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Why haven't we cured the common cold yet?
Researchers think they’re close to a cure for the common cold, but they first need to solve a complex problem that’s perplexed scientists for decades. Polio, smallpox, hepatitis A and B are all serious viruses humanity learned to subdue with effective solutions. Even the flu, which can shift and mutate each year, has a vaccine. And yet, there’s no remedy for the lowly cold.

It's a naming fallacy.

Which common cold? Them buggers mutate so fast we can't even name them properly.

We have cured it, but by common language usage instead of medicine.  Nobody I know has gotten a cold for 20 years.  They still get the sort of infection we used to call a cold, but now everybody calls it the flu.

Masks help. I have been cold-free since the start of 2020, while I suffered at least one cold per late autumn, winter or early spring before that, all my life.

There's also a cost/benefit issue. It's easier to spend billions on research for a disease which can cause deaths (especially if a lot of them), a lot more difficult for diseases which just cause you relatively mild symptoms.

There is one simple reason: Contrary to the viruses you named in your question, which are all caused by one virus (or from the same family), there is nothing like "the" cold virus. This makes it a manageable task to find a vaccine for the former, although it doesn't mean it is simple.
A cold is viral infection of the upper respiratory tract which are caused by a wide variety of different viruses. The term "cold" is an umbrella term for a wide variety of symptoms following such an infection including coughing, sore throat, runny nose, sneezing, headache, and fever. See reference 1.
The paper in reference 2 lists about 200 serological different viruses, with Rhinoviruses being the most common. Other viruses occuring include adenoviruses, human coronaviruses, human respiratory syncytial viruses, other enteroviruses, human parainfluenza viruses, and human metapneumovirus.
Although there are seven human corona viruses (see here), only four of them are associated with the cold:
229E (alpha coronavirus)
NL63 (alpha coronavirus)
OC43 (beta coronavirus)
HKU1 (beta coronavirus)

The other three can cause a considerably more severe disease and are not seen as causing a cold:
MERS-CoV (the beta coronavirus that causes Middle East Respiratory Syndrome, or MERS)
SARS-CoV (the beta coronavirus that causes severe acute respiratory syndrome, or SARS)
SARS-CoV-2 (the novel coronavirus that causes coronavirus disease 2019, or COVID-19)

See reference 4 for a more detailed look on them.
This list should make pretty clear why there will be nothing like a general cold immunization, since the number of viruses is too big. Additionally, all these viruses can change over time due to mutations which would need permanent adjustments to such a vaccine. This is already a big deal for influenza, but there are only limited viruses around there.

Understanding the symptoms of the common cold and influenza
Understanding the symptoms of the common cold and influenza
Epidemiology of Viral Respiratory Tract Infections
The human coronaviruses (HCoVs) and the molecular mechanisms of
SARS-CoV-2 infection

Thanks for this instructive write-up. I was vaguely aware of several viruses being responsible, but you put it together very nicely, and with references, and put it in context with SARS_CoV-2: Good job.


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Can an injection of unipotent stem cells cause teratoma?
I understand that injecting pluripotent stem cells causes formation of teratomas.
Does injecting unipotent stem cells also cause teratoma?
If it does not form teratoma, is the injection of unipotent stem cells a safer way to heal/regenerate the tissue that was damaged?

As I understand it they are less harmful because unipotent stem cells differentiate into only one specific cell type and form a single lineage, whereas pluripotent stem cells can develop into all three germ layers, which can result into teratoma, but an injection of unipotent hESC can also form malignant tumors (which teratoma can as well -> A "benign" grade 0 (mature) teratoma nonetheless has a risk of malignancy. Recurrence with malignant endodermal sinus tumor has been reported in cases of formerly benign mature teratoma, even in fetiform teratoma). Just my understanding - hence the comment

"Can an injection of unipotent stem cells cause teratoma?" No, because they form a single lineage and therefore can't lead to teratoma or so called dermoid cyst/twin cyst. "..is the injection of unipotent stem cells a safer way to heal/regenerate the tissue that was damaged?" remains to be answered by someone with more knowledge and sources of scientific research regarding this topic..

Sir/Mdm, what does hESC stand for?

Human Embryonic Stem Cells - often abreviated as HESC or hESC

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


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How much protein to add for complete binding
I have 7mg of a 74kDa protein $A$ bound to a column. I want to bind another protein $B$ which is 19kDa onto protein $A$ so that every protein $A$ is bound (or as close to 100% binding as possible). I also know the $K_D$ of protein $A$ to protein $B$ is $9\cdot 10^{-8} M$, I am not sure if this is even relevant. How much of protein $B$ to I need to flow through to try to get complete binding?
One protein $A$ binds to one protein $B$. Can I just convert the 7mg into the amount that would result in one to one binding, i.e., 1.8mg of protein $B$? Then does the dissociation constant even matter? I don't have a ton of protein $B$ so I need to be frugal and calculate how much to use.

I would strongly suggest starting with much smaller amounts (micrograms) and figuring out the conditions there before scaling up. Depending on what it is and how you're making it, 7 mg is a lot of protein. You don't want to waste it all (and however much Protein B you use) if you make a mistake.

@MattDMo The problem is the column is somewhat large, I may have to find a different way ultimately. However, I am still wondering about how to calculate the solution to this problem.

Can you figure it out from https://en.wikipedia.org/wiki/Dissociation_constant ? If not, where are you stuck?

One other thing to consider - will Protein B bind to the column itself, either specifically or non-specifically? Also, what kind of column is it - bead-based like a typical liquid chromatography column, solid-phase like a GC column, something else?

@BryanKrause It seems from the dissociation constant, if I were to want all of it to be in the bound state, I would need an infinite amount of the protein according to the equation?

@RuochanLiu That's correct; really, in biology and chemistry, complete anything is usually aspirational at best. Also as MattDMo points out, when you have other things to bind to the situation gets more complicated. So, you'll need to figure out what you really need based on what you're trying to do, which isn't particularly clear here so far.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Identification of a Tettigonia specimen
At least I think it is a Tettigonia sp. but I have problems identifying it exactly because it is still a nymph. OK, it is a female, that is hard to overlook, but is it T. cantans (my guess) or T. viridissima or am I completely misled?
Found in western Germany (quite rural, Lower Rhine region, north of Dinslaken) in mid-june 2014 on a tomato plant.

The tomato plant is a mini cocktail tomato plant and its leaves are a bit smaller, so here is an example of one with a metric measure tape aside for metrological purposes.


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If crossing over did not occur, would pairs of cells after meiosis II have the same genes?
If crossing over did not occur, would there be two pairs of cells with the same chromosomes after meiosis II? This question came to my mind while I was reading through my bio textbook. After meiosis I, there are two cells with 1n chromosomes but the chromosomes have 2 chromatids. It seems to me that, if crossing over didn't occur the chromatids of the chromosomes would be identical and after meiosis II the 2 cells would divide into 2 pairs of cells with identical chromosomes. Is this right?

Your understanding is correct.
After meiosis II, you will have 4 cells: Cells 1 and 2 are identical and each have one haploid set of chromosomes; Cells 3 and 4 are identical and each have the other haploid set of chromosomes. These two sets of chromosomes are mutually exclusive. Note that these sets of chromosomes are not [necessarily] the same as the gametes that formed the organism.


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Can you use calcein to stain milk somatic cells and observe them through a fluorescent microscope?
I am currently working on an image cytometer that could automatically count somatic cells in milk samples. Can I use Calcein (i.e., C30H26N2O13) to stain the somatic cells? If not, what dye can I use for fluorescent imaging?


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Is the offspring of two-sex plants a clone or a child?
Many common plants e.g. tomato, pepper; produce both male DNA carriers and female embrions. In the case that the plant is confined alone, do the resulting seeds carry a carbon copy of the DNA of the parent like when rooting a broken branch in water or do they experience some profound mutations beyond the usual UV induced ones?

A child, in that it's produced by fusing the parent's gametes.
Note that many agricultural and decorative strains derive from "true breeding" or purebred plants - terms that predate a modern understanding of genetics but indicate that the plants are likely homozygous at all the alleles relevant to the observed/desired traits. When you self-fertilize a homozygous plant, the genotype will be the same as if it were cloned. You will still have the plant going through meiosis and therefore recombination processes will still be acting, but there is no variation to yield novel combinations, so in principle it is not much different from a clone (assuming that everything is indeed homozygous).
See also Growing peaches from (supermarket) bought seeds - in many cases, there are actually separate true breeding strains that are then crossed (rather than selfed) to produce the strains you're familiar with. In that case, even in self-fertilizing plants, you can't expect to get similar traits out of the selfed offspring. I believe most commonly used garden tomatoes and peppers are hybridized, so you typically won't want to plant the seeds of the next generation if you're looking for optimal production. Heirloom tomatoes are an exception that tend to be closer to true-breeding as they've been self-crossed for generations.
Some quotes from: https://open.lib.umn.edu/horticulture/chapter/14-4-plant-breeding/

Inbreeding is producing seed by selfing over 5–7 generations to develop plants that are highly homozygous at most loci in their genomes. Homozygosity results in identical plants propagated by seed. This is done so the resulting progeny look more and more alike until, after 4–6 years, plants grown from seeds harvested off the same plant are indistinguishable from each other.

Most new commercial tomatoes, including new garden tomatoes, are F1 hybrids. The seeds you plant in the field are the result of crossing two parents, as described above. (...) Garden catalogs will tell you whether the seed you are buying is hybrid. If you are getting your fruits from the store, you can count on them being hybrids unless they are marked as heirloom.

A lot of big words for my small brain: I wish I had paid more attention during Biology classes at school. Learned so much by reading the basic definitions. Thanks!


