, springtails, nematodes, and pseudoscorpions. And indeed tardigrades are known to be preyed upon by mites and nematodes.
I've looked through the scientific literature on tardigrades on Google Scholar, and I couldn't find any papers that really talked about how tardigrades defend themselves from predators. All of the literature out there focuses on how tardigrades undergo cryptobiosis.


texts: So, recently, I learnt that T4 and T3 are both released into circulation but only T3 is the active form. Why then, do we make T4 in the first place? I read that T4 has a higher half-life, which might be the reason. Also, my professor said that it might be because thyroid peroxidase is not specific enough to control if it adds one Iodine or two. So, what is the actual reason?


texts: Michaelis-Menten equation type - how it is derived?

texts:
Can somebody explain how is the following differential equation found? It is about the blood alcohol content.

See this article (pages 3 and 4).

They say the concentration of blood alcohol satisfies (in the drinking phase): $$\dfrac{dC}{dt}=u-\dfrac{\alpha C}{C+\beta}\quad; \quad C(0)=0,$$ where $\alpha, \beta$ are the liver and the kidney parameters. For the Recovery Phase we have: $$\dfrac{dC}{dt}=-\dfrac{\alpha C}{C+\beta}\quad; \quad C=C_{max}.$$

I can't see how they came to these equations. The only thing they say about the origin of this model is that it comes from a continuity argument: the amount of alcohol that is introduced in the body, equals the amount of the alcohol that leave the body.

I wonder if there is a model which takes into account all parameters in the above article plus the amount of food in the stomach.


texts:
Sorry if this is a naive question, but it occurred to me as I was walking across campus today; How does a tree decide which limb is allocated the most resources, and thus grows the largest?

My first thought is the first branch to deviate from the base receives the most energy investment, and so on, but I don't have the time (or will) to actually test that. Does it have more to do with efficacy of the limb for photosynthesis? Or is it largely due to chance/unknown variables?

Thanks in advance, I feel this is something I learned back in botany and just forgot completely.


texts: Is there any size limit to the amount of information a human (or other) brain can hold

texts:
Im not sure how this would ever be tested but is there a limit to how much the brain can 'hold' before it reaches capacity ?

I guess this could also be interpreted in terms of memory, as how well some one remember something before reaching capacity / forgetting 'old' memories to make way / space for new ones.


texts: How long can one leave sample in lysis buffer for DNA extraction?

texts:
I am trying to do some DNA extraction for my professor, and I make a lysis buffer with proteinase K. I did not have the time to continue the procedure so the hair and the buffer have been sitting together at room temperature for about 12 days. My professor stated it would be "fine" to continue on with my DNA isolation procedure, but I have my doubts.

Should I continue my DNA extraction( vortexing, boiling, centrifugation and collection of supernatant, storage at -20 degree Celsius) or would this be pointless at this time? My goal is to run PCR and then a gel.

EDIT:

Here is the composition of the lysis buffer:

In 20 ml of Lysis buffer:

final concentrations are $0.1 M$ TAE, $0.5M$ $\ce{NaCl}$, 0.2% SDS.

To $800 ul$ of Lysis buffer I added $5 ul$ of proteinase K at a concentration of $250 ug/ml$.

(Proteinase K was made via:  $ 0.0025 g$ up to $10 ml$ of TAE buffer( $1 M $))

This was in a $1.5 ml$ centrifuge tube that has been now sitting for 12 days.


texts: Examples of extant animals in a submature morphologically unstable evolutionary state?

texts:
I'm fascinated by evolutionary theory and the predictive aspect of it-the notion of an animal entering a strongly divergent state of evolution whereby it is evolving into a new form yet remains suboptimal, and is therefore undergoing rapid morphological change, and the idea that this allows us to project onto possible new variants of life.

To give a past example, the praying mantis is believed to have split from the cockroach around 250M years ago. During this period the mantis developed its upright stance, large range of vision and pronounced raptorial claws, and has seemingly stabilised into this optimal new form over the past 50M+ years.

The interesting thing is that this change could actually have been predicted by analysis of the animals evolutionary history, niche and further available advantageous adaptive forms.

Can someone give a good example of a current animal in this volatile state that we could make accurate projections for?

