texts: Attachment of muscles during molting in insects

texts:
Normally, insects' muscles are attached to their exoskeleton but what happens to this attachment when they are moulting?

Sorry if this is an extremely silly question but I have wondered about it for a long time and have tried searching it.


texts: Can immortality of the Turritopsis dohrnii be learned or adapted by other species?

texts:
I have heard that Turritopsis dohrnii is a species of jelly fish which is immortal, as it can grow old and then back to growing young.

So, how is it possible?   Can other species (marine and/or land) species adapt or  evolve into such a system?


texts: What is cross-immunoreactivity, and how does it impact vaccine development?

texts:
What I understand about cross-immunoreactivity is that the antibody induced by one specific antigen is also fairly effective against another antigen. How would this be used for vaccine development?

Moreover, cross-immunoreactivity is related to epitopes. And how is how is cross-immunoreactivity defined among epitopes? Are variants of a specific virus hypervariable region some kinds of epitopes? What does antigenic convergence have to do with cross-immunoreactivity? Any comments or directions to further references are greatly appreciated.


texts: I saw A documentary many years ago that said that hemoglobin will take in O2 in the fingers and toes. I have Not been able to find any information on this. But it would seem that being so close to the surface some gas exchange would occur, and more so in the fingers and toes than the teunk.


texts: How would our vision be improved if our photoreceptors were not backwards?

texts:
I'm curious to how much better human eyesight would be if the nerves from our rods and cones were correctly placed behind the receptors?
Are there any Animal Models with correctly placed photoreceptors that we can use as a benchmark?


texts: What is the step by step procedure that leads the T cell to release chemokines?

texts: When T cell receptors bind to the receptor of an antigen presenting cell, is this what leads to the release of chemokines? I know that T cell release of chemokines leads to the migration of other T cells to the area of infection. What is the step by step procedure that leads to this release of chemokines from a T cell?


texts: What is the evolutionary advantage of menstruation?

texts:
I was wondering why woman have fertile periods. Based on some simple reasoning I would expect that if woman were always fertile this would increase the chance of reproduction(one of the important things in life). But having menstrual periods would decrease this chance because only the period close to ovulation would result in fertilization.

So why did evolution result in woman having menstrual cycles?


texts: Evolutionary explanation of the bicuspid on the left and tricuspid on the right

texts:
The left heart handles more pressure and logically it would make sens to have a valve with three leafs on the left (If I had got to choose, I'd have put three on both sides).

Other than being more susceptible to valvular disease (also because the pressure is higher on the left), the bicuspid having 2 leaves don't do any good (To my knowledge).

Since this is not the case, there might be some evolutionary constraints that might have caused this difference.

Any explanation according to valvular evolution along the phyla?


texts: Name/term for mechanisms by wich the relative size/number of cells of some tissue/organ are preserved

texts:
The cells of some organ or tissue are dividing and also dies (apoptosis). But this happens in somehow controlled manner so that the total size of the organ is approximately preserved or the total number of cells approximately stays the same. As far as I understand, this is somehow collective process, because cells in one side of the tissues should somehow coordinate the division/apoptosis processes with the cells of the far side. I have read in one book about cells, that such controlling mechanisms are purely undesrtood even today. Of course, such mechanisms work only approximately (or - to be more precise - they are more complex than just static preservation of the size/number), e.g. numberadipose cells can increase with time.

But anyway - my question is - what is the name/term for such controlling mechanisms and what are other important keywords/terms which I can use for searching more research papers about this theme?

I have specific interest in the control of those processes, e.g., with the aim to bound those processes for adipose cells and to encourage those processes for the muscle cell.

"cell cycle control" and Hippo-pathways mechanisms can be the answers, but I am still searching for the matter.


texts: What is the close and related genome used for in Gene models?

texts:
all

I am a little bit confused about using the related genome or reference genome.

When we have a reference genome, we can do alignment. Also we can do the assembly.

Can you give some more reason why a related genome can help to improve gene model ?

And if we do use a related genome, what kind of problems or caveats may occur there ?


texts:
I am a recent transplant from academia to industry.  I would like to follow-up on some experiments in the literature, for which I need cloned plasmids.  Addgene of course doesn't (for the most part) send material to for-profits, and I was wondering if there was a commercial entity I could order from.
There are a number of 'cloning services,' but these seem to require that I send them the backbone and insert.  When in fact a lot of the work is getting the organisms and amplifying the genes of interest into a cloning vector.  I suspect there is a commercial service with big libraries of genes that can do 'full stack' cloning, for a price, but I haven't come across one yet.
Does anyone know if one exists?
Thanks!


texts: Can someone identify the species of this frog/ toad?

texts:
Location: Tirupati, Andhra Pradesh, India

I found it at night time near a lake

It was quite small in size ( 5-6 cm Approx.) having dark brown spots all over its body and three prominent green stripes running along the length of its body and 2 stripes running across its upper body ( one crossing over its eyes).


texts: What large "package" is carried by this large spider underneath itself?

texts:
One night in early May in northern Taiwan a strange looking spider carrying a large white "package" underneath itself ran in front of me and stopped, so I photographed it. The package is roughly the size and shape and color of a round dental floss dispenser that one would carry in one's pocket, perhaps a little smaller, about 2.5 cm in diameter.

I took some photos with a flash and without. The total span of the spider's legs was about 10 cm.

I'm guessing this would be an egg case, but it's surprisingly large, could it be prey? I suppose if a spider didn't have a home of any kind it would have to carry its meals with itself. It seems to be well adapted to this and moved quickly even with the large load.

Question: What kind of spider is this and what is it carrying underneath itself?


texts: Does carbon dioxide from carbonated drinks enter the bloodstream?

texts: When drinking soda or any other carbonated beverage, does some of the CO₂ find itself in the bloodstream? And if so, how long does it take until the carbon dioxide levels in the blood return to normal?


texts: What does vitamin B6 and B12 absorption depend upon?

texts:
I'm looking at my question about homocysteine metabolism and am doing a followup inquiry into vitamins B6(Pyroxidine) and B12(Cyanocobalamin). I've found this interesting bit about vitamin B12 and am looking at its implications:

  Approximately 56% of a 1 mcg oral dose of vitamin B12 is absorbed, but absorption decreases drastically when the capacity of intrinsic factor is exceeded (at 1–2 mcg of vitamin B12)

Quote from vitamin B12 fact sheet

I'm trying to understand the implications of an intrinsic factor involved in B12 absorption. Lets say that a person gets vitamin B12 from both food and a single supplement pill. Will taking that pill "use up" the absorption factor and prevent food's vitamin B12 from being absorbed over time?

This is the first time I'm hearing of additional "factors" that may limit vitamin absorption in the human body. Is this common across vitamins, or is it B12 specific?

Thank you for your input!


texts: Good source that explains the evolution of single-celled organisms "from scratch"

texts: Are there any books or sites that detail, step-by-step, the evolution of the first single-celled organisms (bacteria, archaea) from a Miller-Urey-like beginning? That is, assumes only amino acids, then from there to self-replicating proteins, until culminating in the formation of a basic cell?


texts: Does any molecule other than DNA have a double-helical structure?

texts: DNA is known to have a double-helical structure. Do any other molecules have this structure?


texts: High Glucose vs Low Glucose DMEM for Cell Culture

texts: I've noticed that in mammalian cell culture, there are often two types of DMEM available. High Glucose and Low Glucose. Does it matter which type I use for culturing of cells (e.g. Hela or HEK293)? Which is the type people normally use?


texts: What kinds of animals does insular dwarfism affect and how large does an island need to be to escape it?

texts:
3
down vote
favorite
1
I've been wondering about insular dwarfism, and would like to know if it only affects certain animals (Since some animals grow larger upon colonizing an island, often due to the absence of predators.) Do only big animals get smaller, and if so, how big is "big"? Are there any taxonomic groups that are more or less prone to insular dwarfism?

The second thing that I'd like to know is the minimum size of an island without insular dwarfism could be. Also, I'm not sure if resources, biodiversity or climate affects it too (Considering Bergman's rule, the increased competition in jungles, etc.) This may sound like a lot of questions, but the main components of an answer I'd like are shown in the title - who and where.


texts: Difference in ATP synthesis in mitochondria and chloroplast

texts: The mechanism of ATP synthesis in mitochondria and chloroplasts are almost the same, but there is a big difference: the f1 particle in mitochondria uses 2 H+ ions to synthesize one ATP, whereas in chloroplasts the f1 particle uses 3 H+ ions for the same. What make the difference?


texts:
$ E.coli $ has circular DNA which I guess implies one strand forms the outer circle and the other the inner one. So, is there a way to know if the replicated DNA forms the outer or inner circle?
In the image attached it is seen that the replicated DNA forms the inner circle. Also mentioned is the fact that it is not possible to make out individual strands by TEM.


texts:
I found it in Toronto, Ontario, during early June, 2015.

When prodded it seemed to jump around, or at least to move very fast.

I can also post a short video of it if needed.


texts:
I have to do a task for a university task and I need to understand some things
before figuring out how to do it.

The task is the following:

  Find matches of known proteins (DNA-PolyI,II,III) to the specific E.Coli DNA, sequence.

I downloaded in FASTA format the protein sequence of DNA-Poly3 DNA-Poly1 of E.coli (strain K-12) and the entire DNA sequence
of the E.Coli.

I've studied a bit on-line and using the BioRuby gem and the Ruby programming language I wrote a program that translates DNA to protein sequence.
Then I tried to match the known DNA-Poly3 sequence but it did not match. After searching a bit on-line again, I learned about ORF and
and the 6 possible reading ways of each frame. The longer, in terms of codons, ORF conformation is chosen but there's no way of telling for sure that the protein was made using
this frame.

Then I've read about TATA boxes, but I can't use those since they can be found only in Eukaryotic and Archaea.

So how should I proceed in order to solve this problem: How can I prove that the DNA-Poly3 gets produced by a specific area (gene) in the DNA sequence?