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They look like tiny black ants but they're not I find them only in my son's toy box
I find these only in my son's toy box not in the kitchen or not around food I have bleached all my son's toys and they still come back they are not crawling along the wall or anywhere else in the room or any other toy box in the room there is no food in the toy box as I've cleaned it thoroughly but I don't know what they are they seem to live for a little bit and then just die they only stay in the bottom of his toy box can you help me figure this out or how to get rid of them
They are tiny and black as you can see

Unless your toys include grain of some sort, it's not likely these are actually living on the toys. I'd check your food stocks more carefully, especially rice and grains. Do you have neighbors?

Check for a bag of corn, rice, wheat, cereal, etc. That's the source. They will spread through the whole house given enough time. They're small enough to crawl "under" carpet surface and so move about great distances before being found. Are pretty harmless to everything but your food other than being a "gross" infestation. Mechanical removal + sealing available food necessary to slowly eliminate.

Seeing as it has three legs to a side, which are visible towards its right side (zoom in as far as you can) relative to the rest of the picture, appears to have a protruding set of mouthparts, and has a body that's visually divided into two parts, I'm tentatively going to call that a weevil.
As Bryan Krause pointed out: check any food you might have in your house for them. Weevils like eating things.
Alternatively, it might be a member of a weevil family that feeds on dead wood. Is the toy box made of wood?

Unlikely to be Anthribidae ("family that feeds on dead wood") due to wrong habitat, size, morphology, etc..... Also, all animals "like eating things"

@theforestecologist More specifically, weevils like eating things that people would prefer uneaten.


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What genetic biomarkers are the best place to obtain histopathological images for the purpose of cancer classification?
I am doing a science-fair project and wanted to know where I could obtain the best possible histopathological images of both non-cancerous and cancerous subjects. I would require roughly more than ~50k images.

It sounds like you might be doing some form of image analysis for features followed by statistical analysis, with needs for a dataset that size. I would suggest looking at what others have done in the past and see if you can find their datasets. For example, here is a recent review. One possible resource might be here. All of this would show up in a google search. If those don't answer your question, feel free to edit your question to explain why.

Do you mean biomarkers (e.g. proteins such as CEA or other biologic substances whose expression/appearance or lack thereof correlates with cancer) or databases? I think some clarification to your question could help others answer your question. Also, for 50k+ images, I think it is likely that you need to partner with an institution to obtain this data.

Maximillian, are you sure the resources of cancer imaging archives that you sent me is trustable? Because it is asking for access to transfer files to and from my computer. Otherwise, these are some really good images for my project and will most likely help me succeed.

The grammar in the title of the question here doesn't make sense to me. "Genetic biomarkers" are not a place. Additionally, "best" depends on some criteria, which are not specified here.

Additionally: At what cancer are you looking? Biomarkers differ widely and are often not very good. Reliable biomarkers for certain cancers are a "one million dollar" question.


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Why is it so that phloem parenchyma is absent in most monocots?
I am currently studying anatomy of flowering plants and came across this statement in my textbook:
'Phloem parenchyma is absent in most of the monocots.'
We learnt that the main function of phloem parenchyma is to store food material and other substances like resins, mucilage and latex. Do monocots have some other structures for the same purpose? Why is it that they lack these type of cells?

@MaximilianPress I did look up as many Q and A forums as I could (posting questions only after thorough research) and mostly the answers I saw didn't actually explain the reason and instead wrote it down as a fact. Answers on Quora especially , were very vague and not that helpful. I'll edit the question accordingly , thanks.

@MaximilianPress please don't recommend users look up info on such disreputable (and low quality) sites such as Quora.  -_-

@theforestecologist fair enough, deleting comment.


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Is there a term to designate the property for an enzyme of catalyzing several reactions from the same substrate?
LacZ (beta-galacosidase) catalyzes the hydrolysis of lactose into either galactose and glucose or allolactose.
Is there a term to designate such property for a single enzyme of catalysing several reactions from the same substrate (i.e. forming different alternative products)?

There is a problem with the nomenclature of enzymes that catalyse more than one reaction because they fall into (at least) two structural types. One can refer to both of them as:

multi-functional enzymes or multi-functional proteins

The latter term is used in a 1976 review of the topic.
However for precision it is necessary to employ terminology that distinguishes between them, especially as the term multi-functional has also been used to indicate the different physiological functions that a single enzyme activity can have (e.g. in this review of cysteine cathepsins).
The more common type — to which the lacZ gene product does not belong — can be considered as fusions of proteins containing separate catalytic activity. Examples include the AROM complex of the shikimate pathway of fungi and protists, and the fatty acid synthase complex of eukaryotes. The Wikipedia entry for fatty acid synthase uses the term:

multi-enzyme protein

The term, multi-enzyme complex, is often applied to such proteins (as above) but is also applied to complexes of individual enzymes, and so is not suitable as an unambigous descriptor for this type of enzyme.
In the case of the product of the lacZ gene there is a single catalytic site, with a single binding site for the substrate but an additional site to which the glucose produced by hydrolysis of the β-galactoside may or may not bind to produce allolactose. The authors of the linked paper describe this as:

an enzyme with bifunctional activity

This is a description, rather than a ‘snappy’ term, and even so requires further elaboration to remove all ambiguity:

an enzyme with a catalytic site possessing bifunctional activity

But this class of enzyme is relatively rare, which is why I suppose no ‘snappy’ term has (to my knowledge) arisen.


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What's the procedure of the antigen recognition by the B cells in a clear way?
Before presenting my confusion, I really sincerely thank everyone for any advices or clarifying , every  single comment  is helpful.  And my english writing skill is still very bad, Just ask anything if you are confused.
I have first referenced JaneWay's immunobiology textbook and this question about roughly the same question.
However, the exact process is still not very clear in my mind.
So for clearance, Let's imagine the entire  process at the beginning, that is, the time a pathogen having already successfully invade to our body and start circulating throughout blood vessel.
So the first question: The antigen could be distinguished into two types, one of which we have already identified and one of which is totally new to our body,is this understanding correct?
Then, the second question:for the identified pathogen, our antibody which is circulating throughout our body will somehow bind the pathogen and triggers a series of immune response, is this understanding correct?
And then The third and seems like the most untrivial question: for the antigen which is totally new (didn't remembered by our immune cells) to our body, How does our cell knows it is at the first place indeed a pathogen?
Just give me some references  will be enormously helpful for me, thank you!

I can't pull resources for you at this time, and my response is too long for a comment, but just to give you some direction to research:
Firstly, if you are not clear, I would try to understand how antigen and pathogen are different terms. Understanding "epitope" and "hapten" may also help with your understanding.

Yes, BUT it's less "type of antigen" and more "state of immune system" - either there is immunologic memory [to the particular antigen] or there is not.
Yes, there is an antibody binding domain on the variable region of the antibody. Keywords: "Fc/Fab, Constant region/Variable region, Heavy chain/Light chain, V(D)J recombination, CDR1/2/3."
It does not "know." Ideally, it recognizes all foreign particles (of sufficient immunogenicity) as "antigens," but this process is not perfect. Common examples of "improper" recognition are autoimmune disorders and allergies. Try looking into T/B Cell Maturation/Activation, Thymus cells, and B Cell Dual Recognition (the classic/dominant method of activation in response to pathogenic infection). I think this will give you a better understanding of how the body tries to limit its immune response to what we consider "pathogenic."

If the question doesn't get locked, hopefully someone can provide a more complete response to you.

Sorry to bother you again, but if let's say if our innate immune system will automatically attack those pathogens which has "Pathogen-associated molecular pattern" PAMPs, then why does those benign bacteria living in our guts doesn't get attacked by our immune system?

I don't think it is well known and upon cursory search, appears to be an area of active research. The question warrants a separate post.


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Doesn't pasteurization kill gut bacteria such as Akkermansia muciniphila?
I've recently watched two presentations on YouTube (this and this) about Akkermansia municiphila, a commensal bacteria that feeds on the mucus of the gut.
What I find confusing is their claim about stabilizing Akkermansia and making it commercially available via pasteurization.
How can it be used as a priobiotic if they pasterize it? Doesn't that make it inactive?

This is interesting since Akkermansia muciniphila is a strict anaerobic and does not produces spores (which was my first thought on it). However, digging up the original publication (see reference 1) solved the question:

Unexpectedly, we discovered that pasteurization of A. muciniphila
enhanced its capacity to reduce fat mass development, insulin
resistance and dyslipidemia in mice. These improvements were notably
associated with a modulation of the host urinary metabolomics profile
and intestinal energy absorption. We demonstrated that Amuc_1100, a
specific protein isolated from the outer membrane of A. muciniphila,
interacts with Toll-like receptor 2, is stable at temperatures used
for pasteurization, improves the gut barrier and partly recapitulates
the beneficial effects of the bacterium.

The effect on the experimental animals by these bacteria seems to be mediated by the Amuc_1100 protein which interacts with the Toll like receptor 2 and is responsible for bacteria-host interactions. It turned out that the protein is stable at the temperatures used for pasteurization.
The pasteurized bacteria seems to influence the energy expenditure and decreased the the food efficency (see reference 2):

We confirmed that daily oral administration of pasteurized A.
muciniphila alleviated diet-induced obesity and decreased food energy
efficiency. We found that this effect was associated with an increase
in energy expenditure and spontaneous physical activity.

However why this effect can be seen with the pasteurized bacteria still seems unknown (at least I haven't found a scientific article yet).
References:

A purified membrane protein from Akkermansia muciniphila or the
pasteurized bacterium improves metabolism in obese and diabetic mice

Pasteurized Akkermansia muciniphila increases whole-body energy
expenditure and fecal energy excretion in diet-induced obese mice


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EDTA in DNA extraction
I thought the EDTA solution binds to metal ions and deactivates the (metal-dependent) nuclease present in the cytoplasm which protects DNA from degradation. But I wondered how that would be the case because if the DNA and nuclease are both found in the cytoplasm, the DNA would just be degraded. (Eukaryotes have a membrane-bound nucleus which prevents the nuclease from degrading DNA, but as prokaryotes do not have one, DNA is just loose in the cytoplasm along with the nuclease) And after some research, I found out that bacteria protect their DNA from autodegradation by modifying their DNA bases.
If that is the case, then why is EDTA used in bacterial DNA extraction?? Wouldn’t the DNA be safe from the nuclease regardless of the metals in the first place?

