texts: How does alum help in blood coagulation?

texts:
I recently came across a test in my chemistry book which says that potash alum, $\ce{K_2SO_4.Al_2(SO_4)_3.24H_2O}$ is used on cuts and bruises, because it coagulates the blood quickly. The explanation it gave, was that blood is a colloid of proteins in water and the $\ce{K^+}$, $\ce{Al^{3+}}$ and the $\ce{SO_4^{2-}}$ ions coagulate(=precipitate) them, causing a blood clot (quickly). However, from biology, I know that blood coagulation(=clotting) is brought about by formation of fibrin network which traps the WBC and RBC in blood. The formation of fibrin from fibrinogen involves a series of reactions with many factors like $\ce{Ca^{2+}}$ , but not $\ce{K^+}$ or $\ce{Al^{3+}}$.

So, I was wondering what the actual explanation might be.

Do people actually use alum to stop bleeding, or only as a disinfectant? Does alum have any disinfectant effects?
Does precipitation of proteins in blood help clotting?
Does alum contribute in any way to the process of blood clotting?

Note: This is a question involving both chemistry and biology, but I posted the question here as I thought that this is more of biology than chemistry.


texts: Evolution of the haplo-diplontic life cycle

texts:
From wikipedia > Biological Life Cycle:

haplontic life cycle - the haploid stage is multicellular and the diploid stage is a single cell, meiosis is "zygotic".
diplontic life cycle - the diploid stage is multicellular and haploid gametes are formed, meiosis is "gametic".
haplodiplontic life cycle [..] - multicellular diploid and haploid stages occur, meiosis is "sporic".

To my knowledge, all mammal species are diplontic. It might even be true for all vertebrates (but I am not sure). In plants and in fungi, there is a much greater diversity of life cycle however. In many (all?) bryophytes for example, the sporophyte (the diploid phase) is multicellular and its life is completely dependent on the gametophyte. This diversity of life cycle lead to the following question:

What drives the evolution of the relative time an organism spend in the haploid vs in the diploid phase of the life cycle?

This post comes as a follow up to @JAD's comment here


texts: we know that resistant strains (MDR, XDR, PDR) have arisen in single incidents around the globe but why are these bacteria not common and not spreading quickly as humans keep using antibiotics and killing the non-resistant strains which these Amr strains have to compete for resources. One might say that they ARE spreading but my question is why is the increase in population so slow. compare it with malaria parasite 'plasmodium' which despite being a higher organism with slower reproduction cycle kills so many.


texts: Coronavirus origin could be bat, why this happen while people have been eating bats for centuries?

texts: Sorry for my lack of understanding, Why now, when people been eating bats for centuries? If bats are simply a vector, where does that virus come from?


texts: Are tongues red because they contain blood?

texts:
Many animals have red tongues, though not all of them - blue-tongued skinks and giraffes come to mind. Are they red because of the blood (and therefore haemoglobin) in them?

It sounds plausible, but it also sounds like a post-hoc explanation.

I'd be especially curious about any other species having blue blood, like horseshoe crabs, but still having red tongues, unlike horseshoe crabs, which apparently don't even have tongues.


texts:
Four years ago I found a spider so big that I'll never forget. Unfortunately I don't have a picture but I guess there isn't a lot of big spiders in Mexico. So here are some things I remember:

It wasn't a brown spider, I think it had red legs with some parts black and others white.
Its legs were skinny and very long
The main body was tiny compered with the spam of its legs.
I found it at noon, after I moved to my new house. Unfortunately it wasn't moving when I found it
The spider didn't have any visibly hair.

That's all I can remember. I know that this may be impossible but I don't know what else to do.


texts:
This post at Mental Floss stated that a group of tortoises is called a 'Creep'. I had never heard of that before, and in trying to find the references for the name, I was surprised that I couldn't actually find anything.

Wikipedia showed no results in either of their lists for animal names.

http://en.wikipedia.org/wiki/List_of_animal_names
http://en.wikipedia.org/wiki/List_of_English_terms_of_venery,_by_animal

Neither did the Northern Prairie Wildlife Research Center: http://www.npwrc.usgs.gov/about/faqs/animals/names.htm

The closest I found was that a group of turtles is called a nest or a bale.

Is there an actual source for what a group of tortoises is called?


texts: What is a synonym of the word design that can be used in context of evolution?

texts:
For example let's take two sentences; "engineer made a design for camera", "evolution made an X for eye". What is the best X that could be used?

I need it for an essay about evolution.


texts:
My grandma is a great fan of mushrooms and knows quite a lot about them. About 10 years ago, she started throwing out mushroom remnants in one special place, in order to grow her own mushrooms. In fact, for last three years we found some parasol mushrooms (Macrolepiota procera).

Today she found something, that nobody at home can classify. From what I searched, it might be  Cortinarius privignoides, but it is marked as almost extinct here in Poland, so I doubt this classification. Maybe you have seen this or know what it really is:

The hat is light brown with faint violet shades, the leg on the outside is partly violet too, but the inside is all white.

Some more photos:

All three

The gills are lighter brown, also with a violet tone

The cut through the leg

The cut through the hat

At my parents' house I found one more mushroom atlas, and a new candidate: Cortinarius traganus, but one thing is not right - the ones that I have don't have a smell and gassy webcap should smell and taste bad.


texts:
I came across a passage on enhancers that sounds out-of-whack to me:

  ...an enhancer sits on just one of DNA's two strands (usually the same strand as the protein-coding DNA gene itself).  This is unlike a protein-coding DNA gene, which might need to be on both DNA strands——in a so-called homozygous state, in order to surface as a phenotype——like the classic case of blue eyes.

This is what makes no sense to me, since, AFAICT, whether something is in one or two strands has nothing to do with zygosity.

The authors continue:

  And this is [an] evolutionary advantage: an organism doesn't have to wait for a change on both DNA strands.  The bottom line is that evolutionary tinkering is in principle much easier with enhancers...

Is there a grain of truth in what the authors' write, despite their muddled explanation?  IOW: does the fact that enhancers "sit on just one of DNA's two strands" somehow facilitate "evolutionary tinkering"?


texts:
I have recently done a fair amount of online research about gypsy moth caterpillars and sources I looked at say that older caterpillars feed on the trees primarily during the night and drop down and hide in dark sheltered areas during the day.

I work for someone who had a severe gypsy moth infestation last year and we tied burlap around several isolated trees to see if we could reduce the damage. At the height of the infestation we noticed that there were, at any given time during the day, 20-40 caterpillars circling the base of the burlap and sometimes successfully crawling over it. It looked like they were actively trying to climb up into the trees during the day, which seems to contradict everything I've read.

Can anyone offer any insight into this behavior?


texts: Why are bovines different genera if they can interbreed?

texts: Why are bovinae a "subfamily", above Genus, when members can interbreed?  Some like the beefalo are fertile, which is the normal defining characteristic of a species. And Genus are groups more distantly related, so by definition they should not be closely related species.


texts: Cause-and-effect questions about growth and development of plant

texts:
I need to solve some cause-and-effect problems. The problems are related to growth and development of plant. "Growth and Development" chapter is the first chapter in third level of high school (senior high school).
Show your answer with "Is the statement true?", "Is the reason true?" and "Are the statement and reason have cause-and-effect relationship?"
Problem 1

Anthurium should be sprayed with cytokinin hormone to prevent from wither easily.
Reason
Cytokinin hormone promotes/stimulates the growth of axillary buds that will produce lateral branching.

Problem 2

The stem of Avena sativa with the coleoptile is being cut, couldn't elongate.
Reason
Phytohormone that used for growing is only available at the end/peak of coleoptile.

My attempts to those problems are here:
Problem 1
What I know about cytokinin is when you soak the green leaves in the water with cytokinin, the green color will stay longer than without any soaking. I don't have any idea about the effect of cytokinin to flowers. I think I need to dig more knowledge about the hormone.
I'm not sure with the reason too. Quick searching in Google Cytokinin and Wikipedia gives this:

... This promotes shoot growth, and restricts lateral branching.

The problem is my textbook clearly said that the cytokinin promotes the producing of lateral branching.
Because I couldn't prove the statement and reason, I couldn't give their relationship.
Problem 2
I think even the coleoptile is being cut, the flower must not easy to die. The phytohormone must be related with auxine hormone or other thing.
Because I couldn't prove the statement and reason, I couldn't give their relationship.
Any idea or answer is appreciated!
Feel free to edit my grammar. English is not my native language, but I could understand your post in English.


texts: Does too much Genetical Modification leads to formation of new species?

texts:
I think Genetical Modification can be termed as 'Artificial Mutation'.
Is it possible that genes can be modified so much that it leads to the introduction of new Species i.e Can integration of large no. of Helpful mutations lead to quick evolution?


texts: Is it possible to directly uploaded controlled imagery into a person's conscience?

texts:
I was wondering, is it possible to use electrical charges and/or EM waves to induce imagery directly into a person's mind?

I got this idea because since almost everybody dreams, and dreams are images created by the brain, i wondered if it was possible for an outside source to forcibly make someone see a different image without harming them.


texts: Why do spiders have a leaf at the bottom of a piece of web?

texts:
I've lately seen a lot of instances where a leaf is dangling from a piece of web coming down off a tree. What purpose/s does this serve for the spider? Is it some sort of mechanism for the spider to determine the wind / disturbances in that region?

I've seen a suggestion that it's to help act as a plumb during web construction to keep part of it tight, but do we actually know for sure?

Here's a national geographic image showing what I mean:

http://ngm.nationalgeographic.com/ngm/photo-contest/2012/entries/177963/view/


texts: Why is triclosan not considered an antibiotic?

texts:
Triclosan is a chemical often referred to as a "biocide" instead of an "antibiotic". However, its mode of action seems to suggest that it is an antibiotic.

  Triclosan binds to bacterial enoyl-acyl carrier protein reductase
  (ENR) enzyme, which is encoded by the gene FabI. This binding
  increases the enzyme's affinity for nicotinamide adenine dinucleotide
  (NAD+). This results in the formation of a stable, ternary complex of
  ENR-NAD+-triclosan, which is unable to participate in fatty acid
  synthesis.

