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why does water go from high to low osmotic pressure to decrease the size of the nucleus?
I am reading this paper "Volume regulation and shape bifurcation in the cell nucleus" (linked below)
https://jcs.biologists.org/content/joces/128/18/3375.full.pdf
I am confused by this sentence "During cell detachment, because the cytoplasmic osmotic pressure decreases dramatically, water flows out of the nucleus and the nuclear volume shrinks."
Since water flows from low to high osmotic pressure, I would have thought that this decrease in osmotic pressure of the cytoplasm would cause water to flow into the nucleus, not out of it. Why does the opposite happen here?
The article also states that the volume of the cytoplasm will decrease. So is this something to do with the extracellular space?

After reading a snippet of the article, it seems like you just found a simple mistake that wasn't caught during review, but really shouldn't cause much confusion in the context of the paper. It's clear enough from the preceding paragraphs what they concluded is happening. Cell volume is reduced after detachment, primarily due to water efflux. Because of that change, the difference in osmotic and hydrostatic pressures between the cytoplasm and the nucleus favors water flux from the nucleus to the cytoplasm, reducing the volume of the nucleus and causing it to shrivel.


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How does imbibition and turgor pressure generate much force?
Both imbibition and turgor pressure together create a large force in plants such as force required to burst the seed coat open?

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When a 'v' letter should be changed to 'w' in botanical nomenclature?
When should be 'v' changed to 'w' in botanical names? (especially ones derived from names originally written in cyrillics).
The International Code of Nomenclature for algae, fungi, and plants says that

The letters w and y, foreign to classical Latin, and k, rare in that
  language, are permissible in scientific names
When the original publication of a name adopted a use of the letters
  u, v or i, j in any way incompatible with modern nomenclatural
  practices, those letters are to be transcribed in conformity with
  modern nomenclatural usage.

Where should I look for the rules on such usage?

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Why are chickens passive when their eggs are taken?
Most species don't seem enthusiastic when their eggs are taken, yet on farms with domesticated hens, they seem more passive when their eggs are harvested. Why does this occur?

You might ask a similar question about cows and milk.  I suspect that at least part of the answer is that chickens that showed the most resistance to having eggs taken became roast chicken or (if they were old and tough) chicken soup.  Thus over thousands of generations, the "protect your eggs at all costs" was selected against, and chickens were domesticated.

That is certainly one possibility, but I do not know of anything that strongly supports it. –

Preferential breeding so you don't get attacked every morning at the hen house supports it. If you've ever worked on a farm or raised chickens you'll know that some breeds are more aggressive than others, but those "heirloom" breeds are typically found only on small family farms where the hens have a lot more room. Factory farming has provided incentive to breed any kind of violence or aggression out of their layers, because you can have thousands (or more) chickens living together, especially if they're "free range" with no barriers, and you would want them to be as docile as possible.

Okay, that makes more sense. How long did this process take exactly for hens to become docile through selective breeding?

@jamesqf - I had a saying on my farm: if it draws blood, it's dinner. Exactly as you stated. Young=meat, old=broth. Selective pressure in action. The chickens and roosters who were aggressive didn't get to breed for long.


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

How would you get near infrared through the skull?

@Chris take a look at this link


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Should I consider one or two DNA chains to find how many nucleotides are in a gene?
I am trying to solve an exercise.

How many nucleotides does a gene contain if information about 287 amino acids is encoded in it? What is the molecular mass and length of this gene?

AFAIK, I have to consider two DNA chains to find molecular mass, and one DNA chain to find the length of the gene (am I right here?).
But I am stuck trying to find how many nucleotides are there in a gene. Should I consider both or only one DNA chain? I suppose that both (as for the molecular mass of the gene) but I am not totally sure.

This is a bad question from two perspectives. First, counting either one or two strands are equally correct or incorrect as there is nothing in the definition of a gene that specifies strandedness ( or even DNA). Second, the length of a gene is always longer than the DNA needed to encode the amino acids. All mRNAs have 3' and 5' non-coding regions of varying length, and, of course, there is always a stop codon. I approve of making students do calculations. I disapprove of questions that are biologically stupid.

@David, thank you very much for your reply. I agree with you. But this is exactly the question asked by my school teacher. Actually, these nuances are why I got stuck with this exercise.

Only your teacher can decide what the "right answer" is to their poorly thought out question. Either consult with them directly to find out what they want or give multiple answers and state clearly what assumptions you are making for each answer. Something like "If I assume that the gene only consists of an open reading frame and is single stranded then my answer is ###. However, if it is double stranded then my answer is #### etc." This has the advantage that you might be able to teach them ...

@tyersome, thank you for the advice. I have written exactly that way)

Counting both strands is admirably correct, but most people will multiply the number of amino acids by three, not six.  For example, nucleotide positions in a reference sequence will increase by 3 for each amino acid in the presumptive coding sequence.  Besides, if you want to be that pedantic, you should say zero, since the DNA contains nucleotide residues, not individual nucleotides, as they have undergone dehydration synthesis.  I think in biology the right answer will almost never be marked correct by a machine. :)
The answer you come up with will also be influenced by whether you would like to include a stop codon (+3) to avoid nonsense-mediated degradation, and a transcriptional start site and polyadenylation sequence (in eukaryotes).  The ''gene'' itself, in the genetic sense, will include enhancer elements over a much longer region of the chromosome and regulatory 3'-untranslated regions.  And then there's alternative splicing to consider...

Thank you very much. I understand now :) You've helped me a lot!

In fact, counting the nucleotides only one chain is mathematically the correct answer! The second chain does not contain any new information, since it is unambiguously determined by the first chain. On the other hand, the second chain does contain additional mass.

Well, you could have a mismatch.  The mRNA produced will use the complement of the base on the template strand, unless mismatch repair alters it to match the coding strand.  All six positions therefore may contain some information about the amino acid.


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Measuring the protein content using UV Vis
The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ethanol. Since ethanol precipitates the protein can I still determine the protein content of my sample using UV Vis at 260nm absorbance? or the protein content can be measured by its precipitate using a different method?

How do you want to measure the concentration of a solution when part of the dissolved content is not in the solution anymore?

ohh.... Even if the pure ethanol is at low temperature, still it cannot measure the protein content of the solution?