Why does bacterial DNA not get degraded when it's not protected by a nuclear envelope from endogeneous nucleases in the bacterium? Why ever use EDTA to block nucleases if DNA seems safe in its presence?

Prokaryotic genomes are composed of DNA which is indeed not enclosed in nuclei, but it is regardless compacted into a nucleoid. Thus one major way bacteria protect their genomes is through supercoiling of their DNA, to compact it and render it less easily accessible. Another major way, as you mention, is by modifying their bases, most commonly through methylating nucleotides. Methyl groups are added specifically onto bases in recognition sequences which nucleases otherwise act on, thereby protecting this target from being cleaved by hydrolysis. As with supercoiling, this allows the strand to be nuclease-inaccessible. There are also other ways that bacteria control the activity of their enzymes; their expression is controlled, they may be inactivated or purged, etc.
Also consider that nucleases are usually specific in some way, which means that protecting DNA becomes a lesser task: some target DNA ends only (exonucleases) which can be shielded. Some nucleases target within strands (endonucleases), these can have specific recognition activity, and other (rarer) kinds don't and hydrolyze DNA non-specifically. When you extract DNA you want to make sure that for the entire process - from lysis to isolation to storage - the DNA is free of contaminants and conditions which could potentially degrade DNA.
This means we must consider controlling biological, chemical and physical aspects which may contribute to DNA damage. One instance of each:

We don't want other microorganisms there which may secrete nucleases or digest DNA; thus, we sterilize.

We don't want enzymatic activity which may compromise DNA stability; thus, we chelate ions which otherwise are required for nuclease activity using EDTA.

Last, we don't want the DNA to get lost in isolation, so we control things like temperature and pH and salinity to solubilize, denature, precipitate things differentially, such as DNA, RNA, short strands, long strands, etc. For instance, if you want to isolate plasmids (rather than nucleoid DNA), one quick and dirty way of doing it is to add an alkaline (high pH) reagent after lysis. This is called "alkaline denaturation". The broken cells release their contents, the DNA inside separates into its component strands, or denatures. When you lower the pH once more, the plasmids reanneal easily but the very large, bulky nucleoid DNA can't and you separate them on this basis. In this case you'd also add EDTA out of abundance of caution to protect the nucleoid DNA from fragmenting into smaller bits that would be co-isolated along with the small plasmids. EDTA would also prevent the nuclease digestion of plasmids too, since they are composed of DNA too. EDTA is a well-motivated, preventative measure to upkeep the quality of the DNA during artificial isolation procedures wherein cells and compartments get homogenized and all sorts of things occur which normally don't in nature.

Last note, in the spirit of science and good lab practice: try skipping the addition of EDTA and compare your DNA yields. You may notice it doesn't make much difference, which would suggest that cytosolic nucleases may not have much activity for the bacterium's own DNA!


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Does lower stomatal conductance of water influenced by elevated CO2 decrease overall evapotranspiration?
From what I understand, elevated CO2 levels decrease the stomatal conductance of water in plants. What I remember from irrigation sciences, higher temperatures should be more demanding on evapotranspiration. What will be more decisive for (evapo)transpiration of Canopy - higher temperature or higher CO2 levels?
Thank you!

Still not quite sure about this topic - some new article about it...
https://modernfarmer.com/2022/12/plants-have-mouths/


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Would a size-specific, electrophoresis-based RNA quantification kit work for ssDNA as well?
I'm using a custom library of ssDNA oligos to test the performance of some qPCR assays with mismatched bases in various primer and probe regions, and I'm trying to come up with a good way to verify whether or not my results are due to differences in assay performance or differences in the copy number of fully synthesized templates.
Basically, the fragments I was asked to order were only available with the most basic desalting purification protocol, which does not include any fragment size selection and can therefore include incomplete or degraded templates. After verifying quantifications with absorbance- and fluorescence-based methods, there's not enough of a difference to explain my qPCR results. But, again, this doesn't account for any potential differences in fragment length/completeness.
I have access to an instrument that provides size-specific quantification and integrity assessment based on electrophoretic separation. But the available DNA kits use SYBR Green I, which is really a dsDNA dye and only weakly interacts with ssDNA. They sell RNA quantification kits using SYBR Gold, a better choice for ssDNA, but when I called tech support to ask about ssDNA, I got the boilerplate response. They haven't tested their kits for that application so they can't recommend it or comment on whether or not it will provide good results.
So I'm just here asking if there's some difference in buffer or gel properties that would prevent ssDNA from properly running on an RNA-specific electrophoresis platform. I've looked up a few standard RNA gel electrophoresis protocols and they all seem similar enough to DNA gels, so I'm assuming the instrument's RNA kit would probably work for DNA as well. Just wanted to see if anyone on here had specific experience that might contradict that assessment.


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Is there any drawback to breathing deeply all the time?
Normal, relaxed breathing (eupnea) uses the external intercostal muscles. Diaphragmatic breathing (deep breathing) is more efficient because it balances the ventilation/perfusion ratio across the lungs by ventilating the lower half of the lungs more (as far as I understand), allowing for more efficient gas exchange. It also has various health benefits. The respiratory center in our brain controls breathing to regulate carbon dioxide and oxygen levels in the blood. Is there any drawback to breathing slowly but deeply all the time, or is it just that humans are inefficient?

Why question on how something didn't evolve are pointless. Most likely it simply didn't happen. There is no reasoning in evolution, it happens by chance.

I edited my question to clarify the real meaning of what I was trying to say.

What does it mean to be "more efficient"? What is the survival/reproductive benefit of that efficiency?

Many online sources claim that it is "more efficient" than normal breathing, as well as having various health benefits.

If they don't explain what thing is being optimized, that's a meaningless statement, like claiming something is "healthy" is a meaningless statement.

This link states many health benefits. https://motherhoodcommunity.com/diaphragmatic-belly-breathing/

@mathlander note that you are on a site for biology - the science for it. Our responses on here are scientifically backed and generally discount anecdotal evidence, such as almost all of that on the website you linked. I checked out their references - most of them are not scientific at all, and almost all of the actual scientific links have no mention of diaphragmatic breathing or breath control, or are very badly misinterpreted by the website authors.

@mathlander also note that your body has a natural mechanism to get you all the oxygen you need at any given time. This is highly efficient in energy terms (which is a serious evolutionary constraint) because you use minimal muscle effort to do so. I don't see that deep breathing and exerting more effort could be more efficient.

@bob1 i actually experienced benefits of deep breathing all the time myself. Tho leaving that aside, my only question is that is it in anyway harmful to deep breathe all the time scientifically?

@vipulratiya note that anecdote =! science. You may personally feel that it has helped you, which is fine and good if it works for you, but it isn't scientific. Has anyone looked at the benefits of doing it all the time - maybe. Try searching pubmed for yourself and/or ask a question about it.

Short answer no, no evidence to support this at all.
Longer answer:
The adult respiratory rate is about 12-16 breaths per minute - this equates to about one breath per 3.75-6 seconds.
A study that I found looked at gas distribution in the lung during inspiration and breath hold found that in healthy volunteers, the lungs had approximately even distribution of gas throughout the lungs within about 1.7 seconds1 (see fig 3.2, also reproduced below), and that this rate was more affected by posture and gravity effects on the lungs than by breathing rate. This means that even if you do slow your breathing rate and use your diaphragm more, you aren't getting more oxygen than if you breathe normally.

Reproduced from reference 1.
There are some autonomic responses to breath control, such as lowering heart-rate, but I don't know that these have any scientifically validated benefits beyond this.
1: J.M. Wild, F.C. Horn, G.J. Collier, H. Marshall,
Chapter 3 - Dynamic Imaging of Lung Ventilation and Gas Flow With Hyperpolarized Gas MRI,
Editor(s): Mitchell S. Albert, Francis T. Hane,
Hyperpolarized and Inert Gas MRI,
Academic Press,
2017,
Pages 47-59,
ISBN 9780128036754,
https://doi.org/10.1016/B978-0-12-803675-4.00003-8.

@mathlander what benefits did you mention? I only see your statement saying "various health benefits" without mention of what those benefits might be.

Are the benefits in the link I commented scientifically proven?

@mathlander No - see my comment about the link in the comments section for your question. Also please don't delete comments that then make subsequent comments meaningless.

I know that the link is not scientifically proven, but are the benefits given there proven anywhere else?

@mathlander may I direct you to pubmed - if you want to know, you can first research on there and then, if needed ask specific questions about each topic. General questions don't fit well with the Stack Exchange format and questions here require prior research attempts by askers, as outlined in the [help].

https://www.passy-muir.com/wp-content/uploads/2018/10/51083-133296-1-PB.pdf claims lots of benefits.

@mathlander if you have a look at the object in your link you will find that it isn't Passy-Muir's, but a review from Advances in Respiratory Medicine, which is a very low ranked scientific journal from a semi-predatory publishing group; not a great publication, but credible information I suspect.


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Is there a standard protocol for isolating bacteriophages from biofilm?
We are planning to screen soil, water, and biofilm for mycobacteriophages, particularly the environments where the bacteria have been found in the past.
We have already isolated phages from soil but have had trouble finding a good protocol for isolating them from biofilm. Nelson et al. isolated Mycobacteria by swabbing the biofilm of rocks. A Google Scholar search for isolate bacteriophage from biofilm gives us results about the phages' ability to penetrate biofilm but not much about isolation.
We found this paper, which described a protocol for extracting phages from skin swabs, which we could try to extrapolate to biofilm swabs.
Is there a paper that describes phage isolation from biofilms on hard surfaces such as rocks and human-built environments?