Thanks for your time,

ps. Insights and hints are very much welcomed as this is just the tip of the iceberg for me and I'm very willing to study bioinformatics :-)

EDIT: This is an update for info requested in relevant answer

The files I have used are the following:

➜  Bioinfo  ruby dogma.rb
----------------
DNA Length: 4639675
gi|48994873|gb|U00096.2| Escherichia coli str. K-12 substr. MG1655, complete genome
----------------
DNA Poly-1 sample: 928
gi|16131704|ref|NP_418300.1| fused DNA polymerase I 5'->3' polymerase/3'->5' exonuclease/5'->3' exonuclease [Escherichia coli str. K-12 substr. MG1655]

You can download them here: E.Coli DNA and E.Coli DNA-Poly1.

NOTE: My sample protein is DNA Polymerase I (and not 3).


texts: Question regarding genetic variance and heritability

texts:
According to early studies (performed by Wright) on guinea pig coat
color, the total variance in a randomly mating strain was 0.573. The
variance in an inbred strain was 0.340. From correlations between
relatives in the randomly mating population, the heritability (gene
effect) was determined to be 38 percent of the total variance. Find
the following:
(a) variance due to gene effect;
(b) variance due to epistasis and dominance.

I understand the terms gene effect, epistasis and dominance but how should I use them in a question like this? I have never worked with numbers in genetics before. That's why I want some sort of a hint that I can somehow proceed the question with.


texts: A drone bee is male and is the product of only a queen bee. How is it that the drone bee can be male. I know that a drone is produced by an unfertilized egg, but this does not explain where the two X chromosomes come from. To me, this means that the one X chromosome from the queen must some how be duplicated.


texts: Did we first have swimming birds or flying birds?

texts:
Looking at the swimming birds building nests just across my garden, I suddenly wondered how evolution came to swimming birds and whether flying birds started swimming or whether swimming bird like animals started flying.

What came first and when and why?


texts: Where is the cartilage plate in this electron microscope image of the trachea?

texts: Also how could you tell? Assuming you were shown a photo of the cartilage only, how would you identify it?


texts:
In humans, the ability or inability to roll the tongue is a single
  gene trait.  The allele for tongue rolling (R) is dominant to the
  allele for not being able to roll the tongue (r).  Whether or not an
  individual can taste PTC is also an single gene trait.  The allele for
  being a taster (T) is dominants to the allele for not being able to
  taste PTC (t).

Claudia cannot roll her tongue but can taste PTC. Her mom also can taste PTC but her dad is not a taster. Claudia's grandparents were all unable to roll tongues.

1)  Based on the Info, what is Claudia's GENOTYPE?

I know she is "rr" because she cannot roll her tongue and it is recessive. However; I do not know the complete genotype for the PTC taster.  I know it for sure is a "T," but is it "TT" or "Tt?" How do we know? Do we have enough info to figure it out?


texts: What kind of beetle is this (found on landing windowsill)?

texts: found this beetle on my landing windowsill, would like to know what it is, very small, this was a zoomed picture on my phone.


texts:
http://de.wikipedia.org/wiki/Hühnerei says it takes up to 24 h for a chicken to produce an egg.

Is that dependent on the chickens nutrition, i.e., if it does not get enough food or the wrong kind, meaning it can survive on the food but it does not have everything to produce an egg?

Do we have data on this?


texts:
Often, after waking up from a night's sleep hard, flaky, pale yellow crystals are deposited around the eyelids (which easily wash off with water).

What are these? Why are they yellow? What are they made of? Is their amount proportional to the length of sleep?


texts:
Both snake and weasel hibernate. Which of the following is correct?

  A. They will die when temperature decreases below the critical
  temperature.

  B. Weasel will die when temperature decreases below the critical
  temperature.

  C. Snake will die and weasel will wake up when the temperature
  decreases below the critical temperature.

  D. Weasel keeps low body temperature and slow heart rate during the
  entire period of hibernation.

I don't think any of them should die, they would have some adaptation to prevent that. So,is the answer (D) ?

What is the snake's adaptation in this situation ?


texts: An over-simplified model of cell division and its relation to stem cells

texts:
I am a mathematician, and I decided to try to model cell division with math and see what conclusions came out of it. I had some questions concerning stem cells that came up in the model.

In an extremely simplified model of cell division, each cell decides what cells it will divide into with no output from the outside workd, including from neighboring cells. I also assume the time frame is small enough that cells do not die, and that there are only finitely many 'programs' telling different cells how to divide.

Given these assumptions, I came to the conclusion that one of two things could happen:
1. The number of cells grows exponentially, or
2. Most cells will never divide into other cells.

In fact, if growth is going to remain constant (e.g. 300,000,000 cells per month, every month in a sample), then eventually there will be two kinds of cells:
1. Normal cells, which never divide, and
2. 'Starter cells', which divide into normal cells but NEVER create other starter cells. The number of starter cells is eventually constant.

I hypothesized that these starter cells would eventually be far outnumbered and become a very small part if the body proportionally. I hypothesized that hair follicles, nail roots, growth plates, and bone marrow contained starter cells. I further hypothesized that these are adult stem cells.

  Question 1: Is this what stem cells are? Are they the cells that divide to create other, non-dividing cells?

After this, I realized that if the starter cells die, they would not be replaced under my model, because no cell is allowed to divide into new starter cells. I hypothesized that stem cell transplants fail because the host body kills off stem cells one by one and they can it be replaced. I also hypothesized that in the host, outside signals like hormones (which weren't allowed in my model) tell the body to create new stem cells as needed.

  Question 2: Do stem cell transplants fail because isolated stem cells do not replicate themselves?

Finally, I noted above that the alternative to a bounded amount of stem cells is exponential growth, where stem cells divide into stem cells.

  Question 3: Do embryo stem cells divide into other stem cells exponentially? Is this why embryo stem cells are easier to work with?

Thanks for your time. Even answers like "no, this is obviously wrong because ..." would be appreciated.


texts: I google the scientific name for black panthers. I get panthera onca. I google panthera onca, and I get jaguar. Can someone explain what is going on? Are they the same? What is the real scientific names for them? Because panthers are black and jaguars are yellow with black spots.


texts:
I have found these thingies in my institute at Tiruchchirapalli in India. I have no idea what they are:

Can someone tell me what they are, exactly?


texts: Stem cell research and female egg synthesis

texts: In terms of years, how far is stem cell research from being able to produce a female human egg from other female body cells?


texts:
This website introduces the "Icosahedral Matrices".

What are the locations of the other half?

It only shows around 30 numbers of the 60 facets. So how to know the other 30 numbers on the back?

The 60 transformation matrices are shown below in the website. Are they rotational matrices? What are the exact meaning of those 9 numbers for a particular matrix? For example,


texts:
I had some potentially infested clothing (and shoes) in a bathtub, and just after I bagged them to wash, I spotted this little fellow running away.  I put it in a plastic food container and snapped a photo as close up as my phone could get:

Is this a bed bug?  Its length is about 3 mm, so presumably it would be a nymph if so.  Compared to pictures on the Web, it certainly looks similar.  However, it seems too thin (even for a nymph), and the antennas don't have that outward crook that all of the pictures (even of nymphs) seem to have.  Also, at the time that I took the picture, it could not have fed on blood in the previous 12 hours.  So hopefully it's not a bed bug at all; but maybe there's nothing else that it could be, and the pictures give the wrong impression of what's possible.  Can anyone tell?

This is not a StackExchange that I'm used to, so if this is an inappropriate question, then I apologize, and I'd appreciate any suggestions of where to ask instead.

ETA:  This is in the Midwest/Great Plains region of the USA.

ETA:  Having seen more pictures, the thinner (or really, longer) form seems to be after they have fed.  But as I said, this could not have fed within 12 hours at least (when the clothes it might have been in were removed, plus the people had no apparent bites).  And that doesn't explain the relatively straight antennas.  But it does seem closer now.

ETA:  The picture doesn't seem to match any of the false IDs of bed bugs on this site, nor the related insects at bugguide.net.  (And it compares to the actual bed bugs with the slight differences that I noted already.)


texts: Why did the sensitive plant (Mimosa pudica) evolve its leaf-closing mechanism?

texts: Why did the sensitive plant, Mimosa pudica, evolve its leaf closing mechanism? Does it help in a heavy storm? Does it scare off whatever animals might think it a good meal?


texts: Rejection of valid theories of biology on theoretical grounds

texts: Is there a theory in biology that was initially disregarded as false (because of critical or contrasting perspectives) and only recognized as important after a considerable time, possibly only in recent years, thus significantly impeding its development?


texts:
What does "Niche Complementarity" mean?

On this website they define "Niche Complementarity" as:

  The tendency for coexisting species which occupy a similar position along one niche dimension

I don't quite understand this definition. The tendency to do what?

Notes:

I know what is an ecological niche and therefore what is a niche dimension. There is no need to define this.
I am particularly interested in the use of this concept in speciation and adaptive radiation.


texts:
I'm from Brazil. And I have this plant at home.

Can anybody identify this plant?


texts:
In Molecular Biology of The Cell (Alberts, et al., 2015), it lists the various RNAs that are trafficked through the Nuclear Pore Complex (NPC) into the cytoplasm.

The list includes snRNAs, but I have seen it stated elsewhere that snRNAs don't leave the nucleus, that they are made there and perform their function there.

Is MBOC's version correct and snRNAs leave the nucleus, or are the other sources correct and the snRNAs are made, remain, and function in the nucleus?


texts:
So imagine a parasite of a parasite. Imagine a parasite of that parasite. Then imagine a parasite of that parasite, then a parasite of that parasite, and so on and so forth.

Is there a formal term for this?

How frequent does this occur in nature? If it varies, what does it vary by? How many levels down do parasites typically go?

What is the deepest level that has ever been observed, and with what organism?

Thanks


texts: Can hepatitis B also infect vaccinated persons?

texts: If a person is vaccinated against hepatitis B: Is there any chance that he also gets the infection by physical contact? Is it a congenital disease or not (if the parent is hepatitis positive is the offspring is also affected or not)?


texts: Why is the thalamic reticular nucleus called a nucleus?

texts:
In the Wikipedia article on nuclei I read:

  A nucleus is one of the two most common forms of nerve cell
  organization, the other being layered structures.

Is there a specific and plausible reason, why the  thalamic reticular nucleus is called a nucleus, even though it is - anatomically - a layer?

