What's the meaning of the label MRE and a number like 162 or 600 in the names of bacteria? I've stumbled across labels like E. coli MRE 162 or E. coli MRE 600 for different kinds of E. coli bacteria.

What's the meaning of MRE and the numbers like 162 or 600 in this context?

MRE is an acronym for the Microbiological Research Establishment at
  Porton Down, UK.

It was applied to Escherichia coli strain MRE600 as that was where the strain was first deposited, according to this paper.

I tracked the answer down in an article by Chris Morris on the Culture Collection Page of Public Health:

“My association with Porton Down, the current location of the European Collection of Animal Cell Cultures (ECACC), started at an earlier date than the inception of ECACC, and was when the site was known as the Microbiological Research Establishment (MRE), part of the Ministry of Defence.”

The numeric portion of the strain designation (600 etc.) that follows MRE is presumably just a reference or accession number within the institute, with no biological meaning.

(As a matter of interest, Porton Down had a certain notoriety in Britain back in the ’60s as a secret military establishment.)


Typical firing patterns of (some) motor neurons Since it is not so easy to imagine and visualize the behaviour of the muscles in the fingers, hand, and arm of a violinist performing a fast and accentuated trill vs. a slow and soft vibrato, I try to imagine and visualize how corresponding motor neurons do fire.

I assume there are some motor neurons that are immediately responsible for the speed and amplitude of the movement of a finger performing a fast trill, and — partly the same, partly others — that are immediately responsible for the speed and amplitude of the movement of the same finger performing a slow vibrato.

The behaviour of these motor neurons — during the trill or the vibrato — can be recorded as corresponding sequences/trains/bursts/chats of spikes.

I wonder:

  How may these spiking and/or bursting patterns look like?

Maybe like this?

fast and accentuated (= large amplitude) TRILL, each group corresponding to one movement (up-down) of the finger

slow and soft (= small amplitude) VIBRATO, each group corresponding to one movement (to-fro) of the finger

I can't answer the whole question, but what I do know:
An actionpotential can't have a small amplitude, the amplitude is always the same. If a neuron gets excited enough there will be an action potential, otherwise there won't.

"When the depolarization reaches about -55 mV a neuron will fire an action potential. This is the threshold. If the neuron does not reach this critical threshold level, then no action potential will fire. Also, when the threshold level is reached, an action potential of a fixed sized will always fire...for any given neuron, the size of the action potential is always the same. "
quoted from https://faculty.washington.edu/chudler/ap.html

Neurons have a maximum firing rate, a point where they cannot fire faster. (http://blog.eyewire.org/why-do-neurons-fire-at-a-maximum-of-about-200-hz/)
So to move faster your body can't fire faster. But it can fire more: more neurons fire if you want to move faster, and less neurons fire if you want to move slower: https://blogs.scientificamerican.com/scicurious-brain/when-you-run-fast-your-brain-runs-faster/

I do think your first row of spikes is kinda correct. Neurons fire as long as you move your hand/finger(s) in a certain direction, and as soon as these neurons stop firing and their complementairy neurons start firing you move your hand to the opposite direction.


Does a virus that spreads more rapidly have less chance to evolve? Now that the COVID-19 pandemic has been going on for a while, there are reports of many new variants, which have presumably arisen in the past year through mutation and spread through natural selection.
I'll assume that the outcomes of COVID-19 infection are either death or a successful immuse , others would have developed antibodies. Suppose for the purposes of discussion that those are the two end consequences (or correct my answer in your thinking.)
If eighteen months ago, everyone in the planet had been infected with COVID-19 in one very bad day, then many people would die, and the others would end up with antibodies. That might stop the spread of the disease, which would stop its evolution. (Feel free to address Typhoid Mary-like scenarios in the answer; or of course any misconceptions in this paragraph.)
Is there a perspective from which—or set of circumstances under which—drawing out a pandemic can actually worsen the effect of a disease by giving it more chance to evolve?
(I've put the question in terms of COVID-19, but I think it's really a generally question, no less applicable to COVID-20 and above. :-) Please feel free to answer in general terms. I am not looking for a discussion about what public health measures may or not be appropriate to the current pandemic.)

Any evolutionary process has two components to it:

generation of genetic diversity in a population, and
shifts in the distribution of genetic variants under selective pressure.

For a virus like SARS-CoV-2, every infection results in a vast amount of replication, some of which will be variants generated through imperfect replication. Thus, the more rapidly a virus is spreading, the more opportunity it has to generate genetic diversity. Conversely, if there's not many infections going on, then there won't be much evolution because there won't be much diversity generation.
With regards to selection, the more actions that we take against the virus (e.g., mask wearing, social distancing, vaccination), the more selective pressure that it is under, since these actions differentiate between strains that are more or less effective in evading them. If the pressure goes too high, however, this breaks down. With highly effective countermeasures (e.g., rapid vaccine distribution while not letting our guard down), then there won't be much evolution because most variants won't have an opportunity to infect any new host: each new generation of infections will be driven more by countermeasure failures unrelated to viral efficacy, and thus there will actually be little effective selection.
The highest opportunity for evolutionary change, then, is with poorly coordinated countermeasures. This produces an intermediate rate of spreading, with both much viral replication and many opportunities for selective pressure on infections.  It's really much the same as the problem with stopping a course of antibiotics prematurely, only on a societal rather than individual scale.
Bottom line: countermeasures are still a good idea, even when potential evolution of variants is included. People and governments that don't take the problem seriously, however, are threats to all the rest of us.


How did the huge dinosaurs cope with gravity and loads on bones, etc.? It's very costly to be a huge animal. Your mass grows in cube when you scale up, but you still only have two/four legs to support the same weight. This increases the pressure that your body needs to cope with.(this is easy to see if you compare an ant with an elephant. The elephants legs are much thicker and strudier in comparison to it's body)

Looking at a T-rex for example, speciemns have been found that are believed to weight more than 9 tonnes, compared to an elephants 10 tonnes. T-rex has ofcorse has only two legs. The heaviest dionsaur is believed to have weight 80 tonnes. That is the weight of about 20 cars on each of their feet.

How could they support such massive weights?

Assuming that gravity was essentially the same (other answers to this question notwithstanding), very large dinosaurs were dealing with the same forces that they would today. There are two clades of dinosaurs in which gigantism evolved, Sauropoda (quadrupdeal sauropods) and Theropoda (including T. rex). Each "solved" the problem of large size in different (but also somewhat similar) ways.

The main reason why large size was not a problem was that, if posture changed to align the forces between the animal and the ground, the bones are compressed. Bone is very strong in compression.

Theropoda

Theropod essential operate as a see-saw, with a large muscular tail balancing a large head. As such, they did not likely use much active muscular force to balance. The analogy is a human standing. Just standing, you don't need much muscle force to balance.

Hutchinson and Garcia (2002) showed that, because of a lack of plausibly large leg musculature, T. rex could not run. For a range of postures, they estimated how much muscle would be required to balance the animal and found that running behavior was unlikely.

Hutchinson, J.R. and M. Garcia. 2002. Tyrannosaurus was not a fast runner. Nature 415:1018-1021.

Sauropoda

Sauropods show many similar adaptations as elephants, the largest extant land mammals. Their limbs were held upright (erect), which requires less energy for balance. Some sauropods had air-filled bones, which would also lighten the skeleton. Wilson and Carrano (1999) document the evolution of posture through sauropod evolution from a biomechanical perspective.

Wilson, J.A. and M.T. Carrano. 1999. Titanosaurs and the origin of “wide-gauge” trackways: a biomechanical and systematic perspective on sauropod locomotion. Paleobiology 25:252–267.


Is it safe to feed an adult fire salamander with slime maggots? As a reminder, maggots feed of a flesh, while fire salamander consumes his prey alive, without killing it.
Can it happen that the maggot will start eating the salamander from the inside?

Although I am afraid I don't know much about fire salamanders specifically, it is certainly possible for ingested fly larvae (or larvae hatching from ingested eggs) to survive ingestion and subsequently cause intestinal damage. Parasitic infestation by fly larvae that grow inside the host while feeding on its tissue is called myiasis. Enteric myiasis (also called gastric, rectal, or intestinal myiasis to indicate the affected part of the digestive system) occurs occasionally in humans following the ingestion of cheese infested with cheese fly maggots. Casu marzu, a traditionally produced Sardinian cheese, is supposed to have live cheese fly maggots in it, and cases of bloody diarrhoea following its consumption are known. If they're dead the cheese is considered unsafe to eat (although personally I'd correct that to 'more unsafe').


Protein content in sprouted beans I have checked on Wikipedia which says that sprouted mung beans has way less protein than normal one, while on web you will find articles saying sprouted beans are best, which is true, how do I eat unbaked mung bean anyway without any processing they are so hard. Does soaking moon beans overnight really reduce protein content drastically ?

Short answer:

Yes the legume seed protein content decrease when it germinates.

but still;

The sprouting seed is healthier.

Long answer:

Yes it is true that after germinating some of the protein decrease. It is mostly due to breakdown, transport and consumption of protein stored in seed. All fabaceae (former Leguminosae-sensu-stricto) members use a large amount of protein storage, such as Vicillins, Legumins, etc in their seed cotyledons . All edible true-pulses , including pea , mung, etc belong to fabaceae.  When the seed germinates, theses proteins breaks down into simple amino acids and small peptides, and get reallocated*.  In addition, a part of this work as food (respiratory substrate) through amino acid oxidation  **.

  Fig-1

  Protein mobilization in seeds... simplified.
  Source... *

  Fig-2
  .
  The cellular process of protein mobilization in Mung bean cotyledon.
  Source ... *

We are commonly advised to eat sprouting seeds not for their protein content (we get the major portion of protein from daily major foods like meat, fish, eggs, leafy vegetables, etc.); but it is for the vitamin content.

This paper says

  " Mung bean sprout produces several kinds of hepatoprotective compounds such as flavonoid and chlorogenic acid."

There are also many papers related to sprouting mung bean; such as this but I do not have full access to them (sorry for that), such as this, this etc.

