texts: Why are people unable to develop lasting immunity against Norovirus?

texts:
Infection with many viruses will result in decades-long if not lifetime immunity, for example chicken pox.

Because of the large number of viruses responsible for the common cold, lifelong immunity to the common cold isn't possible; we will still be susceptible to those we haven't encountered before. But we do develop immunity to those we've been exposed to.

Influenza virus mutates quickly enough that there will nearly always be strains which will be new to us. Immunity to HIV is difficult because of the particular cells the virus attacks (as well as mutations).

However, Norovirus, while there are many strains, is particularly problematic because immunity to a strain lasts less than a year, making reinfection with the same strain repeatedly possible.

Is the reason Norovirus infection doesn't confer longer-lasting immunity known?


texts: Why do we need to diversify our food sources to live healthy, where other animals live happy on one source?

texts:
We read about eating different food to get all vitamins and minerals our body need, and often you find people fail to get the daily amount of a certain thing.
I wonder why we humans need to do this where other animal live fine on grass only or leafs only


texts: Why is an intron (or exon) still called intron (exon) if retained in (excluded from) mRNA?

texts:
In most explanations, the sections of RNA removed during splicing are called introns, and the remaining segments that are stitched together are called exons.  That is, introns and exons are defined in terms of the splicing process.
But I've come across several counter-examples.  For instance:
From A simple answer for a splicing conundrum:

Exons without these elements [exonic splicing enhancers (ESEs)] are
generally not recognized and tend to be excluded from the mature
mRNA.

And from Wikipedia on alternative splicing:

Intron retention: A sequence may be spliced out as an intron or
simply retained...

In what sense is an exon still an exon (and not an intron) if it tends to be excluded from the mRNA?  In what sense is an intron an intron if it included in an alternatively spliced mRNA?


texts:
the question is already in the title. If possible, it might be extended to:
Have animal taxa (mammal) who tend to live in a family structure have a monogamous sexuality? Or are there cases of these taxa, where the sexual partner is not the social one.


texts: Are there any organisms that are made of more than one (~5-12) cell?

texts: Prokaryotes and eukaryotes are unicellular, made of one cell. Great. Eukaryotes are unicellular or multicellular. But the typical examples of multicellular eukaryotes we have are made of, often, trillions of cells, like us humans. Ants must still be made of many millions of cells. Are there known eukaryotes with very few cells that make them up? Like, 5, or something? Or maybe a dozen cells making up the whole organism in its fully developed state?


texts: What kind of flying insect is this? It kinda resembles a dragonfly but it had what looked like a stinger on the end of it's tail. It was found in Franklin, Ohio.


texts: Can humans survive without consuming life?

texts:
Some people say that it's awful that humans eat animals.  They feel that it's barbaric, because you're killing life and then on top of that, you're eating it, and that you should eat vegetation instead.

But isn't vegetation life too?  Personally, I see no difference between animals and veg as all life has cells, dna etc

So my question is, is it possible for humans to live healthy long lives without eating any type of life, i.e no animals, no plants, no cells (dead or alive) etc? If it is possible, how would it be done?


texts: What factors affect the likelihood of auditory stimuli causing arousal during sleep?

texts: I've noticed that the sound of water drops makes me wake up from sleep but other more strong sounds don't make me wake up. I can't find anything about this. The only reason I can think of is maybe because the sound of drops is continuous. Is there any research about the qualitative aspects of certain noises that affect the likelihood of causing arousal  from sleep?


texts: What's seen when stress echocardiography shows ischaemia? Can this happen without angina?

texts:
What can be seen on the screen when stress echocardiography (a pair of heart ultrasounds before and after exercise) suggests ischaemia? Can this happen without chest pain?

Illustration from Wikipedia:


texts: How do I test if microbes have survived after dehydration?

texts:
I have a solution containing various bacteria and fungi.
My aim is to place solution on filter paper, and wait until it dries.
I then wish to test if the organisms have survived, either on the dried paper, or by rehydrating it (maybe placing the paper into water).
Can someone provide advice on the type of test(s) I should perform to achieve this result?
Preferably the test would be easily sourced (purchase online?) and relatively cheap and easy as I am quite inexperienced in this area.
Thank you in advance for any advice that you can provide.


texts: If osteoarthritis (osteoarthrosis) is a degenerative condition, where the cartilage in joints wears down, what causes the joints to become inflamed? I'm reading through a book called Understanding Disease: Arthritis by Steven Tiger, and it mentions that Heberden's nodes are caused by osteoarthrosis. if things inside the joint are wearing down, why does it get bigger?


texts:
I s'pose this is a variant of the age-old question, "Why are leaves green?"  It's fairly easy to ask teh internets and find plenty of answers for that one.

I have a different but related question: why aren't leaves black?  That is, chlorophyll varieties in leaves' cells mostly absorb red and blue wavelengths.  Why isn't there a pigment in photosynthesis that absorbs green?

Instead, the green gets reflected back to the atmosphere.  Its energy is otherwise lost to the plant.  Nature is awfully well optimized to so many niches; why would this band of light be wasted?

There are some plants that do absorb green (and have dark leaves).  These pigments -- such as anthocyanins, betalains, and carotenoids -- don't have any role in photosynthesis, and play other roles (such as protection against extreme temperature, or acting as an anti-oxidant).  Am I missing some pigment in my list that is green-absorbing and participates in photosynthesis?  If there were such a plant with a pigment like that, why wouldn't these plants dominate?  Is there a large cost to producing the green-absorbing pigment that mostly negates the advantage of the extra energy gained?

After a little more searching on SO, I found the top answer to this question.  In slightly different words, it says that light arrives in quanta, the chemistry in photosynthesis is driven by a certain threshold of energy, and any excess energy from a photon goes to waste heat (that tends to denature some of the proteins involved).  The answer points to another answer with similar reasoning.  However, their explanations don't account for the fact that chlorophylls strongly absorb blue in addition to red, where blue photons have nearly twice the energy of red ones.

Moreover, the answer goes on to say:

  Of course, this is still no explanation why leaves are not simply black — absorbing all light is surely even more effective, no? I don't know enough about organic chemistry, but my guess would be that there are no organic substances with such a broad absorption spectrum and adding another kind of pigment might not pay off.

Are there nothing other than educated guesses at an answer?  And why not use a combination of pigments, instead of a single, broad-spectrum absorbing pigment?  For example, some metabolic pathways use parallel processes.  Quoth the Wackypedia:

  Sometimes more than one enzyme can catalyze the same reaction in parallel; this can allow more complex regulation: with, for example, a low constant activity provided by one enzyme but an inducible high activity from a second enzyme.


texts: Could I use spiders to catch unwanted insects?

texts:
I was wondering if its possible to catch spiders and place them in my greenhouse in order to kill unwanted insect that feast on my plants? I don't really mind presence of spiders since then are not dangerous in my country (Czech republic).

Common species that live outside are Araneus diadematus, we got many that live in presence of human like Tegenaria domestica, but I read that they are type that live at human build constructions and can't really survive outside.


texts:
This is a World Building question, but it's biology specific (I think).

I'm looking for an approximate answer on how long, evolutionary, a specific venom has been roughly the same.  Is it pretty much species based (although I know that's a problematic term), so it would be the same as the "age" of the snake's evolutionary tree since it last branched?  Or is it based on something else?

Specifically looking for information on the Eastern Diamondback.  I am ok with extremely approximate/vague answers, or even just a hypothesis/educated guess.

If it helps, a possible rephrase of this question would be:

How far back in time could you time travel before a modern anti-venom starts to lose effectiveness?


texts:
Background

GC-content refers to the frequency of base pairs that are either C or G in the genome, or in other words the number of GC base pairs divided by the addition of the number of GC base pairs plus the number of AT base pairs.

$$GCcontent = \frac{N_{GC}}{N_{AT}+N_{GC}}$$

Question

How does the GC-content evolve and why does the GC-content differ between populations/species/lineages? Does it evolve under Genetic drift only? Under selection? Intuitively, I'd say that the ratio of the probabilities of mutating from A or T to G or C should be an important factor driving the evolution of the GC-content. Does it? Does the overall mutation rate influence the GC-content? What other traits/forces influence the evolution of the GC-content?


texts:
If I understand correctly, the steps of gene editing with CRISPR-Cas9 are roughly as follows

Cas9 nuclease and guide RNA form a complex.
Cas9+guide RNA complex scans genomic DNA and recognizes the sequences homologous to the guide RNA
Induces a double strand break in DNA upstream of the PAM sequence (only breaks when the homologous sequence of the guide RNA is in the vicinity of the PAM).
Genetic modification using the mechanism of DNA repair (NHEJ, HDR) after double-strand break.

If so, in the gene editing with CRISPR-Cas9 , gene editing is likely to continue as long as the Cas9 does not lose its activity, am I right?
My question

When does the Cas lose its activity?
What was the logic of the experiment that identified the timing? / If the matter itself is unexplored, what kind of experiments could be done to find out the timing when the Cas lose its activity?

As this movie shows, if the gene editing occurs successfully, it will indeed introduce a mutation in the target gene.
However, even if it does,-this is just my guess from here on out- it is likely to remain complementary to the target gene, at least upstream of the guide RNA. However, even if the target gene is mutated, there is likely to remain complementary sequence to the guide RNA, at least upstream of the mutation. So, even if one successful gene edit is completed, I think it's possible that gene editing could happen again in the same location. Moreover, even if the targeted site is successfully edited, there is still the possibility of subsequent off-target editing elsewhere. That's why I think the tools exist to stop CAS.