How do you know how much precipitated?

From what I know protein binds with ethanol forming a precipitate but I don't know if the temperature affects the precipitation because I also don't know if I can still read the protein content of the sample solution at 260nm using the UV Vis spectrophotometer. Some are saying that it can still be read when cold ethanol is used but I don't know if its true because most of the solutions that are subjected to UV vis are usually clear solution or clear colored solutions. that's why I'm asking.

How would precipitating (some of) the protein with ethanol or any other method help you to measure the A280 of a protein solution? The Bradford or Coomassie dye is to measure absorbance around 600 nm.


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Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI
I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic tree for these species but since I'm working from home, I'm using my old laptop that makes it hard for me to process data. Can you recommend any software/ site/ tutorial/ paper that I can use to generate a phylogenetic tree easily? This is also the first time that I will create a phylogenetic tree and I'm not sure how to proceed without downloading and processing too much data that my current laptop can't handle.
Thank you!

What file format(s) is your data? standard phylo tree format is i.e. Newick or New Hampshire format... So you can just go on google and search "freeware Newick tree display program" or something.

My data is actually the WGS in NCBI for 55 bacterial strains. Is there a way to create a tree out of these without downloading and processing a large size of data?

what about their tree viewer? genetics informatics forum is called BioStars.

@aliential The OP wants to create a tree, not just to visualize a tree. Rimuru show us a few of your bacterias, everything is about the size and the alignement step. If it is your first time then use blast to extract a well-aligned 2000 nucleotides region, then use online tools such as http://www.trex.uqam.ca/index.php

Will you be comparing each one of the virulence genes to each other? If the WGS sequence is annotated for your gene you can take those sequences and use software like MEGA to create a phylogenetic tree. But you have good internet and your laptop does not have enough processing power (you haven't provided laptop specs) use an online tool like @reuns mentioned.


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Why do denatured proteins tend to be less soluble than the native protein?
Why do denatured proteins tend to be less soluble than the native protein?
In terms of hydrophobic effects, could anyone explain this phenomenon for me?

Put bluntly, soluble proteins have shielded as many hydrophobic residues in their sequence as possible from the solvent (say cytosol, primarily aqueous). As the solvent then has access primarily to hydrophilic residues, the protein is largely soluble. Denatured proteins with large, exposed regions of hydrophobic residues become insoluble because hydrophobic molecules do not dissolve in water. As this is what amounts to a homework question, however, do keep in mind for subsequent questions that this site requires some personal effort to obtain a good answer!

Background information
A native protein has it's hydrophobic amino acids folded inwards, so it has a hydrophobic core. why? Because it's thermodynamically favoured. When a protein is denatured the hydrophobic amino acids won't be longer inside the core of the protein, but instead will be exposed to the hydrophilic environment (assuming you are talking about a protein inside an organism). But this isn't thermodynamically favoured because hydrophobic parts cannot form H-bonds with water and so aren't much soluble in water:

So when this happens, many protein molecules will aggregate like soap micelles (because hydrophobic interactions are favored). This will lower the total surface area of hydrophobic amino acids in contact with the water, thus lower disturbance in H-bonding in water molecules.
Here's my self-made depiction of effect of organics molecule on H-bonding in water (its quite rough, so don't care about fine details).

Summarized
hydrophobic amino acids will be exposed to the hydrophilic environment --> the proteins will aggregate together --> insoluble plaque.

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Earliest to use media after autoclaving?
I am autoclaving media to use later to inoculate yeast. How much time do I have to wait before using the media and adding the culture? Can I use it a few hours after autoclaving?

There is a relatively simple (and yet logical) answer: You can use the media as soon as they are cold enough for your desired culture temperature. So if you want to use the media at 30°C, there is no need to wait longer. The media will only warm up again in the incubator until this temperature is reached.
The addition of antibiotics is also uncritical, since the media is ways to hot to be directly used when they still inactivate antibiotics. Your cells wouldn't survive this either.
There is also no waiting period necessary to use fresh media after autoclaving, since there are no processes going on when the autoclaving was done properly. If not, you will see contaminations pretty fast.

If not using antibiotics or other additives, it's just a matter of medium being cold enough. If it's too hot, the yeast (or whatever you are inoculating) might get killed or heat-shocked, which you maybe don't want.
Since the incubator will bring the culture to 30C anyway, there's no point cooling it past that point. Yeast are probably fine at 37C, maybe even 42C depending on what experiment you are running.
If you put the hot medium into your culture vessel first then wait, it will cool faster, since the glass won't be as hot. When I feel impatient I like to run cold water down the outside of the flask while swirling, cools it off very fast.

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Pooling already extracted dna?
I had ethanol precipitated a large amount of DNA (2ml) and had to split the sample in half to spin down because only the microcentrifuge has the correct rotor to spin that fast. I want to get as concentrated of a DNA sample as possible. Is it possible (correct) to combine the resuspended DNA? I wanted a total of 30 ul of extracted DNA. Could I resuspend each of the two sample in 15 ul and then combine them?
What is the best way to go about this. I realize just keeping them separate might be the best option. I also realized I could've lost DNA when transferring the sample to a smaller tube. I did this because I don't believe it is correct to spin for longer at a lower speed...

Assuming you are using standard 1.5ml microcentrifuge tubes, it is completely possible to resuspend a dried DNA pellet from an ethanol/isopropanol precipitation. I have resuspended RNA pellets in 10µl water frequently with no issues.

But then can I combine the resuspensions?

I see no reason it will cause any issues.

If it were me...

You can resuspend the two separate pellets (A and B) in 10ul each.
Collate in one tube (add A to B).
Use the remaining 10ul  from your desired volume to 'wash out' tube B and add the wash to tube A.

So long as the DNA is from the same sample this is a perfectly reasonable step that should not result in a substantial loss.


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Converting miRNA names
I need to convert all of my microRNA names e.g. hsa-miR-30e-5p to e.g. entrez gene IDs, ensemble IDs or another ID. Does anyone know a good ID conversion tool for microRNAs?
(I managed to convert it to miRBase ID e.g. MIMAT0000692, but David does not recognise them apparently)

Does this help? https://www.biostars.org/p/85571/

miRbase is kind of an official database for miRNAs. So it is better to have miRbase ids for miRNAs rather than other (ensembl, entrez etc) ids.