A 2019 paper in Viruses used sonication to monitor the phage titer of P. aeruginosa biofilms associated with "stainless steel coupons".

In order to better understand the repartition of phages after the treatments, samples were taken to determine the quantity of planktonic viruses in the mineral minimum medium around stainless steel coupons, but also to estimate the amount that was biofilm-associated. In the first case, samples were collected directly on the liquid medium of the jar after 14 h of phage activity and titered by following the previously detailed protocol. In the second case, at the end of treatment, the liquid medium around the coupons was discarded and replaced by the same volume of medium. The biofilm was then resuspended by sonication (Figure 1), allowing the sampling and titering of biofilm-associated phages.
Sonication of controls was assessed by adding the same phage titers in each jar (3 × 1010 PFU/jar). The titer was then evaluated by the spot test method when jars had not been sonicated and after 1, 3, and 5 min of sonication.

Unfortunately, their methods include neither the frequency of sonication nor the specific sonicator used.
A 2016 paper in Frontiers in Microbiology investigating phage mitigation of catheter-associated biofilms found that sonication reduces the viability of phage particles. Anecdotally, vigorous vortexing is sufficient to break the tails off of Myoviridae and Siphoviridae phages when making TEM preps, so it's not surprising that sonication has an effect on phage infectivity. However, if your goal is phage discovery and not phage titer determination, I wouldn't worry too much about viability -- some phage will survive the sonication process.
Riffing on the insights from these papers, here's a simple protocol on which you can build:

Scrape biofilms from hard surfaces using a sterilized razor blade and (carefully!) transfer the biofilm to a conical tube using a sterile toothpick or pipette tip.
Wash the biofilm in phage buffer or similar medium by repeated centrifugation. This will help to remove phage that aren't strongly associated with / contained within the biofilm.
Add the appropriate volume of fresh buffer for sonication. Note that buffer volume is an important parameter in efficiency of sonication (see Figure 1 of this paper).
Sonicate! If you don't have access to an ultrasonic probe homogenizer, water-bath sonicators are relatively affordable and will probably work for your purposes.
Use the sonicated sample as input for your favorite phage enrichment protocol.

Happy hunting!


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Tiny black mushrooms growing from veggies?

I've found these tiny black mushrooms sprouting from my scallions.  I'm in Salt Lake, UT, but the scallions are store-bought, so I'm not sure where they're from or where they've been. Anyone know what these are?  Are they dangerous?

Related: What are the white eggs growing from a black stem on the Napa cabbage plant?

@theforestecologist that looks spot on.  I flagged my question as a duplicate


text:
What's the exact mechanism of oral tolerance?
I have mainly two matters of confusion need to be clarified.
First question:

The immune system does not necessarily kill everything hat has PAMPS, the bacteria living in the gut, have PAMPS (Pathogen-associated molecular pattern) in their surface, but they are not harmful to the body

Is this proposition correct?
and the second question is about my confusion of the following statement

the mechanism by which the immune system tolerates the presence of the bacteria that live in the gut is not fully understood

So I am wondering, is there some textbooks or reference particularly talk about oral tolerance?
Moreover, I am especially curious about the fact that, since PAMPS trigger innate immune first rather than adaptive immune system, How can oral tolerance even avoid innate immune? is there some resources about that particular topic?

Please define acronyms that you use. And I wouldn't use chatGPT to study things....

@Bryan Krause Sorry about that, I just make the first citation  also a susceptible question which needs references, thank you!


text:
Can stand-alone DNA (no nucleus, no membranes, organelles...etc.) create cells?
I have been searching for an answer to the following question as part of my research but can't find a direct/complete answer yet.
Can stand-alone DNA (no nucleus, no membranes, organelles...etc.) create cells?
From what I have learned about the biology of the cell, it seems to me that it is virtually impossible, but I will like an answer from an expert on the subject matter.
Regards,
Alfredo Archilla

Too much information is missing. E.g. what is the DNA standing alone in (water? Saline? Primordial soup? Eukaryotic cytoplasm minus organelles?) Can you define "cell"? If you're asking if DNA can do anything by itself, it can't. It's just a language, a code, a blueprint, a complex set of instructions. A blueprint can't build a building. DNA can't build a cell.

Welcome to SE Biology. Please finish reading the [Tour] (we know you have not) and then the Help on asking questions. You will see that you are expected to do some research and thinking of your own before posting a question and demonstrate it in the question. What have you learned about biology that makes you think it is impossible? If you are correct, this does not make a question of interest to biologists, but more the use of this site to check whether you have the correct answer to some assignment. If so, this is not what the site is for.

DNA absolutely not, RNA maybe...
DNA can't even replicate itself without help
RNA on the other hand makes almost everything. It makes proteins, it makes DNA and we know it can at least bind and alter phospholipids. It can also make more of itself.
keep in mind the simplest living cells (prokaryotes) do not have nuclei nor most of the things we call organelles either.

https://www.ncbi.nlm.nih.gov/books/NBK26876/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC17937/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122455/

Ribosomes are necessary for protein synthesis. Without organelles, RNA is basically useless, depending on your definition of "cell". Without membranes, what does RNA's ability to alter membrane permeability matter? Without mitochondria, there's really no energy for the cell (again, depending on what you consider a "cell".) I think this answer is incorrect, but that's just an opinion. The OP has not given us enough useful information, but as stated, RNA can't make a cell.

RNA doesn't make proteins. Ribosomes (which include proteins) and tRNA-complexed amino acids make proteins. You need chaperones to help fold proteins, post-translational modifications need to be made for proteins to be active, and they need to be localized correctly. You also need a supply of lipids and phospholipids to build membranes. All of this requires pre-existing "stuff" that is not RNA. If your answer was correct, I could leave my total RNA extraction sitting around long enough and cells would form in it. Obviously, that doesn't happen.

@MattDMo all the functional parts and the bulk of the molecules of ribosomes are made of RNA, the proteins are only some stabilizers. tRNA is amazingly also made of RNA. you absolutely do NOT need chaperones to make proteins fold the right way. chaperones make it more efficient they are not necessary. one way you can tell is viruses often have no chaperones  or post translational modification for their proteins.  lastly make is not the same as made of, I never even tried to claim membranes were made of RNA.

@anongoodnurse most cells do not have mitochondria, mitochondria is only in eukaryotic cells. please learn what actually makes up the simplest cells. also ribosomes are made of RNA. Proteins synthesis in its simplest form is rRNA reading mRNA using tRNA carrying amino acids to make proteins.

Is a ribosome an organelle? Yes, it is (OP stated "no organelles".) Can a ribosome assemble itself from RNA? No, it cannot. Please don't tell me what to learn; I've had more schooling than most (Physician, former Molecular Biologist). Your answer is simply wrong. Surprising, given your profile claims, that you can't see the errors in your answer. Besides, you spent your answer on what the OP's didn't actually ask. Cells have cell membranes. @MattDMo is correct, as am I.

@anongoodnurse can a ribosome assemble itself, yes, https://pubs.acs.org/doi/abs/10.1021/ar2000474 I note no mention of mitochondria, do you still think they are necessary? If you define a cell as having a membrane sure it has a membrane could something without a membrane cells have membrane replicate, yes, could it make a membrane quite possibly.  you seem to be confused about what the OP asks, it is not is something without organelles IS a cell, it is could it make a cell.

I'm not going to argue anymore after this. Even "simple" ribosomal formation requires the proper preexisting ribosomal proteins, a complete buttload of enzymes, rRNA, a cell-membrane dependent protein localization, etc. I'm not confused about what the OP asked. It's clear: "Can stand-alone DNA (no nucleus, no membranes, organelles...etc.) create cells?"


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Is there any difference between microplastics from health perspective?
I wonder if there is difference between plastics if we talk about the negative health effects of microplastics. For example wood is just a bunch of polymer and some other components from chemical perspective and it is neutral from health perspective if it is not fungus infected. So I wonder if the polymer type matters by microplastics or it is just the size and maybe endocrine disruptor additives like BPA.

What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Our goal is not simply to be an answer site, but rather a site that promotes self-learning with some expert help along the way.

@MattDMo Well I found some article that talks about different polymer types and has a hazard model, but it is for marine life. I did not find an article which assesses human health risks of different polymers. https://www.sciencedirect.com/science/article/pii/S030438942200187X I found another article for human health, but it is too general, no cell tests, etc. https://link.springer.com/article/10.1007/s40572-018-0206-z

it would be helpful to have those citations directly referenced in the question, noting your specific objections to each and why they don't answer the question.


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Through what mechanism does ingesting Saturated Fat (but not Mono unsaturated Fat/PUFA) increase Serum Cholesterol.?
I know that the saturated fats you ingest is broken down in the intestines by the bile acids from liver and then re synthesized as triglycerides after crossing the enterocytes. Then these triglycerides along with cholesterol (either from diet, or from the liver in form of Bile acid)  is packaged into lipoprotein particles called chylomicrons..and they leave the intestines through the lymphathic Systems.  These  chylomicrons deliver triglycerides (converted to FFA) to adipose, muscular and other peripheral tissues.The remnants of the Chylomicrons are taken up back by the liver at a LRP receptor?
Once these Chylomicrons remnants are taken up by the liver..it somehow triggers greater  synthesis of ApoB particles and VLDL, as well as down regulation of LDL receptors on liver. Then the VLDL particles (loaded with Triglycerides and endogenous cholesterol?) leave the Liver and deliver FFA to peripheral tissues (similar to Chylomicrons)...and progressively lose their Triglyceride content and become IDL (reptaked by the liver). and finally LDL..since LDL receptors are also downregulated and their is presumably no other equally effective mechanism for LDL reuptake this leads to a net increase in LDL particles in Serum and measured Serum cholesterol. My question is How does Chylomicron remnants returning to the liver trigger the synthesis/Genesis of greater amount of ApoB and VLDL production? Do these remnants act as a signal to the liver to produce more VLDL/ApoB, or are Components from Chylomicrons  used to produce the VLDL, and how about LDL reuptake downregulation.
I am an engineer with no background in physiology/biochemistry. Could you please provide a relatively layman's explanation of the mechanism. Thank you.