A guide RNA binds to the target gene that has been bitten by CAS. The strand opposite the strand to which the guide RNA was bound has just been cleaved.
Quoted from this video.
An idea for an experiment to detect when CAS goes quiet
If a single cell colony was created from a gene-edited population and there was genetic variation in the cells born from that colony, then I think that would mean that there would have been Cas9 activity even after the single cell colony was started in culture. Is this idea correct? Could there be a smarter experiment?


texts: Should I design a primer to detect virus based on NCBI genebank?

texts: When I searched HIV on NCBI gene bank, I found 2 results from 1997: http://www.ncbi.nlm.nih.gov/genome/?term=HIV. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?


texts: Are they somehow dangerous? What are they and how can I get rid of them?


texts: Solution based measurement of Solvent-Accessible Surface Area of macromolecules

texts:
The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA from a solved (and generally static) structure.

Chemical probes like diazirine and hydroxyl radicals show some bias regarding where they tend to bind. I'm realizing while I'm writing this question that NMR is a perfectly valid method to determine a solution based structure and then calculate the SASA. Similar strategies has also been used to examine structured RNAs. I'm curious about the variety of these methods and how accurate they are.


texts: How much oil you can get from a dead animal

texts:
This is purely speculative, but is there a formula to calculate how much oil you can get from 1 Kg of biomass?
I've seen bioreactors in farms where they put dung, vegetable scraps, and all bio scraps, where bacteria transformed the biomass in methane gas which then was used in powering electric generators or cooking stoves.


texts:
An acute instance of anxiety can cause a sudden sharp chest pain for a very brief period of time.  What is the mechanism behind anxiety leading to chest pain?

Is the pain coming from the heart itself, or surrounding muscles?  What structure is in pain and what is the physiology behind it?


texts: Why does the gc content deviate from 50% in prokaryotes

texts:
I have read quite some articles but I can't figure out the main reason for gc content deviation in prokaryotes. In eukaryotes I can understand it, because the genome isn't composed at random, like TATA boxes and CpG island, because they are important for functioning in the production of proteins.

However in prokaryotes there is such a variety, GC% is ranging from 20% up to 70%. Most of the time it depends on the environment, high temperature needs a stable genome (= high gc content).

I also read the answer to this question How does GC-content evolve? however it's still not clear to me. I hope someone can explain the deviation a little bit more.

Question

Prokaryotes have an AT drift, but what mechanism causes some of these bacteria to higher their GC% instead of lowering it.


texts:
In practice, when you have vasoconstriction of the glomerular capillaries and subsequently an increase in blood pressure, glomerular filtration rate increases. However, this seems counterintuitive to Bernoulli's principle.

During vasoconstriction, because the radii of the capillaries are getting smaller, we should expect an increase in flow rate and blood velocity. According to Bernoulli's principle, the outward hydrostatic pressure should drop.

How does this lead to an increase in filtration rate?


texts: Blast a sequence against multiple databases

texts:
I would like to BLASTP a list of protein sequences in fasta format against multiple protein databases. Since I'm only interested in the first hit of each database, it is possible that BLAST result would need to be parsed.

Do you know if this strategy is a good one, or you suggest me others?

Thanks for your help. Best regards, Bernardo


texts:
I confused myself during studying, and wanted to confirm something. Since transcription via RNA polymerases only takes place in the 5'to 3' direction, that would mean that that 5' to 3' strand is the only one that contains the information to be translated later into a protein or mRNA or w/e.

So then the 3' to 5' strand would NOT contain any genes, but just the base pair complement to them? Or am I thinking of the concept of a gene wrong?


texts: Why is haemophilia unviable in later stages of life?

texts:
A sentence in my textbook is:

The possibility of female being haemophilic is extremely rare because mother of such a female has to be at least carrier and the father should be haemophilic (unviable in the later stage of life)

I know that haemophilia is an X-linked recessive disorder. Hence mother should be carrier and father must be affected for daughter to get affected. But I'm unable to understand what "unviable in the later stage of life" means.


texts:
My question is about small non-coding RNAs. miRNA and siRNA are both known for mRNA regulation. miRNA can both transcriptionally inhibit and degrade mRNA by cutting it. For inhibition just a small fragment (seed) of miRNA is complementary to the mRNA while for degradation miRNA and mRNA must reach 100% match.
siRNA is almost the same molecule and its only function is to 100% match mRNA and degrade it.

So if siRNA appears to be just a subtype of miRNA, can we confirm that? Or are there any other differences that make these two molecules different kinds of small non-coding RNAs?


texts: Why don't antibodies generally bind to food and drugs?

texts: Are these excluded thru central tolerance?  What if you ingested something with a unique molecular structure that you hadn't ingested before?


texts: How thick is the residue from a fingerprint?

texts: I am trying to work out the mass added to a small glass sphere when it is picked up with bare fingers.


texts: Aspirin - does it inhibit enzyme of thromboxane?

texts:
This is a diagram a friend showed me about the drug aspirin, where we were arguing which enzyme it prevents.

Aspirin is known to inhibit the production of prostaglandins. However, it also serves fit as a purpose to inhibit production of thromboxane.

My question is, does the drug inhibit enzyme a to prevent the production of both thromboxane and prostaglandins, or only enzyme B?


texts: Is it possible to color sperm cells so they look more clear under a microscope?

texts: Im working on something that requires me to check the velocity of a sperm cell under a microscope but I imagine it would be very hard for a program to keep track of the sperm cells.


texts: What is the mIU unit as used in hCG hormone levels?

texts:
My girlfriend is in her very early pregnancy, and has provided several blood samples by now where the doctors measure her hCG levels.

The hCG hormone level is measure in a unit called mIU/ml which I figure is milli-something per milliliter blood. But what is that something? What is the IU?


texts: In human embryology, what starts ovum cell division?

texts:
Maybe I am not using the correct search keywords in Google, but I cannot seem to find anything beyond basic information taught in schools about fertilisation of the egg by the sperm.

After the sperm has fertilised the ovum, I know that the zygote starts with one cell, then divides into two cells, then four cells and so on, but what initialises cell division, and how does the cell divide?


texts: What does "~mitochondrial DNA ~bp linear DNA" means?

texts:
I'm surfing NCBI website -Nucleotide- to find some examples of real DNA sequences to use in my small homework project.
My question is related to the title of a DNA sequence below:

Sus scrofa mitochondrial DNA, D-loop region, isolate: Europeanwild boar 3
1,045 bp linear DNA

I thought a mitochondrial DNA is different than a linear/nuclear DNA, especially that a mitochondrial DNA is circular while a linear/nuclear DNA is linear. So what does the above title actually means (in simple terms)? Is it still linear or not?


texts: use of adjuvants and peptides in modern vaccines?

texts:
when preparation of modern vaccines we generally use a part of the microbe or the antigen such as polysaccharides to create an effective vaccine against the vaccine. so when the preparation of sub unit and conjugate vaccine we use adjuvant? so what is the use of using an peptide in case of babies having week immune system?

Basically my question is What is the use of peptides when we are using adjuvants to enhance the immunogenic response?


texts:
This is a medicine-related question that I've been wondering about. I've been watching medical lectures on YouTube regarding the human body and was wondering about how surgeons treat a severed artery or vein (think Juggular or Carotid)? Specifically I was curious about what kind of tools they use and what the technique is for performing this operation.

And before anyone asks, no, I don't need to treat someone with this kind of injury :).

Thanks,
mj


texts:
First of all, I am not a biology guy; I am in Computer Science. But, I have a strong interest in all the mysteries of nature, from universe to human body. So, I want to ask a question related to genetics.
As I have read that all(both male's and female's) the biological traits of a person are passed genetically to the offspring(of course assuming the crossing). So if my mom's eye color is blue and my dad's eye color is also blue, I will get blue color too, but what about the core architecture of the body? I mean I have 2 legs at a certain location from my body(my waist but, not from my head!) and similarly other orientations. Why they are that certain way? If they somehow got changed, would the resultant body be stable?Is the answer different in case change is artificially engineered or natural?
Where is this core architectural information exactly stored(If the answer is DNA then how?) and in what form is it stored?How come that information is not changed in thousands of years or even millions of years? And is that information of such nature that it contains "exact" steps to develop a healthy say, brain structure(which is a really complex)?
My another question is: If there is a community of mutated people, will their offsprings be mutated always with 100% certainty?

I know these are a lot of questions but you can see that, they basically revolve around the information that I am curious about. Can someone address my curiosity?


texts: Can I train my non-dominant hand and make it dominant?

texts: Are our dominant limbs decided on birth or is there some way in which I can train my non-dominant hand and make it as coordinated as my dominant?


texts: Does the DNA sequence of a butterfly match that of the caterpillar it used to be?

texts:
Just had this thought occur to me.

If one were to take a DNA sample(or is it RNA?) of a caterpillar before it became a chrysalis, and attempt to match the sample against one taken after the chrysalis matured to a butterfly, would the two samples come up identical?


texts: Does our eyeball increase in size as we grow?

texts: Does the size of the eye increase as we develop from the stage the complete eye first forms to infancy and then to adulthood ?


texts: Is it possible to derive the Michaelis-Menten equation under conditions where the product formation is reversible

texts: Text books etc generally derive the Michaelis-Menten equation for the irreversible case i.e $$\ce{E + S <=> ES -> E +P}$$ I can't see how to do it for the reversible case i.e  $$\ce{E + S <=> ES <=> E +P}\;$$ Is it possible?


texts: What is the difference between "dikaryotic" and "heterokaryotic" states in the sexual lifecyles of fungi?

texts: Many fungi undergo a reproductive phase in which more than one genetically distinct nuclei (from 2 separate mating types) is present within the same cytoplasm. In the Ascomycota and Basidiomycota, this phase is termed "dikaryotic", whereas in other fungal phyla the phase is "heterokaryotic." What is the difference here? Is it purely number of nuclei per cell, or does the difference depend on how many genetically distinct nuclei are present (2 or >2)?


texts: Why is there such a long interval between ages of sexual maturity and of reproduction in female chimpanzees?

texts:
There seems to be some disagreement on the ages at which female chimpanzees typically reach sexual maturity and when they typically first give birth, but regardless, different sources seem to agree that a number of years elapse between these two milestones.