It seems there're no ids for a mature sequence. You better search for a parent sequence ids. You could check, but it also seems that HGNC ids are -miR-30E- part.
So you could try Ensemble search (you should input names in 'Filter'-'GENE' section) or use Genenames. As you see, it has API, and you could use it programmatically with HGNC ids.


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Are the words biology and Ecology ever interchangeable?
I often hear people use the word "Ecology" when i think they mean "biology." This got me wondering: are the words ever interchangeable, or are these people really just that frequently using the wrong word?
My understanding is biology is the broader study of life while Ecology is the more specialized study of life interacting with other stuff (life + earth).

You pretty much nailed it with your definitions. Good guess. Wikipedia should also be able to help you

Ah... So you've heard people to use words despite they don't know what they mean?


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What kinds of bacteria live in water bottles?
I've always heard not to re-use disposable plastic water bottles.
According to this Huffington Post article, the reason is because:

everyday wear and tear from repeated washings and reuse can lead to physical breakdown of the plastic, such as visible thinning or cracks. Bacteria can harbor in the cracks, posing a health risk.

Also, a study from the Canadian Journal of Public Health found nearly two-thirds of bottles sampled had bacterial levels that exceeded drinking water guidelines. (See here).
So my question is: What kinds of bacteria (or other microorganisms) live in water bottles? In other words, which species should we worry about in these cases?
This Livestrong Article lists species found in the water itself, but I'm more curious about what organisms get introduced and grow through re-use of the bottle.
This is relevant because bottled water just became the most sold consumer beverage in the US.

I usually follow the rule: reusable until perma-stank condition achieved. The water in your faucet is not sterile. It is host to many bacteria, molds and yeast. This is one contributor to contamination. Plus the air you breath is host to microbes, therefore opening the water bottle contributes to contamination. But, if you rinse and wash with soap between uses, it should be good for a few weeks before it's time to be recycled.

In addition to the cracks providing a better place for bacteria to grow, all plastic bottles, when reused, are subjected to high levels of bacteria due to contact with hands and mouths. So your water bottle can potentially host a range of bacteria.
Your water bottle traps humidity inside and provides a perfect growing medium, especially near the threads of the mouthpiece and along/within cracks in the bottle which provide better bacteria accumulation.
Microorganisms that Grow

Overall, most sources I could find remained very vague (numerous News stories) or mentioned bacteria generally:

Staphylococcus and streptococcus species, [Source].

Norovirus [Source].

The seemingly most detailed studies I could find came from Watanabe et al. 2014 and Ohnishi et al. (2012) who examined microbial growth in numerous beverage types. However, I could only find their their abstracts online, which report:

microbial growth was detected in ~20% of poured samples, and in ~51% of drank samples.

225 bacterial strains, 27 mold strains, and 77 yeast strains were isolated

Bacteria: Streptococcus spp. (e.g., S. salivarius) and Staphylococcus spp. (e.g., S. aureus), made up the majority. Enterotoxin-producing S. aureus and Bacillus cereus were also isolated.

Molds: Cladosporium spp., Tramets spp., Bjerkandera spp., and Penicillium spp.

 [I Will hunt down these articles to get more details and will update accordingly when I find them...]
Microorganisms in the Water

Based on a study found here, brand new bottles of water can have fungus spores (typically harmless), but opened bottles can show signs of greater diversity (e.g., fungi, skin Staphylococcus, and yeast.

Igbeneghu & Lamikanra (2014) found Staphylococcus species (notably S aureus) and strains of Pseudomonas in bottled water available in Africa.

Your Livestrong article lists a number of non-human pathogens such as: Ralstonia Pickettii, Acidovorax Temperans, A. Delafieldii, Agrobacterium Rhizogenes, Burkholderia Glumae, and Bacillus Thermoglucosidasius.

Juvonen et al.'s  (2011) "Microbiological spoilage and safety
risks in non-beer beverages" provides a thorough list of organisms found worldwide in different bottled waters and other beverages.

Other Issues

According to Rose State microbiologist, Dr. Amy Hurst:

The plastic materials degrade into the water, so then you're drinking very small plastic molecules. [Source].

PET plastics tend to leach when exposed to realistic though extreme conditions, such as exposure to sunlight, heat and storage time. [See UF article]

Bisphenol-A (BPA) and phthalates present in the bottles can leach into the water and possibly cause harm to humans.

Rochester (2013) provides a good review of BPA effects in humans and other test organisms.

New research shows that BPA alternatives such as BPS aren't any safer either; in fact, in some cases they are considered more dangerous to humans. All bisphenols are capable of mimicking the body's sex hormones, says Robin Mesnage, research associate with King's College London.

Al-Saleh et al (2011) found that  76% of the bottled waters they tested in Saudi markets contained measurable amounts of phthalates.

So Reusable Plastic Bottles are Better Right?

Well, from a bacteria standpoint, this isn't necessarily true.  According to a small study  of 12 reusable bottles being used for a week:

Avg bacteria load: 300k CFUs (colony forming units). Ranged between 25 - 900k CFU/cm$^2$.

Notable types found: E.coli, salmonella, and various gram-positive cocci and gram negative rod bacteria.

They found that different bottle types harbored different amounts and kinds of bacteria.

True enough the re-usability of plastic bottles is quite a problem even in the area I live. This is due to multiple factors; one of those factors is the symbiotic microorganisms that could be living in your mouth (from my lectures)
as well as any contaminant from anything you've eaten$^1$. That however isn't the only thing that could be contaminating your water bottle. The exposure to the air itself may contaminate. (that's why in microbiology we use a laminar flow cabinet or work close to a flame).
That's also why hospitals have air purification systems to avoid infections$^2$.
As a result, the amount of possible contaminants are too big to list. We could list those that I personally think would be more relevant to list -- these include our mouth natural flora since saliva is the most common contaminant of reusable bottles:

lactobacilli;
Candida albicans;
enterococci;
Streptococcus salivarius;
Fusobacterium nucleatum;

List obtained from Almståhl et al.$^3$
Almost all of these microorganisms are associated with some sort of disease or another.
I didn't actually find any specific study on the reuse of water bottles so i apologize for not being capable of giving a more definitive reply.
Sorry if i have failed to answer your question in any way or have misinterpreted what was required, I hope my research was some help to you.
Citations:

(Mahvash Navazesh, DMD, Satish K.S. Kumar, MDSc1, Measuring salivary flow : Challenges and opportunities)
(W.D. Griffithsa, A. Bennettb, S. Speightb, S. Parksb. Determining the performance of a commercial air purification system for reducing airborne contamination using model micro-organisms: a new test methodology.
Almståhl A, Wikström M, Fagerberg-Mohlin B. Microflora in oral ecosystems and salivary secretion rates--A 3-year follow-up after radiation therapy to the head and neck region.