  Reference

  * Protein Storage and Utilization in Seeds; by Rod Casey, J.Derek Bewly and John S. Greenwood. Published as a chapter in a book, Plant Metabolism, Edited by Dennis, Turpin, Lefbvre, Lyzell. Second Edition.
  ** Amino Acid Catabolism in Plants; Tatjana M. Hildebrandt , Adriano Nunes Nesi, Wagner L. Araújo, Hans-Peter Braun (NCBI-PMC) (Full-text Free Open access link)


Can pathogens enter the bloodstream if the epidermis has been scraped off? Assume that the epidermis has been scraped off by a fall (not just scratched). Also assume that the dermis is completely untouched. Does this allow pathogens to enter the body more easily, or does the dermis still provide adequate protection?

Our epidermis is the first line defence against natural infections; it is also a part of the innate immune system. This is due to

it contains a layer of dead cells that separates the living cells of the deeper layers of epidermis and dermis from the environment.
This part of the epidermis is avascular and so pathogens can not easily enter into the bloodstream through it.
It contains natural bacterial flora (like in our gut) that kills a large number of pathogenic microorganisms with their toxins.
secretion of sebaceous gland contains some antimicrobial substances.

There are lots of other protective features of epidermis.

Dermis is richly supplied by blood vessels. So even if all the layers of dermis remain intact its high vascular nature will act as an open entrance of microorganisms. By definition abrasion involves only the epidermis or some parts of the dermis but still we need to take tetanus vaccine after getting an injury contaminated with soil. In diseases like Stevens-Johnson Syndrome (where epidermis separates from dermis) or in burn patients the skin is covered with antibiotics and dressings. The patient is also given high dose of antibiotics to fight those bacteria that still entered into the bloodstream.


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

A bear usually kills its prey by biting it on the back or neck. The bear uses his forepaw to strike very hard, usually breaking the prey's spine so this is why usually his killing instinct is on the back part of a prey. Bears also bite their prey on the snout.
this information can be found at the end of this article: http://www.largecarnivores.fi/species/brown-bear/bears-diet-and-hunting-behaviour.


Identify a small bug, possibly a plant bug? We found this bug in a bedroom in southern California. It's small: the body is about 5mm and the length including legs and antenna could be up to about 10mm. It's mostly black, though the abdomen from the bottom appears to have gold highlights under light when I used a flashlight. In sunlight it appears somewhat brownish. It looks like it has wings which forms sort of an "X" pattern on its back. The legs are dark black or brown but may be somewhat translucent in sunlight to appear an orange-gold color.

What species is it? It looks to me a little like a plant bug (phylinae?) or roach or beetle but I'm not sure. And could this species bite?

This is a plant bug (family Miridae); going deeper isn't possible on the basis of a photograph, except for some common economic species (the key to genera in How To Know the True Bugs is almost 200 couplets long!).  Most species of the family are plant feeders (hence the common name); biting humans is unlikely.

Reasoning (from Comments):

The top right photo [from the OP's post] shows that the front wing has a cuneus (a section of the hardened part of the wing on the outer margin set off by a groove), which is characteristic of that family and the broad-sense "Anthocoridae" (which includes three smaller families); none of the photos show simple eyes (the eyes we see are compound), which eliminates "Anthocoridae" and the subfamily Isometopinae of Miridae; the remaining seven Nearctic subfamilies are still possible


Peptide oxidation bias during sample preparation for LC-MS/MS Problem description

In bottom-up proteomics, a commonly observed amino acid modification is the oxidation of methionine (Met-O). I wonder if the observed Met-O reflect natural protein oxidation or if they rather stem from oxidation during sample preparation.

Observations

During sample preparation, several factors could influence the Met-O:

Typical sample preparation protocols include reduction of the sample by either DTT or TCEP. This step serves to reduce disulfide bridges. I wonder if this step would also lead to reduction of oxidized methionines. Still, this reduction step seems to be used even in studies that analyse natural protein oxidation (e.g. Walker et al., PNAS, 2019, Methods)
Sample preparation takes several hours at least, typically the digestion is even prolongued over night. Several modifications typically happen during sample preparation or during the measurement, e.g. deamidations. I did not find studies about the extend of Met-O happening during sample preparation. Klont et al. report differences between Met-O in four different sample preparation methods, but it is not clear where the differences stem from. They could either happen during sample preparation or the four methods have different capacities of detecting natural oxidations.

My questions

Does the use of reducing agents modify oxidized methionines?
Do methionine oxidations occur during LC-MS/MS sample preparation and measurement? How strong is this effect?
Does anyone know a technique that discriminates native protein oxidations from those occuring during sample preparation? I found this publication, using 18O, but I cannot access it and thus cannot estimate if the protocol would be useful.

I know this was posted a long time ago and I'm not sure if you have found your answer but I am an author on two of the publications you  andcite can offer some insight.
1.) Methionine oxidation, unlike cysteine oxidation, is irreversible without the action of a dedicated enzyme or catalyst. Neither TCEP nor DTT is able to reduce methionine sulfoxide. The only reducing agent that I know of that is strong enough to reduce methionine sulfoxide is MMA.
2.) The in-vitro oxidation of methionines during sample preparation is a well documented issue in LC-MS/MS analysis and it is known that the majority of in-vitro oxidation occurs during peptide digest as well as during electrospray ionization. The strength of the effect is highly variable and dependent on how long you digest proteins. For a typical overnight digest we observe effects that range from 0%-400%, depending on the peptide.
3.) The use of 18O labelled blocking reagents is the only currently available method that can prevent the accumulation of in-vitro oxidation. I'm the first author on the publication you cite and would be happy to send you a copy if you email me (jbetting@ur.rochester.edu) I have also been working on improved methods using the same general strategy and would be happy to share those with you after publication


Why should benzalkonium chloride (an antifungal agent) be used during your laundry machine's "rinse" cycle, not its "wash" cycle? I'll first provide lots of background information. My actual question is at the very end.

Background

The spread of athlete's foot

Athlete's foot is a fungal infection which is mildly contagious. The infection can be spread by skin particles left on towels. (Source.)

If one person in a family has a fungal infection (e.g. athlete's foot or jock itch), their laundry may also contain fungi. I suspect that towels and laundry machines might make it easier for these fungi to spread: e.g. from the patient's feet to their groin. See, for example, here.

Water at 140 °F

You can kill fungi using water at 140 °F (60 °C). Unfortunately, your water heater probably doesn't produce such hot water, because such hot water is dangerous and can kill unsuspecting individuals. (Sources.) Still, you can make such hot water in other ways. (Source.)

Antifungal rinses

Another option is to use a suitable antifungal rinse.

The most common cause of athlete's foot is T. rubrum. (Source.)

T. rubrum is a dermatophyte-type fungus. Dermatophytes spread through spores. These spores can sometimes live for up to 20 months. (Source.)

Canesten Laundry Hygiene Rinse is 7% benzalkonium chloride. (Source.) A competing product is Bluo Laundry Sanitiser, which is also 7% benzalkonium chloride. (Source.) These products are sold in Australia but not in North America. (How safe are they? I dunno; I'm not a toxicologist.)

The Canesten rinse label makes an impressive claim: "eliminates ... fungi from your washing". Still, it looks like these rinses' fungistatic effects are stronger than their fungicidal effects. In reality, they're not perfect at killing T. rubrum, but they're still better than nothing. An Australian lab found that, in 20 minutes, these types of rinses reduced T. rubrum by between 90% and 99%. (Source.)

(Each rinse is marketed as both antifungal and antibacterial, though there's limited evidence that people can catch bacterial infections from clothing. I'm not convinced that their antibacterial effects are really necessary.)

Use during the rinse cycle, not the wash cycle

Each manufacturer says that its benzalkonium chloride rinse should be added during your washing machine's final rinse cycle, not its initial wash cycle.

You can do this using your clothes washer's fabric-softener dispenser, if present. On a top-loader, this is usually a cup-like device on top of the machine's central agitator post. (Source.) Or you can buy a softener dispenser ball, though they're not always 100% reliable. Or you can add the rinse manually at the correct moment.

A sample washer program

Washing machines can vary. Here's a description of the normal program of certain inexpensive top-loading Whirlpool agitator-type washing machines:

Fill - agitate: 16 minutes.
Drain: 2 minutes.
Spin: 2 minutes.
Rinse, fill, & agitate: 4 minutes.
Drain: 2 minutes.
Spray & spin: 2 minutes.
Spin only: 4 minutes.

Total: 32 minutes.

(Based on: wiring diagram W10118358, rev. A.)

The wash cycle is longer than the rinse cycle.

My question

To summarize the above background information: Canesten laundry rinse (7% benzalkonium chloride) has both antifungal and antibacterial effects.

And so I wonder: Why does the manufacturer recommend that it be used during your laundry machine's rinse cycle instead of its (longer) wash cycle?

Any answers or guesses are welcome.

The label of the veterinary product Fung-A-Way, which is Benzalkonium Chloride 0.15%, states that "Efficiency is neutralized by soap or detergent residues."

The website http://www.mpbio.com has the following under its description for Benzalkonium Chloride:
"Incompatible with anionic detergents, such as soap, and with nitrates."


How does human body keep track of its age? How does the human body knows that it's time for a event that happens around a certain age like puberty or something that's periodic like menstruation or gestation time of 9 months?

Please note I'm NOT talking about day-night biological clock .

It doesn't always. Some people have an undistorted slown down aging. Jyoti Amge is over 18 and looks like an undistorted little girl. Yesterday, I saw a TV show that showed a 22 year old who looked like an undistorted 8 year old girl. There are also people who have distorted aging. People with progeria look like a distorted older person. I think nodoby has an undistorted sped up aging. Gabby Williams looked like a distorted toddler when she was 12. Nicky freeman from https://thewest.com.au/news/australia/forty-year-old-trapped-in-childs-body-ng-ya-220462 has a distorted bone structure of a ten year old boy and is all wrinkly. The girl in the YouTube video at https://www.youtube.com/watch?v=xoBetcKAxII&t=96s has the undistorted bond structure of a 13 year old girl and is all wrinkly.