This is nearly identical to the action of many other antibiotics, such as penicillins (inhibits cell wall synthesis enzymes), quinolones (inhibit DNA gyrase) or sulfonamides (inhibit folate synthesis).

In fact, this paper describes the mechanism of resistance to triclosan and notes that it is identical to many antibiotics. Why then, is triclosan not classified as an antibiotic and is still prophylatically used in so many places (such as hospitals)?


texts: Very high 260/230 absorbance ratio of an RNA sample

texts:
After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25).

I've never gotten numbers like this and I know the ratio is supposed to be ~2 in general.

What could be the reason for such a high 260/230 absorbance?


texts: Why does HIV chooses the Macrophage cells to infect first?

texts:
Upon entering our body HIV directs the macrophage cells to manufacture more virus particles. It injects the Viral RNA into the Macrophages. With the help of the enzyme reverse transcriptase the Viral RNA converts into viral DNA that embeds into the DNA of macrophage cells. In this process the macrophages remain alive.

Just Curious-

Since Macrophage cells have phagocytic activity, why does HIV chooses them to be their Virus producing factory and not some other cell like RBCs which are apparently much more abundant and have no phagocytic activity at all.

In other words what facilitates the macrophages to be HIV's manufacturing plant?


texts: What is Oncogene, and how do you get it?

texts: I was looking at my family tree and it said that one of my family members died by Oncogene. What is it and how do you get it?


texts: Why don't birds in flocks fly into each other?

texts: I've seen videos of hundreds of birds flying in the same general direction but creating incredible patterns in the sky seemingly instantaneously! How do they all know in what direction to turn at the same time? Is there a "Lead" bird dictating this somehow?


texts:
I stacked my bike and split my head right open.  About three weeks later the scab falls off and the skin is sealed over, like magic!  How does it all work?  How does the brain know that part of the body is injured and needs repair, or does the brain know at all?  What kind of signals between brain/cells/body are involved.

Sorry it's probably a basic question for a biologist, but I come from a different field and have always wondered about this amazing process.  It's also a very hard topic to google about, because most results are about spiritual healing, crystals, prayer and a lot of pseudoscience rubbish.


texts: Can stress echocardiography show coronary blood flow difference before and after exercise?

texts:
Stress echocardiography means a pair of cardiac ultrasound imaging examinations, before and after exercise. I assume that coronary blood flow is increased after exercise. Is cardiac ultrasound technology capable of showing this blood flow difference?

Update: I emphasize that my question concerns stress echocardiography, i.e. two echocardiography sessions before and after exercise (or pharmacological stress test) - not simply echocardiography.


texts: How do proteins get into the blood stream?

texts:
So I'm asking this in reference to the injection of insulin, which is commonly done subcutaneously (in the hypodermis, a fatty part of skin). Now I know proteins usually get into the blood when digested through the stomach/intestines - but I was wondering how they manage to get into the blood when injected into muscles/fat? I know there are capillaries pretty much everywhere, but from what I've researched proteins are too large to get through capillary walls.

That begs the question then, how do proteins manage to get into the blood stream when injected? I can't really envisage large capillaries, because surely they'd have huge holes in them or whatever to allow large proteins like insulin in. Any help on this one? Cheers


texts: cell proliferation assays for research proposal

texts:
I'm an undergrad Biology student and I'm working on a research proposal for a certain course. I need help or guide on cell proliferation assays. I have a target gene , recent papers show that this gene's haploinsufficiency increases cell proliferation. However the most recent paper (published in 2020) showed that haploinsufficency decreases cell proliferation instead. I want to investigate this discrepancy but I don't know what methods should I use. In both papers they used immunostaining with Ki67 antibodies and SOX2 and TRB2 markers and in 2020 they also tested cyclin D levels. I'm not an expert at this field and I want to know what methods I can use for my experiment.
Thank You


texts:
First of all I am a physicist, so I apologise for my non-existent understanding of basic biology. However, I have what I think is an interesting question and this seems like a good place to ask it...

I’ve recently been thinking whether there is a way to measure time using biological processes. In other words some system, a characteristic of which can be correlated to elapsed time. One example I can come up with is counting the number of divisions of a cell. I guess this can be done, but will most likely be highly inaccurate…

So this is my question: Do you know of any papers even tangentially related to the idea of a biological system that can be used as a clock?

Any ideas will be greatly appreciated!


texts: What are mutator genes which cause copying errors in other genes?

texts:
Reading Dawkins' book "The Selfish Gene," I came across this line: "There are even genes--called mutators--that manipulate the rates of copying errors in other genes." (The context is his argument that such a gene is looking out for its best interest by killing off the competition.)

What are these "mutator" genes, and how do they function?


texts: Help with analogy: Competition among similar species

texts:
I'm not from this field, but I'm trying to make a biology/ecology analogy for companies with similar products competing for the same market segment.

I was thinking of using the competitive exclusion principle to illustrate that the products will have to each find their own niche, or disappear from the market.

In a market, when opportunity arises (lots of capital available, and interest from the consumer side for an new product) many competing products spring up, and then we slowly arrive at an equilibrium similar to the exclusion principle mentioned before.

My question is this: Is there a similar "opportunity stage" of this process in nature? Like an increase in resources available that drives many different species to "appear" and compete for the newfound wealth?

Pointers to Wiki articles etc. for further research will be appreciated.


texts: Are there any examples in nature of two polypeptides joining into a single, continuous, third polypeptide?

texts:
Are there any examples in nature of two polypeptides join into a single, continuous, third polypeptide like this:

(Where all the indicated  amino and carboxyl groups are on the main polypeptide chain ( located on Cα of the respective amino acids )

And if this exists, is there any term for the phenomenon?


texts: Any examples of life forms on Earth that could have survived on Mars or Moon?

texts: Do we know of any living forms on Earth that could continue to live on Mars?


texts: What happens to the absorbed blue and red light in the chlorophyll molecule?

texts: If the chlorophyll molecule (its chromophore) absorbs red and blue light and reflects green light, shouldn't the absorbed blue and red light be emitted back when its excited electrons relax?


texts: Why do dragonflies have these special little spots on their wings?

texts:
The wings of several kinds of dragonflies I've seen here in Taiwan all have an apparently special little pigmented spot near the ends of each wing.
Does this spot have a name and a function?
below x2: Taken today in Hsinchu county, Taiwan. Note arrows. I've also asked Identify these two large dragonflies in Taiwan?
Click for full size

below left: from Identify this black dragonfly with bluish coloration along its flat top, yellow on it's mid-body and green on its head  below right: from Identify this black dragonfly with a bright bluish-white band around its body
Click for full size


texts: Hearing system as in visual system: exists well also - in protecting the inner mechanical parts of both sensing systems - a similarity?

texts:
I prefer answers, not just discussing.

In the mechanical part of the human eye the control system to protect for overload of the diaphragm in the iris with a strong coupling to the light intensity that falls on the retina has his place in the visual system as close as possible to the light source in the chain of control devices of the human visual system. The iris is disk-shaped and consists of two muscles. Like a diaphragm for light, the iris regulates how much light comes into our eyes. In bright conditions, the muscles of the iris limit how much light comes in. In lowlit conditions, the muscles of the iris increase the amount of light comming in.

Basic hypotheses is that the protection device in mammalian human hearing system is based on similarity as in the visual system and therefore should well also be using similar protection tools as used in the visual system and should well also be placed in the chain of control devices as close as possible to the signal source, as an experienced system engineer will always place a protection device in the chain of control devices as close as possible to the signal source.

Exists such an continuous functioning simalarity analogue in the protection system for sound signals ?
Both the iris in the eye (two muscles) and eardrum+ossicular chain in the ear (two muscles): in protection.
Exists that similarity ?


texts: Unknown plant, please help me identify it

texts: Years ago I was into keeping tropical fruit trees/bushes indoors. One of them didn't do well under my care so I planted it outside to enjoy the final year before European winter gets it. It somehow survived, barely. Each year it did better though so 5-6 years later it's full of edible fruit. I don't know what it is. Can somebody identify it?


texts:
Considering the short supplies of blood in hospitals, why can't we freeze on our blood from time to time and and have it stocked for reuse in an emergency?
That could make ourselves responsible for own our blood supply in case of an emergency.


texts: Are there any animals that celebrate communally?

texts:
Are there any animals that are known to celebrate events? For example, we humans might celebrate a birthday or passing an important test. An event causes us to perform some sort of celebration that is motivated simply by joy and not any sort of survival instinct.

To clarify, I am more interested in positive celebrations. I know a number of animals having mourning behaviors (which absolutely count as a response to external events, no denying); I'm just more interested in celebrations in a positive sense.

I'd like to take this one step further.

Are there any cases proven or postulated of animals celebrating. I don't necessarily need something firm and proven, could be a theory.


texts: What are the biological mechanisms behind the increase in cancer risk and alcohol consumption?

texts:
Alcohol consumption is known to be a risk factor for developing cancer. Compared to obvious causes like tobacco where one is exposed to known carcinogens, I don't see an obvious mechanism by which alcohol consumption would increase the risk of cancer.

Is there anything known about the mechanisms by which alchohol consumption affects cancer risk?


texts:
During my study of the immune system,  I came across 2 very contrasting explanation as to how prions work.

Firstly, scientific American pointed out this:

link here:

  "A major breakthrough occurred when researchers discovered that the infectious agent consists primarily of a protein found in the membranes of normal cells, but in this case the protein has an altered shape, or conformation. Some scientists hypothesized that the distorted protein could bind to other proteins of the same type and induce them to change their conformation as well, producing a chain reaction that propagates the disease and generates new infectious material. Since then, the gene for this protein has been successfully cloned, and studies using transgenic mice have bolstered the prion hypothesis. The evidence in support of the hypothesis is now very strong, though not incontrovertible

However based on this website

  The guess was that they infected cells by causing normal prions to become misshapen, too. That theory, though, has been proven false, though it is still commonly believed. (See Sanctuary: Bad Bad Prions from Discover, dated 9 January of this year for an example of the ongoing belief.) The first serious attack on the prion-as-infectious-agent theory was reported in Medical Hypotheses in 1997. The article makes the case that prions trigger an autoimmune response.(1) As becomes clear the more one looks into the issue, this makes sense and fits the facts as known.

