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Can methylation of a promoter induce gene expression in some rare cases?
Can methylation of a promoter induce gene expression in some rare cases?
I've read somewhere that methylation of an intron can induce gene expression (eg. Igf2). How is that even possible?
Thank you in advance!

Can you decide if you read this about a promoter or an intron? This makes a difference. Additionally: Do you have any idea where you read this?

@Chris: I'm intersted if a methylation of a promoter can induce gene expression in some rare cases, but I've only read about introns- if they are metilated they can induce gene expression. I really don't remember where I've read this, probably on a website but don't know which so I'll try to find it, though.

There is nothing intrinsic to DNA methylation itself that requires it to repress transcription. Simply, it affects sequence recognition by proteins. CpG methylation can prevent transcription factor binding and/or recruit proteins that inhibit transcription, either competitively or through chromatin condensation. This is why it's generally associated with transcriptional repression.
I have found some articles which describe methylation in intergenic regions and introns activating transcription but, since you're asking specifically about promoters, I'll limit the examples to methylation in the 5' flanking region. Please note that I'm grossly oversimplifying these articles, you should actually read them to get the full picture.

Bahar HK, Vana T, Walker MD. 2014. Paradoxical role of DNA methylation in activation of FoxA2 gene expression during endoderm development. J Biol Chem 289(34):23882-23892
This study reports that, during development, high levels of methylation of a CpG island in the FoxA2 promoter is present in expressing tissues and absent in non-expressing tissues. Their hypothesis is that CpG methylation prevents binding of a protein that represses transcription by condensing chromatin through histone modifications.

Hantusch B, Kalt R, Krieger S, Puri C, Kerjaschki D. 2007. Sp1/Sp3 and DNA-methylation contribute to basal transcriptional activation of human podoplanin in MG63 versus Saos-2 osteoblastic cells. BMC Mol Bio 8(20)
Here, PDPN expression was associated with CpG methylation. They hypothesize that methylation could affect chromatin state or recruit, what they term, a methylation dependent factor, which activates transcription.

Niesen MI, Osborne AR, Yang H, Rastogi S, Chellappan S, Cheng JQ, Boss JM, Blanck G. 2005. Activation of a methylated promoter mediated by a sequence-specific DNA-binding protein, RFX. J Biol Chem 280(47):38914-38922
This study describes a DNA binding protein (RFX) that can recognize and activate the methylated promoter of MHC. They suggest that RFX can competitively inhibit binding of methyl-DNA binding domain proteins that condense chromatin.


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What is the most condensed form of (stored) energy used in biology?
When considering how organisms store energy for later use, I was wondering what substance known in Biology is best for compacting the most energy in the smallest space(volume-wise).
With my (limited) knowledge, I would guess that it would be what we would normally call "body fat". However, I know I am probably not aware of most forms of stored energy, and I considered that perhaps substances like egg-whites may potentially contain more energy in the same amount of volume.
So, the question as in the title: What is the most condensed form of (stored) energy used in biology?
Alternatively, if there is no known "best": What would the leading competitors be?

The best ratio between weight and energy content (and of course also stability) has indeed fat. It's energy content is more than twice as high as for carbohydrates (sugars).
See this table from here on the energy contents:

This is the reason why animals which hibernate or migrate fed up to build up fat resources before the winter or their journey. With carbohydrates they would need more than the double amount of stored carbohydrates to get the same energy. Proteins are approximately on the same level as carbohydrates.
If you look on this problem not by energy per mass but volume per mass, fat still wins. For this we need the density of protein (muscles in this case) and fat. Paper 1 (see reference below) say that the human muscles have an average density of 1.06g/cm³. Paper 2 lists a density of 0.92g/cm³ for fat. So fats (this is practically only valid for the human body, but should be in the same range for other animals) are about 15% less dense than muscles. As the energy density per weight is about double as high for fat, this compensates for the lower density.
Carbohydrates are better, but are still not as good as fat. It's a bit hard to find specific densities for carbohydrates in the human body, so let's use Glycogen (which is a widely found carbohydrate used for mid-term storage of energy) for this purpose. Paper 3 lists a density for Glycogen between 1.40–1.62 g/cm³, so fat has only 55-65% of it's density. Since the energy density of fat is about 2.25x that of carbohydrates, fat is still better.
If you look at ATP in comparison, it has relatively little energy to provide. ATP delivers about 32.3 kJ/mole (with 507.18 g/mole this make around 64 J/gram) per phosphate released from the molecule, which is 128 J/gram if both phosphates are released. This is approximately 300x less energy per gram than fat. This makes sense, since fats are completely oxidized (down to water and carbon dioxide), while in ATP only the phosphate bonds are broken. ATP acts as an energy carrier in the body and not as an energy storage molecule.
References:

Specific Force Deficit in Skeletal Muscles of Old Rats Is Partially
Explained by the Existence of Denervated Muscle Fibers
Association of adiponectin and resistin with adipose tissue
compartments, insulin resistance and dyslipidaemia
Shifts in the Distribution of Mass Densities Is a Signature of
Caloric Restriction in Caenorhabditis elegans

Do you have any information on more exotic chemical stores, such as the bombardier beetle's hydroquinone and hydrogen peroxide?  The peroxide alone is a mere 2.9 KJ/kg, but I could not find a figure for the reaction of the two.

What about "pure" energy (in terms of biology) like ATP? I guess this is probably not what the question means though.

@Sparhawk I added a paragraph on ATP.

Huh, interesting! Thanks for doing the maths.

@Sparhawk: It's interesting. I didn't expect the difference to be so big.

Yes, absolutely! I always imagined that that ATP was utilised not only for ease in energy exchange, but also some measure of efficiency. I guess not!

The question says "volume-wise", not "mass-wise", so a comparison of the density of fat to the others seems in order. Just to establish whether it wins both ways despite being less dense than protein. (Or at any rate, fatty tissue is less dense than muscle tissue).

@SteveJessop Interesting point. But even if you put this into account, fat still wins. I updated the answer.

Shouldn't "volume per mass" be "energy per volume"?

What about PHB? IIRC, PHB has similar energy per mass as fat, but a higher density, so the same amount of energy would take up less space. Can't find references at the moment though.

What do you mean with PHB?

Polyhydroxybutyrate

http://en.wikipedia.org/wiki/Energy_content_of_biofuel has a table of biofuels by density, it seems that oils and biodiesel beat fat slightly in both density and weight.

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HELP hepes preparation
I need help: I would like to prepare an HEPES solution, without using the powder. It is possible? I remember that I did it once, but maybe I'm wrong...does someone know a protocol for HEPES preparation without using a powder? thanks!!
I need It for morpholino dilutions. 5mM, ph 7.6.

Why don't you want to use the powder? If not, you can only buy stock solutions from the usual providers of lab chemicals.

I'm voting to close this question as off-topic because this is not about biology but about preparing buffer solutions.

HEPES is a particular chemical, not a mixture of chemicals so unless you have the ability to synthesise your own chemicals you cannot produce it without having the dry chemical preparation.

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How can they know that they found "all the PERVs"? (porcine endogenous retroviruses)
The New York Times article Gene Editing Spurs Hope for Transplanting Pig Organs Into Human links to the recent Science publication Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9
 Niu et al. Science  10 Aug 2017: eaan4187, DOI: 10.1126/science.aan4187.
The highlighted section of the abstract says "...we inactivated all the PERVs in a porcine primary cell line..." where a PERV is a porcine endogenous retrovirus, an RNA virus which carries its own reverse transcriptase molecule and converts to DNA before incorporating into the host's genome.
Question: Do they mean to say all currently known PERVs or is there some way to be absolutely sure that every PERV in the pig's genome is known. In other words, could they have missed one? Could there be an as-yet unidentified PERV? I don't really want to ask about the possibility of an entirely new and unknown class of retroviruses; rather I'm trying to understand how all PERVs as currently defined can be identified in a pig cell line.
The reason that this is important is that the motivation here is to generate pig organs for transplantation into humans. The concern is that the pig genome may contain retroviruses that could then infect the human host, and the further possibility that it could be passed infectiously to others. As pig to human infectious disease is always a concern, starting with a "clean" pig genome is of particular epidemiological importance.
The first sentence of the NYTimes article:

In a striking advance that helps open the door to organ transplants from animals, researchers have created gene-edited piglets cleansed of viruses that might cause disease in humans. (emphasis added)

Abstract of Niu et al. 2017:

Xenotransplantation is a promising strategy to alleviate the shortage of organs for human transplantation. In addition to the concern on pig-to-human immunological compatibility, the risk of cross-species transmission of porcine endogenous retroviruses (PERVs) has impeded the clinical application of this approach. Earlier, we demonstrated the feasibility of inactivating PERV activity in an immortalized pig cell line. Here, we confirmed that PERVs infect human cells, and observed the horizontal transfer of PERVs among human cells. Using CRISPR-Cas9, we inactivated all the PERVs in a porcine primary cell line and generated PERV-inactivated pigs via somatic cell nuclear transfer. Our study highlighted the value of PERV inactivation to prevent cross-species viral transmission and demonstrated the successful production of PERV-inactivated animals to address the safety concern in clinical xenotransplantation. (emphasis added)

You are right, they should have written "all currently known PERVs".
Although the structure of ERVs is generally well understood (https://www.ncbi.nlm.nih.gov/pubmed/26104559; https://www.ncbi.nlm.nih.gov/pubmed/26818261) there may be some complex cases that have been missed. Also, the map of the porcine genome is not fully complete yet (nor the human one) so you cannot be sure that there are no ERV-derived sequences hidden in the unsequenced regions.

More intriguing than I realized Sequences derived from ERVs make up at least 8 to 10% of the human and mouse genomes and range from ancient sequences that predate mammalian divergence to elements that are currently still active Mager & Stoye, and "Despite state-of-the-art genomic tools available for retroviral discovery and the large number of retroviral sequences described to date, there are still gaps in understanding retroviral macroevolutionary patterns and host-retrovirus interactions and a lack of a coherent systematic classification particularly for HERVs" Escalera-Zamudio & Greenwood


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Why I cannot find dendritic cells in blood smear?
According to many sources including Wikipedia, there are haematopoietic stem cell derived dendritic cells in the blood.

figure 1 - haematopoietic cell lines - ref

Despite of this, when I examine a blood smear, I cannot find dendritic cells and I did not find any blood smear example on the internet, which depicts dendritic cells.

figure 2 - blood smear cell lines - ref

Why is that?