Thanks so much for the edit! It is indeed much better. I apologize for the noobish mistakes.

This is not a problem, but one of the strength of the stackexchange communities. People correct mistakes that happen. Welcome to biology, btw. :-)

Great answer here, +1 and I edited your other post - don't emphasize being a newbie. This style of answering is awesome and a lot better that the average user accomplishes here.

Really? I'm glad to hear that my way of answering is usefull, I have to admit I got corrected and the credits arn't all mine.

@Kiny - my first posts were not only edited; they were blandly shot to pieces. That's how people learn right :-)

@AliceD xD Had that happened to me i would totally learn to fear the community. I'm glad my teachers teach me properly!!

@Kiny and that is exactly my biggest concern of harsh reactions to new users. People need to be given the freedom and help to find their way.

Kiny - sometimes I still correct @AliceD's posts, 30k rep later (and even though I am relatively quite new) ;)

@BryanKrause - never too old to learn :-) Thanks for your efforts !

@Kiny I'm glad you're taking the edits in stride and learning from them. Just know we're all here to help each other learn :). And I agree with AliceD -- we like details and citations here! Good Answer :).


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What senses are active while sleeping?
During sleep, our body activity decreases. I am wondering on the extent of the lowering of this activity regarding our five senses. Clearly, the sense of touch is still very efficient since shaking a body is the most common way to awake someone, and hearing is also quite unaffacted (most, if not all, alarm clock, rely on this sense). Most deaths due to fire are due to intoxication rather than the burnt of the fire, so it suggests that smell and taste are pretty dimmed during sleep.
My main question: To which extent each sense is dimmed during sleep?
For example,

Can we smell during sleep? I don't remember having been awoken by the smell of something during my life...
Similarly, can we taste? If someone gives me delicious food during my sleep, would I be able to feel its taste and remember this experience?
Can we see? REM are well known but it is a mechanical feature of the sleep. Some people sleep with the eyes opened: what do they see?

Note: This related question tries to explain how senses are dimmed during sleep but not how much they are.
Note 2: I am aware this is person-dependant: any sound would awake my mother (a skill during my nightly escapades) whereas I would not notice a party around me when I am in deep sleep. But there should be some kind of average... It also depends on the phase of sleep; I am mostly interested in deep sleep and REM sleep, but an answer detailing every phase would be awesome.
Note 3: This question is certainly naive in its current form. Please help me to improve it.

Hmm, technically all senses are active, but their imput has "access denied"  to your "standard output" until certain variable intensity is reached, I think.

Certainly sight is active, at least to the extent of being aware of and woken by bright light, such as sunrise.

@Taladris - I think you'll be interested in this question I just asked, which is similar to yours but doesn't quite duplicate it.

The answer is of interest not only in sleep but also the perceptions of patients under anesthesia, comatose states, etc.
Our senses aren't 'dimmed' in sleep. There is no effective way to turn off our senses. The best way to explain what happens in sleep is that at some point (the last point, actually), our cognitive processing of sensations changes. That is, our higher brain functions allow us to ignore certain sensory input. This effect has been most studied in sound perception.
In a sleep study involving sound and EEG/fMRI during all phases of (drug-free) sleep,

The first significant result of this study is that the pattern of brain activation associated with auditory stimulation was strikingly similar in wakefulness and sleep, suggesting that sensory processing occurred in both conditions. However, we found qualitative differences in brain activation associated with auditory processing during sleep compared to wakefulness. The reduced regional activity during sleep, compared to wakefulness, in the left parietal and, bilaterally, in the prefrontal cortex, thalamus, and cingulate gyrus (part of the limbic system) suggests that these areas may be involved in the further processing and perceptual integration of sensory inputs likely to occur during wakefulness only.[1]

Supporting this is evidence that some sounds awaken someone no matter at what stage they are in sleep, for example, young mothers are woken up by their infants' lightest movements[2], and the fact that we respond to our own names in a similar fashion in sleep and in wakefulness, but such responses are not shown for presentation of other first names.[3]

These results suggest that the sleeping brain, during SII and PS, elicits a differential cognitive response to the presentation of the subject's own name, comparable to that occurring during wakefulness, and therefore that the sleeping brain is able to detect and categorize some particular aspects of stimulus significance.[3]
Thus, the results suggest that when subjects were listening to their own name during sleep some brain regions were selectively more responsive than in any other condition. ...we have demonstrated that the sleeping brain is able to process auditory stimuli. In addition, we postulate the existence of a functional network capable of detecting and facilitating processing of emotionally relevant inputs during sleep.[1]
Our results support the view that PS is not a state of "sensory isolation"; failure to respond to external stimuli during this stage may depend upon mechanisms occurring only after the sensory input has undergone cognitive analysis.[4]

However, as you noted, odors are not good at waking people up.