The problem right now is that my campbell 11th edition textbook, which is the newest edition and just recently revised also points to the same explanation as the first source.

Which source is correct in showing the method in which prions cause diseases?


texts: Activation of Glycogen Synthesis by Insulin - mechanism and cellular location?

texts:
My textbook states the following...

Insulin activates enzymes that convert glucose to glycogen.

Does this conversion occur inside or outside the liver and muscle cells?

If it is inside, does the Insulin act as the primary messenger and activate an enzyme cascade that activates glycogen synthase?


texts: Why do most fish move fins orthogonally with their axis of symmetry?

texts:
So recently I read the question why are most fishes vertical (in the sense of distribution of their body mass) and it got me thinking what is the reason behind the direction they move their fins. My explanation is that they need to catch the image they several times to truly percieve it, so the eyes have to be orthogonal on the direction they move their fins. Am I correct, therefore they swim like this  rather than this
 because there is more to see on the horizontal dimension in shallow waters?


texts: Which animals where the first in which ova were not simply released, but instead provided with some additional nutrition and/or protection in the form of a larger egg?


texts:
A ruminant's digestive system contains 4 chambers: The rumen, reticulum, omasum and abomasum. The food travels from the mouth to the rumen, then to the reticulum, back to the mouth, then back to the reticulum and to the omasum as can be seen in the below diagram:

After the cud (the regurgitated food from the reticulum) is further chewed in the mouth, how does it pass back to the reticulum (and subsequently omasum) instead of the rumen? In other words, how does the cow choose in which way the food should go?


texts: Why does our voice change when we get affected by cold or cough? I observed the voice change thing in so many people including me.


texts: Does any one know which species of insect is this one?

texts:
I found this insect, in multiple zones of Imbabura - Ecuador. https://en.wikipedia.org/wiki/Imbabura_Province

Sorry for not having something to scale with, but it's about 15 cm long.

Another picture here:


texts: What is the leaf venation of a scuppernong vine leaf?

texts: I googled around and I didn't find anything that says its leaf veination. Anyone know?


texts: What are the pros and cons of eating earth (soil)?

texts:
I wonder if there are any benefits to eat earth. What I mean by earth is the topsoil that is sometimes on vegetable (I eat organic vegetables and some of them like spinach are full of topsoil).

I found this article (a study about why people, in certain culture, eat earth) but it doesn't clearly answer my question as it's about clay and not topsoil. Topsoil has a highest concentration of organic matter than clay.

I wonder if we can digest the soil nutrient (Phosphorus, Potassium, Calcium, Magnesium, Manganese, Zinc, Copper) just as we would if there were coming from vegetable and fruits.

What are the other pros and cons of eating earth (soil)? (I am aware of the cons about parasite and bacteria but my question is not about these risks. It's about nutritive value of earth.)


texts: Why do some Brown Pelicans have orange or reddish parts on their bills?

texts:
I am doing research on Brown Pelicans and have photos/descriptions of the breeding and nonbreeding appearances of adults, esp. the California and eastern subspecies here on our southern Pacific, Gulf of Mexico, and southern Atlantic coasts.

One question is really puzzling me:

The birds are described as having long pale bills, some with some brown on them. The bill of the California subspecies is described as acquiring some orange or red during the breeding season (along with the gular pouch which turns bright red/orange/pink). But I see photos of nonbreeding birds (with completely white necks) with either a little or quite a bit of orange on their bills, usually on the lower half.

There are so many pictures like this that the orange cannot be just a breeding color.

Do some Brown Pelicans just have some or quite a bit of orange on their bills, even when they are not breeding? I have looked at just about every link that comes up under Brown Pelicans and no one explains the presence of orange in some of their bills (except during the California subspecies' breeding season). In the official descriptions of the appearances of nonbreeding adults, orange in the bill is never mentioned. I would like to know the answer to this detail in the appearance of some of them!


texts: This video suggests that the first cell to be the victim of viral infection of ebola is the dendritic cell which acts as the leader of immune system cells.But I am unable to understand how the dendritic cells get infected if they are the leaders?


texts: Human can't digest cellulose.....but the length of small intestine is approximately same in humans and herbivores

texts: My question is why herbivores are able to digest cellulose and why can't we??


texts: Have there been any "chopstick gene" mistakes in genetics?

texts:
I've heard of the "chopstick gene" fallacy - wrongly assuming an association between genetics and some characteristic, confounded by non-genetic factors.

Has this fallacy happened in real life?

I'm not really interested in cases deliberately focusing on race, where people have argued that there's an innate difference between people of different races based on certain genetic differences, such as the putative "warrior gene" ("warrior allele"?) being described as more common in Maori people. As far as I can tell, the "chopstick gene" isn't about arguing that Asian people are better with chopsticks because of genetic differences between Asians and non-Asians.

I'm more interested in research that was done in good faith, which ignored the possibility of genetic variations having different frequencies in different groups, that produced erroneous conclusions.


texts: Is there a single word, or brief phrase, that denotes the state of the total genetic machinery (genome + transcriptome + proteome + ...) of a cell or organ or organism at a particular point in time?


texts:
I'm going to undertake an siRNA experiment soon, but I have only read about them. I want to address the role an enzyme plays in processing a protein.

From what I understand, I will need to pick two specific siRNA's from  a screen of multiple siRNA candidates. As a negative control, I should also make a non-sense scramble siRNA. Of course the specific siRNA should show a significant knock-down of the enzyme; the control should not affect expression. As well, there should also be a validated positive control (such as GAPDH) and a mock treated control.

Is this experimental design sufficient? What are some common things to keep in mind, or pitfalls to avoid when doing siRNA studies?


texts: I found this strange tooth in Galveston, Texas. What does it belong to?

texts:
I found this on May 7, 2017, on Bolivar Peninsula in Galveston, Texas. What's not visible are the treelike rings inside the tooth and what looks like a tiny interior porous center. It looks like it was considerably larger but broken off.

We're all taking bets on what it is!


texts: In which phenomena does one gene pair hide the effect of other unit?

texts:
This question was asken in an exam,

The answer they are saying is "Epistasis". But I think "Dominance" fits better,  because it is not mentioned whether genes of same allele are to be considered or different allele. Also it is not told whether genes in same locus are being talked of or different.

Please give some reference if you can. I know only school level biology. I do not know even in detail what allele and locus are. As far as I could understand from wikipedea and other sources I think "Dominance" is correct.


texts: Is the function of adjacent genes correlated?

texts: Do genes that occupy a similar locus on the genome have correlated function, specifically in human beings? It is my understanding that adjacent genes are inherited together, and so location plays a role there. However it terms of function, I don't know to what extent location plays a role. Furthermore, if say two adjacent genes have the same expression, does this necessarily mean that their function is correlated, or is that interpretation stretch?


texts:
Can someone help me identify this plant? Flowers bloom in summer, then red seeds form afterwards.  Leaf length is about 10 inches max.  I live in Southern California and it is grown in a container under my patio.

Thanks for your help.


texts: Question about production of CFTR protein

texts: How do organelles such as ribosomes, ER, Golgi and vesicles produce CFTR protein and mucus?


texts: What trajectory do action potentials take, from initial visual stimulus all the way to motor function?

texts:
Say we see a mosquito, and our brain tells us 'hey that's a mosquito, you should kill it.' Then we move our hands and slap/clap it.

The initial visual stimulus is translated to an action potential via the phototransduction cascade. Light hits retinal, bla bla, glutamate release is decreased, turns a few cells on and off, which eventually sends the action potential down the optic nerve through the lateral geniculate nucleus and to the 'final' target, the occipital cortex.

Then, something happens from this point in the occipital cortex, which eventually 'translates' to action potentials beginning in an upper motor neuron (UMN). This UMN located in the  motor cortex of the brain, propagating its message eventually reaching the muscle.

The question is, what happens in this intermediate phase, where visual input lands on the occipital cortex, and then eventually translates to an action potential being propagated at the UMN located in the motor cortex? Do neurons directly synapse from the occipital cortex to the motor cortex? Is there a particular neurotransmitter responsible for communication between neurons of the occipital lobe and motor cortex, or whatever lies in between (glutamate, acetylcholine, etc)?

And finally, the hardest question... light provides a simple stimulus which translates to an action potential, making it the 'origin' of the action potential in this case. But if we close our eyes, and imagine a mosquito, we'll still have activity in our occipital cortex, and willingly provoke the same motor response. What was the stimulus for this visualization, if light wasn't the firestarter? Does some other molecule isomerize cis-retinal to trans-retinal, or affect some other step down the photoreception cascade?


texts: I want to take a sample of skin infection bacteria (I suppose combination of staphylococus, strep, etc) and give it to the doctor for analysis but the appointment is in two weeks. The bacteria will be dead by then, right? Is there any home-made nurturing solution that I can put them in to preserve them until then?


texts:
I amplified my DNA with real time PCR. The amplification curve shows good amplification but not a single band is observed in my gel after gel electrophoresis. What would be the possible reasons?

I am attaching a photograph of my gel below. My ladder opened correctly but not a single band can be observed:


texts: Somehow I haven't found anyone on the internet can answer this: during muscle contraction, does the thin myofilament slide past the stationary thick myofilament, or does the thick myofilament slide past the stationary thin myofilament?


texts: How does one choose PCR conditions? Does it depend on the taxon, on the DNA concentration, on the primers or anything else?


texts: Which is the proportion of metagenomics reads that cannot be mapped in any genome?

texts:
I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable?