And please, no trivial answers like "everything is constantly in a state of evolution", I already know that and thats not I'm referring to.


texts:
To my understanding, an allergic response is a non-adaptive response of the immune system to some molecule. The molecule in question is therefore "thought by the immune system" to be infectious although it is not. An allergic response is triggered by immunoglobulin of type E ($IG_E$) and causes an immune reaction.

I'd expect immune responses to not be instataneous, that is I would expect that it takes some time in order for the immune system to achieve some reaction peak. In consequences, I have been wondering whether someone that is under an allergic reaction is more resistant to early development of infectious disease because the immune system is already "switched on" prior to the infection. On the other hand, I would have thought that the body resistance to anything is lowered during an allergic reaction 1) because the allergy diminishes "general health" and 2) because allergic response may kill body cells.

Are we more/less resistant to infectious diseases during an allergic reaction?


texts: Why aren't plants and animals capable of assimilating $\ce{N2}$ directly from the atmosphere?

texts:
From a E-book  written by Hungary scientists, the reason is $\ce{N2}$ is inert.

Is this correct?
How does the chemical properties of gas species ($\ce{SO2}$, $\ce{O2}$, $\ce{NH3}$, etc) influence the assimilation process by organisms?


texts: Confusion regarding seedless grape and the normal process of germination

texts:
In general, does seedless grape by definition contains seed or is the seed small enough that the process of ingestion creates the illusion that there is no seed?

If the latter is true, is the seedless grape capable of germination?

Lastly does the fruit part of the seeded grape function as an incentive for animals to ingest it and provide nutrients for seeds in the form of feces, or can it function as nutrient itself?

Thanks


texts:
A recent post at a sister site Best field remedy for small cockroach in the ear has an answer that says

A few drops of baby oil (light nontoxic mineral oil) to suffocate the cockroach then tweezers to carefully remove it once dead and motionless.

This seemed unlikely to me, in the given scenario I suspected the baby oil had an additive. Per this link "some roaches can go up to 40 minutes without breathing" further suggesting suffocation was not the cause of roaches lack of motion.
I have done some more research and it appears this does actually work as described.

Doctors Settle Cockroach-In-The-Ear Controversy
The proper way to remove a cockroach from someone’s ear, it seems, has been the subject of little-publicized disagreement. The time-honored method is to drop some mineral oil in the ear, then try to pull the little critter out. A newer, competing technology is to squirt it with lidocaine, an anesthetic, to make it bug out on its own. Source

Both solutions above were ultimately successful. They found the lidocaine more effective.
Lidocaine does have draw backs as outlined in this article

Cantrell removed the dead roach with a set of alligator forceps, but the patient complained of dizziness for five hours after leaving the hospital.
"It is known that topical anesthetic agents entering the middle-ear cavity can be absorbed by the oval and round windows and cause vertigo," he said. The oval and round windows are parts of the middle ear used to transmit sound. Source

Putting aside which is the more appropriate choice. I just want to know how the mineral oil kills a roach quickly when it normally takes up to 40 minutes to sufficat one.
NOTE: Roach toxicity of Mint Oil is a completely different subject. (PDF)


texts: Can Omega 3 Fatty Acids prevent chest pain in periodic Atrial Fibrillation?

texts:
It is debated if omega-3 polyunsaturated fatty acids (N3PUFa) may be effective in preventing AF (atrial fibrillation), meta-analysis here.

However, much less has been considered this: Do N3-PUFAs prevent acute symptoms of periodic Atrial fibrillation?

The meta-analysis concentrate only in the long-term effects of prevention.
My proposal focuses on the short-term i.e. the fact that the user can recognise AF first and then uses N3-PUFAs.

Please, assume that there is a validation method by which the user can easily detect that he has AF - he does this if he suspect it, i.e. feels special discomfort and special wave-like-pain the chest.

He takes each time in this case 20 ml of Müller omega-3 oil which has also vitamin D.
The effect of recovering is immediate in prophylaxis.
Assume the user has less than < 20 ng/ml vitamin D in blood each case, most of the time, 9 ng/ml so avitaminosis.

My conjecture is that N3-PUFAs can prevent the acute symptoms of periodic AF.

