texts:
Reading the following paragraph:

  After staring at the red and blue shamrock, you saw a green and
  yellow afterimage. Opponent-process theory proposes that as you stared
  at the red and blue shamrock, you were using the red and blue portions
  of the opponent-process cells. After a period of 60 to 90 seconds of
  continuous staring, you expended these cells' capacity to fire action
  potentials. In a sense, you temporarily "wore out" the red and blue
  portions of these cells. Then you looked at a blank sheet of white
  paper. Under normal conditions, the while light would excite all of
  the opponent-process cells. Recall that white light contains all
  colors of light. But, given the exhausted state of your
  opponent-process cells, only parts of them were capable of firing
  action potentials. In this example, the green and yellow parts of the
  cells were ready to fire. The light reflected off of the white paper
  could excite only the yellow and green parts of the cells, so you saw
  a green and yellow shamrock.

  (Ellen Pastorino & Susann Doyle-Portillo, What Is Psychology? Essentials, 2010)

I've been wondering:

Can the negative afterimage appear only if there is light or is it possible in darkness?

In other words does the red color make the ganglion continue working even when there is no image and the afterimage appears green or is more light required in order for the afterimage to appear?


texts: Are all cone cells connected directly to the brain?

texts:
Coming from a computing science background, I noticed that cameras have orders of magnitude fewer wires than pixels. For example, the Raspberry Pi Camera v2 has 8 megapixels, but only 10 wires connecting it to the board. In human-made systems, it is preferred to time-multiplex pixels over few wires or, even better, already compress or encode image information on the camera.

I was wondering if the human optical system features something similar. Does the eye compress, encode or time-multiplex the image "pixels" it captures before sending the information to the brain? Or is each cone cell ("pixel") connected directly to the brain?

(In case the latter: Wow! The optical nerve must have a huge bandwidth.)


texts: Range for which the Verhulst-Pearl model is a good approximate

texts:
The Verhulst-Pearl model describes the growth of a population using the differential equation,
$$\frac{dN}{dt}=rN \left(\frac{K-N}{K} \right)$$
where N is the population (no. of organisms), r, the intrinsic growth factor and K the carrying capacity of Nature for that species.
Solving the differential equation, we can obtain a relation between time and instantaneous population, given as,
$$\frac{N}{K-N}=\frac{N_o}{K-N_o}e^{\frac{rt}{K}}$$
Where $N_o$ is the initial population.

For a general value of $N_o$, the logistic growth model can predict the the population fairly accurately. But I don't think the graph would be entirely correct if we have very low or very high values of initial population (nearing saturation).

So, What is the range of initial population where the logistic model works as a good approximate?


texts:
The pig is only an example, just an animal. Leydig cells have protein inclusions (Reinke crystals) that are mostly made of crystallised lipofuscin. They are secretory inclusions i.e. cells formed in secreting cells.

An example of Leydig cell in pig's testicle:

My teacher told me that there is a difference in the existence of some cells between humans and animals.
However, I cannot find such a difference. I have not been provided a slide of human Leydig cell so I have not been able to compare.

What is the morphological difference between Leydig cell in human and pig?


texts:
What is this snail? (Location: Bangkok, Thailan; size: 3 cm long, 5 mm wide; color: mostly black)

Video:  https://youtu.be/vxig5QOSoss


texts:
Discovered attempting to hide on bathroom sink handle at night, though bathroom light had been left on.

Barely reacted to attempts to capture it at all. No flying. No jumping. Just really slow crawling.

Found Eastern US. 2017/11/18


texts:
Two models have been proposed to explain how ATP hydrolysis by mitochondrial hsp70 drives protein import.In the thermal ratchet model (Figure 12-28A), the emerging chain slides back and forth in the TIM23 translocation channel by thermal motion. Each time a sufficiently long portion of the chain is exposed in the matrix, an hsp70 molecule binds to it, preventing further backsliding and thereby making the movement directional. Thus, a hand-over-hand binding of multiple hsp70 proteins translocates the polypeptide chain into the matrix.

What does thermal motion mean here? I will be obliged if somebody could explain it.


texts: Is the transcription starting site located before or after the promoter?

texts:
It's maybe a stupid question, but I really want to know the answer.

The definition of Promoter (From Wikipedia):

  In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes

And the definition of the transcription start site (From Wikiversity):

  The transcription start site "is the location where transcription starts at the 5'-end of a gene sequence.

I also Found this image (The source):

I'm asking this question because as far as I know, the RNA Polymerase binds to the TSS, and a friend of mine told me that's it binds to the Promoter.

PS : I'm interested in bacteria.


texts: Stopping all intracellular activity in a reversible fashion

texts:
I have never studied biology but the following question seems meaningful to me. Suppose I take a cell, not that of a unicellular organism, but a human cell. Normally, there are some intracellular processes going on. If I understand correctly, one way a cell is going to die is that enough mistakes happen during these processes and it can't take it anymore.

Suppose I really need this cell alive and well in two hundred years and I do not really care what happens in the meanwhile. Is there a way to stop all the intracellular processes (protein synthesis, intracellular digestion, etc.), in a reversible fashion, so that I (or probably not me but a great-great-great-great-great-great-great-grandchild) could "start" this cell again after two hundred years pass? Now, two hundred years seem like too much for an experiment, but you get the idea; say, a month would be OK too.

Surely, some biologist thought about this at some point. Any references studying this question would be great.

EDIT: Wikipedia says that

  Many bacteria can survive adverse conditions such as temperature, desiccation, and antibiotics by endospores, cysts, conidia or states of reduced metabolic activity lacking specialized cellular structures.

So at least some unicellular organisms can temporarily slow down the rate of metabolism.

I also think that some mammals can enter the state called hibernation, when their heart rate significantly decreases. I think this is different from above in that the amount of time mammals can spend in this state is less than the amount of time bacteria can spend in the dormant state (see here). From this I infer that the maximum metabolism slow-down factor is lower in mammals than in bacteria.

Ultimately, I am interested in learning how far we could push, via artificial means, the slow-down factor in complicated organisms like mammals. However, taking an entire organ and making all of its cells to go to sleep and then waking all of them up in an organized way seems to be much harder than achieving the same for a single cell. Thus my question: can we, in a reversible and controlled way, slow down the metabolism within a single human cell? What is the maximum slow-down factor then?


texts: Is Rheumatic fever more Chronic than acute?

texts:
It follows from the complication of S.pyogenes' pharyngitis.
I am thinking how the inflammatory response behaves: acute or chronic or something between.

I think chronic disease is better description here than acute, however not sure.

What is the type of inflammatory response in the Rheumatic fever?


texts: Is there a risk of localised die-off when plants bud too early?

texts:
I've been taking a few walks in the countryside in Scotland and England this winter (end of December 2014). Some parts of England haven't had any frosts yet, which is very unusual, and it's been generally quite warm since summer ended.

My friends and I agree that there's quite a lot of stuff putting out shoots and buds, as if it's April already. I can imagine that this means a lot of small fragile plants could get killed if a hard frost comes in the next few weeks. If so, it seems natural to expect that next summer will be marked by an absence of these plants, and, being dead, they won't put out seeds or otherwise reproduce for next year. In other words, we're expecting some species to experience localised die-off.

Is this plausible or are we just imagining it? If it's actually happening, is it something to actually be worried about? i.e. will a large portion of the seeds/shoots/buds/whatever refrain from growing even if some are being tricked by the mild winter, or will they be cold-resistant if they're coming up now, or is some other mechanism going to make it all okay? Alternatively, is this winter likely to trigger a large ecological change?

I realise this question doesn't single-out any particular species for attention, and perhaps it's too much of an open question for StackExchange's taste, but I'd very much appreciate some insight into how fragile or robust is the distribution of British plant life when the weather is abnormal, as it is right now.


texts: What exactly is this small puffer fish doing and how did it manage to accomplish such a feat?

texts:
I recently saw a video on youtube  where it shows a puffer fish making intricate designs in the sand:

OZZY MAN VIDEO

The puffer fish made this design on the sand:

What exactly is the puffer fish doing and how is it capable of accomplishing such a feat?  Is this behavior learnt, or innate?


texts: Determine similarity in percentages between species A and B, A and C, and B and C

texts:
The chart above is a graphic that shows the amino acid sequence differences between different organisms for a protein keratin.
The question I am required to answer begins as, "Keratin is made up of about 450 amino acids. Determine the similarity in percentages between species A and B, A and C, and B and C. Explain how amino acid sequences can be used in determining how closely related two species are."
My initial solution to finding the percentages is dividing the respective differences in the chart above by 450. Then, subtract that number by 100, and hence, find the similarity percentage. For example, for species A and B, I would divide 4 by 450, resulting in 0.89%. I would next subtract this percentage from 100%, resulting in 99.11% similarity. Is this the correct procedure?
My initial solution to explaining how amino acid sequences can be used to determine how closely related two species are is as follows: The larger the difference in amino acid sequences between two species, the less closely related two species are. Is this explanation correct as well?


texts: Are chromosomes from each parent split between gametes with equal probability (esp. in humans)?

texts:
I've recently read a little on Wikipedia about genetics, but I can't find a direct answer to this question.

My rough understanding is this:

Both males and females have pairs of chromosomes, one copy from each parent
Both produce gametes (eggs in females, sperm in males)
The gamete is produced during something called 'meiosis' to take only one set of genes

What I can't find an answer to though is whether that selection is completely random, such that every chromosome in a gamete has an equally likely chance of being taken from the male parent set and the female parent set.

Another way of putting it, perhaps: Would the range of 100% male parent to 100% female parent chromosome selection in the gamete be a binomial distribution?

My background is computing, so please assume very little knowledge of biology.


texts: Explaining the simpson's diversity index

texts:
In my biology class, we were trying to compare the biodiversity of two site. In doing so, we were instructed to use the Simpson's Diversity index as follows:

$$ \frac{\sum_i n_i (n_i - 1)}{N (N - 1)}$$

Where $n_i$ is the total number of organisms of a particular species; and, $N$ is the total number of organisms of all species.