For example, this 2018 paper from Jane Goodall and colleagues found

  … an average age of 11.5 years (range 8.5–13.9) at sexual maturity and 14.9 years (range 11.1–22.1) at first birth. These values exceed previously published averages for wild chimpanzees by one or more years. Even in this larger sample, age at first birth is likely underestimated due to the disproportionate number of non-dispersing females, which, on average, give birth two years earlier than dispersing females.

In humans, there is also a substantial lag between these two events, but we understand this as a very common cultural dividing point, which places the first firmly in childhood, and the second (generally/ideally) in adulthood. The maintenance of this interval is controlled by a variety of social and societal practices and institutions, across cultures.

Do we know what maintains the lag between the biological capability for reproduction and the actual first birth in chimpanzees? Presumably there is also some sort of set of social practices among chimpanzee society that maintains this. Do we know to what extent it is controlled by mature matriarchs or patriarchs, or by actions taken by the young females themselves, or some other set of behaviours?


texts: Purpose of dilution streaking or streak purification

texts:
In dilution streaking a drop of liquid culture is collected with an inoculating loop and then streaked across the agar plate surface. At the end of the streaking the number of organisms clinging to the loop until only single cells are deposited at a given location and you get colony-forming units.

I am wondering now what exactly the purpose of this streak purification is. If you want to grow your bacteria why would you not just put a few drops of the liquid culture on the agar plate? Why is it particularly useful to use this technique? Or, why would you choose this method over the "spread plate" technique, where a liquid culture undergoes a set of dilutions first and each dilution is then placed directly on the surface of separate agar plates.


texts: What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and highly contaminated by other DNA).


texts:
Given that bonobo chimps are more sexually active then humans, are the females almost always pregnant? if not how not?

also are they so sexually active in the wild as well or is it just in captivity?


texts: Why isn't the upper limit of pain lower in humans?

texts:
From what I understand, pain is an useful mechanism that signals us that something is not quite right with our body (in particular, we're under attack). It's good - it alert us and tells us that we got to do something (stop the threat, or run away, etc). From Wikipedia:

  Pain motivates the individual to withdraw from damaging situations, to
  protect a damaged body part while it heals, and to avoid similar
  experiences in the future.

However, there are damages that cause too much pain. If you are stabbed in a particular place, you will most likely have so much pain that you simply can't fight back or run away. The shock makes it incredibly hard to do something or even think properly.

So my question is: is there a reason why pain can elevate to such high levels? I'm just assuming that if we had some sort of hard limit on the amount of pain we receive, we could perform better in several dangerous situations. In other words: instead of hurting so much that we can't even think properly, it hurts enough to let us know we are in grave danger but still capable of assess the situation and perhaps even act accordingly.

Obviously some physical damages will render you unable to act anyway. Like, damages on the spine that may cause your limbs to malfunction. But I mean damages such as a large open wound on the abdomen: if that didn't hurt so much, I'd imagine you could probably stand up and run away (you'd probably bleed out but at least you'll have a chance to escape the threat).

My guess is that it "cannot be helped". Pain are signals from different parts of the body to the brain, and once a signal is sent, the brain has no choice but to process it accordingly.


texts: Do cockroaches have less health issues than humans?

texts:
Cockroaches are known to live in very dirty places like sewers. Does this cause them to evolve to be stronger against parasites and bacteria? Recently I read online that cockroaches can sustain radioactive harm 6-15 more than humans, so does that mean that cockroaches are less likely to get cancer?

refernece for the radioactive exposure:

http://www.abc.net.au/science/articles/2006/02/23/1567313.htm?site=science/greatmomentsinscience


texts: Is it possible to genetically modify a plant at home?

texts: Would I be able to genetically modify a plant at home? What equipment will be necessary? I think it might be a fun change from the 'norm' of regular hybridisation, to try some inter-family gene insertion, instead of staying within a genus. Are some plants easier to modify than others?


texts: How do individual plants adapt to changes in temperature?

texts:
If you grow a plant from seed in your nice warm house, then plant it out in your temperate garden, it will stop growing for a while, possibly die, and if not, subsequently resume growth. Standard gardening practice is to 'harden off' plants, moving them to an area of intermediate temperature for a while before planting them out.

Why does this happen? What is the difference between a plant adapted to a warm environment and one adapted to a cold environment?

Expression of cold-tolerance genes? Levels of some secondary metabolite? Thickness of cell walls? Density of root hairs?

An unidentified author on the Royal Horticultural Society website states that
"The effect of hardening off is to thicken and alter the plant's leaf structure and increase leaf waxiness", which is not quite detailed enough to satisfy.


texts:
I am trying to read literature on Alzheimer's disease.
A very important phenomenon that occurs in AD patients, is hyperexcitability in neurons close to A-beta concentrations.
Some authors only describe the phenomenon of hyperexcitability in excitatory cells as an indirect phenomenon, which results due to the suppressed function of inhibitory cells.
Some other authors only describe it as the direct result of excessive concentration of Glutamate in a synaptic cleft which, due to the dysfunction of Astroglia, remains there and causes hyperexcitability and excitotoxicity.

I haven't found yet a paper where both are mentioned as distinct ones. At least I haven't found any that I could comprehend, given that my background is not biomedical.

I would like to know if these two cases I mentioned before, are indeed distinct ones, or if they are the same, and I cannot see it due to lack of knowledge.


texts: Why is glycerol supplied/used as 87% solution?

texts: While preparing glycerol stocks of my transformed bacterial cells (DH5alpha) the protocol I had to follow was that I would make one 50% glycerol stock (500µl culture, 500µl glycerol 50%) and another 87% glycerol stock (850µl bacterial culture, 150µl glycerol 87%). 87 seems to be a very specific number. Any particular reason why 87% glycerol concentration is used?


texts: What is the maximum/minimum temperature humans can survive at for an extended period of time, and what rate does the body temperature change at?

texts:
3 questions:

At what rate does the body temperature of a human change at? That is, assuming the outside temperature is x, is there some sort of formula that can determine how long it takes for the human body to reach any temperature above or equal to x? I understand this is quite variable, but any data will be useful.

a) What are the harshest conditions currently on Earth that we can survive at (That is, the maximum temperatures people actively live at every day for a period of years, and the minimum temperatures they do so).
b) In what ways have their bodies adapted to allow them to do so?

Thanks!


texts: Why re-label the strand ends in 3' DNA labelling?

texts:
I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works.
I took a diagram from my lesson and tried to understand with it; this is what I understood.
If I’m wrong, please tell me and correct me.

We take a restriction enzyme which will cut both strands. The bottom strand will be a 5’ end. So, the top strand is shorter than the bottom strand.
We will add a Klenow fragment which, with its polymerase activity, polymerizes in the 5’->3’ direction the missing part of the top strand, with dNTP α 32P (labelled by a radioactive phosphate in the alpha position).
We get two strands which have the same size, of which one will be strongly labelled.
We finish with a terminal transferase which will catalyse the addition of dNTP α 32P on the 3’OH ends of both DNA strands (in order to label these ends).

But, if I’m right, could you explain the necessity of the last step; why label both ends since we have already labelled the top strand?


texts: Ripening bananas artificially: What is the biological theory behind?

texts:
I am a resident of the tropical island of Sri Lanka, and we have a strange traditional method to ripen our banana harvest quickly.

What we do is this: We dig a pit in earth that is enough to put the whole banana cluster in. Then, after safely laying the bananas in the pit, we cover up the pit with a sheet such that only a small hole from a side remains: visualize a small 3-4 inch door to the pit.

After that, we light a fire with semi-dry leaves just outside the pit's door. (Semi-dry leaves are used to get as much smoke as possible. Dry leaves do not give that much smoke, because they completely oxidize quickly). And the smoke is sent through the door by blowing it with the aid of a bamboo.

This sends a good amount of smoke and warms the inside of the pit considerably. And by experience I can tell you that this makes the bananas to ripen really quickly. I have done a controlled experiment where half of the cluster was not put into the pit. Bananas in the pit ripen overnight and the control sample took days to ripen.

Can anybody explain what are the bio-mechanisms that are working here?


texts: What would happen if two different viruses penetrated one cell?

texts:
I want to know what would happen if two different kinds of viruses took over one cell.

Would nothing happen? Would the cell create both kinds of viruses? Would it make a fusion of the two viruses?


texts: Function of testosterone in women and estrogen in men

texts:
I was recently surprised to find out that testosterone and estrogen are found in both men and women albeit in different amounts.
I know that testosterone is related to the development of facial, body and pubic hair, deepening of the voice, and muscle development in men.  And that estrogen helps in maintaining the condition of the vaginal lining and its elasticity, and in producing vaginal lubrication in women among other functions.
But what could be the function of testosterone in women or estrogen in men? A simple Google search could give me no good results except for here where it says:

  In men, estrogens have no known function. An unusually high level, however, may reduce sexual appetite, cause erectile difficulties, produce some breast enlargement, and result in the loss of body hair in some men.

and that

  Large deficiencies of testosterone may cause a drop in sexual desire, and excessive testosterone may heighten sexual interest in both sexes.

Does anyone have any further knowledge?


texts: How can census population size be smaller than the effective population size in some species? is that possible?

texts: The only way I can think this could happen is through a recent population bottleneck. Can it be possible though ?


texts: Mechanism in which HSCs regain stemness in the niche

texts: I'm reading this review: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6854531/ which cited Schofield, 1978 (https://pubmed.ncbi.nlm.nih.gov/747780/). In the review, it was described in figure 1 that quiescent HSCs dissociate from the niche and become a daughter cell, and if the daughter cell reoccupies the niche then it regains its stemness. Does anybody know any recent research regarding this concept? Also, I'm interested in how HSCs away from the niche eventually lose their stemness over time as they go through cell-division. I've tried googling, but the keywords I am hitting did not give me the results I wanted.


texts: Summarising ChIP-seq and controls needed

texts:
As part of my study I have to present on a method of discerning binding sites of proteins to DNA, for which I have looked at ChIP-seq. This is a brief overview of what I have so far, and was wondering if there are any particularly glaring omissions that I have made so far.