Some suggest that the human olfactory system during sleep is sufficiently well tuned to ensure arousal to such threatening stimuli as odors associated with smoke from fire. Our results strongly suggest otherwise. The intensity, strength, and noxiousness of the pyridine stimulus elicited behavioral arousal or EEG activation on fewer than half of stage 2 trials, less than one third of REM-sleep trials, and virtually no stage-4- sleep trials. This is a nontrivial lack of response, since pyridine is a component of coal tar and is also used as a herbicide for firewood, and thus is a likely by-product of many real fires. In practical terms, therefore, olfactory awareness in humans is low to absent during sleep, and human olfaction appears insufficiently sensitive and reliable to act as a sentinel system. We further note that auditory arousal threshold is highest in young and sleep-deprived individuals, increasing the likelihood that olfactory processing is even worse for children and sleep-deprived adults.[5]

The methodology in the olfactory study varies quite significantly from the auditory study. Better studies may shed more evidence on why olfactory stimuli are processed differently from other stimuli.
As to what percent? That probably differs from person to person, and I did not search the literature for that.
[1] Auditory Processing across the Sleep-Wake Cycle: Simultaneous EEG and fMRI Monitoring in Humans
[2] Changes in sleep patterns of young women from late pregnancy to postpartum: relationships to their infants' movements
[3] A differential brain response to the subject's own name persist during sleep
[4] Brain Processing of Stimulus Deviance During Slow-Wave and Paradoxical Sleep: A Study of Human Auditory Evoked Responses Using the Oddball Paradigm.
[5] Minimal Olfactory Perception During Sleep: Why Odor Alarms Will Not Work for Humans


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Did migratory birds' ancestors live in the places of migration?
I was studying birds' migration as a type of instinctive behaviour. But my textbook points out that other than for warm climate and easy food, migratory bird migrate to places where their ancestors lived.
Is it a real point? Or the writers just made it up.

An anecdotal comment, as it doesn't address your question about birds: This is the case in eels. European (Anguilla anguilla ) + American  (A. rostrata ) eels are sister taxa; both go to the Sargasso Sea to spawn. The working hypothesis is that the original N. Atlantic eel pop migrated through the Tethys Sea to the spreading Atlantic, and spawned in what would become the modern Sargasso. As the Atlantic Basin spread through continental drift, the 2 spp differentiated--but both still return to the Sargasso to spawn. ref: Aoyama, J. 2009. Aqua-BioSci. Monogr. (ABSM), Vol. 2, No. 1, pp. 1–42

do migratory birds have same kind of analogous history?

ancestors can refer to 2 generations ago and to 1000ds of years ago. that's why my interpretation of it was vague.

haven't the foggiest. @comprehensible -- I actually really liked your answer.

Edited for a different consideration: Do birds migrate to and from zones defined only by ecological and climate choice, or do they evolve to migrate away to and from an ancestral home?
Later studies of migration searched for evolutionary definitions of bird migration as opposed to ecology/geography definitions which were the initial focus. Various theories of evolution and migration have been developed, although ice ages and climate change make the definition of a bird ancestral land vague.
If you search google for "sister taxa, migration, evolution" you will find a lot
A study for American Thrush species starts with previous research:

range expansion and speciation for the
evolution of long-distance migration. In brief,
resident, tropical species expand their ranges
into the seasonal subtropics. Further range
expansion into temperate areas due to competition
and other selective pressures creates a partially
migratory species. The partially migratory
birds continue to expand into higher latitudes,
where they breed successfully; migratory behavior
becomes fi xed (Stiles 1980).

It's results for the thrush are very complex, and you can see the map and the conclusions at the end, which state that:

The migratory species tree does not have a clear single ancestor.
The ancestor's range was probably very widespread, over 1000ds of
kilometers.
They migrated by stepping stone, rather than by diet
constraints of being frugivorous versus insectivorous.

http://www.sonoma.edu/users/g/girman/outlawetal2003.pdf
also
http://www.bioone.org/doi/abs/10.1642/0004-8038%282007%29124%5B410%3AASROMM%5D2.0.CO%3B2?journalCode=tauk
The data is erased in history, the migration routes and maps are very complex, the ancestral homeland shifts as forests and boreal ranges change latitude, so it's a balance in between the ability for birds to have fixed ancestral lands, given their great mobility, and the speed of their evolution. For the moment there are some theories on mechanisms and causes for selection by migratory advantage which are not general enough to apply to many clades of bird.
for precise and recent return to homeland:
Yes it's absolutely true, that many birds return to the exact same nest in Europe for example after wintering in Africa, and they also return to the same cliff/forest as where their parents were born, and some species vaguely follow the flocks very broad zones:
One study showed that most swallows returned to the same colony, with 44 per cent of pairs reoccupying the same nest. “This is remarkable given the length of a swallow’s return migration from its wintering grounds in South Africa,” says Rob Robinson, associate director of research at the BTO. Robinson has studied this iconic species’ unusually strong nest-faithfulness, a phenomenon called natal philopatry.
https://en.wikipedia.org/wiki/Philopatry

I don't think your answer really answer s my question. have u read Kara's comment? My question is do migratory birds have same kind of analogous history?

some birds have specialized into migrators millions of years ago, like Geese, and some of them are more generalized species, like thrush, with recent ancestry that can be studied. There are geese in hawaii and S africa. The hawaiian goose may have evolved from an off-course flock that arrived there 500,000 years ago. euro and ozzy swan also demonstrates geography vagueness of bird origins, and euro small bird species ranges are normally pan european for 1000ds of km so it makes the geography of ancestry complex, same as eels except radiative/ ranges that change easily.

Now it's a very nice answer.

Thanks, someone knowledgeable about evolution of bird ecology would give a summary of different types of migrating species, coastal, forest, boreal, tropical, thrush, goose, range geography and climate change, which selective pressures are prevalent for temps and predators in different ranges and seasonal foods, and combine that knowledge with current research of migration genetics and evolution to give a very good text about it, it would be interesting to read an actual textbook chapter on evolution of migration with examples and theory. At my town have 1000ds HiRondElles which are martins.


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Why is there debate about thymus being an endocrine gland?
I read on my textbook that there is debate about whether thymus is an endocrine gland. But they do have glandular cells no? Is producing T Cells the only point for thinking it not as a part of endocrine system?
So, Q: What's the reason behind this debate and has it reached any conclusion?