We were given a method to calculate the index in a class that required almost naught mathematical understanding for the purposes of the experiment. From what I have read, the Index calculates the probability that any 2 randomly selected organisms belong to the same species, and it is thought that the closer the result is to zero, the more diverse the region is.

What I can't understand, is the math behind the index; for example: why is it multiplying n by n-1? And how is this better than dividing the sum of all the organisms by the number of species?

I'm in Pre-Cal, so when explaining, please do so with minimum emphasis on "advanced" math terms.


texts:
So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk.

I'm curious whether it would be possible to use fastq-dump to write to a named pipe (using mkfifo) and feed that into another program, for example Trinity, to run an assembly on the FASTQ file without ever having to write all that data to disk. For large datasets, this could actually save quite a bit of time in aggregate.

Has anyone done something similar? I am going to try and experiment with the technique soon, but I a) don't know much about the mkfifo process to begin with and b) am unsure of how this procedure would work for paired-end data where fastq-dump is splitting the SRA file as it goes. How would one specify which output would go to which pipe?

EDIT: A (hypothetical) example:

  mkfifo fileStream

  fastq-dump SRR123456 > fileStream

  Trinity --single fileStream misc_args

That should take the fastq-dump data and stream it into the named pipe "fileStream", which can then be used to stream data into Trinity. I don't know enough about all of the commands, however, to know if this makes any sense.

I would welcome any thoughts from more experienced users!

EDIT: Added update as an answer below.


texts: Why's there no vaccine against Respiratory Syncytial Virus (RSV)?

texts:
RSV was discovered in 1956. Here’s why we can’t rush a COVID-19 vaccine | AAMC

Respiratory syncytial virus (RSV): This pervasive respiratory virus has proven resistant to vaccination. Children treated with one vaccine in the 1960s developed an  enhanced form of the disease, suffering high fever, bronchopneumonia, and wheezing. Many were hospitalized and two died.
“That set the field back years,” Poland said, as researchers and manufacturers “were afraid” to try again.
Researchers have since tried but still not developed an RSV vaccine for public use, according to the CDC. Babies at particularly high risk for RSV are sometimes injected with an antibody to help fight off infection.

I don't grasp the Canadian government's Overview of the respiratory syncytial virus vaccine candidate pipeline in Canada, CCDR 46(4). E.g. so what if "amino acids do vary in prefusion specific epitopes"?

Challenges to RSV vaccine development
Antigen diversity
A successful vaccine candidate will account for the diversity of antigens presented by RSV in the form of the structural variability of the proteins on the surface of the virus. The protective, neutralizing antibody response to RSV is dominated by antibodies targeting the prefusion F protein on the surface of RSVFootnote 17Footnote 18. Although the genetic sequence of F does not vary substantially between strains of RSV [89% of its sequence is identical in both A and B strainsFootnote 19], amino acids do vary in prefusion specific epitopes [bolding mine]. As new products are authorized and make it into broad usage, it will be critical to understand the sero-epidemiological responses at a population level to understand whether prefusion or postfusion antibodies are dominant responses, and whether these demonstrate equivalent protection against both RSV type A and B.
RSV infection dampens the immune response
[...]
There are no clear correlates of protection
[...]


texts: What does this mutation notation mean: MAP2K41161fs*12

texts: I received a report that had a mutation notated as: "MAP2K41161fs*12". I'm used to seeing this sort of thing: BRAF(V600E) or BRAF(T1799TA). Can someone tell me how to interpret "MAP2K41161fs*12" ?? Is it a deletion? An insertion? A translocation? Or What?


texts:
In Texas, there is lot of grassland and many cotton fields, which need a great deal of water. However, I have not seen any forests or areas with many trees.

Why are there no forests or heavily-treed areas in Texas?


texts: Which cell organelle is more important in giving colour to petals?

texts: It was a question in our school test and given answer was vacuole. But I think it should be chromoplast as they are the organelles specialised to provide colour. But options were given, so which is more accurate? Is the question controversial (both are correct?)


texts: Problem with Caspr antibody in western blotting

texts:
I have been working on optimizing western blotting for Caspr (contactin associated protein), but I am having difficulties and would like suggestions.

I ran my proteins on a 40% acrylamide gel,
I used TBST for washing and BSA as blocking buffer.
I incubated the blot with primary antibody overnight.
The secondary antibody is linked with HRP.

I could  not find any bands in the blot.(Same problem was faced in case of contactin) What might be the reason?

Edit:-

I repeated the experiment a couple of times and found that secondary antibody(Anti-mouse,1:5000)wasn't working anymore.
I made freshly diluted secondary antibody again and found bands.
The old secondary antibody dilution was only few months old.What may have gone wrong with it?


texts: What are some examples of undirected weighted networks in ecology?

texts:
I'm a math major with a current interest towards network theory. A network can be considered as a collection of nodes, and edges between these nodes signifying some relation between them. The most ubiquitous example would be a social network like Facebook with nodes representing people, and an edge connecting two nodes if they're friends.

A network is called directed if the edges have a direction. This means that if there's an edge directed from A to B, it's not the same as an edge from B to A. An example of this would be a food web network, where the nodes represent species and an edge from species A to B means that A eats B. Obviously, this does not necessarily mean that there's an edge from B to A (rarely does the prey eat the predator).

A network is called undirected if it is not directed, i.e. none of the edges have any direction; if there's an edge from A to B, it necessarily means that there's an edge from B to A.

Now, one can assign weights (numerical values) to the edges in a network to signify the relative importance of edges. In the Facebook example above, this can be considered akin to assigning values to edges which indicate the strength of friendship/distance between the residences of friends, etc.

I wish to study ecological networks to see if I can make interesting inferences from my study of weighted networks.

So can you give me some examples of undirected, weighted ecological networks?


texts: Calcium and nitric oxide: does a numerical relationship exist?

texts:
Currently, I am trying to understand how nitric oxide and calcium are related during the production of the former (I am not a biologist nor a chemist, so my knowledge about these topics is very poor). I would like to know if there are some papers or experiments that present a model (or, at least, some numerical data) that relate the concentration of nitric oxide with the concentration of calcium.

I've read somewhere that one of the effects of nitric oxide in synaptic transmission is the reduction of calcium influx, but how does it happen quantitatively? I've started my research considering the model reported here where NMDA is assumed to be main calcium source so that the time derivative of calcium concentration is directly related to the NMDA current. Now, I think this model should be slightly modified if I would consider the effects of nitric oxide; I've found a model that describes how nitric oxide synthesis occurs, but what is missing for me is the link between calcium concentration and nitric oxide concentration.


texts: Will this strategy work for verifying successful cloning of a DNA fragment into a plasmid vector?

texts:
So I am in a bit of a time constraint. Essentially, I inserted a DNA fragment via molecular cloning which contains a unique RE site. I need to confirm whether my colony has or does not have the fragment.
I need to do this in one day so would this work as a confirmation strategy:

Pick colony and perform colony PCR with primers around RE site.
Cleanup the PCR product and digest using the enzyme which was inserted.
Run on a gel. If a cut is noticed, this confirms that the colony had the inserted fragment (containing the RE site).

Would this strategy work? Are there any notable issues people can for see in this strategy?


texts: How are we able to selectively inflate our cheeks?

texts:
First an observation - I noticed that I can not inflate my cheeks with my mouth open. This means that inflating cheeks is not a muscle property and that only pressure of air from lungs trapped inside my closed mouth is responsible for any inflation. Also, once inflated I can move my tongue anywhere and still retain the inflation. This means that tongue is also not responsible for air regulation inside mouth.

Moving on, we all know that we can either inflate both our cheeks, or we can inflate only cheek from one side or we can inflate *portion of face between lips and chin* (I don't know what it is actually called). Put simply, we have complete control over which part of my face would I like to inflate.

I don't understand how this is possible without muscle control? Air has tendency to occupy all space therefore my entire cheeks should get inflated without me having any control whatsoever, but as it turns out I can control and redirect the air to apply pressure only at a particular cheek without any help from tongue. How?


texts: What are the sources of energy that alcohol provides?

texts: Milk contains sugar and proteins which give energy. What compounds in alcoholic beverages (edited) give energy? Are they more likely to turn into fat (as in beer belly) than blood glucose?


texts: Aligning multiple sequences in heterogeneous group

texts:
I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have seq1, seq2.... seq10, seq1 might align to seq3 and seq8, but be completely unrelated to the others.

There are also some differences in the lengths sampled, so the above example might represent:

Seq1-------------------------------------------------

Seq3----------------------   seq8-----------------

Such that seq3 and seq8 don't align to each other, but both align to seq1

So what I'd like to do is go through and somehow generate a list of groups of sequences that align to each other, as well as the alignments. eg:

Group 1

Seq1-------------------------------------------------

Seq3----------------------   seq8-----------------

Group 2

seq2------------------------------------

.       seq6-----------------------------

.   seq7--------------------------xxxxxx

Group 3... etc

Trying ClustalW or MUSSLE to align everything doesn't work (or takes an unreasonable amount of time), I'm guessing because there are so many sequences that don't align at all. I tried making a custom BLAST database and then BLASTed each sequence against it, but then I get multiple hits for the same alignment (with the group 2 example above, seq2:seq6, seq2:seq7, seq6:seq2, seq6:seq7, seq7:seq2 and seq7:seq6 all get returned as 6 unique hits, when they should be grouped together.

My current coding knowledge is fairly basic, but I'm willing to read docs and figure stuff out, I just don't want to reinvent the wheel.

Edit2:
Really, the grouping is the important part - once I have the groups, I can do the alignment separately with little effort. I'd just like to have groups where each sequence is in a single group.


texts:
A relatively frequent, completely penetrant recessive disease variety of mutations in the gene. The gene has been recently cloned. Analysis of the region flanking the gene reveals that the population has at three (3) RFLP (this is a type of DNA marker; they are not SNPs so have much larger sizes) alleles in this region. The sizes of the RFLP alleles are 7, 10 or 13 kb in length. Shown here are two small pedigrees of families in which affected individuals are shaded in black. The size of the RFLP alleles each individual carries is shown below the pedigree. enter image description here

Question: If the male child from the left pedigree marries the female child from the right pedigree, What is the probability their child will be a carrier?