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Did neanderthals need vitamin C from the diet?
Modern humans need to get vitamin c from the diet, because we do not make it ourselves. Did neanderthals produce vitamin c? At what point of evolution exactly was this ability lost?

Humans can't synthesize vitamin C due to a dysfunctional enzyme L-gulonolactone oxidase, or "GULO".
From Wikipedia:

Loss of GULO activity in the primate order occurred about 63 million years ago, at about the time it split into the suborders Haplorhini (which lost the enzyme activity) and Strepsirrhini (which retained it). The haplorhine ("simple-nosed") primates, which cannot make vitamin C enzymatically, include the tarsiers and the simians (apes, monkeys and humans)

All of our relatives under Haplorhini, including monkeys and apes, are unable to synthesize vitamin C; that would certainly include neanderthals.


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DNase annotations of Drosophila melanogaster
I am familiar that the RedFly database provides annotations for 1,458 sites in the genome of Drosophila melanogaster subject to cleavage by DNase I. It seems the vast majority of those annotations come from the original FlyReg database originally reported in 2005, which merged with RedFly early on. I have looked, but not found any additional sources of annotations of the Drosophila genome of DNase cleavage sites. I wanted to ask, to be sure, if there are no additional studies / experiments which record DNase annotations in the Drosophila genome outside of the ones recorded by RedFly.

I think that DNAse-seq is no longer the favored assay for chromatin accessibility.
These days, I believe ATAC-seq is favored, or even single-cell variants of ATAC-seq. (links to drosophila papers)
I can't comment on a general Drosophila regulatory database beyond what you already know about, beyond what's obvious via google (here, here).

Very useful answer but are you sure it's no longer favored? 2021: "DNase I is still the reagent of choice for TF footprinting, which can determine the location of TF binding sites due to the protection of the site by the TF itself." https://doi.org/10.1038/s43586-020-00008-9

@arara interesting, I don't have access to the review unfortunately so it's hard for me to evaluate. I suspect that there is a subtle distinction between "TF binding sites" and "chromatin accessibility". Chromatin accessibility is a rather more generic phenomenon. What I would bet is that ATAC-seq is more common these days in large part because it's easier methodologically. But I could readily accept that DNAseI is a more diagnostic, less biased reagent at the single molecule level (or for e.g. one locus probed on a Southern blot). But I'm also not an expert in the field!


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NMDA receptor depolarization
I learnt that two factors for NMDA receptor channels opening are:
1)Binding of glutamate
2)Depolarization of postsynaptic cell (to remove the Mg+2 block)
Given that depolarization starts in axon hillock and NMDA receptors are on dendrites, how does it all work?

"depolarization starts in axon hillock" - this is not true, why do you think this?

Seemingly I confused the term with action potential. So NMDA receptors need a depolarization which is below +30?

Yes, that's correct. Also read about backpropagating action potentials.

Alright, I will. Thank you!


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Is harmonic resonance in Photoreceptors explored?
Look at the resonance curves of the L-cone (OPN1LW) in humans, it has its peak at ~570nm and rises up in the lower wavelength (higher frequency) area. For me as a musician, that looks like a natural harmonic 2/3 response – the fifths – of the frequency. But all spectral response charts I've found so far for the different receptors in humans don't really go beyond the borders of the range visible to humans.
Has someone a link to a study that tested for harmonic responses or general response in a field extending at least one octave in both directions, hence about 200nm - 1600nm, for the actual receptors (rods/cones) without surrounding effects like the lense being a low-pass-filter etc.

See https://physics.stackexchange.com/questions/229046/why-do-we-see-just-one-octave-of-light and https://biology.stackexchange.com/questions/57708/what-is-the-biological-potential-for-vision-of-wavelengths-outside-the-human-vis.

I’m voting to close this question because a request for a link is not a question about Biology in terms of SE Biology.

I think a few things are muddled here. The frequency response profile of a cone (which is an entire cell) is a functional response to excitation of that cell's photoreceptors. It's easy to show that these cells only function over the range of wavelengths that are considered "visible range." So that's why you won't readily locate experiments that address your query. (I think a link to the data you're asking about would help.)
Since the underlying light-detection event here is the photo-isomerization of rhodopsin, there's no reason to think the process (at that scale) would occur at harmonics you're familiar with from music theory. That's because electronic transitions correspond to well-defined frequencies (as with the photoelectric effect). The rhodopsin molecule, like most pigments, isn't well-approximated as a harmonic oscillator (unlike, say, a guitar string) which is the whole reason classical electromagnetic theories failed to predict the emission spectrum of hydrogen.
So you're mixing-up your natural phenomena; biological photoreceptors behave somewhat-like the hydrogen atom, not like a guitar string. As you can see, the emission or absorbtion spectra of hydrogen do not have simple overtones of a fundamental frequency.

Vision works by a pigment molecules changing conformation by absorbing a photon. A certain range of energies is necessary for this conformation change.
More generally, molecules can potentially absorb multiple photons simultaneously rather than individual photons, and the combined energy of multiple lower-energy photons can excite the molecule to the same state as a single higher-energy photon. This is commonly utilized in biological experiments via 2-photon microscopy. Because 2-photon excitation requires simultaneous arrival of two photons, you need much higher intensities of light.
Here's an example of a paper discussing this in rhodopsin:
Palczewska, G., Vinberg, F., Stremplewski, P., Bircher, M. P., Salom, D., Komar, K., ... & Palczewski, K. (2014). Human infrared vision is triggered by two-photon chromophore isomerization. Proceedings of the National Academy of Sciences, 111(50), E5445-E5454.


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Accessing the recombination map of Drosophila melanogaster
I'm looking for some information on the data of a recombination map of Drosophila melanogaster. In 2012, an extensive study by Comeron et al. appeared saying that they had reconstructed a recombination map for D. melanogaster. I want to access the data files themselves, and the Data Availability section of the paper included:

Estimates of recombination reported in this study are publicly
available, for any genomic region or gene in D. melanogaster, from
www.recombination.biology.uiowa.edu and www.recombinome.com.

So two websites are listed for where the data can be accessed. But neither site exists anymore. A data file can be downloaded from Comeron's work on FlyBase here. The problem is, however, this data file only seems to list crossover (CO) recombination rates in windows, but not the same thing for gene conversion (GC) recombination rates, despite both being reported separately in the paper. So this makes me think that there's a lot of supplementary files from Comeron's paper not saved here on the FlyBase page. I found another indication of the limited access there seems to be of Comeron et al.'s original files. Reading this 2019 paper which appeared to make use of Comeron et al.'s recombination map data:

The resultant D. simulans recombination map was used in parallel with
the D. melanogaster recombination map produced by Comeron et al.
(2012), downloaded from the D. melanogaster Recombination Rate
Calculator (Fiston-Lavier et al. 2010, last accessed April 19, 2019 ).

So the paper for the Recombination Rate Calculator (RCC) was published in 2010 to introduce this web tool. And when the Comeron et al study came out in 2012, the website incorporated that papers data. And that's how this 2019 paper is accessing that data, ie via the RCC website. The RCC website is old and not updated, as you can only query recombination map coordinates in Release 5 of the D. melanogaster genome. But when you do submit a query for the recombination rates of regions of the Drosophila genome to the website, you suddenly get these additional columns of information referenced back to the Comeron et al. study: minimum, maximum, and average recombination rate over the genome. This is not listed in the FlyBase file at all, and the RCC website doesn't specify if this is CO or GC recombination rates. Also, from what I can see you can't actually download the supplementary data files from the RCC website for yourself either.
So, how can I actually access the full supplementary data from Comeron et al.'s original recombination map study of Drosophila? It doesn't seem that there is any sort of full access from the sources listed in the paper, or FlyBase, or the RCC website. If any additional recombination maps have come out since and the data files are available, I'd be happy to use those as well.
EDIT: FlyBase unfortunately doesn't have additional files to those I've found. The Comeron lab also lost some info when those websites went defunct, but will attach some of the per-chromosome recombination amp files to the website in R5 and R6 coordinates.

We don’t know. Write to the authors of the paper, and if they don’t reply, try writing to FlyBase, which provides excellent professional support.

@David Thanks for the suggestion, I've sent FlyBase an email and will update if I get what I'm looking for.

Yes, the original links stopped working, apologies. I have now added a file/link in my current website with per-chromosome recombination maps in R5 and R6 coordinates.
https://comeron.lab.uiowa.edu/recombination-rates
Josep

Josep Comeron is still at the University of Iowa Biology Department, and his lab has its own website. Browsing around, I found this page on recombination rates, but no apparent way to access the data. His contact information is available on both the UIowa Biology Dept. page and his lab site, so I suggest emailing or calling him directly to see where the information you're seeking is currently available.
I tried to use the Wayback Machine to see if the data from either recombinome.com or the uiowa.edu was archived there. recombinome.com has been crawled repeatedly, but clicking on some random results from 2013-2015 only gave the main page, with no links to the raw data. www.recombination.biology.uiowa.edu was never archived.

I originally encountered the same issue trying to access those sites with the Wayback Machine unfortunately.


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What is the earliest known animal that could run?
By "running" I mean a land gait that at one point has all propulsion limbs off the ground. Jumping, like a flea or a frog, is not running.
The earliest land vertebrates could not run, I assume. The ability to run would be an advantage when pursuing prey or evading predators.
Our data from the period where running would first evolve is limited to bones and footprints. Is that enough to tell what an extinct animal's gait would be?