Does probiotics bacteria from yogurt live in the mouth too? Does it populate the mouth/throat or just the gut? Yes I was basically just wondered this as I've taken probiotics in a pill form but those only go to the gut. I guessed the mouth needs probiotics too and I wondered if yogurt can accomplish that.
I also found conflicting stuff on the internet: some say enzymes in the mouth kill the bacteria in yogurt, others say yogurt helps bad breath for example which means it does have beneficial bacteria that live there in the mouth probably.

of course they do... the question is for how long.
Probiotics will tend only to affect the microbiome in the digestive tract for a while.  For yogurt supplemented with probiotics subjects microbiomes drifted back within 48 hours.  Depending on your diet the individuals can hang out for a while or persist.  Children, who tend to drink more dairy have a more persistent Lactobacillus signature.


Allele frequency question You are heterozygous at locus A. Both of your alleles, A1 and A2, have a 10% allele frequency in the population. If you are one of 22 people in a room, how many people do you expect to share a locus A allele with?

I come up with 6.8, working like so:

22 people = 44 locus A alleles in the room = 4.4 A1 alleles and 4.4 A2 alleles at 10% frequency.

I have one of each, leaving 3.4 of each allele to the rest of the room. So, looking at both alleles, there are 6.8 shared alleles out there.

My answer assumes that these alleles are all in different people - I don't know how to account for the probability of someone else having two of them. So I know I am wrong already. Is that last step all I'm missing, or have I gone wrong in a more fundamental way?

(Context: This was a question on a grad-level immunology exam. None of us students could agree on the answer afterwards, and the confused wording (I rephrased it above) made us strongly suspect the professor doesn't have the right answer either, so we wanted to see what the answer actually is for when the exams are graded.)

Same as @bpedit but stated a little bit differently.

  You are heterozygous at locus A. Both of your alleles, A1 and A2, have a 10% allele frequency in the population. If you are one of 22 people in a room, how many people do you expect to share a locus A allele with?

There are 5 possible genotypes that could share at least one allele with "you" A1|A1, A1|A2, A2|A2, A1|A3 and A2|A3, where A3 is the allele (or set of alleles) which frequency is $0.8$. Under Hardy-Weinberg assumptions, the frequencies of each of these genotypes are

$f(A1|A1) = 0.1^2$
$f(A1|A2) = 2 \cdot 0.1^2$
$f(A2|A2) = 0.1^2$
$f(A1|A3) = 2\cdot 0.1\cdot 0.8$
$f(A2|A3) = 2\cdot 0.1\cdot 0.8$

which sums to $4\cdot(0.1^2) + 2(2\cdot 0.1\cdot 0.8)=0.36$.

As the frequencies of both A1 and A2 are $0.1$, the frequencies of each of the three mentioned genotypes are all $0.1^2$. Therefore, the expected number of individuals that share at least one allele with "you" at this locus is $21\cdot 0.36 = 7.56$ people.

Why did we need Hardy-Weinberg assumption to make this calculation?

This section comes in reaction to @Atwo comment below.

To give you the intuition for why you need H-W for this calculation. Imagine all A1 where in heterozygous A1|A2 (and therefore same for A2), then the only other genotype that would share an allele with you are A1|A2 genotypes that would be present at frequency $0.2$. And therefore the expected number of people the share at least one allele with you in the room would be $21\cdot 0.2 = 4.2$ people.

For exercise, I would like to invite the reader you to repeat the same calculation for a case where all A1 and A2 alleles are only found in heterozygous A1|A3 and A2|A3.


Does anyone know of any resources that detail an extensive number of receptor types, their effects, and signalling pathways? In a similar manner to this Wikipedia page, although I am not too concerned about the localisation of the receptor, or any known ligands, as I can already access this knowledge easily.

https://en.m.wikipedia.org/wiki/Alpha-2_adrenergic_receptor

From the comment section:

The IUPHAR database is one of the most extensive database for receptors and ligands. It also contains a lot of additional information and direct references to the literature.


Why are bruises not lethal? Given the following:

bruises are caused by minor trauma which breaks blood vessels beneath the skin, causing bleeding
the mechanism by which bleeding stops is clotting
blood clots inside the body have an unfortunate tendency to get into the bloodstream and cause blockages, leading to severe problems such as strokes or heart attacks

why is it that people don't die from bruises?  What mechanism does the human body have to keep this from happening?

blood clots inside the body have an unfortunate tendency to get into the bloodstream and cause blockages, leading to severe problems such as strokes or heart attacks

This statement is primarily true only for blood clots within blood vessels, especially in the veins. When you are talking about bruising, you are talking about clots outside of the vasculature.

When a blood clot occurs in an artery, it can block that artery or break off, flow downstream, and block some smaller distal vessel. These events are most severe when they affect crucial organs like the brain and heart ("stroke" or "heart attack"), though of course any organ can be damaged in this way. However, blood clots in arteries can't ever directly affect a tissue that is not distal from where the clot starts, because they can never pass through capillaries or travel backward.

When a blood clot occurs in a vein and is dislodged, it can follow the increasingly larger venous system back to the heart, where it can cause a pulmonary embolism (blockage in the lungs) or, via a patent foramen ovale, travel to the left-side circulation and end up anywhere, including the coronary arteries or blood vessels of the brain. Similarly, clots that form in the venous return from the lungs to the heart or in the left side of the heart itself can travel anywhere (except the lungs) and create a blockage.

For a clot outside the vasculature, for it to have an effect somewhere else systemically it must re-enter the vasculature. This is simply not possible in most situations, because the vessels involved are very small, and during bleeding the blood is flowing out of vessels: there is no pressure gradient to push the clot back into the vessels.

In more severe cases of injury where major vessels are involved, clotting in those major vessels can indeed be a problem, but not for common occurrences of bruising.

(see also @anongoodnurse's answer that contains a good clarification of what exactly a bruise is, as well as how there are risks from very serious bruises but not the same way the original question implied)


What would happen if VEGF was injected into a person? Couldn't VEGF help with ligament recovery? I looked it up and found some studies in rats, but nothing on people. VEGF inhibitors tend to be used more often then VEGF.

Why isn't VEGF being used in people? What would generally happen if VEGF was injected into a person?

EDIT
Here is the one study that examined injection VEGF in rats for increasing skin viability.

Also I am not really asking about the effect of VEGF on ligaments. I just figured that because there is little vasculature surrounding ligaments (and cartilage), VEGF could in theory improve recovery of such injuries. The bigger question is why aren't people ever injected with VEGF?

VEGF is a family of growth factors that promote angiogenesis and vasculogenesis.

Vascularization is a key step in the progression of cancer, so the VEGF family has often been a target for suppression: preventing vascularization of tumors can stop their further growth.

That said, your premise that VEGF hasn't been tried clinically is false: there have been several clinical trials of VEGF (and no doubt more that I didn't find).

Hedman, et al 2003 used catheter-based VEGF gene transfer at the time of angioplasty/stenting, though they found it did not prevent restenosis they did see increased perfusion (it seems to me that further research didn't show sufficient effects on long-term outcomes). Ripa, et al 2006 used VEGF gene transfer as part of a treatment for ischemic heart disease. It seemed like the treatment was safe, but the efficacy was limited. Ropper, et al. 2009 attempted VEGF gene transfer for the treatment of diabetic polyneuropathy. They found some improvement of pain, and report a fairly high rate of adverse events but their control group also experienced adverse events.

It seems like a similar VEGF plasmid is available in Russia as Neovasculgen for use in limb ischemia; the company developing the drug is in the process of beginning to get approval elsewhere.

VEGF as a topical application has been studied under the name telbermin, for example Hanft, et al 2008.

There may be others, but I stopped my search there. https://clinicaltrials.gov/ is a good place to start looking for what research has been done in humans if you have trouble finding journal articles at first.

Hanft, J. R., Pollak, R. A., Barbul, A., Gils, C. V., Kwon, P. S., Gray, S. M., ... & Breen, T. J. (2008). Phase I trial on the safety of topical rhVEGF on chronic neuropathic diabetic foot ulcers. Journal of wound care, 17(1), 30-37.

Hedman, M., Hartikainen, J., Syvänne, M., Stjernvall, J., Hedman, A., Kivelä, A., ... & Närvänen, O. (2003). Safety and feasibility of catheter-based local intracoronary vascular endothelial growth factor gene transfer in the prevention of postangioplasty and in-stent restenosis and in the treatment of chronic myocardial ischemia: phase II results of the Kuopio Angiogenesis Trial (KAT). Circulation, 107(21), 2677-2683.

Ripa, R. S., Wang, Y., Jørgensen, E., Johnsen, H. E., Hesse, B., & Kastrup, J. (2006). Intramyocardial injection of vascular endothelial growth factor-A165 plasmid followed by granulocyte-colony stimulating factor to induce angiogenesis in patients with severe chronic ischaemic heart disease. European heart journal, 27(15), 1785-1792.

Ropper, A. H., Gorson, K. C., Gooch, C. L., Weinberg, D. H., Pieczek, A., Ware, J. H., ... & Kirchmair, R. (2009). Vascular endothelial growth factor gene transfer for diabetic polyneuropathy: a randomized, double‐blinded trial. Annals of neurology, 65(4), 386-393.

Simovic, D., Isner, J. M., Ropper, A. H., Pieczek, A., & Weinberg, D. H. (2001). Improvement in chronic ischemic neuropathy after intramuscular phVEGF165 gene transfer in patients with critical limb ischemia. Archives of neurology, 58(5), 761-768.


Red bug with white tips on antennae These red bugs can be found in hundreds in our locality in Bangalore, India.

They are just about 3.5 cm and have these white (or maybe pale yellow) tips on their antennae.

Can someone identify them and suggest a link where I can find substantial information on their morphology and general behaviour?

I think they are called "Red Bugs" (really), otherwise known as Antilochus conquebertii (aka Antilochus coquebertii).

The black coloring changes from location to location. These were found in India. They were even described by the querent as eating black seeds.

Viet Nam Red Bugs are pretty as well:

  The family Pyrrhocoridae is commonly called the Red Bug family, and the family includes the Cotton Stainers as well as the Firebugs, so Red Bugs is the more general family name that includes the other genera and species.


Is Asteraceae and Compositae the same family? I'm wondering what taxonomic family sunflowers (Helianthus) belong to. Although it's mentioned it belongs to family Asteraceae it is also a composite flower. So it belongs to Asteraceae or Compositae or both?
And do they refer to the same family or to different families?

They are either treated or even declared to be synonyms in all the texts using both of the terms that I have ever read.