I said that there isn't enough information to tell since the parents genotypes are unknown.


texts: Real unipolar neurons do indeed exist in human?

texts:
I studied that the unipolar neuron in human body are not really unipolar but they're pseoudounipolar neurons. On the other hand according to what I understood from wikipedia (neuron) there are real unipolar neuron.

In fact, I'm confused (if unipolar cell does exist in human body or doesn't) and I would like get you help about it.


texts: Would modifying the human microbiome to digest cellulose be worth it?

texts:
I've read that cellulose has a lot of calories that go unused. I was wondering how practical it would be to incorporate a bacteria capable of suggesting cellulose into the human gut.

I would say that it is worth it if a human could gain a substantial amount of calories by digesting cellulose in a "normal" diet. To compute the amount of calories, I would like estimates for how fast bacteria can process the cellulose (like half life per billion bacteria) and how efficient the process would be.

Then given the average duration of the digestive process and a reasonable bacteria population, estimates could be made on how much energy could be gained by digesting the cellulose in an average diet.


texts: can the face of a person be accurately predicted from DNA information?

texts:
http://blogs.smithsonianmag.com/artscience/2013/05/creepy-or-cool-portraits-derived-from-the-dna-in-hair-and-gum-found-in-public-places/?utm_source=plus.google.com&utm_medium=socialmedia&utm_campaign=20130503&utm_content=collageartdna

Can the face of a person be accurately rendered just from analysing a DNA sample of that individual?


texts:
I've been studying evolution for some time and was wondering whether the emergence of different races is an example of micro evolution within our species?
Bonus Question: is it impossible for homo sapiens to undergo to split into separate species via macro evolution?  I think it's impossible since were so interconnected (due to globalization and transportation), therefore speciation could not occur.

Thanks


texts:
This tiny monstrosity (~2mm in length) was inside of some kind of "flat tent cocoon" on a pepper plant leaf in Washington state, USA.

Not sure what's going on here. Is it malformed or infected?


texts: Will a 0.2g/mL sugar concentration cause vomiting in humans?

texts:
This infographic claims that the sugar content in a can of Coca Cola would cause vomiting if not for the phosphoric acid.

  In The First 10 minutes: 10 teaspoons of sugar hit your system. (100% of your recommended daily intake.) You don’t immediately vomit from the overwhelming sweetness because phosphoric acid cuts the flavor allowing you to keep it down.

Now this question came up on skeptics.SE and the remaining question is whether (flavourless) water with sugar would cause vomiting. Very specifically we're talking about 200ml of final concentration and 39 grams of sugar. I would try it out myself, but per the rules of skeptics.SE I am not allowed to do this so I am posting it as a question here.


texts: Do Traits Have to be Adaptive in Order to Survive?

texts:
I'm reading Michael Pollan's book 'How to Change Your Mind', which is largely about psychedelic mushrooms. In discussing the biology of the mushrooms, he writes:

'Even if psilocybin in mushrooms began as 'an accident of a metabolic pathway', the fact that it wasn't discarded during the course of the species' evolution suggests it must have offered some benefit.'

I'm wondering if this is actually true. In general, I'm wondering if it is true that traits that do not confer advantage will eventually be weeded out.

Being ignorant of the finer points of evolution/natural selection, I can make arguments both ways. On the one hand, it seems that the intense competition would make investing any resources at all in a trait that was not beneficial a totally losing proposition. Therefore no traits that weren't positively adaptive would survive. On the other hand, there seem to be all kinds of traits that are 'neutral' in fitness terms but which survive anyway. E.g. coccyx, male nipples, appendix, whale legs, etc.

I am not talking about information encoded in the genome, which can be present but not expressed. I am talking about phenotypes, i.e. traits that get expressed in interactions with the environment, such as the psilocybin chemicals in these mushrooms. (Though I suppose unexpressed genetic info could never be selected for or against by natural selection by definition.)

So to put a very fine point on my question: Is it possible/likely that psilocybin mushrooms produce a chemical that happens to engender hallucinations, not because doing so is adaptive, but just incidentally? So that this property would be something like the redness of blood, i.e. not adaptive in itself but just a matter of happenstance?


texts: Is it true that it is mostly impossible, for any kind of antibiotic, to succeed in killing off every bacteria in a very rich environment?

texts:
It is commonly believed that the resistance to antibiotics by micro-organisms is truly evolution at work, and that the recent surge in superbugs may very well be attributed to it.

When we refer to a bacteria's ability to "evolve" into resisting this antibiotic, I assume we mean that when we introduce antibiotics into the environment, a lot of bacteria die but some who by mere chance and luck didn't do so and that these lucky bacteria go on to survive and multiply, thus aiding in the creation of so-called superbugs, or rather, bacterial resistance to sophisticated drugs.

This whole situation already suggests to us, or at least to me, that there's much inherent complexity in these organisms and indeed a certain uniqueness to each.

I have, however, been troubled recently by the following question: is it truly impossible, for any kind of wholly new antibiotic which was not used before (no matter how complex), to succeed in killing off every single bacteria in any rich habitat/environment (no matter how populous)? And that there'll always be some bacteria on whom this shall not work apparently due to uniqueness in something of their structure?


texts:
At my med school we have human samples (body parts, organs, etc.)

They are soaked in some sort of solution for long term storage. I'm quite sure that it's not formaldehyde as that would be really toxic and we're allowed to pick them up from the tubs.

What sort of solution could this be?


texts: Correlation between morphology of neurons and neurotransmitters

texts:
Are there known significant (positive or negative) statistical correlations between the morphology type of neurons and the neurotransmitters that they use (presynaptic, i.e. transmitters that are released, and postsynaptic, i.e. transmitters that are received)?

This question assumes, that a definite set of morphology types has been defined. The answer depends on this definition, of course.


texts: H3K36me3 role in RNA polymerase II elongation

texts:
I found a paper describing the association of RNA polymerase II with the histone methyltransferase Set2 that methylates H3K36.

At the end they say:

  While our results strongly implicate K36 methylation as having a direct role in RNAPII elongation, the precise role is currently unclear. We propose three possibilities: (i) K36 methylation generates a chromatin structure that is more permissive for RNAPII passage. In this scenario, the loss of Set2/K36 methylation would result in a chromatin structure that is more difficult for RNAPII to pass, which might appear as an increase in RNAPII occupancy along the gene through increased pausing. (ii) K36 methylation generates chromatin structure that is less permissive for RNAPII passage. In this case, K36 methylation acts as a negative regulator of RNAPII elongation, and the loss of this “mark” permits increased RNAPII passage.

I am a bit confused about the (ii) point. If the loss of this mark permits increased RNAPII passage we would not see the H3K36me3 pattern in the active genes. Why is then H3K36me3 said to mark active genes?


texts: Giving minimal credence to estimates in popular media of the average biomass of  insects/arachnids, etc. in an acre of land, it seems that a "free-range" cow (I don't mean to pick on cows) might be something of an omnivore. Is there any evidence that herbivores derive essential parts of their diet from sources other than cellulose? Or that they do not?


texts: Why we need an egg cell donor and a surrogate mother in an organism cloning process?

texts: Could a whole set of artificial organism-cloning process only be operated on the  somatic nuclear donor ,which means for example ,can we extract the somatic nuclear from animal "A" and put it into the egg cell plasma also from animal "A"  then implant it into the animal"A"'s uterus to clone "A" ?


texts: How does a base pair weigh approx. 650 Da (which is two paired nucleotides) but an amino acid (3 nucleotides) weighs only approx. 110 Da ?


texts: The heart of a Pigmy Shrew beats 1300 per minute then why is it so fast?

texts: A pygmy shrew is such a small animal. Even with such fast heart beats their average life span is 1.5 years. So can we consider faster heartbeats to not be good for health?


texts: If dolphins can see sound, can they say images?

texts: Dolphins determine their surroundings by listening to echoes. Can they mimic those echoes and communicate it to other dolphins, transmitting an "image"? Does the same go for all echolocators?


texts: A suggested ancestor of cyanobacteria consumed manganese. Why not magnesium?

texts: Joseph Kirchvink and others have suggested a theory that a precursor to cyanobacteria consumed manganese (I believe in the form of Mn2+ dissolved in water). Why wouldn't dissolved Mg2+ work equally as well? It was more abundant and is the central ion of the porphyrin ring in chlorophyll.


texts: What is the fastest but not venomous snake?

texts: Is it known which non-venomous snake can attack most quickly? I guess it is a snake that attacks its opponent by bites, and not some kind of constrictor.


texts: Has there any mutations been recorded which cause harmful effects due to change in the part of pre-mRNA responsible for proper m-RNA splicing ?


texts: How to distinguish processionary from other caterpillars

texts:
Processionary caterpillars have a vast and harmful presence in southern Europe. In northern Italy, in parks and gardens, I often see caterpillar nests in trees, but I do not know how to tell if they are processionary, with dangerous urticating hair, or other innocous (for humans and pets) kinds of caterpillar (such as tent caterpillar, for example).
I've read from Wikipedia and other sources that processionary "usually" nest in pines and oaks, but it is not clear to me if it is only a matter of preference or if they cannot nest in other trees. Does seeing a caterpillar nest in an another kind of tree safely imply that it is not a processionary nest?
Besides, the photos I have found show very different kinds of caterpillars,  what easy visual clues could I use to tell them apart? Ideally, I would like to be able from a distance to decide if I should get my dog away from an "infested" tree or if I can safely ignore it.


texts: How do I go about traveling with DNA extract samples?

texts:
I am traveling from Fairbanks, Alaska to Vienna, Austria in six weeks and need to bring 10 very small (~50 ul) samples of extracted arctic ground squirrel DNA with me.

I need to travel with these on dry ice in a little carry-on cooler.

