texts: How does Topoisomerase II inhibition affect cancer cells?

texts:
Topoisomerase II poisons represent some of the most important and
  widely prescribed anticancer drugs currently in clinical use. These
  drugs encompass a diverse group of natural and synthetic compounds
  that are commonly used to treat a variety of human malignancies. At
  the present time, six topoisomerase II-targeted anticancer agents are
  approved for use in the United States, and additional drugs are
  prescribed elsewhere in the world. These agents all act as traditional
  topoisomerase II poisons and function primarily by inhibiting
  enzyme-mediated DNA ligation.

Briefly describe what TopoII does and how it works. Explain what "inhibiting enzyme-mediated DNA ligation" means.

My thoughts for the first question are Type II topoisomerases cut both strands of the DNA helix simultaneously in order to manage DNA tangles and
supercoils. They use the hydrolysis of ATP. It changes the linking number of circular DNA by ±2. After the ends are
cut, the ends of the DNA are separated and a second DNA duplex is passed through the break. The cut DNA is re-
ligated. This  allows the enzyme to increase or decrease the linking number of a DNA loop by 2 units.  It also
promotes chromosome disentanglement. Inhibiting enzyme-mediated DNA ligation means that it prevents the enzymes are not allowed to ligate. This is
prevented by not allowing the formation of a phosphodiester bond.

Cancer cells grow much more rapidly than most cells in the body. What would be the consequence of "inhibiting enzyme-mediated DNA ligation" and why might this be particularly deleterious in cancer cells?

I am really unsure on this one.

I have looked at the Wikipedia answers to this question and they are wrong.


texts: Which are the last cells of the human body to die?

texts:
When somebody dies, which are the last surviving cells of his/her body? Those of hair, nails, or some other obscure but resilient cells?

Shedding light on why and how they are so vital might boost our knowledge of survival pathways.


texts: Confusion about the brain regions - temporal cortex, hippocampus and and white matter

texts:
I am a computer scientist working with brain data. I have some data from different brain regions, and the regions are called temporal cortex, parietal cortex, hippocampus and forebrain white matter. I want to show those regions on a brain image in a presentation.

The problem is, when I search the brain images online, I cannot find the regions my data mentions. The regions in the search results are usually called "lobe" rather than "cortex". And when I search for "forebrain white matter", the results are usually about "cerebral white matter". I am totally confused. Here are a few questions:

Are "cortex" and "lobe" the same thing? Or does cortex means gray matter while lobe contains both gray and white matter?
Does hippocampus contain gray and white matter? Or does it reside in the inner side of the temporal lobe, meaning it is in the white matter part of the temporal lobe?
Are "forebrain" and "cerebrum" the same thing?
Why is hippocampus considered part of the temporal lobe although it has the long side of it outside of the temporal lobe?


texts: How does heart rate change when entering N1 sleep?

texts: I would like to know how the heart rate changes as a person enters N1 (NREM 1) sleep from a wakeful state. The focus is on entering N1, and it would be great to have time-series data to see the pattern of the decrease, but a  textual description of the decrease would be good too. Most importantly, by how much does heart rate decrease from resting to N1, and how quickly does it fall?


texts: Do RuBisCo and Haemoglobin have any similarity?

texts: In RuBisCo and haemoglobin both can bind to CO2 as well as O2. Do these proteins have any structural similarity?


texts: Which processes are during the latent period of ventricular contraction?

texts:
The latent period is the time between the start of depolarisation and the start of contraction.
I know that the contraction of ventricles starts after sufficient influx of Ca2+ and threshold potential is met.
The influx of Ca2+ is at start of Phase 2, so Phase 0 and 1 are included in the latent period.

Comparing to electrocardiogram is not simple, since there is always at least some time lag between the event and the recording.
I think there not much sense to compare cellular model events to ECG recordings here.

Which cellular processes does the latent period include?


texts: What does "Pandercetes" (genus of spiders) mean?

texts:
"Pandercetes" is a taxonomic genus, and refers to certain Huntsman spiders (found in Australia/Asia).
It was named by Koch, a German entomologist, in 1875.
What does the name itself mean or connote? What are the defining characteristics of this genus?
I could not get a clue as to what roots the word is made of .. pander + cetes? pan + dercetes? My understanding leads nowhere this far.


texts: What happens if an IV drip with a saline solution slips out of the vein, but keeps dripping into the body?

texts:
A patient has a saline solution IV drip into the vein. They have somehow moved around and the needle has fallen out of the vein, but remained in the body. Nobody has noticed and for a few hours water has accumulated like a balloon in the arm.

What happens? Is it dangerous? If untreated, would the body absorb the water, or would it remain as a balloon / pocket? If a pocket of water forms, what is the treatment?


texts: I can’t for the life of me find an identification of these snails. They’re thriving in brackish water, but may be freshwater naturally. They’re about .8cm long at their largest. I believe they have live birth due to the lack of eggs but presence of baby snails over the year and a half that I’ve had them.


texts: Why are fruits so large compared to their seeds?

texts: Why do many plants produce such large fruits(apples and strawberries,for example) if those contain only relatively small seeds?


texts: Why does increasing concentration of extracellular sodium have no effect on electrical gradient of potassium?

texts:
I learnt that the permeability of an ion across the membrane contributes to the membrane potential as much as(or even more than) its concentration and electrical gradients. And so far I've made peace with the fact that Sodium, having a very low permeability, doesn't contribute much (through its own movement) to membrane potential despite having a high electrochemical gradient directed towards the cell's interior.
Now, the confusing thing is that, if I imagine dumping some sodium ions (with their positive charge) on the cell's exterior, this would affect the electrical gradient of potassium (and in fact other ions)--because more positivity is recorded externally-- making potassium in particular less "ready" to diffuse out of the cell. The result of which would be a depression (that is a more negative value ) of the resting membrane potential.
If potassium's extracellular concentration were increased instead, a similar effect would be observed.
What exactly is wrong with this reasoning?
I'm putting this forward because my Professor mentioned only extracellular potassium ion as having an effect on membrane's resting potential.


texts:
I live in a flat in the UK and have caught such mites a few times on my skin. I think they are responsible for my bites. On one occasion one mite had one dark spot in the middle instead of two.

Does anyone know what it is?

Regards


texts: Reduction of size in diatoms due to asexual reproduction

texts:
From this we can see that diatoms reduce their size after asexual reproduction.

This would ultimately lead to nonviable small size. Is there any mechanism to avoid this ?


texts: How much of a DNA difference is between Chicken of the Woods, and Hen of the Woods?

texts: I've noticed that when a COW is touching the ground it turns a gray color, but when on a log/tree it's bright orange. Is there a correlation between the DNA, and where it grows?


texts: Why does the ring finger not move independently?

texts: Why is it that we need to move little finger in order to move ring finger with it? For example, put your palm on a table and fold your middle finger inside. You won't be able to move your ring finger unless you move your little finger along with it. Why? Paul Gilbert and Buckethead and various other guitarists are the only people that I'm aware of that use the ring finger and looks independent. Is it possible to have surgery to make the fingers independent or is it not functional to do that?


texts: Multi-modal distribution for gene expression data

texts:
Why would some genes have more than two modes in their expression distribution? What external factors would cause this anomaly?

I'm referring to the expression distribution of a gene across different tissue samples. For example, if one was to download a bunch of data from NCBI GEO, and pinpoint one gene and plot the expression level versus the frequency for that gene across all those data sets, some genes would have more than 2 modes (2 expression levels with very high frequency). This is the only case I'm interested in: more than 2 modes - not bimodal. So what would cause more than two modes?


texts: Why are these nesting magpies building another nest

texts:
Pair if eurasian magpies occupy a nest visible from my balcony. It's the nesting season for them here, and I assumed they have laid eggs. I can't see the eggs directly, but one of the magpies has been regularly sitting inside the nest (at least for last two or three weeks) and they always attack other birds that come too close.

Today, they've started building a new nest on another tree. It's pretty close, the nests are about 20 meters apart. They still visit their original nest.

What does it mean? Is it a sign of nesting failure? Does it mean their original nest is no longer sufficient?


texts: How many generations are required for a specific neutral mutation to reach fixation?

texts: In population genetics, the term “time to fixation” is defined as the time it takes for a specific mutation to appear in a population, plus the time required for this mutation to spread throughout this population. My question is, how many generations are required for a specific neutral mutation to reach fixation? I need a general formula for number of generations as a function of mutation rate and population size, valid for all kinds of biological entities. Note that a neutral mutation is not fixed by selection, it is fixed by genetic drift.


texts:
A few years back my Physics professor made a joke that his myopia (i.e., nearsightedness) gave him a "superpower" that allowed him to see close objects much more clearly than someone with typical eyesight. For example, reading small fine print or tiny details on a surface. The physics made sense, as a person with myopia should have a closer near focus point.

Recently, this belief was challenged by a normal-sighted friend. I did some Google-ing and couldn't find any evidence or articles confirming or refuting this belief. All I found was a lot of anecdotal evidence.

My question is: Is this belief correct? Are there any scholarly articles or similarly trustworthy sources confirming this?


texts:
For example, all big cats have killer instinct.
They go straight for the throat or neck of their prey, killing it before consuming.
I've seen videos of bears and wolves hunting prey. I've never seen any where they bite the throat or neck deliberately.
Bears just bash their prey till they die or eat them alive.
Wolves eat their prey alive when the prey literally exhausted all of their energy.


texts:
What is this larva/insect that I saw crawling on one of my books?

It moves by wriggling motion and seems to be able to retract it's head(?) when disturbed. It is about 8mm long.
Location: Chennai, TamilNadu, South India


texts: How does Genetic drift and selection affect fixation of an allele?

texts: I want to know how does genetic drift, and selection coefficient (s) together affect the fixation of an allele? For example, if there is a neutral allele (s=0), will only genetic drift cause the fixation or loss of an allele? Similarly, if an allele is beneficial which means that s > 0. In that case, how do genetic drift and selection coefficient together determine the fixation and loss of an allele? And what happens when s < 0 that is an allele is deleterious. Lastly, how do genetic drift and selection coefficient gets affected by the population size? I am reading about population genetics, and I am totally confused by this point. I would appreciate if someone can clear this to me.


texts: plant crossing for creating breeding population

texts:
I read some material about plant breeding. For a self-incompatible plant with high heterozygosity, it said that after selecting the plant population based on phenotype/desired trait, a cross was done among plant with the desired trait to create the breeding population. However, as far as I know, the breeding population was usually phenotypically selected for desirable traits. I'm not experienced in this field, could you please kindly explain to me why crossing is conducted for creating breeding population?