How can N3-PUFAs prevent the acute symptoms of periodic AF?
What is the role of vitamin D here?


texts: It is said that iron deficiency anemia is characterised by microcytic-hypochromic RBCs. I would like to ask how iron deficiency causes decrease in the volume of RBCs? If the volume is decreasing because of low hemoglobin, then why  does the concentration of hb too decreases causing hypochromic RBCs? Why don't they decrease in same pace?


texts: Meaning of "optical" in "Optical cap, 8X Strip" (used in qPCR)

texts:
I'm translating an English document that lists equipment used in a qPCR procedure:

Reagents/Materials

Optical cap, 8X Strip

I googled and found that the meaning of this line is "a strip of 8 caps for PCR tubes". What is the meaning of optical though? I'm not sure how to translate it into Russian.
Does the word indicate the the cap is fully transparent? Or that the cap creates no visual distortion (it is flat)?
Screenshot:

I'm googling but I can't seem to find any definition of "optical cap". It is used in a lot of books and documents as if the term is self-evident, while it's not.


texts: Paralogous genes in genome-wide association studies?

texts:
Has anybody tested if paralogous genes are over-represented among the genes identified by genome-wide association studies (GWAS)?

For example, if a GWAS study finds 200 genes associated to the disease/trait, and a number X of those can be classified as belonging to Y different gene families, is there a test to see if X and Y are bigger than expected, given the total number of genes and gene paralogies in a genome? Here I am talking long established copies within a species, not CNVs in different individuals of the same species.

I am thinking there is an interesting question behind this: if a gene has duplicated during the evolution of a genome, and the different gene copies have taken specialized, yet related, roles, an unbiased analysis like GWAS should be able to find cases where different paralogous copies associate to different subdiseases/subtraits within the same global disease/trait.


texts: Is it better to take a half dose of paracetamol and a half dose of ibuprofen together rather than a full dose of either?

texts:
Recently, I heard on this health-related radio programme that it was better to take a half dose of paracetamol and a half dose of ibuprofen together, rather than the full dose of either one, for acute pain. Could anyone explain the reasons for this ? Could it be something along the lines of there being diminishing returns to higher doses, so you get more bang for the buck, as it were, for the first half of a dose than the second, but due to possible toxicity or drug interactions, two full doses are not recommended ?

In the same radio programme it was stated that caffeine also helps. Can anyone explain that ?


texts: Which of these methods is both effective and reliable in elongate muscle and tendon for use in humans: growth factors or stem cell technology

texts:
Which method is it the most effective, but also the most reliable for elongating muscle and tendons for clinical trial; using modern growth factor technology or using modern stem cell technology?

Being able to stimulate muscle elongation is a key step towards improving the standard of living for people afflicted with severe Poliomyelitis or people with limb Malformations. There are already techniques to culture living bone implants in the lab from stem cells for human beings. I am looking for an analog for muscle tissue.

Please provide references with your answers.


texts: Is in the process of making soy protein isolate all (or most) of the protein trypsin inhibitor removed?

texts:
Being lactose intolerant and going to the gym I looked for lactose free protein powder. Soy protein isolate seemed like a good option until I read something about the protein Trypsin Inhibitor (TI). Which soybeans have the highest content of of all legume.  When reading up on this I discovered it isn't something that you want to be eating. Now I am far from an expert on this kind of topics and 2 days of reading papers has given me some information but I cannot get to a proper conclusion because I do not understand the half of it.
In this article https://onlinelibrary.wiley.com/doi/full/10.1111/1750-3841.13985 they test different methods on how to remove TI. Where cooking removes most of the TI. However, they also state that cooking above 80 degrees Celsius damages important nutrients.
https://link.springer.com/chapter/10.1007/978-1-4757-0022-0_20
In this article they say "In the processing of defatted soy flour to prepare a soy protein isolate, generally no heat treatment is used. Instead, a high percentage of the trypsin inhibitors (TI) is physically removed in the whey fraction. However, depending on their mode of preparation, soy isolates may contain trypsin inhibitor activity as high as 40% of that found in raw soybeans"
What do they mean with "whey fraction"? Does the commercial available soy protein isolate still contain trypsin inhibitor activity even if they have treated it in some way?
This article they show in the first diagram a simplified version of how soy protein is made and one of the last steps is cooking the product. This process also occurs for protein isolate as far as I understand.
Horan, Frank E. “Soy Protein Products and Their Production.” Journal of the American Oil Chemists' Society, vol. 51, no. 1part1, 1974, p. 67., doi:10.1007/BF02542094. (This was available through my university online library tool)
To summaries:
Does the process of making protein isolate contain any of the treatments needed to remove Trypsin Inhibitor mentioned in the first article? If yes, then did that not damage other nutrients within the product? How much of the TI is removed from the soy protein isolate in the process of making it?
Thanks for anyone that reads this and trying to figure this out as well.
I also don't know if this is more a biology or chemistry topic...