Has anyone flown with DNA samples? Any advice on how to go about it? Questions to ask customs?


texts: Serotonin - Does being aroused make you sleepy?

texts:
My Psychology text book says Serotonin causes "Sleep, arousal levels and emotion"

Does this really mean that when you are being aroused, Serotonin is released, which in turn makes you sleepy? If so, what evolutionary benefit would that have??


texts: How much tissue is required to do RNA-seq analysis on a single organism?

texts:
How much tissue would be required to do RNA-seq analysis on a single organism?
More specifically, if a person wanted an RNA-seq analysis of expression for a single organ, how much tissue would they need to donate?


texts: What species of duck is this? See below photo. Head colour is green like a mallard, but that's pretty much the only similarity. Spotted in Leicestershire, UK.


texts:
I've heard in many documents said that :

  There are 25 million to a billion different T-cells in your body. Each
  cell has a unique T-cell receptor that can fit with only one kind of
  antigen - quoted from askabiologist.

But I haven't found the mechanism of this. How our body produce too many different T-cells? Does our genome need to have 25 million to billion genes to encode for 25 million to billion unique receptor for those T-cells? Does each T-cell have a different gene region on their genome or they have a different turned-on/turned-off genes ?


texts: General Enhancer Questions (Methylation Patterns, ect.)

texts:
I have a biological question(s) for ya'll involving enhancers.

1.) Enhancers work by being the binding sites for TFs. But how does this increase transcription? (Especially when enhancers can be extremely far away from the gene they control.)

2.) Enhancers can become methylated. When they do, does this usually prevent transcription factor binding? And if it does prevent the binding, how does this affect the role of the TF and gene expression.

EDIT:  Here's what I found.

It seems that enhancers can be far away from the gene they act upon, but the binding of TF via their DNA-binding domain can cause looping of DNA to help them reach the promoter region of the gene of interest. Thus, increasing the rate of gene expression.

On the reverse, methylation can sometimes be seen to act as silencing of gene expression. So, if our enhancer region is methylated, this may prevent TF binding and the enhancer from increasing gene expression.

BONUS:  Methylation in promoters can also cause silencing by preventing RNA polymerase II, and the required proteins (ect) from carrying transcription.

If anybody wants to add (or correct anything, let me know!)


texts: Does the spray of a skunk affect only mammals, or can it also affect birds, reptiles, amphibians, fish, or invertebrates?

texts:
The spray of a skunk is said to affect dogs, bears, and humans.
Can it also affect other mammals or members of other groups of animals such as birds (other than the great horned owl, due to their poor sense of smell), reptiles, amphibians, fish, or even invertebrates (insects, spiders, crabs, etc)?


texts:
I read the wikipedia article and am confused if a chromosome is the pair of two chromotoids or if each chromatoid is considered a chromosome.

I've heard someone say we have 23 pairs of chromosomes for a total of 46 chromosomes.

I am trying to be precise with my words here.

Even more confusing they always seem to pick this certain state of the chromosoes lifepsan to describe them.

The point at which it replicates to create a pair.

Why not just describe the chromosome before it replicates for simplicity sake.

Would it be correct to say that before the chromosome divides, there are simply 23 of them?


texts: How EGDS (endurance genetic distance score) is calculated?

texts:
Can anybody please make me understand how EGDS5 has been calculated to 40.8 in this paper at page#31?

The formula has been described in this paper but when i tried the same, I am not getting the same results.

According to paper describing the formula:

$EGDS = 100 - \frac {100\cdot d} { n \cdot w }$

where

$n =$ number of studied polymorphisms

$w =$ score given to worst genotype

$d =$ euclidean distance calculated as follows

$d = \sqrt{ \sum_{i = 1}^{n} (2 - x_i)^2}$

$x_i =$ genotype score of corresponding polymorphism

$2 =$ optimal genotype score

here is what I tried. Given below is the genotype score of 5 genes:

$ x = (1,1,1,1,0)$

$d = \sqrt { (2-1)^2 + (2-1)^2 + (2-1)^2 + (2-1)^2 + (2-0)^2 }$

$= \sqrt { 1 + 1 + 1 + 1 + 4}$

$= \sqrt 8 \approx 2.82$

Now, $EGDS5 = 100 - \frac{ 100 }{ 5 \cdot 4 } \cdot 2.82$

$= 100 -  5  \cdot 2.82 $

$= 85.9$

which is not equal to 40.8.


texts: How does Celiac's Disease cause people to stop growing?

texts:
In all of the sites I've looked on, one of the symptoms of Celiac's Disease is the failure to grow in children. Why would an immune attack against gluten cause stunted growth?

Celiac.org states:

  When people with celiac disease eat gluten (a protein found in wheat,
  rye and barley), their body mounts an immune response that attacks the
  small intestine. These attacks lead to damage on the villi, small
  fingerlike projections that line the small intestine, that promote
  nutrient absorption. When the villi get damaged, nutrients cannot be
  absorbed properly into the body

Journal of Pediatric Gastroenterology & Nutrition published a study on catch-up growth in children diagnosed with Celiac's before the age of nine.

Is the lack of nutrients what causes the impaired growth, or is there more to it than that?


texts: Is the glomerular filtration rate, per kidney or for both?

texts:
We say in a healthy human being the average glomerular filtration rate is about 120 mL/min. Is that for both kidneys together (60+60), or just one kidney?

Pardon me if this makes me sound like an idiot, because I have a feeling I'm thinking about this wrong.


texts: What makes diffculty to make a human bio-tooth compare to a mouse's?

texts:
Some time ago I read a news article that said a bio-engineered tooth based on a mouse's would be available around 2015. There was some research about it at King's College in the UK, and many other institutes.

Now, I haven't heard any news that such a thing is available. It seems to be a basic result of stem-cell research, how much difference can there be between a human's tooth and a mouse's?


texts: Do tarantulas and humans have the same mechanism for growing hair?

texts:
There's hair on my arms.

Tarantulas also have hair on their arms.

Is this the same type of hair?


texts: How does the social structure of lion prides prevent incest?

texts:
I assume that lions don't have a concept of incest and they will just mate with any adult lioness in heat, daughter or not.
If so, is incest inevitable as the female cubs will grow up and remain in the pride? Their brothers will be kicked out as they reach mating age. But the females stay, so what is the mechanism that will prevent their fathers from mating with them?
I suppose that their fathers will be driven out of the pride by incoming males sooner or later. But if it doesn't happen soon enough, then what prevents them from mating with their daughters?


texts:
A few friends of mine told me that salt provides zero nutritional value to us, and in fact can harm our bodies. Now, these guys are medical students, and being an engineering student myself, I decided not to argue with them. The rest of this question assumes that this fact is true, so if it's not, you can just go ahead and call me out now...

So here's my understanding of things: we 'like' doing things because of our instincts, which have slowly become refined over millions of years. For example, I 'like' eating foods with fat in it because my instinct compels me to do so. Fat is 'good' for my body, since it provides a lot of energy (obesity problems aside).

So are there certain things, such as eating salt, that are not in fact beneficial in any way, and we only do these things because we were trained to as children? This is the only thing I could come up with, but it's not a very satisfying explanation for a few reasons. First, I think humans have been eating salt for a long time. This would mean that most likely, it is actually our 'instinct' to eat salt. Also, salt is eaten in every culture today, which has the same implication.

So is there some better explanation?


texts: What relation do glycerol-3-P DH and acyl-CoA DH have with Complex II of the ETC?

texts:
I am sorry if this may be a purely definitional/nomenclature question.

Complex II of the electron transport chain (ETC) would be succinate dehydrogenase, transporting electrons to ubiquinone (and forming ubiquinol with the addition of 2 protons).

Both glycerol-3-phosphate dehydrogenase (DH) and acyl CoA DH are integrated in the inner mitochondrial membrane, and form an ubiquinol, which can be used by Complex III of the ETC - very similarly to succinate DH. I was wondering why, then, these 2 enzymes weren't also part of "Complex II" or whether they were just not part of an "ETC complex" because they aren't part of the TCA cycle, or something? Are they in any way also related to the ETC supercomplex/respirasome?

Thank you.


texts: Reason behind using inducible promoter for heterologous expression

texts:
Protocols often seem to use regulatable promoters when expressing a heterologous gene in a host like yeast where they add something like IPTG to induce expression from (say) the lac promoter.

Is there a reason to do this as opposed to using a constitutive promoter? i.e. Is there reason to think that regulatable (inducible) promoters have higher expression levels than constitutive promoters?

In other words, what utility is there in having an external "switch", i.e. the IPTG to turn on expression on-demand rather than just boost the default expression level using a promoter not requiring induction?

The goal here is small biomolecule synthesis by industrial fermentation of a transgenic yeast.

Example Protocol:

L21 Star™ (DE3) E. coli cells (Invitrogen) were co-transformed with the plasmids pACYCDuet-4506 and Ct94-pETDuet and transformed cells were selected on carbenicillin (50 μg/ml) chloramphenicol (34 μg/ml) LB-agarose plates. Single colonies were used to inoculate 5 mL LB medium with 50 μg/ml carbenicilin and 34 μg/ml chloramphenicol. The culture was incubated overnight at 37° C. The next day 2 mL of TB medium supplemented with the same antibiotics were inoculated with 0.2 mL of the overnight culture. After 6 hours incubation at 37° C., the culture was cooled down to 28° C. and 1 mM IPTG, 2 mg/mL mevalonate (prepared by dissolving mevalonolactone (Sigma) in 0.5N NaOH at a concentration of 1 g/mL and incubating the solution for 30 minutes at 37° C.) and 0.2 mL decane were added to each tube. The cultures were incubated for 48 hours at 28° C. The cultures were then extracted twice with 2 volumes of ethyl acetate, the organic phase was concentrated to 500 μL and analyzed by GC-MS as described above in Example 3. In these conditions sesquiterpene production above 200 mg/L was routinely achieved. Beta-santalene was produced.


texts:
Often, genetics studies, especially genome wide ones, talk about "focal copy number variations" in genes or regions of the chromosome. I know what a copy number variation is. What does "focal" mean, exactly?

Are there non-focal CNVs? What are they? Where did the term "focal" originate? Is there a specific paper that coined (and hopefully unambiguously defined) the term?

A search for "focal copy number variation" on Google Scholar should turn up plenty of papers about it. The GISTIC algorithm is a popular computational method for finding putative CNVs- so information about this algorithm may have some clues.