I found a figure for viromics, which seems to indicate that only about 6% of the sequences correspond to known virus (http://www.pnas.org/content/111/29/10714.full). But I couldn't find a more general percentage.


texts: I was always curious, why do chameleons have this strange gait?


texts:
I m a student at computer science and I'm working in a project called Plant Breeding and for moment I need to extract genes from a file with genomes.
I know that the start sequence of a gene is ATG and the stop sequences of a gene is TAA,TGA or TAG.Should I know about inside more apart of the fact that inside I will find only A,T,G,C and inside are exons and introns?


texts: What does it mean for a type of plant to "vegatatively dominate" as opposed to "taxonomically dominate"?

texts:
I'm reading Plants and the K-T Boundary, by Douglas Nichols and Kirk Johnson. On page forty-seven the authors write the following: "By the Campanian many floras were vegetatively co-dominated by angiosperms, conifers, and ferns, but taxonomically dominated by angiosperms."

My first intuition was that this means angiosperms, conifers, and ferns were equally dominating the available resources in many ecosystems, but that at the same time the angiosperms had become more evolutionary diverse. But I'm very new to reading about paleobotany, and biology in general, so I thought I'd better check that. Thanks for your time.

What is the difference between vegetative and taxonomic domination in the above example?


texts: Regarding benign tumors and what 'stops' them

texts: Benign tumors can grow to dangerous size yet are they capable of metastisizing ; if not what stops this? Also with a benign tumor if you call its cells 'near' its edges its tumor 'cell wall' I was wondering if the cells in its Tumor Cell Wall still have apoptosis mechanisms in them that function?


texts: All living things need water to survive. Worker ants can drink directly from the source. But a queen ant would need help from the colony to get its daily supply of food and water. I have seen ants carrying tiny bits of food, but I have not really seen them carrying water. Do they use their hands like how they carry food? Do they use a receptacle like us humans? Or are there some other innovative ways?


texts: Why is dimethyltryptamine (DMT) being released during death?

texts:
I'm not very well informed about all the things related to biology and the current achievements of science in this field so if I'm wrong in anything I say, please let me know.

Many times I've come across a theory that the meaning of life itself is procreation - we simply live in order to make our species exist as long as possible. In the light of this theory, units like homosexuals or infertile people are totally useless and there's no really reason for them to exist from biological point of view. Though it's pretty obvious that in order to make us want to reproduce, something like joy of having sexual intercourse and life in general has been created. That's why units who only lack in ability to reproduce do live and most of the time they're fine.

Evolution doing adjustments in us in order to make us feel happy during our life seems to be understandable, but what about death? I've read that during death, a larger amount of DMT substance is being released in the brain - compound which is known from it's psychedelic effects, which in most cases are euphoric. It looks like we're not meant to feel 'bad' while dying, which is nice, but my question is - is it known why? What could be the evolutionary reason to create this mechanism? The unit which is about to die is not going to be useful anymore, so why bother? I'd like to somehow understand logic behind this.


texts:
I see on http://en.wikipedia.org/wiki/Upper_limb that the term "upper extremity" seem to include hands. However, in many hospitals, there is a "Hand & Upper Extremity Service", which would tend to indicate that the term "upper extremity" does not include hands.

Does the term "upper extremity" include hands?


texts: I learned that water enters xylem vessels in the roots after absorption by osmosis, but also that xylem cells are impregnated with lignin that doesn't allow water to pass through them to prevent water loss. Does that mean xylem cells in roots of plants aren't impregnated with it?


texts:
My experiment involves pulling down cells on to a filter plate for a variety of assays. However, I want to ensure that my cells are alive so I am trying to resuspend them so that I can do an accurate cell count. However, I am unable to close off the mass-balance which suggests that the cells are either getting through the membrane or getting stuck.

Any suggestions on the appropriate way to fully resuspend cells? I'm currently using a P200 to mix the solution.


texts: What is this small black spider found in NY?

texts:
I found this small, black, spider with a yellow mark at the top of its abdomen, crawling on my desk in my office (located in the Lower Hudson valley in NY). I have never seen a spider like this before.

What is this spider, and is it native to NY, or is it an invasive species?


texts:
If left unpicked after the fruit ripens, what fruits may ferment instead of just rotting? My perception is that most fruits just rot.

I know figs will ferment. I'm guessing that this is because the wasp that pollinates the fig carries yeast inside what will become the fruit.

Eating ferment figs got me thinking about how humans first discovered ethanol. I'd guess that they ate ferment fruit and fiddled around until they could reproduce the process.


texts: What chemicals can be detected in sweat?

texts:
This question came to mind after reading this article. The article speaks of inducing sweating to determine, by a roundabout fashion, the amount of salt therein. I'm no medic but I find myself wondering whether sweat may be used directly to measure any other chemicals secreted by the body.

For instance:

If one's kidney/liver were to suffer some malady would the body attempt to discharge some additional waste through one's sweat

What chemicals may be detected by analysing sweat?


texts:
I have heard that chilli peppers and coffee evolved to contain toxic chemicals which help to protect them from predators.  And recently I learned that star anise, liquorice and aniseed are not actually related plants, but each independently developed the ability to produce anethole, which can also deter predators.

However humans have evolved resistance so they can ingest all these substances, and tend to enjoy their extreme flavours.  Some more examples are onions, garlic, peppercorns and tea (for its stimulative effect rather than for its flavour).

It made me wonder:

Did the active ingredient in chocolate also evolve to deter predators?

And I am also curious, are there any other foods which I haven't mentioned that humans also enjoy due to their toxic or deterrent components?  (I'm thinking more about flavour than psychoactive effects here, as I know there are many examples of the latter.)


texts:
First off, let me start by outlining the problem:

Your laboratory has established a technique for examining DNA replication in a cellular extract. To the cellular protein extract, you add nucleotides, a small amount of radiolabeled 32P-dGTP to aid visualization of the synthesized DNA, and a 4000-base-pair linear double-stranded DNA molecule that contains an origin of replication in the middle. After allowing the reaction to proceed for 30 minutes at 30°C, you boil the mixture to denature the proteins and the DNA strands, separate the components on an acrylamide gel, and detect the radiolabeled DNA products. This complete reaction is shown in lane 2 on the gel in the Figure below.

Problem A:

You perform the assay by yourself for the first time with no one else is in lab. The tube labeled “nucleotide mixture” has only enough for a single reaction, but you find a tube with a label that reads “dATP, dTTP, dGTP, dCTP” and you use this in a second reaction. You find the first reaction looks like lane 2 and the second reaction looks like lane 3. Why was no DNA synthesized in the second reaction?

My answer:

Because deoxyribose triphosphates do not have a –OH group to attach. You essentially can’t build with them.

Problem B:

Your lab partner has recently isolated a mutant strain that can replicate its DNA normally at 30°C but exhibit no DNA replication at 40°C. He calls the mutant tsr1, for Temperature Sensitive Replication. The wild-type strain replicates efficiently at both temperatures. You believe that you can use the biochemical assay of cell extracts to identify which genes are defective in the mutant. You grow wild-type cells and tsr1 cells at 40°C, make the extracts, incubate the DNA replication reaction at 40°C, and detect the products on a gel. You observe the pattern shown in lanes 4 and 5. You are so excited by the results that you run to your lab partner and tell him that you know what enzyme is defective. He is delighted by your results but says that there are three different enzymes that can account for your results. What are they?

I am 100% lost on this one.

I understand from the figure that the wild-type at 40 degrees has 4000 nucleotides so it's not being cut off. The mutant, trs1 is being cut off one into two slices of 2000 and one of these slices has been cut off into slices of 500? Am I understanding this correctly?
I also don't understand why the 500 line is so thick compared to the others?

Anyhow I feel really confused on this. I've been learning about Sanger sequencing and it makes 100% sense with ddXTP added into the mix to view the length of each sequence and therefore be able to read the sequence, but I'm not even sure if that's what's happening here.


texts: What is the name of this plant with 4-5 lobed leaves?

texts:
Location is India, It has 4-5 lobed leaves with flowers & pointy seed pods.

I am thinking it is Wild raddish.


texts:
The Gorgon--a terrifying, monstrous female with hairs made of live snakes and a stare so horrifying that it would literally turn you to stone.

The Gorgonopsid--a predatory protomammal that hunted down its prey via saber-like teeth.

Herein lies the problem.  The gorgonopsid looks nothing even remotely like a snake, nor is it likely that it could stare down its own prey into a statue.  So why call this family of predatory protomammals "gorgonopsids", anyway?


texts: Can crossing over between X and Y chromosome of sex chromosomes take place?

texts: Can it? If no, what would happen if it did?


texts: Approx 1cm, white and brown insect feeding on fruits, what are they?

texts: I found these insects yesterday that were feeding on a guava that I left outside for days. We have a tropical climate here (Mauritius). These insects are about 1 cm long. They have a white abdomen, brown wings, 6 long legs and they have segmented bodies divided into three regions: head, thorax and abdomen. Can someone help to identify them. Thank you in advance.


texts: Why does fetal distress (hypoxia) cause bradycardia?

texts:
In a non stress test performed in the labor room, fetal bradycardia is a danger sign indicating fetal distress (hypoxia).

Why does fetal hypoxia cause bradycardia while hypoxia in adults cause tachycardia? What is the mechanism for both and why is it reverse?


texts: When I download CNV SNP array data for ovarian cancer from TCGA data portal, I see some very small numbers like -5, -6 in the "Segment_Mean" column of the segmentation data files. I am very new to genetics, and I don't understand how that much deletion can occur in the gene. We have 2 copies of each gene in our normal cells, and my intuition tells that the minimum loss for a gene in a cell can be -2 (both copies of that gene are lost). So, could someone please explain shortly how this -5, -6 copy number losses are computed?


texts: Why does it hurt more when you touch a nerve directly?

texts:
I am not a biologist nor know much about biology (so please explain in layman's terms) however I have always been curious as to why this is.

What causes the difference in pain between touching an open wound and pushing down on your skin? In both circumstances you are applying pressure to the nerves except one is a foreign object touching the nerve and the other is the nerve's natural surroundings in your body.

Why is it that a foreign object causes so much more pain?


texts:
I was recently reading about non-coding RNAs being a counter example to Central Dogma of Biology. Can someone add more cases which violate the Central Dogma? Thanks!