Just one reference: the nearest Flora on my desk, G. Marconi, F. Corbetta, Flora della Pianura Padana e dell'Appennino Settentrionale, uses the notation Compositae = Asteraceae.

It is worth to note that Compositae, 'composite ones' in Latin, refers to the their typical capitulum inflorescence, while Asteraceae comes from Aster, a genus belonging to the family, meaning 'star' in Latin, which represents an allusion to the shape of the inflorescence of Aster, and of many other species, which is supposed to look like a star whose rays are represented by the ligules of the ligulate tiny flowers of the capitulum. Nevertheless, there also are species of the family having no ligulate flowers, for ex. Tanacetum vulgare.


Flow cytometry data Analysis everyone.

Since I am new in the flow cytometry technique, I am not really sure how to analyze the result.
We use cell U-937 Lymphoblast.All Cells

Could Anyone help to explain me this one?

Thanks in advance!

Disclaimer: Assumes you know how flow cytometry works.

You've done a flow-based AnnexinV apoptosis assay here.

Annexin A5 (AnnexinV) protein binds to phosphatidylserine (PS), which is typically in abundance of the inner leaflet of live cells. Upon the initiation of apoptosis, PS is known to flip to the outer leaflet. Thus, you can use AnnexinV conjugated to a fluorescent molecule such as fluorescein isothiocyanate (FITC) to look at externalized PS.

7-Aminoactinomycin D or 7-AAD is a fluorescent intercalator that can be used to detect DNA and is excited on the 488nm laser (emits on a 650nm longpass filter or the like). The dye is not permeable to live cells, and so for dead or dying cells with compromised membrane permeability, it binds freely to DNA.

The problem with either alone is you cannot say a 7-AAD+ cell is apoptotic and you cannot say an AnnexinV+ cell is apoptotic, because we know that you have early apoptosis and late apoptosis, and in either the cell isn't wholeheartedly dead, yet. You also have necrosis.

And so on a dot plot of 7-AAD and Annexin V, you can create 4 quadrants based on the mechanism of the two components:

Double-negative: No external PS or DNA binding means these are viable cells.
Double-positive: Both external PS and membrane instability means late apoptosis.
AnnexinV single-positive: Undergoing early apoptosis, nucleus isn't yet permeable.
7-AAD single-positive: Completely dead or necrotic, membranes have probably disintegrated.

The basis of the assay is you're trying to determine at what stage of cell death your cells are in.

The unstained control is a way of looking at your cells alone, and allows your to correct for autoflorescence, florescence generated by your cells just from excitation alone. You also want to run single-stain controls to see where your positive, and negative populations lie. Without FMO (fluoresence minus-one, basically your full staining panel minus a color) controls, it's hard during gating to confidently say where your positives and negatives are delineated, due to the effects of spillover and noise.

A note about the AnnexinV single-stain control: You can see that in the untreated sample, there's basically no AnnexinV, but in the control it's 22.0% of the cells. Single-stain controls where you assume positives exist have to have positive and negatives. Without positives, where do you set the gate for them? What if the population shifts during acquisition? They probably used cells that were dying on purpose to generate confident controls for that sample.

That's the left half of your data. The right half are treatments. Basically you've stained the cells for both markers and then treated them with Torin2, Rapamycin and Mitomycin to see how those compounds affect the viability of the cells. There's a control where you added nothing.

Based on the gates set with the controls, you can see that the mitomycin sample has the greatest effect: The cells are 6.54% AnnexinV positive, undergoing early apoptosis, and 14.3% are double-positive, undergoing late apoptosis, and 8.09% are dead or necrotic.

The conclusion you'd derive is that mitomycin, but not the other compounds, has a profound effect on the viability of the cells.


What are the (evolutionary) advantages of secondary transport? Secondary active transport uses electrochemical gradients as a source of energy for the uphill transport of substrates (coupled to downhill transport of the ion).

However except for in a few cases (e.g. Electron transport chains) the electrochemical gradient is formed by ATPase pumps which use energy from ATP to pump the ions.

So why not just use ATP in the first place (and not have to set up the gradient). (I do understand that the gradients are useful for signalling, action potentials etc. but that is a seperate issue.) i.e. What is the advantage of secondary transport.

My (complete) speculation:
Is secondary transport perhaps used because it allows a sort of inherent regulation. Stop the gradient forming pump and you immediately stop all the secondary transport using that particular gradient? If that is the case are secondary transport proteins in groups with similar functions/pathways utilising the same gradient?

I think an easy analogy for why this approach evolves is to think of how humans use electricity (or energy more broadly).

Although it is feasible to have localized electricity generators (for example, a solar panel on a simple calculator), it's typically more efficient to have centralized electricity production. With that organization, changes to the electricity generating machinery can proceed without any changes needed at the end user. If the power plant improves efficiency by 10%, that improves the efficiency of the entire system without a change needed in every lightbulb, refrigerator, and phone charger.

Once an ion gradient is established, different independent systems can use it to perform otherwise energetically unfavorable tasks. Of course this is not the only way evolution could proceed: as linked in a comment there are several general explanations for why evolution doesn't produce every possible combination. There are in fact a lot of proteins that use ATP directly.

The sodium-potassium ATPase that powers one of the major secondary transport systems is particularly interesting because it moves 5 ions at a time, making it very efficient. It would waste ATP if it only exchanged 2 ions at a time. By producing that gradient, other proteins can then evolve to use this gradient at an appropriate energy level rather than needing to work on a "1 ATP = 1 cycle" basis.


How do you calculate the charge on a polypeptide chain with changing pH? I understand the charge placement on the N & C-terminus and also the utilization of the R-side groups in the amino acids.

For example,
What is the overall charge for a chain Glu-Cys-Arg-Asp with pH 11.0 buffer?

In theory, you can calculate the charge on every individual ionizable group (i.e. looking up their pKa and calculating charge by henderson hasselbalch) and just add them up to get the total net charge.

In practice you would need to measure it with something like isoelectric focusing, since polypeptides fold and certain groups end up interacting with other groups/being shielded from solvent, meaning you really can't calculate it accurately unless you had structural data and even then it would be extremely difficult.


Can non-carbonated energy drinks boost alcohol intoxication? I just read news article about

banning caffeine in alcohol drinks and
about that energy drinks increase the urge to drink alcohol.

Energy drinks cause sugar intoxication - answer about it here in the thread Decreasing the alcohol proof and faster in hangover, why?.
Sugar dehydrates faster as well as causes a cascade of hormonal changes that are more immediately troubling than the alcohol.

I want to understand why energy drinks boosts you to drink more alcohol.
This suggests me that

malaise (caused by energy drinks) can be improved shortly by alcohol drinks

by some unknown mechanisms to me; and this can be the reason why people like to drink more alcohol after energy drinks.
I think that the mechanisms are related to some cascade which I do not know.
This mechanism can lead to improvement in the dehydration very shortly

by acting on the membranes of the cells
or by stabilising the architecture of the endothelium i.e. stabilising the hormonal changes.

My conjecture is that the alcohol can affect on the secretion of the substances from endothelium (EDRF, EDCF).
There are three types of substances secreted by the endothelium

NO
Endothelium hyperpolarising factors
Endothelins

So sugar intoxication causes changes in the endothelium architecture which alcohol intoxication reverts shortly back which boosts people to drink more alcohol to recover from the malaise caused by the energy drinks.

How can non-carbonated energy drinks boost alcohol intoxication?

A very well-written question, so I'm sorry if my answer is a bit too simple. Perhaps it will attract attention of somebody with a better answer.

I think the effect could be mainly caused by the fact that sugary drinks slow down alcohol absorption. So while those who drink just alcohol already know they've had enough, those who have had a couple of energy drinks still feel fine and continue drinking, not knowing that they are about to become even more inebriated.

Also, the stimulants in energy drinks can somewhat reverse the sedative effect of alcohol, leading to higher overall activity of the person and thus faster drinking.


Can immunity to diseases vary by populations? A common explanation for the massive population decreases of isolated societies upon contact with Europeans during the Age of Discovery is that the natives lacked immunity to newly introduced diseases.

What does this actually mean?

Is it just a shorthand for "the adult population was not subjected to these pathogenes during childhood and is therefore more susceptible to them" or is there maybe a certain genetic component to it?

Is it just a shorthand for "the adult population was not subjected to these patogenes during childhood and is therefore more susceptible to them" or is there maybe a certain genetic component to it?

It's a little of both. You can read some of the math behind this in Infectious Diseases of Humans: Dynamics and Control, by Anderson and May.  Chapter 2 gives an overview. The behavior of an epidemic depends a great deal on the specifics of the host-pathogen interaction, but generally you can say that the epidemic curve in a a naive population will have a larger and sharper upswing than in a previously exposed population. You can attribute some of this different behavior to lack of adaptive immunity in the adult population. Again, depending on the pathogen, you can also attribute some of this different behavior to lack of selective pressure in the naive population on highly variable loci involved in the immune response.
To address more directly what seems to be your primary question: yes, there is a genetic component to the susceptibility of a host (e.g., a human) to a pathogen (e.g., a microbe that can cause disease).
Non-heritable aspects:
There are certain aspects of what we call the adaptive immune system in jawed vertebrates that are not directly heritable. You are a jawed vertebrate, and the DNA in each of your B-cells and T-cells that produces B-cell receptors (BCR) and T-cell receptors (TCR) goes through a number of changes outside of the germ line. You can read about these changes in, for example, How the Immune System Works, Chapter 3, by Lauren Sompayrac. It's an excellent introduction if this is new to you.
In addition to the exact set of BCRs and TCRs in the pre-immune state, your current repertoire of cells and molecules is determined by your history of exposure. While some of this can be vertically transmitted, the majority of it is not. This is one of the reasons why, when you look at this repertoire, much of the variability is attributable to non-heritable factors. A not insignificant proportion is attributable to heritable factors, though. So if TCRs and BCRs are not encoded in your germ-line, and your environment obviously has a strong influence on your current immune state, where does the heritable component come from?
Heritable aspects:
All of the other proteins involved in the immune system response are encoded in the germ line, and are thus heritable. Some of them are highly variable, and since they are very important they are under strong selective pressure. You can see important changes in the population distribution of these loci over a relatively small number of generations. There are many other heritable components of an individual or population's susceptibility to infectious disease. There is a great deal of work on this. Casanova has a great article about this in PNAS, which I've linked to in another answer to a related question. A more traditional review of his is here. Of course, he's not the only one working on this. I just like the way he writes. Here's a good one by Baker and Antonovics.
A simplified and speculative example
Re: your comment about measles in the Polynesian islands, we don't have scientific consensus about the relative importance of non-heritable and heritable factors for this particular case. Instead of getting into the nitty gritty details, I'll walk you through a hypothetical:
Imagine an isolated population with a lot of variability in germline genes that code for a special protein that helps their immune system mount a full response to viruses.
A very nasty, very contagious virus is introduced to this previously isolated population. The characteristics of the population help determine the outcome of their interaction with this new virus. Here are 3 important characteristics:

Because nobody has ever been exposed to this virus, nobody has neutralizing antibodies or the rapid immune response that happens the second time you're exposed to a pathogen.