A documentation text for one GISTIC implementation on the Broad Institute's website states the following:

  (8) Broad or Focal: Identifies whether the region reaches significance due
  primarily to broad events (called “broad”), focal events (called “focal”), or
  independently significant broad and focal events (called “both”).


texts: What is the meaning of a reported OD600 value?

texts:
I can't find a reference that explains what, for example, OD600 = 0.1 means.

For example, Wikipedia states

  OD600 is an abbreviation indicating the absorbance, or optical density, of a sample measured at a wavelength of 600 nm.

In other words, the OD600 value reports (a function of) what percent of light goes through a sample. But that depends on the thickness of the sample. More light will go through 1 millimeter of fluid than through 1 meter of the same fluid. So what is the thickness of the sample involved when reporting OD600? Or is the OD600 independent of that, so that it actually has units that people simply omit? In that case, what are the units? What is a precise physical interpretation of what is meant by the measurement OD600 = 0.1?

Suppose OD600 = 0.1 for some sample. I shine 1 mW of 600nm laser light through a 1 cm path length of the sample. What is the transmitted power?


texts: How do bumblebees and hornets avoid the negative effects of inbreeding?

texts:
I just learned that all hornets and bumblebees except for the queen die at the end of the year and the queen starts a new nest in spring.

But that means the next generation of queens have only brothers to breed with.

Should this lead to severe inbreeding, which over a couple of years would cause serious problems for survival?


texts: Bird ID (greenish passerine, Sacramento, CA)

texts:
Can anyone identify this small, greenish bird I saw in Sacramento, California, in May 2016?  I tried using whatBird.com but wasn't able to come up with anything convincing.

It looks a little like a willow flycatcher (Empidonax traillii) or dusky flycatcher  (E. oberholseri), but their heads don't seem so strongly two-coloured.

(Photo: own work; sorry about the not-great quality)


texts: Can the Donnan effect be reversed so phospholipids follow ions?

texts: I know that there are flipases and flopases that facilitate this sort of thing, but I'm curious about other possible influences. Can the Donnan effect be reversed so that phospholipids follow ions? For example, calcium efflux from cells causes it to be more energetically favorable for phosphatidylserine (slightly more negative, and thus slightly more likely to follow a positive charge) to be ejected from inner to outer leaflet.


texts: Has anyone tried using functional near-infrared spectropathy to quantitively measure sodium concentrations in the brain?

texts:
Functional near-infrared spectropathy "fNIRS", is a biophysics/medical technique that uses the near-infrared part of the electromagnetic spectrum (around 680nm to 810nm in wavelength) to image the blood oxygenation level dependent "BOLD" effect in the brain to image brain function for more on BOLD look here. Recently, in 2018 a study was done link to study showing that High-field MRI could be used to functionally image sodium quantitively in the brain.
I'm wondering if the same thing (functional sodium imaging) can be done with fNIRS or an Infrared spectropathy type deal.
Does anyone know if this has been attempted?


texts:
I have been given a project involving a plasmid that contains long stretches of Adenine (60 or 120 bases each). These PolyA stretches are interrupted by the occasional G or C.

I understand that performing PCR, cloning, DNA synthesis, mutagenesis, and sequencing on repetitive sequences is difficult. What techniques and practices should I follow to improve the accuracy when dealing with these PolyA sequences?


texts:
Early this morning, I found this beautiful caterpillar specimen crawling over a leaf:

This specimen was found today morning (spring season) in Brazil at Porto Alegre City 30°01′59″S 51°13′48″W. With approximately 1 Inch long.

What kind of specimen is this?


texts:
They closed my question on the Physics Stack Exchange because it wasn't a purely physics question, so I'm trying here.

Recently I've come across the topic of scrapping microwaves, and the various warnings about the potential dangers. I've found out that generally speaking higher frequency radiation is more harmful, also that frequency itself is not the sole factor of harmfulness; as one question on the Physics site remarks the fact that microwaves and Wi-Fi use the same 2.4 GHz range, yet Wi-Fi doesn't cook. Anyway, I saw on a website:

  Don’t take apart the magnetron or play with it for several good
  reasons! First, there is the obvious danger of 2.45 GHz microwave
  radiation.

There are two problems I see with this warning. First of all isn't 2.45 GHz well into the radio wave category? And also radiation of 2.45 GHz wouldn't be harmful in and of itself, right?

Also a comment from the Physics site:

  wifi would be dangerous because of the microwaves, but it is limited
  to very low powers

This seems to imply that microwaves in and of themselves are harmful.


texts: What makes a DNA sequence motif a DNA sequence motif?

texts:
I've read about DNA sequence motifs, but still don't understand what makes some sequence a DNA sequence motif. Is this a well-defined concept? For, example,
What are DNA sequence motifs? says:

  Sequence motifs are short, recurring patterns in DNA that are presumed
  to have a biological function. Often they indicate sequence-specific
  binding sites for proteins such as nucleases and transcription factors
  (TF). Others are involved in important processes at the RNA level,
  including ribosome binding, mRNA processing (splicing, editing,
  polyadenylation) and transcription termination.

For example, I've been working with Recombination Signal Sequences (RSS), which are important in immunology. However, from what I can tell, RSS are not themselves motifs, but they do contain motifs. E.g. Conservation of sequence in recombination signal sequence spacers
says

  Previously, the RSS has been described as possessing both a conserved heptamer and a conserved nonamer motif.

So, apparently, the heptamer and nonamer component of the RSS are themselves motifs, but the RSS itself is not. Can anyone explain why? Thanks.


texts: Using formulas to explain why contraction of blood vessels leads to increased blood pressure

texts:
I know, I know this is probably a question too simple to be asked on a forum like biology stack exchange. Problem is, I looked many places and can't seem to find a more mathematical approach to explain why the contraction of a BV leads to increased blood pressure (BP).
The main formula i'm looking at is Flow = Pressure/Resistance. In addition, Flow = Area x velocity so Area x velocity = Pressure/Resistance. As the BV constricts, the radius, ie. area, decreases, and so the pressure decreases. But clearly, that is not the case.

What am I missing here?


texts: How to set threshold in ImageJ for quantifying relative fluorescence?

texts:
I have taken images from two different samples that have uptaken EdU during DNA synthesis (S-phase). The experiment setup is to find which condition had uptaken more EdU. Therefore I am detecting EdU with fluorescent to be able to quantify them in two conditions and compare them. The images are taken under same exposure. However in ImageJ when I want to adjust threshold I am not sure if I need to have the same threshold for both images or they can be different? Any tips are appreciated and let me know if I need to provide more info.

cheers!


texts: Cocoon like bug on exterior walls south florida

texts: Can anyone tell me what this is? One side of my house has 30 to 40 of them. when I try to pick them off they leave either brown spots or fibers from the cocoon. Is there anyway to deter them?


texts:
Are there known life forms that are able to transform mechanical energy into chemical energy?

This question asks a similar subject, but more specific and has no answers.

The background of this question are thoughts about hypothetical life on tidally locked exoplanets of red dwarf stars, where light for photosynthesis is scarce but mechanical energy (storms and/or water currents) aplenty.


texts: Why aren't gene drives extremely common?

texts: The ability for gene drives to sidestep the Mendelian mechanism and rapidly spread through populations (even if the gene is slightly fitness reducing) is extremely powerful. Why aren't normal populations riddled with parasitic gene drives?  What mechanism keeps naturally occurring gene drives suppressed to (apparently) very low levels?


texts: How does injecting low doses of allergens cure allergies?

texts:
Allergy shots (aka. allergen immunotherapy) help people adapt to allergens by injecting a gradually increasing doses of one or more allergens.

Does this procedure tell the body that this allergen is safe and there is no need to mount a response to it? In other words, does this mean that there will be no reaction at all rather than just a reduction in the allergic reaction.


texts: Challenges of Industrial-Scale Fermentation

texts:
I was reading the wikipedia article on industrial fermentation, and it mentions that

  It is well established in the field of industrial microbiology that what works well at the laboratory scale may work poorly or not at all when first attempted at large scale.

Why is that?  What are the barriers to large-scale fermentation of bacterial culture?

Also, I know that cell cultures have distinct phases of growth and decay, but what happens after the cells die?  Would an industrial fermentation process have to "re-culture" the bacteria?


texts: Is it possible to simulate the effects of high altitudes for plants?

texts:
Note- I considered asking this on gardening.stackexchange.com but i believe it is better suited for this site since it deals with more complicated material.

As I understand it, certain plants (Camellia sinensis, Coffea, etc.) grow best at higher altitudes. What factor, biologically speaking, is responsible for this?

I know that the oxygen concentration at higher altitudes is lower, is this the reason?

If so, is it possible to use machinery to alter the gas concentrations in a grow room and simulate the effects of high altitudes? Are there any other factors such as pressure or anything that can also be altered? Would simulating this environment be practical for large scale applications?


texts: How was birth control realized in ancient days?

texts: In ancient days, there were no birth control methods like condoms or contraceptive pills available. How did they control pregnancy?


texts: Why are fatty acids synthesized in two carbon units?

texts:
Why does long-chain fatty acid synthesis involve the two-carbon precursor, malonyl CoA, rather than the one-carbon acetyl CoA (or even a three-carbon precursor).
Is this because fatty acids with an even number of carbons are somehow ‘better’ than those with an odd number, or does it reflect some aspect of the chemistry involved?


texts: What are the theoretical and actual (measured) minimum water potentials in plants?

texts:
I'm a plant physiology researcher, but water potentials are not really my thing, so I don't have a great grasp on the literature. I'm dealing with water potential data right now though, and it seems questionable to me. Some of the measured water potential (solute + metric potentials, after lysing cells to break turgor) are as low as -48 bars (most in -10 to -35 range).

That would, if my math is correct, translate to a solute concentration in the 2000 mOsmol range, which seems extremely high to me. Consequently, I'm trying to determine if there is an analytic issue with the data collection. I've run through the equipment chain, checked calibrations, and everything seems ok. I've also been combing plant physiology lit. for comparable data, and I find some in that range, but I can't find any theoretical work that would help set a 'ceiling' for what constitutes a reasonable solute + metric potential.

So, my questions are these:

What is the theoretical maximum capacity for dissolved ion concentration in water, and what pressure potential would that represent, compared to pure water.
Is anyone aware of plant physiology research that has attempted to establish a minimum in vivo water potential in plants (either total potential, or S+M if it's broken out)?


texts: Is there a biophysical causation from local field potential (LFP) to spikes?