Has the TRN once been a somehow spherical nucleus and evolved into a two-dimensional layer? Or does the TRN play a functional role that normally nuclei play, but not layers?


texts:
What's the least number of tRNA molecules needed to form a polypeptide chain that contain 50 amino acids of 15 types?

  I know that each type of amino acid has at least one unique type of tRNA that recognizes it and transport it, so according to my understanding the 15 types of amino acids need at least 15 tRNA molecules of different types unless there was a reason that prevents one tRNA molecule from transporting two identical amino acids (two alanine) to the same polypeptide chain

•In other words:
Can one tRNA molecule carry two identical amino acids (ex: two alanine) to the same polypeptide chain that's being synthesized or not?


texts: Can frogs see clearly under and above water?

texts:
If humans attempt to see underwater, the image is blurred due to refractive differences in air and water that disrupt the normal refractive effect of the lens in the eye. A diving mask overcomes this issue. How then do frogs accommodate their lenses in both air and water? Are their images clear in water and blurry above, or vice versa?

As far as I know, their lenses are made up of epithelial cells and fiber quite similar to the human eye lens, or am I incorrect here?


texts:
I'm not a biologist, but it seems that plants with disgusting taste have evolutionary advantage to tasty plants. Same about animals.

There are some species that can not be eaten by man (sharks have poisonous meat). Being eaten by a human — is one of major threats for a shrimp. Does it mean that shrimps are going to become less and less tasty (for a human taste)?


texts: At what g force do bacteria start to pellet down a tube?

texts: I am working with C. elegans and bacteria and I want to get rid of the bacteria they eat by centrifuging the worms without centrifuging the bacteria. I am using a g-force of 600 and the bacteria sometimes still centrifuge down. What g-force would be ideal to pellet the worms but not the bacteria? Does this depend on the bacterial species?


texts:
I'm studying modified Mendelian ratios. I've got a theoretical problem that I'm stumped on:

A species of bird may have normal wings, or a mutation that causes frazzled wings.

I do 15 identical breeding pairs, crossing a male bird with frazzled wings to a normal winged female. The progeny obtained are 46 with normal wings (22 male/24 female) and 23 frazzled, all male.

Afterwards, I mate the normal winged females to the normal winged males obtained from the above cross. The progeny obtained all have normal wings.

I figured out a possible solution, and would like to know if it makes sense:

Z(f) = Z sex chromosome with normal wing gene, recessive
Z(F) = Z sex chromosome with frazzled wing gene, dominant
W =  W sex chromosome

Z(F)/W = abnormal wing female bird (does not survive as not enough
gene product produced)
Z(f)/W = normal wing female bird
Z(F)/Z(F) = abnormal wing male bird (does not survive as not enough gene product produced, or possibly survives as just enough is produced by 2 mutant genes, doesn't matter anyway)
Z(F)/Z(f) = abnormal wing male bird (survives as wildtype gene produces enough product)
Z(f)/Z(f) = normal winged male bird

My crosses:

P1: Z(F)/Z(f) × Z(f)/W
Progeny: Z(F)/Z(f), Z(f)/Z(f), Z(F)/W (fails to survive), Z(f)/W

F1: Z(F)/Z(f), Z(f)/Z(f), Z(f)/W in 2:1 normal:frazzled wings
F2: Z(f)/Z(f) × Z(f)/W produces Z(f)/Z(f), Z(f)/W

This would account for the phenotypic ratios seen in the problem, and also uses the ZW sex chromosome system found in birds. The genetic explanation would be that a single Z(F) does not produce enough product to thrive, for whatever reason. The trait is sex-linked dominant on the Z chromosome.


texts: At what cancer stage do tumors release circulating tumor cells into the blood?

texts: And would a very accurate sensitive system for detecting circulating tumor cells (which detects 1 cell per 50 billion) be useful as a screening tool ?


texts: Original paper about the all or none law for neurons

texts:
I am looking for the original paper about the all or none law for neural activity.

I know that there is a very old article about the all or none law for mammalian heart muscle fibers, but I'm specifically interested in when this idea was first stated about neural activity.

In A logical calculus of the ideas immanent in nervous activity from 1943 this law is already mentioned like an established hypothesis, so it is probably quite old.


texts: What really causes the toxicity of wrongly-thawed meat?

texts:
(Note: I've seen multiple related questions over at Cooking.SE, but I'm looking for a scientific explanation, not cooking advice!)

I've been researching this for a couple of hours but the more I read, the less I seem to understand the situation. Many sources claim that thawing meat in warm water is wrong and that I should instead opt for cold water to prevent bacteria from growing and producing toxins. I found a wide variety of toxin-producing bacteria that can live and reproduce in meat, such as Escherichia coli, Salmonella, Corynebacterium diphtheriae, Listeria monocytogenes and Clostridium botulinum.

There are two things I don't understand:

If I thaw the meat quickly, the bacteria have less time to reproduce before I cook the meat. This is especially true for Listeria monocytogenes which seems to be able to quickly reproduce in cooler temperatures. Why is it bad to thaw meat in warm water?
If the sources I've read are true, it leads me to believe that Listeria monocytogenes is not a bigger issue than the other species of bacteria growing in the meat. I suspect that bacteria compete for resources and that it is probably only one of them that is the main factor in making a piece of meat toxic for consumption even after cooking. What is the primary cause of meat toxicity?

Or is it possible that I've been overanalyzing the situation and the exponential relationship between bacterial growth and temperature is the main reason?


texts: Did researchers evolve multicellular yeast or did they just turn on multicellularity?

texts:
In this new paper "Experimental evolution of multicellularity" found via Ars Technica the researchers describe having developed multicellularity and apoptosis within 60 days from a unicellular yeast species.

Is it possible that what they have done is merely turn on an ability of that species that evolved previously and just lay dormant?  Do we know that that yeast species and all its ancestors were never multicellular?  The paper doesn't even mention the possiblity of this.


texts:
I have a few questions I can't seem to get a straight answer to, regarding the .gen file format and also biology in general.

The .gen file format specifies SNPs for individuals.

Since each SNP has associated allele A and allele B, I assume that the file only contains Causative SNPs, and not Linked SNPs, since the former reside in the gene, and the later don't. Since each SNP in the file has an associated gene (actually genotype, some combination of allele A and B). Correct?

SNP indicate a single position in genome, so why can allele be identified with a sequence larger then one? Or does it indicate just a starting point, where each allele can be of different length, which can be greater than 1?

Allele should be a particular variant of a specific gene, but in other places I saw the definition "Alleles are alternative forms of a particular sequence.". The later seems more logical, if looking at the .gen file, but it's contradictory to the first statement. So, what's the correct definition?

EDIT:

After further research I came up with findings, demonstrated in an example row for .gen file:

--- rs200405949 10023   CCAA    C   0.249   0.745   0.007   0.005   0.84    0.155 ...

--- - chromosome number, which is missing because it can be inferred from the filename, belonging to each chromosome

rs200405949 - ID of the SNP - a single nucleotide which can vary between samples/people; there are usually only two possible variations, but in rare cases there is a third or even fourth - which are ignored in .gen?

10023 - allele pair (base pair) coordinate/position inside the said chromosome. Either both major and minor allele are made of a single nucleotide (in which case the SNP coordinate/position inside the said chromosome might coincide with this position), or one of the alleles will have more than one nucleotide and the other allele will be the same as the first nucleotide of the former allele - because we need only one distinct sequence, and all other combinations of same nucleotide length are automatically the other allele?

CCAA - (usually?) major allele - the most common allele (specifically in this context, a single nucleotide or a sequence of nucleotides) for a given SNP (or near it, i.e. somehow connected to it) IN the cohort in question, i.e. the cohort being all the samples/people in the experiment/.gen file (hence, the number of samples equals the number of triplet columns after the 5-th column onwards). It occurs in more than 50% of the times COMPARED to minor allele. Compared to minor allele, they both start with C - shouldn't they differ at this SNP position by definition? Also, more than one nucleotide is specified here - why? SNP always has one nucleotide...

C - (usually?) minor allele - the second most frequent allele (specifically in this context, a single nucleotide). The SNP site can be bi-allelic (mostly picked/studied), in which case the major and minor alleles are the only possible alleles, but some sites are tri- or quad-allelic - in which case we don't have the info for the third (and fourth) allele variants, but we know they are even less common then the major and minor alleles?

0.249  0.745   0.007
0.005   0.84    0.155
... - each subsequent triplet of values then indicate likelihoods of homozygote CCAA/CCAA, heterozygote CCAA/C, and homozygote C/C genotypes (allele pairs) at this SNP, respectively, for one sample/person (each allele is present on one of the two copies of the said chromosome, either maternal or paternal). If one of the three values has a value 1 and the other two have 0, I guess this actual SNP was (somehow) tested for, hence we can be 100% sure which allele pair it is, and if not, then the probabilities were somehow deduced (e.g. from other, somehow related SNPs perhaps). What if they add up to less than one? Or even what if all of the three values are 0?

Are my conclusions correct? And what about the open question?


texts: Can Mono-Cell or other organism self-replicate?

texts:
I have a question regarding how organism replicate them self to create an other organism,

We know that in animal reign, we need a male and female that will generate a new being.

what I want to know is if there is a micro organism that can create another one without a partner of the same kind? and in that case how this organism can do that?

hope my question was clear!

Thanks!


texts: Why isn't suppression of immune system for organ transplant not as dangerous as AIDS?

texts:
I've read that when AIDS symptoms show up, life expectancy is about two years if no treatment is applied. On the other hand, I've also read that people having an organ transplant need to take immune system suppressors for the rest of their lives so that their body does not attack the transplanted organ. So, if I understand well, it is a sort of induced AIDS. I do not understand then how it is possible for people with an organ transplant to live more than about two years.

Can someone explain with details the differences between the suppression of the immune system by medicine for organ transplants and the one due to AIDS?


texts: What happens to those molecules that are not received by receptor proteins on the cell membrane?

texts: I am studying cell communication and come to know that proteins from outside environment gets received by receptors on the cellular membrane and then the signal is transduced inside the cell. My question is given a certain concentration of proteins are disseminated in the environment what happens to those protein which are not received by any receptor molecule, are they denatured and get destroyed in the extracellular environment after some time in case if the answer is yes can one provide a reference for the same Are they bounce back or absorbed by cell membrane?


texts: Do river sharks (genus Glyphis) have reduced rectal glands for salt removal?

texts:
Do river sharks of the genus Glyphis have reduced or absent rectal glands for salt removal?