texts: I've seen it in Nordic countries (Sweden, Latvia). It's a tree that reaches maybe 5 or more meters high and its flowers have a beautiful scent.


texts: Why does a frog's oxygen intake through the skin and lungs vary throughout the year?

texts: Why does a frogs oxygen intake through the skin and lungs vary throughout the year?  And why does the intake through the skin vary slightly while through the lungs dramatically? (Blue line = oxygen intake through lungs and orange line = through skin.) Thanks.


texts: Low Density Lipoprotein (LDL) in the endosome

texts:
I am learning vesicular transport of LDL endocytosis. I understand as pH of the endosome is lower (around 6.0) than cytosol (around 7.2) due to the H+ pump, so LDL disassembles from the LDL receptor at the endosome.(wiki)
What I don't understand is how cholesterol can be effectively separated from the empty LDL receptors in the endosome, as cholesterol clusters at the central region of the endosome but the receptors cluster at the tubular region (wiki) before budding (the retrieval/recycling pathway to plasma membrane).
My current thought is cholesterol cluster is too large to get into the narrow tubular region. But I cannot find information about how empty LDL receptors can be directed to the tubular region for COP-I mediated retrieval.
Please correct me if I have made anything wrong.


texts: Why are the most heat tollerant organisms prokaryotic?

texts:
Prokaryotic organisms are able to grow at far higher temperatures than are
eukaryotes.

Archaea are known to group, among some mesophiles, the most extremophiles organisms (es. Pyrococcus furiosus), but also some bacteria can reach quite high-temperature habitats, such as Thermus aquaticus.

Eukaryotes instead are far less tolerant in terms of maximum growth temperature.

Also most of the hyperthermophiles are chemoorganotrophs or chemolithotrophs, being autotrophs (Cyanobacteria) far less heat tolerant.

My question is about the physical or chemical limitations that block eukaryotes from adapt at extreme habitats like prokaryotes do.


texts:
If I'm right, there are two types of pluripotent stem cells: naïve and prime. The naïve form is more undifferentiated.
It would seem to me that it would be easier to make genetically engineered animals if some kind of mutation were made in the cells and the cells that could successfully produce the mutation were iPS-transformed and injected into the blastocyst. But, I don't know of any transgenic animal that has been created in that way, with the exception of the mouse.
Recently, common method seems to be to administer Crisper Cas9 directly into the blastocyst.
My question:

For which animals, can we make iPS-derived reproductive chimeras?
Preferably, the chimeras can produce offspring derived from genetically modified iPS.
However, the question is about animals other than mice.

It would be great if you could also tell me about the following;

What are the strains of animals that have been genetically modified in this way?
If it is difficult to create genetically modified animals in this way, what are the barriers?
However, the questions are also about animals other than mice.


texts:
I have always wondered, if dolphins sleep with one eye opened, do they really sleep at all?
According to this article dolphins indeed shut down their brains.

I already googled it. No help from wikipedia or other articles and publications found.


texts: Flower identification (Singapore, April)

texts:
I saw some flowers growing by the roadside today, and was wondering about the species of this plant.

The plant also appeared to be fruiting, and it produced small fruits that formed small clusters.


texts: Do Asian women have more difficult births than Europeans?

texts:
I recently heard a claim that Asians in general have more difficult births than Europeans. Is this true?