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

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


texts:
We yesterday got our biology-exams back and there's one exercise where I don't agree with my teacher. However, since he is the expert and not me, I need the support of external sources, i.e. experts in order to justify my statement.

  Now in the exercise, we first had to identify the parts of a cell (which was shown in form of an image) and then in part b) reason whether it was an animal or plant cell.

I had identified a chloroplast and a vacuole and stated that the only cell with this organelles was the plant cell. My teacher answered that I had missed the fact, that the cell had also a cell wall (which is indeed a difference between plant and animal cells).

My question is

  Is the fact that the cell had a cell wall necessary in my argumentation, i.e. are there other cells having chloroplasts and a vacuole without being a plant cell?

Could you provide a source which supports, or doesn't support my statement so that I can show it to my teacher?

Thanks in advance


texts:
It is known that large animals have lower heart rates (beats per minute) than small animals. Is it the same situation in humans?

That is: if we have a group women, about the same age and fitness, and if we record for each women her body size (relevant indicators of body size are height, weight, BMI, body surface area) and her heart rate, will we see a trend that the heart rate decreases as size increases?

References to paper and studies about this issue are also welcomed.


texts: What is the classification for animals with full tube digestive tracts?

texts: What is the formal name for animals with full digestive tracts, by which I mean a mouth and an anus, and what is the classification for animals that have a single hole for exchanging food and waste?


texts: What is the reason for cats not liking water?

texts:
I have two cats myself, a Siberian and a Maine Coon, neither of which like water. In fact, they detest it - like most cats. I was wondering what the reason for this was and if any of you have any interesting theories as to why this is the case.

Thanks in advance!


texts:
Why people die of infection from microorganism, when germs can keep breeding for longer if they dont kill host?
Would not millions of years of evolution make germs evolve to not to kill human but feed on them just enough to not to kill them ?


texts: I am trying to identify this little "bug"

texts:
I am trying to identify a bug. I find this little guy in Paris, at the rooftop near plants, in the streets without plants. I let one on my t-shirt, and it was trying to unpick it. I took a picture :

I think remembering having seen such bugs in old closets, on clothes, when I was kid, but I am not sure.


texts: Is there a real lantern fish existing in the world? If yes, kindly share a picture if one exists. I searched online for images, but most of them seem to be fake. The pictures I have seen on the internet were of a fish with a hanging lantern over its head. Are these possibly real pictures?


texts: Does a fully-resolved phylogenetic tree have to be dichotomous?

texts:
I read that wherever there is polytomy there is an unresolved pattern of divergence. I don't understand why this is so.

When divergence takes place, is it necessary that there will be division into only 2 paths? Can't there be more than 2 paths with all the paths being equally related to each other (that is, no 2 paths being related more to each other than to a third path)?

In other words, does a fully-resolved phylogenetic tree have to be dichotomous?


texts: I've read a recent Nature Methods paper by Moon T.S. et al, in which a synthetic genetic circuit consisting of layered logic gates was created. For example, the paper, a circuit is modelled in Figure 4a. How is this circuit computationally modelled? Can you refer me to any graduate level texts on the subject?


texts: Oxygen dissociation curve and temperature

texts:
So, we have a container with a mixture of gases. The concentration of oxygen is $C_{oxy}$ and its partial pressure is $P_{oxy}$. Then we introduce a sample of hemoglobin(deoxygenated) in that container. A certain fraction is then saturated  with oxygen. Then, I increase the temperature of the gas in the container keeping everything else the same. $P_{oxy}$
obviously increases. Does, this mean the percentage of saturated hemoglobin increase too according to the ODC curve although the concentration of oxygen is same?
Or, will it decrease?

I believe saturation actually depends on the concentration. So, although $P_{oxy}$ increases, the saturation percentage remains the same. Hence, we have same saturation percentage for a greater partial pressure. thus the curve shifts to the right with increase in temperature.


texts: How do infectious bacteria determine when their numbers are high enough to attack a host?

texts: When you get sick, you generally don't contract enough bacteria at once for them to succeed in battling your immune system, right?  Their numbers must gradually increase in the host's body before they know that they can attack.  How does that work?


texts: Can genetics be an answer to our human flaws?

texts:
Ok I have been thinking genetics is that part of biology wich has the ability to change the genes of an organism as such it changes their abilities as well if so why cant we use this technique to change the problems that we face for example:
The cells of plants contain chlorophylle as such they can create their own food thanks to sunlight+water+CO2 what if we take the gene responsible for this and transfer it to a human being like this he will not have any need to eat(but he still can if he wants for more energy like meat-eater plants) however a downside would be green skin but I think is worth another one would be the lizards wich have the ability to regenerate limbs and other body parts that were lost this can help those who suffer from absence of body parts. Wouldn't this be amazing like a human with different abilities to adapt and survive these that I mentioned are simply core of our problems these days there can still be more to it.  SO why isn't this technique used for a solution to our problems?


texts:
I live near Paris, France. I would like to know if this small flying insect was some kind of pest or not. More specifically, I want to know if it might be a meal moth or a clothing moth. Here is the little fella :

It's approx 1.5 cm (0.6 in) long


texts: Why cancer does not occur in myogenic heart cells? Is there any special ability in heart cells to resist cancer ?


texts:
Wikipedia says Caliciviridae Family.
My notes say that Norovirus includes the following

Noroviruses

Norwalk-like viruses
Caliciviruses
Astroviruses and some small gastroenteroviruses

which is a larger definition including at least two families than the Wikipedia definition.
I think

Caliciviruses $\subset$ Caliciviridae
Astroviruses and some small gastroenteroviruses $\subset$ astroviridae

so the note is taking subsets among different families and classifying them into abstract class called Noroviruses.

Extension based by Chris' excellent answer.

Criteria of Noroviruses

(+)sense ssRNA viruses
Structure and replication:

1) only (+)sense ssRNA,
2) simple nucleocapsid viruses,
3) only viruses transmitted by fecal-oral route,
4) size about 30 nm in diameter.

and then final classification of Noroviruses by these criteria

Noroviruses

Noroviruses $\subset$ Norwalk-like viruses ($\subset$ F. Caliciviruses)
Some Astroviruses ($\subset$ F. astroviridae) and some small gastroenteroviruses (what?)

which, however, does not make sense since Caliciviridae $\not\subset$ Astroviridae.
I do not understand what is the point of referring to the viruses by the sentence

  Astroviruses and some other round/small gastroenteris viruses

which are not part of Astroviridae.

Which viruses of Caliciviridae are similar to Astroviruses that are apparently round and small gastroenteritis viruses?


texts: Could someone please explain this AP Biology question? I know the answer is C but I do not understand why. Doesn't Smo prevent gene transcription? If you "block its activity" then wouldn't it cause gene transcription, whereas the goal of treating cancer is to prevent transcription? Please help!


texts: How is single nucleotide polymorphism denoted?

texts:
Currently I'm studying an article on TERT promoter mutations in human melanoma and find myself unfamiliar with included denotations,I would appreciate it if someone could explain to me what C228T in the sentence below means.

  Two tumors with a C228T transition also contained an adjacent C>T transition (at position chr5,
  1,295,229), which is indicative of a dinucleotide CC>TT transition


texts: Why do plants have green leaves and not red?

texts:
I know plants are green due to chlorophyll.

Surely it would be more beneficial for plants to be red than green as by being green they reflect green light and do not absorb it even though green light has more energy than red light.

Is there no alternative to chlorophyll? Or is it something else?


texts: Why would a horse-fly quickly dip into water?

texts:
For several years I have noticed a large horse-fly, flying very quickly down to the surface of my pond (in Sweden), touch the surface, and fly off. Sometimes it dips down a few times, taking some quick turns above the surface in between. Once, I caught it, and could see that it was a male of some Tabanus species.

(Since they are so quick, I haven't been able to tell if they are all male, but considering the size I believe they are all Tabanus sp.)

Now I want to know why they are doing it. It seems too quick for drinking water, and they shouldn't be feeding there. Could it be some sort of mating or territorial behaviour? I have only ever seen them one at a time, though. In sunny weather it seems to happen at least a few times per hour, all through the day.


texts: What is the thickness of endothelial lining in blood vessels?

texts: In capillaries, endothelial lining is one cell thick. Is same the case with bigger blood vessels?


texts: How is the fluoride in toothpaste absorbed?

texts:
How is the fluoride in toothpaste absorbed by our body? Does the tooth absorb the molecule directly, or is it absorbed by the mouth?

The answers to this question suggest that some materials can be absorbed by the mouth, but fluoride is absent. Additionally, many municipalities add fluoride to tap water which I should imagine is actually absorbed in the stomach by a different mechanism than that of toothpaste.

Note that toothpaste generally comes with stern warnings not to swallow. Looking at the ingredients it seems the only thing that may be harmful is the fluoride itself. Therefore I suspect that toothpaste has a much higher fluoride concentration than tap water, which supports the notion that its fluoride is absorbed by a different mechanism than tap water.


texts:
In order for a woman to become pregnant, sperm is needed. Why is sperm count so important for pregnancy?

http://en.wikipedia.org/wiki/Sperm


texts: Phenotype-Genotype for multi-hybrid crosses

texts:
It's generally easy to figure out genotype and phenotype frequencies using a Punnett square for monohybrid and Dihybrid crosses. But what about situations involving 5 or 6 traits? Is there a simpler way to get about this?