UPDATE - Reference of lncRNAs violating Central Dogma:

  Although the central dogma remains a core tenet of cellular and
   molecular biology, the appreciation of lncRNAs as functional genomic
   elements that defy the central dogma may be essential for fully under-
   standing biology and disease. [Iyer et al. Nature, 2015]


texts: Why basement membrane thickens in diabetes mellitus?

texts:
Untreated diabetes mellitus may lead to blindness and kidney failure because the basement membrane of small blood vessels in these organs thickens due to increased production of collagen and laminin.

My questions : why are these organs most susceptible ? Why will collagen and laminin production increase in diabetes mellitus ?


texts: I am asked to fill the genotypes in the spaces provided but looks like I am aving a little bit of trouble. can anyone help? thanks in advance!


texts: How much energy would it cost to synthesize all cholesterol requirements de novo?

texts:
Imagine a scenario in which some person is unable to absorb any dietary cholesterol because of some intestinal mutation (for example). Thus, they have no cholesterol available from their diet for steroid hormone synthesis, bile acid synthesis, or any other process that requires cholesterol.

If that person had to synthesize all of their cholesterol requirements de novo (i.e. from acetyl-CoA), how much energy would that require on a daily basis? In biochemistry we talk about de novo cholesterol synthesis, but a lot of the time it is glanced over because it would be so energetically unfavorable to synthesize it when you can get it from your diet.

I'm curious to know... if we could somehow inhibit all cholesterol absorption and forced the body to make all its own cholesterol, then how much excess energy could we burn? Could we use that as a weight loss therapy?


texts: Could someone identify these microorganisms on microscope?

texts:
I'm new in this StackExchange forum, so I don't know if this is an appropriate question.

Can someone please help me recognize these micro-organisms on these photo taken with my phone during my biology lesson using microscope.

Location: Kyjovka river (Czech Republic)

Magnification: 200x


texts: Why is it important to study chromatin to understand cancer?

texts:
Many labs and many projects in biology institutes and university departments have been starting to study chromatin. Chromatin states, chromatin interactions, chromatin loopings, chromatin behaviours, etc. seem to have become the new priority of cancer scientists.

I'm new to this field so there are many things that I still have to understand about chromatin and its relationship to cancer. These questions just flowed into my mind:

What is the relationship between chromatin and cancer?

In cancer research, why is it so important to study chromatin and how chromatin loopings form?

What do scientists would like to find out about chromatin when they investigate it?


texts: Why are omega-3 fatty acids so easily oxidized when they're incorporated in cellular membranes?

texts:
Apparently, this has led to results with clinical significance, as we can see at http://extremelongevity.net/2011/10/03/daily-fish-oil-consumption-may-reduce-lifespan/...

  The researchers fed a special genetic variety of mice diets that
  either included 5% daily fish oil + 5% safflower oil or instead 10%
  daily safflower oil. The mice used were SAMP8 mutants that were bred
  to have accelerated aging and shortened lifespans. These mice are
  often used in longevity experiments because their average lifespans
  are only typically one year. They were fed these diets from 12 weeks
  of age on. The researchers hypothesized since fish oil is so easily
  oxidized it may lead to greater oxidative stress within cells and thus
  actually accelerate aging, a process believed in part due to
  accumulative damage from oxidative stress. Safflower oil is an omega-6
  fatty acid and is not readily oxidized – it could have beneficial
  effects without causing oxidative stress.

Let's not debate the clinical significance here - but I do wonder - why are omega-3 fatty acids so easily oxidized as compared to omega-6 fatty acids?


texts:
How many different chemical substances are there (on the average) in a human cell?

I saw of an estimation of ~ 1 billion (10^9) in sci-pop books.

Is there any reliable estimation rooted in the scientific community?

There is this question, but it does not have any answer. It only states that modern researches use (model) only a very limited number of chemicals within a cell. But what is the estimation of the real complexity of a problem.


texts: I saw this insect crawling on a wall in the UK (Birmingham) today (March 28th). It's about 5mm long. I assumed it was a white fly, but having looked at other images of white files on google, I don't think it is! I assume the fact it has jet black eyes means it's normally nocturnal?


texts: What is the difference between differentially expressed genes and deregulated genes?

texts: Can anyone explain clearly what is the difference between differentially expressed genes and deregulated genes?


texts: Anaerobic respiration in yeast experiment

texts:
We performed an experiment to prove that yeast respires anaerobically.

Had 1g of yeast in test tube with 10cm (cubed) of glucose solution.
Heated it up to 40 degrees Celsius in a beaker, where there was water.
When it reached 40 degrees Celsius we took it off of the Bunsen burner and stirred it for about 5min.
couple of drops of oil were added to stop air from getting in

To prove it was anaerobic respiration we had 2 delivery tubes with 10cm (cubed) of lime water. The solution then had a line of white starting to form indicating carbon dioxide was present.
In my experiment report I have a question that I need to answer:
"It is further argued that by bubbling air through lime water, the same results could be achieved. What control experiment could you carry out to show that this was not the case with your experiment?"
What is the controlled experiment?


texts: How do high-throughput/NGS sequencers calculate quality scores?

texts:
I am confused as to how quality scores are actually calculated by DNA sequencers like Illumina. For each base call, some quality predictor value is computed, based on various properties of the sequencing machine, like intensity of light during the read.

Do we know exactly how these quality scores are computed? Exactly how many factors go into computing these QUAL values?


texts: I found this question about how many taxonomic families there are. That made me wonder how many are just in the animal kingdom alone. I want to know about families not species. Now the linked question was three years ago, so there should be some new information and numbers. A good answer would preferably include a breakdown of the phyla.


texts: What is the point of storing biological samples in Trizol/TriSURE before RNA extraction?

texts: The Wikipedia article on Trizol says that it helps break the cells and maintain RNA integrity during homogenisation of samples. Does anybody know by how much Trizol improves RNA integrity compared to homogenisation without it? If somebody is extracting RNA from tissues without first storing them in Trizol, can you please tell me about the quality of your RNA?


texts: Biology Intuition and Origin of the "facts"

texts:
I am a graduate physics student but also taking biology classes. I am new to the field of bio. Most of what we do in class seem like memorizations and stating-facts. I am wondering:

How can I develop intuition for biology? (Aside from memorizing and practicing.) I am not even sure what intuition would be like in the case of biology?
Where are all the known facts in biology (and chemistry) come from? Have to be from EXPERIMENTS though, I hope to understand the origins of the I-was-being-told-this-way facts such as the composition of DNA and the types of bonding. By understanding, I don't necessarily mean the exact experimental procedure, but the general idea of how everything came about. (I am mainly interested in molecular and cell bio).
Much appreciation for any input!


texts: Correlations between tool use and evolution

texts:
We humans would be nearly defenseless against large predators without weapons. Even small mammals can outrun humans. Our canines have degenerated to the point where they're almost useless as weapons. A young chimpanzee is far stronger than a human.

So how could our ancestors have survived before the invention of tools and weapons?

Apparently, our species didn't necessarily invent these things at all. As I understand it, more ancient hominids were using tools and weapons even before our species evolved. I would therefore assume that we essentially inherited tools and weapons from the species we evolved from.

At any rate, we are incredibly weak and defenseless compared to chimpanzees and other apes. One might speculate that big canines and physical strength became more irrelevant as our ancestors began to rely on artificial weapons for protection.

Are you aware of any research that supports this? Do our ancestors exhibit a trend towards smaller canines or a decrease in physical strength?


texts: What are the differences between how latewood and earlywood forms and how does this effect it's properties?

texts:
In trees the earlywood forms a somewhat abrupt transitions to the darker latewoods that happen during the summer months.
What are the chemical differences that arise in this wood at the cellular and inter-cellular level and what changes occur in the plants that lead to latewood forming instead?


texts: How the atoms-residues-amino acids structure information prioritized? Specifically, I am trying to understand how the first atom is identified since it does not seem to correspond to the first amino acid in the sequence. I assume it's based on the structure but is it bottom to top, left to right and such. Thank you.


texts: Why differentiated cells can't "undifferentiate" (under normal conditions)?

texts:
In a process called differentiation, the cells of the developing organism undergo huge changes, which result in cells, functioning "completely" differently. Two cells are considered to be of different types if they are having different sets of template-competent genes, though most of the genes in the human genome are common even in highly differentiated cells. Being able to produce specific proteins from the same genome is achieved by something called open chromatin state of the DNA. What I would like to ask is why can't this specific conformation of the DNA be reversed as this would likely answer the title of this question? I would also like to have some tips on further reading in the topic of DNA conformations and about DNA generally.

I used Gabor Forgacs's and Stuart A. Newman's book called Biological Physics of the Developing Embryo


texts: Do invasive species cause long-term damage to ecosystems they invade?

texts:
Growing up in the U.S., I was warned at various times of the dire consequences of a variety of introduced pests (usually insects).

Japanese beetles, gypsy moths, and most recently the brown marmorated stink bug are all introduced pests that, at various times, were described as serious threats to our ecology.

These threats aren't confined to arthropods, either.  The giant African land snail is causing a stir in Florida (indeed, Florida seems to suffer from an excessive variety of introduced species.

"Lack of native predators" is frequently cited as the primary reason many invasive species are considered such a risk to the ecology.

I understand that these introduced species can place tremendous pressure on native species that fill similar ecological niches, and may even push these species out of the region due to competition for food and habitat.  However, do the overall ecologies that these species are introduced to adjust over long periods of time?

The numbers of Japanese beetles and gypsy moths don't seem anywhere as high as when I was a child.  Has the ecosystem adjusted, or has the overpopulation self-corrected as the species ran low on food through over-consumption?  Or are the populations still just as problematic now as they were 30 years ago, and I just am not seeing the bigger picture?