Thanks in advance


texts: Animal with "advantageous" trait in a environment where the trait is never utilized (high cold tolerance in mild climate) - natural selection occur?

texts: If you were to put an animal with a certain type of seemingly advantageous "trait" into an environment where the trait was not necessarily needed, ex: Putting an animal with a high tolerance for cold into a mild climate, what kind of natural selection occur? Balancing?


texts: What are these lines that connect into cells called?

texts:
I just recently watched a very interesting video that showed cell division under a microscope. In the video, you can see cells that have either one, two or more lines connected to them. What are these called?

Source: https://youtu.be/rgLJrvoX_qo


texts: Will lipid molecules 'flip-flop' over a membrane without the use of an enzyme?

texts:
All of the references to this I can find refer to enzymes like Flippase making it 'easier' or 'more likely' that the translocation will occur, rather than actually make it possible.

The following is from Alberts

  In the ER, however, phospholipids equilibrate across the membrane within minutes, which is almost 100,000 times faster than can be accounted for by spontaneous “flip-flop.”

Does this mean that left unattended, any phospholipid membrane will 'flip-flop' spontaneously, just very slowly, and can this be observed?


texts: Does the brain store information and personality traits in different areas?

texts:
I'm aware that muscle memory, language etc can remain largely intact after brain injury that impairs other forms of memory, suggesting that different kinds of memory are stored in different places in the brain.

Are your personality traits also stored separate from memory?

If I'm a bigot, I probably came to be that way because of my experiences and what people who are influential in my life have told me. If I forget those experiences and people due to memory loss following brain injury, will I not be a bigot anymore?
I may have certain nuances in my personality because I'm rich - like body language, or that public transport makes me uncomfortable, never having been used to it. If my memory loss is so severe that I don't recall anything about my life so far, will I still have my nuances?


texts: In a Sanger sequencing, what would be happen if different DNA sequence binds to same primer? And how this situation avoided if problematic?

texts:
Sanger's PCR chain-termination sequencing, by its theory, is a simple method to sequence DNA from organisms. But what will happen if there are 2 allelic DNA with same primer binding site, but variations in some-other part?

My question is; 1. Is such overlap practically happens? 2. If it happens, then what problem it creates? (or does it create any problem at all); and 3. if it is problematic, then what techniques used to avoid or reduce such noise?


texts: The difference between "Hunger" and "Appetite"

texts: When I am "hungry", I need something to eat physically. But what about "appetite"? I think it is a psychological phenomenon. Is that correct?


texts: What are the evolutionary reasons behind men being taller than women?

texts:
Human men and women are sexually dimorphic: there are some phenotypic differences between men and women.
Men being taller than women is an accurate stereotype. Overall, men are on average 13 centimeters taller than women. The most extreme example is Macedonia, where the average man is 18.5 cm taller than the average woman.

When you look at animals, I think it's pretty intuitive to think that females are often larger than males from the same species. Spiders, fish, insects, some birds, there's an endless list of examples of bigger females than males. This is explained by a variety of different reasons depending on the species, from mate competition to the ability to bear children. So why would human males be so much bigger than women?

We all know that there are a lot of factors behind the height - and, on a related subject, strength - differences between the sexes. There are some genetic factors, as pointed out in this interesting Quora post about the topic. We also know that nutrition has a large impact in growth. In a word, we know what causes the height difference between men and women. There is a great post about it here. But I couldn't find any conclusive evidence as to why men are taller than women.

Is this because women naturally like tall men? Did prehistoric men have to be taller than women in order to thrive? Or is it just genetic drifting that, more or less randomly, led to this height difference?

The motivation behind my curiosity is feelings-driven. A while ago, my dad said during a conversation that he once "saw a documentary in which they explained that early men stole all the good proteins from the women, so they could grow taller and stronger unlike the poor females." As much as I love and respect my dad, I have a hard time believing that men are natural culprits and thieves. I am by no way making this post just to "prove him wrong" - I am absolutely interested by the topic and would love to know more. Also, if anyone knows the documentary he was talking about, I would be glad to give it a watch.

All apologies for any bad English you might find. Please tell me if I make recurring grammar mistakes.


texts: Coagulation of protiens of different products

texts:
Protein of egg coagulates on 60 degree but proteins of milk do not coagulate at high temperatures..why?
What is the main reason behind all this?


texts:
Cross-posted on r/labrats.
I haven't done cell or tissue culture in about 4 years.
Protocol:
Volume: 200ml media (academia so using sparingly, not the whole 500ml bottle!)
1% L-Glut (250uM)
My L-Glut comes in a 100ml bottle of 200mM.
What should I make up a stock dilution of 250uM in? Distilled H2O? PBS?
Should I then add 2ml (1%) to my media? Or should I add 250uM of L-Glut directly to the media?


texts: Examining milk for presence of harmful bacteria

texts:
I am not experienced in diagnostic bacteriology and am interested in understanding more about it in the context of analyzing food purity.

For example, imagine I have a supply of raw milk which might be, for example, a 20 gallon tank. I would like to ensure that listeria, e. coli and salmonella are not present in the milk.

Is it sufficient to take a single drop of the milk and examine it under a microscope or do I have to do more extensive sampling, for example, sampling every inch vertically or something like that?

What is the procedure to make sure my milk is free of the bacteria, or is that impossible?

I am not interested in procedures to kill the bacteria. I know those. I want to understand the diagnostic processes to tell if bacteria is there.


texts: Is there an "Adam and Eve" for each new trait during (not just human) evolution?

texts:
Do new beneficial mutation evolve simultaneously and independently with several individuals of the same specie or only with one specimen who then transfers it to all of the specie?
In other words, when we talks about common ancestor we usually mean a specie, so for example, all earth dwelling reptiles, birds and mammals are the descendants of Tiktaalik (to the best of my knowledge), and we know that Tiktaalik was the first (or one of the first) species to come to land, but was there a first individual Tiktaalik who went to the land, like Tim Minchin's Tony the fish.

Imagine being the first dude ever to have feet...
Imagine you're a fish, and you are swimming in the ocean ... and suddenly out of nowhere Tony just goes "I'm getting out, I'm freezing, I'm just gonna pop out for a bit, maybe lie on my towel, I'll bring you an ice cream"
-"Don't bother ,Tony, you are a freak! Tony is a freak, let's go, let's ostracize him for being different"

It seems to me that from the same species of ancestors there are several descending distinct species, so it seems to me that that that there was a species of reptiles that at some point some individual of that group developed Dinosaur features and traits and whose descendants became Dinosaurs and then Birds, and another individual of that specie or a descending specie (not necessarily at the same time) developed mammary glands whose descendants became mammals, and other individuals who didn't mate with those two whose descendants remained reptiles.
Was there ever a first dinosaur with feathers who is the father or mother of all birds, or the first fish with lungs, the first monkey with opposable thumbs from whom all apes descend, or the first mammal that decided to go for a swim and all dolphins, whale and seals are his direct descendant of that first swimming mammal?
And also for traits that don't lead to speciation, was there a first human who was lactose tolerant, and all the lactose tolerant people on the world are his/her descendants, or the first person with no wisdom teeth, the first person with slanted eyes, and the first person with red/blond hair?
*- If there are gross inaccuracies and/or over-simplification in my understanding of the evolutionary process, this is because I'm not a biologist, and I would accept happily any correction.


texts: Why do some bad traits evolve, and good ones don't?

texts:
If a trait would be advantageous to an organism then why hasn't it evolved yet?

Conversely, if a trait is not advantageous or mildly disadvantageous, why does it exist?

In other words why does evolution not make the organism more "perfect"?

This is a general question that would be applicable for any kind of trait. Please keep the answers precise and scientific.

Read this meta post for more information: Questions asking for evolutionary reasons


texts: Basic step by step methods for PCR & Gel electrophoresis class

texts:
I'm teaching a class how to do PCR & gel electrophoresis soon and would like it if you could check through my basic step by step instructions - it's a while since I've done one. Is there anything there that is wrong, missing, or should be excluded in the following?

A)    Collect all ingredients from the refrigerator and keep cool (on ice). Leave the TAQ in the freezer until required.
B)    Make master mix by adding all ingredients (ddH20, MgCl2, PCR Buffer, F Primer, R Primer, dNTP) (excl. TAQ)
.......
W)    Take the gel to the UV camera and take a picture. Large DNA molecules move through the gel slowest so will be nearest to the wells.

(The students will use primers they designed to sex 6 DNA samples from 3 species of birds, males should produce 1 band & females 2 bands in the gel)

for the full version see the answer below


texts: Does endocrine noradrenaline stimulate sympathetically innervated cells?

texts: Cells that are innervated by the sympathetic nervous system, does endocrine noradrenaline target the same receptors on them? Are they dually activated by both nervous and endocrine noradrenaline?


texts:
I spotted a grasshopper standing on a pavement with a long sting placed in asphalt. I also recorded a video of it moving:

https://youtu.be/JoDdg2yUuYo

What is it doing?


texts: psychological database with sequenced DNA records

texts:
I'm looking for an epigenetic database which includes for each example the psychological history of the persons DNA. Right now I can only find DNA and epigenetic databases. Sadly none of the databases provide "thick data" (qualitative data eg. history of person) to the sequenced DNA.