Some versions of that special protein with all that variability don't do a good job of helping the immune system mount a response to this new virus.

Luckily though, some other versions of that special protein with all that variability do an especially good job of helping the immune system mount a response to this new virus.

Because of (1) the disease spreads broadly throughout the population. Because of (2), a specific group of people get especially sick, die, and (because they are dead) don't reproduce, and don't pass on their version of the gene that codes for special protein. Because of (3) a specific group of people do very well, are only sick for a little while, and do an especially good job at generating long lived immunity, and (because they are alive and well) reproduce a lot, and pass on their version of the gene that codes for that special protein.
The epidemic is eventually controlled. Years go by, and the virus starts circulating again.
Now the characteristics of the population are quite different, so the dynamics of the host-pathogen interaction will be different.
Many of the people that were alive during the first epidemic now have neutralizing antibodies and a memory response, so this second epidemic will not spread as quickly or as broadly. This is a non-heritable factor. Previous exposure to the virus has changed the repertoire of cells and molecules in people's blood.
Among the younger generation, more of them have the helpful version of the special protein that helps the immune system generate a response, so not as many of them will die. This is a heritable factor. Previous exposure of the population to the virus has exerted selective pressure, changing the frequency of the helpful and unhelpful alleles in the population.


What is the rationale behind IgM being the default antibody? I know that the$\ C _\mu $ gene appears first in line for class switching and hence the IgM is the default antibody. But what is the rationale for it being so? There must be some advantage (evolutionary?) of having the IgM first in line over the IgG or so on.

The IgM is different from the IgG in being a cluster of five, better agglutination, having more avidity, and more cross reactivity (correct me if any of these is wrong). How do these properties help in containing the infection only for the very first time? Or, why is the IgG is not good for the initial response?

When the Naive B cell gets activated and begins to secrete antibodies the affinity of the antibodies is low, as it hasn't yet gone through several cycles of affinity maturation. The increased avidity of the IgM balances the decreased affinity of these initial antibodies. If IgG were released at this stage, the body would have a much lower immune reaction to the antigen.

However after affinity maturation, the IgG has sufficient avidity and affinity to mount a stronger immune reaction than the initial IgM antibodies. If the body still produced IgM after affinity maturation, there would likely be a significant amount of crosslinking. This could potentially cause aggregates to form in the blood/lymph which could cause occlusions.

Edits:

  If the affinity of the antigen-binding sites in an IgG and an IgM molecule is the same, the IgM molecule (with 10 binding sites) will have a much greater avidity for a multivalent antigen than an IgG molecule (which has two binding sites). This difference in avidity, often 10^4-fold or more, is important because antibodies produced early in an immune response usually have much lower affinities than those produced later. Because of its high total avidity, IgM—the major Ig class produced early in immune responses—can function effectively even when each of its binding sites has only a low affinity.

Molecular Biology of the Cell

The claim on aggregation after affinity maturation is speculation based on the crosslinking that occurs with IgA antibodies (e.g. Phlegm) when there are only two high-affinity Ig molecules joined together rather than five.


Does inhaling glue (glue sniffing) reduce appetite? I have heard from many homeless people that they sniff glue just to reduce appetite, as it comes cheap and is more affordable than actual food.

Is this true, and if yes, why? This is totally opposite to the effects of marijuana where people feel hungry.

  GLUE SNIFFING : Involves inhaling the fumes from domestic and
  industrial products (glue etc.).

Short answer
Various inhalants, most notably organic solvents including those used in paint and glue suppress appetite.

Background
From the Division of Alcohol and Drug Abuse I learned the following:

  Initial effects [of various inhalants] include nausea [...], and a loss of appetite.

And the Humanitarian Irin News reports the following on Nepali street youths:

  The adhesive glue contains toluene, [an] intoxicating hydrocarbon [...]. The solvent [...] causes hallucinations as well as dampening hunger pangs [...].

Indeed, acute exposure to organic solvents has been associated with a loss of appetite (Gregerson, 1998), and chronic exposure to toluene in the industrial workforce has also been linked to appetite suppression (Kishi et al., 1993).

References
- Gregerson, Am J Industr Med (1998); 14(6): 681–701
- Kishi et al., Environmental Res (1993); 62(2): 303–13


Is alternative splicing possible in the same cell? I know alternative splicing is possible in different cell types of an organism, or within the same cell at different developmental stages. There are several examples like this. But are there any instances of alternative splicing within the same cell at the same time? Perhaps some melanin variants producing shades of different color for example. Normal cells, not cancerous.

In complex eukaryotes like humans, alternative splicing is the rule, rather than the exception.
Eukaryotic splicing is managed by a complex regulatory system, including more than 100 different elements, some of which are enhancers and regulators.
Thus, while one form will often be dominant, one should generally expect at least some alternatives to be present in a cell.
While the amount of work on population-level heterogeneity is still much larger than that on variation within single cells, studies of splicing heterogeneity have identified that multiple forms are often present simultaneously within a single cell. For example, in this recent study, Figure 2 shows that although the distribution between two splicing alternatives is bimodal, single cells exist with the full range of fractional mixes between the two forms.


How do biologists determine the parents of a child I am not well-versed in biology so this question might be wrong. As far as I understand meiosis, two germ line cells with 23 chromosomes each (one cell from the father and another from the mother) combine and after meiosis we get recombined chromosomes from the haploid cells with 23 chromosomes that will develop into an embryo. So, the child has different chromosomes than the ones of his father and mother. Then how can we know, by analyzing the child's DNA, who are the parents?

My simple question comes, in part, from this video about meiosis

I apologize for any errors.

Your description is not totally correct (or understandable). There is plenty of source of information online so, I won't repeat the whole thing here. In very short and very simplified, talking about humans...

Ploidy, meiosis and fecundation

Both parents are diploid (2N=46). Both parents have specific cells that are undergoing meiosis (in testis and in ovaries). After meiosis, the cells (spermatozoids and ovules) are haploid (1N = 23). The spermatozoid and the ovule fuse (fecundation) to make another diploid (2N = 46) individual. This diploid individual will grow for about 9 months in the mother's uterus before coming out!

Crossover

Now, during meiosis, cross-over occurs. It is a mechanism where the two chromosomes mix up their material. When the cross-over occurs in the father for example, it is the chromosome that the father receive from his father and the chromosome that he received from his mother that mix-up their genetic material.

Possible chromosomes

Let's say the maternally inherited chromosome of the dad is

AAAAAAAAAAAAAA

Let's say the paternally inherited chromosome of the dad is

BBBBBBBBBBBBBB

Then, in the meiosis (where spermatozoids are produced), the two chromosome might mix up and the haploid spermatzoid can end up with something like

BBBBBBBBBBBAAA

Now, on the mother's side, her two chromosomes are, say,

CCCCCCCCCCCCCC

and

DDDDDDDDDDDDDD

The mother might therefore transmit

DDDDDDDCCCCCCC

The (diploid) baby would then be

BBBBBBBBBBBAAA
DDDDDDDCCCCCCC

So of course, the chromosomes present in the baby are a bit different form the ones present in the parents but we can still recognize them. If there is doubt who the father is, a genetic analysis of another father might return the chromosomes

BBBBBBBBBBBBBB
FFFFFFFFFFFFFF

, then we would know this individual cannot be the father because he could have not transmitted the AAA part of the chromosome found in the kid.


Why can CO₂ be transported dissolved in plasma? Is it because CO2 is more soluble in water or has it got to do with the alkaline pH of plasma ?I here mean only aqueous CO2 transport from body cells to lungs.

The bulk of CO2 is transported as bicarbonate/carbonic acid.  The conversion between CO2 and carbonic acid is catalyzed by carbonic anhydrase in red blood cells, otherwise the conversion would be very slow. The bicarbonate is then shuttled out of the RBCs and into the blood plasma. The CO2 (gas) in blood plasma accounts for <10% of CO2 transport, and the solubility isn't that much different from that in water.

Source: Guyton and Hall Textbook on Medical Physiology


Will genetically modified food affect our health? It's a popular public sentiment that - GM foods like tomatoes (flavr savr) will affect our health.. Is there any logical scientific explanation behind this?

It's a popular public sentiment that - GM foods like tomatoes (flavr
  savr) will affect our health.. Is there any logical scientific
  explanation behind this?

GM organisms can have different genes and gene expression than natural ones, so they can create more protein or different proteins. Proteins can be toxic, can cause allergy and can catalyze reactions which can lead to toxic products.

To create a GM plant you need dollar millions, so it is not a cheap business. The GMO food regulations are very strict (at least in the EU), so it is unlikely that you will eat a GMO which contains toxic compounds.

  Whereas food safety organizations find nothing inherently unsafe in
  the process of genetic engineering, they note that new plant
  characteristics developed in the next wave of agricultural
  biotechnology could present new risks. At the same time, future
  generations of biotechnology may well provide food products with
  higher vitamin or protein content and lower allergenicity, yielding
  benefits to food consumers.