I have found a few studies(1,2) on the effect of ethnicity on birth outcomes but they seem to be limited to a small geographic area or focus on aspects such as risk of premature birth, neonatal and/or maternal mortality, etc. Those are of course important facts, but I am more interested in whether an otherwise normal birth is likely to be longer and/or be perceived as more difficult by this specific ethnic group, on basis of their ethnicity alone.

I found a few articles dealing with possible effects of specific genes on duration of labor. Debiec et al. (3) write that

  Asian women had slower active labor than other ethnicities (P < 0.01). Asian women also reported less pain during their labor compared to all other patients (P < 0.001). Slower labor progress was associated with less rapid progression of pain, but this did not obviate the effect of Asian ethnicity on pain.

According to Reitman et al.(4,5) the genotype CC at the SNP Rs1042714(9), which is more prevalent in ethnic Asians, is associated with longer duration of first-stage labor. Polymorphisms in the oxytocin receptor (OXTR) gene have also been tied to variations in labor progress (6,8), but I haven't found data on the prevalence of these polymorphisms in Asian populations.

Greenberg et al. (7) write that "Nulliparous Asian women had a significantly longer second stage and higher rates of prolonged second stage". However, after controlling for confounding variables the actual increase in mean second-stage duration compared to white women was only  5.2 and 5.9 minutes for nulliparous Asian women with and without epidural analgesia, respectively. They also write that

  When the rates of second stage of >3 hours were analyzed by epidural subgroups in the multivariate analysis, black women with epidural analgesia had lower rates than white women, and Asian women with epidural analgesia had higher rates than white women, regardless of parity, although no differences were demonstrated among women without epidural analgesia.

Considering the above sources and any other that may exist, is it reasonable to state that Asian women in general have more difficult births than white/European women?


texts: Hamilton's rule: When to change the equation?

texts:
So, in class, my teacher gave two examples of using hamilton's rule. Let b= 4 and c=2.5.

The first was whether altruism would evolve between two diploid full siblings given these values. Since r=1/2, the equation was (0.5)(4)-2.5.

The second question was the same but from a daughter to her mother. He used (1/2)(4)- (1/2)(2.5).

I was confused as to why the teacher outlined this difference. I know that it has to do with the asymmetrical and symmetrical relatedness concept but don't know the details.

Would it continue to apply to grandparents and aunts/uncles as well?


texts: Do dogs have something different about their physiology that allows them to pant without hyperventilating?

texts: I was wondering this as I considered how effective panting would be for humans as a means of cooling.


texts: What organs are absolutely needed by the human body?

texts:
The title is my question: what organs are absolutely needed (fatal if injured/removed) by the human body and perhaps animals in general?

I'm not asking which organs are mechanically replaceable, but more what organs cannot be removed (and not replaced) in order to maintain human life.

--update--

To clarify the question, I'm wondering what organs when removed (and applied no medical intervention) would cause fatal effects in a short amount of time, or cause semi-fatal effects (ex. shortened lifespan). A list perhaps of importance, if possible, would be nice.

note: I have no medical knowledge so I'll leave 'short' open to interpretation.


texts:
I feel pretty silly for asking this but I don't want to damage these coverslips.

I just ordered a 100ct box of coverslips and see no way to open them without destroying the container they are in. How are these little boxes typically opened? It seems smooth and sealed on all sides.


texts: Are there any pre-Holocene venomous animals?

texts:
The novel (and subsequently movie) Jurassic Park featured a dinosaur called Dilophosaurus, that was purported to be venomous and had an ability similar to that of the extant spitting cobra. Unfortunately, the whole setup isn't real.

This got me wondering though. Modern venomous snakes, to give a particular example, ought to have had ancestors that already had appropriately modified salivary glands, and similarly for most other extant venomous species. (I suppose I'll restrict myself to vertebrates so as not to be too broad.)

I now ask: have fossils of animals that are likely to have been venomous ever been discovered?


texts: Is human zygote unicellular or multicellular

texts: Is the human zygote which is formed by fusion of sperm and egg a unicellular structure? Bcz at some places the 2 celled stage which is formed due to cleavage has been labelled as the zygote. So is the zygote 2 celled stage or the unicellular structure which is formed initially.


texts:
After reading -

(wikipedia) Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other.
( a paper) A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides.