I want to investigate the effects of psychology on epigenetic and vice versa.


texts: If due to some reasons a small portion of our neurons die, how does our body remake them?

texts:
There are various reasons such as intake of neurotoxins, and possibly traumatic injuries, that can cause neurons to die.
After several hundreds, or thousands of our neurons die, how does our body remakes them?


texts: Microscope parameters for whole blood alalysis

texts:
I wonder, what are the minimum requirements for a microscope for blood cell analysis. I'm interested in:
-Counting erythrocytes
-Counting and differenciating all typed of leucocytes
-Counting of thrombocytes

What is the minimum magnification of the objective required?
Which type of objective is sufficient?
What is the minimal price-class of such an objective?


texts: Why do microarrays require a priori knowledge of the genome?

texts:
Reading this paper they said this:

Contemporary microarrays emerged in the wake of genome sequencing
projects for one obvious reason: arrays require a priori knowledge of
the query genome

Why do you need a priori knowledge? Thanks.


texts:
Are there any organisms that do not want to reproduce?
As humans, there are people who do not want to reproduce with the opposite sex. Do any other organisms replicate this behavior? Also, why does this behavior exist? If the end goal of an organism is to reproduce, why has evolution allowed organisms that do not want to reproduce to exist?


texts:
I've always wondered how toxins in certain organisms have evolved. Particularly, organisms that produce toxins as a deterrent to predators as opposed to organisms that use it to paralyze their prey.

Where did this toxicity come from? How did it develop to what it is today?

There must've been a drawn out period where evolution 'tested' and 'fine-tuned' the toxin. Presumably until it was somewhat efficacious to the target.
What are the current popular theories on this?


texts: Which of the above has naturally ink blue hyphae? Are there any that make both Ochratoxin A and fumononis toxin and have hyphae that color?


texts:
While walking back from our routine evening stroll through the hills, we stumbled upon some insect(?). It was the size of an index finger, and it appeared to have some sort of wings. While I tried to take pictures of it, it started turning towards me with it 'claws'.

Additional info:

Origin: Romania, in the hills
Date/time: 17 August 2017, 19:15, sunset
Warm sunny day, just started to cool down, 19 degrees celcius

My wife doesn't want to go outside anymore unless she knows what it is, and she won't allow me to go and pet it.


texts: Duplicity Vs. Singularity of Mammals Organs

texts: Are there known evolutionary reasons why mammals contain 2 of some organs (such as lungs and kidneys) and only 1 of some (such as liver)?


texts:
CRISPR-cas9 uses a string of RNA that matches with DNA and makes a double stranded cut at that point.

If the RNA is just a few letters in length, the enzyme would cut DNA in many places. It would be unspecific. But if you can make the RNA string very long, it would only cut at the exact place where you want to cut.

So how long can you make the RNA sequences?
And is this enough to avoid unintended cuts?


texts: When did mouth pipetting stop becoming a way to handle liquids in a lab?

texts:
Almost all modern lab protocols have an addendum prohibiting pipetting by mouth, instead mandating that a Gilson pipette, a rubber pipette ball, or a serological Pipet-Aid be used.

However, it was clear that some time in the previous century, prior to the invention of the aforementioned tools, many labs did in fact use mouth pipetting to transfer liquids, some of which were highly hazardous. An example can be seen here (from this IO9 article, which dates the photo to the year 1943):

When did pipetting by mouth stop being recommended in labs?


texts: Does the cell internal temperature changes in response to a change in external temperature?

texts:
Background

Some species are homeotherm (internal temperature is not affected by a change in external temperature) and some are poikilotherm (internal temperature changes in response to external temperature). These concepts apply to individual levels.

How about cells (unicellular cells as well as cell in a multicellular organism)? I know that cells react to temperature change. For example, the amount of cholesterol in the cell membrane can vary in response to temperature in order to keep a membrane fluidity roughly constant (ref). But that doesn't prevent the internal temperature to change.

Question

When the external temperature of cell changes, does it affect the internal temperature? I am hoping that the process is general enough so that I don't have to specify a particular organism. If it is needed to talk about a particular organism, then consider a yeast for example. How does the internal temperature of a yeast vary with a change in the external temperature?

EDIT

My knowledge in Physics being very limited, I didn't even think of Fourier's law before reading @Eli Korvigo's answer and comment and @AMR's comment. So let's make some calculations:

If we consider a spherical cell of area $4\pi r^2$, where $r$ is the radius, then the loss of heat is $4\pi r^2 \cdot \Delta T \cdot K$ (Fourier's law), where $\Delta T$ is the temperature differential and $K$ is the thermal conductivity. Then the ratio of heat production $H$ over the thermal conductivity $K$ (in order to deal with this change of $\Delta T$ °C) is $\frac{H}{K} = 4 \pi r^2 \Delta T$. If $r = 10^{-6}$ meters and $\Delta T = 2$ °C, then $\frac{H}{K} ≈ 10^{-11}$. Am I right?

Is this ratio really not realistic for a cell? The thermal conductivity for water is $k=0.56 \frac{W}{m\cdot K}$(ref.) and the heat production per cell is $34 \cdot 10^{-12}$ W (ref.). So the ratio is of the order of $10^{-11}$ as well! Am I right?

So is it really impossible for a cell to regulate its temperature?


texts: How can epigenetic changes be erased if they are inherited?

texts:
I’m a little bit confused about DNA methlyation reprogramming and about the nature of an epigenetic phenomenon. According to Wikipedia:

  After fertilization the paternal and maternal genomes are once again demethylated and remethylated (except for differentially methylated regions associated with imprinted genes). This reprogramming is likely required for totipotency of the newly formed embryo and erasure of acquired epigenetic changes.

I don't understand how something can be thought to be both heritable and erasable. Any help would be greatly appreciated.


texts: Do Alicyclobacilli produce carbon dioxide?

texts: Do Alicyclobacilli, especially guaiacol producing ones, still produce carbon dioxide? Alicyclobacillus spp. are well known spoilage organisms in the fruit juice industry. Apparently there is no "blowing up" of the packaging (often caused by carbon dioxide production) which makes it difficult to visibly detect a potential contamination. Thus the question, do Alicyclobacilli produce carbon dioxide at all?


texts:
I have been thinking about how adrenaline increases blood sugar levels, but have not been able to find an answer to the target cells. Does it affect the hepatocytes and muscle cells, like glycogen?

Thank you in advance :)


texts: Most human cancers are not (very?) contagious (perhaps besides a couple of incidents). But the Tasmanian devil seems to have a form of cancer which is contagious. Now what makes the difference between a contagious cancer and a non contagious cancer in the DNA mutations of a cell?


texts: How is duration of efficacy estimated for vaccines?

texts:
Vaccines, especially those given in adulthood, usually have term limits attached, eg: 10 years for yellow fever or 3 years for typhoid. Since presumably the time course of an immune response is no great respecter of our calendrical conventions, and since there is also presumably a spectrum of responses across the population, how are these durations estimated? What are the criteria for deciding a cutoff time?

Also, do the estimates get revisited and updated as time goes on and new data become available? Do new data become available? Is there continuing follow-up research into this, or does the estimate just get made before the vaccine comes to market and then get taken as gospel?


texts: Does anyone know what type of Cocoon this is?

texts: I am really concerned with this since I've never seen a cocoon this color before and can't find it anywhere on the internet. I found it just laying on the ground not attached to anything, but it seems to be alive because when you touch it, it will wiggle abit. Any answers are appreciated.


texts:
My textbook says this:

Osmosis is the diffusion of water.

Wikipedia says this:

The diffusion model of osmosis is rendered untenable by the fact that osmosis can drive water across a membrane toward a higher concentration of water.

It's my understanding that diffusion is passive transport, and it moves material from a highly concentrated area of that material to an area where it is in lower concentration. By this definition, it looks like Wikipedia is correct. But if for example, a cell is put in saltwater, water from within the cell would go out. Is this diffusion now? Which definition is correct?
I would just go with the Wikipedia definition because it actively describes its own definition as a refinement of the textbook definition, but the paragraph above in the article is a bit confusing to me.


texts: Which comes first, PCR or Gel electrophoresis?

texts: If I want to find out wither a group of patients have the abnormal BCR-ABL cancer gene, how do I benefit from the PCR and the gel electrophoresis techniques? I'm kinda lost trying to determine which comes first and what is the exact function of each device, I have read the whole gene cloning process in my biology book but couldn't absorb it because it's so complex.


texts: sweet receptor's affect on insulin release

texts:
So I understand the basics of how the body releases insulin to keep blood glucose levels in check and (loosely) that higher insulin levels can lead to more (or at a faster rate) glucose being stored as fat rather than being made readily available for energy. For this reason, I try hard to keep a good balance of carbs/protein/fat with each meal... operating on the principle that the protein and fat will slow the breakdown of carbs into glucose and eventual absorption into the bloodstream.

Recently, I have heard some chatter suggesting that in addition to the absorption of glucose into the blood stream, the mere activation of our sweet receptors can/does cause the release of insulin as well.

If this is the case, when I have a snack of say an orange and some cheese, while I think I'm avoiding the insulin spike (by adding the protein and fat of the cheese) that an orange ingested by itself may cause, it's actually still occurring due to, not the high glycemic index of the orange, but it's sweet taste.

Does anyone know if there is any truth to this? And if so, what does the data say... are the spikes elicited by activation of the sweet receptors of similar levels to those from actual high glucose levels in the blood?

In Googling cephalic phase insulin release, I've read abstracts for a few studies that seemed to be more focused on the effects of artificial sweeteners... which isn't really what I'm looking for. But one study seemed to indicate that solutions of sucrose tended to elicit higher insulin levels (than other solutions tested), but not being from the bio/physiology world, it quickly became over my head. I know some fruits (such as my aforementioned orange) are quite high in sucrose.

In practical terms, I'm trying to figure out what other foods, if any, may cause this response and if it is significant enough that one concerned with maintaining consistent, low insulin levels should stay away from such foods.

Can anyone help shed some light on this for a curious layperson? Thanks!


texts: Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?

texts:
I'm thinking of the human genome specifically, but more general answers are welcome.

As RNA polymerase moves along the DNA helix it follows a single strand.  The two DNA strands are unwound locally by a helicase enzyme. However, after some distance, I imagine that either the polymerase must move around the axis of the DNA OR the DNA must somehow be rotated along it's length to relieve the twisting by the polymerase.