2014 - Agricultural Biotechnology: The Promise and Prospects of Genetically Modified Crops

Despite all the effort to make GMO foods safe, there are issues:

  Pesticides associated to genetically modified foods (PAGMF), are
  engineered to tolerate herbicides such as glyphosate (GLYP) and
  gluphosinate (GLUF) or insecticides such as the bacterial toxin
  bacillus thuringiensis (Bt). The aim of this study was to evaluate the
  correlation between maternal and fetal exposure, and to determine
  exposure levels of GLYP and its metabolite aminomethyl phosphoric acid
  (AMPA), GLUF and its metabolite 3-methylphosphinicopropionic acid
  (3-MPPA) and Cry1Ab protein (a Bt toxin) in Eastern Townships of
  Quebec, Canada. Blood of thirty pregnant women (PW) and thirty-nine
  nonpregnant women (NPW) were studied. Serum GLYP and GLUF were
  detected in NPW and not detected in PW. Serum 3-MPPA and CryAb1 toxin
  were detected in PW, their fetuses and NPW. This is the first study to
  reveal the presence of circulating PAGMF in women with and without
  pregnancy, paving the way for a new field in reproductive toxicology
  including nutrition and utero-placental toxicities.

2011 - Maternal and fetal exposure to pesticides associated to genetically modified foods in Eastern Townships of Quebec, Canada

  The study of combined effects of pesticides represents a challenge for
  toxicology. In the case of the new growing generation of genetically
  modified (GM) plants with stacked traits, glyphosate-based herbicides
  (like Roundup) residues are present in the Roundup-tolerant edible
  plants (especially corns) and mixed with modified Bt insecticidal
  toxins that are produced by the GM plants themselves. The potential
  side effects of these combined pesticides on human cells are
  investigated in this work. Here we have tested for the very first time
  Cry1Ab and Cry1Ac Bt toxins (10?ppb to 100?ppm) on the human embryonic
  kidney cell line 293, as well as their combined actions with Roundup,
  within 24?h, on three biomarkers of cell death: measurements of
  mitochondrial succinate dehydrogenase, adenylate kinase release by
  membrane alterations and caspase 3/7 inductions. Cry1Ab caused cell
  death from 100?ppm. For Cry1Ac, under such conditions, no effects were
  detected. The Roundup tested alone from 1 to 20 000?ppm is necrotic
  and apoptotic from 50?ppm, far below agricultural dilutions (50%
  lethal concentration 57.5?ppm). The only measured significant combined
  effect was that Cry1Ab and Cry1Ac reduced caspases 3/7 activations
  induced by Roundup; this could delay the activation of apoptosis.
  There was the same tendency for the other markers. In these results,
  we argue that modified Bt toxins are not inert on nontarget human
  cells, and that they can present combined side-effects with other
  residues of pesticides specific to GM plants.

2012 - Cytotoxicity on human cells of Cry1Ab and Cry1Ac Bt insecticidal toxins alone or with a glyphosate-based herbicide

  Though GM crops promises to meet the world's food need and eliminate
  the world hunger and starvation, the potent harmful effects cannot be
  overlooked and these need to be taken seriously. The long term impact
  on the society cannot be overruled as it includes the health risk of
  all the people involved be it producers (farmers) or the consumers
  along with the scientists who are working in the laboratory. Hence, it
  is the need of the hour to reach and try for sustainable development
  that meets the needs of humans and the balance of nature maintained.

2013 - Cry1Ab Treatment Has No Effects on Viability of Cultured Porcine Intestinal Cells, but Triggers Hsp70 Expression

I think it is the same story as by food, pharma and plastic industry. The billion dollar profit can be more important than the consequences. Btw. if you check a regular food, which you can buy in the shop, you will find a lot of unhealthy components e.g. trans fatty acids, omega-6 fatty acids, fungicide remnants, etc... which can affect your health as well.

My conclusion is that in most of the cases it is safe, however in rare cases it might have a mild harmful effect. To filter out those cases and their causes we need further studies and better regulation.


What are the roles of cadherins in epithelial mesenchymal transitions? I know that cadherins control the expression of cancer cells involved in the epithelial-mesenchymal transitions, but I was wondering exactly how the process worked.

So let's just quickly define what cadherins are, using general information from wikipedia,

Source: Wikipedia
Cells express E-cadherin (epithelial), N-cadherin (neuronal, or P-cadherin (placental). These generally interact with ß-catenins to modulate cell adhesion. There are pathways intrinsic to cancer which downregulate the expression of cadherins,

Source: Epithelial–mesenchymal transition in development and cancer: role of phosphatidylinositol 3' kinase/AKT pathways
We see in the above pathway described in a study of PI3K/Akt signaling in cancer, some of the ways E-cadherin (encoded by CDH1) becomes downregulated. We also see that ß-catenin may be sequestered by E-cadherin at the plasma membrane, and cytosolic ß-catenin actually interacts within the nucleus as a transcription factor for SLUG (or snail2) where Snail2 is an essential mediator of Twist1-induced epithelial mesenchymal transition and metastasis. In the above figure this modulates reduced cell-cell adhesion, but we also see there's a number of other pathways which modulate the entirety of the EMT process.
What I found interesting, maybe unrelated
An interesting concept currently being investigated involves many of the shown membrane receptors, most of which are involved in some sort of crosstalk in aggressive cancer types. ROR1 was identified as a critical component for modulating EMT, and was shown to participate in Wnt signaling through it's frizzled domain, as well as crosstalk with Met tyrosine kinase, EGFR, and TGFß in some way. These interactions were able to increase expression of snail1/2, vimentin, etc. i.e. characteristics of EMT in breast adenocarcinoma (The linked article provides most of this background, but some may be missing, I'm unsure), and decrease expression of epithelial biomarkers like E-cadherin. When they used a ROR1 Ab to target ROR1, they found cadherin levels could be rescued, and morphological components returned to a more epithelial phenotype. Other articles showed this targeting could induce apoptosis in CLL and this occurs through interaction with PI3K/Akt.


Are there single-celled organisms that have evolved from multi-cellular ones? I'm reading this paper about transmissible cancer cells in clams (Metzger et al. 2015) and I was wondering if there are any single-cellular organisms that are around today that are suspected as having descended from a multicellular organism

My question is different from this question as I'm not asking about cancer specifically but rather single-celled organisms evolving from multicellular organisms in general.

I would consider HeLa cells to be an example of a unicellular eukaryotic organism that evolved from humans. It can survive independently and replicate within cell culture plates, but cannot survive in the wild, however.

HeLa cells are, like in your example, cancer cells, in this specific case human cervical cancer cells. They were propagated as an immortal cell line, and completely match the replication characteristics of eukaryotic cell lines when propagated in the laboratory.

It can be even considered the case that HeLa cells are actually a kind of unicellular eukaryotic model organism not unlike S. cerevisiae, since they are widely used in experiments involving human-like cells.

As WYSIWYG has said in the comments, some biologists have even assigned the binomial name Helacyton gartleri to the cells (albeit with some controversy).


What causes sleep inertia? Sometimes after a nap, I wake up in a state of grogginess. I learned that this is actually called sleep inertia. I'm able to find lots of methods to overcome this, but what causes it in the first place?

This is due to states of brain activation promoted by the reticular formation, specifically with the ascending reticular activating system that mediates the general activation of the upper areas, for sleep these areas should promote states of relative low activity promoting the cerebral activation profiles during sleep, it is also interesting to study the descending reticular activating system that mediates the general muscular activation that is generally inhibited during sleep (except clinical problems among others) (that is why you can not make muscular efforts when waking up, try an experiment: try to clench your fists strongly when you are awakening).


Can I compare Shannon-Wiener diversity indices between plots of different sizes (area)? Can I compare the Shannon-Wiener (a.k.a. Shannon-Weaver) Index of diversity ($H'$) of plots (communities) with varying sizes (areas)?

If not, what steps do I need to take and/or which tests should I use to compare the diversity of different-sized plots?

I also wonder if this is possible for Simpson's Index of diversity?

Shannon-Wiener Index:

$$H' = -\sum \limits_{i=1}^S p_i \ln p_i$$

Simpson Index:

$$D = 1 -\sum \limits_{i=1}^S {p_i}^2$$

Where $p_i$ is the proportion of species $i$, and $S$ is the number of species.

Theoretically the index for two habitats of different areas are not directly comparable. Consider the species area relationship. You see more species when you look over a larger area. So you will potentially see a different index just from considering a larger area, and not necessarily because there is something different about the habitats.

Borda-de-Agua et al tackle this head on. They use fractals to account for differences in area when comparing diversity indexes. It's complicated and I won't try to put the methods here because I don't understand them. Definietly worth looking at yourself though.

I would also consider using species abundance distribution (SAD) curves for comparison. They give information about diversity but don't sum it up in one nice number like indexes. I feel they are area invariant too. Since if you keep increasing the area of your sample, the total species will only increase from relatively few rare species, while abundances will increase mostly with the abundant species. This will not change the slope of the curve but just the intercept (My hypothesis, not sure if it's actually true). Checkout a good comparison of SAD's and diversity indexes in the intro to McGill et al.

References

Borda‐de‐Água, L., Hubbell, S. P., & McAllister, M. (2002). Species‐area curves, diversity indices, and species abundance distributions: a multifractal analysis. The American Naturalist, 159(2), 138-155. Link

McGill, B. J., Etienne, R. S., Gray, J. S., Alonso, D., Anderson, M. J., Benecha, H. K., Dornelas, M., Enquist, B. J., Green, J. L., He, F., Hurlbert, A. H., Magurran, A. E., Marquet, P. A., Maurer, B. A., Ostling, A., Soykan, C. U., Ugland, K. I. and White, E. P. (2007), Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters, 10: 995–1015. Link


Reproduction in horses and donkeys How are horses and donkeys able to interbreed and produce a mule. Don't their genetypic variation or chromosomal difference prevent them from doing so? If not, then why not?

In closely related species chromosome has only some genetic variations. Therefore there is chance of their chromosomes joins. But if interbreed occurs the species will not be fertile. The ova of female species can take the most compatible from the closest male type .

It's not like that different species can't breed, in many cases they can. For example Donkey and horse , tiger and lion, etc, but the fact is that when different species breed they do not Produce fertile offsprings. Hinney, mules, liger and other animals that are produced by breeding between different species are infertile.


educational sources for learning biochemistry I just finished high school and am going into a biology undergraduate degree, I'm getting into biochemistry too and would like to learn more about it through online platforms or even non-fiction books to use my time effectively this summer. So far I've been using online flash cards to learn more about the jargon and would like to hear some suggestions of platforms or books to read that teach concepts strongly tied to biochemistry beyond what a basic high school curriculum would teach.

