texts: Is there a practical upper limit to ploidy?

texts:
In my AP Biology class, we were discussing polyploidy, specifically, its deleterious nature in mammals and its prevalence in plants.  We also learned that commercial crops, especially fruit, are often selectively bred for high magnitudes of ploidy.

Fascinated, I googled the subject and ended up reviewing the Wikipedia article to get a little more background info, where I read this:

  Polytene chromosomes of plants and fruit flies can be 1024-ploid.[44][45] Ploidy of systems such as the salivary gland, elaiosome, endosperm, and trophoblast can exceed this, up to 1048576-ploid in the silk glands of the commercial silkworm Bombyx mori.[20]

From this, I have three questions. The first is, is there an upper limit to ploidy that can occur in nature? I understand that polyploids can "lose" ploidy by haploidisation, but is this as common as increases in ploidy? I believe that the answer to this would imply the answer to my first question, however, I could not find much literature in the way of this area.

My second question is, is there an upper limit to synthetically induced polyploidy? Is the Bombyx mori's ploidy arbitrary, or is it at the max that technology can produce? Can it's ploidy be expanded further?

Lastly, does arbitrarily high ploidy serve any purpose in agriculture or science? Is there a threshold where utility is no longer maximized?

Thank you in advance.


texts: How exactly are genes swapped during the process of recombination?

texts:
I am studying recombination in Meiosis and the idea of crossing over doesn't make sense. My understanding is that 46 chromosomes in our germ-cell (23 from mom + 23 from dad) line up next to each other and recombine (swap areas of DNA). My confusion is that, since, for example, Chromosome 1 from mom is same as Chromosome 1 from dad, how is swapping areas of DNA going to exchange any information. Brown eye gene from dad would just be swapped with brown eye gene from mom. How will have any affect on the offspring? OR is it that if mom has brown eyes, the brown eye color gene in mom has something attached to it?
OR is my understanding of genes incorrect and not every nucleus has all possible genes? (except the difference of X and Y chromosome.)?


texts:
In the literature I have found that action potentials behave differently when gravity is changed (cannot access fully).

Action potential properties are gravity dependent.
http://link.springer.com/article/10.1007/BF02870977

Are there any ion channels in the neurons that are more or less likely to be sensitive to changes in gravity?


texts: Is there a reason why human eyesight and plants make use of the same wavelength of light?

texts:
The accepted range for the wavelengths of light that the human eye can detect is roughly between 400nm and 700nm.  Is it a co-incidence that these wavelengths are identical to those in the  Photosynthetically Active Radiation (PAR) range (the wavelength of light used for normal photosynthesis)?

Alternatively is there something special about photons with those energy levels that is leading to stabilising selection in multiple species as diverse as humans and plants?


texts: What Is This Tactic Called? (Banishing Adolescent Females)

texts:
I was watching a documentary about Meerkats the other day and one thing that stuck out to me was how the Mother of a family will banish her daughters once they reach adolescence. If the daughters try to return to the family then the mother will viciously attack said daughter, it's quite sad.

Anyway, the reason for this makes sense (in terms of evolution) because if the adolescent Meerkat were to fall pregnant, she would need more food & support from the clan, thus jeopardizing the original Mother's chance of survival.

I think this is an example of animal behavior/population control where there can only be 1 mature female in the group, like there is with bees. Am I correct in assuming this? Do all animals show this behavior for the same reasons? Also is there a general term that can be applied to this phenomenon?


texts:
Cells come in all sorts of sizes. How do they regulate their cell size to the point where similar cell types have a fairly mono-disperse size distribution?

Reasked from http://www.quora.com/How-Does-a-Cell-Know-Its-Size


texts: How is mRNA directed out of the nucleus to its ultimate cytoplasmic location?

texts:
In the process of translation, I learnt that following formation the mRNA must exit the nucleus through a nuclear pore and attach to a ribosome.

My question is how does mRNA navigate itself out of this pore, and find itself a ribosome to bind to?
Is this a process of diffusion or is there any other mechanism involved?


texts:
I am able to calculate frequencies for allele and genotype, but I don't understand how to tell if the population is at equilibrium. Or how to determine how many generations of random mating would be needed to reach HW equilibrium. I thought the proportions didn't change from generation to generation?

number of individuals: TT-200, Tc-200, cc-600
observed frequencies : TT-0.2, Tc-0.2, cc-0.6
HW frequencies       : TT-0.05, Tc-0.35, cc-0.60

p=.33, q=.77


texts: Would humans eventually evolve to fight off fatal diseases if we didn't treat/vaccinate for them?

texts:
I am definitely pro vaccination, and the question is a bit morbid because people would die, but assuming that we didn't treat or vaccinate people for fatal diseases such as Ebola or the black death, would the surviving people pass along a trait that eventually would lead to near immunity for that disease?

Are there any examples of diseases that humans "contract" but they are immune to? Or any examples of immunity through human evolution?

What about in animals? Are there diseases that have been naturally eradicated?


texts: Whenever I read or learn about prediction tools or aligners or motif detectors, I also hear that they are lacking in something called biological intuition. But I haven't been able to find a solid definition of what that is. Can someone please explain?


texts: If wolves (or foxes) are fitter than rabbits, why rabbits have not become extinct?

texts:
I do not pretend to "demolish" the Darwinian theory of biological evolution and the "survival of the fittest", that's far from my intention.
I have this doubt because of the fact that humanity, as Homo sapiens sapiens, extinguished the Homo sapiens neanderthalensis because we were fitter to survive.

Please consider this question as if the humanity hadn't appeared yet (because we have domesticated rabbits).

Thanks in advance.

Edit: I have assumed that wolves and rabbits (or hares, maybe) live in the same ecosystem.


texts: What is an adjective that describes the property of conferring fitness?

texts:
I find it wordy to repeat

  trait X is a trait that confers fitness.

I wonder if I can instead write

  trait X is useful.

If not, is there an adjective that describes this property of conferring fitness?


texts: Is there a GPS super tiny for passerine birds?

texts:
I wonder if there is a really tiny GPS device that can be mounted on passerine birds (or circa 10 grams birds) without affecting their flight. This web site shows information for bat’s GPS. But it also only last for 24 hours. I wonder if there is some lightweight and long battery life about 2–5 grams. I found this also, but haven’t found if it contains a long battery life.

Is there a study on GPS tracking small birds?


texts: Blood draw from the elderly or those with tiny veins

texts:
A lot of people have very small veins making it next to impossible to draw blood.

Would a nitroglycerin tablet (or some other vasodilator) before drawing blood help to enlarge veins?


texts:
The cancer literature often refers to the deletion of certain sections of a chromosome (e.g. "17p del" or "Del(17p)" for the deletion of chromosome 17's p-arm.)
Does this mean both alleles of the chromosome were deleted for the specified cytoband (i.e., copy number analysis would show zero in this case)? Or does it mean one of the alleles was deleted, and thus one remains (copy number analysis would show a copy number of 1 in this case)?
Thanks


texts: What determines if a small protein / large peptide is immunogenic?

texts:
I'm wondering if there is some threshold in size or a specific structural property that determines if a small protein or large peptide would cause an immune reaction.

Context: there are a number of drugs being developed based on antibody mimetics (small protein scaffolds with stable folding).  These tend to have a size around 50-60 aminoacids (6-7 kD).  These tend to be much easier to design than human / humanized antibodies.  However, it is not uncommon for these to cause anaphylaxis, especially if administered repeatedly.  It may be good to somehow design a version of a small antibody mimetic which itself does not cause an immune reaction.

Are peptides around 10-20 aminoacids typically immunogenic?  What about slightly larger ones up to 30 aminoacids?  Does it matter if they have a stable secondary or tertiary structure?


texts: What is holding the immune system back to not attack human body cells?

texts: There are plenty of loose proteins or other macromolecules free floating everywhere. Why wouldn't they be seized and presented to T cell to trigger an immune response? Does each of these molecules have a signature portion? Or do the presenter cells have some sort of friendly molecule database? Would a normal person's immune system ever possibly generate something like Tocilizumab, i.e. an antibody targeting a normal receptor in most cells?


texts: "producer cell line" vs. "host cell line" in biopharmacology

texts:
I'm translating a text that describes the creation and testing of a cell line that produces a drug (a protein) and also procedures for creation and maintenance of cell banks.

Example sentence:

  Assessment of the morphology, viability, and cell concentration of the producer cell line

I wonder if I can use host cell line instead of producer cell line, or "host cell line" would mean "a line that has not yet been subjected to transformation using viral vectors" (a line that cannot yet produce the needed drug; a "pure" line). Just making sure.


texts: How to wash the column during protein purification with GST tag?

texts:
I have been working with GST tagged proteins for the last 4 years and after loading the cell lysate into the column I was washing it with 20-30 column volumes of PBS and sometimes my proteins were eluted very pure sometimes with a lot of impurities.

A few times I tried washing with NaCl gradient (0-400 mM) but later decided not to do that because it may denature the protein and some of my proteins may not refold.

What do you suggest for washing step?

Note: I don't have any UV detector to see the washouts/flowthroughs/elutions.


texts: Are humans hardwired to continue gathering resources after the costs outweigh the benefits?

texts:
An animal will stop foraging in a berry bush if the perceived cost of searching for berries remaining is greater than the cost of finding another bush which isn't as picked over. People do the same thing on websites. We'll stay on a website searching for our information berry if we feel it costs less than jumping to another website bush.