  Cells treated with formaldehyde to cross-link proteins such as transcription >factors (i.e. HIF) covalently to DNA and incubated for 2-30 minutes. After >incubation glycine is added to terminate the cross linking and dissipate the >formaldehyde.

  Cells are lysed, and sonication (application of sound waves to agitate a >sample) is used to fragment the DNA into sizes between 200-1000 base pairs.

  HIF–DNA complexes are selectively immunoprecipitated by using antibodies >specific to the HIF protein of interest, complexed with a matrix of either >agrose or superparamagnetic beads.

  HIF-DNA-antibody-matrix complexes are isolated through the use of either a >centrifuge or magnetic field (depending on the matrix employed). Several >washings take place to further purify the sample.

  Cross-linking of the protein to the DNA is reversed by way of heating, >separating the DNA and protein-antibody-matrix complex. Proteinase K is used to >digest proteins, leaving only the DNA.

  Oligonucleotide adaptors (primers) are then added to the small stretches of DNA >that were bound to the HIF to enable rapid simultaneous sequencing.

  DNA sequences are then mapped to the reference genome to determine the binding loci.

I would also like to discuss controls that are used in these procedures. So far I have found limited mention of negative controls, positive and negative control loci, non-template control and positive control antibody, but am having trouble discerning what any of this actually is referring to.

I would seriously appreciate any help available on this topic!


texts: MOPS Media Recipe Protocol - Well Defined

texts:
I am trying to find a clear protocol for making MOPS media. However, when looking online, I am finding that this media is loosely defined and I can not find a good protocol. (I have been looking for a couple of hours now)

In addition, there seems to be something called 'MOPS buffer'. What is the difference between the two?

Additionally, if someone could direct me to a good protocol for this media I would appreciate it.


texts: What is the meaning of 'state of nature' in On the Origin of species by Charles Darwin?

texts:
I have started reading "On the origin of species" by Charles Darwin.
The beginning paragraph is:

When we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ much more from each other, than do the individuals of any one species or variety in a state of nature.

What does he mean by state of nature here?
Note:
The term state of nature is very often used in this book, so for anyone reading this book my question would be helpful for greater understanding.
Edit: One user has requested for more context for better understanding...I would like to provide the next paragraph and also a related paragraph.

When we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ much more from each other, than do the individuals of any one species or variety in a state of nature.
When we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, I think we are driven to conclude that this greater variability is simply due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species have been exposed under nature. "

Another paragraph in which State of nature has been used:

Sterility has been said to be the bane of horticulture; but on this view we owe variability to the same cause which produces sterility; and variability is the source of all the choicest productions of the garden. I may add, that as some organisms will breed most freely under the most unnatural conditions (for instance, the rabbit and ferret kept in hutches), showing that their reproductive system has not been thus affected; so will some animals and plants withstand domestication or cultivation, and vary very slightly—perhaps hardly more than in a state of nature.


texts: Why does contracting the iris allow less intense light to go in?

texts:
The iris contracts automatically in the presence of bright light. This makes a flashlight appear bright in darkness, but outside in daylight you can't even see it's light.

The iris is changing your sensitivity to the intenseness of light. But physically all is happening is the iris is getting smaller or larger. I can see how this allows less light to go in if it gets smaller, because it's less surface area. However, I would imagine this would change the field of view though if I didn't know any better. Why does it change the intenseness of light instead?


texts: Why do BRAF mutations appear more in skin cutaneous melanoma?

texts: When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the Parathyroid gland, but the expression in the Skin is about average. So how does it make sense that for example in tumor samples of skin cutaneous melanoma (TCGA-SKCM) the BRAF mutations are so dominant (about 50% of the cases contain a BRAF mutation)? And on the other hand, it occurs less frequently in other cancer types?


texts: Are there any small peptides with protease activity?

texts:
I'm looking for a very small protease to base an engineered protein on.  I did a search for "peptides with protease activity" but all the results seem to be as peptides to be used as protease substrates (eg in assays); I couldn't find any catalytic peptides.

What is the smallest protease or domain which has independent proteolytic activity?  (Ideally looking for something very short, a dozen aminoacids)


texts: How do viruses die outside of host cells?

texts:
I am posting a question that a friend of mine has asked.  My friend wrongly assumes that SARS-CoV-2 virus can be transmitted through blood, although there is no such evidence.  However, his question remains a valid one.

  With so much news about COVID-19 all around us, I have been doing some
      study on viruses.  I do understand that viruses are not really living
      creatures.  They just have some genetic information, which they can
      pass on to the host cell, causing the virus to proliferate, and in some
      cases interfere with the normal functioning of the cell.  Outside of a
      host cell they are completely inert.  In fact they show all the traits
      of a non-living entity.  I get that.

  My question is based on the following scenario.  Imagine there are two
      doors, next to each other.  Let’s call them A and B.  There is a door
      knob on each.  A COVID-19 patient sneezes near the doors, and some SARS-
      CoV-2 viruses land on each door knob (i.e. door A and door B).
      Unfortunately within a few hours someone with a cut finger touches the
      knob of door A and gets infected.  So far no dispute.

  Fast forward 5 years.  In the meantime the knob on door B never got
      cleaned/wiped.  In other words, the inert viruses are still on the door
      knob.  Again someone with a cut finger touches the knob of door B but
      in this case the person does not get infected.  Why?

  Obviously something happened to the virus during these 5 years that
      caused it to lose the ability to pass on its genetic information to the
      host cell and replicate.  What exactly happened?

Addendum:

We received a response for the query that seemed reasonable to us but was voted down, and presumably deleted by the author.  Fortunately I was able to recover a screen capture.  To keep the discussion going, I would like to temporarily include the response here till a better response is posted.  Here it goes:

  This isn't very professional, but there are the basics. Viruses are obligate parasites, which means they can't live outside a host (in this case, a cell) for long. Viruses get damaged as everything else, the damage taking many forms, such as hydrolysis, photolysis, free radical damage, reaction with other molecules (like detergent), conformation changes, dehydration, maillard reactions, and changes induced by heat of labile molecules (like decomposition). All types of damaging processes happen at an increased reaction rate with increasing light and heat. Viruses have rudimentary repair mechanisms if any, so it's a matter of time before they become inactivated. A damaged virus entering the body wouldn't be able to do much harm if any, as their genetic information would be damaged beyond repair, and so, not able to be replicated to make more viruses. Their proteins and genetic bits would still trigger an immune reaction and immunize against intact and not very damaged viruses (which is why damaged viruses are used in vaccines). Those damaged viruses that remained outside just become microbe food.


texts:
I want to write an expression to model exponential growth of a microbe that scholastically and irreversibly acquires a mutation at a fixed rate that slows growth.

I can do it iteratively, but am curious whether a simple expression can be written.

I started with:

$P_{total} = P_{wt}e^{r_{wt}t} + P_{mutant}e^{r_{mutant}t} $

How do I factor in the mutation rate that converts $P_{wt}$ to $P_{mutant}$?


texts: What does the gene name "lexA" stand for?

texts: It is an important gene expressed in E. coli that represses the SOS response and also the expression of lambda lytic phase genes. UV light and damage to DNA is responsible for its breakdown and hence the expression of repair genes and, if present, lambda phage genes. However I couldn't find a reference for its original name.


texts: Why do oranges in the US have a small separate part?

texts: Why do oranges in the US have a small separate detachable part at the tip which is separate from the other pods? It looks like a tiny orange itself and has a long fiber attached to it.


texts: In textbooks, it says that myelination doesn't really affect the time constant as tau=RC where R is the membrane resistance and C is the membrane capacitance. Myelin increases membrane resistance while decreasing membrane capacitance so there isn't really an overall effect on the time constant. However, during active regeneration of the action potential, the current only goes the path with least resistance i.e. the nodes of Ranvier, so wouldn't the R be the resistance of the node of Ranvier instead of the resistance of the entire membrane as stated in the textbooks? If this argument is correct then wouldn't myelination increases decreases time constant? Thanks!


texts: Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability in Drosophila melanogaster and yeast, both genomes much smaller than mammalian or plant genomes. Could it be that DNA methylation is needed to help activate/repress certain genomic regions on top of other epigenomic marks when the genome is so vast that there is a need for an extra level of marking? Is there any evidence along those lines?


texts: Mathematical/statistical models for forecasting population distributions of age, sex, weight, and height

texts:
I come from a mathematical background but I have no experience with the topic of mathematical biology.
Are there well established mathematical/statistical models for forecasting the evolution of population distributions of biometric parameter such as age, sex, weight, and height? For instance, I have often heard that the proportion of elderly people in the population is projected to increase. What models are being used to generate forecasts such as these?


texts: Can you "spam" bird sounds so that birds no longer interpret them right?

texts:
Is it possible to make birds confused by repeating recorded chirping or singing? Or do they always perceive them as usual, even if the situation is clearly not as described by those sounds?

For example:

mating song when there's no mate
danger/alarm cries when nothing's going on

Specifically, I'm interested in public placed with a lot of traffic using looping speakers to scare off birds that like to dump upon almost unsuspecting citizens. Like underground entrances and city malls. Does the effectiveness decrease over time because of that?


texts: It seems to be quite difficult to find an answer to this. Are SNPs the same thing as alleles?


texts: How do castes evolve in eusocial species?

texts:
I have been reading about eusocial species and have some questions. What is the basis for caste differentiation? Is it entirely genetic? Does the queen have the code for soldiers, workers etc in her own genes, so only a mutation to the queen results in change of the whole colony's castes? As a related question, how do different castes evolve?