I can't quite understand how the DNA is free to rotate, being part of a very long molecule. However the other option is also causing me a problem: the growing (nascent) mRNA can be tens of thousands of bases long while still attached to the RNA polymerase and the DNA template.  If the RNA polymerase follows the helix of the DNA, does it also drag the full transcript around with it?


texts: Can a human actually be "frightened to death?"

texts: I've been watching some classic horror movies as of late, and a trope I see in many of them is where a person will see the big bad monster and "die of fright." I'm curious, for the average person, could this happen? Or would it require a prior medical condition of some kind?


texts: Analogous organs: coevolution or opportunism?

texts:
The question reads as: "The lens of many vertebrate eyes is a crystallized form of a protein that also functions in digestion as a metabolic enzyme. This shows that

A. Vision and digestion co-evolved

B. Digestion necessarily evolved prior to vision since it is a more basic function

C. Evolution is opportunistic

D. Vision and digestion evolved around the same time"

My approach: Based on the given information it appears the protein might have given rise to analogous organs. I don't feel B has to be true in all cases. C is a good candidate but its meaning isn't clear. I'm not sure about D. To me the answer appears to be A but I would be happy to be have this confirmed.


texts: Computing Percent Identity between DNA / Amino Acid Sequence

texts:
What are some tools where I can input a pair of DNA sequences (or alternatively a pair of Amino Acid Sequences) and compute a percent similarity identity metric between them?

Is BLAST the right algorithm for this or something else?

The context is that a certain patent protects all sequences at least 90% or more identity to a given sequence. I wanted to test some candidate sequences and verify the percent identity metric.

Below I post a patent-snippet where they actually define their identity metric.


texts: Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?

texts:
I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this may have been optimal for GAIIx data (35bp) but is it still ok to use such a kmer for 150bp data?

All inputs will be greatly appreciated!

Thanks!


texts: Data repositories for data on the Tumor Microenvironment?

texts: Does anyone know of any data repositories for data on the Tumor Microenvironment? I know of the The Cancer Gene Atlas and the Gene Expression Omnibus databases but I'm more curious about data on the (molecular) composition of the TME. (I'm also curious about any databases with data less specific.)


texts: Why is Fast Fourier Transform applied to raw EEG data?

texts:
I am trying to understand why Fast Fourier Transform (FFT) is used in the analysis of raw EEG channel data.

My understanding (at the 30,000 ft view) is that FFT decomposes linear differential equations with non-sinusoidal source terms (which are fairly difficult to solve) and breaks them down into component equations (with sinusoidal source terms) that are easy to solve. It then combines each of these component/partial solutions to solve the original equation. In laymen's terms, it's like taking a smoothie, and breaking it down into its recipe of ingredients. Doing so would allow us to study and analyze each ingredient as it relates to the final product (the smoothie).

But how does this relate to raw (non-FFT-decomposed) EEG data? My understanding of a single channel of EEG data is that it is essentially a measurement of voltage over time.  What is to be gained by using FFT to break this voltage/time signal down into its constituent frequencies (alpha/beta/gamma/delta/mu waves), etc.? What additional information can each frequency tell us about the raw data?

Update:

Here is my updated understanding of how FFT relates to raw EEG data per @Mark's description below:


texts: What is this strange worm-like creature?

texts:
Hi! While I was in my front yard this morning, I happened to look down and see this little guy wiggling thru the grass. He isn't like anything I've seen before.

He is about 2 1/2 inches long. He has a small horn coming out of his back near what appears to be his behind. His belly is a light green color. Also, he starts to flick around when I touch him (To catch him, I scooped him up in a small pot.)

I live in north west Mississippi in the hills near the delta. I am also surrounded by a large forest with all kinds of both pine and normal trees, if it helps.

Thank you in advance!


texts: is there a limit to how much humans can taste?

texts:
kind of a weird question, sorry, but i was wondering--is there a threshold at which our taste buds become overwhelmed? if i, say, put some supersweet compound in my mouth, would there be a point at which adding more compound would not increase the level of sweetness i perceive? i'm sure that if i experienced too much sourness or spiciness, my tongue would probably go numb, but what about sweetness and bitterness? and what is that amount? does it vary from person to person, or are people's opinions on different sorts of food just preferences, and the threshold at which they become unable to process more of a specific taste the same for everyone?
thank you. i hope this makes sense.


texts: miRNA analysis just using BLAST against mirbase.org

texts:
I have sequencing data (Illumina). Library prep was focused on short ncRNAs. I would like to identify human miRNAs. Do you think it is feasible to simply BLAST against a current version of mirBase and filter the output for mature, human miRNAs without using bowtie/tophat against hg19 first?

Thanks


texts:
From Ecosystem Ecology
edited by Sven Erik Jørgensen

After the initial capture of energy across a boundary, ecosystem growth and development is possible by

an increae of the physical structure(biomass),
an increase of the network (more cycling)
an increase in the information embodied in the system.

What is meant by increase in information embodied in the system?
Does it mean increase in diversity of the genes (genetic information)?


texts:
Protein G (the bacterial antibody binding protein) is often used to pulldown antibodies, for example in chromatin immunoprecipitation (ChIP) experiments.

However, I was unable to find a site describing the history of the said protein, and how the name of Protein G came about, due to the fact that the similarly named (but completely different) G protein came up higher in search results.

What was Protein G named after? For example, Protein A was named after the antibody fraction in which it was found, and G protein was named because it bound GDP and GTP.


texts: I have a really basic question. Studying ChIP coupled with q-PCR or sequencing, I see different levels of a certain protein among a genomic region. I cannot really understand how can we have different protein levels. I thought that the binding of a protein in a region is bivalent-it occurs or not. But, as I can understand, we can have different concentration/quantity of protein bound to a region? And if this is the case, how in ChIP-qPCR we get finally DNA fragments, so how can we measure this binding from the quantity of fragments?


texts: Confusion about how to compute probabilities for linked genes

texts:
I am confused about how to compute probabilities for linked genes.
The problem that I am solving is this:

P generation: AAbbddEEff X aaBBDDeeFF. If A and B are 40 centimorgan apart, what is the probabilty to get aabbddeeff in F2?

Here is what I have:

F1 is: AaBbDdEeFf.
The next cross it goes through is this: AaBbDdEeFf X AaBbDdEeFf.
To compute this cross, I drew the 2 chromosomes for AaBb (in coupling), and then the probability for a is 0.5 (A or a) and the possibility for no recombination is 0.6. So 0.5 x 0.6 = 0.3. The same goes for b, so aabb is: 0.3 x 0.3 = 0.09.
For ddeeff: 0.25x0.25x0.25 = 0.015625.
Multiplying these gives 0.09 x 0.015625 = 0.00140625.
Extending that and for 2 gametes gives this: (0.00140625)^2 = 0.00197x10^-3.

But the correct answer is not what I have computed, but instead is 0.000625.
I'm really confused with this question. If we know that only 2 of the 5 genes are linked, is it still correct to multiply: 0.09 x 0.015625 = 0.00140625?  Maybe I should use a Punnett square somehow? Because in that case, the probability for a recessive homozygous is 0.0625 but I'm not sure it fits to this question.


texts: First discovery of long-term depression?

texts:
LTP was first described by Tim Bliss and Terje Lømo in their paper Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path.

When was LTD first described? By whom?


texts: Does having to urinate imply that you are becoming dehydrated?

texts:
This question came up after I read another question that coffee does not dehydrate you, but instead acts as a mild diuretic.

Does having to pee imply dehydration?

Allow me to elaborate: When you have to pee, that liquid is already in your bladder, right? If so, it is not in use by cells. However, since that water must have been previously absorbed in the body in order to be filtered through the renal system, having to pee indicates that you are less hydrated than you once were.

So in the case of coffee, while it doesn't directly dehydrate you, doesn't it indirectly dehydrate you by causing you to pee?


texts: Why are vaccines containing attenuated microorganisms preferable to those containing dead microorganisms instead?

texts: My teacher said it more closely resembles a real infection but I didn't get that.


texts: Do all different types of neurons serve different roles?

texts:
I know from my basic education in neurology that the brain has various sorts of neurons. These are usually bunched into 3 different categories (sensory, moto and interneurons).

I read in a recently published book, and papers on modern neuroscience that there have been thousands of different types of neurons identified in the brain. Does this mean that there are different types neurons each dedicated to a very specific task in the brain? If that is true, then what is each individual neuron's job (a few examples would be sufficient)?


texts:
Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments?
Particularly the Acs1 protein (Acetyl-CoA synthetase) seems to be a protein I often see in a TAP-MS experiment so I am starting to think it is a false positives but I can't seem to find a good paper or website where it is mentioned as a commonly found false positive interacting protein.

Any insights will be helpful.
Thanks.


texts: Is the CDC's reported drop today in COVID-19 cases by date of diagnosis meaningful?

texts:
I was waiting with bated breath for the CDC update on cases of COVID-19 in the U.S. by date of onset.  To my eyes this looks like absolutely wonderful news - that it means that the exponential growth of the virus has been "flattened" - but I'm still afraid I may be misinterpreting what I see.  It bothers me that the headline for the graph hasn't changed.  But it APPEARS that the number of new cases stopped increasing after 3/3.  Am I missing something?

Top: before noon on 3/16, bottom: after noon on 3/16.  Data from https://www.cdc.gov/coronavirus/2019-ncov/cases-in-us.html

Note: In today's update (the first in three days) the CDC page shows the number of cases with onset on 3/4 to be 159, and 3/9 is 307.  This doubled in five days rather than every two or three as other numbers would suggest, but given the dramatic changes in this curve, and their overall direction, I think the top answer below has been vindicated.


texts:
I am a PhD student and stuck with the no band in the gel  results.

I am using the following

1 microliter  Primer R (20mM)
1 microliter  Primer f (20mM)
1 microliter  dNTP  (10mM)
1 microliter  DNA Template ( 448 ng)
1 microliter TAQ polymerase
5 microliter Buffer (10x)  added MgCl2  by 1:1
30 microliter PCR grade water

Program:

95 for 4 minute
95 for 45 sec
55-65 for 1.20 minute
72 for 1 minute
Gradient 35 cycle
72  for 4 minutes

Gel:

110 volt, 200 mPA for 30 - 45 minute

I get PCR products as in the images. There are no bands  while there are intense bands at the bottom and some of the wells.