In my mind as an immunologist, there is no debate. In order to be part of the endocrine system, a body structure needs to be a gland that secretes one or more hormones to induce signaling at distal targets. These hormones can have multiple chemical forms. However, the thymus does not do that. It was proposed beginning back in the 1960s that the thymus contained and produced something called thymosin, which was eventually separated in 40 separate substances, none of which acts as a hormone, and most of which are now known to be present in many other tissues. T cell production and maturation occur as a result of signaling induced by cell-cell interactions (ligands and cognate receptors on the cell surface) as well as the action of many cytokines and chemokines. These compounds are not classified as hormones, though.
It is possible that some hormones might be expressed in the thymus in very small quantities; however they are not secreted. This is due to a part of T cell development and maturation known as negative selection, where the thymus can ectopically express proteins typically only found in other tissues, such as the nervous system, pancreas, or lung, for example. This process allows for the removal of potentially auto-reactive T cells, which recognize self antigen.
Basically, knowing what we do about the function of the thymus in human and mouse, and how it does what it does, I honestly don't see how someone today could classify it as part of the endocrine system, even though histologically it may appear similar to glandular structures, and small traces of one hormone or another may be found in thymic extracts.

In short, yes the debate has reached a conclusion (years ago), and no the thymus is not an endocrine organ as it does not produce any real hormone.

@Armatus you are absolutely correct. Now, we just need to find an image to replace the one in the Endocrine system article on Wikipedia...

Well, I went and did it myself. Hooray for Photoshop!


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Does RNA-LPX expression of antigen by DC induce only T-cell with that antigen specificity?
There was a recent publication concerning use of IV administered RNA-lipoplexes with an adjusted electrical charge to encourage dendritic cells (DC) to pick up the RNA package encoding viral or mutant neo-antigens, for example, a sequence of melanoma tumor cell coded to RNA. The paper is at Systemic RNA delivery to dendritic cells
After reading that abstract and related papers (see Dendritic Cells Pulsed with RNA are Potent Antigen-presenting Cells In Vitro and In Vivo By David Boczkowski et al I came away with the concept that the RNA segment of encoded tumor protein was taken up by a DC and the DC translated that to a protein (antigen) that it presented with MHC of the appropriate class (class I I believe in these tests) to a naive T-cell, which would subsequently amplify and pursue and kill tumor cells with that antigen (by becoming CTL cytotoxic T cell leukocytes).
A quick look at my immunology text from NIH tells me that this mechanism (DC's bringing antigen to naive T-cells in lymphatic tissue) ensures "that rare antigen-specific T cells will encounter their specific antigen on an antigen-presenting cell surface."
My question is does this mean that the so-called "mutant neo-antigen" of a particular tumor in an individual must still find a T-cell receptive to that sequence (epitope) at least in part (say fractionally)? I guess I'm wondering whether there might be the case where a particularly diabolical tumor presented such novel sequences that no existing T-cell rare or otherwise could be receptive to a fraction of its sequence (even when a customized RNA delivery of a selected portion of the sequence was delivered via DC to the T-cell).

After I posted this I looked at link and more or less answered my question. I gather I'm supposed to wait 24 hrs before answering my own question. Preview: Computer methods are used to identify sequences from a tumor mutanome that are likely to express non-synonymous protein present in a peptide presented on MHC molecules, so it is likely at least one mutated epitope would be immunogenic (T-cell druggable).

The OP (me) was unclear whether or not the new therapy had to ultimately present antigen specific to a particular naive T-cell. The answer is yes: Each T-cell is specific for a single antigenic determinant. An antigenic determinant is a small portion of an antigen, such as a certain sequence of amino acids in a protein, that the immune system (a T-cell receptor in this case) recognizes as non-self or altered self. The antigenic determinant is also known as an epitope. Typically an antigen has many different epitopes, each able to react with a specific antibody or T-cell receptor (when presented with MHC).
The confusion arose from the description of the RNA as encoding "mutant neo-antigens" (among other possibilities, e.g., viral or endogenous self-antigens). At first glance this seemed to imply that a tumor antigen constituting a novel polypeptide antigen ("mutant neo-antigen") was able to induce T-cell response (effector and memory T-cell responses) in the absence of any T-cells with a T-cell receptor specific to that neo-antigen. That would not be possible.
Through somatic gene rearrangement in development, T-cell receptors (TCR)  have a wide range of antigen specificity, such that each T-cell has a unique receptor on its surface able to recognize foreign protein antigen associated with MHC molecules. Some estimate that human TCR and antibodies can respond specifically to 10 million different antigens.
Apparently the distinction is made between classical tumor-associated antigens that typically constitute autoantigens (which may appear frequently on the surface of cancer cells in conjunction with MHC and therefore generate some antibody response, possible ineffective) and neo-epitopes, the latter being the result of the estimated 25 – 30% of antigenic mutations (mutations not normally found in the genome) in tumors that could be made to induce immune response on the single- or poly-epitopic level. It appears that autoantigens are more modified normal protein that tend to appear somewhere in the disease process on a particular class of tumor than the result of entirely novel mutations. Since tumors usually have tens to hundreds of non-synonymous mutations, the mutanome of a tumor provides many possible targets for custom poly-epitope vaccines for each individual patient. Coding messenger RNA (mRNA), i.e., synthesizing mRNA to encode multiple transcripts for synthetic poly-epitopic nucleotide sequences, is an attractive antigen delivery format.
In order to locate a sequence that would be likely to act in this capacity (that is, to select tumor mutations likely to exhibit immunogenecity), an approach like the following serial selection has been suggested: (1) next generation sequencing (NGS) of an patient's individual tumor mutanome and patient genome (2) identify triplicate sequences present in the tumor mutanome but not in the patient genome, i.e., identify the mutations in the tumor that distinguish it from normal self (3) identify those mutations that are likely to code for a protein (4) identify those mutations that are likely to cause a non-synonymous protein change (5) identify those mutations meeting all the previous criteria that a predicted to be in a peptide presented on tumor MHC. An example quantifying this selection process is that of the murine B16F10 melanoma mutanome: The NGS exome profile (coding exons) predicted 12,842 mutations; 3570 of those predicted as somatic mutations; non-synonymous mutations 962; mutated peptide predicted to bind MHC 462; 50 of those selected for testing and of those 50, about a third of those tested strongly immunogenic when encoded to RNA and transfected to dendritic cells, i.e., inducing strong T-cell response. As a test of actual anti-tumor effect, mice were immunised with the encoded mutations identified and achieved complete tumor protection and survival in 40% of the group, compared with death of all control group animals.
Generalizing, a poly-epitopic vaccine formed from a tumor mutation should be selected to be specific to the tumor and not in the patient germline genome, to occur in a protein-coding transcript, to cause a change in protein sequence and that protein be expressed in tumor cells. In order for the mutation to induce a robust T-cell response, the mutation-containing epitope must be presented on the patient's MHC molecules in the dendritic cells during vaccination (and at least one T-cell must possess a receptor specific for one of the epitopes) and in the tumor cells for recognition (on the surface of the tumor cells). With the patient HLA haplotypte, MHC-binding epitopes can be predicted with computer algorithms. The immunogenecity of the computationally predicted epitopes can be tested in vitro with T-cell stimulation.
One of the challenges to RNA delivery has been degradation by ubiquitous extracellular RNAses. The study noted [Systemic RNA delivery to dendritic cells] solves that issue by protecting the RNA with lipid carriers to form RNA-lipoplexes (RNA-LPX). This has the additional adjuvant effect (the RNA-LPX) of triggering interferon-a (IFNa) release by plasmacytoid DCs and macrophages in a manner similar to early phases of viral infection.