Things like sea scorpions walked on the ocean bed so shouldn't be discounted, especially when buoyancy makes it a lot easier to satisfy for your running criteria.

Welcome to the site. Interesting question - but you could improve it by telling us what you have found already, and what criteria you measure running by. Note that the [help] has a page on "homework" questions and what you can do to avoid getting closed for this reason.


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If RNA transcription is 5' end to 3' end, what is the directionality of the promoter for?
I am confused. If RNA transcription always grows from the 5' end to the 3' end, what does the direction of the promoter do for the mRNA transcribed?
From what i understand the RNA polymerase always extends the mRNA from the 5' end to the 3' end. Yet promoter sequences define the direction of transcription?
Which one is correct? Does mRNA transcription always extend from 5' to 3'? Or does the promoter dictate the direction in which the RNA polymerase extends mRNA?
Or it the truth somewhere in between?

Can you explain your thinking a bit further to focus the problem?

Think! DNA is double-stranded. What exactly do you understand in molecular terms by the statement "(the) promoter sequences define the direction of transcription"? Draw yourself a diagram.

Ok Sir, so there are 2 strands of DNA, so depending on the direction of the promoter, either one of the strands of DNA becomes the coding template (get transcribed)?
Is that correct?

I’ve just seen your comment. You need to address me as @david so I am alerted to your reply to me. (I don’t have to do the same as I am commenting on your post.) In answer to your query, that’s almost right. But it’s not only the DNA strand that is different, it’s its location or direction relative to that of the promoter.


text:
Cell culture experiments, technical or biological replicates?
Experimental design:
Cells are grown, counted, and seeded in 96-well plates.
Cells recover 24 hours.
Cells are treated with different doses of a drug, 3x per treatment.
Cell survival read via MTT.
This is repeated twice, on two additional times.
In other words, on three independent days, we seed out this plate and measure it one day afterwards (measurement kills the cells):

A
B
C
D

1
1 µM
2 µM
5 µM
10 µM

2
1 µM
2 µM
5 µM
10 µM

3
1 µM
2 µM
5 µM
10 µM

Each Dosage (columns) is measured in triplicates (rows). This is repeated three times, so in the end, each dosage has a total of nine datapoints.
Does this experiment have 3 biological replicates, each of which has 3 technical replicates or is there another way to group this?
My inclination is to use a mixed-level model where each of the plates is a level in a random variable.

I don't think your description of the experiment is very clear.

@ Bryan Krause: I disagree, I understand his setup very clearly, it‘s a standard procedure in cell culture. Also, this question should  not have been closed, since these matters aren‘t trivial and their impact is often underestimated

@markur Disagree, it's still unclear. It may be standard, but it's unclear.

@BryanKrause please specify what exactly is not clear. I have ideas how to improve this post, but I don‘t want to change things that you already understand.

@markur How the replications are administered: what is measured in the same wells and what is measured in different wells. Total N is important too.

@BrianKrause ok I applied some edits

It's a bit complicated, because your cells at each replicate are single source, so biological replicates are not truly replicates - but it gets very difficult to escape that when you consider that most established cell lines are from a single source. If you want to do it as close to properly as you can, you should get up 3 separate vials of your cells and maintain/use them individually.
In your case you can consider that different repeats are biological replicates (so you have initial with 2 repeats? so 3 replicates total(?)) - your wording is unclear here, I interpreted it to mean you have done the experiment twice, not an initial with two additional repeats, but the next line says "3 biological replicates". These give you information about the biological variation in your cells over time.
The replicates at each repeat are technical replicates and provide information about how well you are able to do things like pipetting or making dilutions.

The experiment was done three times. Regarding cell lines, yes, all the cells came from the same lot of the same ATCC catalogue entry (albeit different "break-outs" from frozen stocks). So, there are actually zero biological replicates?

@Bryan it's a philosophical debate as to whether they are biological or not. Most would consider them to be biological replicates, because if you reductio ad absurdum the argument, it makes it impossible to ever have biological replicates in a cell line.

It is not philosophical. Technical replicates measure technical variance while keeping biological variance as low as possible. Hence, you measure technical replicates on the same day. Biological variance is introduced by prolonged culturing (react to differences of FCS, culture flasks, Selection by splitting, etc.). To display biological variance, you measure at different timepoints and minimize technical variance by taking the mean of tech replicates. Even if the cells have the same background, some cell lines do have great internal time-dependent variance, like the ones I work on.

Also, it‘s important to never mix technical and biological variance. If you measure triplicates on three different days, show technical variance by plotting three separated groups, each group consisting of the three technical replicates, (not one group with nine datapoints). To show biological variance, take the mean of the triplicates and display the three means, each mean measured on a different day (not as a ‚time series‘, just on a different random day). If you mix technical and biological variance (n=9) , that‘s pseudo-replication and and bad practice.

Source: Harvey Motulsky (the CEO of Graphpad Prism), Intuitive Biostatistics


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Why are lymph nodes located where they are?
According to the National Cancer Institute, a subdivision of the National Institutes of Health, clusters of lymph nodes are found in the neck, underarm, chest, abdomen, and groin. Why are lymph nodes located in these places?
Edit: This article claims that about 60% of the lymph nodes are located just under the diaphragm, and breathing (particularly deep breathing) creates a pressure gradient, pulling lymph through the lymphatic system. This could be a reason why most of the lymph nodes are located there.

"Why" questions of this kind invite "just-so" explanations that are rarely rigorous. As sites of information processing, lymph nodes could be expected to be concentrated near sites of potential infection. Dendritic cells migrate from infection sites to their proximal nodes, to present molecular patterns of interest. I am not sure whether any lymph nodes' locations are adaptations to receiving circulatory boosts from movements, or whether the effect mentioned in your cited article is an exaptation or a spandrel.

Reasons I can think of (N.B.: teleological): aggregating lymphocytes further from a source of infection helps fight infection better than WBC's spread out everywhere,  and they need to be in soft tissue that can expand without compromising function. Swollen lymph nodes (LN) in your hand would cause a lot of pain (can hardly use hand) and could compromise LN function. But swollen LN in the axilla? Piece of cake and protected. They're especially plentiful below the diaphragm because of all the crud we ingest; they drain the entire GI tract.


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Has there been evidence that there has been coevolution in E. Coli strains with the T4 bacteriophage?
According to Evolution of T4-related phages, there have been multiple instances of evolution in the T4 coliphages. Per the article, there are many T-even phages that have insertions from other coliphages. Per Oechslin's paper, different bacteriophages have different effects with different strains of E. Coli. Has there been evidence that there has been coevolution in E. Coli strains with the T4 bacteriophage? I have found a paper on the coevolution of E. Coli and PP01 at Coevolution of bacteriophage PP01 and Escherichia coli O157:H7 in continuous culture. Still, I have not found any information regarding T4 coliphages and their coevolution with E. Coli.

High-level answer: Yes. Almost by definition there might have to be coevolution between a phage and a host, in the same way that humans coevolve with our viruses (in the form of e.g. immune repertoire). Pathogens kill/disadvantage susceptible hosts, imposing a selective cost to susceptibility.
Detailed answer: Yes. E. coli has CRISPR arrays that target T4, and T4 has mechanisms for escaping CRISPR processing by E. coli. This is pretty textbook coevolutionary arms race. This is reflected somewhat in the different host ranges of phage, as you suggest.


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What is a crypt in a histopathological image?
I am doing a science fair project on using histopathological images for cancer diagnosis, and I came across something that says a characteristic is exemplified by superficial serrated architecture and elongated crypts, I was wondering what that meant.

What tissue? Could you give more information on the sample, "cancer" is incredibly broad.

You should give more details and information to this question as we don't know what tissue/cancer you're referring to.
If I'm just taking a guess I'd say you might mean intestinal glands which form tube-like glands called crypts found in the lining of the gastrointestinal system (i.e., digestive tract). Cancerous tissue including the crypts can be colorectal carcinoma for example. Superficial serrated architecture most likely refers to sessile serrated polyps or colorectal serrated lesions.

Colorectal carcinoma: Pathologic aspects
Superficially serrated adenoma: a proposal for a novel subtype of colorectal serrated lesion
Sessile Serrated Polyps: Detection, Eradication, and Prevention of the Evil Twin


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What safe, accessible enveloped virus should we use for beginning experiments?
I need to know which virus meets the following criteria:

It has to be enveloped.
It has to have a DNA packaging scheme similar to Adenovirus (basically, sticks most of itself together then draws in the DNA like the way a human eats a noodle).
It can’t infect humans (for obvious reasons).
It has to be easily propagated, either in a microbe such as ecoli or in embryonic chicken eggs.
It has to be virus stock that can be easily derived or purchased.
It has to be BSL1 rated

Avian adenovirus met all but the sixth criteria, unfortunately.
Is there something else that you are aware of that would meet those criteria? It does not even have to be in a particular family.

While Phages (as in Acvill's answer) are probably the most tractable and safest option, another option would be insect viruses of the family Baculoviridae

Enveloped
dsDNA
Incapable of infecting humans or plants, generally species/genus specific I think
BSL-1 use in general (see classifications of some recombinant viral vectors here; note that 1* indicates parent virus containment level)
you can buy baculovirus expression systems from a range of companies and suppliers.
Easily propagable in common insect cell lines.

Consider the dsRNA bacteriophage Φ6, which has been used as a surrogate virus to study Ebola and SARS-CoV-2.