It seems to me that if only one individual in a colony is reproducing, the rate of evolution must necessarily be much slower because any genetic change in the queen would affect all castes, which is likely to have some negative effects.


texts:
The silicon bead micro-array technology for SNP scanning is a marvellous example of human ingenuity. Is anyone aware of a non-technical history of its development accessible to the lay reader?
As an aside, can someone explain how the immediately adjoining nucleotide, that I understand to be the SNP being scanned for, is captured? And how can the two alleles be distinguished?


texts: Assays to determine competitive binding versus non-competitive

texts:
I'm looking for both simple and complex assays or technologies than can be used to determine if two competing molecules are competitive or noncompetitive.  I figure xray crystallography is a clear one, but say I can't get crystals to form.  What other techs or assays could I use to determine this?

It's a protein-protein interaction with a small molecule competing with one of the proteins.  This particular set has not been done before. All interactants are purified.


texts: Cells of umbilical cord - mom's or son's?

texts: Let's say we have a mother giving a birth to a son. In a very clear manner the cells of these two individuals are very different, of course. Yet there is an umbilical cord connecting them. Then there should be a clearly defined "border" somewhere on its way where the mother's cells meet the cells of her son, is that so? How is it even possible?! ;)


texts: What is the name for the opening in the mouth for the nasal passages?

texts: Is there a proper anatomical name for the opening in the soft palette where the nasal passages enter the mouth?


texts: In the context of genomic imprinting, how does a human cell "know" whether a chromosome is paternal or maternal(out of a homologous pair), in order to silence genes?


texts: What exacly happens at chromossome level during fecudation and in the first zygotic division?

texts:
I was reading about the viability of animal hybrids and found the following sentence here:

  Previously, this idea was not widely accepted, because, in general, different species have different numbers of chromosomes, the structures within cells that contain genes. This difference can prevent the normal development of the embryo, as each chromosome that came from the male parent must be aligned with an equivalent chromosome from the female parent when the fertilized cell divides for the first time. Without this proper alignment, the cell usually cannot divide and, thus, dies.

However, I couldn't find more information about the first zygotic division and this alignment of homologous chromosomes. This bugged me a little since, during mitosis, there's no alignment of that chromosomes.

So, anyone could clarify what exacly happens at chromosome level during fecudation and in the first zygotic division? How can this block the development of an "embryo" formed by two very distant species' gametes?


texts:
I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity in vitro, I would argue that the substrate and enzyme concentrations resemble those in vivo. As a result, conclusions made by such assays do not apply 100% to the naturally occurring reactions. Are there any examples in literature that address this issue?

Along those lines, what is the concentration of fatty acids/nucleic acids in the cell?


texts: Why are both glucagon and cortisol released in hypoglycemia?

texts:
Cortisol is released in response to prolonged stresses; one situation when cortisol is released is when blood glucose level is low. In this situation cortisol acts on adipose tissue promoting fatty acid mobilization, and also promotes gluconeogenesis by degrading muscle proteins and converting them into pyruvate. Cortisol also stimulates gluconeogenesis by increasing the expression of PEP Carboxykinase the enzyme of gluconeogenensis pathway promoting the TCA Cycle intermediates or Oxaloacetate to convert into Phosphoenolpyruvate and promoting gluconeogenesis to balance the blood glucose level.

These are the same effects produced by glucagon to increase the blood glucose level when it is low.

My question then is what is the need for release of Cortisol? Also, if its release is important to control other pathways I haven't mentioned here, then why does cortisol produce the same effects as glucagon? Why is glucagon alone not enough to maintain blood glucose level?


texts: What is the evolutionary reason behind the fragility of teeth?

texts:
Almost all organs in the human body have a rather large threshold within which the organ or tissue is capable of repairing itself using materials supplied by the body, whether it's made from organic tissue or structural proteins. Wounds and minor damage to the skin or flesh for example heal by themselves, skin, nails and body hair can grow back if damaged or removed, even most bones can be repaired autonomously by a biological body. Cutting off a significant chunk from the human flesh or removing over 90% of a hair or a nail would cause no permanent injury, and the body is capable of repairing the damage over time with ease. The vast majority of the human body (not counting critical organs such as the heart or the brain) can be "grown back" to an extent by itself, because such parts have a rather large damage threshold.

On the contrary, teeth do not. There is a certain threshold in which tooth enamel can be supplied and "repaired" by the body to an minimal degree, but past that point virtually any damage caused to teeth are permanently irreparable by natural means. Which is quite strange, given how fragile a set of human teeth is, be it chemical or physical damage. Especially if you take more "artificial" causes into account. A moderately heavy object aimed towards a human mouth, for example, can easily render ten to fifteen teeth permanently damaged past the point of recovery within a heartbeat, also causing the said person's digestive process to be heavily impaired.

Another strange fact worth noting, is that the human body is capable of producing two separate set of teeth due to biological growth and size differences, but not more than that. Wouldn't it be beneficial for a biological body to be able to supply new teeth in the place of ones that have been damaged or removed? One could argue that such an action would be too complex and impossible, similarly to growing back an entire limb or a spare heart, but given the material that makes up teeth and its fragile nature, it would be safe to assume that it is biologically possible, especially given the fact that the human body DOES produce two separate set of teeth over its lifespan.

However, even stranger still, is that the only element capable of damaging or deteriorating  teeth by natural means, is the consumed food itself, and the acidic bacteria found within. Several types of edible food consumable by human means are capable of damaging the enamel to critical levels within relatively short periods of time, even non-artificial ones. What happened before the invention of the toothbrush and various dental cleaning methods? Why haven't humans evolved in the past tens of thousands of years to the point where repairing or regrowing teeth by natural means is feasible? Simply put, why don't teeth grow back contrary to hair, nails or skin?

What is the biological and evolutionary reason behind teeth being so fragile and indisposable?


texts: It is said that genes are partly responsible for the choices we make in our life; our genes help to create our environment, and then that environment can influence our personality. So, beside genes, what else is responsible for the other choices? Is there something else at work?


texts: Ammonium sulphate precipitation assay pH dependence

texts: In general does the pH effect the precipitation, e.g. would a pH of 6 cause less precipitation than pH 7.5. Or are they unrelated?


texts: Speed of electric signal vs chemical diffusion

texts:
I'm currently reading the book, "An Introduction to Nervous Systems" by Ralph J. Greenspan.
On page 20, there is a sentence that confused me. It was, "Electrical signaling has the advantage of being able to cover large distances very quickly, much more quickly than chemical diffusion". It is in the context of the primitive signaling mechanism in Paramecium.
My doubt was, isn't the electrical signal caused by the movement of ions? Then how is it any different from chemical diffusion? And again, it's not a electrical signal that travels, but a changing potential, right? Then how does it move at a faster pace than diffusion?


texts: In my lab class this week my partner and I were making a SDS-PAGE Laemmli Gel. We made the resolving gel solution which was made of 30% Acrylamide, DI water, 1.5 M Tris-HCL pH8.8, and 20% SDS. We mixed the measured amounts into a conical vial. We then added 10% APS and TEMED and mixed carefully. We then immediately pipetted the solution into the casting stand so the gel could solidify. We then pipetted DI water onto the top of the gel so it would not dehydrate. We left some solution in the conical vial so we knew when the solution would be solidified completely. After waiting 45 minutes the gel in the conical vial was solidified but the gel in the casting stand was still liquid. How come the gel did not solidify in the casting stand but solidified in the conical vial?


texts: Are all healthy animals more likely to defecate near the end of a rest-cycle?

texts:
Just what the title states.
It stems from observation & personal experience that a person/dog/cat/monkey is more likely to relieve oneself immediately after it wakes up from the peak-sleep cycle of it's body-clock. Is this observation true? What causes this behaviour ?


texts: Can I compare Shannon-Wiener diversity indices between plots of different sizes (area)?

texts:
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.


texts: Why are skin moles (pigmented spots) circular in shape?

texts:
I have never seen a rectangular or triangular shaped mole.
Is there any reason for why moles are roughly circular in shape?


texts: Why doesn't muscle strength depend on its length?

texts:
In case of tug of war the more people participate the more strength they represent. And in case of muscles - the longer it is, the greater the number of myosin heads bind to actin when muscles contract. So why doesn't length matter?
UPDATE:
Since I've found multiple answers that compare muscles to ropes, let me comment on why those explanations don't work for me. Ropes don't have "muscle" strength, they have tensile strength. So this analogy can only compare tensile muscle strength to tensile rope strength.
In the end I'm pretty sure I'll find out that tensile strength constraints the muscle strength. And that's probably going to be the reason why muscle strength doesn't grow with length - something does not allow it, otherwise it would get damaged.
But I'd like find out what exactly prevents further contraction. Is it mechanical receptors on the muscle cell which block deploarization? Mechanical receptors in tendons which send nervous signals (but then - do tendons get thicker in proportion with the muscle)? Something else?


texts: This is the only image my the TA was able to get for us. And, we're using it for our lab report. The image isn't even ours. It's another group's image that we're sharing. But I don't understand why in the first lane there seems to be some bulging/ tapered form of the ladder? Can someone explain why has this happened and how? I am very confused...


texts: If I grow microorganisms on agar plates and I expose them to UV light. How exactly will I know that the microorganisms have been killed? I was watching a video that showed spots in the petri dish where the microorganisms were killed when viewed under microscope but will this be visible to the naked eye? If not, is there any way that I can show without the use of a microscope the fact that the organisms have been killed?


texts: Why do tendons require over 100 days to make new collagen?

texts:
{1} says:

  Tendons require over 100 days to make new collagen.