The rectal gland of marine sharks removes excess salts to maintain osmotic balance (Oguri 1964).  In freshwater stingrays (Potamotrygon spp.), the rectal glands are greatly reduced in size  (Thorson et al. 1978) but are apparently functionless (Goldstein and Forster 1971). This is not surprising because freshwater rays do not experience the regular influx of salt water.

I have been unable to determine whether such degeneracy or loss has been observed for the river sharks of Australia (genus Glyphis). Pillans et al. (2009) suggest that osmoregulation is probably similar to bull shark, which would not be surprising because they are in the same family. However, bull sharks that live in salt water but regularly enter fresh water have rectal glands that are normal size (Oguri 1964). River sharks are obligate freshwater species and thus have no need to maintain a large rectal gland for the same reason as the freshwater rays.  From an evolutionary perspective, I would predict reduction or loss of the rectal gland.


texts:
Could somebody point out the neuroscience literature dedicated to the modelling of 3D objects in the human mind?

I'm interested in the brain regions, and particularly the details of the circuitry, involved in simulating/manipulating (or planning to manipulate) and/or recognizing 3D objects, or in relating them to the "2D" sensory information. Ultimately, my interest is quantitative, i.e. I'd be especially interested on more computational outlooks on the topic.

Edit: I am aware of the visual recognition pathway, which roughly speaking culminates with the inferior temporal gyrus (in the "what pathway"). However, some animals (not just humans) can simulate object properties (e.g. how will this plastic figurine warp if I bend it a certain way? What is that moving ballerina likely to look like in the next second?). This is more complex than object recognition alone.

Note: my question is asking for pointers to the foundational literature of this topic. I know it's somewhat broad, but I'm essentially asking where to start reading. Thanks! :)


texts: Is there an ecological scenario where terrestrial insect larvae can show food choices?

texts:
I have been going through literature on insect food choices. I plan to study the effect of prior experience on food choices in both adults and larvae of the red flour beetle, Tribolium castaneum. There are plenty of studies that focus on larval and adult experience having an effect on adult preference. I would like to look at how larval experience changes larval choice, but only if it has some ecological relevance. However, I could not find a single study that provides an ecological relevance to larvae making food choices.

This appears to be due to the fact that larvae are usually sessile, and since adult females are the ones making the oviposition choices, therefore most studies seem to assume that the choices of the larvae don't matter. (Preference Performance Hypothesis)

Larval food choice might be ecologically relevant under conditions where females make "mistakes" during oviposition, say if the environment is spatially/temporally fluctuating. But if they show limited dispersal (or slower dispersal than adults), then does their choice really matter?

Does anyone know of any examples (published or unpublished) where insect larval food choice is ecologically relevant? It would help me out a lot to design my study.
Thanks in advance!


texts: In what ways have plants and animals evolved to support each other throughout history?

texts:
I'm curious about how plant and animal life have been able support each other throughout time and how each has evolved in a way that would help the other?

For example I have heard that plants have evolved to attract animals, such as bees in order to allow for pollination.  These plants produce smelly flowers that are usually white....  or colorful, non-smelling flowers.  By allowing bees to collect nectar for themselves and their hive, the plants are able to be pollinated in the process.

Earlier today I was noticing a bird hopping up branches of a tightly branched tree, which made me think of how plants and animals would support each other throughout time.  Trees are usually homes for a lot of animals, including birds, so I was curious about the evolution of trees to allow for tigher canopies to protect animals from the weather/elements.

My question is, how have plants and animals influenced each other's evolution, by helping each other throughout history?


texts: Is it possible to reduce maturity time of plants with biotechnology?

texts: I've heard of speed breeding which makes use of optimal circumstances in glasshouses and growth chambers. Is it also possible to shorten a plant's maturity time (i.e. the time it needs from being planted until the time its yield can be harvested) using genetic modifications?


texts: When a species of bacteria is referred to by its strain, are they a clone of single founder or is a certain amount variation allowed?


texts: What causes a 'stuffy' or 'runny' nose when you have a cold?

texts: When humans get the common cold, a common symptom is a stuffy or runny nose. Is that the body's immune response or is that the virus's doing?


texts: Is vision a vestigial sense for deep ocean species?

texts:
Sunlight doesn't penetrate beyond a couple of hundred feet from the surface of the ocean. Species that exist at greater depth probably live in a state of perpetual night; yet from a quick google image search (i agree it isn't a very authoritative source) for deep ocean species I see that plenty of these have eyes.

So ...

Are the sight organs in deep oceans species merely a remnant from an earlier era?
If they are a remnant, has evolution/mutation modified these organs over time?
Regardless of whether the organs of sight are vestigial organs for deep ocean species, how do the eyeballs withstand the extreme pressure of water in the deeps?


texts: Interchromosomic vs Intrachromosomic Recombinations

texts:
What is the difference between interchromosomic and intrachromosomic recombinations?

I did a research about them and saw some videos (e.g. this and this) with animations on YouTube. But I'm still lost between them and can't differentiate between these two expressions.


texts: Identify this tuber like object found on beach

texts: Can anyone identify this tuber-like object I found on a beach in South Wales, UK? It's about 25 cm long and looks like a deflated football. Pretty spongy, saturated with water. I was hoping it was ambergris, but that seems unlikely.


texts: How does beta branching stop alpha helices from forming?

texts:
I am told that beta branching interferes with alpha helix formation.

Problem is that I don't see how beta branching has anything to do with alpha-helix formation. Beta-branches are on the outside of alpha helices and internal hydrogen bonding holds the helix together.

My book (Lehninger) also doesn't say anything about beta branching interfering with alpha helix formation.


texts: Is vermiform appendix no more a vestigial organ?

texts:
The appendix has a role in the immune response.

So is it therefore recently removed from the list of vestigial organs?


texts: Difficulty in finding protein inhibition drugs

texts:
I was reading an article on a recent identification of a PARP-14 protein in cancer cells that is responsible for production of additional glucose which keeps cancer cells from dying, and that a PARP-14 inhibiting drug is still a long way from becoming reality.

Would like to ask any medical researchers/anyone with adequate knowledge, what is the difficulty in producing drugs that inhibit production by a certain protein? Isn't it about analyzing the chemical makeup and structure of the protein and finding ways to neutralize it? As how other types of drugs are made? Please give some specific examples regarding this topic. Your help is much appreciated.


texts: I'm rather new to bioinformatics, so this might be a rather basic question, but what are sequencing artifacts, in the context of variant calling?


texts: I have read the phrase 'T3 is three to four times more potent than T4' several times both in books and websites. But isn't T4 a prohormone of T3? Why do then these sources talk about its potency as a hormone(I suppose)?


texts: Why does Nature use a 4-level system to encode information in DNA?

texts:
First, I am not a biologist, so this question might be naive:

Computer information processing and storage is based on 2-digit system of bits with values 0 and 1. Now, DNA stores the information in a 4-digit system: A, C, G, T. Three base pairs form a codon and can encode 43 amino acids.

Is there a good reason why a 4-level system (which can store 2 bits per encoding entity) evolved rather than a 2-level or a system with a larger number of symbols in the alphabet?

Put differently: Why was a binary system not preferred for storage and processing of data? In computing, binary is much easier, and the very few tests of exotic higher-level data processing have not really been successful.


texts: Recently I underwent a wisdom tooth extraction, and while there is still numbness I have observed something peculiar. If I drink cold water, it tastes sour, however the same effect is not observed with room temperature water or hotter. What is causing this effect?


texts: Where are the evolutionary "inbetweeners"?

texts:
The problem I've always had with evolution is the actual lack of variation between animals. More specifically, the lack of observable gradual change between species.

Take for example the hammerhead shark. It obviously has a strong connection with a normal shark, but where's the "half-hammerhead" shark? Where's the species that only has a SLIGHTLY wider head?

I really doubt that a single mutation on a normal shark resulted in a head shaped like that, it had to happen gradually. Right? As far as I understand, evolution works by random mutation in a child being somehow slightly beneficial to that animal so it get's to live longer and reproduce more, eventually resulting in it's genetic material in dominating the inferior ones before it. But if it was for whatever reason beneficial to have a slightly wider head, why don't all the sharks have slightly wider heads now? On the other hand, if it wasn't beneficial, how come the hammerhead still exists?

Furthermore, I feel like some characteristics of a certain animal can't really have gradual benefits. There's a lizard that shoots blood out of it's eyes. The original ancestor certainly didn't, and I'm sure that if it's child only bled slightly from it's eyes it wouldn't really help if much in life. So for it to actually become beneficial, it seems to me that there had to be a ton of lizards that had a disadvantage of bleeding slightly. In fact, there had to be so many that they evolved even further in the same direction and kept doing that until they bled so much it's an actual benefit (sorry for this turning so gross). So why did the inbetweeners survive long enough to evolve even more, and why did they THEN die out?


texts: What governs the distribution of blood vessels?

texts:
Whenever someone is sick, doctor places 2 fingers on wrist & observes the heart-beat-rate by feeling pulses of a certain artery.

To me it seems the distribution of blood vessels are pretty standard across all variations of humans (I mean identical blood vessel positioning seen across Caucasians, Africans, etc. members)

So when someone is born with extra finger or joined skull - which rule/gene/algorithm decides the distribution of network-of-blood-vessels in those special parts?

PS: I am definitely / apparently not a biology student, so pardon my ignorance

Is positioning of blood capillaries random or they too are identically positioned among all humans, although we can't see them.


texts: Recommended sequence clustering algorithm for transcriptome data

texts:
I'm working on a project where I'm going to analyze a large amount of transcriptome data. After assembling our RNA-Seq reads into contigs using Trinity, it looks like I'm going to have about 10GB of sequences in fasta format. Since these sequences are from several hundred tissue libraries but from a single species (chicken), I'm expecting there to be a lot of redundancy, so I'd like to cluster these sequences and just use a representative sequence from each cluster as I go forward with my analysis. I see there are quite a few tools that exist to do things like this, and I'm wondering which you all would recommend. I'll be running this on a Linux machine with 64 CPU cores and ~500GB of RAM.