I've identified both plasmacytoid and myeloid DCs (albeit at very low numbers) in PBMCs derived from whole blood of (presumably healthy) volunteers by flow, so they are there. I don't recall off the top of my head the exact numbers, but it was far less than 1% of PBMCs (dozens to hundreds of counts in a 1-2 million cell sample, IIRC), meaning an incredibly small proportion of overall cells in the blood. Therefore, the chances of seeing and correctly identifying them in a smear are rather low.

@MattDMo Does it look like this? https://www.google.hu/search?docid=pK94a0h-wQhUsM&bih=730&biw=1536&tbm=isch&tbs=simg:CAQSJgmQDCJQTlxphRoSCxCwjKcIGgAMCxCOrv4IGgAMIaSveGtIfsEI&sa=X&ved=0ahUKEwj-4LO8zqfMAhUIJpoKHZz0BUYQ2A4IGSgB#tbs=simg%3Am00&tbnid=kAwiUE5caYWUhM%3A&docid=pK94a0h-wQhUsM&tbm=isch&imgrc=kAwiUE5caYWUhM%3A It is extremely hard to find an image about them. In theory this is an activated mature DC moving from the skin to the lymph nodes. It appears to present antigens in the blood too. Actually I don't have deep knowledge about them right now, I just want to show an image to somebody.

@MattDMo According to this http://www.sciencedirect.com/science/article/pii/S0022175916300217?np=y normally about 0.5% of the WBC-s are some kind of DCs. Interesting. :D I probably confuse them with monocytes, and the image I linked is probably fake. Not sure yet.

This was by regular flow cytometry, so I wasn't taking images of them. All the images I've seen of DC in vivo are along the lines of these - the staining is somewhat diffuse because of all the ruffles and extensions. If you do a search for "mature dendritic cell SEM" you'll find a bunch of scanning electron microscopy images of the cells in 3D.

The dendritic cells are antigen presenting cells that process and present pathogens to the T Cells.
As such they are present in interfaces where foreign organisms are frequently present. Eg: Skin.
When these cells get activated i.e. come in contact with pathogens, they process them and move to lymph nodes to present the processed antigen.
Thus these immune cells do not circulate in blood once they reach the target tissue but reside in the tissues and found in lymph nodes on activation.
Further, from Kuby's Immunology:

Dendritic cells can be difficult to isolate because the conventional procedures for cell isolation tend to damage their long extensions. The development of isolation techniques that employ enzymes and gentler dispersion has facilitated isolation of these cells for study in vitro. - Kuby Immunology 5Ed. P.42
Since blood is the most accessible tissue for clinical studies, we set out to extend the findings that were reported in mouse blood to humans. However, when we tried to induce DC growth by adding GM-CSF to human blood, we identified actively proliferating DC aggregates only infrequently -
Proliferating Dendritic Cell Progenitors in Human Blood
By Nikolaus Romani, Stefan Gruner, et.al.

I need some references about the "do not circulate in blood" part. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809702/figure/fig02/

"conventional procedures for cell isolation tend to damage their long extensions" - I think this is about flow cytometry. I don't think that blood smear creation would damage their long extensions. E.g. sickle cells and reactive lymphocytes are not damaged by this procedure. According to my previous link DC-s in blood do not have such long extensions, they are not mature enough... I believe they can easily confused with other cells, and some of them are derived from monocytes.

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Modern research or study on patterns in nerve signals
I am trying to find any recent study on pattern recognition in nerve signals. It does not really matter the part of the body where the research is focused on. It can be anything from studying activity of one group of nerves to signals coming from an entire limb.
I was only able to find old (1996) research, which could be much more complete with the modern advancements in computing and manufacturing of micro-instruments. Here is an example of an old paper.
P.S. I am generally looking for information on how nerve signals differ within multiple subjects of same specie. For example, how would nerve response to a stimuli differ for two mice from same offspring and how will they differ from it's parents.

what kind of a pattern do you want to find; what do you mean by signal ?

@WYSIWYG some kind of logical sequence of neural activity caused by the stimulus. For example I would want to know if applying hot/cold object to skin of both right and left limbs would cause the sensory neuron to send the same or similar signal (electrical impulse) to the spinal cord. Would it be possible to identify what happened with the limb, having access to part or all of the electrical activity in central and peripheral neural systems, even theoretically. Is it possible to learn what each impulse is about and if it is, should you learn anew for every new body or signals are universal?

I meant what will you capture: Voltage changes ?

@WYSIWYG Yes, it would be synaptic potential.

You might want to read about event related potentials (recorded by EEG) or event related fields (recorder by MEG). The idea is simple:
1) Pick some stimulus, e.g. a person touching the hand of a subject. Pick another stimulus, e.g. the subject seeing a person touching the hand of another subject. Record EEG/MEG.
2) Repeat each condition for at least few hundred times. Throw away bad data, and average the repetitions. You do the averaging because the signal-to-noise ratio is low in all non-invasive electrical measurements, and the signals are always riddled with movement, cardiac, and eye-blink artefacts.
3) Compare the conditions in each sensor. Rest is statistics, though not very easy.
Actually, the experiment above would be about mirror neurons, a relatively hot topic in neuroscience. (See e.g. recent issue from Nature)
The more general situation is that using pattern recognition/machine learning algorithms to study brain signals is already a standard thing to do. There are for example graduate/undergraduate programs in computational neuroscience.
If you would study some other signal (e.g. measure from a hand, leg), they are going to dull. Very dull. Mostly because then you have 1 time-series, instead of several hundreds of time-series to analyse.

For example I would want to know if applying hot/cold object to skin of both right and left limbs would cause the sensory neuron to send the same or similar signal (electrical impulse) to the spinal cord.

This you could too study with the event related fields/potentials.

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

What is unique about them, is that each print, has 3 points, and there is only one straight line of prints, about 2-3 feet apart, where as I would imagine a deer, or other 4 legged animal would leave staggered footprints. We have a lot of deer in these parts but these dont seem to match deer print patterns I've seen online.
Each print is about 5 inches by 4 inches at their widest/longest points (they are longer then they are wider).
Note, the snow has melted somewhat since they were initially made.

The only candidate I could imagine is hare.
Sometimes it leaves a single track from its fore-limbs (from a theoretical point of view, I'd say it happens when the snow is relatively deep.)

I'd say hare too - seen them leaving tracks here!

Excellent, thanks. Upon closer inspection and watching some videos on youtube on how hares move, it seems that the "dot" may be its front paws close together and the 2 longer lines are its hind legs. Seeing them walk its common for them to cross their hind legs in front of their front paws creating this pattern.

O, I wrote "hind-limbs" - now corrected.

@n00b I had the same confusion when I first encountered these tracks, it wasn't until I found some very fresh ones where I could even see the pads of the paws that I worked out what it was.


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DNA & mRNA During Transcription
Just a simple, quick question: how are the mRNA and the template strand of the DNA structured during transcription? I've seen models and videos of them when they're both flat/straight (is that just for simplicity?) and others where they're spiralling around each other. Could someone just briefly shed some light on my situation please?

Transcription occurs in a special structure known as transcription bubble. Inside the bubble are present the mRNA, template DNA being transcribed and the RNA Polymerase. Upstream of bubble is the DNA already transcribed and downstream is the DNA to be transcribed. There is not enough space in cell to have completely unfolded DNA for transcription, so transcribed DNA has to be re-annealed as soon as it is transcribed, giving a bubble-like appearance to the RNA polymerase-bound DNA. Hence it is called a transcription bubble. See this image for illustration:

Source
The mRNA formed quickly leaves the bubble and hangs behind like a thread coming from RNA polymerase.

Source

Cheers, is that RNA polymerase enzyme below? Why are there so many sections to it? All it does is separate the DNA strands and form an RNA strand, why would it need so many sections...

I did not explain it because it was not related to your question. RNA polymerase has many subunits which all come together to become the fully functional enzyme. It actually does much more than separating DNA strands from RNA strand. :)


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Please identify this plant
I don't know anything about plants

Welcome!!! to Biology Stack Exchange. You should add [tag:species-identification] tag to your question. And also please provide information about your location and size of the leaf.

Try to use a more descriptive title. Give details about what you observed.

Any fruits ever develop? Looks like Solanaceae to me.

Not my area of expertise... but looking at the pictures, it looks like it has a distinctly square stem. This is a characteristic of the mint family
Lamiaceae; the leaves look reasonable... but that's obviously an incomplete answer and not definitive.
Note that there are some iPhone & Android apps that help; look up 'LeafSnap' for example (I think that one's iPhone only and perhaps limited to trees)

I'm no plant expert, but it looks a lot like a cucumber plant.  We used to have them in our vegetable garden.

Welcome to Biology.SE! You are more likely to get a positive response to your answer if you explain why your identification is correct. Specifically, please [edit] your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. ——— You may also wish to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!


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Impact of Natural Selection on Population Size
I have conducted a lab with my IB Biology 11 class, regarding changes in allele frequencies within generations overseeing the natural selection of an advantageous phenotype. We were looking to conclude some sort of link between the changing allele frequencies and an overall changing population number of the species. Lab results saw, that as the frequency of the advantageous phenotype increased, the total population dipped and then increased after the 3rd generation. Can anyone point out any possible reasons as to why this occurred - regarding any factors at all? The image below depicts frequency of the advantageous allele vs total population.

Can you give more detail because I don't understand?  Was this an experiment or a simulation?  What was the advantageous phenotype and did you know in advance that it would be advantageous ?
In your graph, what is on the x axis and what is on the y axis?

@remi.b Can you provide some illumination?  I don't understand it.

@JohnnyToff The question is unclear to me. Your picture does not contain any axis labels, you talk about both population size and allele frequency but I don't understand what connection you're making in between them and I do not understand exactly the pattern you've observed. If you're dealing with population, it is also unclear the population dynamic before the introduction of a mutation and it is unclear whether the mutation was beneficial or deleterious. I am voting to close as unclear.