As a sample problem:
If we have two organisms crossed, one with genotype AaBBcCddEe and the other with genotype aaBBccDdEe (lowercase is recessive and upper case is dominant), how many individuals would have the genotype AaBBCcDdEE?


texts: How high is the energy yield of photovoltaics compared to photosynthesis?

texts: I'm not an expert in plant physiology. I was wondering if, per square centimeter, leaves are converting more or less energy than photovoltaic systems. Can this be estimated? How?


texts: Why doesn't the body optimize how many fatty acids it burns?

texts: Ketone bodies are produced due to an excess of fatty acids being burned (accumulation of acetyl-CoA) so my question is: Why doesn't the body simply regulate how many fats it burns so it doesn't have to produce ketone bodies?


texts: Which steps occur in each phase of Meiosis and Mitosis

texts:
MITOSIS

In mitosis am I correct in saying that the spindles attach to the centromeres at the end of prophase/prometaphase? (I read this in an answer to another question)

MEIOSIS

Does the nuclear envelope disintegrate during prophase (as occurs in mitosis), or during metaphase? (this is what it says on my textbook)
When do the spindles attach to the chromosomes during the first phase? (during prophase I, or anaphase I? On my textbook it says anaphase I)
And when do they attach to the sister chromatids in phase II? (on my textbook it says metaphase II).


texts:
I spotted this guy in Switzerland. It's clearly an Opilione (Harvestman), but I really know nearly enough about this diverse group to be able to identify the species.

Sorry, I didn't think to place any reference near it for scale. Can anyone tell me the species or at least the genus? (Bonus points if anyone can guess what it's feeding on)


texts:
Saw this on the street in the UK. To my eyes it looked and moved distinctly tarantula-y (although I don't have any firsthand experience with them) which I'm pretty sure we don't have any of natively. Most of the spiders you commonly see here are thinner generally and move much faster. This guy lumbered.

For scale, it didn't span more than a couple of inches.


texts: What is the name of this plant has dazzling look like leaves?

texts: I am living in India. My neighbours are growing this plant and they even don't know what it was, but its leaves really dazzled me.


texts: Are mosquitoes repelled by high frequency sound?

texts:
I am totally confused whether ask this question to physics or biology stackexchange.

I downloaded a mobile application which claims to repel mosquitoes. This application basically produces sound from 16kHz to 22kHz (I doubt that it even produces more than 20kHz because we can't hear more than 20kHz naturally).

I totally doubt this application. Do mosquitoes go away in higher frequency of sound?


texts:
I'm designing primers for species-specific amplification (inside ITS1-ITS2 region). The problem is that when I blast (GenBank) my primer pair, the Forward primer anneals with some isolates (of the same fungus species that i'm targeting) that have one base polymorfism:

Ex:

Predicted Tm= 58-61ºC
product length = 189
Forward primer  1    TTCATCTCCGACTCGCATGT  20
Template        130  ........G...........  149

Reverse primer  1    GAATACCAAGGAGCACAAGGT  21
Template        318  .....................  298

My goal is to amplify only the 100% specific sequences. Would a higher annealing TºC be able to prevent this unspecific binding?

Question 2: The fungus species i'm targeting have isolates with a diversity of polymorfisms (deletions, insertions, one nucleotide substitution,..) and sometimes the predicted amplicon lenght may vary: 189bp, 190bp, 191bp. Will it be problematic for a RT-PCR quantification assay?

Thanks in advance


texts: After getting fully vaccinated for HBV why does the antiHBs titer last for so long?

texts:
When a newborn child is fully vaccinated with HBV and let's assume he's responsive, his antiHBs titers will be high. But since the antigenic stimulus is withdrawn, shouldn't the titre fall to nill in some time? Rather, the titers stay significant for around 40 more years. (>10 IU/L is significant)

So, how are there circulating antibodies for so long if there is no more antigenic stimulus?

I understand that memory cells have large half lives but what is producing the antibodies is the plasma cells which have very short half lives.

So how do the antibodies persist for so long?


texts: Why fingers in human fists get folded in absence of neural stimuli?

texts:
Background:

I noticed that the fingers in our fist tend to get folded in absence of neural stimuli. The same thing happens in case of our hands and legs.

Question:

What is the mechanism behind this phenomenon?
Is there any positive or negative outcome of this phenomenon?


texts: How do the connections from V1 to V2 form during early development of the human brain?

texts: I am wondering how corticocortical efferents from layer I and II in V1 develop to forward visual information to layer IV in V2. Is there topology preservation in these connections from the beginning on or does it only emerge later?


texts: Datasets of aligned nucleotide sequences

texts:
Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there?

(I would like to use such datasets for training the alignment model I am working on. In particular, to help me get an estimate on some parameters such as the frequency of single nt INDEL at some locations.)


texts: I found this praying mantis in Bangalore, India. It is around 6 cms in length and has a distinct marking on the forelimbs. Can I know the species ?


texts: I know that if species are on the same height level, they existed at the same time and indicates extinction. Does that apply to synamorphy? Did hair and eggs with shells evolve at the same time or did one evolve last?


texts: Can kit foxes and red foxes produce offspring?

texts:
Can a kit fox (Vulpes macrotis) and a red fox (Vulpes vulpes) together produce offspring?

Would such a hybrid be fertile?


texts: How do the flowers of Diphylleia grayi become transparent after rain?

texts:
Known as the skeleton flower, its flowers turn transparent in rain. How does it do so? How can it gain transparency in rain when water is already present in flower? Or is it because other components present in the rain? Also is there any  advantage of this for the plant? I research using Google, but I couldn't find an answer.

YouTube


texts: What is the primary cause of death for small animals in urban and suburban areas?

texts:
Small birds (sparrows, robins, jays, finches) and mammals (squirrels, rats, opossums, raccoons) are a common sight in many urban and suburban communities with green space. However, I observe carcasses of these animals relatively infrequently.
I imagine that the following are some of the most common causes of death:

Predation (the species I mention are small, and somewhere in the middle of the food chain)
Age-associated decline in foraging ability, leading to starvation
Disease
Fatal contact with infrastructure (collisions with buildings or wind turbines, contact with electricity lines)

I can think of two reasons why we don't see carcasses very often:

predation is the most common cause of death
individuals that succumb to disease/starvation end up in their nests/dens

Is this plausible? Has this been studied systematically, e.g. in populations of birds with tracking bands?


texts: Are there statistics on Sickle Cell Traits based on country of origin?

texts:
And where was it originally from and how does it spread?

Thanks.


texts: Are there any plants that parasitize on animals?

texts: It seems, fungi often infect animals, while plants it seems, never. Is it because the cellulose cell walls make them incompatible with animal tissue?


texts: Why isn't direct diagnosis of infectious disease through microscopes a common thing?

texts: I'm not sure if I am being accurate about this but from what I know about diagnostics (watching House MD etc), if a doctor has a suspicion of a pathogenic infection then he/she usually prescribes corresponding medication without doing some kind of a confirmatory test. But isn't it possible to just have a look at the blood sample under a microscope and then confirm it? I guess it can't be done for viruses because they need an electron microscope to resolve them apart but I guess normal bacterias can be identified using more commonly available microscopes.


texts:
I live in Puerto Rico and I'm trying to identify this tree and if possible how to kill it since it is infested with termites.
https://imgur.com/gallery/Xbmq0g8
Tree

Closer view of flowers and leaves. The rectangles on the floor are about 3mm x 6mm.

Seed pod


texts: What is meant by "heads" and "tails" in the context of gene orientation?

texts:
I have a hard time understanding what this paper is talking about when it says:

  We observed maximal cleavage at sites oriented tail-to-tail and separated by -10 bp to +30 bp (Fig. 2d). Finally, adjacent sites on the same DNA strand (head-to-tail orientation) did not show damage by NHEJ

Then it shows a figure/chart that I don't understand. I don't know the head and tail or the gene is, in terms of what it is relative or with respect to.

Any help would be appreciated.
Thanks.


texts: Why sympathetic and parasympathetic nerves originate in different parts of CNS?

texts:
Curious if there is a reason for having:

parasympathetic nerves originating from brain stem and pelvic part of spinal cord
sympathetic nerves originating from thoracic and lumbar parts

It looks well-organized, so maybe there is a good reason for that.


texts: When do the spindle fibers attach to the chromosome

texts: At what phase does this occur in mitosis (or even meiosis); some text books say prophase while others say metaphase.


texts:
If you google visceral and parietal you get: The parietal layers of the membranes line the walls of the body cavity (pariet- refers to a cavity wall). The visceral layer of the membrane covers the organs (the viscera).
but
the first image that pops up is this :

I don't understand how the inner layer is covering and the outer is lining ?


texts: Protein structure prediction from amino acids sequence

texts:
Information given at this resource https://predictioncenter.org/ is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict tertiary protein structure now - I would be grateful.

Also would love to hear your thoughts on 'why a cell can make exactly the same protein structure thousands of time using known to us physical laws, but we have to guess it using machine learning'? Why is it difficult?


texts: What does breathing through the mouth have to do with cracked lips?

texts:
https://www.healthline.com/health/mouth-breathing#symptoms3

Symptoms in children
Children who breathe through their mouths for most of the day may also have the following symptoms:
...
...
dry, cracked lips
...

Why can breathing through mouth result in dry, cracked lips?


texts:
I need to have a book which covers following topics two may also be fine:

(a) Structure and role of carbohydrates, fats, fatty acids and cholesterol, proteins and amino-acids, nucleic acids. Bioenergetics.

b) Glycolysis and the Krebs cycle, oxidation and reduction, oxidative phosphorylation, energy conservation and release, ATP cycle, cyclic AMP – its structure and role.

(c) Hormone classification (steroid and peptide hormones), biosynthesis and functions.

(d) Enzymes: types and mechanisms of action.

(e) Vitamins and co-enzymes

(f) Immunoglobulin and immunity.


texts: Is there an organism which has a common English name which overlaps with another organism's scientific name (or vice versa?)

texts:
Many organisms have their common names identical to their scientific names. For example, there exist apes of the genus Gorilla known commonly as gorillas, and plants of the genus Delphinium known as delphiniums.

However, are there any examples of the common name of an organism overlapping with the scientific name of another organism, therefore causing ambiguity when the organism's name is spoken aloud? If written with correct formatting, this should not cause a problem in any case, due to the formatting specifically describing a genus/species.


texts: Why is muscle force more dependent on cross-sectional area than on fiber length?

texts:
I was looking up why smaller animals are proportionally stronger than larger animals. The answer that comes back everytime is that muscle force depends on the number of muscle fibers, which is proportional to the cross-sectional area of the muscle.
However, I don't understand why muscle force wouldn't depend on fiber length.
I'm not a native english speaker, so I'll try my best to articulate my reasoning in the most concise way possible.