Why does it take so long for tendons to make new collagen?

References:

{1} Bass, L. M. T. "Tendinopathy: why the difference between tendinitis and tendinosis matters." International Journal of Therapeutic Massage & Bodywork: Research, Education, & Practice 5.1 (2012): 14-17. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312643/


texts: Is there a cellular physiological response to desiccation in animals?

texts:
There has been much research on the molecular effects of high levels of temperature for animals, specifically regarding heat shock proteins, protein denaturing and energy investment into stress tolerance.

I understand generally, the effects of desiccation with respect to the importance of moisture, specifically for aquatic animals (eg. oxygen uptake), but I can't seem to find much information on cellular-level responses to desiccation stress.

Are there are well established effects of desiccation on a cellular level or if there is a physiological response in the cell (eg. production of hsp)?


texts:
In the BMI formula= (Weight)  X  703) / (Height^2) , what does 703 represent? What is a reliable source that I can cite for this answer?

weight= lbs    height= inches


texts: Can a human acquire a memory of an animal?

texts:
I would like to know if it's possible for a human to acquire an animal memory.

I mean, animals store their memories in their brain, right? And so do we, humans, store our memory.

So, is it possible to cut off an inch (or something like that) of an animal brain,
also to cut off an inch of a human brain, and to replace that animal brain-piece in the missing part of the human's brain?


texts: Is there a term for when a detrimental gene can be positively selected for because of linkage to a very fit gene?

texts:
Let's say that some piece of DNA would be subject to extreme negative selection if it were independently inherited, but it is very closely linked to an extraordinarily fit gene, and so the complex it belongs to is positively selected for.

Is there a term for this phenomenon?


texts: Which is better adapted for global warming: deciduous or evergreen trees?

texts:
Evergreen photosynthesise for longer and don't lose their leaves all at once, whereas deciduous plants do and enter periods of hibernation during winter, among other differences (correct me if I am wrong).

Is there any significance in these differences considering the future impact of global warming on trees?


texts: Any forms of pneumonia that can be caught?

texts:
I am aware of the fact that there are several different types of pneumonia.

However, I am wondering if any of these types of pneumonia are contagious from person to person.
Is this possible?


texts: Isolating a specific gene (specifically TRAV* series of genes) for sequencing

texts:
I'm trying to figure out (for pedagogical purposes) the right way to isolate and PCR the regions coding the T-Cell receptor.

My understanding is that I would need to use restriction enzymes that target regions near the start and end of the gene. I was looking at a bunch of different restriction enzymes on this site: https://www.addgene.org/mol-bio-reference/restriction-enzymes/

What I'm not sure about is: how do you pick the combination that will specifically cut out that gene and not any of the other ones? It seems like the restriction enzymes only consist of a few base pairs, and I would guess they can slice at many many sites.

Furthermore once it is cut, how do I isolate just the DNA for the gene I want to sequence as opposed to the rest of the junk DNA?


texts: How does increased heat increase the rate of metabolism?

texts:
I have heard that taking a hot shower helps

blood circulation
metabolism.

For (2) metabolism, I think that the rate is increased since kinetic energy is given to compound to bond with enzymes to react. Is this the only reason? In addition, why is (1) true?


texts: Why do typical acetylcholinesterase inhibitors (like carbamates) have a greater parasympathetic effect than a sympathetic effect?

texts: I understand that the post-ganglionic neurones of the sympathetic system are adrenergic, but surely these neurones will be excited to the same extent as the parasympathetic post-ganglionic neurones (due to the ganglionic synapses being cholinergic), and thus target organs/tissues will be receiving equal and opposite sympathetic/parasympathetic stimulation, or rather equal and opposite activation of the muscarinic/adrenergic receptors. (Sub-question: Why does caffeine, a perhaps atypical acetylcholinesterase inhibitor have a greater sympathetic effect than parasympathetic effect?).


texts:
What exactly happens to myosin during isometric contraction? I suspect that either myosin heads just "freeze" in the middle of crossbridge cycle, or go through full crossbridge cycles repeatedly at the perfect rate so that the rate of extension becomes equal the rate of contraction (basically, a muscle isn't still, but repeatedly extends by like <1mm, and then myosin immediately contracts to compensate for this extension to keep muscle at static length - and so back'n'forth it goes).
Why isometric contractions spend energy, when physics make it clear that energy is spent only when we change velocity of something? If my second hypothesis is true and the muscle isn't in fact still, then energy is obviously being spent. But if myosin heads freeze in the middle of the cycle glued to actin, there's no reason why energy should be spent.
Say, a person is trying to lift a 10-ton rock with all the strength they got.  It's also an isometric contraction, but in this case, the second hypothesis shouldn't work, because if myosin could finish a crossbridge cycle under such resistance, it would mean that the muscle is strong enough to lift the rock. So in this case, it must get stuck mid-cycle, with the mass of the rock not letting it to finish its conformation change. If so, then why do muscles spend energy then? Myosin is literally stuck in place, and until it finishes a cycle, it won't bind another ATP.


texts: Relationship of the DNA of a eukaryotic gene to the 5'-UTR of its mRNA

texts:
In eukaryote pre-mRNA I am having a little trouble grasping exactly what the 5 prime untranslated region is defined as.

It seems that it could be defined as the difference in pre-mRNA between the transcription and translation, is that right?

If so, does the transcription begin immediately after the end of the promoter sequence? Immediately after the promoter region on the DNA ends, does the next nucleotide become part of the 5'UTR?


texts:
These worms appear soon after the rain lilies flower and slowly nibble on the leaves growing big and chubby. They are about 5cm long, have many small red legs underneath, have no spines or spikes, and are soft-bodied.
They leave tiny green balls of excreta. I have never seen them metamorphose.  I live in Andhra Pradesh in India. Can anyone tell what species they are? Are they dangerous?


texts: Main mechanism of the evolution of sexual dimorphism

texts:
Sexual dimorphism is very common and (normally) requires the evolution of sex-specific genetic variation/regulation so the genetic correlation between the sexes can be <1. Is there consensus as to how this type of variation predominantly spreads?

I can see it could evolve by drift and selection and I expect it is predominantly via selection (sexually antagonistic selection for different optimal genotypes)- We typically associate sex differences in traits with sex differences in selection (ecological, sexual selection...).


texts: Bacterial Conjugation/Horizontal Gene Transfer -- how does the plasmid exchange work?

texts:
So according to a PPT I'm reading, bacterial conjugation works by the two bacteria joining pili and exchanging plasmids. So how exactly do the plasmids get across the gap? If I understand this correctly, the pili are little hair-like things on the outside of the bacteria -- so unless the plasmids were actually able to somehow be pushed through the pili, there would be gap. Right?

The only other possibility I can think of would be that the membranes fused or something like that. But that comes with it's own whole set of problems.

How does this work?

Thanks!

evamvid


texts: A flower has grown on a leaf in our garden. What is the name of this flower? Give some description.


texts:
http://www.youtube.com/watch?v=3QJ4CjFsflA

This is a link to Hershey and Chase experiment. According to this experiment, we conclude that DNA is the genetic material. But how do we conclude that DNA is the genetic material? They only proved that DNA of virus enters into the bacteria, not the protein coat of virus.

The DNA of the virus later destroys the bacteria because the virus reproduces inside them. Does this demonstrate that DNA is the genetic material?


texts: What is the relationship between radiation and evolution?

texts:
There is always a certain amount of background radiation present, for example due to ionizing radiation from the sun and other stars. Also certain materials like granite may emit relatively large amounts of radiation.

Ionizing radiation may cause mutations in the DNA (Gevertz et al, PNAS 1985). Mutations, in turn, may lead to altered phenotypes. Altered phenotypes and survival of the fittest are key to evolution and formation of new species.

What is the (relative) contribution of background radiation on the formation of new species?. In other words, is background radiation a critical component in evolution and would the course of evolution have changed substantially when there would be no such background radiation?


texts:
On average, do we know what kind of lights attract moths best?
LED, filament bulb, candle...?

And what about colour? Does that matter?


texts: Is the "concept of time" coded into the genome?

texts: What I'm interested about is whether environmental changes' effects are coded into the genome, like metamorphosis, deciduous plants. Can it be explained by morphogens, or it's something completely different?


texts: How does Bernoulli’s Principle apply to the cardiovascular system?

texts:
Below are graphs which illustrate the cross-sectional area, velocity, and fluid pressure through each vascular segment of the cardiovascular system.

It makes sense that velocity and cross-sectional area should be inversely related graphically (by the equation of continuity, ($v_1A_1=v_2A_2$). However, Bernoulli’s principle states that where velocity is high, pressure is low, and vice versa. However, in the graph above, clearly pressure is decreasing as you move away from the aorta, regardless of velocity.

I can understand how the pressure in capillaries will be higher than those in venules, since a higher pressure in capillaries would accelerate the blood as it moves into the venules with a lesser total cross-sectional area. This agrees graphically, since, past the purple stripe, the pressure curve decreases as the velocity curve rises. Yet the mean arterial pressure in the aorta and arteries seems to violate the relationship between velocity and pressure stated in Bernoulli’s principle. What is there to make of this?

(Image taken from Campbell Biology, 10th edition)


texts: Why is Psoriasis treated with Cortisone, when stress (which releases Cortisol) is known to aggravate the condition?

texts: It is well known that stress isn't good for psoriasis , yet why do we treat the illness with Cortisone, a compound very similar to cortisol (and "has a similar name, genesis, and function", according to wikipedia) whilst cortisol is released in the body in stress situations?


texts: I am wondering if anyone who is well versed with VDJ sequencing for TCR repertoire analysis (specifically CDR3) would know if DNA or RNA is a better starting material? We are looking at the effects of radiation therapy on immune system of mice. Thanks


texts: electrostatic charge of viruses, especially Coronaviruses

texts:
I am searching for (and failing to find) literature about the electric charge (+/-) of viruses, specifically the Coronaviruses.  I am aware that it is a complicated issue, including interaction of pH and electrostatic charges, etc.  However, I note that electrostatic charge of various materials is investigated for barrier protection, suggesting that there are normal average or overall charges for viruses.  Can anyone comment on this?