My question is,  is that at the bottom products??
what can be done to make them real? If not then why there are differences between the two lane of wells. Each 12 well are representing a one type of DNA template (I used three different organisms DNA).


texts: Why are Merkel cells innervated by an axon, and not a dendrite?

texts:
Here are two images from Google. Afferent neurons receive input and send it to the central nervous system. Input is received by the neuron's dendritic end and send away centrally via axon terminals that are sheathed with Schwann cells. Axon terminals synapse to motor neurons (muscles and glands).

How is it possible that Merkel cells, which supposed to be a sensory cell, synapse with an axon, and not with a dendritic end?


texts: How do you express and detect GLP-1 receptors?

texts:
I am currently working with a peptide which is an analogue for glp-1, but during invitro studies am not able to detect for the presence of GLP1- receptors.
The cell line used is Min-6. How do I detect it?


texts: Why is the ratio between action potential and threshold value called the 'safety factor'?

texts:
"AllorNothing Principle. Once an action potential has been elicited at any point on the membrane of a normal fiber, the depolarization process travels over the entire membrane if conditions are right, but it does not travel at all if conditions are not right. This principle is called the all-or-nothing principle, and it applies to all normal excit- able tissues.

Occasionally, the action potential reaches a point on the membrane at which it does not generate sufficient voltage to stimulate the next area of the mem- brane. When this situation occurs, the spread of depolar- ization stops. Therefore, for continued propagation of an impulse to occur, the ratio of action potential to threshold for excitation must at all times be greater than 1. This “greater than 1” requirement is called the safety factor for propagation."

This might be a more basic, straightforward question but for some reason, there's not much info on it on the web.

I'm guessing its called the 'safety factor' because it means that not any stimulus can cause an action potential and that the cells remain at equilibrium/their un disturbed state for most of the time, but this is only a guess.

Source of Info: Guyton & Hall Medical Physiology textbook


texts: Why do PCR manufacturers recommend assembling the reaction mix on ice?

texts:
Many PCR manufacturers recommend preparing the reaction mix for the reaction on ice. For example, here is NEB's recommendation for their Q5 polymerase. Other manufacturers also include similar steps:

  We recommend assembling all reaction components on ice and quickly
  transferring the reactions to a thermocycler preheated to the
  denaturation temperature (98°C).

However, I can't think of a good rationale for this. This ResearchGate thread describes a few reasons, but they don't seem to make much sense.

Primer mispriming onto bacterial gDNA - Highly unlikely, since the initial melting step would melt away these misprimed primers and allow them to prime the correct sites.

Polymerase is proofreading (3'-5' exonuclease) - Proofreading activity should not affect any of the components, since the primer oligos are present in very large quantities, and the template should not be significantly affected by any proofreading, since they already have the correct sequence.

RNA is degraded by the polymerase - An extremely ridiculous answer, since PCR does not use RNA as a template, and RT-qPCR uses reverse-transcribed cDNA as the template. Whether the RNA is stable or not has no bearing on the activity of a DNA-only PCR once the RNA has been reverse-transcribed.

Polymerase is thermolabile - This is probably the most ridiculous answer to the question. The whole point of using polymerases like Taq, Pfu and Q5 is that they are from thermophile organisms, and they are highly thermostable to withstand the high temperatures during PCR.

What, then, is the reason PCR reactions are recommended to be assembled on ice?


texts: Scatchard Plots and Total Receptor Concentration

texts:
Im having trouble understanding Scatchard plots.
Y Axis = Bound/Free Ligand
X Axis = Bound Ligand
The graph has a negative slope.
Why when there is almost no Bound (Y axis = 0) do we get a high positive number for Bound ligand on the X Axis corresponding to Receptor concentration? if there is no bound how is there a positive bound number?
it looks like the less bound ligand on the Y axis, the more bound on the X axis!


texts: Have there been any positive public health effects due to UV lights?

texts:
Occasionally, in hospitals and in eating establishments in the US, they have industrial grade UV lights in sconces attached to the wall (though they seem to be less prominent as the years go by).  I understand the anti-microbial properties of UV light, but are these devices anything more than show pieces?

Have there been any lasting, significant public health gains that have been correlated with the use of UV light in public places?


texts: Is galvinoxyl antioxidant assay possible using NMR spectroscopy?

texts: I would like to perform an antioxidant assay using the galvinoxyl protocol. The protocol states that we need EPR spectroscopy, but only NMR spectroscopy is available at my institution. Is there an alternate way where I perform a galvinoxyl assay using NMR spectroscopy.


texts: What is the simplest way to demonstrate the germicidal property of UV light?

texts: This is intended for a high school project. I am familiar with the one that studies growth of e coli over time in a petri dish but I a bit concerned about as to how safe a demonstration of this nature might be. also no idea as how one may obtain such e coli sample safely.


texts: Is it possible for a human being to live on a different day cycle?

texts:
I am considering writing a story where a character lives on a 30-hour day cycle.

That is, this person sleeps for 9.5 hours and is awake for 20.5 hours.  Then this person repeats the schedule.

I'd like to know from those of you whom are more knowledgeable about biology and physiology whether this is possible.


texts: Is it possible to create an experiment in house conditions to prove the existence of germs?

texts:
I realise that the best way to prove the existence of germs or single-celled organisms is by looking at them through a microscope.
But I don't have a microscope at my home, how can I design an experiment in a normal house environment to show the existence of germs (or other single-celled organisms) without spending too much money?

By "house environment" I mean that I have access to normal stores and the internet. If it's something that can be bought in a "normal" store or on-line without getting me into trouble, and doesn't cost a lot then I can have access to it. I don't have access to lab grade equipment or conditions, so no sterile rooms or special growth environment.

I thought about the following experiment, inspired by the mythbusters pyramid power episode. In the episode they cut an apple in half and put one half under a pyramid and the other not under a pyramid. In the first attempt one of the halfs rotted quicker than the other, they concluded that it happened because the saw they used to cut the apples wasn't sterile.

So I thought about taking 3 apples, contaminating a knife (by rubbing human saliva on it). Cutting one apple with the contaminated knife, one apple with a sterile knife (using rubbing alcohol to sterilize it) and one apple by a knife that has 1 contaminated side and one sterile, which is a contaminated knife, that had only 1 side sterilized with rubbing alcohol. Then leaving the 6 halves in separated sealed containers (some tupperware) for a few days and then looking examining the rott. The expected result is that the "contaminated apple" will have a lot of rot on both halves, the "sterile" apple will have no (or close to no) rot, and the half and half apple will have one rotten side and one not rotten side, and the sides will coincide to the contaminated/sterile sides of the knife touching them.

Will this experiment work?


texts: Botany related question: liverwort sporophyte

texts: Is perianth part of the sporophyte or gametophyte in liverworts (Marchantiophyta)?


texts: What is the difference between these worms: Caenorhabditis elegans and Eisenia fetida?

texts: I love worm composting (I use red wiggler worms), but wondering how similar or different the Caenorhabditis elegans and Eisenia fetida are?


texts: Is there a organ or type of cell that makes Nagalase?

texts: Schindler disease / Kanzaki disease is being described as alpha-N-acetylgalactosaminidase deficiency. So then, which organ or cell(s) produce this alpha-N-acetylgalactosaminidase (Nagalase) ?


texts: What are the alternatives to using a histidine-tag in detecting protein-protein interactions? Why would they be more beneficial than his-tags?


texts: Does vaccination lead to short-term secondary infection suceptibility?

texts:
For clarity, here is a summary of my question, per anongoodnurse's comment:
Does a lower peripheral lymphocyte count resulting from recent immunization render us more susceptible to infection by other viruses?

There are many bad-faith arguments circulating that suggest COVID-19 vaccines are doing more harm than good. One talking point is that COVID-19 vaccination leads to a temporary reduction in circulating white blood cells, leaving vaccinated individuals susceptible to infections in the short term.  Former NYT reporter Alex Berenson has been making such claims on Twitter:

1/ The fact the mRNA vaccines transiently suppress lymphocytes after vaccination has come up repeatedly on the feed as a possible explanation for post-vaccination deaths.
Fact check: This is TRUE. @BioNTech_Group
acknowledged it its papers (both 162b1 and 162b2 did so)

2/ By the way, they also lead to a sharp rise in C-reactive protein.
Would love immunologists or virologists to chime in on whether these changes may be in any way clinically meaningful

As sources, Berenson cites two papers detailing the results of phase I/II trials for mRNA vaccine candidates.1,2
Derek Thompson addresses this Tweet and other claims made by Berenson in an article in The Atlantic 3, in which Thompson asks experts to challenge the misinformation shared by Berenson. Regarding the Tweet above, virologist Shane Crotty said the following:

The claim he is making is simply fearmongering, connecting a simple physiological event with bogus claims of deaths ... The observation of lymphocyte numbers temporarily dropping in blood is actually a common phenomenon in immune responses ... The cells are not gone. They come back to the blood in a few days. It is generally a good sign of an immune response, not the opposite.

While Berenson's claims regarding post-vaccination deaths are derived from his (willful?) misinterpretation of the data, Crotty's response got me thinking about the immunological dynamics of vaccination. My question: Does the localization of lymphocytes to secondary lymphoid tissues the site of a vaccination  (re: bob1's comment) lead to reduced circulating lymphocytes and a subsequent increase in susceptibility to secondary infections? By secondary infection, I mean a challenge from a pathogen that is different from the one for which the vaccine was received.
For example, a person receives a dose of one of the SARS-CoV-2 mRNA vaccines, then, sometime during the critical period when circulating lymphocytes localize to the site of vaccination, the same person comes into contact with an influenza strain for which they have no adaptive immunity.  Would that person have a lower chance of contracting flu had they not received the SARS-CoV-2 vaccine, all other factors being equal?
I found one publication that shows reduced risk for infection by influenza in patients who already had SARS-CoV-2, though this is attributed to pathogenic competition.4 Considering total pathogen dosage, it is logical to me that challenge with two pathogens is more likely to lead to illness than challenge with a single pathogen, but is there anything in the literature that suggests co-infection by an immunogenic "mock" pathogen (vaccine) and a secondary pathogen leads to a greater incidence of infection by the secondary pathogen?