Φ6 is enveloped.
During Φ6 assembly, an NTPase recognizes pac sequences and sequentially packages three ssRNA segments into the capsid; minus strand synthesis then occurs after plus strand packaging. See figure 6 from Mindich 2004 for a helpful schematic.
Φ6 is a Pseudomonas phage and cannot infect human cells.
Φ6 is readily propagated on Pseudomonas sp. DSM 21482, which itself is a Risk Group 1 organism (German equivalent of BSL1).
You can purchase Φ6 from DSMZ.
Like its host, Φ6 is in Risk Group 1.

Not saying this isn't the right choice (because phages were my first thought too), but phi6 isn't enveloped and is RNA rather than DNA

Is Phi6 not enveloped? This paper says it is: https://www.nature.com/articles/s41598-020-79625-z

huh, I thought none of the phages were - turns out I'm wrong. Looks like only the Cystovirus genus is though.

Excellent -  thank you to everybody!  Yes this paper https://www.mdpi.com/1422-0067/19/3/790/htm also says Phi6 is enveloped.


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Can you alter your hearing range by changing air pressure in your nose?
I caught a bad cold recently and found that increasing air pressure in my nose causes some clicks in my ear. I understood from this site that this is because ears and nose are connected. But what I didn't understand however, was that I my hearing range got completely shifted after doing so (not permanently of course). If I am right, it tends to make low frequency sounds clearer. The opposite happens when I decrease pressure. The higher frequencies become more crip and clear. I have the feeling that the answer is related to the way hearing works but would like to hear how exactly. It would be great if any of you could confirm or deny this or provide some explanations.

Questions based on personal anecdotes are hard to answer. Perceptual quality of sound may depend on a lot of things besides middle ear pressure.

Just fyi: the ear(s) and the nose are connected by the eustachian tube, not the sinuses.

@AliceD Agreed. I have also experienced the shift in audible range while travelling on a plane. This is why I think this is related to pressure.

Thanks for the info @anongoodnurse

The sound equation I = Xi^2.Omega^2.c.Rho (Xi = particle displacement, Omega = frequency, c = speed of sound, Rho = density of medium)  implies that the sound pressure (i.e. volume) changes with air pressure  and frequency- which explains the aeroplane problem, but I don't know how much effect in the small volume of an ear.


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electrotonic spread and screening
(In physics.stack I have been suggested to post my question also here.)
In the classical theory of passive neurons (where the action potential is not yet excited), the voltage is successfully described by cable theory. The (unmyelinated) axon is modeled as a series of cylindrical sections in series. Each section is described by an electric circuit (in 1D) with an axial resistance, and the membrane is modeled as a capacitor.
If charges are injected at one end of the cylinder, the "cable equation" gives the transmembrane voltage at steady-state in the shape of an exponentially decreasing function of space. Here the characteristic 1/e decay length of the voltage can be long in large axons, of the order of mm.
Question
My question is about the apparent lack of charge screening in this picture. At physiological conditions (where ions and counter-ions are present), I'd expect that an excess of charge, like the one injected by a micro-pipette, or generated by the opening of channels, is screened very quickly (microseconds), so a few Debye-lengths (nm) apart, the voltage should not be seen.
How can the theory and experiments show a voltage that persists at millimeter distances at physiological conditions where screening should be present?
EDIT from a comment:
The electrotonic transmembrane potential is exponentially decreasing along the membrane. If we assume one side isopotential (say the interior), the other side should then have a voltage that decreases along the membrane. So measuring the voltage on two points along the membrane, one should see a drop in voltage, if the points are distant enough. Therefore on that side there is a current, and the charges on that side are not screened.
Is this description correct?

In biological membranes, the primary physics principle resisting change in voltage is described by capacitance of the membrane, which is a key aspect of the cable equations. If you model some instantaneous change in charge (not particularly biological, but something like it is possible using an amplifier in patch-clamp electrophysiology), the change in membrane potential will be smoothed by the membrane capacitance.
When people talk about voltages in biological systems, they're talking about an electrical potential difference across the membrane, not measuring within nanometers inside the cell. Yes, if you somehow placed two sensors nanometers apart in the cell you'd have some difficulty measuring a voltage between them - for practical intents you can consider the intracellular space to be isopotential over the distances relevant to molecules.
Thinking about other ways to phrase this: maybe it will make sense to you to think about a distinction between charge of a solution and a particle (e.g., a single ion in that solution). When you have more positive than negative ions on one side of a membrane compared to the other, you're going to have a voltage where it's more energetically favorable for positive charge to move on the negative side than vice-versa. Charge-screening refers to how the total charge of the extra positive ions (or lack of negative ions) distributes in solution, such that it's not like you have "islands" of positivity on the positive side around each positive ion (as long as you're viewing from outside Debye lengths), but rather the charge is still somewhere in the solution when you measure compared to the other side - that's the membrane voltage. Note that when you look at the equation for voltage over a capacitor:
V = Q/C
the equation just involves the charge and the capacitance, not the specific locations of the charges.

thank you for your answer. The electrotonic (transmembrane) potential is exponentially decreasing along the membrane. If we assume one side isopotential (you suggest the inside one), the other side should have a voltage that decreases along the membrane. So your two point measurement should see a drop in voltage, if the points are distant enough. Therefore on that side there is a current, and the charges on that side are not screened? Does this sound correct?

@scrx2 No, it doesn't sound correct, when I'm talking about being isopotential I mean over the short distances where charge screening is relevant. You're not appreciating that charges can't move across the membrane freely, where the actual membrane potential is realized.

Maybe here's a different way to think about it: you have net 10 charges on one side of the membrane, and net 10 on the other. Now you move one across so you have 9 charges on 1 side and 11 on the other. If charges now cannot move across the membrane, how would you arrange those charges in space on each side such that there is no voltage across the membrane?

yes, there will be a voltage difference across the membrane, following an exponential profile along the membrane (say X). But, because of this exponential profile in X, there should be a potential difference also along X. Along X, as an electrical resistance is present, there will be a current. Do you agree?

Are you saying that the extra charge brought, by say one ion pump, from one side to the other cannot be screened? I'd agree

So measuring the voltage on two points along the membrane, one should see a drop in voltage, if the points are distant enough. Therefore on that side, there is a current, and the charges on that side are not screened.

You are correct that in theory along an axon membrane for example, the decrease in voltage is exponential in space. However, you need to consider saltatory conduction. There, the action potential propagation occurs from one node of Ranvier to the next. This mechanism increases the conduction velocity of action potentials and also decreases the exponential voltage drop.

How can the theory and experiments show a voltage that persists at millimeter distances at physiological conditions where screening should be present?

The uninsulated nodes of Ranvier are the only places along the axon where ions are exchanged across the axon membrane, regenerating the action potential between regions of the axon that are insulated by myelin, unlike electrical conduction in a simple circuit. That's where cable theory falls short.
The saltatory process also allows for maintaining voltages along a vast distance of biomolecular membranes. In addition to increasing the speed of the nerve impulse, the myelin sheath helps in reducing energy expenditure over the axon membrane as a whole, because the amount of sodium and potassium ions that need to be pumped to bring the concentrations back to the resting state following each action potential is decreased. Also, keep in mind that the axon potential propagation is unidirectional because the absolute refractory period (of the channels) prevents the initiation of an action potential in a region of the membrane that has just produced an action potential.
This literature might touch on the physics in more detail: The Membrane Potential and its Representation by a Constant Electric Field in Computer Simulations

thank you for your answer. I'm specifically interested in passive conditions, under the firing threshold, to forget the voltage-dependent channels. And as you correctly mention it, I'd add that I'd like to consider unmyelinated axons. Thank you for the ref too, seems interesting!

Under the firing threshold, the ion exchange over the membrane is in a steady-state model. In such physiological conditions, a couple of important physical principles need to be considered: The electrochemical potential is NOT in equilibrium. Meaning that Nernst-potentials and cable equations fall short! Meaning a steady-state model is more accurate. In this case, the Goldman-potential or Goldman equation is used to describe the state of no net flow of ions.

But even with this model a couple of assumptions are made:

Steady-stateI: on-concentration are in
steady-state dc/dt=0. The membrane
potential Vm is constant (dV/dt=0) and there
is no net current across the membrane (I=0).
The membrane has a thickness d and is physically homogeneous
The different ion fluxes are uncoupled.
We have a distribution equilibrium for an ion i between the solution and membrane interface.
Simplification: Only monovalent ions.
Flux in the membrane is conservative, nothing gets lost.

I feel like you might want more sophisticated mathematical models so check out Goldman–Hodgkin–Katz flux equation, Hindmarsh–Rose model, Hodgkin–Huxley model, Morris–Lecar model


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Is there an estimate of the number of enterocytes in the human body?
I've been looking for this information but I haven't been able to find it. Does anyone know if there are estimates of the number of enterocytes or epithelial cells in the intestinal tract? Otherwise, would a simple division of the volumes of the intestinal tract and of a cell work as a rough estimation?

Difficult to estimate given the considerable variation in human gut length. Related post: Does variation in human gut length vary predictably with diet of ancestors?

It might be easier to estimate the density of some small area and try scaling up based on length and other volume measures. However using such a model to do so would require density estimates from each variable segment. For example, as circular folds decrease in robustness from duodenum to ileum and eventually disappear in the colon, I would expect cell density to decline dramatically

Why are you asking? General interest (and therefore requiring low precision) or for perhaps some sort of metabolic calculation(and therefore requiring greater accuracy)?

Also, I'm not sure to what degree localized cell densities (e.g., of the duodenum lets say) vary between people. I think a more answerable question underlying yours that must be addressed in any answer you ultimately receive is whether and to what degree cell density of given anatomical regions varies between people

@theforestecologist I just want an approximate range for modeling purposes. But as the other comments have pointed out, this seems to vary significantly from person to person.

It might help if you explained why you wish to know something that on the face of it has the intellectual content of the Guinness Book of Records.