If we had significant resources such that the cost of predatory/foraging behavior out-weighed the energy benefit from gaining more resources, would we stop? There seems to be a biological and cultural drive to keep getting more stuff. As people, could we ever reach a point where we're satisfied? The logic says yes, but common sense says we're hardwired to feel compelled to never stop gathering resources.


texts: Alfred Jost's rabbit experiment: how did he actually do it?

texts:
I was watching a Crash Course on Biology YouTube video by Hank Green: Great Glands - Your Endocrine System.  Hank humorously describes a sex determination experiment by Alfred Jost as follows (beginning at time 9.17 in the video):

So, he, ah, very carefully... very, very carefully (and this is a little disturbing) removed bunny embryos from their mother, and then, also very carefully, removed the part that would become the ovaries or the testes from the bunny embryos.  And then, also very carefully, he put the embryos back in the momma rabbit.
What Jost found, after the bunnies were born, was that the ones that he performed the surgery on turned out to be girls.  So, in the absence of gonads, and therefore hormones that specifically instructed the development of testes and the growth of a pee-pee and a deep bunny voice, he discovered that the default setting for mammalian embryos is "make it female".

Q: How did Alfred Jost actually perform this experiment?
Essentially I'm after a less superficial description of how Jost implemented this experiment in practice.
I did a bit of Googling; what I found was consistent with Hank's description, but still omits a description of how Jost excised rabbit embryo gonads (instead just asserting that he did it).


texts: I have a gene of of interest that I would like to compare between homologues. How does one go about finding a gene from known coding sequences across phyla? Afterwards I imagine I could do a Clustal sequence alignment to see how the sequences match.


texts: We all carry two copies of each gene (outside of male sex chromosomes).  If the two differ from each other often one is dominant and one recessive.  How does this mechanism work on a molecular level?  What mechanism determines which gene gets expressed?


texts: Book on the history of Darwin's discoveries and development of his theory

texts:
This question is a book request. I am wondering if there are any books with these elements:

Tells the history of Darwin's discoveries.
Captures Darwin's changing views of the origins of species, because of his discoveries and his thinking on the subject.
Is a modern text but incorporates some of Darwin's writings (e.g. from the Voyage of the Beagle, etc).

Note: I am not asking for a book that is just explaining the process of natural selection, rather I am looking for a historical book about Darwin's discoveries and the inception and development  and eventually his publication of his theory of natural selection.


texts: Do human somatic cells have 46 chromosomes all the time?

texts:
As far as I know, a human somatic cell has the cell cycle:

Interphase and Replication (mitosis). In interphase, the cell has 2 growth phases (G1 + G2) and a synthesis one (S phase being in between G1 and G2). After G2 ends, the cell will start entering mitosis.

Until the S phase, the cell has only 23 chromosomes right? And only after the DNA has duplicated the number of chromosomes doubles (to 46).

Please correct me if I am wrong? And will the cell in the G0 phase (after duplication and before G1) have 23 or 46 chromosomes?


texts: I did Laemmli-SDS-PAGE for my Ammonium sulphate precipitate but I had very weak band and have very weird part at the end of gel. Please help me to solve that problem. Thanks


texts: What Role Antagonists Play in the Study of Drugs?

texts:
I am pretty unfamiliar to pharmacology. I'm doing a research on drug abuse, particularly opioids' mechanism of action. I encountered several times evidences that come from studies using antagonists especially naloxone that are to prove something is 'a specific opioid effect':

  Opioid-induced miosis in the human ... This action is a specific
  opioid effect as demonstrated by its antagonism by naloxone.

I wanted to know the rationale behind these kind of conclusions. Also an elaboration on the role antagonists play in drug research will be appreciated.


texts: Examples of genes involved in plastic responses

texts:
Adaptive plasticity involves sensing the environment and responding adaptively to it. Intuitively, I would think that this process may ask for a more or less complex genetic machinery of regulation of gene expression.

Can you give me examples of genes and genetic pathways that are famous for their role in adaptive plastic response?


texts: Can we develop a nucleos(t)ide analogue to cure rabies?

texts: Nucleos(t)ide analogues have been successfully used to treat HIV, HBV and HCV. Since rabies virus is also a RNA virus that uses RdRp to replicate. If we develop an nucleos(t)ide against its RdRp, will it be able to save rabies victims? What would be potential obstacles?


texts: How much pollen is needed to pollinate a flower?

texts:
Assuming 100% of the pollen gets delivered to exactly the locations it needs to pollinate a female flower, how much pollen is needed to pollinate a flower? If it's more than one unit of pollen, what, if anything, prevents more than one plant's pollen from pollinating the flower?

If we need an example plant to answer this question, let's assume zucchini. For instance, if you plant a zucchini in the middle of a spaghetti squash and an orange-fleshed squash, is there any likelihood at all that you'll get a single zucchini pollinated by both in one generation (such that the next generation of cross-pollinated zucchini would be both stringy and orange-fleshed instead of just one or the other)?


texts: Exocytosis of mast cell secretory granules

texts:
I've been doing a bit of reading about mast cell degranulation and have become thoroughly lost while trying to understand how the secretory granules are actually secreted.

I understand that there are many ways in which mast cells can be stimulated to degranulate, but I have been focusing on the example of IgE bound to FcεRI receptors. I believe I'm right in saying that antigen binding causes cross-linking of FcεRI receptors (since the antigen epitopes bind with the IgE paratopes and the IgE antibodies are themselves bound to the FcεRI receptors.) This recruits Lyn which phosphorylates ITAM motifs on the β and γ chains of the FcεRI receptors. This recruits Syk which is phosphorylated and activates LAT. This phosphorylates PLCγ which catalyzes the breakdown of PIP2 into IP3 and DAG.

All of this leads to the activation of PKC. I understand that PKC is (at least in part) responsible for the exoctyosis of SG but my question is by what means? Wikipedia, KEGG and this handy resource are all very cursory, whereas the academic papers which google turns up are way over my head.

So, if I might, what is it that PKC does and, in general, how are the secretory granules transferred from within the cell to the plasma membrane and out into the environment around the cell?


texts: i'd like to know the name of this flower.


texts: What is the max amount of photons per second of the rods and cones in our eyes?

texts:
The title says it all. I just cannot find any information about this - I have tried for so long now. Therefore, I figured that I could reach out to some clever guys in this forum for help instead:)

Also, if it is possible, I would love a link to read more about it.


texts: What is the efficacy of an Ebola antibody response

texts:
There is contradictory (~?) evidence in the literature that antibody responses against Ebola are effective in clearing the virus and protecting the patient. Some time ago, I wrote a bit about the literature on this in my blog (which you can find here) that one of the primary problems faced in developing an effective antibody response against Ebola is that antibodies may actually be hijacked by the virus in order to mediate entry (Takada et al).
My question is, has this observation been supported? And, if so, how do more recent vaccines address / avoid this problem?


texts: What is the difference between average and monoisotopic mass calculations of peptides?

texts:
I often have to calculate the mass of peptide sequences using calculators such as here.

I have the option of calculating the average and monoisotopic mass, but what is the difference?


texts: What is the spacing between stop codon and transcription terminator?

texts: When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?


texts: Why is this spider wound in such a dense web?

texts:
I saw this thing yesterday on my window curtain, and I've been wondering what this is.
It looks like a dense network of spider web, and the spider inside it is visible. I thought the spider was dead, but I saw the spider making very small movements inside it. So, that made me more curious to know what it is.


texts:
Why are fertilizers with polonium 210 used when growing tobacco?

I'm thinking of pursuing a science fair in which I create my own fertilizer for tobacco that doesn't contain polonium or lead. However, I need more background research. Does anyone know why these fertilizers are used?


texts: Does SARS-CoV-2 kill its host cell or not?

texts:
Wikipedia says that

Initial spike protein priming by transmembrane protease, serine 2 (TMPRSS2) is essential for entry of SARS-CoV-2.After a SARS-CoV-2 virion attaches to a target cell, the cell's protease TMPRSS2 cuts open the spike protein of the virus, exposing a fusion peptide in the S2 subunit, and the host receptor ACE2. After fusion, an endosome forms around the virion, separating it from the rest of the host cell. The virion escapes when the pH of the endosome drops or when cathepsin, a host cysteine protease, cleaves it. The virion then releases RNA into the cell and forces the cell to produce and disseminate copies of the virus, which infect more cells

What happens next? Can this cell stop to produce the virus and start to divide ?
For example this article (SARS-CoV-2 RNA reverse - transcribed and integrated into the human genome) suggests that virus also inserts its portion into DNA so the person can have PCR-positive tests even if "no replication - competent virus was isolated or spread from these PCR-positive patients".


texts: I just saw this bird outside my apartment. Anyone know what it is? (Texas, US)

texts:
Saw this bird outside my apartment in College Station, Texas  and have never seen anything like it before!
It is about the size of a hand.


texts: How do I tell if the mosquitos in my New York City apartment can carry Zika?

texts:
The species that carries Zika, A. aegypti, is unlikely to be found in New York. However, the related species A. albopictus is prevalent and quite concerning. So this question is focusing on A. albopictus (if I may editorialize I would suggest leaving the title closer to the real question of interest, and disambiguating the species as the first step in resolving it).

According to the CDC

  Zika virus is transmitted to people primarily through the bite of an infected Aedes species mosquito (A. aegypti and A. albopictus).

I understand New York has IIRC the aegypti species and Zika has appeared.

My apartment gets mosquitos rather randomly every couple months. Understandably I want to figure out how much effort I should put into preventing or getting rid of them. I can describe their behavior here and maybe that's enough information. If not, do I need to get out a magnifying glass or sequence DNA? (Which I did once in college but I wasn't very good at it).

Their behavior:

I get "bursts" of them at random times in the year - more in the warm months but also in November. We had a warm winter but this still surprised me.
They seem to bite me at night but I've never had a mosquito bite on me. I've had mosquito bites from being bitten by mosquitos before, so unless I've developed a resistance to that in the last few years, that's strange.
I haven't found any evidence of standing water nearby. They don't hover around my sinks or toilets. I read once the Zika carrying strain is on the hardy side and can live off of moisture in walls so this is troubling.

If you're curious my preferred life hack is keeping my living room slightly warmer than my bedroom. And also, you know, killing all of them.