There are several reference books for biochemistry, some more readable than others. I personally recommend two of them: (1) Lehninger et al. Principles of Biochemistry and (2) Voet, D., Voet, J., et al. Fundamentals of Biochemistry: Life at the molecular level. Both books contain the most important and basic features of each subject. The chapters are generally well written. I have to say that, from my own experience, I consider that Voet's book is more enjoyable, given that some of the sections of Lehninger's can be a bit tricky. Whichever book you choose, make sure you get relatively new editions. Good luck!
As a side note, even though biochemistry is one the first proper biology classes one takes in undergrad, there are some background requirements. Taking organic and inorganic chemistry courses before is important and some understanding of thermodynamics will certainly come in handy.


What is meant by 4 –12% or 8% SDS-PAGE? I am reading a journal paper and I am looking at the materials and methods section. Regarding the Western blot method in the paper, I have come across the following statement:

Proteins were separated by 4 –12% or 8% SDS-PAGE and electroblotted to
nitrocellulose transfer membrane.

I am not sure what is meant by '4-12% or 8% SDS-PAGE' in the above statement. Do the percentage values refer to the percentage of acrylamide in the gel? Any insights are appreciated.

Do the percentage values refer to the percentage of acrylamide in the gel?

Yes. The 8% gel is 8 g acrylamide per 100 mL. The “4-12%” gel is a gradient gel, which are useful for separating proteins over a large range of sizes. Read more about the uses and formulations of gradient gels here.


Normalizing Metabolomics data First time posting. I recently started working in the field of metabolomics. I have semi-quantitative (not absolute concentration) LC-MS data from in-vitro cell experiments under different experimental conditions.

What is the best way to normalize the data so that I can compare across experimental conditions correctly ( + across different cell types)? I've found many people scale their data using different methods (pareto scale, auto scale, zero mean)  each of these leads to different results when I run something like a PCA between experimental groups.

Thanks.

Jon

Scaling is not the same as normalization.  You have empirically discovered how scaling affects PCA, and it's purpose is to control whether large peaks dominate the analysis or not.

Normalization on the other hand is typically done when samples were in a solvent and the concentration could vary due to the extraction method, the hydration of the tissues etc.  So normalization tries to compensate for these varying concentrations.

Normalization would normally be applied across the peak intensity vs time dimension.  Two typical normalization schemes are 1) normalization to constant sum (usually 1) and 2) Probabalistic Quotient Normalization which uses a slightly more complex approach (and is frequently preferred).  I don't work with LC-MS data, there may be other methods that are preferred with this type of data.  Whatever software you are using probably has several options built-in.

Probabalistic Quotient Normalization is reported in F. Dieterle et. al. Analytical Chemistry vol. 78 pages 4281-4290 (2006). The exact same mathematics are called "median fold change normalization" by Nicholson's group, reported in K. A. Veselkov et. al. Analytical Chemistry vol. 83 pages 5864-5872 (2011).


Shouldn't recording electrode have as low resistance as possible? Following quote is from this wikipedia page on single unit recording.

Intracellular single unit recordings require electrodes be inserted through the cell membrane to record from within the cell. Glass micropipettes or metal electrodes may be used for intracellular single unit recordings, but glass micropipettes are preferred because their high input resistance allows more precise recordings for measurement of resting potentials.

How high input resistance helps better recordings? Shouldn't recording electrode have as low resistance as possible?

For accurate measurement of the membrane potential, it is crucial to have as little current flow through the measurement device as possible. Otherwise, the equilibrium of leak channels that generates the resting potential would be disturbed. See diagram and text from Axon Guide 3rd edition below:


Percentage of understood human DNA I want to know what's the approximate percentage of understood human DNA, as in, which part does what. I'm not asking for details, just the amount.

Thank you.

The devil is in the details, and therefore we cannot just state that we have understood X% of the DNA. We know e.g. that 2% of the human DNA encode proteins. And for a good number of proteins we know what they do. So you might know that a particular codon AGT encodes a serine residue in a protein, which could have a catalytic activity. Or it has a structural activity. Or we are not sure what it does. Sometimes protein-coding and regulatory sequences overlap. So even if we first understood the protein-coding function, there was still the regulatory function to be discovered.

The upshot is that there are multiple levels of understanding, and big controversies of what they actually imply (see e.g. the ENCODE saga).


What can cause a lump in the middle of the neck? (homework case study) What can cause an erythematous, fluctuant, nontender mass in the middle of the neck?

Full Case Study: (Its the last of 6 cases and I just can't figure this one out,  because of all the possibilities, there is always something that doesn't line up.)

The 26-year-old man presented for evaluation of a neck mass and a right axillary mass. The patient, who came to the United States from Vietnam 6 1/2 years ago, noted  midline neck mass. The mass gradually increased in size. Approximately 3 weeks prior to admission, he noted a midline neck mass. These masses were incised and drained twice. Samples of purulent material were sent for routine bacterial culture at an outside hospital. The patient had lost 3 kg (ca. 7 lbs) in the 2 months prior to admission but denied fever. Travel history was notable for his having lived in Arizona for 6 years prior to moving to Boston.

On examination, he was afebrile. An erythematous , fluctuant, nontender mass (8cm x 6cm) was present in the midline of the neck. (Fig. 5.1)  (computed tomogram[CT] scan in fig. 5.2).The right axilla demonstrated incision sites that were draining and were tender to palpation. He had no adenopathy elsewhere. His (PPD) purified protein derivative skin test was reactive, and his chest x-ray was notable for apical scarring in the right lung.

Because of the positive PPD and apical scarring seen on the patient's chest x-ray, the clinical suspicion of cervical ________ was high, and the patient was begun on a four drug anti- _________________ regimen.

Several days after the neck mass was drained of several milliliters of purulent material for culture, a mold was found to grow on the blood agar plates in the routine bacteriology section of the microbiology laboratory. The mold was white (Fig. 5.3) and initially did not have any identifying characteristics when a lactophenol cotton blue preparation was examined under a phase-contrast microscope. It was subcultured at both room temperature and body temperature, and after subculture began to demonstrate the presence of  spores microscopically (Fig. 5.4) The identification was confirmed by using a commercially available genetic probe.

You ask for the fungus causing An erythematous , fluctuant, nontender mass (8cm x 6cm) was present in the midline of the neck.

On the brink of question closure I decided to do a quick search. Based on your descriptions, I found a possible culprit.

In the referenced paper they talk about a fungal Cryptococcosis infection causing, and I quote:

  [A] fluctuant, non-tender mass, five by five cm. in the right costal vertebral angle which was not red or warm.

So this mass was found on the costal vertebral angle, but the remaining symptoms seem reminiscent of your case study. Fungi generally appear white when plated, as far as I know.
However, more information is likely necessary to confirm this genus and identify the species.

costal vertebral angle (CVA). Source: Pinterest

Reference
- Moore, J Invest Dermatol (1957); 28: 159–82


Is there a biophysical causation from local field potential (LFP) to spikes? Many experiments showed that neurons tend to fire at some phase (usually trough) of local field potential (LFP) oscillations, such as theta or gamma rhythm. LFP is supposedly generated by a population of neurons with coherent currents induced by spikes. So there is a causal link from spiking activity to LFPs. Is there also a significant influence on the spikes directly from LFP (not via the hidden spikes that generated the LFP)?

Is it just an epiphenomenon, and or is there a possibility that it is partly a serious mechanism for neural computation?

I am not sure that kind of action would be a "significant influence", but the general understanding is that LFP and spike frequency are inter-correlated (1, 2). An interesting recent publication on the topic (3), however, doubts this correlation as the nature of LFP recording and signal processing might introduce some artifacts to the recordings.

It would be interesting to see a correlation between the spike shapes and LFP, but I failed to find a relevant paper here.

References:

 Belitski A, Gretton A, Magri C, Murayama Y, Montemurro MA, Logothetis NK, Panzeri S. 2008. Low-frequency local field potentials and spikes in primary visual cortex convey independent visual information. The Journal of neuroscience : the official journal of the Society for Neuroscience 28: 5696–709.
 Rasch MJ, Gretton A, Murayama Y, Maass W, Logothetis NK. 2008. Inferring spike trains from local field potentials. Journal of neurophysiology 99: 1461–76.
 Zanos TP, Mineault PJ, Pack CC. 2011. Removal of spurious correlations between spikes and local field potentials. Journal of neurophysiology 105: 474–86.


If coelocanths are more related to humans than groupers -does a Coelocanth's DNA literally have more sequences in common with a human than a grouper? Would a coelocanth and a human still have more sequences in common than a coelocanth and a grouper? Would the coelocanth and human dna basically "look" more similar than either would to a ray-finned fish based on sequences?

Yes, in virtually every way. In terms of pairwise distances, measured in percentages, humans and coelacanth are closer to one-another than coelacanth would be to any ray-finned fish. In terms of individual genes, there would be genes that humans and coelacanth share with their common ancestor, but are not found in any ray-finned fish. Remember, humans are bipedal terrestrial fish.


What species is this fast-moving spider? This is a frame from a recent recording:

Location

Forest in Central Europe at around 1pm.

Abiotic factors at the time of recording

Temperature = 23°C
Humidity = 38%
Wind = 6 km/h

Description

Approximate size = ~3 cm including limbs
Semi-transparent limbs and cephalothorax, opaque abdomen
The abdomen presents a pattern which reminds me of the coat pattern in giraffe G. camelopardalis tippelskirchii
its general morphology makes me think it might be part of Pholcidae family but I'm not entirely sure because the height of the abdomen seems a bit too bulbous on the Y axis
web structure rather irregular

Observed behavior

Very short reaction time (dropped a piece of leaf on top of its web), very fast moving spider. I can't provide a better estimation for the speed, but here's is the 3rd frame after the one above (on the previous two frames it just very slightly flexes its limbs):

And one frame later it's already gone.

Internet search

Google image search: no results using the first image you see in this post
Google text search: different sentences like "long-legged transparent forest spider" only returned the usual daddy long legs you can find at home in urban areas.
Finally I tried https://spiderid.com/spiders/ selecting white and brown but none of the displayed spiders matches anything that resembles the frame above.

Any help will be much appreciated. I guess the pattern on the abdomen is key to identify this species but I haven't had a lot of luck while looking for abdominal spider patterns.