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What are these white, fuzzy dome-shaped contaminants growing on my LB agar plate?
We are attempting to extract bacteriophages from environmental samples. We recently had an issue with an unknown contaminant when trying to grow a lawn of M abscessus for a bacteriophage isolation spot test.
Briefly, we mixed molten top agar with a saturated M.abscessus culture and poured it over a prefilled LB plate. Then we split the plate into nine squares and placed a single drop of environmental sample filtrate in the square—the environmental samples were filtrated by a .22um PES filter.
The result looked like this:

As you can see, a lawn of what appears to be M.abscessus is forming (the yellow-white smaller colonies). But there are also eight circular white colonies of unknown origin.
Here is what we know:

The unknown contaminants are dome-shaped and look fuzzy in structure. They are roughly 5mm across.
They seem randomly distributed across multiple squares, which likely means the contaminant did not come from the environmental sample filtrate drops.
The contaminant could have been in the M.abscessus culture. But we did add Carbenicillin (100ug/ml final concentration) and Cycloheximide (1ug/ml final concentration) to the culture to inhibit bacteria and fungi.
The contaminant could have come from the top agar, which was stored in a 55°C water bath.
We created four of these plates at the same time, and they all had the same contaminant.

What species could these dome-shaped white colonies belong to?

Did you pour control plates without M. abscessus and without filtrate? That would tell you exactly where the contamination is coming from. As for identification, it's going to be pretty difficult without microscopic images of the colonies and without biochemical tests or sequencing.

From a practical laboratory standpoint, it seems like performing the sorts of controls that MattDMo suggests is going to be far more useful to you than identifying the specific contaminant. Assuming all you want to do is grow your organism free of others, it doesn't matter what is contaminating but rather what step in your process introduced contamination.

@MattDMo  that makes sense. We will definitely use more negative controls on the future. We discovered that our final Cycloheximide concentration was accidentally too low, so our best guess is that this is because of that.

Did you use a spreader and sterilise it? If you cold sterilise in pure ethanol you can pickup bugs from the alcohol.; which won’t occur with 70% ethanol. The contaminant I saw for this was Staphylococcus.

If you want to identify this bacterium or any other contaminant, you need a PCR of the 16S rRNA gene, sequence it using Sanger and then blast the results against a database. This is the easiest, cheapest, and most reliable way to know exactly what you are dealing with.


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How do we logically infer large time scales using Molecular Clocks?
If molecular clocks are uses in genetics to determine the mutation rate of genes to estimate times speciation occurred between two or more life forms, are there genes that have mutation rates that we can observe that allows us to deduce mutation rates over hundreds of thousands to millions of years?
For example, Homo Sapien speciation occurred 300,000 years ago from Homo Erectus that existed 2 million years ago. How did we get those time scales? Are there mutation rates in simple bacteria or viruses that are constant that we can use to logically build up to those longer time scales?

There are a few different questions going on here.

Mutational clocks are not the only, or even the primary, means of dating specimens of these species. More common is to use carbon dating, for example as done here, to establish when certain species existed.
Mutational molecular clocks are calibrated based on observed mutation rates. It is fairly routine to measure mutation rates per generation using whole-genome DNA sequencing. We have a good vision of what substitution rates are on average throughout the genome.

For an intuition of why this works, consider that there are roughly $3*10^9$ bp in a haploid human genome. The human mutation rate is about $1*10^{-8}$ per generation. So every generation, we expect around ~30 new mutations on average per haploid genome. It's simply a matter of observing the whole genome to find them.
Mitochondrial genome mutation rates are quite a bit faster, and were some of the first genomic regions used to do this kind of dating, before whole genome sequencing became so routine.
Using that kind of information, we can make some statistical guesses about the relationships between Homo species (I'll let you look at some of those references to see how that is done).


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What are the common dental traits of fungivorous mammals?
What are the dental adaptations for eating mushrooms that are commonly found amongst fungivorous mammals?


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Do animals have the notion of fair share and fractions?
There are already several experiments showing that animals (not only humans) can do some math: counting and problem solving.
My question is: what about the notion of fair share and fractions? I am looking for any reference or study!

Welcome to the site. Please take a [tour] and visit the [help] for more information on the Biology Stack. Please note the homework policy. So - what have you found in your searches, and what do you mean by "animals" - note that we are animals, as are insects, fish, birds, primates, other mammals...

please take a look here https://www.youtube.com/watch?v=meiU6TxysCg


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Is there any bloodstream chemical composition software simulator?
Let's say I'd like to know how certain substance affects bloodstream levels of certain drug during a period of time. Is there any simulation software available publicly to run such kind of simulation?

Pretty much any spreadsheet can be used for this, you just need the requisite data (and to know how to program equations). Can you be more specific about the drugs and the context in which you're needing the data?

@Jiminy Cricket it's necessary to know what to drink/eat in order to increase suction rate  (into bloodstream) of a certain drug. Where to get data for a spreadsheet?

@Jiminy Cricket or some substance instead of a drug.

This is all very vague at present, also the question you ask doesn't seem to be the question you need an answer to. Please take our [tour] and read up in the [help], paying particular attention to the [ask] section - then [edit] your question to ask what you intend and include the details which are missing such as your prior researches and the substances in question.

Usually you give someone (or a rodent) the drug, and take measurements of their blood regularly after that. How you actually detect the drug in the blood depends on the drug.

In addition, the drug taken isn't the active one sometimes, it's the breakdown products that are the active ones. You'd need to be specific about the substances in question.

@Jiminy Cricket two things: benzimidazole type of substances and caffeine.

Could you please do as suggested - take our [tour] and read the [ask] section of the [help] then [edit] your question into shape. Comments don't last and the question itself should contain all the requisite information necessary to answer.

Welcome to the site Ya Y! I would love to see this question be edited to add some of your clarifying details that you've brought up in the comments.


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Conjugate vaccines in the context of the original antigenic sin and antibody feedback inhibition
How come we can get an antibody response against a polysaccharide bound to a carrier protein, that we have antibodies towards, when antibody feedback inhibition exists?
If we have antibodies against the carrier protein then surely this will lead to inhibition of the B-cells that express B-cell receptors for the polysaccharide?
What's going on here?

Check out this review. Antibody feedback regulation can go both ways. Downregulation is associated with antigen masking, but that won't happen if the (new) polysaccharide antigen isn't masked by the existing Abs. So, the answer is, it depends.


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MTT assay data pre-processing
I was handed MTT assay data, consisting of drug doses and raw OD scores. The drug treatments were performed three separate times, each followed by MTT assay.
I applied some non-linear mixed-level dose-response modeling (log-logistic model) to the data and generated dose-response curves, ED50, etc.
I got the feedback that I first needed to subtract mean blank values of each plate from each OD on a plate, then divide the blank-subtracted values by the mean blank-subtracted value for dose = 0, again on each plate. THEN the PI wanted me to "propagate error" for the modeling.
What is the function of the division-by-zero-dose mean OD? Will that suppress plate-to-plate variation, which  means any aggregate model will be less trustworthy? I was told that all that pre-processing was the standard procedure "in the field". Is this the case? If so, why is it "standard procedure"?
If one assigns random effects to each plate, one can account for plate-to-plate variation without suppressing it, after all.

I’m not sure the poster is expecting an answer to this question, so why it has been edited escapes me. He would have been well advised to define MTT, as “mean transit time” seems hardly appropriate, but it’s too late now, I imagine.


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Are there women that can always "select" a spermatozoon with X or Y chromosome?
In women when there are spermatozoons near to perform a fecundation, their egg cells emit some substances to attract the spermatozoons they "consider" would be a best match.
Here a link for that study: https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0805
I'd like to know if in that selection there would be cases where the female would only select spermatozoons with the X or the Y chromosome; this would explain cases along the history where a woman couldn't give birth to a child of a certain sex.
Is this selection possible in some women?

I would say almost impossible to answer because 1) you'd need to extract eggs and work on it, 2) statistics says that the observed even will happen just by chance. For historical cases; how do you know that their next pregnancy wouldn't have been the opposite sex?

@bob1, if they have done the study that the eggs get to "select" the spermatozoons, I see no reason they could go on the study further to check what it exactly can "select". About historical cases sure, there are not evidence for anything, but they support my hypothesis.

I'm not sure that there has been any study that shows that the ovum selects sperm based on anything other than being the first to reach it. There are selections based on motility and survival in the different environments of the genital tract in women (pH, mucus, distance...) but nothing to do with the egg. see here for a review (2015).

I looked at the study briefly and I honestly don't see evidence of a "selection" effect in the way that you're talking about. They find that there are non-random attractant effects between particular male/female donors. But I don't find a convincing mechanism, or even any evidence that particular kinds or classes of sperm can be chosen. There is simply no evidence that the eggs "consider" or "choose" sperm, as opposed to more or less random attraction phenomena. Granted, the researches themselves misleadingly frame it as "mate choice", but that appears to just be hype.


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What Type of Color Vision do Mantises have?
I am trying to figure out what type of color vision mantises have, but stuff about mantis shrimp keeps coming up instead. All I was able to find was this one paper from 1971. It found evidence that the ocellus have 2 photoreceptor and the compound eyes have 1 photoreceptor, but acknowledges that more could still exist:

Although a second or third receptor type (blue or ultraviolet) was not established as present in the mantis compound eye in these studies, this lack of experimental evidence does not preclude the possibility that a second or third receptor type exists.

Have anything more definitive been done regarding mantis color vision?


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Was Spinosaurus bipedal or quadrupedal?
Different sites told me different things. I tried looking it up but I haven’t found anything. So which was it? Was Spinosaurus quadrupedal or bipedal like all other theropods? Either seems possible.

The Wikipedia page is pretty thorough on the subject. Is there a particular point you needed clarifying?

Hi. According to previous research's Spinosaurus was a bipedal like other theropods while recent research conducted by Nizar Ibrahim states that Spinosaur was a quadruped