So, are these behavior traits useful? Can I identify them as opposed to other New York inhabiting mosquitos? Is a DNA test necessary?


texts: How exactly do microfillaments change the cell membrane's shape?

texts:
I understand that they are concentrated under cell membrane and can contract, but the details aren't very clear. How do they attach to membrane, and in what direction do they pull? Do they draw two points of cell membrane together or what?
Also, actin in muscles doesn't just contract itself but anchors to myosin and "crawls" along it: it's not actin that contracts, but the entire actin-myosin complex. Does something similar happen in microfillaments?


texts: What do the signs +/+ +/- mean in this image?

texts: I don't understand what this graph is supposed to explain, especially what the signs +/+ or -/- mean. I just know it characterises some rats.


texts: Is there a maximum testosterone limit, or is it more accurate to say use?

texts:
I am constantly amazed at how we cannot differentiate between male and female.

The International Olympic committee sets the target testosterone at 5 nmol per deciliter with active androgen receptors.

What are active androgen receptors? Do they count sex hormone binding globulin (SHBG) bound Testosterone, especially in the brain? If I was serious about asking someone who would I ask ?


texts: Why does pharynx have an internal longitudinal muscle layer and external circular muscle layer, while oesophagus and the rest of gastrointestinal tract have inner circular and outer longitudinal muscle layer?


texts: Genetic Drift: Models, assumptions and empirical observations

texts:
There two main mathematical models to describe the process of genetic drift are Moran model and Wright-Fisher model.

My questions concern the assumptions of these models, the existence of other models of genetic drift, explanation of the advantage/disadvantage of these models and the empirical results supporting one or another model.

What are the assumptions of each of these models?

stable population size?
iteroparous/semelparous
what about the probability density function of the fitness?
…?

What advantage/disadvantage do these models have? Or I should say, to which population do these various model applies?
What kind of biological population has been empirically shown to fit better one model rather than another one? What are the key experiments to test the validity of these models?

Please do not hesitate to post even if you answer only partially to the questions! Thank you!


texts: Identification - What kind of animal leaves these tracks?

texts:
I live in the suburbs of Washington DC where it recently snowed. I was admiring all of the tracks left behind by wildlife of all kinds when I came across these prints, that I was unable to recognize from charts of common animals prints online.

What is unique about them, is that each print, has 3 points, and there is only one straight line of prints, about 2-3 feet apart, where as I would imagine a deer, or other 4 legged animal would leave staggered footprints. We have a lot of deer in these parts but these dont seem to match deer print patterns I've seen online.

Each print is about 5 inches by 4 inches at their widest/longest points (they are longer then they are wider).

Note, the snow has melted somewhat since they were initially made.


texts: Why does the HPV vaccine not work on already infected people?

texts:
With my limited knowledge, I understand that the vaccine works by inserting fake HPV-like material in the body, thus inducing the immune system to build up defenses against it, so when the body is exposed to real HPV on the wild the immune system will be able to handle it.

That makes sense, however, why can't the body still build up the defenses when there was already an exposure? Specially when the HPV virus is "dormant" and undetectable.

EDIT: After the discussion with @Bob in the comments section below, the hypothesis is:

  In an infected person whose immune system was able to clear the acute
  infection, the virus (single infected cells) is constantly trying to
  enter lytic cycle again, only to be defeated by the immune system
  (because one infected cell leaving dormant state alone might not be
  effective); and then when the immune system is compromised for some
  reason, the virus is successful into entering lytic cycle and then
  there is a new clinical infection.

  If this is all truth, then the answer to the question is that the vaccine
  does "work" in the sense that the body still reacts correctly (by responding to the antigen)
  to it, but it is, in practice, useless because: 1) when the virus is
  dormant there isn't anything for the immune system to do; 2) when the
  virus strikes, the immune system was already exposed to it anyway, so
  it is generally able to fight and there is no need for the vaccine; 3)
  the infection will get clinical again only when the immune system is,
  for some reason, defective.

  The whole point of the vaccine is to never let the virus infect many (or any?) cell in order to avoid this situation where it is always trying to come back - and will do, when the immune system can't fight it off for some reason.

Please, if some specialist can analyze and comment on that it will be awesome.

More questions around it:

Is there the possibility that, while in this "dormant/attack" cycle, every single infected cell is defeated over the course of time, meaning an actual "cure"?
How does the cell replication process impacts the 1) hypothesis? (Maybe it is not possible for the immune system to achieve a natural cure because the virus keeps constantly replicating.)
How "much virus" would be needed for a successful strike in a compromised immune system (and how much compromised that system would have to be to fail)?
If the virus acts locally, is it possible for the vaccine to help other still-not-infected sites? In other words: is the natural immune response from the first infection in, say, the anus, worth anything for a subsequent infection in, for example, the oropharynx?


texts: Amount of variation between a canonical gene sequence in various samples

texts:
Suppose there is a GeneBank DNA sequence listed that produces a specific enzyme in a specific species of plant. e.g. A terpene Synthase.

Now if someone samples various trees of the same species would one expect to get the exact same sequence each time? Or is a certain amount of variation expected from tree to tree?

The drift behind my question is: Obviously not all tress of the same species are exactly identical in phenotype. So are the causative factors seen in sequence variations of various enzymes etc.? Or can we expect the various samples to have exactly identical amino acid / DNA sequences for particular genes / enzymes.

e.g.  e.g. Take this specific sequence: http://www.uniprot.org/uniprot/E3W202 If I sample from various trees of this same species and sequence this particular gene how much variation should I expect? Or would they be almost 100% identical?


texts: What's the minimum, if any, concentration of atmospheric nitrogen needed by plants?  Would plants be able to grow in an atmosphere with just carbon dioxide and oxygen?


texts: Offspring of parents with different number of chromosomes

texts: Many papers report that dog-whelks (Nucella lapillus) show a distinct chromosomal polymorphism between populations of 2n = 24 up to 2n = 36. Could somebody please tell me how many chromosomes the F1 generation of parents with (male) 2n = 24 and (female) 2n = 27 would have? What would happen to the three unmatched chromosomes?


texts: Could large plants grow out of large, solid rock in some way? What is primarily stopping them?

texts:
Roots of plants are known for being able to pierce through the firm soil and even solid stone to some extent. However, it occurred to me recently that I might be overestimating this ability as soil isn't the continuous material it seems from a large scale, but rather it is made of many small but firm granules connected by softer organic material which got me wondering just how important the granulation of soil is.

Typically, I don't see large stemmed plants growing out of solid rock despite that many granules of soil have a similar hardness to solid rock. But, could a plant that normally grows in soil grow instead in solid rock under the right circumstances? Soil is granulated, whereas solid rock is not.

I'm no expert, so I can only imagine different possible scenarios.

Could a large solid rock support a large and stemmed plant if it was porous enough? In other words, is it unimportant that the rock is very firm so long as there is enough exposed surface area to allow the chemical reactions that take place during the ion exchange at the roots and possibly break down the stone?

Or alternatively, it may not even be the porous or granule nature, but it might simply be the solution water carries. Could an large plant grow off of a large and smoother solid stone alone with roots rested near the base, but, if there was water running fast enough and warm enough to dissolve the surface of the rock and allow the ion exchange to take place in roots once the water was carried downstream to those roots?

Perhaps it's neither of those possibilities and it is solely the ability of a plant to anchor itself that matters the most in this issue. Even if a plant could pierce through the stone with its microscopic roots, since its stem also grows proportionately, if a plant can't anchor itself then it will just be blown away or washed off, so only small plants can anchor themselves to rocks.

Which of these traits is the most important factor in why plants don't typically grow out of larger solid rock, and can it be overcome to successfully grow large stemmed plants out of large solid rock?


texts: How did researchers find out that it was only the maternal chromosome that underwent deletion in Angelman syndrome?

texts:
It is known that in Angelman syndrome, the chromosome 15 undergoes deletion in the maternal chromosome while in Prader-Willi it's in the paternal.

I understand it can be detected by FISH or other chromosomal staining methods (which would have been used those times), the chromosome number which underwent the deletion.

How could they figure out which chromosome (maternal or paternal)  had undergone the change. My question is, which technique allows the chromosome to be marked maternal or paternal? Which technique was originally used?


texts: If so many different hormones/molecules work by activating adenylyl cyclase, how do they have different effects?

texts:
It seems that many hormones and molecules work by activating adenylyl cyclase to convert $\text{ATP}$ to $\text{cAMP}$, such as adrenaline and glucagon. Both of these seem to bind to $\text G$ protein receptors, cause an alpha subunit to dissociate and bind to adenyly cyclase to activate it, and then adenylyl cyclase forms $\text{cAMP}$. If so many molecules work in the same way, how can they have different effects?

My guess is that perhaps they may have different molecules inside which respond differently to elevated levels of $\text{cAMP}$? I presume both cells affected by adrenaline and by glucagon have the protein kinase which, when activated by $\text{cAMP}$, is able to activate glycogen phosphorylase to break down glycogen, as both adrenaline and glucagon increase blood sugar levels. Perhaps liver cells have more of the glycogen phosphorylase enzyme for a greater rate of breakdown of glycogen?

But then when I consider the heart, adrenaline increases heart rate but glucagon does not. If they have the same mechanism of action, how can this discrepancy arise? Could it perhaps be that adrenaline increases heart rate not by acting in the heart cells but in the medulla oblongata to increase the heart rate? But then again I come to the problem of why glucagon does not have the same effect. In this case I could hazard a guess that the glucagon molecule is too large to pass across the blood brain barrier.

But this is just one example of a possible problem in how two different molecules use the same mechanism. Although I cannot find a link now, I think I remember that long term potential ion to for new memories involves activation of adenyl cyclase. If that is so, it doesnt make much sense becaus adrenaline certainly doesn't help in the formation of new memories!