Can you add a better image with proper axis labels? Also use imgur to upload your images or use HTML (as I have edited your original post).

You should always label axes on a graph. I know it's explained in the text, but it's best practice to label your graphs to facilitate understanding of the data you're presenting.

Related: https://xkcd.com/833/

Take the following thought experiment.
A population off 100 fish, 90 red and 10 blue. On average, a red fish has 0.5 children and a blue fish has 2. This is how the population develops after each generation:

90 red, 10 blue, 100 total, 10% blue
45 red, 20 blue, 65 total, 31% blue
23 red, 40 blue, 63 total, 63% blue
12 red, 80 blue, 92 total, 87% blue
6 red, 160 blue, 166 total, 96% blue

Notice that even though the percentage of blue fish strictly increases, the total population decreases and then increases. This is because the initial population had red fish who died off before the growth of the blue fish become noticeable. I suspect that something similar happened in your experiment, although I cannot say for sure since your description of it was vague.
I also want to make it explicitly clear that having my starting population be more red than blue fish made this effect much larger, but was not necessary. Even if I started with 50 red fish and 50 blue fish, this decrease in population followed by an increase could have still happened. It would have required less clean numbers for the fish reproduction rates, which I did not want to deal with.


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What type of ants are these?
I live in NYC and these fellas started popping out near my computer screen and desk. They don't seem interested in food as my sister usually leaves candy wrappers around. They however are stinky, I tried to catch one with a tape and I can smell the odors they give off like 4 inches away. They got these stingers on their butt so I think they could be a species of fire ant. They're also really tiny. As shown on a q tip here.

(click to enlarge)
Finally could these be bites? They are really itchy and I get them overnight.

They look like termite, rather than ants.

@JackRod all wrong for a termite.

A close up on one of the ones that is curled up and dead would be a big help. a side shot would be best.

Many, ant species have stinger.

These ants are definitely in the subfamily Myrmicine Ants (Myrmicinae):

Myrmicinae is a subfamily of ants, with about 140 extant genera; their distribution is cosmopolitan. The pupae lack cocoons. Some species retain a functional sting. The petioles of Myrmicinae consist of two nodes. The nests are permanent and in soil, rotting wood, under stones, or in trees Source: https://wikipedia.org

After further research, it appears these ants are Doubtful Acorn Ants (Temnothorax ambiguus). They are fairly uncommon to come across, as they are very small and hard to take photos off. They don't even have a page on Wikipedia. Most likely, you have rotting wood around (perhaps your desk) and they are nesting in it.

Image ref: https://www.inaturalist.org/photos/209974453, Photo 209974453, (c) Aaron Stoll, all rights reserved, uploaded by Aaron Stoll
Here is their range: (credit to https://inaturalist.org for the range map)

odorous house ant
Without a better picture I can't be certain but based on what anatomy we can see and you mentioning smell I would guess the odorous house ant.
They do stink when crushed, it should smell like blue cheese and turpentine.  They are common house pest in NYC drawn by sweets and water.
They do not sting or bite so they are likely non connected but again without a better picture it is hard to be certain. I suggest asking about medical concerns on the medical stack as they are off topic here.
As a small consolation at least they are a native ant species.

My first thought was that these look like bethylids (bethylidae) which are aculeate wasps. Some species can do a bit of damage with their stings apparently, notably Scleroderma which I was reading about recently. At least in the second picture it looks like they dont have a petiole which makes me think its a flightless wasp. Better pictures would probably clear things up.
https://www.ajtmh.org/view/journals/tpmd/103/4/article-p1352.xml article about Scleroderma stings

They should be Red Imported Fireants.
https://en.wikipedia.org/wiki/Red_imported_fire_ant

thorax shape is all wrong and head is too small for red imported fire ants. red imported fire ants should have pretty prominent petiole


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Why do muscle spindles send impulses at a constant rate when the muscle is at rest?
According to my book, the sensory neuron around the muscle spindle is sending impulses at a constant rate, while the entire muscle itself is relaxated (at rest).
So when the muscle stretches the impulse frequency gets higher, right?
According to the book, the reason why this 'constant rate frequency at rest' is happening is because otherwise the muscle spindle wouldn't been able to know the difference between a relaxed and contracted muscle.
I don't understand this reasoning, could anyone explain?


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Pyruvate oxidation - where did the hydrogen come from?

(source: resource12ubio at sites.google.com)
As shown in the diagram above, NAD+ is reduced and becomes NADH by gaining two electrons
Now, where did the hydrogen come from?
In the diagram, pyruvate has 3 hydrogen, but it still has 3 hydrogen in acetyl CoA.

@Astrolamb has given you a good answer here. In general, be aware that counting atoms will often result in a headache in biochemistry. There are large parts of key molecules that are often not represented.

@DeNovo is absolutely right; when looking at biochemical systems, if something doesn't seem to make sense, try to find a diagram that includes ALL the puzzle pieces.

The Wikepedia page has a really good diagram of the reactions involved. The Pyruvate Dehydrogenase Complex facilitates the removal of CO2, and the addition of two hydrogen atoms to the overall reaction come from the FADH2/FAD molecule.

This is an example of how, in biochemistry, the rules for writing a reaction equation are much more flexible, and generally based on convention. NAD+, for example, has a negative charge at physiologic pH. We write it as NAD+ to emphasize the active moeity in the oxidation/reduction reaction. H+s, in particular, are often poorly accounted for in our short hand.


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Aneuploidy in meiosis
I am quite confused about nondisjuction in anaphase II. If the double chromosome is not segregated, isn't it double. On pictures they are drawn as single but I don't understand why, and if they are double do they duplicate themselves in the S phase?

What is confusing me in picture above is cell (n+1) , why are all chromosomes single? I thought, after end of division in the third cell (labeled as n+1) there should be 3 chromosomes with single chromatid,  and 1 chromosome with 2 chromatid joined at centromeric region, as it is drawn in picture above that show nondisjunction in cell during anaphase ii . When and how do these 2 chromatids get physically separated?

can you add a little explanation about what is confusing? what pictures are you referring to? could you add them?

From Study.com >>
On the off chance that nondisjunction happens amid anaphase II of meiosis II, it implies that no less than one set of sister chromatids did not isolate.
In this situation, two cells will have the typical haploid number of chromosomes. Additionally, one cell will have an additional chromosome (n + 1) and one will miss a chromosome (n - 1) due to the nondisjunction of the chromosomes.
Here is a picture reference taken from Google.ca >>

In the image provided in the question, the chromosomes are not indicated clear and concisely, so it is very hard to follow through the logic of segregation of the daughter cells to (n + 1) and (n - 1) chromosomes.
As you can see from the updated image reference in the answer, we can notice that the cell that underwent nondisjunction in anaphase 2 gives rise to 2 daughter cells, in which, one cell receives the non-segregated chromosome plus one copy of a sister chromatid which makes it (n + 1) and the other daughter cell receives one segregated sister chromatid ONLY which makes it (n - 1).
On an additional note, from Biology Exams 4 U >>

Fusion of n+1 gamete with normal gamete (n) = 2n + 1 or Trisomic.
Fusion of n-1 gamete with normal gamete (n) = 2n - 1 or Monosomic.
In short, Nondisjuntion in meiosis II leads to trisomy (2n+1) or
  Monosomy (2n-1).

What is confusing me in picture above  is cell (n+1) , why are all chromosomes single. I thought there should be 3 single chromosomes and 1 double as it is drawn in picture above that show nondisjunction in cell during anaphase ii . I hope i am clear. :)

Look at the updated answer with a more clear and concise image. Hope it helps.


text:
What happens to snakes that swallow rodents as a whole?
As we all know, a few species of snakes swallow rodents as a whole. My question is what happens to the teeth and bones of these animals? Won't they cut into the flesh of the snake and hurt it? Are the digestive acids strong enough to dissolve bones and teeth? Even so, I'm sure the process takes time, and during this period won't the snake get injured?

Almost everything the snake eats is completely digested. They have a very efficient digestive system. Things that wouldn't be digested would be the rodent's claws and hair and feathers of birds. And during digestion, the snake's intestines go into overdrive mode and expand when necessary. When the snake isn't eating, the intestines are usually dormant.
If something goes wrong though, or if the snake is threatened, the snake regurgitates everything in order to increase its mobility.

It would be a nice complement to this answer to add some references.

Owing to their narrow structure, no chewing mechanism nor limbs, a snake has to swallow its prey as a whole. In fact, their success and diversity is partly due to their ability to swallow  prey relatively larger than their own body size. So inevitably, they need to process the parts like teeth, bones, exoskeleton and things of such nature.

Snake saliva not only eases swallowing by lubrication, but also
  contains powerful enzymes to break down tissues and even egg shells.
  But snakes generally cannot digest keratin (claws, hair) or chitin
  (arthropod exoskeleton). Many prey are covered with tough hide and if
  a snake relied solely on its digestive juices, it would take a long to
  time to get through to the nutrients. So this is speeded up by snake
  venom. Venom not only immobilises prey but also starts digesting the
  prey from the inside. A study showed that when a fer-de-lance
  (Bothrops asper) is deprived of its venom it took 12 days to digest
  a rat instead of the usual 2-3 days.

However, there is no consensus among different theories arguing the utility of a snake's venom. The above mentioned opinion is based on digestion hypothesis of venom utility.
Please refer to this excellent review and a summary of a snake's eating habits

It is not acceptable to copy and paste directly from another site without indicating that you have done so by using inline quotation marks/blockquote and stating your source with a link.

I have no idea about the convention. I shall follow it in future if I were to cite an external website.

Please follow the instructions Rory M gave it right now. You are given the option to edit your post, so please do so for this post as well. Don't ignore this post, and give due credit to every source you are using.


text:
Purpose of poly(A)+ RNA?
I am learning RNA-seq analysis. I always encounter this phase "poly(A)+ RNA". After searching, I got this: "Most messenger RNAs contain a poly(A) tail, while structural RNAs do not. Poly(A) selection therefore enriches for messenger RNA. The technique has proved essential for construction of cDNA libraries."
Does it mean that when constructing the cDNA, we always use the ones with a A's tail? Then other RNAs like tRNA are filtered and not used to get their cDNA? I do find some RNAs records on UCSC where microRNAs are included.
When we say poly(A)+ RNA library, what is the difference between normal one? Or normal RNA library is a poly(A)+ RNA library? Thanks.