I deduced that the portion of oriC containing all four 9mer-s
was to be called a tandem repeat and it together with all three 13 mer-s, two tandem repeats.
But again while reading Principles of genetics by Simmons I stumbled upon the following-

The single ori in E.coli has been characterised in considerable detail. It is 245 nucleotide pair long and contains two repeated sequences. One 13-bp is present in three tandem repeats. The three repeats are rich in ...

So here it says that each 9-mer in the series is a tandem repeat actually.
Which meaning is more accepted?


texts: Some kind of better oxygen-transport protein or something... Can you help me find it?

texts:
I remember reading about artificial or man-made, oxygen-transport protein that is somehow an improvement on hemoglobin, and that it is possibly immune to sickle-cell anemia, or something... But I forgot where I found it and what exactly it is...

Can you guys help me find it?


texts: How do I prepare a PDB for submission to the Protein Data Bank?

texts:
I have a couple structures that are nearly ready to be deposited in the PDB.  Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked all sorts of additional records (TER, SEQRES, HETNAM, etc.) that my refinement and modelling tools don't seem to care about.

From what I understand/guess, the online submission tool will help fill in all the metadata (REMARKs, etc.), but how do I turn my coordinates into something acceptable?


texts: Why do cockroaches and flying beetles survive high levels of radiation?

texts:
Apparently it's a fact that cockroaches survive nuclear radiations.

How can they survive this?


texts:
Does anyone routinely do RNA isolation from zebrafish embryos?

I have embryos from different stages but all below 24hpf. This is the protocol I follow:

Take 10-20 embryos
Wash once with milliQ water
Treat with 1mg/ml Proteinase-K (5min with gentle shaking) to dechorionate
Wash again with milliQ water
Remove water and add 250 µl Trizol
Homogenize by pippeting
add 750µl more of trizol
Do the standard trizol extraction step (with chlorofom)
Take the aqueous phase and wash again with 200µl chloroform
Precipitate RNA with isopropanol
Wash thrice with 70% ethanol
dissolve in nuclease free water

Despite all this I get a poor A260/A230 : ~0.4

Moreover, this happens consistently in all samples. The RNA bands look fine on the gel.

I have done RNA isolation many times from cell lines and tissues and never faced this problem. Is this common with zebrafish embryos? Is there a way to fix this other than by using kits?


texts: Why do death cap mushrooms not warn of their poison?

texts:
This has been puzzling me for a long time now. There is an evolutionary predilection for living things which have evolved strong defensive measures (that may not themselves be visible) to give distinct visual or audible warnings advertising these measures.
Wasps, hornets, snakes, and bees are all brightly coloured. Snakes may even have rattles to advertise their venom. These things by in large don't want to have to use their poison in a defensive capacity. Getting revenge on a predator who has mortally wounded you is a Pyrrhic victory.
These warnings are so potent that many animals without such measures will mimic these warnings in order to piggy pack on a general evolutionary bias towards an instinctive avoidance of anything that warns of being poisonous.
But take the death cap mushroom.

This innocuous fungus looks identical to completely harmless mushrooms. It has no foul smell. In fact, evidence shows that it actually has a pleasant taste! That picture above actually looks pretty tasty in my opinion.
This fungus has gone to the trouble of developing one of the most potent poisons in nature (humans have a seriously robust digestive systems by animal standards, and yet a single death cap can easily kill an adult human).
So why so secretive about its arsenal?
I know this same question about evolving poisons that are not well advertised could be applied to a large number of animals, insects, and particularly fungi, but I think the death cap is the most extreme example in both the lethality of the poison considered, and combined lack of advertising.


texts: What is the definition of "Natural Selection"?

texts:
Natural selection is the differential survival and reproduction of individuals due to differences in phenotype.

Natural selection, a process that results in the adaptation of an organism to its environment by means of selectively reproducing changes in its genotype or genetic constitution.

Natural selection, then, can be defined as the differential reproduction of alternative hereditary variants, determined by the fact that some variants increase the likelihood that the organisms having them will survive and reproduce more successfully than will organisms carrying alternative variants.