I started looking at USEARCH, but it seems I'm going to run into some memory issues with the free 32-bit version and as much as I clicked around on their site I couldn't figure out how much the 64-bit version costs or how to buy it.


texts: What pattern can be learned from the data of RNA seq counts and HiC matrix?

texts: I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between the two types of data such as the level of expression of gene segment and the interaction of the gene segment, since it seems that they are correlated. Thanks


texts: Is it possible to make a cancer cell that doesn’t encode any neoantigens?

texts:
The cell still has mutations, but those mutations only occur in the noncoding sequences, such as promoters, which drives over expression of proto-oncogenes and downregulation of tumor suppressor genes. So the cell will proliferate uncontrollably, but won’t express any neoantigens.
Will such cell be invisible to our immune system?


texts: Allergy desensitization: what is the mechanism? Could it happen with other immune responses?

texts: Allergy is a type of immune response against an otherwise harmless substance. If I understand it well, the aim of allergy immunotherapy is not to stimulate an immune response like the immunotherapy for for other diseases, but to progressively reduce it by controlled exposition to the antigen. Is the mechanism understood? Could the repeated long-term exposition to an antigen reduce other types of immune responses (to virus or bacteria for example?)


texts: Why do humans lose subcutaneous fat from the extremities with age?

texts:
Why does fat tissue die and shrink on the hands, knees, and lower legs of most people as they age, even when they are overweight?
In most people, their bone definition becomes much more visible around their extremities.

I'm aware I asked a similar question before, but the previous question wasn't specific enough.
Why do humans lose subcutaneous fat tissue with age?

With age, humans store more visceral fat because of multiple factors that include physical inactivity, higher FSH levels, androgens, a drop in estrogen in women, and other factors.


texts: Prostaglandin F2-alpha production in men

texts: I am trying to find information on Prostaglandin F2-alpha, specificaly production in men. Could somebody explain how this prostaglandin is produced? What types of cells are producing it, production signaling? Any books on this subject?


texts: How does having an empty stomach affect absorption of compounds?

texts:
From personal experience, compounds such as nicotine, caffeine and alchohol appear to absorb much quicker into the blood on an 'empty' stomach', or after extended periods of fasting. If this is the case, why would that occur?

Does time play a significant role in absorption in an average 'healthy' individual? Are there any srudies published on this phenomenon?


texts: Is it possible that the recipient of a heart transplant would display some of the donor's personality traits, as if the heart has memories?

texts:
I've read somewhere that after a person has a heart transplant, it is possible that his/her attitude, action or behavior would change slightly or significantly, as though he/she possesses some aspects of the organ donor's personality because he/she is using the donor's heart.

Anything to support this phenomenon? Does it suggest that there are actually memories 'stored' in the heart and these memories may be retrieved by the person that owns the heart even if he/she is not the original owner?


texts: What techniques can be used to link environmental conditions to crop yield?

texts:
Im interested in how we can determine what are the optimal conditions for crops and how deviations from these optimal conditions affect yield. In the literature I have found two main approaches and I was interested if there were more ways that are used or if anyone can think of a more creative way to test the link.

Approach One

Use a greenhouse experiment to isolate all variables bar one and vary it. Measure the change in yield based on that variable.

But this approach is time consuming and it is difficult to include interactions.

Approach Two

Use a model that relies on some base knowledge of that plant - i.e. the base temperature at which growth is zero, and a rough idea of optimal ranges. But requires this base knowledge already.

Potential Approach Three

Use multiple linear regression in combination with field data to create a linear or polynomial model of each variables effect on yield. Interactions can be included easily. But relationships are unlikely to be linear and without prior knowledge it is hard to decide on non-linear models.

Can anyone think of other ways that could be used to test these links?


texts: how to solve gap reactions in genome scale metabolic reconstruction

texts:
I'm making a project about modeling of nannochloropsis metabolism. My model is in the refinement stage. However, it is not running in the FBA test. Then i found there are 87 reactions that did not run. But the reactant/metabolites for those reactions to run are there in the model.

Is there any one know what is the possible reason for this, and how to solve this problem?

Really looking forward to see your answer.

Thanks,


texts:
I've stumbled upon the article "Telmisartan Treatment of Refractory Proteinuria in a Dog."* What is refractory proteinuria?

*Bugbee AC1, Coleman AE, Wang A, Woolcock AD, Brown SA. J Vet Intern Med. 2014 Sep 30. doi: 10.1111/jvim.12471. [Epub ahead of print]


texts:
This old common question is still not clear to me. I got this explanation:

Bananas go through a unique process known as negative geotropism. Instead of continuing to grow towards the ground, they start to turn towards the sun. The fruit grows against gravity, giving the banana its familiar curved shape.
But why? The answer lies in the botanical history of the banana. It originated in the middle layer of the rainforest, where there is little sunlight. If the fruit were to grow towards the small amount of light that penetrates sideways through the vegetation, the plant could overbalance and topple over.
So bananas developed a way of growing towards the light without destabilising the plant.

source
So, evolutionarily, the bananas are 'forced' to grow towards the light. But how is this capabilty 'grown into' the banana? Is it something epigenetic or is it just light that attracts them? So how does this mechanism works?


texts: Why does the mass increase in this question?

texts: So, on 'http://filestore.aqa.org.uk/sample-papers-and-mark-schemes/2016/june/AQA-BL3HP-QP-JUN16.PDF', question 1.b., they show a partially permeable bag of glucose solution, in a less concentrated solution. Since sugar is more dense than water, why does the bag get HEAVIER, when there's more sugar, and less water?


texts: What happens to the human ear as it naturally goes deaf?

texts:
I was always told that when the human ear goes deaf to a specific sound (auditory frequency), then that sound is heard one last time, and upon fading away, will never be able to be heard again.

Is this in fact true? If so, why do we hear that sound (which seems to happen randomly and is somewhat loud for a split second) just before the ear becomes deaf to it?

Ultimately speaking, what exactly happens as the human ear naturally goes deaf?


texts: Is there a durable surface that ants can't pass?

texts:
I'm looking for a surface, that will be impassable for ant's yet not poisonous or easily decaying.

One idea is water - they really can't cross that. But water easily dries and is quite uncomfortable.

Is there something their legs will find uncomfortable? Something spiky for example?


texts: What biological processes cause leaves to change colours in Autumn?

texts:
I am curious to learn what are the biological mechanisms that cause leaves of deciduous plants to change colour? What happens to the chlorophyll?

What environmental phenomena (temperature/air pressure/length of sunlight) are they responding to?


texts: Where can I find a list of diseases and their incidence?

texts:
Say I am studying a particular disease and I know that its incidence is 0.8 per 100000 children below the age of 18, how would I find the incidence of a whole bunch of other pediatric diseases (or even not just limited to pediatrics)?

Essentially I want to find diseases that would be familiar to a medical audience and provide an example of a disease with an incidence of about 0.8 per 100000, another one that is one tenth the incidence and another one that is ten times the incidence.


texts:
I'm studying biology for the first time seriously. I've been reading OpenStax College's material.
In the section of "The Cell Membrane", I have the following problem:

Choose the answer that best completes the following analogy: Diffusion is to ________ as endocytosis is to ________.

filtration; phagocytosis
osmosis; pinocytosis
solutes; fluid
gradient; chemical energy

I chose number 1, but the site says the correct answer is number 2. Could someone please explain why?

[EDIT]

I chose number 1, because diffusion and filtration were passive ways to transport, while endocytosis and phagocytosis are active. I didn't not take in to account that 2. fitted better, because the osmosis part was confusing me.


texts: Why can't humans use dietary citric or acetic acid as a primary source of energy?

texts: As the Krebs cycle is involved with the conversion of food in to citric acid, why can't eating citric acid be used as a temporary primary source of energy - in place of fat/carbohydrate/protein?? It seems like a waste of energy to convert food into citric acid if there is freely available citric acid in your diet why wouldn't that preferentially be used for energy - as it would skip a lot of steps and therefore be more efficient. And what about drinking acetic acid for similar benefits, as "it is changed to citric acid by combining with oxaloacetic acid with the help of CoEnzyme A and ATP".


texts: Why do some tissues have insulin-dependent glucose transporters and others not?

texts: Insulin upregulates GLUT-4 glucose transporter insertion in skeletal muscle and adipose tissue. But there are many tissues in the body that use insulin-independent glucose transporters (like GLUT-3 in the brain). Would there be any disadvantage to have the entire body use insulin-independent transporters like GLUT-3? Why involve insulin in this? Wouldn't the concentration of glucose in the blood regulate the influx of glucose via concentration gradients anyway?


texts: I have read wikipedia but don't understand it well. Do we mean Complex I, II,III and IV when we say respirasomes?


texts: What is meant by the term synaptic targeting?

texts:
I am studying whether a protein interacts with the mitochondria in the synapses of neurons and I have come across the term "synaptic targeting". I am reading this paper and I have come across the following:

During synaptic development, proteins aggregate at specialized pre-
and postsynaptic structures. Mechanisms that mediate protein
clustering at these sites remain unknown. To investigate this process,
we analyzed synaptic targeting of a postsynaptic density protein,
PSD-95, by expressing green fluorescent protein– (GFP-) tagged PSD-95
in cultured hippocampal neurons.

I am not sure what exactly is meant by the term "synaptic targeting". I have tried Googling the definition but all I get are links to journal papers. I think that synaptic targeting refers to where in the synapse (e.g. presynaptic or postsynaptic ending) a protein is located, but I am not certain. Any insights are appreciated.


texts: Is it possible to make anaerobic media too reducing?

texts:
I've been struggling to grow an anaerobe (P. gingivalis), I take every precaution to keep the culture conditions free of oxygen, I was wondering if the conditions can be so reducing that they inhibit microbial growth of an obligate anaerobe.