What is the long-term impact that we've seen from invasive, introduced species?  Is there a significant difference on the long-term impact between introduced flora, arthropods, or mammals?


texts: How would you use readthrough as part of a genetic circuit design?

texts:
Traditionally, in synthetic biology, researchers tried to avoid some transcription phenomena (like roadblocking of tandem promoters or readthrough of weak terminators) since they are not in line with the discipline's strive to design modular, digital genetic circuits. However, some researchers have started using these "problems" as part of the intended design (see Bordoy et al., for example).
How do you think transcriptional readthrough could be used as part of a genetic circuit design? When would you want to have a readthrough? What kind of logic or function would this emulate?


texts: Ok carnivores are "animals that eat other animals," so what are bacteria that eat animals? Or are they just not important


texts: Is there a record of species kept in zoos worldwide and number of individuals? If yes, can one have access to it?

texts: Looking for the number and species of wild cats kept in zoos to assess the potential pool of individuals available for reintroduction programmes.


texts: Biological advantage of electric synapses

texts:
Electric synapses are synapses that do not process information but simply foward one action potential from one neuron to the next. There are no neurotransmitters, no inhibitory and exitatory postsynaptic potentials that would cause different responses in the post-synapse.

So, I'm wondering: What are the biological advantages over just one long axon? My research has only told me the advantages over "normal" synapses (speed), but I couldn't find any advantage over just using one longer neuron which, I suppose, would be even faster.


texts: How are the two mating types, a and α, for S. cerevisiae pronounced?

texts:
In reading about S. cerevisiae there are two mating types, one being the Latin letter a and the other being the Greek letter α.

How are these two types pronounced such that they can be differentiated?

In other words when I pronounce the text I don't want to say 'a' for both of them; there should be a different word or phrase for each one so that they are known to be different.

Is it simply that a is pronounced as a and α is pronounced as alpha?


texts: Does cat urine really fluoresce? If so, why?

texts:
I temporarily got caught in the Sad and Useless website, and found Science is Fun.

Most of the claims seem plausible, but I can't guess why cat urine would fluoresce.

Comments have directed me to Why Does Urine Glow Under a Black Light? which says:

  You can use a black light to detect body fluids. It's actually a good way to look for pet urine or make sure a bathroom or hotel room is really clean. Cat urine, in particular, glows very brightly under ultraviolet light. Urine glows under a black light primarily because it contains the element phosphorus. Phosphorus glows yellowish green in the presence of oxygen, with or without black light, but the light imparts additional energy that make the chemiluminescence easier to see. Urine also contains broken down blood proteins that glow under a black light.

Certainly other mammals including humans have both phosphorus and broken down blood proteins in their urine, so is the proposed specificity to cat urine just an issue of concentration perhaps?


texts:
The Addax (Addax nasomaculatus) is critically endangered species of a desert anetelope with impressive long horns. Today there are small populations in the Sahara desert and the Arabian desert (Saudi Arabia). The addax is mentioned in the bible ("Dishon"), though the identification is not uninomous. Today in Israel there are breeding centers for the addax, one in Hai-Bar Yotvata (near Eilat, the rift valley, bay of the Red Sea) and the other in the Zoological Center at Ramat Gan ("The Safari"), but as far as I know, there are no plans to release addax in the wild in Israel (although I think it can survive and flourish there).

The question is: was the addax native to the Land of Israel (before it was eradicated from it by overhunting)? Do the conservation organizations support reintroduce it to the wild in Israel (in addition to the Sahara and the Arabian desert) addax herds from the breeding centers? The reintroduction of Oryx to the wild in Israel was pretty successful.


texts: Why do we need two markers to measure a recombination rate?

texts:
In calculating recombination,

Why is it necessary to take into account pairs of loci where one marker is heterozygous?

Why is it necessary to take into account pairs of loci where both markers are heterozygous?


texts: Is there an entry-level circadian model of serotonin, ghrelin, dopamine and the sense of well being?

texts:
I've long been interested in circadian rhythms and recently came across a variety of articles that appear to indicate that the following neurotransmitters, transferases and hormones are connected. There are mentions of some circadian rhythmicity and maintaining homeostasis for these compounds(Are serotonin levels in humans affected by light?):

Serotonin
Dopamine
Melatonin
HIOMT, NAT
Ghrelin
Leptin

Additionally, their expression is related to Suprachiasmatic Nucleus and light exposure.

I'm interested if there's a good article or a talk that discusses the homeostatic system that those compounds are a part of. I'm particularly interested in their effect on the feeling of well being.

It seems to me that all these compounds are in some way related to moving and feeding. However, I cannot wrap my mind around multiple separate articles that describe how, and am looking for a single paper that may shed light on the connection between these compounds.


texts:
The standard answer found in intro course to evolutionary biology to the question:

  what is evolution?

is:

  It is a change in allele frequency over time!

I believe a complete definition should encompass the following concepts:

mutations
copy number variation (CNV)
codon usage
chromosome numbers
phenotypic change (whether heritable or not)
Complex phenotypic trait such as plasticity and developmental noise
maybe some other things...

My questions are:

Would it be worth it to talk about phenotype in a definition of evolution?
What are the alternative definitions that have been proposed?
What is your definition?

Note: I would rather talk about genetic evolution, but if you think it is worth making one definition for genetic and cultural (and some other stuff maybe) evolution, you're free to suggest it!


texts: Person-years and relevance to incidence of condition

texts: If the annual incidence (age and sex-adjusted) of a particular condition x is 21.8 cases per 100,000 person-years and this data was determined in one geographic location, then is it correct to say in a city of 1 million people that we may see that same condition, in one year, in approximately 21.8 x 10 = 218 people? I'm just trying to provide some relevance to a group of students on how common some conditions may be. I understand that the exact incidence would vary along with demographic, geographic and environmental features.


texts: Mean and standard deviation of human bone density?

texts: Are the human bones about equal in density? Or is there any published data on the mean + s.d. density for a given bone available?


texts: Why are interneurons needed in the spinal cord for polysynaptic reflexes and somatosensory tracts to the brain?

texts: The single explanation I found for the polysynaptic reflex is that the interneuron diverges into more pathways, such as the efferent motor neuron, the inhibitory neuron to the opposite extensor muscle, and a ramification that goes to the brain. But why couldn't the afferent neuron axon solve for these ramifications? Furthermore, it is counterintuitive for a nociceptive reflex, that must save the damaging tissue as fast as possible, to be slowed down by an additional synapse.


texts: Is there any case in which excitability increases with lowering the RMP?

texts:
My professor says , at a more negative RMP, less sodium ion channels are inactivated, so if you take 2 of the exact same neuron with the same threshold potentials, and try to excite them starting from different membrane potentials, the one you try to excite from a more negative membrane potential excites faster and fires an action potential faster because more sodium ion channels are activated .

I might have missed something from what he said, and I hope I did because this makes no sense to me.
Shouldn't excitability increase with an increasing positive resting membrane potential ? The closer I am to the threshold potential the weaker the stimulus that I need to fire an action potential, isn't that right ?

The only article I found on this is https://www.sciencedirect.com/topics/neuroscience/excitability and its specific to cardiac muscle so perhaps the excitability in cardiac muscle  is an exception ?


texts: Was 14,000+ year old DNA "laying around in cave dirt" protected from degradation, or is it just naturally this robust?

texts:
In the NYTimes news article No Bones About It: Scientists Recover Ancient DNA From Cave Dirt I've read:

Although DNA sticks to minerals and decayed plants in soil, scientists did not know whether it would ever be possible to fish out gene fragments that were tens of thousands of years old and buried deep among other genetic debris.

I haven't read the original article yet, but I'd like to double check, this is bare DNA molecules, stuck to minerals or other detritus in 14,000 to 550,000 year old compacted dirt? Roughly speaking at least? In layman's terms, just laying around in some caves?
Has something protected the DNA from degradation, or is DNA just more environmentally stable and robust than I thought?
There is also discussion in the Science commentary No bones? No problem: DNA left in cave soils can reveal ancient human occupants.
The NYTimes article goes on to say:

The new study involved searching for ancient DNA in four caves in Eurasia where humans were known to have lived between 14,000 and 550,000 years ago.
Dr. Meyer and his colleagues figured out which DNA in the cave sediment was prehistoric by looking for telltale signs of degradation at the ends of the molecules.

What are the "telltale signs of degradation at the ends" of DNA molecules described in the paper?


texts: How can paternal chromosomes be present in an egg cell during meiosis I or crossing over, if fertilisation has not yet occurred?

texts: I am very confused about crossing over. It is said that crossing over increases genetic variation as it is a combination of paternal and maternal chromosomes. However, crossing over occurs in meiosis 1 but meiosis 1 occurs before fertilisation, so my question is how are there paternal chromosomes in an egg cell prior to fertilisation.


texts: How does one identify a seed's species & variety?

texts:
How does one identify a seed's species & variety, could it be done by some means of DNA or by use of a microscope?
Say for example, I had a pumpkin seed, I knew that it was a "small sugar pumpkin" variety, but how would one scientifically identify it to know that it was infact a small sugar pumpkin as well as a pumpkin without going through the process of planting it. Is there some kind of indicator on a DNA level that shows "This is what I am?"

My knowledge regarding biology is extremely basic, but I am very interested in knowing the full process of how this would work.


texts: How to add oxygen to indoor air without opening windows?

texts:
I'm not a biologist. I have read that low oxygen levels in the home can have a negative effect on health. I am interested in increasing the amount of oxygen in the air in my home.

To open the windows would be the most effective way but the air outside is cold and measurably polluted (PM2.5 usually greater than 30µg/m3) so I would like to find other ways.

I know that plants add oxygen to the air but I have read that an unrealistically large amount of plants would be needed to make a meaningful difference to the oxygen levels.

I am wondering what other methods I can use and also whether what I have written above is correct.

Please forgive me for my ignorance. If this is the wrong place to ask this question then please help me to find the right place. Also sorry for not knowing what tags to use.


texts: Other than olfactory senses do sharks use some kind of sense that uses electromagnetic waves? Is this similar to an electric eel? I saw a book with the cover statement 'Sharks never get cancer'. IS this possible or just 'quackery' ? Could being constantly 'bathed' in some kind of electromagnetic field cause pre-cancer cells ( that are already unstable) to be 'disrupted'?


texts: Which is the more accepted theory for the opening and Closing of stomata : the sugar concentration theory or the k+ ion theory ?


texts: In Ganong's Review of medical physiology it is mentioned that plasminogen is converted to active plasmin when tissue type plaminogen activator hydrolyses the bond between Arg560 and Valine 561. Can anyone show the molecular mechanism ? What happens to the two different parts of the hydrolysed chain.


texts: Is there a difference between an organizer and inducer substance?

texts: There is a question in my Embryology textbook's exercise that asks about an organizer and inducer substance. I found their definitions and now I am wondering if they are the same things?


texts: Is there anything that tells me how Lichens Grow?

texts:
I've done a lot o research about this matter but I could not find anything relevant. So I'm doing a Computer Science project where, using AI and Computer Graphics, we try to predict the growth and aging of lichens on a stone, and at this moment I need some "academic validation", so is there any way like a formula or something that tells me how lichens evolve and grow on stones? Thank you so much!