EDIT: I have just also read that insulin works by activating cAMP in hepatocytes/muscle cells, however it also seems that glucagon works by activating cAMP in the same cells! Two directly opposing effects using the same mechanism in the same cells- I'm very confused now!


texts: What does the decline of serum antibodies after infection mean for B cell immunity, exactly?

texts:
About a month ago there was a small media blip about a report in the New England Journal of Medicine that neutralizing antibodies to SARS-CoV-2 decline significantly within a matter of months. Published op-eds ranged from "a vaccine won't work, why God WHY" to "actually this isn't that weird, stop freaking out." Some key details from the articles I read at the time:

We still got T-cell immunity, and there are some signs this could last longer for COVID-19
Antibodies decline as infections clear for other illnesses.
Remaining memory B cells are (usually) primed to churn out more antibodies upon reinfection.
Nevertheless, the decline of antibodies is less protective and raises concerns of decay of immunity (an opinion in the original report)

I want to ask about the B cell side of this in order to better understand the somewhat conflicting messages and opinions.

If memory B cells worked as advertised, how would serum antibody levels even be a measure of immunity? It would seem that antibodies dropping to negligible levels wouldn't matter if your memory B cells can make them on demand.
Is there some benefit to having antibodies in your blood independent of your memory B cell function? Is it somehow quicker or vital to prevent reinfection or recurrence of serious illness?


texts:
I live in the Caribbean (Puerto Rico) and found this spider in my garage. Is it venomous?

It measures about 8 inches as a whole.


texts: How to interpret a phenotypic frequency density plot

texts:
I just read a paper that ran an evolutionary agent-based simulations aimed to test how genetic preparedness and social learning affect survival in various environmental conditions (changing environment, danger level, etc.). The full paper is here.

I'm a psychology student, and quite new to this area of literature.
About the graph, I get that density refers to the population density of different strategies at the end point of the simulation, but what does x-axis stand for?

I cannot find any specific mention about the x-axis in the paper, so I presume the graph is a standard one that does not need elaboration.
Could someone explain to me how to interpret the graph?


texts: Why not produce protein based on condensation reaction?

texts: I'm fairly new learning about protein. As I know protein can be synthesis by condensation reaction. And the current method to produce protein is purify them from an organism. So why not produce protein based on condensation reaction instead of purifying it from an organism?


texts:
I have been using old style lab book for some time now but with increasing work on computer and storing sequencing results and gel pictures on computer it would be nice to have everything on computer in a form of labbook.

Does any of you uses a good ELN that would be free as I don't think university will be willing to pay for it :)

Thank you for your answers.


texts: What could explain discrepancies between dates provided by the fossil record vs. the molecular clock?

texts:
I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock:

First appearance of Ecrobia grimmi in the fossil record: Middle and Upper Miocene (15.97 to 5.33 million years ago)
Age of Ecrobia grimmi as suggested by the molecular clock: 0.58 to 2.04 million years. The molecular clock was calibrated using an external marker-specific clock rate, and the climax of a geological event.

What could explain this discrepancy?


texts: What makes some viruses more infectious than others?

texts:
This week a new strain of the SARS-CoV-2 virus was discovered in the UK, and reports are saying that it's more infectious than the strains we've been dealing with for the past year. Which made me wonder: what is it about different strains (or different viruses in general) that makes them more of less infectious than others?
They've been saying that they don't think the new strain will be any more resistant to the vaccines. Does that mean they're no more able to evade the immune system? Or is it just the immune system that hasn't been primed by a vaccine?


texts: How do birds learn their tunes in isolation from their own species?

texts:
I wonder what a bird would sing if it didn't have its parents around (or any other birds for that matter) to learn its chirping sounds from.

I'm interested in how a bird would sing...

in complete isolation from creatures communicating through sound;
in isolation from its own species, but with other birds;
in isolation from all birds (other animals and creatures are there for it)

For example,

Would a bird even feel the need to speak up if there wasn't any other vocalizing creature around?
Would a bird learn other species' signals? Would it only learn from one species, the one which it would think of a fitting mate?
Would a bird try to mimic a non-flying creature's signals?

These are similar questions, but if you think they should be separated, let me know in the comments.


texts: Viruses: Adaptation to a new host through repeated host jumps

texts:
A friend told me, during a 3 minute discussion, that viruses that are endemic in host $A$ and make repeated jumps to host $B$ but can't be transmitted between individuals of species $B$, may slowly adapt (through these repeated jumps) to be able to be transmitted between individuals of host $B$ and become epidemic.

I don't know much about epidemiology. I don't understand how a virus population that is endemic to host $A$ may adapt to host $B$ with repeated jumps while the viruses that jump to host $B$ are dead end because they cannot be transmitted further more. Or Are these viruses able to jump back to host $A$ to bring back their newly acquired adaptations to host $B$?

Also, I might misunderstand the meaning of "repeated host jumps transmission". I first thought it meant repeated jumps from a reservoir population in host $A$ to host $B$, but it is also possible that it describes the dynamic of a virus population that is adapted to jump from species to species and they actually gain this ability by keeping jumping and jumping. But then, how could a virus species get adapted to jump from species to species? I'm a bit confused…. Can you give me some hints about this process of cross-species transmission through repeated jumps?


texts:
I've been reading about selective sweeps. And I found a case study that talks about drosophila and how their selection coefficient is between 0.0001 and 0.005.
I want to know what it'll be like for gorillas? That is what would be the selection coefficient range for them and why? Also, I was told that N*s of gorillas is between 100 and 10000 where N is the current population size and s is the selection coefficient.
Help would be really appreciated. I do not have a biological background therefore, it's taking some time to wrap my head around these things.


texts: What are the benefits of statins in terms of prolonging life?

texts:
Recently the UK government suggested that all adults over the age of 50, without exception, would benefit from taking statins.

I have an elderly female relative who may, or may not have had a minor cardiac event (the diagnosis is still out) and low blood pressure. It has been suggested to them that they would benefit from statins and have asked me (a former biologist) to find out more.

I've had a look at the mechanisms of action, which seem clear. But the clinical data is somewhat confusing.

It seems we can state with certainty that a small but significant number of users report relatively minor side effects, and a very tiny minority have serious ones.

In term of the benefits, however, the picture is much less clear. I have found a variety of statistics about how they reduce cardiac events but what this translates to in terms of length of life and quality of life is not stated.

One article I looked at suggested that on average, someone at high risk of heart disease taking statins for 30 years would only live an extra 9 months.

The author of that site has a book to sell, and may have an axe to grind. But there are several other articles out there - such as this, and this and this - which make worrying claims about statins being both more unsafe and less beneficial than clinical trials suggest. In particular there seems very limited evidence of any benefits to women.

I am inclined to treat these as alarmist nonsense - they have that sense of hysteria about them. But given that the authors look legitimate, that clinical trials data do not appear to agree with one another (widely varying in the percentage of users reporting side effects, for example), and that this is a relative, I wanted to get a second opinion.

So - can someone please crunch the numbers and tell me what the benefits of statin use are in terms of life years and quality of life? Is there any benefit for women with or without heart disease? And is there any basis to some of the alarmism around their use?


texts: ID large-thorned plant growing in Turkey

texts: Can anyone identify this plant which is growing in a friend's garden in the Uzumlu area of Turkey. It has very large spikes/thorns. I'm told it doesn't have flowers or seeds so we are wondering how it propagates itself.


texts: What is the genetic distance where linkage can be ignored?

texts:
I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph "degree of linkage vs. genetic distance". Unfortunately I can't remember which paper it was. Does anyone know where this number (1000) comes from?

PS: I'm aware that this topic is much more complex, especially if you are interested selective sweeps.


texts:
I have a relatively simply gene regulatory network I would like to visualize, complete with the common arrow and bar symbols used to show, respectively, which genes enhance or repress with other genes. Is there a way to typeset a gene regulatory network using something like LaTeX or Graphviz?

For very simple networks, I guess something like Photoshop or Illustrator would probably be the quickest solution, but these programs become very tedious as the size of the network grows even a little bit. What do people typically use for this type of task?


texts: Equation for accurate prediction of PCR yield

texts:
It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 grams of DNA. This is clearly absurd and not the case.

Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an upper bound - but even so, a very uninformative one), and in practice, yields will fall far short of it because:

Every single duplex of DNA does not denature at each cycle
Primers do not bind to every single molecule of DNA at each cycle
Not every DNA strand gets bound by a polymerase at every cycle
Not every polymerase that binds manages to complete the entire product in time in every cycle
The reaction inhibits itself by depleting dNTPs
The heat denatures the reaction by degrading enzyme

In fact, cursory examination of qPCR output often follows saturation kinetics:

Mathematical methods for modeling qPCR are obviously well developed.

My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?

For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).


texts: Nature versus nurture regarding aggression in specific dog breeds

texts:
A week ago I was bitten in my face by a dog that originally came from an asylum. That dog is half Rottweiler. Some people claim that the history of the dog is probably different from what the asylum thinks or says, whereas other people claim that Rottweilers or male Rottweilers are unreliable. But let's not focus on this single occurrence and ask the wider question:

Is there scientific evidence to indicate that there are certain breeds that produce significant numbers of dogs that are inherently and unreliably aggressive, or is such aggression usually the consequence of how their owners raised them?


texts: I found this creature climbing on the lower part of a wall inside apartment. Can you distinguish if it's a bed bug nymph or a booklouse? Sorry the photo quality isn't great, because it's so small (2 mm). Thanks in advance!


texts: Does Invertase catalyse the hydrolysis of other sugars other than sucrose?

texts: I recently did a lab where we tested out the substrate specificity of Invertase on different types of sugars such as sugar alcohols and disaccharides, measured by the absorbance of red using a colorimeter. Our results indicated that lactose and maltose were more effectively hydrolysed than the sugar alcohols sorbitol, inositol and mannitol. I'm guessing this could be because lactose and maltose are similar in structure to sucrose, which it normally hydrolyses, however, I was hoping there was a more concrete answer.


texts: Can you Interrupt a promoter region by inserting another promoter region into it?

texts:
I currently have a plasmid (pFPV25.1) which contains a promoter region with multiple cloning sights in it. I would like to place a new promoter I have isolated, and I was wondering whether I could  insert the new promoter into the middle of the old promoter; would that result in the new promoter controlling the gene of interest?