Note that this isn’t always done: there are RNA-seq protocols which do intentionally not enrich for mRNA and hence don’t do poly(A) selection. After all, we might be interested in other RNA as well (but this is much rarer since most RNA-seq is done as a quantification of gene expression).

One of the primary reasons to use poly(A) selection is to eliminate the massive amount of ribosomal RNA (rRNA) present in the samples.  The alternative is to use ribosomal RNA depletion kits / techniques to remove as much rRNA as possible before sequencing.  Without rRNA depletion a large proportion (~60-80%) of the reads would map to rRNAs.
poly(A) selection also reduces the amount of pre-mRNA in the samples, which reduces the number of intron aligned reads.

Thanks, GWW. So if we are not saying "poly(A) RNA", the reads we get will be largely from rRNAs? And for poly(A) selection, is it going to remove other RNAs like microRNA?

@CaiShaojiang, yes it will not bind to miRNAs

@bobthejoe miRNA can be (usually is) polyadenylated as well.

@KonradRudolph: Not exactly. The pri-miRNA is polyadenylated, but what is (eventually) called the miRNA isn't, so ...

@Steve Correct. Unfortunately, I oversimplified.


text:
Why can't certain nucleoside analogs be used to label bacterial RNA?
A 2020 publication in Nucleic Acids Research 1 includes the following passage:

A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among them, 4-thiouridine (4SU) and 5-ethynyluridine (EU) are two most widely used noncanonical nucleosides that can be conjugated via thiol coupling chemistry and click chemistry, respectively (9,10). Although the metabolic RNA labeling technique has been instrumental for studying RNA dynamics in eukaryotes, it is not applicable to bacteria.

The authors give no citations or further explanations for the bolded claim.  Indeed, I have found at least one publication that contradicts this statement,2 showing 4SU labeling in E. coli:

We have defined conditions allowing the substitution of 13 +/- 2% of the uridine residues in bulk RNA by 4-thiouridine.

One explanation is that 4SU is a natural RNA modification in bacteria, as Rogers et al. 3 states that most bacterial tRNAs contain 4SU. So, while bacterial RNA can be labeled with exogenous 4SU, naturally occurring 4SU confounds analysis. Concerning EU, Blenkiron et al. 4 used this analog to label nascent RNAs from uropathogenic E. coli in order to track the fate of bacterial RNAs in membrane vesicles:

We then looked at whether we could track uptake of MV RNA cargo into treated host cells by labelling UPEC nascent RNA in the bacteria before it was packaged with MVs. This was achieved by adding an excess of a modified uracil, 5EU (5-ethynyl uridine), which was incorporated into the newly synthesised and MV associated RNA.

Additionally, the text of this research grant award abstract 5 suggests that EU is suitable for labeling both E. coli and B. subtilis:

We have been investigating whether bacteria can incorporate the “clickable” RNA analog 5-ethynyl uridine (EU) for subsequent attachment of fluorescent label (Alexa Fluor) for microscopic detection or a chemical tag (desthiobiotin) for streptavidin-mediated RNA capture. The results for both aspects so far are a qualified “yes”. Both Escherichia coli and Bacillus subtilis grown with EU can subsequently be detected by fluorescence microscopy, but E. coli becomes considerably more brightly labeled.

I can find no research stating EU / 5EU naturally occurs in bacterial RNA.
My question, in short: What aspects of bacterial metabolism or RNA composition justify the claim that 4SU and EU are "not applicable" for bacterial RNA labeling?

Edit, 1 March 2021 -- I'm adding a bounty to garner more attention. From further reading, I suspect the answer to be one of 3 possibilities.

Per David's comment, the bacterial cell wall may be impermeable to certain formulations of nucleoside analogs or the reagents subsequently used in thiol coupling / click chemistry.
Certain nucleoside analogs are toxic in bacteria to an extent not seen in eukaryotic cells, perhaps by a mechanism that causes the elongating RNA polymerase to stall.
4SU and EU labeling are applicable to bacteria, and the claims of the authors are unsubstantiated.

References

Meng L, Guo Y, Tang Q, Huang R, Xie Y, Chen X. Metabolic RNA labeling for probing RNA dynamics in bacteria. Nucleic Acids Res. 2020 Dec 16;48(22):12566-12576.
Favre A, Bezerra R, Hajnsdorf E, Lemaigre Dubreuil Y, Expert-Bezançon A. Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis. Eur J Biochem. 1986 Nov 3;160(3):441-9.
Rogers KC, Crescenzo AT, Söll D. Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon. Biochimie. 1995;77(1-2):66-74.
Blenkiron C, Simonov D, Muthukaruppan A, Tsai P, Dauros P, Green S, Hong J, Print CG, Swift S, Phillips AR. Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA. PLoS One. 2016 Aug 8;11(8):e0160440.
Click-chemistry labeling of RNA: A new tool for microbial ecology?

I don't know the answer, but could it be something to do with poor uptake through the bacterial cell wall, which isn't a problem in eukaryotes where there is only a cell membrane? That might affect either or both of the nucleosides and the other reagents needed in the method. It might also explain the counter examples if people were working at  the edge.

Perhaps, and thanks for the feedback. It makes sense to me that bacterial cells would be impermeable to NTPs because of the negative charge, but the bacterial studies I've linked all treat with either the free nucleobase or nucleoside (base + sugar). I'm leaning toward a conclusion that 4SU and EU are more toxic to bacterial cells than they are to euk. cells, based on the use of nucleoside analogs as antibacterial agents.

Meng et al. actually give their explanation in the first paragraph of their results section. The main reasons for their claim are that they did not detect any labeling with 4SU or EU and that both analogs suppress bacterial growth. Also they raise the issue with the naturally occurring 4SU in tRNAs.

Aiming to develop nucleoside analogs compatible with bacterial RNA labeling, we first set out to evaluate the two nucleoside analogs widely used in eukaryotic cells. E. coli cells were incubated with 4SU or EU at varied concentrations for 2 h, which resulted in no detectable labeling even at high concentrations (Supplementary Figure S1A, B). Moreover, severe suppression of bacterial growth was observed with both 4SU and EU (Supplementary Figure S1C, D), which was in agreement with previous observations that 4SU impaired cellular metabolism in E. coli (31). Cell viability was significantly impaired with 4SU at concentrations higher than 100 μM, while EU did not induce significant decrease in cell viability (Supplementary Figure S1E, F). In addition, tRNAs of bacteria contain endogenous 4SU generated via thiolation of uracil (32), which may interfere with metabolic labeling if exogenous 4SU would be used. Of note, although EU does not incorporate into DNA in mammalian cells (10), significant labeling of DNA was observed in EU-treated E. coli, presumably due to metabolic conversion of EU to EdUTP (Supplementary Figure S1G). Together, these results demonstrate that 4SU and EU are not applicable for bacteria.

This explanation is not necessarily incompatible with the results in the other references mostly because the strains and the test approaches are different.
In Favre et al. they use a different strain of E. coli,"an Escherichia coli
pyrD strain" that is optimized for 4SU incorporation :
In Material and Methods :

pyrD used to control the level of 4-thiouridine incorporation

and in Results :

a) growth of E. coli AB1157 sfiA pyrD in the presence of 4-thiouridine
Preliminary studies showed that the level of s4U incorporation into the rRNA of strains MRE 600 or K12 AB1157 grown in a standard glucose medium in the presence of 4-thiouridine remained at the detection limit. We therefore use AB1157 pyrD mutant deficient in the pyrimidine biosynthesis pathway. To our growth medium we systematically add 40 μg/ml uridine because it is  the minimal concentration required to supplement growth fully. The growth of the pyrD mutant was first examined at different temperatures and different exogeneous s4U concentrations from 40 μg/ml upwards in the conditions defined in Material and Methods, In Fig. 1 we report  the growth curves obtained for two s4U/U ratios,1 and 2.5, and four temperatures: 25°C, 28°C, 30°C, 35°C. When the ratio is 1 there is practically no growth inhibition. With  a ratio of 2.5 the  growth  inhibition becomes strongly dependent on temperature. The culture does not grow at all at 20°C, the  growth is linear between 25°C and 30°C and for temperatures above 30°C it escapes inhibition, becoming exponential. As will be described below significant s4U incorporation occurs in  conditions where growth is linear.

In Favre et al. as seen at the end of the paragraph above as well as in another publication (Bezerra and Favre, 1990) from the same lab shows that incorporation of 4SU depends on several factors.
Concerning the work of Blenkiron et al., it is harder to explain but they also use a different strain so that may impact the incorporation and they do not use the same approaches compared to Meng et al. to detect it. Confocal microscopy for Blenkiron et al. vs Dot blot and In-gel fluorescence for Meng et al..
Finally as far as the grant abstract is concerned, it's hard to conclude because the information is scarce but as Meng et al. they also observed an effect (although milder) of 5EU on bacterial growth and again, they used a different approach to observe the labeling based on fluorescence microscopy as Blenkiron et al..

References :

Meng L, Guo Y, Tang Q, Huang R, Xie Y, Chen X. Metabolic RNA labeling for probing RNA dynamics in bacteria. Nucleic Acids Res. 2020 Dec 16;48(22):12566-12576.
Favre A, Bezerra R, Hajnsdorf E, Lemaigre Dubreuil Y, Expert-Bezançon A. Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis. Eur J Biochem. 1986 Nov 3;160(3):441-9.
Blenkiron C, Simonov D, Muthukaruppan A, Tsai P, Dauros P, Green S, Hong J, Print CG, Swift S, Phillips AR. Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA. PLoS One. 2016 Aug 8;11(8):e0160440.
Bezerra R, Favre A. In vivo incorporation of the intrinsic photolabel 4-thiouridine into Escherichia coli RNAs. Biochemical and biophysical research communications. 1990 Jan 15;166(1):29-37.

Welcome to Biology.SE! This looks like a good answer, but please do not post text as images. Instead copy and paste the text into your post. Images are not searchable, and can not be interpreted by screen readers for those with visual impairments. Use the [edit] link to modify your question. See this for more information. Thanks!