Especially, I want to know, at neural pH, are Coronaviruses more likely to adhere to a negatively or positively charged surface?

Thanks.


texts: Has it been enough time for evolution through simple natural selection?

texts:
Let first state that I understand natural selection. I am not asking if evolution happened. I see evolution as a fact, but I do not assume the current theory of natural selection as fact.

I wonder if there has been enough "time", or number of generations, needed to create enough mutations that lead to the known genetic complexity of all species today (or even just until dinosaurs), since the Last Universal Ancestor.

Is it possible to prove, or estimate this time?

Note: There was obviously enough time for evolution to occur. My question is if, the known mechanisms of mutation and theory of natural selection, are enough to justify the evolution in this amount of time.


texts:
What did the evolution of multicellular animals look like?

Aspects of this question include:

(1) Are there any living organisms that might be helpful in visualizing "transitional forms" between unicellular organisms and multicellular animals? E.g. I have heard of slime molds as one example. Would love to hear of as many good examples as you can come up with. Not looking for strict hereditary relationships here, and I am fine with plausible but unproven theories. E.g., mudskippers might help a person visualize the evolution of amphibians, even if they aren't in fact closely related to amphibian ancestors.

(2) Do we think that the first animals evolved into sponges, or cnidarians/ctenophoroans, or something else? Did sponges and cnidarians/ctenophoroans evolve multicellularity separately? As this is probably a big topic, feel free to just post a link or two.

(3) For any examples that you can think of for #1, would love to hear of any good citations of articles or books for me to read, but keep in mind that I am not a scientist and not looking for anything extremely technical.


texts: Appropriate statistical test for a student lab?

texts:
I am a HS Bio teacher and doing a microevolution lab involving candy. Essentially students use four candy types and push them together until one cracks (Nat Sel). They also do simulations of migration, mutation and genetic drift. They then calculate the "allele frequency" of each type per generation and look for changes. I want to have my students do a simple statistical test to see whether the change was significant or not from each evolutionary factor. I was going to do a chi square test, but someone told me that is not appropriate to this type of experiment.
So, can anyone confirm, is chi square inappropriate, and if it is..
Can anyone point me to a more appropriate test. These are high school kids with no stats background (and I have forgotten virtually all the stats I learned 20 years ago)...


texts: Why is it so important to avoid infection of lacerations to the scalp?

texts: There is supposedly something unique with regards to infections of the scalp, although I cannot remember, perhaps it was to do with the CSF and its build up? I have scoured the internet for hours but have not found an answer.


texts: Can CRISPR be used in editing primary cells? How is the transfection efficiency?

texts: Sometimes people wanna use primary cells to do gene-editing because the cells normally have more interesting characteristics, but can we really do so?


texts:
In a textbook, I encountered a notation used when writing blood groups down, which was "I" with the blood group type as a superscript. I was curious as to why the letter "I" is used in this notation and what it means. E.g. Iᴬ and Iᴮ.

Thanks.


texts:
I have read about Parthenogenesis induction in a paper : "Hagimori T, Abe Y, Date S, Miura K (2006) The first finding of a Rickettsia bacterium associated
with parthenogenesis induction among insects. Curr Microbiol 52: 97–101 "

I was curious to know what is the evolutionary advantage of parthenogenesis induction for the parasite (in this case Rickettsia bacterium ) ?


texts: Why does all life use the same macromolecules in their genetic code?

texts: There is no biochemical constraint of any sort, so why doesn't some other code work? Why is it specifically RNA/DNA?


texts: Can Bacteria Repair Dephosphorylated Plasmids?

texts:
I have been trying to insert a short sequence of DNA into a plasmid. I wanted to make two different versions, with the insert at different locations. I chose HinDIII and SalI sites approximately opposite each other on the plasmid and designed oligos with HinDIII or SalI sites, and of course extra bases on the ends to allow proper cutting.

I cut the plasmids and oligos and dephosphorylated the vector to help prevent empty vector ligations. I mixed the plasmid and oligos and ligated, then transformed into bacteria, all standard stuff.

The HinDIII version worked the first time, with few colonies on the empty vector control plate, and more colonies on the plates that received oligos during the ligation. I confirmed insertion by using the BpmI cut site the oligos just happened to carry.

However, the SalI version has failed every time I tried it. The empty vector control and all other plates are a just a carpet of cells. There are very few individual colonies, and the ones that exist don't look right, too small. I haven't even tried a miniprep, too likely to get an empty vector back. I did do a nontransformed control, where the cells were not given any DNA and were just directly plated. Those cells died, indicating it's not an issue with my ampicillin.

My hypothesis is that unligated empty vector outnumbers the correctly ligated plasmids, and that cells that pick up a copy of the unligated DNA somehow repair the cut, even though it's dephosphorylated. This is made more likely because I only used a single digest, so the plasmid has matching sticky ends, however the HinDIII version used the same strategy. I have been including a 1 hour 37 C SOC media incubation, which could allow the bacteria more time to carry out this repair. If I skip the incubation, maybe that would prevent unwanted repair.

I am testing this hypothesis with some additional controls, including transforming bacteria with empty vector that hasn't been treated with ligase to make sure the ligation reaction isn't the problem, as well as using the previously ligated DNA without the SOC incubation. I will report that data as it becomes available. I am short on competent cells, so I can't do much else right now.

Also, what do you think about treating the ligated DNA with klenow to blunt any remaining sticky ends before transformation?

EDIT: I have the data for the transformations that skipped the ligation and SOC media incubation. Skipping the incubation did not change anything, neither did skipping the ligation. All plates continue to show a carpet of cells.


texts: Skin (epithelial) stem cells: unipotent or multipotent?

texts:
In a video on the Khan platform on stem cells, epithelial stem cells are described as unipotent stem cells, i.e. only producing one kind of specialised cell: epithelialor skin cells.
However, on a website describing the hierarchy of [stem] cell potency, skin cells are shown to be the product of multipotent stem cells:

Which category is correct for skin stem cells - unipotent or multipotent?
UPDATE


texts:
I heard about Larger cats eating the cubs. Is it some kind of facultative cannibalism or they can eat there own kind like that?

What are the facultative cannibalism present in animal kingdom?

What is the genetic origin?


texts:
For most of the long bones head is the proximal end, but for metacarpals and Ulna, head is the distal end. Why are their distal ends called as heads?

What's the criteria for calling an end as head end?


texts: About artificially induced processes that would normally cause a cell to self-destruct

texts: Are there certain biochemical processes that would normally cause a cell to self-destruct but if the cell being tested has apoptosis mechanisms that have malfunctioned or been 'turned off' the cell will not 'malfunction' because of the induced process ? Are there such biochemical processes that could indirectly indicate which cells have no functioning apoptosis mechanisms? If so would this be a possible test for cancerous cells?


texts:
I am studying ECGs of heart transplant patients.
The difficult thing is that there is so little available data publicly.
I must apply for data in my universities.
It would be also great if something is public.

I have searched several databases and contacted some authors directly.
Some findings

No heart transplant data in Physionet, online search tool here.
No heart transplant data of ECGI with Dr Rudy (personal email)

I am waiting answers or working with application for

Dr Rudy's company
University of Helsinki's database (under process for application)
Some technical universities in Finland (these have connections where are good data but they do not hold data themselves)

Is there any ECG data about heart transplant patients?


texts:
I took samples of tapwater in order to examine concentrations of escherichia coli and enterococcus, in a rural area. I was told, by the analytical lab, to take samples in four sterilized vessels bought from pharmacy. The problem is that at the completion of the last vessel, its cap fell frοm my hand down to the soil and some grains of sand stack on the inner surface of the cap. As fast as I could, I picked it up and washed it off totally with the water of the sampling tap. After that I closed my last sampling vessel with it and this was the completion of the sampling. How great is the possibility my sample has a serious contamination of these twο biological pollutants after this incident?

Thanks and sorry for the long story and bad english


texts:
I would like to make a simulation (concerning genetic evolution) and I want to use a very simplistic model of neurons.

I don't really care there are different kinds of neurons, I don't care much that the extracellular field is different at axons-dendrites and initially, I don't even care that the spike is transferred through the axon. What I really want to know, is whether I can approximate (very roughly) the field with a magnetic dipole pointing at the direction of the axon. Or are the directions of the MF and the axon unrelated?

I have looked around for some image depicting such a relation, but I didn't find any. Is there any resource of some kind available?


texts: Do the individual claws of a bear have names?

texts: The question seems pretty self-explanatory (if perhaps a little odd). Anatomical names or colloquial names are both appreciated, especially the latter if they exist.


texts: I have heard that fasting causes regeneration of memory cells(B- and T-lymphocytes) thereby improving immunity.Is this true? If yes, how?


texts: How big should the human population be, as predicted by body mass?

texts:
I would guess there is a theory in biology which states that the population size for a given species is inversely proportional to the body mass of individuals in that species.  In other words, there are zillions of ants, billions of mice, millions of deer, and just a few elephants.

If humans existed in a "state of nature" (i.e., were not able to manipulate their environment more than any other mammal), what population size would be predicted by their ~70 kg body mass?

(Assume that the human population has spread globally.)