References

Mulligan, M.J., Lyke, K.E., Kitchin, N. et al. Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults. Nature 586, 589–593 (2020).
Sahin, U., Muik, A., Derhovanessian, E. et al. COVID-19 vaccine BNT162b1 elicits human antibody and TH1 T cell responses. Nature 586, 594–599 (2020).
Derek Thompson. The Pandemic’s Wrongest Man. The Atlantic, 1 April 2021.
Stowe, J., Tessier, E., Zhao, H. et al. Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design. medRxiv 2020.09.18.20189647.


texts: Looking for good reference book in molecular biology

texts:
I am starting to work in molecular biology/ molecular genetic and I am looking for a really good book containing the main concepts and mostly the more recent techniques.

I would be interested in a book that has also protocol examples and examples on how to apply the different techniques.
My focus is on bacteria and fungi.

Any suggestion?


texts: Are all emerging viral diseases of the past 100 years zoonoses?

texts:
From my basic understanding: The viruses causing Ebola, Sars and Covid-19 are all the result of a zoonosis, meanings that the viruses have passed from animals to humans.

So my question is: Are all recently (let's say 100 years) emerged viral diseases, with potential for a global epidemic, the result of a zoonosis?


texts:
This plant was found growing in Germany. I have never seen it before, reverse Google image search did not help either. Can you help me identify what type of plant this is?

Thanks, looks like it is something like this:

http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034

Related question:

https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610


texts:
I think it is decreased blood supply to organs and tissues.
I also think it is the stopped circulation.
However, both ones cannot be right, I think.

What is ischaemia exactly?


texts: Why do we anthromorphize evolution and genes and nature?

texts:
Books sometimes says things "Our genes want us to have as many children as possible", or "Evolution
wants the fittest to survive". But genes are not conscious entities who can want things. So, why do we anthromorphize genes, evolution, and nature? I apologize if this question is not appropriate for this stack exchange. Perhaps it can be moved to an appropriate stack exchange if it is.


texts: How many atoms has the smallest known bacterium?

texts:
Background thoughts before this question: is it feasible to simulate a complete bacterium, atom by atom, in a computer simulation? On modern systems, either in an  upcoming exascale computer?

In current research they've simulated an organella with 100M atoms but I don't know on which infrastructure.

On Quora, there is an estimation of E.coli to have about 9x1010 atoms. With 4m base pairs it is though still quite big and possibly would produce too high computational workload in a simulation.

See also:
https://scicomp.stackexchange.com/questions/33941/is-a-complete-bacteria-simulation-with-an-exascale-supercomputer-possible

If they have simulated an organella with 100M atoms atom by atom, possibly you could already completely simulate some viruses, but they are not independent organisms.

So there has been an atom by atom simulation of the polio virus capsid in 2014 on the K computer with 10 petaflops. To include enough water molecules to fill and surround the capsid, Okazaki and colleagues needed to model the dynamics of nearly 6.5 million atoms, which they did for a simulated 200 ns.

Question - which order of magnitude would a small bacterium count on atoms? What about the smallest known bacterium Nasuia deltocephalinicola with its 112K base pairs? How many atoms has it got?


texts: What determines when twining plants twine?

texts:
Some climbing plants, such as clematis and honeysuckle use their leaves like tendrils. Others, like Aristolochia use their stems. The young leaves of these plants are able to twist around slender objects. Twining stems twist around whatever they touch, be it a pole, branch, wire or chair leg. The stems will wind clockwise or counterclockwise, depending on the species of plant.

AFAIK, plants can't see or feel, but the way they climb clearly shows they have some way of knowing when to twine. How does this work?


texts: What is this bird - sound attached - (Atlanta Georgia)?

texts:
We live in Atlanta Georgia (northern suburb) & this bird starts singing in the middle of the night !!

And goes on for almost 2 hours without stopping.

Here is the link to it :

https://drive.google.com/open?id=0B3WzrpCj4uKeQ3l5MnJPY1RfcUpiVzkxRHBsWEN4RnYtTlNB

Any way to politely ask him/her to stop singing at night ? :)

Would highly appreciate any help in this regard !


texts: Species Distribution Modeling: Mammal river species

texts:
When working with mammal river species, what parameters would you use to study them  (I have max and min temperature, average rain, slope and obstacles in the river)
Something like type of riparian forest?
Is there any good example of species distribution modelling of mammal river species?

Thanks, Héctor.


texts: How is the brain kickstarted during development

texts:
The brain is a complicated beast, that operates (generally) by electrical activity. During development, all cells originate from the a single "cell": the zygote.

At some point during development, the cells will begin to form into the specialised cells of the brain. But how does the brain activity start?

Is there some process that gets things going, akin to jump starting a car? Specifically, I'm referring to the mammalian (and more specifically human) brain.


texts: Percentage of mutations caused by radiation?

texts: Consider a gamete in a typical human being. In the interest of being specific, let us say that we're talking about a typical ovum in a typical middle class woman living in a developed nation. What percentage, on the average, of the mutations in the genome of that ovum will have been caused by electromagnetic radiation?


texts: Identification of small fuzzy flying insect (pic)

texts:
These critters were flying around the neighborhood on an autumn evening in Seattle, WA, USA. Their most notable feature was the small amount fuzz on them. They were quite slow in their flight compared to similar-sized fruit flies.

Any ideas?

Here are two close-ups:

One one for size comparison:


texts: Is breathing in deodorant fumes dangerous for my brain?

texts: I noticed that I sometimes get dizzy when I accidentaly breathe in too much Axe. Also, I find the smell of alchohol rich deodorants quite unpleasant. But, I was wondering, is it actually dangerous? Can some chemical (alchohol) pass the blood-brain barrier and hurt my brain? Can it hurt other organs? It might be that I'm just dizzy because of the lack of oxygen...


texts:
Kiwis have the enzyme actinidain. This enzyme will break the peptide bonds from the gelatin. Making gelatin with raw kiwis will not work, because the peptide bonds in the gelatin will be broken down.

But what if you would make plain gelatin, and apply raw kiwis to it? Do the enzymes break down the gelatin when the gelatin already has set?


texts: Usage and mechanism of the Bastien protocol to treat amanitin poisoning

texts: In 1971, 1974 and 1984 a French doctor Pierre Bastien (frwiki) voluntarily poisoned himself by ingestion of Amanita phalloides mushrooms in order to popularise his method of treatment of such poisoning. This method seems to have consisted of vitamin B and C injections and dosages of Abiocine and Nifuroxazide. Is this method still being practiced or has it been discouraged? What would be the mechanism of this protocol?


texts: So apparently we produce roughly 300 million sperm daily. Is there a reason why this is necessary? Wouldn't a much smaller (but still large) number be sufficient? Like, one million?


texts: How can sex ratios remain Fisherian (1:1) in species where only the dominant male gets to mate

texts: In certain species only the dominant male gets to mate (or given strong preference), and yet the sex ratio remains 1:1. (I'm thinking in particular of gorillas). How does this happen? It doesn't seem like Fisher's argument should apply in this case.


texts: Is there any animal known to produce structures of both keratin and chitin?

texts:
I began with thinking about the similarities between keratin in its hardest form (fingernails, horn sheaths) and the chitin that composes the exoskeletons of some few beetles I've seen in my life. To my eye the two materials seem to have comparable properties. Then I found out that tarantula hair is also made out of chitin, so in more aspects than one it seems that chitin and keratin have convergently evolved.
I understand that chitin is a carbohydrate while keratin is a protein, so there's no commonality regarding the origin of the two, but I am curious as to whether an animal has ever been demonstrated to produce both compounds in some capacity?


texts:
I know most people can't enjoy sex if their spinal cord injured.

How spinal cord play its roles in human beings sex?


texts:
While whatching a film, I've been thinking about how does a headshot kill someone, and how long does it take?

For example let's say you've beeing shot by a normal (police) handfired weapon - no shotgun or sniper weapon.

I know that the rhombencephalon regulate the most important vital functions like breathing and if the shoot goes throught it, that there will be no change.

Question:
But if the bullet passed the brain throught the telencephalon, which function is mainly thinking, and don't hurt any
brain regions who handles life keeping functions (like the rhombencephalon)  do you die instantly (like in movies) or have any change (fall into a coma)?


texts: Will a completely removed cat whisker grow back?

texts: I just accidentally pulled out, while playing, my cat's whisker entirely, follicle and all. I feel terrible as I know she is a kitten and whiskers are rooted deep in a place rich in nerves. I'm wondering if the whisker will grow back and if it will cause a lot of pain as it regrows.


texts: Does natural selection select for randomness in development?

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In a podcast with Sean Carroll and Liv Boeree they discuss a result from game theory that the optimal strategy in the face of incomplete information can require random decision making. For example, without more information (e.g. the robot that uses high frame rate video and fast movement to see what the human is picking and quickly pick what beats it), the strategy in rock-paper-scissors that cannot be dominated is to choose which one your going to do randomly with equal probability.

We know that situations where there is not one optimal strategy exist in biology. Examples: male vs. female, side blotched lizards, E. Coli (produce toxins and defense vs. just defense vs. neither).

Now, in most of the examples above the source of the randomness is entirely from sexual reproduction (meiosis). The only example I can think off the top of my head of where this isn't the case is for crocodiles (maybe only some) where the sex is fixed by the temperature the egg is at during a certain stage of its development. In a sense, for them, sex selection is completely non-genetic but is done as a response to a stimulus.

My question is this: are there examples of genes that control development in a non-deterministic way (i.e. are there genes that by their presence will produce a trait with some probability greater than zero and less than nearly 1)?