To make the liquid media I do the following:

TSB supplemented with yeast extract
plus 0.5g/L L-cysteine HCl as a reducing agent
plus resazurin as a redox indicator
heat-sparge with nitrogen until the resazurin goes completely colourless
add hemin (5 mg/L) and vitamin K1 (1 mg/L) from stock solutions (1mL/L hemin in water, 200uL/L vit K1 in ethanol)
filter-inject this media into glass tubes which have had the gas in them removed (this takes place in an anaerobic hood)
all materials (syringes, needles, filters, tubes) had been left in the anaerobic hood before use so that no residual oxygen is left in/on them
swap the headspace for a gas mix of 80:10:10 N2:CO2:H2

I don't get any growth after over 72 hours @ 37oC.

Other protocols I have found are much more vague/lax about removing the oxygen, many just say that the cysteine should be added, and the media should be incubated in an anaerobic hood for 24 hours with the lid loose before being used. This got me thinking that maybe I'm removing too much of the oxygen.

What do you think?


texts: Diarrhea / constipation: why are they associated with failure of the large intestine (and not the small intestine) to reabsorb water?

texts: When I see reference to diarrhea or constipation, it's almost always in reference to the under- or over-reabsorption of water, respectively, in the large intestine. However, if the large intestine plays a much smaller role in water reabsorption than the small intestine (80% vs 20%), why is the small intestine rarely implicated in these disorders? Is it because the small intestine usually doesn't malfunction in this way and malfunctions are much more common in the large intestine?


texts: Question about the consequences of non-random mating and allele frequencies

texts:
I just began studying population genetics, and I don't understand something that is written in my lecture:

Consequences of non-random mating:

More homozygote and less heterozygote individuals in the population
Allele frequencies are constant (not in case of negative density dependence)
Genotype frequencies change

What I don't understand is the second point. If the genotypes' frequencies change, shouldn't the frequencies of alleles change as well? Furthermore, I don't really understand either how this is supposed to be linked to a negative density-dependence case...
Any help is welcome! :)


texts: 3cm Worm Found in a Glass of Tap Water - please help identify

texts: 3cm Stripy Worm Found in a Glass of Tap Water - please help identify. The worm was found in the beginning of July in a glass of tap water, in Ireland. It was about 3cm long, had a round shape and was moving quickly. It had no legs.


texts: How Circumcision could reduce the chance for a HIV infection?

texts: Circumcision removes the foreskin of the penis which mainly acts as a cover to the penis. Normally removing the foreskin makes more vulnerable to any STD, so how could circumcision reduce the risk of a HIV infection?


texts: Why do the fastest runners tend to be black?

texts:
If you watched the last Olympics like me you probably also observed that most medallists in running events were black. Why is that? I discussed this with university grad friends and researchers and we only came up with hypotheses but nobody had an actual explanation. Is it cultural, genetic, other reasons or nobody really know?

Update:

Sprint and distance running requiring different attributes for being the best, let separate this question in two parts: 1) Sprint (i.e. 100m) and 2) Distance running (@Forest already provided a great answer for this).

Note: I know this question can potentially bring disrespectful answers/comments, but I'm hopeful that this site and its members can answer this interesting question. Otherwise, I'll simply erase my question.


texts: VPg priming of the replication of RNA viruses

texts:
I'm doing a presentation on the replication of SARS-CoV-2 for my chemistry class, and I found that to replicate its RNA, the virus uses RNA-dependent RNA polymerase, which is primed by a VPg primer. Since the presentation is for a chemistry class, not a molecular biology class, I would like to know the chemistry behind the way that primers work.

I've tried searching the information on the internet, but could not locate the information I need.


texts: Is Ellman's reagent specific for low molecular weight proteins and thiols?

texts: Is it still possible to quantify cystein rich low molecular weight proteins such as Metallothionein in a given sample using Ellman's reagent if the sample is contaminated with some high molecular weight proteins?


texts: DNA shared by octopuses and modern humans

texts: What percentage of DNA do we share with octopuses? I tried looking it up but couldn't find the answer on the internet. Could someone enlighten me on the same? To make the question more specific, I am more interested in knowing how many genes humans share with octopuses, but answers regarding how different our shared genes are or even a metric of the entire genome alignment would be helpful.


texts: How diverse are the sperm cells of an individual male due to random mutations?

texts: Due to the sheer number of sperm cells in an individual and the rate of mutations, are they likely to be incredibly diverse and encompass most of what we see across our species?  For instance would it be likely to find sperm cells that could result in extreme height, intelligence, different skin colour,etc even if the father didn't have any of those genes in their DNA, but a sperm cell did due to mutations?


texts: How are fragments isolated during shotgun Sanger sequencing?

texts:
For a large genome (say millions of base pairs) -- we split the genome into fragments < 1000bp that are sequenced and can then be put back together computationally.

My understanding is you use some sort of shearing technique to get the DNA into fragments as in: https://en.wikipedia.org/wiki/DNA_fragmentation

Now you have a vat full of random fragments -- how do you sanger sequence these?

From what I can tell if you took the solution with the sheared DNA and ran sanger sequencing you'd get a bunch mixed of fragments mixed together resulting in a lot of noise ... you'd basically get all the runs averaged together. Don't you need to isolate each fragment before running Sanger sequencing?

How is this done?


texts:
I'm confused on what a triglyceride is, from what my text book it says its a type of gylercide, then from a website it said

  Glycerides can be subdivided into two categories. The first group, the neutral glycerides are nonionic and nonpolar. The second group, the phosphoglycerides contain a polar region, the phosphoryl group.

Which makes triglyceride not a directly under a glyceride but under one of these groups. Then it says

  Esterification may occur at one, two or all three positions producing monoglycerides (monoacylglycerols), diglycerides (diacylglycerols), or triglycerides (triacylglycerols). The most prevalent and most important are the triglycerides.

So does that mean that triglyceride can be produced by either of the two groups phosphoglycerides and neutral glycerides. And if that's correct then how are monoglycerides and diglycerides produced.

Source


texts: toxin determination and treatment of wild water

texts:
I am writing an article on the treatment of wild water from a wilderness survival angle. I have come across the term "toxin" and am finding it hard to produce a determination and treatment strategy.

It is first difficult to advise if a water source contains toxins, other than the presence of algal blooms. For example, a lake had blue-green algae. I understand that the associated toxin is produced by the cyanobacteria, but not the bacteria itself.

Pathogen treatment would be boiling or if available, chemicals such as iodine, chlorine or chlorine dioxide. Chemically contaminated water would require distilling.

I don't know if I can treat water containing toxins at all without distilling it or if there are different strategies for different toxins.


texts:
At least, why don't all animals produce no more heat than the tiny amount that's a byproduct of walking or a bonobo climbing up a vine when the outside temperature is above 0°C? They won't freeze anyway.

After all, the amount of food controls the population size at whatever size makes each individual have just enough food, so shouldn't those with a lower energy demand be more likely to get enough food to rear more children? Shouldn't mutations that make a warm blooded animal able to thrive with a lower core temperature and produce less heat be selected for because there's more likely to get enough food to rear more children?

Also, shouldn't cheetahs evolve to produce extremely little heat in the day during rest even on not very hot days so they will be less hot and can chase their prey for longer? Have they already evolved that way?

If a species did evolve to produce less heat, would that also evolve to walk slower because it takes a lower speed to minimize the energy burnt per distance because they're producing less heat? I know there there will be a nonzero speed that minimizes the absolute minimum possible energy burnt per distance possible to evolve for that speed and a lower speed will actually increase the energy burnt per distance because the animal is walking for a longer time but the rate of energy burnt per time varies less rapidly with speed at such low speeds because of the energy burnt to fight against gravity.


texts: Was Raymond Gosling supervised by Rosalind Franklin?

texts:
The story of how the structure of DNA was deduced is fairly complicated and controversial, but most parties agree that a key pieces of data was "Photo 51", an X-ray diffraction image of DNA taken by Raymond Gosling in May 1952 (or possibly other similar images taken at the time as part of the same study).
Ray Gosling, who took the photo, was a doctoral student at the time. The Wikipedia page for the photo indicates that he was supervised by Rosalind Franklin, at least for a while:

James Watson was shown the photo by Maurice Wilkins without Rosalind
Franklin's approval or knowledge (although by this time Gosling had
returned to the supervision of Wilkins).

One controversy in the story is that the photo was shown to Watson and Crick without Franklin's knowledge or permission, which should have been sought first as she was his supervisor.
However, this article discussing a 2015 play about the issue (called Photo 51) includes an explanation by Professor Tony North, who was also supervised by Wilkins and shared equipment with Wilkins and Franklin, that:

Wilkins had to know what Gosling was doing, as he rather than Franklin
was his PhD supervisor. Franklin was ineligible for the role because
she did not have a formal university position, but a personal research
fellowship, Professor North said.
“The result is that Maurice had every right to know what Raymond had
been doing and what results he had achieved, so that he had a right to
see photo 51 without seeking Rosalind’s permission,” he said.

A quote from a primary source seems more credible. I also know from experience that other lab members often play a substantial role in training or supervising doctoral students without necessarily having a formal role in their supervision (i.e. being registered as a supervisor).
Was Rosalind Franklin, at any point, formally supervising Raymond Gosling's doctorate?


texts: Apple-seed-sized black bug, not very leggy - (Canada)

texts:
Can anyone identify this bug:

I'm in Toronto (Canada), 9th floor of a highrise building.  Most of the apartment is wall-to-wall carpeting, though the kitchen, entrance, and washroom are tiled.


texts: How to calculate the effective population size ($N_e$) with overlapping generations?

texts:
From this Source: If generations are overlapping, then the effective population size $N_e$ does not equal the population size $N$.

I know mathematical formulations in order to find the effective population size $N_e$ when the sex-ratio is biased $\left(N_e = \frac{4N_mN_f}{N_m+N_f}\right)$ or when the population size varies cyclically through time $\left(N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}\right)$.

What is the effective population size in a population with overlapping generations?


texts: Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?

texts:
I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription.

Does this mean no new proteins are made during what can be 20% of a cell's life?  How does the cell survive?


texts: Why doesn't glucagon promote glycogenolysis in muscle?

texts: Insulin stimulates glycogenesis in both liver and in muscles. Epinephrine stimulates glycogenolysis in both liver and muscles. But glucagon stimulates glycogenolysis in liver only.  Why is this so?


texts: How exactly does sensory substitution work?

texts:
Sensory substitution, when one of sensory modality changes into another sensory modality to help someone restore the ability to perceive defective sensory using a working sensory modality. For example, blind people who have improvements in their other senses like auditory system or olfactory system compared to normal people. Or deaf person who have enhanced vision ability than normal people.