This image shows what I've accomplished:

In real Life:

http://i.imgur.com/NFo4A8Y.jpg

So is it possible to predict how are they going to spread along the stone in a period of time? Do they start by growing in small colonies and then tend to get together to create a bigger colony? I don't know if this makes any sense, anyway thank you for your patience!


texts: where to find the relative frequency distribution of synonymous codons

texts:
Most amino acids can be encoded by more than one codon. For example, Serine can be encoded by any one of {UCU, UCC, UCA, UCG, AGU, AGC}.

My question is in two parts:

1) what are the relative frequencies of those codons? This question can be equivalently phrased in probabilistic terms: What is the probability that a given amino acid was encoded by particular codon?

2) Is this probability dependent on the context (the neighboring codons/amino acids)?


texts: Is there logic in this sentence? "Authors discovered a gene as one of the genes evolved through natural selection"

texts:
From a news report:

  PhD candidate Daiki Sato and Professor Masakado Kawata have discovered SLC18A1 (VMAT1), which encodes vesicular monoamine transporter 1, as one of the genes evolved through natural selection in the human lineage.

Didn't all genes evolve through natural selection?

I'm self-training myself in translation into Russian, and this sentence stumped me. How do I translate it and avoid an absurdity? I thought that all genes have evolved. That's what genetics is about, isn't it?


texts: What is the difference between a species tree, a gene tree and a phylogenetic tree?

texts:
I have found websites and text books disagreeing over this. For example,

  Phylogenies are also known as “species trees”...

http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/evolution-basics-species-trees-gene-trees-and-incomplete-lineage-sorting/

and

  It is well known that a phylogenetic tree (gene tree) constructed from DNA sequences for a genetic locus does not necessarily agree with the tree that represents the actual evolutionary pathway of the species involved (species tree)...

http://mbe.oxfordjournals.org/content/5/5/568.abstract

Although the second source, being from a journal, would seem to be more reliable, my original thought was that phylogenetic trees do show the evolutionary relationships between species and thus are species trees as opposed to gene trees.

Any clarification on the issue would be much appreciated.


texts: Why does uniprot sometimes not label single-pass transmembrane proteins as "anchors"?

texts: Currently, section 3a) of unitprot TRANSMEM reference page divides single-pass transmembrane proteins into 4 types: I, II, III, IV. I is not explicitly labelled as an "anchor" whereas the others are. What criteria need to be made for a single-pass protein not to be classed as an anchor?


texts: Why exactly were bacteria and archaea kingdoms separated from the now unused kingdom of Monera? Aren't they the same? They are both prokaryotes, so what is the difference?


texts: Do all human cells have all the same organelles?

texts: I know that not all human cells have nuclei (erythrocytes eject theirs before they are fully matured), but do all human cells have all the other organelles? The two I'm particularly concerned with are the Golgi apparatus and lysosomes.


texts:
Location: Jahangirnagar university, Savar, Bangladesh

EDIT: Here is the video from which image is taken


texts: What recovers normal polarisation after hyperpolarisation?

texts:
I have been taught that a $\ce{Na+/~K+}$  pump helps to recover normal polarisation after-hyperpolarisation in neurones. I could not find out how it does that, since I've also been taught that such a pump moves $\ce{3Na+}$  out of the cell and $\ce{2K+}$  into the cell. That implies that the potential can only get more negative. How does this work?

My hypothesis was that the potential 'leaks' out and recovers the 70 mV that way. I couldn't verify that, however.


texts: What makes the electrical charge inside the neuron more positive at the end of action potential and returns it to resting potential?

texts:
When a neuron's stimulated by something, electric potential difference changes immediately and inside of the neuron, becomes more potentially positive than the outside of it.

I've read that sodium-pottasiom pump returns membrane potential back to its resting potential at the end of action potential's process.

How sodium-pottasiom pump returns membrane potential back to its resting potential and makes inside of the neuron more potentially possitive when three sodium ions are transported to the out of the cell and just two potassiom ions are transported back into the cell?

I mean, in this condition, it is expected that inside of the cell is gonna be more potentially negative, not more positive.

(Sodium-pottasiom pump ➡ puts 3 Na+ outside - brings 2 K+ inside ➡ 1 negative charge inside...!??)


texts:
For a long time I've just accepted, because it is just what everyone told me, that mitochondria became organelles in the cell when they were "engulfed" by another cell which acted like it's host. This is the endosymbiotic hypothesis.

  "The endosymbiotic hypothesis suggests mitochondria were originally
  prokaryotic cells, capable of implementing oxidative mechanisms that
  were not possible to eukaryotic cells; they became endosymbionts
  living inside the eukaryote."

However, recently I looked at the wiki entry on mitochondria and saw there that it lists two main hypothesis, endosymbiotic and autogenous.

  "In the autogenous hypothesis, mitochondria were born by splitting off
  a portion of DNA from the nucleus of the eukaryotic cell at the time
  of divergence with the prokaryotes; this DNA portion would have been
  enclosed by membranes, which could not be crossed by proteins."

It also states that, given that mitochondria have some striking similarities to bacteria, the most parsimonious hypothesis for mitochondrial evolution is that of endosymbiosis. (This question here deals with some aspects of multiple-occurence/convergent endosymbiosis).

My questions are;

How strong is the evidence for either of these leading hypotheses (perhaps there is a review article)? Is there evidence that is overwhelmingly in favour of endosymbiosis?
Further, are there any other (plausible) hypotheses to explain the origins of mitochondria (with or without supporting evidence)?


texts: How does the drug MBC effect the depolymerization of microtubules in eukaryotic cells?

texts:
I have tried to look for the mechanism of how methyl benzimidazol-2-yl-carbamate affects microtubules in eukaryotes, but what I found wasn't very useful:

Quilan et al 1980 assert that it acts by inhibiting polymerization of microtubules rather than by directly depolymerizing them.
In "The Cytoskeleton: A Target for Toxic Agents", it is mentioned that

  ..strains of Aspergillus that were resistant to the drug had a lower affinity for MBC in a binding assay, whereas super-sensitive strains had a higher affinity for the drug.

Any references would be appreciated.

In Summary: I would like to know how the drug MBC effects the depolymerization of microtubules in eukaryotic cells. I would also appreciate any scientific references.


texts:
Blue eyes are a recessive trait in humans. I read an article recently which stated:

  People with blue eyes have a single, common ancestor, according to new research.

  A team of scientists has tracked down a genetic mutation that leads to blue eyes. The mutation occurred between 6,000 and 10,000 years ago. Before then, there were no blue eyes.

  "Originally, we all had brown eyes," said Hans Eiberg from the Department of Cellular and Molecular Medicine at the University of Copenhagen.

Which appears to be a mainstream hypothesis today. My question is, if there is a genetic mutation that occurred in one individual which made their eyes blue, and the rest of the population is brown eyed, how does this make so many individuals blue eyed? If the blue eyes are recessive, the individual's children would mix with the other brown-eyed individuals and their offspring will be brown-eyed. How does anyone treat this theory seriously?


texts: Does thyroxine increase BMR or metabolic rate?

texts: I know that thyroxine increases the metabolic rate, but my teacher said it increases the metabolic rate, not the basal metabolic rate, the basal metabolic rate is always the same. What's the difference between BMR and metabolic rate??


texts: Are gametes determined by the sex of an organism?

texts:
In the Wikipedia article for biological sex, I read the following sentence.

  "The gametes produced by an organism are determined by its sex:..."

However, is it not through the gametes produced by an organism that "sex" is defined? Should this sentence be the other way around?


texts: Why are killer whales found in the Gulf of Mexico smaller than ones found in the Pacific?

texts: I recently found out that there are killer whales that live in the Gulf of Mexico, but they are smaller than killer whales that are commonly found in the Pacific Ocean. Why is it they are smaller in size?


texts: Are there macrophages in the blood vessels and within the blood stream?

texts:
Monocytes are phagocytes that "evolve" or "differentiate" into macrophages. I read that there are monocytes in the blood stream and vessels and that macrophages are found mainly in other tissues and in the lymphatic system.

My question: are there macrophages (and not merely monocytes) in the blood vessels and within the blood stream? And if there are, are they numerous there or sparse?


texts:
One day, a bird flew inside my house. I locked the door. It landed on my TV and then I turned off the light. Then I touched the bird and it didn't even to try to fly or move.

Then I went to the kitchen and turn on the light,  and suddenly it flew into the kitchen.