What I understand is that the RNA sequence that would be transcribed will change, but the start codon for translation would be kept consistent by doing this method, resulting in the gene being controlled by the new promoter.

Thanks.


texts: What is the best current understanding of how yeast transformation works?

texts:
I would like to get myself up to speed with what is currently known to science about yeast transformation. Specifically, transformation of plasmids and linear DNA fragments. I am particularly interested in practical aspects, such as:

What is salmon sperm for? What if I don't use it? What if I use more?
What is the relationship between number of cells, amount of transforming DNA, and transformation efficiency?
How does choice of electroporation cuvette gap size affect efficiency?
What can I do to get more colonies after transforming my yeast?
What steps can I skip to make the transformation quicker if I am doing an easy transformation?
How do different genetic backgrounds and media affect efficiency? Are there any common ones that reduce efficiency substantially? Are there any uncommon ones that increase it substantially?
What is the effect of post-transformation "recovery" time (eg. culture 12 h without selection and then plate on selective medium)?
Is making spheroplasts worth it?
Does the same transformation protocol work for different species (S. cerevisiae, S. pombe, C. albicans, etc.)?
Is there a coherent theoretical framework for understanding what actually happens when yeast are transformed, as opposed to "you mix some chemicals with DNA and throw cells in, abra kadabra, transformants come out"? The sort of theory I'm asking about would be useful in predicting conditions for better efficiency.

I am not expecting you to comprehensively answer these questions in your answer. This would make for a very long answer, and each of these could be a question here in its own right.

Instead, I want the answer to name reference materials which can be studied to learn more about the points above. For example, recent reviews or textbooks by established experts in the fields would be quite useful.


texts: What are iPSC cells, and what are their applications?

texts: I also searched it on internet, and just basically know it's related to the Stem Cells, but there are too many resources, can anyone help me find out more about them, like their applications? They really interest me.


texts: Can anyone please help me how will the CD spectra or graph of porin molecule look like. Porin molecule has 14 beta plated structures joined by some random coil, but it's very confusing to draw it. Can anyone please help me?


texts: Is it possible to increase lifespan through controlled evolution?

texts:
A few years back when I was reading The Selfish Gene by Richard Dawkins, there's this short passage where he theorizes about a way to achieve an increased lifespan through controlled evolution.

The theory goes like this: we don't tend to have medical problems until after 30 because we all tend to reproduce before that age.  Thus, people who tended to die before 30 never passed on their dying-prone genes.

So, if you didn't let people reproduce before a age X (where X starts at 30) and then slowly move that age up, you could use evolution to increase lifespan.

The ethical issues notwithstanding, is there any reason why this wouldn't work?  If it would work, how long do you think you would need to sit at each value of X?  How far apart do you think each value could be?  Finally, how many generations, using this technique, would it take before someone would live to be 1000 naturally?


texts: What's a good and reliable database on the pharmacodynamic and pharmacokinetic data of drugs both approved and unapproved?

texts: What's a good and reliable database for the pharmacodynamic and pharmacokinetic data of drugs both approved (in the US and elsewhere) and unapproved?


texts: How can there be a one-to-one correspondence between RNA and genes?

texts: From what I know, multiple strands of DNA make up a gene, so how can for each gene there can only be one RNA corresponding to it and vice versa? Is my knowledge incorrect?


texts: Identification of an alpine blueberry type

texts:
I'm trying to figure out what kind of berry this is. It can be found all over the Swiss, French, and Italian alps, generally right where ordinary blueberries are (the ones one would eat). However, they are distinctly different:

The flower attachment spot (sorry, non-botanist here) at the tip is square shaped (see photo)
Their leaves turn red much later during the season
The berry is more elongated when compared to ordinary blueberries, a bit of an ellipsoid


texts: Stimulating an axon causes impulses to travel both ways?

texts:
A diagram is presented as such above.
The question given states What would be the effect of stimulation to cause a nerve impulse with a microelectrode at the middle of the axon?

I thought the nerve impulse only travels in one direction to the muscle fibres, but the book says "A nerve impulse would pass in both directions."

Why is that the case?


texts: Evolution of leukemia pluripotent short-term cells

texts:
I have a problem in understanding the introduction of this paper entitled  "Stability and bifurcation in a model for the dynamics of stem-like cells in leukemia under treatment". As I have no background in biology, it's difficult for me to get the meaning of some terms like:

Short-term cells
Multipotent progenitor cells
Goldie-Coldman Law

On the other hand, the second paragraph is completely confusing to me:

  Let $Q$ denote the density of stem-cells population. A percentage $\eta_1$ of these ones are supposed to undergo asymmetric division with one daughter cell identical to the mother cell and the other one committed to differentiation. A percentage $\eta_2$ of the stem-like population differentiate symmetrically and go to the line of mature cells. The rest of them, a percentage $(1- \eta_1 - \eta_2)$ is supposed to self-renew: both cells that result from mitosis are identical to the cell that entred to the cell cycle. The same duration $\tau$ of the cell cycle is supposed for all types of division.

Is there a charitable soul to indicate some web page or youtube video on the subject?


texts: Multiple sequence alignment - how to align everything to 1 gene sequence?

texts:
I'm having trouble aligning 3 sequences together - the total gene (~2500bp) and the forward and reverse sequences that are ~1000bp in length. Now I'm using Clustal X2, but the problem is that the program does complete alignment, which is useless for me right now.  Could anyone recommend or suggest any parameters or methods on how to align more that 2 sequences together, but that each sequence is aligned to the first one (the total gene)?
Thanks!


texts:
I've got the following question and I'm afraid that the question doesn't match with the answer...

Factor III (rather than factor VIII) is known as thromboplastin or tissue factor and it makes sense that the factor III deficiency is related to thromboplastin formation. Isn't it?

What does factor VIII have to do with thromboplastin formation?


texts: Is the mRNA produced constant during time?

texts:
I am doing a statistical data analysis of a dataset of P. Furiosus cells exposed to gamma radiation.
For the samples exposed to gamma radiation, I have the values of mRNA produced over time. For the samples not exposed to gamma radiation (reference samples), I do not have the time at which the mRNA has been extracted.
Therefore, I was wondering: under normal conditions, generally, is the mRNA produced constant with respect to time? I thought that maybe the fact that is constant could be the reason for which there are not the values of time.


texts: Do brain cells shrink during REM sleep or a lucid dream?

texts: In this BBC news article a study shows that during sleep brain cells shrink to open up the gaps between neurons and allow fluid to wash the brain clean.  But do the cells shrink and undergo the whole procedure during REM sleep and lucid dreaming?


texts: What is the chemical mechanism by which PcP(c) is converted to PcP(Sc) in Fatal Familial Insomnia

texts: I know the gene PRNP and it's location.  There’s a mutation at codon 178 (asparagine found instead of normal aspartic acid) on the prion protein gene (also found in fCJD) and more uniquely there is a the presence of a methionine at position 129.  My question is how PcP(Sc) converts normal PcP(C) into the mutated destructive form, and whether or not this is a reversible process.


texts: Why do we have to exhale in order to talk? From looking on Wikipedia, it seems like it has something to do with the glottis, but I'm not clear on the mechanism that makes speech sound so different when air is coming in.


texts: Why do anaerobic bacteria require a low redox potential for their culture media?

texts:
I'm reading Clostridium ,which is an anaerobic bacteria in my microbiology text and it says,

  of more importance than the absence of oxygen is the provision of a sufficiently low redox potential in the medium. Third can be achieved by adding unsaturated fatty acids, ascorbic acid, glutathione, cysteine, etc.

Why? Do they reduce oxygen free radicals or something? Well, are these present in Clostridium's natural habitat?


texts: Is it possible to grow brain tissue in vitro? Can we make a super-brain this way?

texts: I wonder whether such experiments were conducted? Is it possible to create a "biological super-computer" this way?


texts: which enzyme phosphorylates sodium potassium pump?

texts:
I know that Na+/k+ pump possess atp-ase function; so the pump will hydrolyze ATP into ADP + Pi. And I see in a figure that the pump is phosphorylated but couldn't really find which protein catalyzes this.

Does the pump act as a phosphorylase??

Or is there a separate enzyme present nearby that does this?


texts: Is there a difference in cytoplasmic pH between prokaryotes and eukaryotes?

texts:
The cytosolic pH in human cells is around 7.4, but fluctuates as the cell is replicating. Prokaryotes and eukaryotes are vastly different in many ways. One thing they share is cytoplasm. Is there any general difference in the pH between these two cytosolic spaces? Any pointers to a previous investigation into this would be hugely appreciated. Ideally I'm after a quantified numerical comparison from a peer reviewed reference, but given the obscurity of the question that might be a tall order!

Googling was to no avail. It's swamped with pH survival data.


texts: Puffball growing on a tree: What kind of mushroom is this?

texts:
What kind of mushroom/fungus is the one shown in the photos?
Description: Looks similar in size (~4-5 cm as I  remember) and shape to a puffball. It is not hard to the touch, unlike typical mushrooms that grow on trees. Several balls were growing individually (not in clusters) from the 2-3 m tall stump of a broken tree, at multiple locations from the bottom to the top. They were breaking through the bark from the inside.
Time and location: Saxony, Germany, in a mixed forest. Early September.


texts:
I consider the existence of a broken GULO gene in humans to be the clearest evidence for human evolution - just what else is it doing there otherwise?

Are there any other examples of vestigial genes in the Human genome? Or perhaps vestigial proteins?


texts:
I am currently on holiday in southern France and have noticed that the house we are staying in has somewhat of a hornet/wasp problem.