Questions :

Does this work the same way as Alternative Sensation ?
Is there any pattern of which senses will probably improve according to which kind of senses someone's lacking ?
Is there actually any method to train which senses someone would like to improve ?


texts: Sex biased gene expression in the X chromosome

texts:
It has been shown that the X chromosome is frequently enriched for female biased genes, and has a deficit of male biased genes. For example in this paper, and this one.

However, I'm struggling to find papers which test the general distribution sex-biased genes. I am trying to find out if the X is enriched for sex biased genes, e.g. if the X hosts 20% of all protein coding genes, it would be enriched if it carried 30% of all sex-biased genes.

Are there any such studies?

I think I found an answer tucked in the methods section at the back of the Allen paper where 15% of sex-biased genes were X-linked, I'd suggest this means that 15.55% ($100 \times (\frac{1075}{1075 + 4938 + 4323})$) of sex-biased genes are X-linked - other examples are still sought:

  "Genes associated with chromosomes 2 (4,323 genes, 37%), 3 (4,938
  genes, 43%), and X (1,705 genes, 15%) were used in the analysis; these
  chromosomes accounted for 10,967 (95%) of the genes... a further 547
  (4.7%) of the genes ... were omitted"


texts: Criteria for compound action potential thresholds

texts: As opposed to action potential thresholds (which are binary yes/no events), electrophysiological thresholds of compound action potentials are arbitrary. Mostly a certain noise level is picked and when the neural signal crosses this 'threshold' it is said to be 'above-threshold'. I have come across various definitions of this threshold, such as SD-based values (2xSD, 4xSD etc), 'visual' thresholds (a bit iffy from my point of view) among other things. Is there a rule of thumb as to define threshold? Alternatively, a review article, book chapter, or a primary research article with considerable impact explicitly dealing with this matter would be very helpful.


texts: Speciation and Phylogeny of Lactobacillus

texts:
The lactobacillus, also called Döderlein's bacillus is a genus of facultative aerobic bacteria. There are several species such as Lactobacillus acidophillus and Lactobacillus reuteri.

I have several questions, all linked, for the concern of speciation of bacteria species used for lactic fermentation by humans.

Are all species that are used for cheese and yoghurt fermentation part of the genus Lactobacillus?
Do all species used for cheese and yoghurt fermentation form a monophyletic clade?
Did the speciation of this clade occurr before or after the use of these bacteria by humans?
What was the ecological niche of the ancestor(s) before humans used them for cheese and yoghurt?


texts: Very high magnification, size of a very small ant. Found in Menorca, spain


texts:
DNA holds genetic information and holds the key to the evolution of living organisms. Transcription and translation mechanisms enable living cells to process information encoded in DNA. To that end, transcription and translation are fundamental mechanisms needed to enable the evolution of organisms. Molecular machines (enzymes) carry out these mechanisms by reading the information in DNA and using it to construct proteins.

Did the first living cell contain the machinery needed for translation and transcription? or  Did they evolve over time?

EDIT: Edited the question to narrow the scope.


texts: How to determine if two mutations in a gene are on the same or different alleles?

texts:
I would like to know, except a familial study, is there another way to determine if a mutation/variation is cis or trans (i.e. on the same or different alleles)? For example by sequencing technique or other molecular biology procedure.

CIS               TRANS

+  +              +  +
|  |              |  |
A  |              A  |
|  |              |  |
B  |              |  B
|  |              |  |
+  +              +  +

Thanks


texts: Identity by descent among unrelated individuals

texts: I was reading a couple of papers which talk about IBD (Identity by descent) among unrelated individuals (for eg. http://www.pnas.org/content/109/4/1193.long). However they do not seem to clearly define what they mean there. I was wondering how IBD is defined in such a context. I'd appreciate any help (especially suggested references to look this up).


texts: Why is gastrin not acing paracrine manner primarily, when it acts mainly on cells nearby its release?

texts: Gastrin is released by G cells and stimulates Parietal cells to secrete hydrochloric acid. Why is it not acting in a paracrine fashion instead of endocrine?


texts: What is the second phase of photosynthesis?

texts:
I really want to know what the second phase of photosynthesis (in the dark) is. I have a fair understanding of the first cycle where molecular oxygen is generated under the influence of light, but I don't understand the second cycle which can take place in the dark. It would greatly help to have a graphic of the second phase of photosynthesis.

Note: it is not for my homework, but for my own understanding. My textbook doesn't explain things very well.


texts:
I notice that certain (wild) flowers have the same colour, although they are not closely related. For example, the yellows of the dandelion (Taraxacum) and the buttercup (Ranunculus) are, at least to my eyes, identical (my observations are in the Netherlands).

I know that the colour is intended to attract insects; is this parallel evolution or are there certain biochemicals which provide colour and are easy for the plant to synthesize? Or something else?
Edit: I used the buttercup and dandelion because that was the first pair I found physically close enough for a photo; the cowslip, celandine and charlock mustard are all (to my eyes) the same yellow. I have also seen similar blues, reds and violets, and shall try to collect examples next time I go cycling on the dyke.
When I look at colour tables like https://en.wikipedia.org/wiki/Web_colors#Extended_colors I see numerous colours which I do not recall ever seeing in wild flowers.
Edit2: I retract my remarks about blues, reds and violets; it's hard to judge colours when cycling past and when I pluck the flowers and compare directly there's a definite difference, for example:

However I still find the yellows very similar; here the charlock (left) is lighter but the buttercup, celandine and dandelion look identical to my eyes.

Comments seem to suggest a biochemical cause; can anyone confirm (or disprove) it?


texts: Reason for seeing grid-like patterns when strobing a solid black-white image?

texts:
I was trying to do some stimulation for SSVEPs by strobing a solid black square and a solid white square. Weird thing was, I ended up seeing weird grid like patterns that looked like this, always of the inverted color.

  _        _
 / \      / \
 | |      | |
 \ / _--_ \ / _--_
  O |    | O |    |
 / \ ---- / \ ----
 | |      | |
 \_/ _--_ \_/ _--_
  O |    | O |    |
     ----     ----

And that sort of pattern repeats itself around the strobing area (where the convex areas are always of opposite color than the current color on the screen).

I'm inclined to think about light and dark adaptation, but it still seems weird that it'd be shaped like that in particular. So... What's going on?

EDIT: Additional info that I should've realized was necessary >_<:

Strobe area: ~14x10.5 cm
Strobe frequency: 2 frames/half-cycle @ Laptop Vsync (~60 Hz) ~ 15 Hz
Viewing distance: ~55-60 cm and shorter.

Screen is backlit. Not sure about brightness metrics.

The pattern isn't offset to one corner like I've drawn, it's more evenly spaced. Horizontal bars are more accentuated than vertical ones (and the dark-on-light phenomenon is more visible for me than the light-on-dark). Moving in closer increases the visibility of the effect (I guess that was to be expected), and changes the number of times the pattern repeats across the screen (but it's hard to count them). The larger the area in my visual field the more times the pattern repeats. I'd say that at about 60 cm it's just one box, but with my nose a handful of cm away from the screen (it's hard to measure by myself >_<), there are maybe three in the horizontal direction... Or at least tens of them (increasingly large as it gets toward the center in both dimensions), depending on how focused in on the screen I am.

It's really really hard to count them.

I haven't had the chance to check with other people yet, but I'll try some time (this is just something I saw while working on a personal project).


texts: Summary statistic that can distinguish between migration from pop2 to pop1 vs. pop1 to pop2

texts:
Given two sister populations that diverged some time ago, say pop2 migrates to pop1 and breeds there, giving offspring with sequence segments similar to those from pop1 but not in pop2. There are stats to find how similar two populations are; for instane, mean dxy takes the average of number of pairwise sequence differences between the two sister populations. Say if there is no migration, mean dxy at a locus of length 10000 is 100. Then with migration, say mean dxy at that locus is 300. Detecting a dxy that's unlikely under the null hypothesis of no migration indicates migration and interbreeding occurred.

I've been thinking for a while on if there are summary statistics which can distinguish between migration from pop2 to pop1 vs. migration from pop1 to pop2 (assuming only one of these events occurs). Do such statistics exist? Without loss of generality assume pop2 members migrate to pop1. Then pop1 will have members that are more similar to pop2 compared to if no migration occurred, but pop2 will be as if no migration occurred.

If we run simulations of a population w/ no migration, we can expect to see some value of pi and # of segregating sites. These measurements may be different in pop1 when pop2 migrates into pop1; some members of pop1 will have SNPs that pop2 do not have, and thus there would be more genetic variation (higher pi and ss) in pop1 compared to its expected pi and ss under no migration. So dxy can say that there's some similarity between pop1 and pop2 that's not expected under null hypothesis, and then pi or ss can say which of the two has a higher genetic variation than expected. Can some statistic that depends on dxy and pi distinguish between migration from pop1 to pop2 vs migration from pop2 to pop1?


texts:
Simple terminology question:

Is there a hard boundary between in vitro and ex vivo?
Is there a hard boundary between in vivo and ex vivo?

Suppose a sensory neuron is electrically recorded in the following settings:

Surgically accessing through the animal's skin, and patch-clamped,
Tissue surrounding the neuron is almost separated, but still dangling from the larger part of the animal, and patch-clamped,
Same as above, but the slight dangling connection is cut,
The sensory neuron is isolated and put in an artificially oxygenated medium

The sensory neuron is assumed to have purely feedforward signal, and is perfectly healthy in all conditions. Which conditions, if any, are in vivo, in vitro, or ex vivo? (Feel free to propose better hypothetical experiments. I know this example is not the best.)

Am I the only one confused about these terminologies?


texts: In plant species' description, does the leaf length include the lamina and petiole, or only the lamina?

texts:
The description (partially pasted below) of Ramosmania rodriguesii in Verdcourt (1996) states that the leaves are up to 30 cm long. Does this length include both the lamina and petiole, or only the lamina?