Pawelek;

Unfortunately, I'm not very experienced at European spiders, but I suspect you're looking in the wrong place.  First of all, this appears to be an adult male spider (large ball-like structures at the ends of the pedipalps, in front of the 'face'), so the body pattern is probably going to be a bit different from the one you see on the females.  Male patterns are often an afterthought in identification references, unfortunately.

Secondly, this doesn't look much like a Pholcid to me - I'm getting more of a Linyphiid impression, from the shape of the abdomen, the visible patterns on cephalothorax and abdomen, and the filmy sheet it's hanging under.
I wish I could be of more help than this - but perhaps Ed Nieuwenhuys can help.  Here's a link to his site; if you look down toward the bottom, there's a contact link you could send him a photo and this question:

https://ednieuw.home.xs4all.nl/Spiders/spidhome.htm


How is oxytocin produced? Is oxytocin (or other peptide hormones) produced from a gene through translation, or is it made some other way?

Oxytocin is produced by cleavage of the protein of the oxytocin/neurophysin I prepropeptide gene. The precursor peptide is cleaved by Proprotein-Convertase 1
. Mice lacking the gene which encodes for this enzyme have reduced levels of oxytocin. The final step in the biosynthesis of oxytocin is carried out by Peptidyl glycine alpha-amidating mono-oxygenase.


What Aquatic Mammal has no Tail? Found in a waterway in Butte County, CA. First thought it was a beaver kit, but it has no
tail.
What aquatic mammal has no tail?

Looks like a mountain beaver (Aplodontia rufa) to me. Location, appearance, and minimal tail all match.

A bit more detail:

Where I'm from on Washington's Olympic Peninsula, they're not uncommon, but Butte County is near the southern end of their distribution (eol map page) and they may be less common there, and limited to cooler higher elevations (Beier 1989), and to wet habitats (their inability to concentrate urine (!) means they need to drink enormous quantities of water).

This white paper from USDA (Arjo 2007) is a great source, and more comprehensive than the  the wikipedia page, which is also good.

Arjo, Wendy M. (2007). "Mountain Beaver: A Primitive Fossorial Rodent". USDA National Wildlife Research Center - Staff Publications. Paper 675.

Beir, Paul (1989). Journal of Wildlife Management 53(3) 649-654


Can translation ever occur without transcription? This question is aimed mainly towards viruses with ssRNA, is transcription required, for the +ve strand RNA? If so, why?

I am assuming that the question is whether, in single-standed +ve RNA viruses, translation of plus-strand RNA can occur before transcription.

First, there are many different families of viruses, and there are bound to be counter-examples to whatever I say here. However, with that rider:

We generally refer to replication of RNA viruses by RNA-dependent RNA polymerase, rather than transcription. I am not aware of any RNA virus that has an RNA polymerase recognizing promotors and transcribing specific genes. These viruses tend to replicate in the cytoplasm and therefore do not have access to host RNA polymerase.
There has to be replication, and this tends to be conservative, rather than semi-conservative. By this I mean that when minus-strands are generated they act as templates for many plus-strands, which are needed for the virus particles.
In the case of picornaviruses, such as polio, translation can occur before replication. As is common with small RNA viruses, there is a single initiation site for translation — in the case of polio, a polyprotein is produced, which is subsequently cleaved into individual polypeptides. The diagram below is from the Wikipedia entry for poliovirus and is reproduced here under the Creative Commons license.

[Nidia H De Jesus (image and caption) - De Jesus NH (2007). "Epidemics to eradication: the modern history of poliomyelitis". Virol. J. 4: 70. DOI:10.1186/1743-422X-4-70. PMID 17623069.
The cellular life cycle of poliovirus. It is initiated by binding of a poliovirion to the cell surface macromolecule CD155, which functions as the receptor (1). Uncoating of the viral RNA is mediated by receptor-dependent destabilization of the virus capsid (2). Cleavage of the viral protein VPg is performed by a cellular phosphodiesterase, and translation of the viral RNA occurs by a cap-independent (IRES-mediated) mechanism (3). Proteolytic processing of the viral polyprotein yields mature structural and non-structural proteins (4). The positive-sense RNA serves as template for complementary negative-strand synthesis, thereby producing a double-stranded RNA (replicative form, RF) (5). Initiation of many positive strands from a single negative strand produces the partially single-stranded replicative intermediate (RI) (6). The newly synthesized positive-sense RNA molecules can serve as templates for translation (7) or associate with capsid precursors to undergo encapsidation and induce the maturation cleavage of VP0 (8), which ultimately generates progeny virions. Lysis of the infected cell results in release of infectious progeny virions (9).]


Can fats clog veins or capillaries? I know that so much fats running in the bloodstream could deposit in arteries, harden forming a plaque and cause atherosclerosis. But what about veins (which are formed from same types of layers as arteries) and capillaries?

I googled a bit but everything was regarding arteries.

Is it because veins have a much wider diameter than arteries that even if some fats deposit they won't clog it?

And for capillaries, they are much smaller so shouldn't they be more vulnerable to this?

In addition, I guess since one of the lymphatic vessels functions are to transport fats from  capillaries in villi to bloodstream, how are they adapted to prevent deposit of fats as they carry out the transportation?

N:B I'm just an OL biology student, and also horrible at chemistry

I know that so much fats running in the bloodstream could deposit in arteries, harden forming a plaque and cause atherosclerosis. But what about veins (which are formed from same types of layers as arteries) and capillaries?

Wikipedia says this:

  Veins do not develop atheromata, because they are not subjected to the same haemodynamic pressure that arteries are,[8] unless surgically moved to function as an artery, as in bypass surgery.

The cited study isn't freely available, but seems to have tested in rabbits by surgically modifying their blood flow and giving them a high fat diet.

As for capillaries, they are continuously remodeled, so while they do become clogged for a variety of reasons, once flow stops they're disassembled and new capillaries formed if the tissue becomes hypoxic.


Why are many fruits sour? Many fruits (like apples, berries, citrus fruits etc.) contain high levels of organic acids, especially malic acid and citric acid. Are there any evolutionary functions of those acids in ripe fruits? In unripe fruits the sour taste may protect fruits from being eaten prematurely by herbivores, but why are those acids still present in ripe fruits? Are they there for increasing osmotic pressure so plants can make bigger fruits in a cheap way by just inserting more water in them? Or do organic acids perhaps play a role in pathogen protection? Or are they just a by-product of some other biochemical mechanism in fruit development?

Short answer

Great question! I have done some research on the topic and found so much interesting information. It still seems like a topic that i being researched on, but so far, the research shows that malate is created by a CAM and C4 like pathway while citrate is created from TCA cycle.  Their functions are that they are important biomolecules in metabolism, in particular respiration.

Background

Malic acid and citric acid are the two main organic acids that are accumulated in the fruits and cause the sour taste. Citrus fruits contain more citric acid and other fruits like apples and pears contain malic acid. I will provide a detailed analysis for both cases.

In an article by Deshpande & Ramakrishnan they mention two hypotheses about the accumulation of the citric acid in fruits. One was that the organic acids are not formed in the fruit, but transported to the fruit, in which the fruit acts like a storage organ. The other hypothesis is that the carbohydrates in the fruit is converted to the organic acid. In their research. they tried to isolate some enzymes from the Garcinia fruit to support the second hypothesis. They say:

This [reciprocal relation between acid and sugar content] would indicate the transformation of sugar to citric acid in the fruit tissue itself due to the presence of the requisite enzyme systems.
They suggest that the TCA cycle is how the citric acid is being accumulated and stored.

The article in the comments by Lobit et al. also supports a similar hypothesis of the accumulation of malic acid. The authors tell us that the malic acid is most likely produced in the fruit itself because the pH of the xylem and phloem (the transporting organs of plants) have a pH of close to 7 or higher. It seems that the malic acid is stored in the vacuoles of the mesocarp cells and that the amount of malic acid in the fruit depends on the transport of the malic acid to the vacuoles in the mesocarp cells.

Pathways

The actual pathways for the creation of citric acid and malic acid are very complex. Here is a picture of the different pathways in the cytosol of the mesocarp cells thst create these organic acids (picture taken from Etienne et al.)

The first pathway described is the PEP pathway, which is really a modified CAM or C4 pathway (which are teo ways to deal with photorespiratin, and are adaptations to hot, dry environments). The PEP is converted to oxaloacetate by PEPC, which also takes in CO2, then that oxaloacetate is converted to malate by NAD-MDH. PEPC is regulated by malate concentration and cystolic pH, showing that the activity of PEPC is to indirectly increase the malate concentrations, not just to create more oxaloacetate.Let me note that I still don't fully understand why C4 and CAM-like pathways are present in Fruits from C3 plants.

The major pathway for citrate synthesis is the TCA cycle. Both are also involved in metabolism. TCA cycle (the citric acid cycle) is an important cycle and the second pathway in aerobic respiration. This pathway occurs in the mitochondria. Malate reacts with acetyl-CoA to make citrate and the CoA is released. The citrate then goes on to be repeatedly oxidized and ends up back to oxaloacetate. Now, for metabolic reasons, for example, if the amount of ATP created is top much at the end of aerobic respiration, the citrate could be transported out of the mitochondria, leading to citrate accumulation.

Control of acid accumulation

The control of the organic acid accumulation is different for both malic acid and citric acid. Malic acid accumulation in the vacuoles is controlled by vacuolar storage and vacuolar transport (Etienne et al). This hypothesis was really the subject of the article in the comments. Their article was about modeling the malic acid based on this hypothesis and compare it to actual biochemical analysis of fruits. Their results supported the hypothesis.

The accumulation of citric acid is more dependent on metabolism, therefore respiration. This is since the vacuolar transport is slower for citrate than malate, and so whatever limits thr speed of malate vauolar transport affects citrate. But citrate concentration in thr cytosol would be the only other main factor affecting the vacuolar transport. A model by Wu et al. was created based on this hypothesis and compared to the actual citrate concentrations, and once again, this hypothesis also supported.

Functions of these organic acids

Suprisingly, the only functions of malate and citric acid cycle is mainly for respiration(mainly TCA cycle), and other metabolic processes. Malate does affect the texture, ripening, and starch metabolism and more of fruits, as described in this article. But, malate and citrate are important for all respiring organisms, including us.