Is there anybody that can help in identifying it? My best guess is a European Hornet but I'm no expert so may be wrong.

Below are some pictures. Sorry they couldn't have been of any clearer quality, they were taken through a window, and I didn't particularly feel like going out to get any closer because I've heard that some hornets can be quite aggressive even if unprovoked.

From what I saw, it has visible fur, and is around 2cm in length. The feature that led me to it being a Hornet is that the waist gets smaller before the abdomen.


texts:
Echolocation is the ability to obtain spatial information of the surroundings from echos generated by the animal. There are bats and other vertebrates that naturally use it.

I was wondering if this is limited to vertebrates, or if there are examples among the invertebrate, especially insects.


texts:
I found this image on Google+

If you shake your head you can see a portrait of a person. Can anyone explain how the image is constructed in the brain?


texts: One particular codon codes only for one amino acid, but an amino acid can be coded for by several different codons. Now according to the genetic code, the codon UUU codes for the amino acid phenylalanine and UUA codes for leucine. But, according to the Wobble Hypothesis, the base on the third position of the codon and that on the anticodon need not be complementary (which helps explain why there are very few types of tRNA molecules, inspite of there being 61 codons). If this hypothesis is true, then we could have a phenylalanine placed in a position which was meant to be for leucine, and vice versa (since the codons coding for them differ only in their third base). The same holds true for pairs like aspartic acid & glutamic acid and serine & arginine. So how does translation of a particular mRNA molecule result in the right polypeptide sequence?


texts: Is there a medical condition in which you can't cut your hair?

texts: Just curious, does there exist a medical condition in which a patient is advised not to or simply cannot cut their (head) hair?


texts: Why are not both alleles knocked out at the same time in knock out mouse?

texts:
I was reading this little 'article' about homologous recombination and knockout mouse. According to this article you first remove embryonic stem cells from a gray-fur blastocyst, then insert the construct and place them back into the blastocyst. Further the text states:

  A knockout mouse has had both alleles of a particular gene replaced
  with an inactive allele. This is usually accomplished by using
  homologous recombination to replace one allele followed by two or more
  generations of selective breeding until an breeding pair are isolated
  that have both alleles of the targeted gene inactivated or knocked
  out.

However what I don't get here is that we have cells from an embryo, and thus have cells with both alleles. Hence, the regions surrounding these alleles will be homologous, so why would this step result in heterozygous (and thus require selective breeding afterwards) instead of homozygous mouse direcly?


texts: Can I find out what resistance bacteria has based on strain? where do I look for that info?

texts:
I have a list of strains across various organisms for example:

Escherichia coli - ATCC 25922, CGSC 6152, W3110RL.

Pseudomonas aeruginosa - ATCC 27853, PAO1, APAE1111.

I'm failing to find any resistance information on these strains, as in what strain is resistant or susceptible to what antibiotic. Is there a way to find out?

Thanks.


texts: How to construct tumor phylogenetic tree?

texts:
I would like to know if anyone has tried any software that constructs tumor evolution trees where the trunks represent the common mutations and the private alterations are noted on each branch. I can do it manually but the sample size is too big (nearly 100 patients). Here's a good example of what I'm after here on Figure4 http://www.nature.com/nm/journal/v21/n7/full/nm.3886.html

Any additional computational model suggestions are welcome.


texts: what is the margarine metabolism in our body?

texts:
margarine is commonly used food ingredients that contribute to both inflammation and

obesity , but actually I want to know the margarine metabolism in the human body

I can find some resources talk about its impact on health but I can't get the idea of its metabolism.


texts: I brought a hibernating yellow jacket queen into my house accidentally. What will happen?

texts:
There was apparently a hibernating yellow jacket queen in my stack of firewood outside.  An hour or so after bringing in the firewood, we saw the queen fly off into the house, where we can't find her.

What will happen?  Will she lay her eggs and start a nest somewhere in our house?  Will she just find somewhere and go back to sleep?


texts: What type of point mutation and chromosomal mutation cause Albinism in humans?

texts:
First of all, I know that OCA1 (Oculocutaneous Albinism Type 1) is autosomal recessive which means that both parents-who are unaffected-have to pass down one copy of a mutated gene in order to activate the mutation (in this case it is Albinism). Based on the following link, "TYR (The TYR gene provides instructions for making an enzyme called tyrosinase. This enzyme is located in melanocytes, which are specialized cells that produce a pigment called melanin) is the only gene in which mutations are known to cause oculocutaneous albinism type 1." Also, there is a table on the website but it does not justify the exact point mutation that causes OCA1...unless I'm wrong.

----> http://www.ncbi.nlm.nih.gov/books/NBK1166/

What type of point mutation and chromosomal mutation?

Point Mutations:
http://www.britannica.com/science/point-mutation

Chromosomal Mutations:
There is good insight on Chromosomal mutations at http://biology.about.com/od/genetics/ss/chromosome-mutation.htm

I would really like help, this information is for my biology project!


texts: What is the evolutionary reason behind human preference for salty foods?

texts:
It's been established that food palatability is related to it's caloric density. This hypothesis is used to explain why humans are partial to sugar and fat. But it is also said that humans are partial to salt.

Given that salt has no calories, are there evolutionary reasons that explain why humans have a preference for salty foods?


texts:
I'm stopped at a stoplight and, with nothing to do, my thoughts wander to the timed don't-walk sign that governs any pedestrians who might wish to cross the street I'm driving along.

I can see two such signs, one on my side of the cross street, and one across the way. They are synchronized: each counts down the seconds at exactly the same time as the other, as far as I can tell, lighting up as "5", then a second later as "4", etc. Nothing's wrong with my ocular nerve or brain, as far as I know. Can you fill in the blanks please?

I can be …% sure that the lights are synchronized within … seconds of one another. (Not something trivial like "100" and "1", of course.)


texts: Is there a circadian component to hunger?

texts:
I'm wondering what produces the feeling of hunger in humans. Checking Wikipedia revealed that leptin and ghrelin are two hormones involved. I've also read that the digestive system produces its own melatonin.

Because melatonin is related to circadian rhythm and the biological clock,Is melatonin involved in feeling hungry? Is there a circadian pattern to the levels of leptin and ghrelin in humans?


texts: Does a man contain all the genes needed to make a woman?

texts:
This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so forth in the landing. With the artificial "wombs" intact, he populates the planet with clones of himself.

If he wanted to introduce enough variation (without making up new genes, only rearranging) in the population to allow them to be able to reproduce naturally without inbreeding problems, would he be able to? In particular, could he make a woman?
Alternately, could a woman (without a Y chromosome) do the the inverse?

At the risk of introducing bias into the answers, the plot as it stands assumes he is a male and he CAN'T do any of the above and he is restricted to clones.


texts: How to prevent e coli from clumping (for FACS)?

texts:
I'm performing FACS on e coli, but the cells are clumping together so each event is multiple cells.

I ran a control where I had one flask of e coli expressing GFP, and one flask expressing RFP. Run separately, I got a clean population of either high-GFP fluorescent events, or high RFP fluorescent events. If I mix 10uL of each population into 200uL TE buffer and immediately run that sample, all the events have high RFP AND high GFP fluorescence, indicating the cells are sticking together immediately upon mixing.

Cell line: ER2566 (NEB)
F- λ- fhuA2 [lon] ompT lacZ::T7 gene 1 gal sulA11 Δ(mcrC-mrr)114::IS10 R(mcr-73::miniTn10-TetS)2 R(zgb-210::Tn10)(TetS) endA1 [dcm]
Host strain for the expression of a target gene cloned in the pTYB vectors.
Carry a chromosomal copy of the T7 RNA polymerase gene inserted into lacZ gene and thus under the control of the lac promoter. In the absence of IPTG induction expression of T7 RNA polymerase is suppressed by the binding of lac I repressor to the lac promoter.
Deficient in both lon and ompT proteases.

Growth media: M9 minimal media

FACS running media: TE

I know there are anti-clumping agents for yeast and mammalian cells, but I haven't come across one for bacteria.

Can anyone recommend:

an e coli protein expression strain that is known to not clump
an anti-clumping agent for bacteria
any other possible solutions
?

Thank you!


texts: Why do plants produce so much more sugar than they use?

texts:
I recently asked the question, "Do plants need O2 to consume energy they've stored via sugar?" to which @canadianer responded, "Yes, plants require oxygen to generate ATP from sugar. However, they generate far more sugar (and O2) than they use." Why do plants produce all that extra sugar, especially given that sugar is thermodynamically expensive?

One reason, I believe, is to produce fruit and so recruit animals to help with reproduction. But are there others?


texts: Genetic engineering for insulin production

texts:
In order to put human DNA inside a bacteria in order to have it create Insulin, from what type of cell would you need to take the gene for insulin?
I thought it should be from any somatic cell, since the DNA is identical, but I'm told it should be only from the pancreas, why is that?


texts: Can animals and humans be ranked in their ability to detect moisture?

texts:
One reason for insects being so successful - about 70% of all animal species - is their excellent ability to detect moisture. Take termites for instance. The soldiers boot out the flying reproductives only when it will rain within 24 hours. Because moisture will be needed to survive and make a new termite nest.

Humans by contrast are hopeless at detecting moisture; humans do not have the senses to be able to predict rain. Except by more indirect methods and science.

So my question is is there any way of ranking the different abilities to detect moisture? This is not a list question. Rather, it's steering for a formula or set of variables. Are there factors that make a dog better at detecting moisture than cat for instance, if that is the case?

I am surprised that nobody seems to have done this for something - water and moisture - that is so vital for life.


texts: Does every human eye see the same visible spectrum?

texts:
It is said that human eye can see light with wavelength approximately between 400nm and 700nm.