In addition, please include the complete reference information since links can break. One easy way to get that information is to search for the paper on Google Scholar and click on the ‟ symbol to get reference information. This is a good example of how to format references. Note also that quotes must always be referenced. Thanks again!

Thanks for the feedbacks @tyersome. I've edited the answer accordingly.

Great that is much better! (+1) I'm gathering that the first quote is from the Meng et. al. (2020) paper — I'm going to edit your answer to make that clearer. Thanks!


text:
Why are men more susceptible to severe COVID-19?
It seems that globally, men are more susceptible to severe COVID-19 than women:
https://www.theguardian.com/world/2020/mar/26/men-are-much-more-likely-to-die-from-coronavirus-but-why
This is seen in other coronavirus diseases (SARS, MERS) but not respiratory diseases generally. Do we know the reasons for this?

Why the downvotes? :(

Update -- In the time since this question was asked, two relevant articles have been published, one in Nature Reviews Immunology and one in medRxiv (note: medRxiv is a preprint server and is therefore not peer reiewed).
Scully, E.P., Haverfield, J., Ursin, R.L. et al. Considering how biological sex impacts immune responses and COVID-19 outcomes. Nat Rev Immunol (2020).
Takahashi, T., Wong, P., Ellingson, M., et al. Sex differences in immune responses to SARS-CoV-2 that underlie disease outcomes. medRxiv (2020).
Besides the genetic factors related to viral entry that I've explained below, these papers explain the immunological factors that may determine the higher susceptibility of males to severe SARS-CoV-2 infection, including sex-specific differences in early antiviral response, innate immune repsonse, and adaptive immune response.  Figure 2 of Scully et al. provides a graphic summary.

Genetic factors
SARS-CoV-2 entry into human cells is thought to depend on two human proteins:

ACE2 -- a transmembrane protein important for blood pressure control.1  The viral spike protein binds the enzymatic domain of ACE2, facilitating translocation of the virus into the cell.2
TMPRSS2 -- a serine protease with a transmembrane domain.  The proteolytic activity of this enzyme is thought to play a role in "priming" the viral spike protein.3

So, a place to start would be to ask if there are sex-specific differences in the expression or localization of these proteins.
ACE2
No significant differences in lung ACE2 activity have been found between male and female mice.4  In rats, however, lung ACE2 levels are reduced with aging in both males and females, with significantly higher ACE2 expression in old female rats compared to old males.5 Assuming that rats are a good model for sex-specific human lung protein expression, this observation counters the simple explanation that men are more likely to have severe COVID-19 due to higher ACE2 expression.
A recent preprint 6 presents an interesting hypothesis -- that ACE2 mosaicism due to X inactivation may be protective against SARS-CoV-2 in women.
From the abstract:

The fact that the human ACE2 protein is encoded on the X chromosome means that males who carry rare ACE2 coding variants will express those variants in all ACE2-expressing cells, whereas females will typically express those variants in a mosaic distribution determined by early X-inactivation events.

So, since males are hemizygous for the X-chromosome, males that have an ACE2 variant that binds strongly to the SARS-CoV-2 spike protein will only express that variant in their lungs.  Females have two X-chromosomes, though only one is expressed in any given cell due to X-inactivation.  If a female is heterozygous at the ACE2 locus, with one allele that encodes a protein that strongly binds SARS-CoV-2 spike protein and one allele that encodes a protein that weakly binds SARS-CoV-2 spike protein, mosaic expression of the maternal and paternal alleles may give partial protection from infection.
The authors found that ACE2 is generally intolerant of loss-of-function variants, though many missense variants occur at and near residues predicted to bind SARS-CoV-2.  Such variants were detected at a rate of 3.9 males per 1000 and 8.5 females per 1000.  However, the most popular missense variant, rs41303171, does not lie in a domain of ACE2 that is predicted to interact with SARS-CoV-2.  Additionally, this SNP is only observed in 1.7% of male and 3.1% of female samples, so it is not obvious that this explanation can account for the sex-specific discrepancy in severe COVID-19 at the population level.
TMPRSS2
Currently, evidence suggests that there are no sex-specific differences in TMPRSS2 expression in the lungs of humans or mice.7  Note, however, that only transcript levels have been evaluated in this context, and that TMPRSS2 activity would need to be evaluated to determine that proteolytic action is not different between sexes.

Non-genetic factors
Worldwide, men smoke five times as much as women.8
Smoking is co-morbid with severe COVID-19 9, likely due to decreased lung capacity, though possibly through a mechanism involving increased TMPRSS2 expression.7  From the same TMPRSS2 paper cited above:

regardless of sex, smoking significantly increases the expression of TMPRSS2, which reverts back to never-smoker levels in former smokers

Indeed, one recent study of more than 1,000 COVID-19 patients reported greater than two-fold increased risk for intensive care unit admission and death in smokers as compared with non-smokers.10
There may be cultural factors affecting disease progression, as well.  If men are less likely to wear masks or follow other guidelines to reduce the risk of infection, then infected men may be exposed to a higher infectious dose than women. Initial infectious dose may be positively correlated with viral load 11, and higher viral load is associated with a more severe prognosis for SARS infections.12
It could simply be the case that symptomatic men are less likely to be tested (a "tough it out" mentality), and therefore would be less likely to receive treatment that prevents a mild infection from becoming severe.

Citations

A Novel Angiotensin-Converting Enzyme–Related Carboxypeptidase (ACE2) Converts Angiotensin I to Angiotensin 1-9
SARS coronavirus entry into host cells through a novel clathrin- and caveolae-independent endocytic pathway
Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites
Sex differences in renal angiotensin converting enzyme 2 (ACE2) activity are 17β-oestradiol-dependent and sex chromosome-independent
Age- and gender-related difference of ACE2 expression in rat lung
ACE 2 Coding Variants: A Potential X-linked Risk Factor for COVID-19 Disease
No evidence that androgen regulation of pulmonary TMPRSS2 explains sex-discordant COVID-19 outcomes
Gender empowerment and female-to-male smoking prevalence ratios
COVID-19 and smoking: A systematic review of the evidence
Clinical Characteristics of Coronavirus Disease 2019 in China
SARS-CoV-2 viral load and the severity of COVID-19
Initial viral load and the outcomes of SARS

The following GWAS finds another ACE2 related X-chromosome allele correlated with COVID-19: https://news.bugbank.uk/2020/05/xpnpep2-is-genome-wide-significant-in.html

Besides biological reasons, men are often more risk-prone and take less precautions, which certainly has some impact. Here in South Korea, the share of men that wear masks is definitely lower than the share of women that wear it (based on anecdotal observations at least).

@Olorun, that would explain a greater rate of infection among men, which seems to be the case. Though I'm not sure how that would cause a greater rate of severe COVID-19 cases in men, unless (1) men are being exposed to a greater viral load, if greater viral loads are correlated with adverse outcomes, or (2) men are less likely to seek treatment at the onset of symptoms, leading to a worse prognosis.  I'll edit my answer to reflect those possibilities.

Both seem like very real possiblities, especially the "tough it out" mentality - if the men with lesser symptoms are less likely to be tested, then the overall share of infected men with severe symptoms will be higher.

What does "priming" mean in simple terms, presumably it alters the folding of the spike protein in some way? Is priming common among viruses in general?

@SingleMalt, TMPRSS2 is a transmembrane protease, which means it sits on the outside of the cell membrane and cuts other proteins. Studies in SARS-CoV have shown that cutting of the viral spike protein by TMPRSS2 increases the likelihood of viral entry into the cell. Similar activation by human protease is observed for influenza A and metapneumovirus.


text:
What does 21q21.1-q21.2 mean?
I am reading a journal paper about the association between NCAM2 and autism, and I have come across the following:

We performed microarray analysis and identified a 1.6-Mb deletion of
21q21.1-q21.2, containing the NCAM2 gene but no other functional gene.

I am not sure what the '-q21.2' after '21q21.1' in '21q21.1-q21.2' means. Does it mean that the deletion goes between band 21.1 to 21.2 on the long arm of chromosome 21 (21q)? Any insights are appreciated.

Cytogenetic map notation uses the following form:
A[p/q]BC.D
Where A is the chromosome number, p is the petit / short arm, q is the queue / long arm, B is the band, C is the sub-band, and D is the sub-sub-band.
So, 21q21.1-q21.2 designates a region on the long arm of chromosome 21, band 2, sub-band 1, between sub-sub-bands 1 and 2.
Source:  NCBI Genetics Review (archived version)


text:
What is the threshold of significance when measuring difference in proteins' radii of gyration?
In molecular dynamics simulations of proteins, the radius of gyration is often used to assess protein compactness. Given two proteins, what difference in radii of gyration can be considered significant? 1 angstrom, 5 angstroms, 10 angstroms? Significant meaning: yes it is definitely more compact or no it is definitely not more compact. I have been searching but can't find any reference related to that.

Welcome to Biology.SE! I think this is actually a statistics question in disguise — whether a difference is significant will depend on the degree of variance in the two values you are comparing! Also note that these answers will always be probabilistic rather than Boolean (yes or no) ... ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

If you need an introduction to statistics, I have found starting with a relatively accessible and reliable source like Khan Academy to be very helpful.

@tyersome The question is more about the threshold one should use to apply a statistical test. The test will tell wheater there is a significant difference or not at a given threshold (1 angstrom, 5 angstroms, 10 angstroms). I think a simple t-test is enough. But a which threshold to use is more biology-related.

Given only the difference of two values, you can make no claims about whether those values are significantly different. In order to determine if two proteins have significantly different radii of gyration (Rg), you will need repeated measures and a statistical test. To demonstrate the kind of analysis you need to do, consider the following examples.
Example 1 -- proteins A and B, 12 measurements each, 0.1 Å resolution
H0: there is no difference in mean Rg between protein A and protein B.
Data

Rg protein A (Å)
Rg protein B (Å)

10.1
11.1

10.2
11.2

10.1
11.1

10.3
11

10.9
11.7

9.8
10.8

9.9
10.9

10
11

10.3
11.2

10.1
10.8

10
11.5

9.5
11.1

Summary Statistics

-----
Protein A
Protein B

Mean
10.1
11.1

Variance
0.113
0.0706

Results
For two independent samples, we can perform an unequal variance t-test. With α = 0.05, we calculate a two-tailed p value of 5.26 × 10-8, so the null hypothesis can be rejected. Despite having a difference between means of only 1 Å, proteins A and B have a significantly different mean Rg.