I think genes that can be switched on and off in response to relevant environmental stimuli shouldn't count (e.g. the development into a queen for a honey bee). I'm just interested in whether there are genes that function in a highly random fashion and if natural selection has lead to such genes being produced (something like the presence of gene X causes trait Y with 30% probability, all other genes being equal). I add the qualifier "highly" to the randomness because these processes are ultimately always going to have some randomness from thermodynamics, and our cells go to a lot of effort to mitigate that randomness in most situations.


texts: Is there an animal which, when eaten by other animal, poisons the predator and gets out of it's stomach?

texts:
It was a question in one competition, but it remained unanswered and i am curious about an answer.
There was a hint: American bullfrog
but i can not find any example of this behaviour on the web.


texts: How did the orchids evolve to support pseudocopulation when they do not have any organ for vision to see how insects look like?

texts: How could they guess so perfectly how a moth or whatever the pseudocopulating organism looks like. They do not have eyes to see the shape or structure. What could possibly be the reason they evolved with such accuracy to deceive an animal?


texts: What kind of spider is this? hoping its not poisonious

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Found outdoors, after it was killed we found little tiny baby spiders on our ceilings throughout our house. really wanting to know if this spider is venomous or not as we have a baby of our own in the house..

Found in Bligh Park 2756, Sydney NSW Australia.
I would say it’s around 10cm.


texts: Where can I find free authoritative images of different species of Lagomorphs?

texts:
I would like to make an infographic showcasing the order Lagomorpha (rabbits, hares, and pikas), which contains a dozen genera and about 100 species. I want to include a picture for most species, or, failing that, a picture for each genus. The difficulty is that I'm not at all an expert on these animals -- I just find them cute and I like infographics -- so if I simply google around for pictures of them, I won't be able to verify that a picture labeled "Bunolagus monticularis" is actually a picture of a Bunolagus monticularis specimen, rather than something else.
Photographs would be ideal, but I'm fine with using sketches instead when no photographs are available. It would also be ideal if the images were free to use and in the public domain (or licensed under some version of Creative Commons)
Is there any source for images of species specimens that is generally considered trustworthy? It's fine if it's limited to lagomorphs, but if it also extends to other animals/plants, that's all the better!


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I've gotten conflicting advice on this: some people believe one can remove RNase contamination simply by spraying the bench, pipettes, gloves, etc. with ethanol. Others think ethanol does not destroy RNase and special reagents are needed to prevent RNase contamination.

So does ethanol remove RNase contamination? If not, what reagent does?


texts: When using a primer to replicate DNA in a plasmid, does it replicate the whole plasmid?

texts:
I've been learning about PCR and plasmids. I understand that the reason for having both a forward and a reverse primer is to extract and amplify the specific piece of DNA between these two primers.

What I'm struggling to understand is that why after the first replication, a fully circular DNA strand isn't formed and hence, why isn't a fully circular DNA strand formed for each replication.

For the following diagram , let the strands be labelled strand 1, strand 2, strand 3, strand 4 from top to bottom. (Diagram from Lehninger Principle of Biochemistry, 5th Ed).

For example, in the diagram here. When cloning a plasmid I assume strand 1 is fully circular, so strand 2 (which was transcribed from strand 1) should also be fully circular and in the diagrams it should show DNA to the left of the site of interest.

Does the transcription stop somewhere along the line, preventing it from copying the whole strand? Or does the strand never join up into a circle, so that the DNA that would appear to the left of strand 2 has been copied, but doesn't join up to the site of interest so wasn't included in the diagram.

Thanks for your help.


texts:
The common garden snail was originally assigned as Helix aspersa and stayed that way for over 200 years. Recently, some biologists assigned it to the genus or subgenus Cornu renaming it to Cornu aspersum, yet other researchers assigned it to Cantareus. Still, many texts still use the name Helix aspersa.

My question is what is the correct or official binomial nomenclature (scientific name) of the garden snail as for 2019?

Remark: I read Wikipedia but even there there are inconsistencies about it. E.g. Wikispecies.


texts: Why does no one get vaccinated against plague in Europe?

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I've read on Wikipedia that only people who work with Y. pestis and people in 3rd world countries get vaccinated against it:

  Since human plague is rare in most parts of the world, routine vaccination is not needed other than for those at particularly high risk of exposure

But I know that it is easy for plague to conquer Europe. All your need is just some fleas and half of the continent dies, as proved in history.

So why does no one in Europe get vaccinated against plague?


texts: What species of arthropod is in this picture?

texts:
I've found exactly one of these, dead, on my kitchen floor most mornings this past week.

It looks like a large flea, is about 1 cm long (picture compares it to a British 10 pence coin, approx. 24.5 mm in diameter) and 2 mm thick with a laterally flattened body.

I believe it to be of the order Siphonaptera, but am unsure as to what exactly it is.

Can anybody identify the exact species of this arthropod?

If it helps, I live in the South-West of the UK.


texts: Why clotting does not occur during Menstruation

texts: As we know when we get injured our body's clotting systems stop the bleeding. So why does it take days for menstruation to stop ?


texts: To what extent does the 260/230 value affect the efficiency of PCR reactions ? Do the constituents leading to a low 260/230 value (EDTA, guanidine salts and oligosaccharides) inhibit PCR ? I have been getting pretty low values of 260/230 (0.5-1.0) for DNA extracted using Charge Switch Protocol using Magnetic beads and the PCR has been failing. Also, is there any reason why I might be getting low 260/230 values in Charge Switch method ? (I was getting good values using Phenol-Chloroform extraction method)


texts: Is there a way to measure the amount of bytes that are possible to encode in a DNA molecule?

texts:
When I saw a DNA molecule for the first time, it kinda reminded me of a hard drive. It consists of slots and there are some possible combinations for each slot; in the hard drive these possible combinations would be 0's and 1's. In DNA, these slots would be G's, A's, T's, C's.

So, is there a way to measure the amount of bytes that are encoded in a DNA molecule?

I've made this question before in another forum, but the answerer provided me only with Shannon's theorem, which is $K=L-\frac{(1-q^L)^n}{q^L}$ and told me a little about genetic redundancy. I could only search for the ammount of slots which are present in the DNA, but this genetic redundancy thing got me stuck.


texts: The role of voltage-gated ion channels in chemical synapses

texts:
I am trying to understand the mechanisms underlying action potential generation on
the cellular level.

Typically, there is an emphasis on voltage-dependent permeability changes of Potassium (K+) and Sodium (Na+) channels which lead to the respective changes of the membrane potential.

Also typically, synapses in the brain are chemical synapses (in contrast to the smaller fraction of electrical synapses, e.g. in the hippocampus, which make use of gap junctions for signal transmission).

My confusion is now this: Chemical synapses depend on neurotransmitters to trigger permeability changes. The canonical explanation of action potentials is with reference to voltage-gated channels -- how do these two things go together?


texts: Is there a comprehensive list of dinosaurs synonyms with indications of which name is now considered correct? Something like "there's no brontosaurus, there's only Apatosaurus", "there's no Anatotitan, there's only Edmontosaurus" and so on.


texts: Where does the exudate comes from during inflammation?

texts: During inflammation transudate and exudate is formed by vessels. I would like to make sure if it comes from arterioles, venules, or both, and the reason why.


texts:
Tissue culture means that cells are propagated and multiplied under controlled conditions. Suppose the following situations:

  a) A seed being is embedded in an Agar medium and germinated under controlled conditions.
  b) An individual cell is extracted from a parent plant and embedded in a medium, resulting in the formation of a callus (germination).

Are these both examples of tissue culture? Both situations seem to fall under my definition of tissue culture.


texts: If a device were created to monitor the nervous  signals from the heart, including stable heartbeats, rapid heartbeats, etc., and this device were capable of transmitting the "stable heartbeat" to the heart, would this have any adverse or advantagious effects for medical science?


texts: Why don't we hear ultrasonic sounds as aliased versions of the original signals?

texts:
The upper limit of hearing is approximately 15 kHz, dependent on age and other factors. According to the principles of digital signal-processing, such an upper limit would mean that the auditory system samples at least at 30 kHz or more.

Now suppose an ultrasonic signal, say a 40-kHz acoustic frequency - why would I hear nothing, instead of that signal aliased at a 30 kHz sampling rate?


texts: How to identify the age of a "living" person?

texts:
An Indian old man claims he is [180 years old] now.

We are not able to tell he is 180 or 181 probably. But can we tell he is 90, 120, 100 or 150?

Different people may age differently.
A 60-year old person may appear to be 80, while somebody else could appear younger than their mathematical age. Some other people may have progeria.

What is the most accurate way to identify a living person's age nowadays?
Are there reliable parameters to measure?

C-14 needs a long time base line. Hence, it is suitable for the bone of dead people.

What kind of method can guarantee it can distinguish a 30y and a 80y old person?  What's the error bar of that method?


texts:
Is it possible that a human or any other creature can die from pain?

I googled and found different answers. Some articles say Yes while others say No.


texts: How did our bodies decide on the right enzymes and where did we get them?

texts:
I have read that enzymes act as catalysts to reactions in our bodies and that they are extremely target-specific.
My question is how did our body know that a particular enzyme could act as a catalyst for a particular reaction? How did de we get the perfect combination of reactants and their catalysts?
Note:- I am not a person who is studying biology so I might not know that which is pretty obvious to you people.
Anyways, the least expected answer is that ancient aliens carried out some sort of Worldwide Enzyme Injection Programme ;-)

Edit:- By the knowledge gained after asking this question I've figured out that it might be something like this -
There were species which had a different set of enzymes than us but as these weren't the right match the species perished. Those who had the right enzymes survived. Am I right ?


texts: Identifying a possible pathogen of a succulent plant (Haworthiopsis attenuata) presenting with small brown scales

texts:
I have a succulent (most likely Haworthiopsis attenuata) that is currently not looking so hot. I recently noticed a number of small brown scales growing on multiple leaves, that I think are some sort of pathogen (or at least are not part of the plant) for the following reasons:

They don't appear to follow any sort of pattern like the white marks on the leaves.
They are easily detachable with tweezers--I plucked two or three off as a test.

The best explanation I've found myself is that they're some sort of scale insects, but they seem really tiny. These are about the size of a Chia seed--only a few mm across. What are these, and as a bonus, how can I get rid of them? Photos are below:


texts: Does the saliva of a person just recovered from an infectious disease help to cure another persons having the same disease?

texts: I have always had this 'weird' thought (But could never quite test it...). Would the saliva of a just recovered person contains antibodies, or other immuno-boosting substances that can help fight off the same pathogen in another person? If yes, is the concentration (dose) of them in saliva enough to have any considerable effect directly (without any further artificial concentration or extraction done)?


texts: Is there really a clear distinction between dinosaurs and birds?

texts:
Traditionally, birds are classified as a class of dinosaurs and the term non-avian dinosaurs is introduced to refer to the rest.