Are these upper and lower bounds same for every human? If not, what are the means and standard deviations of these upper and lower wavelength values for human eyes?


texts: Among primates, is it true that homosexual behavior is extremely unnatural and uncommon?

texts:
I was recently reading a book published by some anonymous biologist known as Lynn Saxon, in which she appears to want to refute Christopher Ryan's thesis in Sex at Dawn that prior to the invent of agriculture, humans were presumably far more promiscuous and had sex not just for reproductive purposes.

In order to do this, she then goes on to show how, in the animal world, the great majority of all sexual activity is directed only towards reproduction. Another author, David Barash, says similar things: namely, that "evolution is very much about reproduction—variation in reproductive success is evolution".

However, homosexual behavior is anything but reproductive. Saxon appears to suggest indirectly that all such "non-reproductive" behaviors that are "useless from a evolutionary point of view" are rare and unnatural among primates, who are our closest relatives.

One more biologist, known as Antonio Pardo, says:

"Properly speaking, homosexuality does not exist among animals…. For reasons of survival, the reproductive instinct among animals is always directed towards an individual of the opposite sex. Therefore, an animal can never be homosexual as such."

Is this true? Is homosexuality really uncommon and unnatural among our closest relatives who are primates? Is sex mostly for reproduction?


texts:
Over the last week or so as warmer weather has arrived, I've noticed small insects crawling around in the bathroom. I'm located in western Europe. They are perhaps 1mm in length, quite difficult to see without a magnifying glass. I used a macro lens to capture these pictures. What might they be? Ticks? Aren't ticks larger? Why are there so many?

Note: these pictures are heavily magnified (they are on an old wooden door with cracking paint), and I've applied lighting auto correction. Actual size of each insect is 1mm or less.


texts: Where to go next with clustered C elegans neuronal time series

texts:
I'm doing some independent research with the C Elegans nervous system (with the OpenWorm project) and was looking for some guidance as to where I should go next.

Right now, I'm dealing with calcium fluorescence imaging time series datasets for a subset of neurons in C Elegans. Here are my five time series clustered by similarity:

and here are correlation matrices for the neurons across the datasets:

There are obvious patterns here.

I have many vague ideas of where to go next, but I'm wondering if anyone with more expertise can provide some guidance as to what approaches I can take to:

Look at this data in the context of known C Elegans neuronal connectivity
Trying to reconstruct connectivity from functional data (develop an algorithm for this, not a simple task)
Understand why certain correlations exist
Look at computations occurring among neurons in these datasets and isolate computational building blocks
Developing a minimal network model for C Elegans.
Understanding information flow

I'm overwhelmed by all of these ideas and need some guidance/a concrete starting point.


texts: Synthesis of Fatty Acids Longer than 16 Carbons

texts:
I understand that the human body when performing Fatty Acid Synthesis can synthesize only until C16 (palmitate). However the ER has desaturases and elongases. I know that desaturases are used to add double bonds, but do humans have elongases to add even more Carbons to a double bond? If so, then this would mean that the human body can synthesize fats longer than C16?

Lets take a hypothetical case and say that humans have both desaturases and elongases. Would it be feasible to add double bonds to palmitate via desaturases, then add more carbons to the chain via elongases and then add more double bonds via desaturases? This way, the resulting fatty acid will have an increased length and more unsaturated character (i.e. more double bonds than the prescribed 4 that humans can add at positions 4, 5, 6, and 9)?


texts: Is there such thing as a bird with infrared vision?

texts:
I am writing a story and I specifically need a bird with infrared vision. Worst case scenario I just invent one but that would break the pattern in my story.

The closest thing I have seen from researching myself was this statement, "tawny owl's retina has about 56,000 light-sensitive rods per square millimetre (36 million per square inch); although earlier claims that it could see in the infrared part of the spectrum have been dismissed."

So apparently it was proven that the Tawny Owl (Strix aluco) does not have infrared vision. I couldn't find a better forum to ask this on (I don't know, is there a zoology forum?) so my last resort would be a biologist.


texts:
Based on the comments in this post and also this chat. For discussions and speculations please comment in the chat.

The basic question is what is the advantage of having a single long axon such as that of sciatic nerve (~1m) compared to a series of neurons?

The primary advantage is surely the conduction speed which will get affected because of chemical synapses. However, gap junction synapses can reduce that delay. The larger volume of the soma of the post synaptic neuron may also reduce the conduction speed, but signal strengthening can also happen. Cell architecture can be adjusted to minimize the loss of speed.

The obvious disadvantage of having a single large cell is that there would be tremendous burden on the nucleus for the cellular maintenance. There would be delays in transfer of non-electrical signals such as biomolecules from axon termini to soma and vice versa. Long axons also means continuous transport along them which in turn demands large number of molecular motors and therefore ATP. Moreover, a small injury can disable the entire conduction channel. It can be imagined that this trait (long axons) can also be selected against; injury leading to inability to move and thereby causing perishment.

EDIT (Based on comments to Anne's answer)

Time is of course a valid advantage for having a single axon as an information conduction channel. However, the energy or the maintenance cost is the factor that I am actually interested in. Maintenance cost would increase with cell volume (in fact surface area) and having serial neurons would demand more energy (cumulative) than a single axon (including costs of maintaining a nucleus). However a long cell would need much higher number of molecular motors to maintain the traffic flow rate. All responses that require transcriptional control would be slow (such as response to injury). Moreover a single soma also imposes a limit on the number of mitochondria. There should be a limit on how long an axon can be. I am especially interested in case of big animals (with long hindlimbs) that also have a good reflex (perhaps camels, even horses).

Has someone tried to analyse the tradeoffs of having a long axon vs series of neurons connected by gap junctions? If not is this problem worth modeling or quite trivial?

Saw this in Quora:

  My first thought mostly agreed with the question details, except I'm
  pretty sure that the dorsal root ganglion (DRG) has a longer axon than
  the motor information carried in the sciatic nerve (which is the
  longest nerve in the body, but not axon).

Does this mean that sciatic nerve has serial neurons?


texts:
I'm somewhat irritated by "mutation" generally being described as a fully random factor in evolution: pure randomness does not seem like something that can survive in a long evolutionary process.

And some basic evolution in some long-lived organisms appears to happen in quite fewer generations than one would consider plausible considering just natural selection over an unbiasedly mutated genetic base.

So I'm wondering whether there have been attempts to view mutation itself as a process influenced by evolution.  For example, couldn't "junk DNA" result in a susceptibility to certain mutations that is determined by environmental factors, like amount and constitution of nutrients, ambient temperatures and others.

The overall discussion of mutagenesis I can find focuses entirely on "damage", again basically assigning all mutations a negative or at least undirected character (like more mutations occuring under stress, with the "aim" being more likely to have more random mutations where one offspring might be more successful than the stressed parent by chance).

In a similar vein, I don't see not much of anything about evolution and competition of gametes: how different environmental factors influence which of an abundance of eggs mature and which of the (asexual) male gamete reproduction mutation in the testes will be favored over time or under environmental conditions.

Basically all of evolution and natural selection seems about how to survive into fertility and select a partner, and that's it as genes are constant apart from random cosmic radiation or toxic substances.

I think that this kind of viewing the message in the DNA as isolated from its medium just does not sound like something that would survive billions of years without something less random replacing the pure randomness.

So are there any major studies trying to figure out whether certain mutations leading to better adapted phenotypes occur in a non-random manner (namely not just affecting mutation rate but also direction) in response to environmental circumstances?


texts:
What kind of biosensor is made by Phages?
I need a list of published paper that used Phages for make LCR(inductance (L), capacitance (C), and resistance (R) of a component) biosensor for detection. for example detection of E.coli


texts: I am studying RNA-binding proteins involved in RNA granules. I am searching the literature for an order of magnitude of the absolute global concentration in the cytoplasm. Although I am aware this quantity can vary greatly from proteins to proteins, I would be happy if I find some papers having estimated it for some given proteins.


texts: About cell membrane; action potential and resting potential

texts:
Ion X is negatively charged and more concentrated inside than outside the membrane potential of a cell
therefore Ex (equilibrium) is positive. Ion X is unknown.
Why is the equilibrium positive?


texts: What are the internal surfaces of body cavities actually made of?

texts: In Ross's book of histology it says that the mesothelium that includes all body cavities is made of simple squamous epithelium but in other places it says that in the gastrointestinal tract it is made of simple columnar epithelium. Is it that the trachea and the the gastrointestinal tract are not classed as cavities?


texts: Styes formed in the eyes are cured by dabbing at them with lukewarm water(I saw this being done many a times as a home remedy.) At times, common salt is added to the water before dabbing. My mother says, NaCl hastens the healing process; why is it so? What does salt do to cure the styes faster? Can salt be used for treating other eruptions anywhere else?


texts: How does (action potential) hyper-polarisation work?

texts:
I understand that after depolarisation, repolarisation and then hyperpolarisaiton occurs and that an area in hyperpolarisation is in its "refractory period".

Why does this prevent Na+ ions diffusing "backwards"? Since an area of the neurone membrane in hyperpolarisation will have a very negative charge so surely positive Na+ ions would diffuse towards them rather than away from them - "forward".

Similarly, why does this prevent another action potential firing too soon?

(I know this is kind of 2 questions in one, but as they are so very related I thought it more prudent to combine them).


texts:
I live in the upper southeastern region of Arizona in U.S. There's a type of tree growing in my back yard that I can't seem to identify. Its growing in an arrangement very similar to an ocotillo plant.  It has single spiny stems coming up out of the ground.  They don't branch out but have large sharp spines with leafs growing out of them.  It doesn't look anything at all like any of the native desert plants in the area.  There's mesquite and sage and various types of cactus.

At the moment the stems are about five feet tall.  I took clippings about two feet in length and photographed them.  It seems I'm only able to post two links so I've chosen the clearest images that I have.  I'm very curious as to what this is and any help would be greatly appreciated.


texts: Why the nails are of white colour from bottom? then why they are pink and again white in the end?


texts: Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

texts:
All humans have the same sort of proteins in our bodies. Take haemoglobin for example.