I would hesitate to say the liposomes "solved" the problem of protecting the RNA in circulation. It definitely helps though. mRNA delivery is a pain, but the study here probably benefited from liposome formulation's tendency to accumulate in liver and spleen. All of these nanoparticles tend to accumulate in those organs.

@user137 Good point. I just read Sahin's 2013 patent application at https://www.google.com/patents/WO2013143683A1?cl=en and that did make clear the difficulties you allude to, although Sahin's method of creating nanoparticle liposomes with electro-neutral or slightly negative charge apparently targets the spleen preferentially over other organs. This is the desired end if you want to get an RNA antigen payload to professional APCs without damaging other organs like the liver and lungs. Thanks for the clarification.

@user137 ...and the Sahin neutral or slightly negative liposomes seem to have some of the advantages of PEGylation in decreasing the RES (reticuloendothelial system) clearance of lipoloplexes from blood, which may have been more of the central thrust of your comment, i.e., that nuclease degradation (protected by lipoplexes) is only one component of the problem of protecting the RNA in circulation (so I was indeed a bit optimistic earlier).

As of December 22, 2020 both the Moderna and Pfizer RNA vaccines for the original COVID-19 are carried by lipid nanoparticles with PEG (polyethylene glycol). One can only hope they can move quickly with the UK variant that has just appeared with modification to the spike protein that is targeted by these two RNA vaccines.


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Repeating sequences of genomes
How can we estimate what portion of a genome is repeating sequences without sequencing it?
Thank you

I'm pretty sure that's not possible. Without knowing the sequence of a genome (which means someone has to sequence it), you can't really know which parts are repeats.

@Nicolai This is one of my study questions, so there must be some way to estimate, although I am clueless to how this could be done.

This site has a policy for homework questions, so you should probably edit your answer to show your previous effort to answer this yourself. I can't think of any experimental way to this (but it might be possible), so the best estimate is probably by comparison with related genomes, that have been sequenced.

No, it isnt a homework question, its for study review

Yes, it is possible to estimate the amount of repetitive DNA in a genome without sequencing. This was an important technique in the 1960s, referred to as C₀t analysis and pioneered by Roy Britten.
The approach taken is to study the kinetics of renaturation of heat-denatured genomic DNA (in a fragmented form). As you can see in this idealised Figure taken from the Wikipedia article on the technique there are components which renature rapidly whilst other components renature more slowly:

The interpretation of this is that repeated sequences renature rapidly because they are at a higher concentration than are single-copy sequences.
As stated at the linked Wikipedia article:

...it was through C₀t analysis that the redundant (repetitive) nature of eukaryotic genomes was first discovered.

And finally here is a quotation from Britten and Kohne's 1968 paper in Science:

The rate of reassociation of the complementary strands of DNA of viral and bacterial origin is inversely proportional to the (haploid) DNA content per cell. However, a large fraction of the DNA of higher organisms reassociates much more rapidly than would be predicted from the DNA content of each cell. Another fraction appears to reassociate at the expected rate. It is concluded that certain segments of the DNA are repeated hundreds of thousands of times. A survey of a number of species indicates that repeated sequences occur widely and probably universally in the DNA of higher organisms.

In agreement with @Nicolai, I don't think you can!
Of course, if you assume having a priori knowledge about the fraction of repeated elements in related organisms, you could try to estimate it. Typically, if you consider a angiosperm, you know you're going to have much more repeated elements than if you consider a bacteria. Also, the size of cells and the size of the nucleus are correlated with the genome size (Gregory 2001) and the genome size is itself correlated with the number of repeating sequences (Flavell et al. 1974, Bennetzen et al. 2005). However, those correlations are pretty lose and it will not be possible to be accurate with these methods.


text:
Why is only one primer used for DNA sequencing instead of two?
I understand that PCR uses two primers that anneal to the two ssDNA's in order to exponentially amplify a DNA and that Sanger sequencing uses only one primer because a sequence can be determined with only using one primer and one single-strand with ddNTPs. However I've read this:
"Sequencing uses one primer, while PCR utilizes two. If we try to sequence with two primers present, you'll get the two sequences back, superimposed on each other and completely unreadable."
I'm struggling to visualize why using two would be an issue though, how will that make the DNA unreadable?
Thanks in advance!

The reaction for the Sanger sequencing reacting contains beneath the normal dNTP (which are needed to make most of the DNA) the dideoxynucleotides, which lack the 3'-OH-Group and which are labelled with a fluorescent dye. Once one of this nucleotides is incorporated, the chain reaction stops here, leading to a product with a specific length and a known (by the fluorescent dye) end base.
In theory this leads to products of a length primer + 1 ddNTP base, primer + 1 base + 1 ddNTP base, primer + 2 bases + 1 ddNTP base and so on. The sequencer seperates these bases by sizes and the sequentially reads out the fluorescent dye and translates this into a sequence of bases. See the image from the Wikipedia for illustration:

If you now add two primers (and of course have a double stranded DNA), this reaction will start from both ends of the DNA (always in 5'--> 3' direction) leading to two sets of marked DNA of the same size (so again the base + 1 ddNTP, base + 1 base + 1 ddNTP and so on). Since these are equal in size, you will always read out two bases at the same time and you will not be able to tell, which signal belongs to which strand. This looks like this (from here):


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Are there ways to genetically increase mutation rate of E.coli?
Are there ways to increase mutation rate of E.coli using genetic modifications? I know possible ways it can be done without genetic modifications by exposing the cells to stressful conditions like anaerobic and radiation but what are some genetic ways?
Thanks!