As recent discoveries suggest that some dinosaurs may have been warm-blooded and that some dinosaurs had feathers, the distinction between birds and dinosaurs seems blurred.

I have often heard statements like "Birds are the only dinosaurs that survived the Cretaceous–Paleogene extinction event.". With recent discoveries, isn't this how the clade of birds is defined rather than a fact about the extinction?

// not sure if this question belongs in biology, sorry


texts: Correlation between threat and odour, taste

texts:
Is there any sort of correlation between threat and taste/smell?
Are we evolved such that things which are harmful to life taste and /or smell bad and things(food) which are useful to us taste, smell good?
How far this conjecture correct?


texts: Could planaria regenerate when cutting vertically to 3 thirds or more?

texts: Reproduction in planaria occurs when we cut it into 2 halfs vertically .


texts: Concentration gradients across membranes with different ions

texts:
I'm trying to gain an intuition for the dynamics of across neuronal membranes. The overarching idea here is they are controlled by ion concentration gradients across the membrane (which we can describe mathematically).

I'm looking for someone to delineate every present concentration gradient across neuronal membranes that are relevant here(involving $Na^+$, $Ca^{2+}$, $K^-$, and $Cl^-$).

It's unclear to me what creates a concentration gradient:

Are the concentrations of each type of ion independent from eachother, i.e. in a world without charge, diffusion across the membrane is individual to the concentration of each ion, or, is mediated by the net concentrations of mass (which makes less sense)?
Is the flow of ions across the membrane driven by net charge on each side, or the charge concentrations of each individual ion?


texts: Meaning of a negative value for non-fiber, non-sugar carbohydrate based on a nutrition label

texts:
One of the questions for my lab is to find the non-fiber, non-sugar carbohydrate per serving of an onion. Now the total carbohydrate for this onion is 11 g, the total sugars for the onion is 9 g, and the total fiber is 3 g.

11-9-3 = -1 g of non-fiber, non-sugar carbs for this onion and this is not making any sense to me.


texts: In reference to genotyping primers, often some are labeling with 'oIMR'. It seems that this often refers to internal positive control primers, but I'm not sure. What does this stand for?


texts: How do we know how long hermit crabs live in the wild?

texts: This article states that hermit crabs in the wild are extremely difficult to track because they constantly change shells and even gender.  Later in the article, they say that hermit crabs can live 4 decades in the wild.  How can they know this if they can't follow a single crab for an extended period of time?


texts: Can a tumor produce something not currently found in our own bodies?

texts:
While speaking with my co-workers, the topic of tumors growing things came up.  The examples were (and backed by images) of tumors growing a tooth, hair, and sometimes even more complex objects such as an eye.

My question is, could a tumor reproduce something that isn't typically found in the human body?  Could it grow something that maybe a very distant ancestor would have had?


texts: Are there toxins that cause heart attack and/or stroke in multiple individuals in short time frames?

texts: Are there any known environmental factors that would cause more than one person to have a heart attack or stroke within a short period of time (e.g. 2-3 months) of one another? I'm particularly looking for causes that are likely to be found around the home (e.g., chronic low-dose CO poisoning), as opposed to industrial sites.


texts: How long do the periods of systole and diastole last?

texts:
The background to this is i'm doing some work using ECGs for an animation of the heart and i'm having trouble defining the end points of these periods, particularly diastole. Currently, the only information the animation uses is the time (in seconds) when a R peak was detected in an ECG.

So i was wondering what the normal lengths of these periods are and what could affect the lengths of these periods.

I assume that the lengths of the periods is mainly affected by pressure/blood volume and not electrical activity so an ECG won't tell you how long these periods are (unless a heart beat is interrupted by another?). Is that assumption correct?

On a side note: what would happens to the heart physically if there is a large gap between beats. Does it sit relatively still during that period?

EDIT:

My original post could have worded better, so: I want to know specifically about long it takes for the ventricles to physical contract and relax. How would i determine the length of these two periods in seconds and where could i find the "normal" lengths of these periods? in the cause of relaxation, i'm wondering about what to do when there is a substantial gap between heart beats.


texts: What produces the strong odor of decaying dead animals?

texts: Are there specific chemicals responsible for producing the strong, putrid odor that is present after an animal deceases? Also, how long does this odor last?


texts: The above picture was taken in western forest of India where a larva attached itself to a frog neck. What is it and how it will effect the frog?


texts: What is the field of view of humans (not just fixed angle eyes)?

texts:
What is the human field of view also counting the maximum vertical and horizontal eye movement (rotation), with the head still.

It is unclear from this question whether the answer relates to the field of view from both eyes when a person is looking at a fixed angle or also what he/she can see if the head won't rotate but the eyes will.
What is the field of view for the human eyes?

There are many articles and diagrams online as well but they too don't make it clear whether the eye rotations are also taken into account or not and it is just the FOV at any given moment at a given eye angle.


texts: Can I simulate a previous and next sequence of my fasta files?

texts:
I have fasta sequences of a virus protein that had suffered a mutation in 2008 and this mutant had increase it fitness when compared to wild strain (according to literature).I want to simulate if my sequences were submitted in 2009(I have sequences from 2009 and 2010) or before to mutation and simulate next sequences to verify if the population of mutants really turns majority.
How can I do that?My virus is a RNA -ss. Any tool to use that i can represent it graphically?
Or simplifying..I want to simulate the past and the future sequences of my dataset.


texts: Where do the 2 electrons and H⁺ go when NADPH is turned into NADP⁺ during the Calvin Cycle?

texts: I was wondering where the 2 electrons and H+ go when NADPH is turned into NADP+ during the Calvin Cycle? I know that during the light dependent reaction, 2 electrons (from water) and H+ combine with NADP+ (from the Calvin Cycle) to form NADPH, but after NADPH is used and is turned into NADP+, where do those electrons and H+ go?


texts: Falling asleep or states of subconsciousness does not stop the mind from making its own fictional images. These seem like sensations just like those received from human eyes. But, how do we define these visual sensations biologically?


texts: Why does cell differentiation start with the morula?

texts:
I suppose that cell differentation has to start by some external symmetry breaking. The first time there are two different types of cells is the morula with roughly 16 cells: there are some 12-15 cells forming the surface of the morula and some 1-4 cells in the interior of the morula. These are exposed to physically/chemically different local environments which might be the initial triggers of cell differentiation.

(source)

Questions:

Is this kind of argument/picture correct?
What are the significant differences in the environments of the outer and the inner blastomeres of the morula that trigger cell differentiation - and how do they do?


texts:
Why do some bacteria kill each other? And how do they do that?
It's really a mind-blowing thing if you think about it. Please give me a simple answer.


texts: What is this vinca like vine? Is it poisonous? 62521 USA Illinois


texts: Why can human viruses that can't infect chickens be grown in embryonic chicken cells?

texts:
Embryonic chicken cells are commonly used in vaccine production.  The viruses are grown in chicken eggs, or in embryonic cells taken from those eggs, and then inactivated or attenuated to produce the vaccine.   But why can human viruses—some of which are not known to infect adult chickens—infect immature embryonic chicken cells?
For instance, according to this WHO fact sheet (https://www.who.int/news-room/fact-sheets/detail/measles), "Measles is a human disease and is not known to occur in animals." Yet the the measles virus prepared for the MMR vaccine is grown in chicken embryonic fibroblast cells.
N.B.:  According to http://www.ogrod.uw.edu.pl/__data/assets/pdf_file/0010/2161/13a.pdf, while measles may have evolved from domestic animals, it is thought to have its origin in cattle rather than chickens: "Measles, for example, is closely related to two other morbilliviruses-canine distemper and rinderpest (a disease of cattle)" [1]
One guess is that, while a virus would normally require interaction with a species-specific surface protein to initiate membrane fusion (see https://www.frontiersin.org/articles/10.3389/fmicb.2011.00247/full [2]), and thus viral (or viral RNA) entry into the cell, the naive nature of undifferentiated chicken egg cells enables such fusion to occur without such species-specific proteins.
Another guess (in the opposite direction) is that the species-specificity of viral infection depends on species-specific cell recognition factors, and because the cells in chicken eggs are undifferentiated, or minimally differentiated, they possess a broad range of recognition factors (where the non-chicken-specific ones are lost as the cells differentiate).
It was surprisingly difficult to find information online about this.  According to the the following (https://www.jstor.org/stable/30105172?seq=1), chicken embryo cells do become more resistant to viruses as the embryo ages; but this doesn't explain the lack of species-specificity:
"Cells dispersed from young embryos were permissive to viral growth, while those from older embryos were restrictive in an age-related pattern similar to that observed in ovo. The mechanism of natural antiviral cellular resistance did not involve viral attachment or release from cells from older embryos, but apparently depended on intracellular events during viral replication. These observations suggest that increasing natural resistance is based partially on intrinsic cellular changes. Sensitivity of a given virus and responsiveness of cells to the action of interferon may be more important to antiviral resistance than the amount of interferon that the virus induces." [3]
[1] Dobson, Andrew P., and E. Robin Carper. "Infectious diseases and human population history." Bioscience 46.2 (1996): 115-126.
[2] Hashiguchi, Takao, Katsumi Maenaka, and Yusuke Yanagi. "Measles virus hemagglutinin: structural insights into cell entry and measles vaccine." Frontiers in microbiology 2 (2011): 247.
[3] Morahan, Page S., and Sidney E. Grossberg. "Age-related cellular resistance of the chicken embryo to viral infections. I. Interferon and natural resistance to myxoviruses and vesicular stomatitis virus." The Journal of Infectious Diseases (1970): 615-623.


texts:
Link to GIF on imgur
What is this flat organism? It is around 1 cm long. I find them in places which aren't cleaned often. Location is India. Are they harmful or poisonous?
Edit: I've found that this is a duplicate question of What insect is this? (India).