Darwin's definition of natural selection his book "On The Origin Of Species By Means Of Natural Selection or the Preservation Of Favoured Races In The Struggle For Life" is:

  The preservation of favorable variations and the rejection of injurious variations

In Evolution 101, natural selection is not defined, but rather the concept "evolution by natural section" is characterized as the outcome of variation, differential reproduction and Heredity, and a clarifying example is provided.

Clearly, the wording in each of the above is different!

I searched Biology StackExchange for any explicit statement of the definition of natural selection, I couldn't manage to find one. There are some discussions about whether it is a tautology or not, but even in those discussions, the definition of natural selection was not quoted.

I tried to search tags "natural selection" and "definitions" of biology StackExchange, and yet I didn't see any particular wording mentioned as the official definition of natural selection.

Actually, the tag [natural selection] mentions this definition in the tag information itself:

Natural Selection is a mechanism of evolution that leads to non-random spread of genes due to the effect that genes have on reproductive success

Natural selection is the process by which heritable traits that make it more likely for an organism to survive and successfully reproduce become more common in a population over successive generations.

Is there an official definition of natural selection that is adopted by biologists nowadays? and what is that definition exactly?

[EDIT] It came to my awareness that this question might be a possible duplicate of the following question: "How is Selection best defined", and indeed in the answers provided to that question the topic of definition of natural selection has been addressed.

I didn't know of this posting. I simply surfed for "natural selection", and not just for "selection", and I didn't notice it. But indeed what's presented in the answers does cover the question present here.

However there is some difference in the question itself from that present here. Here I wanted to know of what I thought would be an official definition, and I was asking in particular about "natural selection", while in the referred question, the question is more general, it's about what qualifies "any" force (apparently he means related to biology and especially evolution) to be labeled as "selection", including artificial selection, sexual selection, etc.., so it's a wider topic, at least as far as terminology is concerned.

Here in this question I've quoted the main results that one would see upon surfing the web for "definition of natural selection", and I wanted to know which one would be the official or as @Remi.b had put it, the most commonly used or referred to in biological research.

I still think, that for precision purposes, exact wordings are important, and such an extremely important concept like "natural selection", it would have been expected that it had an agreeable, kind of, official definition, by some convention or the alike.

Anyhow, I think, whether this question is a duplicate or not, can be better assessed by experts in evolution field present in this website, like those who provided answers, and others.

Thanks.


texts: Difference between sexual and asexual spore

texts:
This Wikipedia article on Spores mentions this:

  In biology, a spore is a unit of sexual or asexual reproduction that may be adapted for ....

What is the difference between the sexual spore and asexual spore?
Are they any different on basis of formation, diploid or haploid, role in life cycle?

By Sexual Spores, I mean the spores that arise in the sexual reproduction process and similarly for Asexual Spores, i.e. spores which arise in asexual reproduction process.

To add to the context, this image shows the Sexual and Asexual spores in a certain fungi (Mycelium) life cycle.


texts: Techniques to show a protein heterodimer-DNA interaction

texts:
It is known that c-Jun and fos dimerize to form AP1 factor that binds to a sequence on DNA containing PyPuGACGTCNNNNGAGGTCPyPU.  In esophageal cancer cell lines there is no expression of the fos gene. However we still see expression of genes regulated by AP1 factor.  One of the possibility is another isoform of fos is expressed in these cells (e.g. fra1).

How will you check that fra1 is expressed or not in these cells.
How will you check that the heterodimer bound to the given DNA
contains fra-1 along with c-jun.

My thoughts on the above questions

For first question we can do immunofluorescence assay or we can do DNA affinity assay in which we chemically synthesize DNA sequence and bind it on agarose gel column pass through it protein extract of oesophageal cancer cells and our fra-1 protein if being expressed in cell line will bind to DNA. later we can elute protein DNA complex and by anti-fra1 antibody we can check if it is being expressed. But the drawback of both these technique is we should have knowledge of epitope of fra-1.

For second question - we can perform ChIP using antibody tagged Against c-jun and then eluting out DNA bound to c-jun. Then we can simultaneously label the complex with anti fra-1 in one sample and anti fos in another sample. We can check for results. If fluorescence is obtained in case of fra-1 sample that means both c-jun and fra are bound to probe and not fos.


texts:
Hepatocytes polyploidy
Why are some hepatocytes polyploid?