I imagine we would fall somewhere between the wolf and bear populations.


texts: The Water hyacinth and its ability to absorb pollutants from the water

texts: What genes makes the water Hyacinth able to absorb pollutants from the water it lives in? (2) can this gene be successfully harvested? And how?


texts: Time lapse between fresh blood's exposure to air and that same blood turning darker red-brown

texts:
For investigative purposes, I'm searching for a tool that can be used as a quick visual assessment of the the length of time that blood has been exposed to air after the blood flow has stopped.. Let's say that you walk into a room and see someone unconscious. Where blood appears, it had already stopped any fresh flow & has already dried to a dark brown similar to mahogany wood.  That person has been there longer than how many minutes? Please understand that I'm not asking how long the person has been lying there but for at least how long?

You come upon a dazed person unsteady on their feet with an injury to the face. The blood flow has stopped: the person may have smeared the blood when touching their face but you  see that the blood has not changed to a deep brown and still retains a bright red color..approximately how much time has likely elapsed between the injury occurring and your encounter with the injured person?

I know there's no exact time estimate possible without testing but simply for quick field assessments, is anyone willing to hazard an opinion?

In summary: How can I tell the age of a blood stain?


texts: What percentage of people today would likely be descendants a man born 4,000 years ago?

texts:
Assuming a particular man was born in  southern Mesopotamia, around 4,000 years ago, and was significant involved in a major religion.

To what degree (if any) of accuracy could his descendants be traced?
What percentage of the global population is likely a descendant of the man?

This question comes from a comment on sister site.

  I don't think most people are really able to trace their entire family tree that far back. But Avraham is so many generations ago, I would expect that either nobody in the world is his descendant or nearly everybody in the world is


texts: Can Eskimos be regarded a distinct species from Kalahari Bushmen based on morphological differences & geographic isolation?

texts:
I was motivated to ask based on the answer to another SE Biology Question that uses the following argument to conclude that two varients of snake are indeed a different species:

  To test whether [Dendrelaphis ashoki and D. girii  were a separate
  species of snake] they (Vogel and van Rooijen, 2011) compared 9
  individuals of D. ashoki with 34 individuals of D. pictus, and found
  statistically significant (p<0.05) differences in five morphological
  characters....

Further:

  The authors didn't rely just on morphological evidence: they note that
  D. ashoki, which is found in the Western Ghats, is also geographically
  isolated from other populations of D. pictus, which are found in
  Northeast India, Myanmar and South East Asia.

Minor differences in morphology of a snake: Why designate it a different species?

My question is, why can't we on the bases of an analogous argument conclude that (say) Eskimos & Kalahari Bushmen are, forget the race debate, but two entirely  distinct species?

I mean if "number of infralabials touched by the first sublabial" can count as a legitimate species-distinguishing morpohological factor, then so can heights, eye colors, hair texture, skin color etc. right? And we won't even have to fish too hard to gain statistical significance given how different Eskimos are from Kalahari Bushmen morphologically.

Further, the geographical isolation must have been pretty strong too.


texts: Can birds suddenly suspend in the air in one position?

texts: I don't know if it was my eyes fooling me or if it was real. I've seen birds suddenly get suspended in the air, flapping their wings but not moving. Like making non-locomotor movement on the air. Is there an explanation for this?


texts: Is the six-layer cortex model of the mammalian cortex still the most accepted model?

texts:
I've been reading a bit about the different layers of the cerebral cortex and its clear that certainly not every region of the cortex has the same number of layers. Thus, the idea that every region has six-layers is clearly false.  And I think this fact is definitely well known.

Do neuroscientists still view the six-layer model as an accurate model? If so, what aspects of it have changed over time that now incorporate the fact not every region has six layers?

Aside:

Let me clarify my question. If not every region has 6 layers, why don't we just say there is a layered cortex and not specify a number? But if we decide to do this, what distinguishes the mammalian "6-layered" cortex from non-mammalian species that have a so-called "3-layer" cortex

See The Microcircuit Concept Applied to Cortical Evolution: from Three-Layer to Six-Layer Cortex by Gordon Shepard for more.


texts: Do ants know the direct (approximately shortest) path to their nest from the food morsel?

texts:
I've been studying a bit on the foraging habits of ants, and one of the things I'm not clear on is whether ants know the shortest path from the food that they find to their nest. I understand that ants can leave different types of pheromones$^{[1,2]}$, they can change their behavior based on those trails, and those trails are often volatile. What I'd like to know is how do ants find their nest once they find a food morsel. In one of the papers,$^{[3]}$ it was shown that ants change their foraging strategy based on the number of encounters they have: they follow a straighter path when the ant density in an area is low, while they follow a more tortuous path if the ant density is high.
Considering a lower ant density, an ant will travel pretty far from the nest in search for food in a path that is not always straightforward. Assuming that the pheromone trails it leaves behind do not evaporate by the time it finds the food, will the ant travel back on the same path laid down by its pheromone trail, or will it actively find a more direct path towards its nest? I might also be missing something in the sense that ants always know where their nest lies when they are foraging, and thus can find the shortest path whenever they find any food. If so, any work reflecting such research would be of great help.
References:

Dussutour, A., Nicolis, S. C., Shephard, G., Beekman, M., & Sumpter, D. J. (2009). The role of multiple pheromones in food recruitment by ants. Journal of Experimental Biology, 212(15), 2337-2348.

von Thienen, W., Metzler, D., & Witte, V. (2016). How memory and motivation modulate the responses to trail pheromones in three ant species. Behavioral ecology and sociobiology, 70(3), 393-407.

Adler, F. R., & Gordon, D. M. (1992). Information collection and spread by networks of patrolling ants. The American Naturalist, 140(3), 373-400.


texts: What are the chemical characteristics of cofactors that functionally differentiate them from the side chains of amino acids?

texts: Cofactors are essential for the function of many enzymes, such as NAD+ in the glycolytic pathway - I was wondering how the chemical properties of these cofactors allow them to fulfil their function and/or what it is about the chemical properties of amino acid side chains that limits their utility in the kind of reactions that require cofactors.


texts:
E. G. Gray is Neuro scientist who found and described first the two major morphologically defined synapse types (Gray Type I (asymmetric) and II (symmetric)) in his work
E G Gray (Oct. 1959). “Axo-somatic and axo-dendritic synapses of the cerebral cortex: an electron microscope study”. In: Journal of Anatomy 93.4, pp. 420–433

However I am unable to find his full name nor further information about his life.


texts:
My study materials use the word vesselcompression chamber of aorta to emphasize aorta's elastic property.

The arch of the aorta only coils, not its straight part.
I think the reason why the arch coils is the elasticity of aorta (artery) is high.
If the elasticity is too low, then the aorta is more stiff.
This means that heart has to work harder so higher systolic pressure and lower diastolic pressure.

Why does the arch of the aorta coils?


texts: Is there any liquid in the bone medullary cavity

texts: I am looking at the effect of intramedullary nails on tibial bones and can't seem to find anything on fluids present within the medullar cavity/canal. Since this is where blood cells are formed I would expect there to be at least a bit of blood in the cavity. I also read somewhere about something called 'liquid bone marrow'. Can someone please confirm whether there is blood in the cavity and whether there are any other fluids present. Thanks in advance.


texts: Difference between curated publications and additional publications in nextProt database?

texts:
With reference to reference papers listed in nextProt database, what is the difference between curated publications and additional publications? Anyone using nextProt, kindly explain the terms. For example, when I search for SLC22A23 in nextProt simple search engine, I get as mentioned below on the left side toolbar.

References

Curated publications (21)

Additional publications (2)

Patents (0)

Submissions (0)

Web resources (0)

Link: https://search.nextprot.org/entry/NX_A1A5C7/

Thanks


texts: Why does T-cell Cancer Therapy require a large tumor mutanome?

texts:
An article I read about Neuroblastoma states that the fact that Neuroblstoma has a small mutanome means that it is not viable to apply the classic T-cell immunotherapy. Why is this so?
The article can be found here: Neuroblastoma: Developmental Biology, Cancer Genomics, and Immunotherapy


texts: I have seen species of birds, insects and fishes with splendid colours. But when it comes to mammals (including us humans), they almost always appear in shades of brown, grey, orange, or in black and white. I don't recall seeing any pink, green and purple. Why is that so?


texts: Using expression vector to express arsenite oxidase genes in E. coli

texts:
So I am trying to express a gene cluster that can oxidize arsenite into arsenite autotrophically. The arsenite oxidase gene cluster sequence is linked here: https://www.ncbi.nlm.nih.gov/nuccore/AY345225.3

I originally was going to clone this gene into the pBAD-DEST49 expression vector, and transform it into E. coli C600, but the vector is out of stock, and I need it quickly. I was looking through Sigma Aldrich, and I found this vector: PSF-OXB20. I plan to clone the genes into this vector.

I do, however, need some advice. I am not 100% sure on if this vector would work, or if the genes would be overexpressed. My question is would this vector work out, or is there any better ones out there. Any advice would be appreciated, and if I need to include more details, just let me know.


texts: System biology and evolution: Book-recommendations

texts:
I have relatively good knowledge in evolutionary biology and in population genetics. I am getting more and more interested in the evolution of ...

genetic developmental processes
gene interactions
gene expression
plasticity
intrinsic or cellular noise
mutational robustness

It seems that i am getting increasingly interested in a field that is in between population genetics and system biology. I know very little about system biology.

Can you please give me some recommendations for books (and other readings such as reviews) that talk about the evolution of those processes that are usually studied by system biologists? I am much more interested in a book that presents concepts and methods than a book listing empirical observations. Also, I am not interested in medicine but in biology.


texts:
Does anyone know any good resources dealing with shapes of trees?

For example, pine trees are cone shaped for optimal absorption of sunlight, but lone pine trees growing in isolation (and other commonly cone shaped conifers) often grow very high above ground and have no well-defined shape. Presumably, when there aren't neighbours to compete with for sunlight or space, the optimal shape is..well, whatever shape absorbs most sunlight; less constraints = more possibilities.

Looking for an answer that explains this sort of phenomenon. Thanks.