Force is exerted by the myosin motors. Force is therefore proportional to the number of myosin motors.
The number of myosin motors is proportional to the fiber length.
The number of myosin filaments is proportional to the cross-sectional area.
Then, muscle force is proportional to muscle volume, and therefore to muscle mass.

What am I missing ? Why is muscle fiber length not that important to muscle force ?

Thank you in advance for your help.


texts: How many cells does the hermaphrodite version of Caenorhabditis elegans have?

texts:
Wikipedia states:

  The male C. elegans, for example, has 1031 cells

How many cells does the female version have?


texts: What is the exact percentage of spectral changes that human pinnae introduces into the acoustic input signal?

texts:
I read somewhere that amount of spectral changes that human auricula introduces into the input signal is 6%.

Now I cannot find that literature.

Does anyone know a source that might confirm this, or may confirm this him/her self? Well or contradict it if necessary.


texts: Do Colorblind People Have Stronger Sensitivity in Their Other Remaining Cones?

texts:
I came across this paper Color defect and color theory. The paper explained about how unilateral color blind (people who color blind only in 1 eye) actually see less bright in their color-blind eye (in graph : filled bullet) compared to the normal eye (in graph : white bullet). Especially to the scene that corresponds to the missing cone (in this paper, Deuteranopes. Missing cones = green)

I have 2 questions regarding this brightness loss in color blind people.

Green cones response are near the red cones response, and they are overlapping. How is it possible that Deuteranopes loss brightness in Green and Blue (which will make more sense if they also loss brightness in Red, thus loss brightness in the whole spectrum) but instead, still achieve the same amount of brightness in Red ? Despite Red and Green color-blind have the same color combination possibility (gamut mapping) that they can perceive ?
Could it be that color-blind people have stronger sensitivity in other cones (for example : stronger in red) and then this red opsin actually replace / fill the missing cones stimuli in retina, so their retina still able to perceive the same amount of brightness on that excessive cones ?


texts: The popular potted plant, Pothos aureus (or Epipremnum aureum) is happy to grow in a jar, with only water, for years. How is this possible when other plants need at least Nitrogen, Phosphorus and Potassium?


texts:
I came across this term in University question paper.

  What is the difference between core promoter and regulatory promoter?

I have googled (Web, Scholar and Books) it but couldn't find any information from any authentic source.


texts: How can I measure bee and wasp population?

texts:
Bees and wasps in our garden disappeared suddenly last year - I asked a question about it at Why our bees might have suddenly disappeared. This year, I see that some bumblebees are active now. I'd like to measure the population of bees and wasps in the garden over the year, and see if the numbers change when the nearby fields are sprayed.

I note the question How best to count bees entering and leaving a hive to measure hive activity? but I don't have a hive to count. Our bees come from far away, and I'm interested in multiple species from multiple nests, and wasps too. So I'd need to count the number visiting the garden. But, can I count reliably? It will vary with weather, and the number on any one plant will vary greatly depending on plant flowering dates.

Is there any established protocol for counting bees and wasps in the wild to look for population changes over time?

I can't spend too much time on this - I might manage an hour every week. Or, I could set up camera recording, if someone knows some really clever software to do the counting. But I still can't imagine how to overcome the variation.

Thanks!


texts:
Could we use viruses that only affect bacteria to act as antibiotics?

The more bacteria, the more times the virus divides, so the stronger it gets. Is this practical?


texts: Does a reduction in stem cells mean possible earlier death?

texts:
The basis of this question relies on my understanding of these 2 facts:

1) A person has a certain number of stem cells from birth
2) Stem cells are the basis of all cells and are used to repair and replenish

I read an article about stem cells being found in fat removed by lipsuction and that the trials that has been done on using these stem cells for repair elsewhere in the body.

My question is, if stem cells are used for repair in the body and you have a certain amount of them, if you "lose" some via liposuction, does this then mean you have less stem cells and therefore less chance of repair and could then theoretically die sooner?

It's more than likely my lack of knowledge on the subject but I would like to understand why.


texts: What in soy are people allergic to and will these allergens be passed along if an animal that has eaten soy is consumed?

texts:
I have two related questions about soy allergies and possible reactions.

What is it that are humans who have soy allergies actually allergic to? What is the allergen?
If an animal eats soy, are those allergens broken down or retained? Can the consumption of that animal cause an allergic reaction similar to direct soy consumption?


texts: Large nocturnal butterfly with red and black hindwings

texts:
Location:

Central Poland, urban environment.

Size:

Around 4 centimeters long.

Time:

Early July.

Images:


texts: I have read that neurons have proportionately less MHC molecules than other cells of the body. What is the advantage of this?


texts: Why these 2 dots frequently occur in dog's eyebrows? Do it serve/served any advantage?

texts:
It has been wonder me, in spite of so-many variations in color-patterns in dogs; these 2 dots (1 on each eyebrow) remains frequently occurring.

 Dog-1  Dog-1 close up.

this one has a white dot. photographed from Kolkata.

 this one is from Uttarakhand, Western Himalayas. Also has white dots.  I've seen brown dots too, which I have not photographed, so I cite an example from internet (wikimedia: )

Now, my question is; why are these 2 dots are so conserved? Is it associated with some conserved region of a chromosome?  or maybe it has/ had served any purpose or advantage (such as recognition or nonverbal communication or to mislead their prey since if the prey think of them as eyes; then they would miss the gazing direction of actual eye) so that it was selected by nature? Some sort of wolves too have similar paired-spots, so could I guess that once upon a time certain ancestor of all dogs and wolves contained these paired dots?

PS. I've not found helpful discussion about that dots. From this webpage it seems to me, it is being called false-white black and tan atat genotype. Don't know have i understood correct or not...


texts: Spike protein production by mRNA vaccines?

texts:
I am trying to understand the spike protein production mechanism of the mRNA vaccines, and during my research I learned that the mRNA (Moderna, mRNA-1273) vaccines hijack the cell machinery to produce spike proteins of SARS-CoV-2 by providing genetic material mRNA (which is encapsulated by lipid nanoparticle).
My question, which cells are subject to the vaccine particules (which factor determines the target cells?) Are produced spike proteins part of the cells (which interacted by the vaccine), or are these proteins emitted into the bloodstream like hormones so immune systems attack only the produced spike proteins?
I am asking this question to understand whether the cells which are used to create spike proteins are attacked by the immune system.


texts: How to do a blast search for similar sequences?

texts:
Tried doing a Blast search for a PPO gene in an advocado genome: https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEFAULTS=on&BLAST_SPEC=OGP__3435__73885&DATABASE=GPIPE/3435/current

However there are no matches, which may be because it is a different species with a slightly different sequence? The genome I am searching is known to contain PPO.


texts: On what basis is each chromosome given a number? There appears to me to be no visible ordering between each pair. Is there any reason other than differentiation?


texts: Haidinger's brush: Is this a by-product of the eye's physics, or are there any evolutionary grounds for it?

texts:
The human eye is, very subtly, sensitive to the polarization of light. This is  an effect known as Haidinger's brush (see Wikipedia article of this name).

What, if anything, is known or at least intelligently speculated about the evolutionary "grounding" for this effect?

Another way to put this question: Some cephalopods and the mantis shrimp have sight that is sensitive to polarization of light and this sense is clearly begotten by evolutionary forces as it helps these animals detect prey and predators. So, is our subtle ability to perceive polarized light a leftover from a genetic forebear that benefitted from this ability? Or is it simply an artifact of the physics of the eye? The physics of Haidinger's brush is quite different from the topology of retinal cells that confers this ability in cephalopods and others I have read about.

A second question and related is: what is our nearest common genetic forebear that is known to exploit polarization sensitivity of its sight?


texts:
I've seen the following insect in Austria at the border to Bavaria (high resolution). It was quite small. I would guess not longer than 1cm:

Could somebody identify it?


texts:
My friend has a mint plant with a spiral-shaped stem, and the leaves are positioned like this:

Why could such deformation happen? Other mint plants, growing in the same pot, are normal.


texts: So, we all know that hybrids are infertile, that's the definition of a species, but how come some parrot species can interbreed and still be fertile. For instance a military macaw and a blue and gold macaw can have offspring that are fertile and can breed to make further hybrid macaws. These two species are definitely different species and not sub-species. How is this possible?


texts: What kind of tree is this — why do its huge leaves change shape and "grow fingers"?

texts:
Edit 2: Confirmation that it's one tree!

Surrounding trees on either side along the sidewalk are completely different, and the ones on the other side of the fence are short and have rounded but far smaller, as well as thicker, dark leaves.

I've taken a 180 degree vertical "panoramic" photograph to show that there are no encroachments from trees with large leaves from behind. I've also included a few more photos of small clusters of leaves coming from a single large branch, again showing all three types of leaves.

Note some of the photos are large, and if you open them in a separate tab or window you can zoom in for additional detail.

I was riding a bike in Taipei recently (November 2017, location in google maps - more views of trees: https://goo.gl/oXPHr3) and I saw two huge leaves on the sidewalk. I stopped to photograph them and realized that they were very different shapes but otherwise looked quite similar. They are both over 40 cm long broad leaves, but while one has smooth edges and is "leaf-shaped", the other has long serrations (roughly 10 cm deep, 5-7cm spacing) on each edge.

I took some more photos of the leaves and branches of this very large tree, and one of the trunk, which looks quite gnarly.

Edit 1: I've cropped and lightened sections of two of the photos where I believe I can show examples where leaves on the same branch exhibit continuous change from smoothed edges to serrated edges. I've used 1 to denote smooth-edged leaves, 2 to denote leaves that show a few "digits" at the far end of the leaf, and 3 to denote leaves that exhibit full "digitization". In each case I think it's pretty clear that they connect to the same branch, and are not from different trees as suggested in the answer. This is strongly (if superficially) reminiscent of the sassafras leave differences.

Question: What kind of tree is this, and why do its huge leaves change shape and "grow fingers"?

It was pointed out to me that Sassafras leaves also come in different shapes with "fingers", I've included one image of those below as well for comparison.

For comparison, here's an image of Sassafras leaves with "fingers", from Landscape Plants, Oregon State University.