Why won't birds move an inch in total darkness?


texts: How does gas equilibration occur in the alveolus, numerically?

texts:
I am attempting to model gas exchange across the alveolar membrane.  My main question is there a direct exchange of O2 molecules for CO2 molecules?  If so, then my model predicts (assuming alveolar PO2 107mmHg and CO2 40mmHg; and venous PO2 40, PCO2 46) an arterial PO2 107mmHg, but PCO2 of only 37mmHg (taking into account pH change and equilibration with bicarb and haemoglobin carbamates).  If I remove the plasma bicarb equilibration process (as this takes ~15 seconds, but alveolar transit time is ~0.75 seconds), then the arterial PCO2 is even lower, ~33mmHg.  The expected results should be somewhere in the range of an arterial PO2 of 107 and PCO2 of 40.
The only alternative I can think of is that there isn't a molecule for molecule exchange, with the O2 absorption and CO2 removal being separate processes.  If this is the case then overall there will either be a reduction in alveolar air pressure and/or volume during gas exchange.  However, I can find no references to inhaled tidal volume being different to exhaled tidal volume.  Nor does there seem to be any evidence for N2 or H2O molecules to participate in this process (at standard atmospheric pressure).
Any ideas??
Ultimately I want to then extrapolate model to deal with pathology (eg high alveolar CO2, high venous CO2 etc).
EDIT to include references...
Mechanistic physicochemical model of CO2 transport in the blood
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5341128/
Modeling of the oxygen transfer in the respiratory process
https://hal.archives-ouvertes.fr/hal-00714239/document
Modeling pulmonary gas exchange and single-exhalation profiles of CO
https://www.frontiersin.org/articles/10.3389/fphys.2018.00927/full
Respiratory Physiology
https://derangedphysiology.com/main/cicm-primary-exam/required-reading/respiratory-system
Other materials I have read include:

Pilbeams Mechanical Ventilation
Nunn's Applied Respiratory Physiology
Guyton and Hall Medical Physiology


texts: From what kind of insect might these eggs be

texts:
Does anybody know what kind of insect might have laid these eggs:
The photo was taken a few days ago in Limburg, Belgium near a pasture with some goats.


texts: Why doesn't Manipulated Virus for Cancer Cure Work

texts:
I'm not a biologist but I have an idea for a cure for cancer and it is very simple and probably has flaws (if it worked it probrably wouldn't be a cure for all) or is not possible but ... I'm still going to ask why because I want to learn why it doesn't work and I want to learn more in general, so you can use all the biology terms you like. The idea is essentially to use a virus and manipulate/change it (this would be mechanized if it were to be mass produced and the type of virus is unknown to me because you want one that is fast growing and goes across only specific parts of the body depending on the cancer). This virus would not have any bad parts (parts that make you sick) to it because when the virus "injects" it's DNA or manipulates the existing for copying it would instead manipulate the DNA in the cell it is going into to have growth limits and other cancer genes that are set to being back to normal and then copy itself. Eventually it would be fought off by the immune system and most of the virus would be gone (along with the cancer) because this virus would last for a long period of time (week(s)).

I appreciate anyone who answers this question because I'm sure it sounds stupid from your perspective but this is the place to learn.

Thanks,
Jackson

Note: This is not an idea I'm trying to make, obviously, I just couldn't get it off my mind and wanted to see what is wrong and if it is fixable.


texts: Are mutations accumulating far faster than selected out?

texts: I just want to see the mutation accumulation rate in human populations. Versus the rate at which mutations are selected out. Just wanted to check if the genome is deteriorating


texts: Species that have evolved to be near identical?

texts:
Are there any species that are near identical in outward appearance but are separate species?
When I say species I mean can’t interbreed.


texts:
Here are the notes I made for an experiment I was doing (I didn't put it here as it is too long)

(please ignore the numbers at the end of the pdf file)

The graph looks like this:

As you see on the graph, the numbers are the same as the ones below

1. The effect running out of glucose has on the yeast growth
Our yeast increased in number by dividing rapidly. They use glucose to respire and release energy. They need energy to grow.

2. Why the yeast starts to grow again
The yeast  starts to decrease in volume when they ran out of glucose.

3. Describing patterns in graphs
The yeast breaks down the starch to glucose

The problem is, why did the yeast rise at the end, I forgot?

Thanks in advance


texts: Why do some cellular organelles like mitochondria and plastids have their own DNA. And what is the basic difference between the DNA of the nucleus and these organelles?


texts: What are differences between formation of embryonic disc in chick and mammal embryo?

texts:
Exam question which got lowest average points in my university: 1/5 average.
No markscheme available so my attempt below.

I assume that embryonic disk prefers to germ disk such that Formation prefers to only to the 3rd developmental week because of the Wikipedia fact.
I also went through the points during 2nd week of development and did not notice major differences. So let's consider only the 3rd week:

Formation of the primitive streak
Genesis of the germ layers
Genesis of the notochord
Location of the epiblast cell target and the development of the primitive streak
The bilaminar membranes
Evolution of the mesoblast
The intraembryonic coelom
Induction of the neural plate – neurulation

The following differences are based mostly on Gilbert's Developmental Biology 9e -book.

Other Differences which seems to at least start at the 3rd week of development

Chick meroblastic cleavage, human holoblastic. TODO do not know how that causes differences yet during the 3rd week.
Chick has yolk, human not so human placenta development and implantation. Chick dependent on yolk nutrients, human not.
Human embryo gets mother nutrients through placenta.
Chorion formation and finally from it the fetal portion of the placenta.
Chorion also includes the uterine cells to form the maternal of the placenta, the decidua.
The decidua will come rich in the blood vessels that will provide oxygen & nutrients to the embryo.
Human oviduct expansion to the uterus.
Chick embryo externally developing from the mother, human not. Chick egg is telocithal with a small disc of cytoplasm: blastodisc - sitting atop a large yolk. The yolk, eggs of birds undergo discoidal meroblastic cleavage. Cleavage occurs only in the blastodisc which is about 2-3 mm in diameters & is located at the animal pole of the egg. The first cleavage furrow appears centrally in the blastodisc; other cleavages follow to create a single-layered blastoderm.
The cleavages do not extend into the yolk, cytoplasm, so the early-cleavage cells are continuous with one another & with the yolk at their bases.
One chick hypoblast streak, human multiple. Chick must have some control mechanism.

What are the differences between formation of embryonic disc in chick and mammal embryo?


texts: Does global sperm count decline also mean lower testosterone?

texts:
So I read about the sperm count decline in men in rich countries.
I wonder if this is accompanied by other changes for example in testosterone levels or in other hormones linked with the reproductive system ?
Also other measures such as semen volume ?
Example report on this issue
https://www.sciencedaily.com/releases/2017/07/170726110954.htm

Also, the report shows a steady decline - will this continue and what would be the bottoming out of this trend ?


texts:
To me, there are two definitions of "random" in common usage: effectively random, where predicting the outcome is beyond most reasonable effort (e.g., drawing a card from a deck); and truly random, where predicting the outcome is beyond known science (e.g., radioactive decay/QM).

With this (possibly flawed) perspective, I'm very interested in sources of true randomness. I started thinking about how parents never know exactly what their child is going to look like. Is this because there are aspects of reproduction that are fundamentally unpredictable (true randomness) or because we lack the sophistication/motivation to predict it (effective randomness)?


texts: Assembling small DNA parts using Golden Gate

texts:
Background
I've always been told that DNA assembly can be tricky when using very small DNA parts due to low efficiency. I've also seen this when using 3A biobrick assembly to assemble promoters and RBSs together. However, there doesn't seem to be any information that I can find which definitively shows what the minimum DNA part size is that can be used before the efficiency becomes so low that assembly is unfeasible. The most I can find are warnings that small DNA parts are problematic (e.g. https://blog.addgene.org/plasmids-101-golden-gate-cloning).
The Question
What is the minimum DNA part size that can be used in DNA assembly before it becomes unfeasible? I'm specifically interested in Golden Gate assembly, but information for other digest-ligate assembly methods could also be helpful.


texts: What is the smallest molecule that can present as an antigen to the immune system in the context of allergies?

texts:
People often claim, in a colloquial sense, that they are "allergic to everything".

Is it possible to have a full-fledged IgE mediated allergic response to very small molecules?  I was always under the impression that the smallest antigen was a oligopeptide, but is it possible for someone to be allergic to something like isopropanol, glucose, or another small organic molecule?

How about allergies to metals, as I know those are fairly common, would they be mediated through a similar mechanism?


texts: In terms of Prions is there a possibility, that other proteins apart from PRPC could be misfolded

texts: This is as from research PRPC seems to be the cause of all Prion related diseases. Thank you


texts: Why can polar molecules like water pass aquaporin better than unpolar like H2 or CO2

texts: We learned in our lecutre, that aquaporin lets Water pass, but blocks Ions like H+ and unpolar molecules like CO2 and H2. The reasons for the Ion blocking are comprehensible, but I dont get, why less-than-water-polar molecules are blocked. Our professor said, it has something to do with the water molecules are orient in the aquaporin towards the positively charged n-terminus of the alpha helix, but why is that an advantage compared to non polar not charged molecules?


texts: Does the location of the double bond in chlorins yield a distinct biological function?

texts:
Chlorins differ by the number of double bonds and their location. Chlorin has 20 pi electrons, whereas bacteriochlorin and isobacterichlorin have 18 pi electrons, but at different locations.

Do chlorin, bacteriochlorin and isobacteriochlorin have distinct biological function due to this double-bond difference?


texts: What's inside the males body in the space where females have the ovaries and the uterus?

texts:
The male penis and scrotum are external extremities, whereas the female sex organs are placed "inside" the body. So as females have the bladder, rectum, other stuff just like males. Does this mean overall females have larger volume of organs? Is this why females have wider hips? Because male penis and scrotum is extral appendages just like female breasts.

Any good animation, videos, references are welcome. Any reason for how these changes came to be from a evolutionary view point are all extra information I would love.


texts: fast metabolism and law of conservation of energy

texts:
Usually if person take more calories with food than he spends, he is gaining weight.

But if he has fast metabolism, his weight stays the same.

Where these calories go? Maybe food is not completely digesting?

PS. How it related to Basal metabolic rate?


texts: How to get phased haplotype from vcf file?

texts:
Although I'm reading all days and nights, still confused in this area. I have hundreds of BAM files (from whole-genome sequencing of a given human population). I was wondering how I can obtain phased haplotype from raw vcf file? I read also about GATK, but didn't find a clear answer to my question. Please kindly tell me if this tool is suitable for this goal?
Would you please introduce me some practical guides and pipelines that explain such an analysis step-by-step?

Thank you for your help


texts: Gene APOA2 SNP rs5082 alleles are A or G, but papers describe it with CC and TT?

texts:
rs5082 is a SNP in the APOA2 gene. It is associated with obesity and heart disease risk.

According to this article the alleles can be A or G
https://www.ncbi.nlm.nih.gov/snp/rs5082#frequency_tab

Why does this article only discuss CC or TT?  Where is the A or G?
https://academic.oup.com/ajcn/article/108/1/188/5036568


texts: If there are bats flying in the cave, and I play the same pitch they use to echolocate from a speaker, what would the bats do?