Is the gene coding for haemoglobin in my body identical to everyone else's gene or is there slight variations in the nucleotide sequence?

Are there examples of proteins that are always completely conserved at the population level?


texts: Is there a biological mechanism for evolution encoded into our DNA?

texts:
Throughout high school, I remember learning about Darwin's theory of evolution as if it were near-fact. But something always seemed wrong about the ideas presented.

Survival of the fittest
Random mutation
Natural Selection

All of these things seem to account for some margin of evolutionary progress, but I always remained skeptical that the extremely complex features of life could have formed from these methods alone, even after hundreds of millions of years.

Here's what I notice:

Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.

I'm going to use this example:

Turtles on an island where shrubbery grew higher up developed longer necks, to reach the leaves.

I imagine that turtle looking up at that food, and sub-consciously wishing to get to it, constantly straining, for its entire lifetime.

It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.

My question:

Is this possible? Does any similar mechanism exist that we know of? If not, how can so many specific (advanced) evolutionary leaps be otherwise explained?


texts: Does destroying a virus envelope make the virus inactive?

texts: Some viruses have a lipid envelope around their protein capsid. The envelope can be dissolved with soap, but does that still leave the capsid and interior genetic material intact? If so, is the virus still active?


texts: Percentage of genome devoted to regulating gene expression

texts:
Recently I've been studying the p53 tumor suppressor gene as a model for regulation of gene expression. It's amazing how many different post-translational modifications are known to regulate p53 activity, and how many different factors are involved in this regulation.

It is postulated that there are between 20,000 and 30,000 genes in the human genome. Is there an estimate for the percentage of these genes whose primary function is related to regulation of gene expression?


texts: Are there any strictly chloroplast/mitochondrion-residing ribozymes?

texts:
A simple question that had occurred to me. Considering the small doubt of transcribed genes in both organelles, I would doubt it, but are there any known ribozymes strictly found in either mitochondria or chloroplasts?

UPDATE: Actually, I just thought of rRNA acting as a peptidyl transferase in mitochondrial ribosomes... Any other ideas?


texts: How to make sure a stem cell culture is cancer free?

texts:
Say I take a blood sample from an adult, extract the white cells and apply to them the process described in <this article>. Assuming this actually turns the adult white cells into stem cells, which I then transfer to a culture in order to grow an arbitrary quantity, how can I make sure in the end this culture is free of cancer stem cells? Is there a last step that can be applied which would eliminate any potential CSCs leaving only healthy cells in the culture?

Thank you.


texts: How is an RT-PCR representative of the RNA contents in a cell?

texts: For example, we first collect all the RNA contents from a mammalian cell line. Say, for instance, we collect 80 uL of RNA with a concentration of 150 ng/uL. Next, to make cDNA, we take 1,000 ng of the RNA. However, this 1,000 ng is a completely random sampling of the total RNA we had. How is that random sample of RNA representative of the RNA contents originally in our cells?


texts: What are the requirements for a stable carbon cycle in sealed "bottle gardens"`?

texts:
The most famous example of a sealed bottle garden is David Latimer's bottle with a Spiderworth plant, pictured below, which has been sealed for 40 years. My own attempt at a bottle garden is failing and I'm looking to "debug" what's going on.

My garden is a 2 litre glass jar filled with gravel, sand and soil, filling about a quarter of the jar. The soil is rather damp. I'm observing the following: When the bottle is sealed, plants such as moss, strawberry shoots and seeds thrive for a couple of weeks. They will then wilt and worms that had hitched a ride in the soil try to escape. When opening the bottle, there is a strong smell exactly like manure. The brief exchange of air when opening the bottle is enough to allow the plants to properly rot over the coming days, with mold only now spreading. (This proves that oxygen was depleted before I opened the jar) I removed the dead plants, sprinkled seeds on the soil and closed the jar. The seeds germinated and thrived for a couple of weeks until the process repeated.

At first look, it appears that when oxygen has been depleted, anaerobic bacteria take over, producing H2S, which I assume kill the plants. Or are they killed by changes in pH under high CO2 concentrations? Why does this not occur for all bottle gardens? Is the problem that there's too few plants to keep up the oxygen level which keeps the anaerobic bacteria at bay, is it the waterlogged soil or some other factor I'm unaware of?

Latimer did something right with his bottle garden, which started with a seedling and some compost.


texts: Janina kolkiewicz who faced Lazarus phenomenon

texts: I've just read about Janina kolkiewicz case who faced Lazarus phenomenon and I was wondering how could her brain and organs survive these long hours without oxygen?


texts: Why is amyloplast produced by some plant cells but not other cells?

texts: For example I know it is produced in Potato's and fruits and its purpose is to synthesize glucose in to starch through polymerization. But why is it only present in some cells? Is it only present in cells with higher glucose content?


texts: Does chicken embryo form the disc called "discoblast" in the cleavage and blastulation of chicken?

texts:
This thread is related to my previous thread which is still unsolved mainly. I need to be able to compare chick and human cleavage and blastulation of zygote.
My friend says that

  Chicken have discoblast, human not. That is the main thing to get the idea of the difference.

I know that chicken have yolk sac with yolk, while human have yolk sac without yolk.

My notes say that

  Cleavage in birds is partial discoidal (embryo forms disc and cells called blastodisc are on top of the yolk).

So embryo forms some disc, lets call it #1. Some cells called blastodisc are on top of the yolk. So are the cells called blastodisc on top of the yolk and the disc #1?

What is the name of the given disc that chick embryo forms?
It seems that human is not forming the given disc. Apparently, the name of the given disc is discoblast, the thing he says is very important.


texts: Do cuttlefish know how to mimic animals since the moment they are born or do they learn by observing?

texts:
I can't seem to find information anywhere else so I hope somebody can help me out.

So, as the question states, I saw a cuttlefish mimicking a hermit crab the other day and I was wondering if cuttlefish carry information of what they can mimic as spiders carry information of how to make a web (innate behaviour) or if they learn how to mimic by observing other animals.


texts: What is the relation between plasmid concentration and mRNA levels?

texts:
Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene:

One of the simplest ways to model GFP transcription is to use an ODE:

$\frac{d [GFP_{mRNA}]}{dt} = a - b{\cdot}[GFP_{mRNA}]$

where $a$ is GFP transcription rate and $b$ is GFP mRNA degradation rate (both constants). Normally, we assume $a>>b$.

Suppose we wish to account for plasmid concentration with the value of transcription rate $a$ - e.g. with higher plasmid concentration, the ratio $a/b$ should increase as the mRNA saturation levels are expected to be reached faster. In other words, suppose we transfect 2 individual constructs depicted above, 10 ng of one and 30 ng of the other - how should this difference in concentration impact the rate constants values, assuming the constructs are otherwise identical?

Assuming this, approximately how does gene transcription rate $a$ change as a function of the amount of transfected plasmid containing the above construct? Ideally, I'd be interested in knowing this for HEK 293 cells, but any other decent estimation is acceptable. One simple option is to simply assume linear relation, but I think that's too simplistic: e.g. if we say $a=1$ at 10 ng plasmid concentration, then $a=3$ at 30 ng plasmid concentration. Note that I'm not necessarily limiting myself to ODE models, just looking for some kind of relation.

I have so far not been able to find anything useful in papers I've examined, so any help would be appreciated.


texts:
Bread gets mouldy pretty quickly. My parents (both of whom are nurses) throw out a loaf of bread after a spot of mould is seen (because "if you can see one spot, it means the whole thing is covered in mould spores") because they say you'll get sick if you eat it. The USDA also has a handy chart on it's mould page telling you when you should discard food with mould on it.

Is it the mould itself that makes us sick or is it something that the mould is releasing?

What are the mechanisms that cause us to feel sick after eating mouldy food?

The USDA says that there can also be bacteria along with the mould on the the food - is this what is really making us feel ill?


texts:
I wonder if there is a place on the internet to get PCR primers for a specific gene.
For instance, exon 15 in CFTR gene. I don't want to design myself because I am sure sombody else already did it.


texts: What is the name of this spider and is it poisonous?

texts: We found it between Palm trees in the backyard of a home in West Palm Beach Florida.


texts: Scientists have documented that it seems to only be male humpback whales who sing structured songs, but do we know what purpose their songs play?


texts: Can the knowledge about torsion angles alone be sufficient for specifying secondary structures of protein?

texts: I have read that Ramachandran plots are used to identify secondary structures of proteins. Also, alpha helices and beta strands cluster around specific regions of the plot which gives us the information about how much of these structures are present in the protein. But, it seems intuitively unreasonable. I can't convince myself "why there can't be other structures with the same torsion angles as alpha helices or beta sheets". Am I missing something?


texts: Is it possible to train allergic resistance by exposing yourself to allergens?

texts:
My hypothesis is that one can decrease the allergic reactions over time by continuously exposing yourself to slowly increasing doses of allergens.

Is there any scientific evidence pointing this right or wrong?


texts: Are there worms/snake traveling by rolling? (see youtube video)

texts:
Someone obtained this from a nature simulator :  https://youtu.be/l-qOBi2tAnI

Is there any animals travelling like this?


texts:
I am reading an article about detection of differential methylation. They use the term "cell type composition" in the following context:

"Researchers need to carefully design studies that associate phenotypes with DNA methylation. Some aspects, such as cell type composition, cannot be readily controlled by design; patients and therefore individual DNA samples simply differ in their cell type composition." (Robinson, MD., 2014)

I would like to know to what "cell type composition" refers?

Does it refer to the composition of a specific cell-type in terms of its methylation pattern (or can it refer to something more general outside this context)? It makes sense to me that different cell-types should have different methylation patterns, that's why there are different cell-types in the first place. But is it that even within one specific cell-type, the composition of methylation pattern is different across different individuals?