Example 2 -- proteins C and D, 12 measurements each, 0.1 Å resolution
H0: there is no difference in mean Rg between protein C and protein D.
Data

Rg protein C (Å)
Rg protein D (Å)

15
5.5

11.5
2.4

12.2
13.3

20.6
14.2

20.2
17.2

11.2
12.6

15.2
17.8

9.3
9.9

10.8
10.1

14.9
8.4

14.2
10.4

8.2
4.8

Summary Statistics

-----
Protein C
Protein D

Mean
13.6
10.6

Variance
15.2
22.9

Results
Applying the same test as in Example 1, we calculate a two-tailed p value of 0.100, and the null hypothesis cannot be rejected. Despite having a difference in means that is 3 times larger than the observed difference for proteins A and B, the large variance in the measured values means that there is no significant difference in the mean Rg for proteins C and D.


text:
Can you design a bacteriophage that attacks the part of the bacteria that makes them antibiotics resistant?
I read in a newspaper about a case where they had found a virus that could attack a specific form of antibiotics-resistant bacteria and managed to save a girl from a certain death by "infecting her" with the virus.
See this article for instance.
I would like to know if it is possible to construct a virus that attacks the part of the bacteria that makes them immune to antibiotics?
I mean if you could combine a certain type of antibiotics with a virus that attacks any bacteria that is immune to that particular type of antibiotics the bacteria is in a bad place.

I have read before, now citing this answer

"Bacteria usually gain resistance mechanisms through horizontal gene
  transfer (such as conjugation and phage infection)."

and that bacteria can be resistent by for instance:

"produce beta-lactamase that inactivate many lactam based antibiotics
  such as penicillin."

then if you can construct a drug that somehow can attack the bacteria because of the specific genetic code that gives the bacteria the ability to produce beta-lactamase then you might be able to attack all bacteria that shares the same genetic code that gives them that ability and the bacteria can not mutate to escape without losing their resistance to penicillin.

Check out phage therapy. For more details check out the reviews by Levin & Bull (2004) and Skurnik & Strauch (2006). The idea was around for quite some time and there is active ongoing research in this field.
However, this idea just involves killing the bacteria using bacteriophages and not reducing their resistance to antibiotics. The bacteria that are immune to antibiotics can be killed by viruses (and vice versa). If you use them in combination then possibly there can be synergistic effects under a certain regime.

Another clinical trial was conducted to evaluate a combination of the
  antibiotic enrofloxacin and intramuscularly administered bacteriophage
  (Huff et al., 2004). Both treatments individually provided effective
  treatments of the E. coli infection, but the synergy between the two
  treatments led to a total protection of the birds, thus suggesting a
  significant value of the combined treatment.

Skurnik & Strauch (2006)

The combined treatment may not always be synergistic; they could also be antagonistic and therefore a good therapeutic strategy should be applied (Chaudhry et al., 2017).

As suggested above for tobramycin, antibiotics can be antagonistic to
  phage because they reduce the density of the bacteria and thus the
  capacity of these viruses to replicate [43]. Worse, antibiotics may
  even interfere with phage replication within the cell, thereby causing
  a reduction in phage numbers [41, 44, 45]. One way to test the effects
  of this possible antagonism is to treat with phage first and
  subsequently treat with the antibiotic, comparing the outcome with the
  case of simultaneous treatment. Here, we used delays of 4 and 24
  hours. Results show substantial effects of delayed treatment with
  phage for some antibiotics but no effect for others (Fig 4). The only
  statistically significant effects of delay are for the 24 hours delay
  using gentamicin and tobramycin, but the magnitude of the effect is
  profound. These are two of the three drugs for which simultaneous
  treatment suppressed phage replication (Fig 4B). The third such drug
  that suppressed phage replication with simultaneous treatment
  (ciprofloxacin) also exhibited greater kill with phage-first
  treatment, but the statistics fail to reject the null hypothesis of no
  effect of delay. This case warrants further investigation.

Unfortunately, bacteriophages are very host-specific and are hence not as broad spectrum as antibiotics. They are just like viruses of animals: the virus that infects a cat would most likely not infect humans. Very few viruses have a broad range of hosts.

For your query:

if you can construct a drug that somehow can attack the bacteria because of the specific genetic code that gives the bacteria the ability to produce beta-lactamase then you might be able to attack all bacteria that shares the same genetic code that gives them that ability and the bacteria can not mutate to escape without losing their resistance to penicillin.

the answer is that it is possible in principle. There are ways to knock out certain genes (CRISPR-Cas is one of the ways). However, the problem is the delivery of these molecules that mediate these knockout, to the bacterial cells. For that, you again have to rely on virus like particles for the delivery which gets us back to square one: how to make delivery machines/viruses that target all pathogenic bacteria. Moreover, the mechanisms of antibiotic resistance are diverse. Considering several other factors (that I am not going to list here), it is very difficult to make an efficient system for targeting antibiotic resistance genes in different bacteria.

It's possible and certain engineered solutions might be even more potent than just phage therapy on its own. For example, imagine if you could deliver CRISPR-Cas with a lysogenic bacteriophage (that is, the phage delivers a CRISPR-Cas payload, and that payload gets integrated into the host genome without immediately killing the bacteria). The CRISPR-Cas system could then activate expression, and maybe not edit genes, but let's say down-regulate specific known antibiotic resistance genes or programs, this is known as CRISPR interference. This regulation could be done to the antibiotic resistance bacteria, and then followed up with antibiotics, resulting in much higher efficacy of treatment. It's like a Trojan horse! Researchers recently have even begun to scale this sort of CRISPRi program to target many genes simultaneously and have demonstrated how this approach could reduce bacteria "survivors" (referred to a persisters by the field) by more than an order of magnitude following treatment of antibiotics such as ampicillin, ofloxacin and cefixime (Reis et al., 2017).


text:
How to get a pdb file of a single atom?
I am trying to get a pdb file that contains a single atom, it doesn't matter if it's Hydrogen or another atom. How can I obtain this? Are there any pdb files with just a single atom available to download? Or do I have to take an existing molecule and remove the atoms manually?

How do you want to make a crystall of a single atom?

I have no idea why you would need sth like that, but you'd have to cut existing one

I'm currently working on a problem on molecular modeling and our software is having problems. I was told that a good way to debug this is to run the program using a pdf file with just a single atom

you'd have to cut existing one can you explain how?

@user4352158 In the PDB file you can remove every other entry except an atom. You can also view a single atom without altering the file itself(at least in swiss-pdb viewer)


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Mitochondrial Genetic code
We know that the genetic code is universal. My query is why the mitochondrial genetic code is different from universal genetic code?

Your premise is incorrect, the genetic code is NOT universal. There is a 'standard' genetic code, which is found among higher animals and plants and most bacteria, but there is a variety of other genetic codes found in the main genome of more obscure organisms. These are listed at: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi .
There is also no mitochondrial genetic code but a variety of mitochondrial (and plastid) genetic codes. One feature of genomes with non-standard genetic codes is small size, so that the number of proteins influenced by a change from a common precursor genetic code would have been small.
In the case of mammalian mitochondria there are fewer tRNAs and these have non-standard anticodon-codon interactions. Thus rationalization of these genetic codes may have been due to pressure to reduce the size of the genome.


text:
Can anyone identify this insect from India?
Found this bug in Chennai. Curious to know what kind it is. Does it pose any danger?

This is definitely a bug - as indicated by the characteristic body form and the segmented (it should be five) antenna. My guess here is that this is Nezara viridula, also known as the "southern green stink bug" or the "southern green shield bug".
See this image (from here):

Besides being a pest for agriculture, they are harmless and not toxic, although they can spread a stinking substance when threatened, hence their name. You can find more about them here and here.

Looks like a common green stink bug - https://en.wikipedia.org/wiki/Green_stink_bug
Give it a test. If you put it into a handkerchief and scare it a little, it should give off a foul smelling odor

Unfortunately the article linked by you limits the distribution of the bug to the US and parts of Australia.

The edges around its body also differ from the OP's images

the exact same bug is present in central Europe. I saw it today. So maybe the wikipedia article needs updating

the edges around it's body might be different because of the age difference. The body shape (hexagonal back) looks identical though


text:
What bug is this? Manchester, UK
The creature appears to have a green body with 5 legs of the same size, and one longer than the rest. It moved this long leg around, and it looked like it was using it to sense it’s surroundings.
Location: Manchester, United Kingdom

Looks like a harvestman (daddy long legs). What size was it? You can try identifying it with the tool here: https://harvestmen.fscbiodiversity.uk/ The image isn't clear enough for me to try.

That looks like what I would call a "daddy long legs", also known as harvestmen. These are arachnids of the order Opilones. There are some 30 species of harvestmen found in the UK. The webpage https://harvestmen.fscbiodiversity.uk/ has a very useful identification tool and based on it, I believe your photograph shows a Leiobunum sp. A:

Please visit the site itself for more details as it doesn't allow copying.

Great ID resource! Bookmarked it for later use.

It's my understanding that crane flies are called "daddy long-legs" in the UK.  So using that name for a harvestman over there might cause confusion.

@EldritchWarlord yep, but I was raised calling them daddy long legs, and I'm not about to change that because I now live in London :) but that's why I mentioned the BrE version too. They're called harvest men there.


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Why do Centipedes always have an odd number of pairs of legs?
Furthermore, centipedes are within the Myriapoda, a subphylum of arthropods which also contains millipedes. Do millipedes also have an odd number pair of legs?

A definitive answer would require an extensive embryology research across many species of centipedes. To my knowledge, Strigamia maritima is the only centipede whose embryogenesis and segmentation has been seriously studied. I'm afraid you won't find your answer.

@A.Bourgoin noted, you provide a relevant / useful caveat.