Reference (source of above paragraph):
Verdcourt, B. (1996). Ramosmania rodriguesii Rubiaceae. Curtis's Botanical Magazine, 13(4), 204-209.


texts: Invading Bacteria are phagocytosed by phagocytes. Phagocytes are specialised white cells. But, if a non-phagocyte cells are infected with bacteria how those cells handle this situation? Do they succumb to the bacteria?


texts: Are there any DNA viruses with junk DNA in them?

texts: I know mimiviruses and pandoraviruses have orphan DNA - DNA that is not found in other species - but this is DNA that codes for proteins. I am not able to find out if they contain junk DNA. By junk I mean DNA that does not have ANY function at all. Sort of like the junk DNA in the human genome put there by retroviruses, DNA that just sits there, doing nothing, just going along for the ride.


texts: Relation/difference between metabolism and cellular organisation

texts: In the highlighted paragraph from NCERT textbook, they mention that cellular organisation is the defining property of life forms while metabolism without exception is also the defining property of life forms. My doubt is whether the term 'metabolism' also includes the metabolism reaction in vitro condition too or metabolism only means all the chemical reactions occuring in the cell excluding in vitro condition. If what I mean is true, does cellular organisation and metabolism both mean the same thing? But then again if both are the same thing, metabolism also should be the defining property of life forms, but it is not the case as mentioned by my textbook. So that means both metabolism and cellular organisation are different things. Is this right?


texts: How do I solve this problem related to specificity and sensitivity?

texts:
Consider an autosomal recessive disease with an incidence of 1/10,000 in
the general population of 100,000. Your best friend comes to you very
upset because he has just taken a screening test for this disease and gotten
a positive result. He is convinced he is a carrier, despite having no family
history of the disease. You try to reassure him, but he says, "Don't bother.
The Clinic said this test has 98% sensitivity and 90% specificity. With that
level of sensitivity, it must be correct!" What is the chance your friend is
NOT a carrier?

I have attempted it in this way:
The reason I used Hardy-Weinberg is because there isn't any other way to determine whether he is a carrier or  not.

Case 1: He is AA (double dominant). This has a 0.99^2 = 0.9801 chance. The chance that his result was positive is 1 - 0.90 = 0.1 since that is the chance that the specificity failed since specificity measures the chance of true negatives. Multiplying this gives us a 0.09801 probability of this case.

Case 2: He is Aa (heterozygous). This has a 2*0.99*0.01 = 0.0198 chance. Again his chance of a positive result should be 1 - 0.9 = 0.1. Multiplying this gives us 0.00198.

Case 3: He is aa (double recessive). This has a 0.01^2 = 0.0001 chance. The chance of getting a positive result is 0.98. Multiplying we get 0.000098.

Adding these up, I have 0.100088. We want the probability he is not a carrier, so 0.000098+0.09801 (cases 1 and 3) divided by 0.100088 (the total). This yields around 0.9802 or 98% chance, which isn't one of the choices. What am I doing wrong?


texts: What is the purpose of Prostaglandin F2-alpha and the Prostaglandin F receptor in the melatonin cell signaling pathway?

texts:
I've been doing a lot of research recently on the melatonin cell signaling pathway for an extra credit project at school. I've included an image in this post, which is a diagram of the MT1 pathway. It seems to be a fairly standard GPCR sequence. I can identify all of the elements depicted in the diagram, but unfortunately I don't understand why some of these elements are present at all.

The portion of this pathway that stands out to me the most is the presence of a Prostaglandin F receptor (FP) as well as the presence of Prostaglandin F2-alpha (PGF2α). From the research that I have done, I've gathered that PGF2α is a prostaglandin found naturally in the body that can been used as an abortifacient in medical applications. I have not found any research that covers exactly why these two elements are present in the MT1 pathway.

Here's what I know: the Gi beta-gamma complex (Gβγi) and the Gq alpha subunit (Gαq) both activate Phospholipase C (PLC), which in this reaction causes the hydrolysis of PIP2 to create IP3 and DAG. My current hypothesis is that FP carries PGF2α into the cell, and PGF2α helps to activate PLC in some way. Unfortunately, I haven't been able to find any information online supporting this. Has anybody done any research regarding this topic, and if so can you provide any insight? I really, really appreciate it.


texts: Any known values of density for spinal cord (pig or human)?

texts:
Need to know the density of spinal cord tissue to evaluate the shear modulus from ultrasound elastography (shear wave velocity) measurements, but need the density of the tissue to compute this.

I am a physicist by trade so unaware of whether white and gray matter have homogeneous properties in the CNS as a whole or whether they are different in the brain and spinal cord.

Could do with density (g cm^-3 or equivalent) of white matter, gray matter or of the cord as a whole.

Also if there are any sources so i can cite this this would be most useful.


texts: I am having confusing about treatment of phorpyria . I read it somewhere that for treating phopyria hemin and glucose is given IV . Please give me an easy explanation of it


texts: What does it mean for a chemical pathway to be conserved?

texts:
In many papers the MAPK pathway, (along with many others) is referred to as being conserved:

Example: "The mitogen-activated protein kinase (MAPK) cascades are ubiquitous in eukaryotic signal transduction, and these pathways are conserved in cells from yeast to mammals"

example 2 "The Hippo signaling pathway appears to be highly conserved."

What does it mean for a pathway to be conserved?


texts: Is it normal to see yeast cells stacked in the Z axis when counting yeast?

texts:
I just got started with yeast cell counting and was surprised to observe yeast cells that are at different z axis depths at 400x. That is, by adjusting the focus (not the x/y stage) I can make some cells go into view as others go out (there is some overlap in some cases but not always).

Is this normal? It means that I will have to count at probably 2 different depths which I haven't seen anyone else talk about. I had assumed everything would be visible at a single depth.

It is possible I did something wrong like not properly seating the cover slide. My filling technique, based on some videos I watched, was to breathe on the cover slide and the hemocytometer, place the cover slide on and slide it around a bit, and then touch the dropper to the edge of the slide to fill the chamber (I did not observe any obvious overflow/overfill).


texts: How do veins's valve pocket sinus tend to become hypoxic?

texts:
For context, this question relates to the formation of deep vein thrombosis as I read that hypoxemia in vein can trigger coagulation cascade and cause a thrombus to form in vein.

I read that vein's valve pocket sinus tend to become hypoxic due to vortical flow. The diagram I attached below has oxygen tension color coded with a gradient from red to blue; the darker the blue is, the greater the hypoxia.

However, how exactly does vortical flow have to do with hypoxemia in those regions? From my understanding, the lack of blood circulation in vein's valve pocket shouldn't affect the amount of O2 bound to the haemoglobin stucked in the vein's pocket? As veins are not permeable to O2 thus O2 can't escape into surrounding cells.

References:

Bovill EG, van der Vliet A. Venous valvular stasis-associated hypoxia and thrombosis: what is the link? Annu Rev Physiol. 2011;73:527–545. doi: 10.1146/annurev-physiol-012110-142305.

Mackman N. (2012). New insights into the mechanisms of venous thrombosis. The Journal of clinical investigation, 122(7), 2331–2336. doi:10.1172/JCI60229

https://www.jci.org/articles/view/60229


texts:
It's rather clear and commonsensical what the genetic code is, how it is inscribed (as a sequence of nucleotides in the DNA), what it means, and most of all: how it is decoded and works.

It's less clear and agreed upon what the histone code is, how it is inscribed, what it means, and how it works. But ideas about this seem to go into some apparent direction.

What's rather unclear to me is, what a "neural code" might be. (see "neural code" at Google Scholar)

What seems clear to me: The neural code is more of a temporal code, having to do with temporal frequencies, rhythmic patterns, and synchronicity (while the other two are more of spatial codes). Probably, it's a spatio-temporal code, but that's all. I completely miss a general picture of how a possible answer might look like.

  What is the actual and agreed upon look on the concept of a neural code?

Side question: Which other (maybe obvious) biological codes I did not come across ("something inscribed/encrypted/encoded to be described/decrypted/decoded")?


texts: What is Genome wide analysis and Locus specific analysis

texts: I am reading some articles on genetic variations and I see there are two types of analysis one is genome wide genetic variation analysis and second one is locus specific genetic variation analysis. I don't understand what these two, genome wide and locus specific analysis mean and what is the difference between these two analysis or why do we need both type of analysis?


texts: Why do negative ions flow into a cell in an inhibitory synapse, even though a neuron has a negative resting potential?

texts:
In my spare time I have been reading an introductory Psychology textbook and this question came to my mind after reading about action potentials.  I have no previous knowledge in chemistry so if I do need some sort of other knowledge I would appreciate if I could be told what I need to learn in order to understand the physiology of the nervous system better. So Why do negative ions come into a cell during an inhibitory synapse even though a neuron has a negative charged resting potential?

I understand this question might be extremely vague and impossible to answer without previous knowledge of the physiology of the nervous system. Any help would be greatly appreciated.


texts: Why is the hippocampus considered to be a cortical structure but not the amygdala?

texts:
I'm having some trouble understanding the anatomical differences that classify the hippocampus as a cortical structure but not the amygdala. I have included the screenshot of a diagram from Gray's Clinical Neuroanatomy.

Medial aspect of the left cerebral hemisphere demonstrating some limbic structures (yellow). The anterior nuclear group of the thalamus is coloured orange, and the rest of the thalamus is magenta. The approximate position of the brain stem is outlined in a heavy interrupted line.


texts: Are non-lytic viruses reproducing themselves in the host cell?

texts: Non lytic viruses can cause cancers like the HPV. But aren't they reproducing themselves as they don't ruptures the cell. Or are they just not reproduced in enough numbers so that the cell keeps working. But if they stays in the cell and/or not reproducing how are other cells infected to cause a tumor? Just by normal division or within a stem cell?


texts: Term of the type xxx-troph for a compound not used by an organism

texts:
A prototroph for compound X can make it
A bradytroph grows faster if X is scavenged
An auxotroph needs to scavenge X
A hyperauxotroph lacks both the biosynthetic pathway and the transporters for X

However, I cannot find the term for when the metabolism is rerouted to not need that compound. A term exists and it isn't with an obvious prefix like para, exo, ecto, juxta or similar, but that is as much as I recall: I cannot recall it or where I read it. Has anyone ever encountered said term?