Centipedes are part of the group of insects that utilize a short germ-band mode of embryonic development.1  One feature of this type of segmentation is that new segments are added sequentially to the end of the developing insect (the "posterior proliferative zone").  This is in contrast to insects that undergo long germ-band gastrulation, like Drosophila, where all segments are created simultaneously.
Additionally, Myriapoda demonstrate double segmental periodicity, meaning that segments are always added two at a time.  See the following informative figure from Damen 2004 2 --

Figure 2. Segmentation in the geophilomorph centipedes involves a phase of double segmental periodicity. The drawing shows a schematic model for segmentation in geophilomorphic centipedes. Segments are patterned in posterior tissue that does not show overt segmentation. Segments become molecularly defined in entities (coloured blocks) that eventually give rise to two segments each. Before morphological segments become visible, these two-segment entities are molecularly subdivided into segmental units
(dashed lines), which each eventually will give rise to one segment. For instance, at stage I C represents an entity that is refined into two units (C at stage II), which give rise to one segment each (C′ at stage III). This mechanism of segmentation provides a developmental constraint that only allows the addition of segments in bits of two and in this way only allows odd numbers of trunk segments in centipedes.

One would expect, then, to only see even numbers of leg pairs.  Arthur and Chipman explain this discrepancy in their 2005 essay 3 on Strigamia maritima, the most well-studied member of the Myriapoda subphylum.

Of course, if everything happens in twos, we would expect that there would always be an even, rather than odd, number of segments. But this apparent discrepancy is probably not real. It seems likely that the poison claw segment immediately anterior to the first pair of legs is really a modified trunk segment.

As for how Myriapoda add segments two at a time, I direct you to sources like Chipman and Akam 2008 4, though be prepared for some heavy reading on signaling cascades and morphogen gradients.

References

Hughes CL, Kaufman TC. Exploring myriapod segmentation: the expression patterns of even-skipped, engrailed, and wingless in a centipede. Dev Biol. 2002 Jul 1;247(1):47-61.
Damen WG. Arthropod segmentation: why centipedes are odd. Curr Biol. 2004 Jul 27;14(14):R557-9.
Arthur W, Chipman AD. The centipede Strigamia maritima: what it can tell us about the development and evolution of segmentation. Bioessays. 2005 Jun;27(6):653-60.
Chipman AD, Akam M. The segmentation cascade in the centipede Strigamia maritima: involvement of the Notch pathway and pair-rule gene homologues. Dev Biol. 2008 Jul 1;319(1):160-9.

[W]e suggest that the myriapods have developed their unique body plan
  largely by expanding the number of segments under the control of the
  ‘trunk’ genes.

https://dev.biologists.org/content/develop/129/5/1225.full.pdf
In a way, Wikipedia states that the Craterostigmomorpha centipede doesn't: "They have a distinct body plan; their anamorphosis comprises a single stage: in their first moult, they grow from having 12 segments to having 15." Albeit, no source for that.
It seems that they always have an even amount of legs or an odd amount of leg pairs on a genetic level, hoc genes:

https://pubmed.ncbi.nlm.nih.gov/11874918
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244043

It gets very technical; if you really want to dig deep, perhaps look at the similar articles (after the abstracts) in the sources.


text:
Is it possible to assert who is the parent/child by looking at DNA sequence only?
Suppose I have whole genome sequences for two people of the same sex. I know one person is the parent of the other, but I do not know who is the parent and who is the child. Is it possible to determine with certainty the direction of descent using the sequencing information alone? Assume that the individuals were sampled at the same age so that you can't tell parentage from telomeres or other age-related markers.

Isn't this the same as asking if DNA testing can identify parentage? (I think you know the answer to that) And isn't this assuming that the genetic material somehow survived for longer than the Carbon 14 did?

@DKNguyen I don't think it is the same, no. I don't care to look if they are relative here, I care to know which one engendered the other, only by looking at their genes. And yes, it is by assuming I have the full knowledge of both genetic codes. I picked 100 k years as an example to remove C14 possibility out of the question, but if you prefer, make it, say, 5000 years ago or even a decade ago (but then please don't cheat using C14 :) ).

What do you mean by 'only looking at the chromosomes'? Staring at them down a microscope? Sequencing them?

@AccidentalBismuthTransform I've edited your question for clarity and to incorporate the information from the comments. Feel free to roll back my edits if you feel they change the spirit of your question.

Take a chromosome of individual A. For each gene check if an identical copy is found in individual B. If it is the case then B is the parent of A.

@rerus if the gene is identical in both, why does that rule out A being the parent of B?

@swbarnes2 B is the parent iff for one of two chromosomes 1 of individual A, all the genes alleles are found in B. This is a naive model due to intragenic crossover, mutations, and mitosis crossover, so you'll need to compute a B->A inheritance score for each chromosome of A.

My main source is https://www.ncbi.nlm.nih.gov/books/NBK21438/ "Mitotic crossing-over is rare" as it is the main thing that can mess entirely what I'm saying.

If one chromosome is identical between A and B, how can that possibly distinguish anything at all between them?  If two students in a class turn in identical papers, how is that evidence that A must have copied from B, and that B could not have copied from A?

@swbarnes2 ... meiotic crossover
https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4353236/ https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC3478297/

@reuns I had to read your comment twice to realize what you mean and that you are right and swbarnes2 just didn't understand you. It would recommend you to turn your comment into answer with diagram. The point is that one chromosome in A is identical to parts of two chromosomes in B. This is not a symmetrical pattern. Another way to look at it is that out of 4 homologous chromosomes involved 3 have at least some part not identical to anything. Problem with this approach is that with current methods we can't get full chromosome haplotypes.

If A is XY and B is XX, if A is the parent, A should pass on their X chromosome intact to the offspring.  If B is the parent, than the X chromosome A receives would have undergone crossing over with B's other X chromosome before being passed to A.
Otherwise, I don't think you could do it from sequence alone.
I guess if the circumstances were right, you could include haplotpye information, and you could tell; if one person had top to bottom haplotypes only found in China, and the other was half Chinese haplotypes and half African haplotypes, the simplest explanation is that the person with one ethnic origin is the parent, and the person with two is the offspring


text:
What are the stretch of amino acids?
I found the words "stretch of amino acids" in a newspaper article.

"This lipopeptide matches the stretch of amino acids in the spike protein of SARS-CoV-2 exactly."

What is the "stretch of amino acids"? Is this different from "amino acid sequence"?
I looked for a definition of the word but could not find it.
From the usage, I guess it means something similar to "sequence", am I right?

Yes, stretch means sequence.  "This lipopeptide matches the stretch of amino acids in the spike protein of SARS-CoV-2 exactly."

Thank you for your answer.　I'm also not sure what the word "match" means in that quote.
Does it mean that the primary structure of spike protein and lipopeptide are the same? Or is it to be a "key and keyhole" relationship with spike protein?

@acvill you can expand your comment and make it a proper answer

I think this question should be closed because it is scientifically trivial and would seem more to relate to a restricted experience of English language usage, for which there are many aids on the internet. As far as Stack Exchange is concerned, English Language Learners might be appropriate.

Unless ones know more or less chemistry, you may not understand the concept of "amino acid sequence" itself. For the non-native speaker of English, making up two or three technical terms that have exactly the same thing is the cause of the confusion, I think.

Yes, stretch means sequence in this context.  See definition #5 for stretch (noun) on Wiktionary:

A segment or length of material.

So, the "stretch of amino acids" in the article refers to the peptide sequence portion of the lipopeptide prophylactic.

I was confused, guessing that there was some point in changing the terms. Thanks to you, my confusion was cleared up. I'll read the paper to see how these inhibit the infection process using the same sequence of peptides. I imagine it's similar to competitive inhibition, though.

English speakers might also say "That stretch of road has a lot of potholes".  It might even be used more loosely, like "a stretch of time".  It's not an exclusively scientific term.

The lipoprotein has a 36 amino acid sequence that is the same (matches) as part of a protein from SARS-Cov-2.
The newspaper article refers to this paper below.
"Intranasal fusion inhibitory lipopeptide prevents direct contact SARS- CoV-2 transmission in ferrets"
Rory D. de Vries1@, Katharina S. Schmitz1@, Francesca T. Bovier#2,3,4@, Danny Noack1, Bart L. Haagmans1, Sudipta Biswas5, Barry Rockx1, Samuel H. Gellman6, Christopher A. Alabi5, Rik L. de Swart1, Anne Moscona2,3,7,8, Matteo Porotto2,3,4
available at:
https://www.biorxiv.org/content/10.1101/2020.11.04.361154v1.full.pdf

Thanks for your answer. Your explanation really helped to understand the followings; The "matches" in the article means that ”part of the primary structure of the spike and part of the amino acid sequence of the lipoprotein are identical".


text:
Do viruses or bacteria have a flavour?
My 9 year old niece asked me this when I was explaining some stuff to her about the coronavirus. She asked "What does this virus taste like? Can I tell whether my sandwich is contaminated for example?"
That sounded like a silly question and I immediately responded by saying that they are too small to have any taste, and even if you manage to eat a whole lot of viruses it would taste like water.
The day after, I searched a bit just to make sure that I haven't fed the wrong information to the kid. As I expected, there wasn't a single page mentioning this question (except this quora post with a vague answer). Now it may sound like I am overthinking and the question is too naive and isn't worth the time, but then again, I thought what's the harm in asking?

Has there been any research on the likely taste or maybe smell of a specific virus or bacteria?

While I don't think it's the bacteria themselves that cause the taste, there are quite a number of foods - cheese is a prime example - that acquire their taste as a result of bacterial action.  And if you want to expand that a little to include microorganisms in general, there's bread, wine, beer and more.

I think this is a very good question, but from the title i had assumed it would be about the sensory organs of bacteria.

same; too few characters for a title edit: ... have [a] taste [to them]?

... have a flavour (or "flavor" according to, er, taste)

I know that mold has a taste.

As you could imagine, a systematic cataloguing of bacterial or viral flavor profiles would violate a number of biosafety protocols. However, in a laboratory setting, different bacteria definitely have distinct odors. In some cases, the odor is even included in guidelines for laboratory identification of an organism. However, that odor is typically not a result of smelling bacteria directly, as very few bacteria are aerosolized from a lab culture. More likely, the odors of bacteria are a result of volatile chemical metabolites produced by the organisms. For example, the spoiled milk smell comes from a number of odiferous compounds produced by bacteria. Sometimes these bacterial metabolites have rather colorfully descriptive names, such as putricine or cadaverine.
Viruses are different though. They don't generate new metabolites on their own (outside of an infected cell) and they are incredibly tiny, even compared to a single cell. The human sense of taste is sensitive enough to detect some compounds in the low parts per million range. To even approach that range, you'd have to cram around 100 billion virus particles into a single milliliter of water (based on back of the envelope calculation). That's about 100,000 times more virus than most COVID19 positive clinical specimens, so I don't think you'll have to worry about tasting it under most circumstance. However, some research has been done to see if dogs can sniff out viral infections (likely by detecting volatile compounds produced by the infected cells, not by detecting the virus directly). Of course, they're trying to train them to detect the novel coronavirus as well.

To add another back of the envelope calculation, assuming the virus particle to have density 1 (order of magnitude) and a diameter of 80 nm (for the solid sphere), we'd expect roughly 1e-16 g per particle, so 10⁴ - 10⁷ SARS-CoV2 particles/ml should be 1 pg/ml - 1 ng/ml. Humans odor detection threshold for geosmin in water is 6 pg/ml, so in the mass concentration range of the SARS-CoV2 samples. Of course, I picked geosmin because we (those of us who do have the receptor) are extremely sensitive for geosmin. But then, that's maybe not an accident: geosmin is produced by molds, and this warns us

of mouldy water. (Geosmin also occurs in other mixtures such as some plants and actually in substantially higher concentration and IIRC contributes to the smell/taste - but in those combinations doesn't produce the ugly/warning sensory impression we get if it is in [more-or-less pure] water)

dogos? doctor doggo? :) too small for edit

It's an okay generic answer, I hope it's not too critical to say it avoids the question a little and makes it about odorants; the questioner is asking about flavour (taste!). I mention it because it's unclear from your answer that taste is a different beast from smell. Certainly a little misleading to discuss concentration (parts per million) when there exist no chemoreceptors to even detect viruses or cells... There are <1 elephant parts per million in a gallon of water too, but I'd bet you wouldn't be able to taste whole elephants, regardless of how sensitive our noses and tongues would be!

So I think this is a more conversational kind of question. I will address some misconceptions you have, and I will try to keep it brief, considering the nature and depth of your question. One could comment on the question very deeply, so I'll stick to addressing some misconceptions.

Can I tell whether my sandwich is contaminated for example?

Usually you can taste contamination because of the (action of) metabolic products of microorganisms. You do not taste nor smell the microorganism directly; you taste their metabolites or the effect of their presence, such as products of fermentation, or oxidized molecules which are normally not present because air does not penetrate through e.g. apple skins. Take filamentous fungi, for instance; they release enzymes that act on complex carbohydrates to break them down. You cannot taste the cellulose which makes up the majority of a stalk of celery, but you may be able to taste its broken down products once a fungus has begun to digest it prior to absorbing its nutrients: sweet glucose, sucrose, trioses, some acids. It depends on the food and the extent and kind of contamination.

they are too small to have any taste and, even if you manage to eat a whole lot of viruses it would taste like water.

You can taste molecules which are far smaller than a virus. Indeed, pheromones and volatile or sticky chemicals and all that jazz are definitely much smaller than viruses. Viral particles themselves may actually be too big to taste, because your sense of gustation and olfaction depends on the interaction between tastant or odorant molecules and corresponding receptors, which are situated on the membrane of sensory neurons (nerve cells which are responsible for detecting and relaying information to the brain about the outside world). These receptors harbor ligand-binding pockets that are too small to capture entire viruses. This does not rule out the ability for you to taste broken bits of viruses, but I think this is unlikely or coincidental (i.e. the particle may bind to receptors weakly and not very well).

it would taste like water

Water is a requisite for taste and smell, things have to be dissolved in water for you to be able to detect them. Water by itself has no taste! Only impurities, oxygenation and carbonation and mineral content give water flavor. I understand that you factor in temperature and texture into the 'perception of water', but these are not gustatory phenomena and use different mechanisms of detection.

Water is a requisite for taste and smell, things have to be dissolved in water for you to be able to detect them - Why is that so?

Re "things have to be dissolved in water for you to be able to detect them", is this really the case?  Most tastes are the same as smell, and the odor molecules are generally not dissolved in water, unless you're including water that's present in body fluids at the odor receptor.

"pheromones and volatile or sticky chemicals and all that jazz" are even on the large end of the spectrum. We can taste NaCl, and it doesn't get much smaller than that!

Capsaicin can certainly be tasted, and that's negligibly soluble in water.  It's fat-soluble though; the fat isn't even miscible with water.

@ChrisH Capsaicin does not activate taste buds though, it works via TRPV1 channels and at least in humans is part of the nociceptive system via the N. trigeminus, not the olfactory system via the Nn. olfactorii. @S Pr we might actually be able to taste water in itself because of its dilution of acids and interactions with carboanhydrases

@Narusan that comes down to the semantics of "taste"; in the context of the question "taste" would certainly seem to include not just the taste buds but the olfactory system.  It's not stretching things much further to include other receptors in/near the mouth that respond to foods.

@ChrisH It's a pretty clear cut distinction.  Taste receptors are part of a well defined subset of the nervous system that processes gustatory inputs from specialized sensors.  Olfactory receptors are part of a separate system that process smells with their own specialized sensors.  Capsaicin triggers pain receptors, which are of a totally different sort.  TRPV1 is a nociceptor that forms part of the body's thermoception system.  There's no way we could consider it related to taste.

@J... biologically yes of course.  In everyday language taste is a superset of taste, olfaction, and other stuff.  Ask yourself this: how many people would say "this curry tastes hot" (referring to capsaicin) compared to how many would use another verb.   Think also of "this cake tastes of vanilla" -- purely olfaction, not strictly taste at all. The question is asked on behalf of a 9-year-old; in that context the broad colloquial meaning of "taste" can be expected to apply.

@ChrisH  True, but this is bio.SE and the target audience is academics, researchers, and students on a path thereto.  I guess I'm labouring from the perspective that the discussion here intends to adhere to standard scientific terminology and that it behoves us to dispel the misconceptions that can sometimes brew in colloquial circles.

@J... I'd be the same in physics, which is my field. Then of course there's the whole fruit/veg - tomato/rhubarb - biological/culinary definitions issue). One issue I'm familiar with is that there's often no more suitable/scientific word for the superset of scientific terms.  Can you suggest anything that encompasses taste, olfaction and capsaicin-heat (whether or not it also includes real heat/cold or mouthfeel that wouldn't be culinary "taste")? "Detect" doesn't work without quite a lot more explanation, for example

@ChrisH I don't know of such a word, specifically.  Still, I wouldn't say 'taste' is appropriate in a scientific context - no more than a hot cup of coffee 'tastes' hot.  It burns just the same whether you put it in your mouth or dump it on your skin.  To call it 'taste' simply because it happens in the mouth is misleading, I suppose.

I am anosmic with no sense of smell.  I taste things but have no olfaction.  "Things taste and smell the same" is not a valid statement, as they are different senses with non-overlapping domains of subjective experience, but it points at how people with taste and smell run them together perceptually.  A mild synesthesia maybe even.  They loosely use "taste" to mean "perception of flavor" which is some synthesis of the two disjoint inputs.

It was really hard not to accept your answer. But for some reasons, I thought the other answer could be a better fit. Thank you

@terdon: we taste H⁺

"Viral particles themselves may actually be too big to taste, because your sense of gustation and olfaction depends on the interaction between tastant or odorant molecules and corresponding receptors" -- so perhaps the process in a way resembling tasting/smelling viruses is the interaction with antibodies. This does not lead to a sensory perception, however, except indirectly for the usual symptoms of your immune system being busy. At any rate, this won't help at all "tasting" infectious material beforehand.

@cbeleitesunhappywithSX oh wow, that's what we detect as "sour"! I had no idea, thanks!

Hi all, I arrive to see a nice comment section, good points too! They are a case in point why I included a disclaimer on brevity at the beginning, the conversation gets deep quick, since it's a well studied branch of neuroscience :) @J... the term which encompases reception of taste/smell/capsaicin would be chemosensation, even though capsaicin works via the noci- or thermo-ception pathways. I am aware some detectable (and delectable!) compounds are immiscible in water and thus may need to be fat soluble - as long as they are free to bind with our 'repertoire' of receptors.

@jamesqf Even odor molecules must become dissolved in the watery mucus at the olfactory epithelium to be detected; odorant receptors are not air-exposed. Even in invertebrates such as worms and insects, odors enter into specialized structures called sensilla through nanopores, whereby they dissolve into an aqueous lymph where sensory neurons project into. Never a bad time to remember how water-based all life is, even terrestrial life ;)

@S Pr: Yes, that's the distinction I was trying to make.

Already 2 good answers (MikeyC and S PRr), but one point missing:
We are very good at detecting the presence of some bacteria and fungi in our food in unhealty amount. We detect (by smell or taste) the products of these microorganisms as "food gone bad".
That's how we survived when the food didn't have expiry term labels mandated by the government.
We are also very good at avoiding places and things that smell bad. Bad smell is an indirect indication of an unhealthy thing, probably having bad viruses and bacteria ready to get us.
Then again, most microorganisms that make us ill actually don't eat much of our food. They hide in the food (or elsewhere) in order to eat us. That's why we cannot detect most of them. They don't leave much of a chemical trace.
Viruses are even harder - they do nothing outside of the host and there is too little of them in order to sense them directly.

We detect (by smell or taste) the products of these microorganisms as "food gone bad". isn't that because of bacterial products instead of bacteria themselves? Since OP asked specifically about the taste of microbes, the other answers didn't talk much about their products (but still touched upon it). Not saying that your answer is bad, but it sure needs some references ;)

@another'Homosapien' a lot of taste and smell sensation comes not from the main substance or object one smells and tastes, but from the product of the object interactions with the environment and/or degradation/decomposition of the substance or object, and/or some by-product from the object/substance creation. We say "smell of rotten eggs" and not "smell of the substance that rotten eggs evaporate".

Yup, I get that. But my point was that OP specifically asked about the taste of microbes, not their products (maybe I'm being pedantic here). There's nothing about your answer that is wrong or I don't understand, it's just that it doesn't answer the exact question. Also, the answer lacks the much-required references :P