Mutations are caused by the insertion of the wrong bases during replication, or by chemical changes to bases, either by chemical agents or by radiation.
The rate of mutations could be increased by exchanging the E.coli polymerases with other polymerases displaying higher error rates (or with less proofreading capabilities). A lot of errors are quickly repaired via different mechanisms, knocking out all or a few of those mechanisms might result in an E.coli strain with an increased mutation rate (if they survive).
https://www.ncbi.nlm.nih.gov/books/NBK9900/
A more elaborate way would be to engineer E.coli to contain a pathway that synthesizes a mutagenic compound. The easiest way to to this would be 1 enzyme that generates reactive oxygen species, as those also cause DNA damage. You could also delete some of the catalases and other enzymes that remove reactive oxygen species instead.
https://www.ncbi.nlm.nih.gov/pubmed/16824196


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How medical studies induce cancer in lab animals?
To test the effectiveness of drugs, they are typically tested on animals. How cancer is induced in lab animals to test the effectiveness of cancer drugs?

That depends on the cancer. There are many mouse models which are susceptible to develop cancer or can be induced to do so. This might be a starter: https://www.ncbi.nlm.nih.gov/pubmed/20936938 Another way is to inject cancer cells from humans into immunodeficient mice, which then can be able to "settle" and grow.

What is the success rate of cancer transfer from human to mouse method? And why not extract cells from the mouse,   induce cancer in vitro and place them back in original organ? In this case there will not be any immune response?

I am not an expert, otherwise I would have written a full answer. You can induce some cancers directly in genetically susceptible mice, but not all of them. Also, doing that many operation on small mouse organs is quite likely to kill them before they develop any cancer (not speaking of the ethical implications of the amount of additional discomfort they would have to endure).


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Is it better for a person's stomach to have 1 big meal or 2 small meals? Does this change as a person gets older?
Is it better for a person's stomach to have 1 big meal or 2 small meals? Does this change as a person gets older.
Also what about water? Is it the same way or different and why?

How do you define 'better'?

"Also what about water?" Try drinking all you daily water in one go. Your body will instantly let you know it's not okay with that.

I’m voting to close this question because it is both unclear (see comment by @user438383) and seemingly asking for a medical opinion. Please take the [tour] and then consult the [help] pages for additional advice on [Ask] effective and appropriate questions on this site and then delete or [edit] your post accordingly.


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What types of spider and caterpillar are these, and what are they doing?
What varieties of spider / caterpillar(?) are these?
And what is the spider doing to the caterpillar?
This is in Texas.
This went on for hours, with the spider dancing with the caterpillar in the spider web where the caterpillar was caught. After 10+ hours, this morning, I found the caterpillar -- still intact -- curled up on the ground beneath. Was the spider sucking the juice out of it or something? I don't understand what parts of it, if any, was consumed by the spider.

Are you aware how spiders eat?

@DKNguyen Probably not by sucking the juices/blood out of its prey like a mosquito? Which is why I was particularly confused, as the spider didn't seem to be 'eating' it. Now the caterpillar is just dead. So I'm not sure what the spider did to it..

Not like that no. I assume you're younger if you're not aware, but they do drink their victims. Spiders pump digestive enzymes into the prey to externally digest it then drink it, whereas you ingest your prey and the digestion is done internally.

Thanks! I did not know this. I also looked this up just now, and yes, that's in fact what happened: "When feeding the spider regurgitates enzyme rich stomach fluids over and into its prey. This external digestion... reduces the prey's body and tissues to a chitinous soup. The liquid is sucked up through the spider's tube-like mouth, aided by the action of the pumping stomach, leaving the hard parts behind. Spiders... inject digestive fluids into the bitten prey and suck out its liquefied internal tissues, leaving an almost intact body husk behind." (src: australian.museum) @DKNguyen

The spider is a cobweb weaver - family Therididae (can be determined from the bulbous abdomen, thinness of legs and small cephalothorax) and appears to be Steatoda triangulosa from the brownish colour, white markings on the abdomen, and rings/annulations on the legs. S.triangulosa is found widely across North America and Europe.
The prey is not a caterpillar but a myriapod, I believe in the order of flat-backed millipedes.
As @DKNguyen already answered, the spider was preying on the millipede. The 'dancing around' was the spider trying to subdue the prey by wrapping it up in silk, but for prey that size, it takes a long time to get enough silk on it to hinder its movements.
Once the spider gets a meal out of the prey, they detach it from the web and let it fall to the ground below. This is often a way to detect when you have a cobweb spider in a corner or under a stair or something - when you see a clutter of dead bugs. The clutter also tells you that the spider is helping take care of pest control while staying in one spot.

Spiders pump digestive enzymes into the prey to externally digest it then drink it, whereas you ingest your prey and the digestion is done internally.
That's not even the only way animals eat...starfish bring their stomachs out of their body onto their prey and digest the prey there. Might seem even weirder, but arguably less roundabout than the spider's method.

I dunno about that. Regurgitating your stomach to surround a victim outside of your body would seem to be a very risky proposition; it could be damaged. I’ll take my meal with a straw, please, like the early astronauts.

@anongoodnurse I think it is less like a straw and more like throwing up on your food, letting it sit and then drinking it up.

Ooooo, that does sound awful indeed, but safer for keeping my stomach out of harm’s way. I saw this once at a tiny aquarium in Maine. Fond memories! (Ugh.)


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Why does the concentration gradient of one ion represent the entire cell in the equilibrium potential of an ion?
The Nernst equation for the equilibrium potential of an ion(in this case potassium),
$$E_{eq,K^+} = \frac{RT}{zF} \ln \frac{[K^+]_{o}}{[K^+]_{i}}$$
includes the ratio of the concentration of that specific ion outside of the membrane to the concentration inside. If this is for calculating the diffusional force, why does it ignore other ions? Wouldn't the concentration of other ions inside and outside of the cell also affect this ratio?
For example, some ion might be more abundant inside the membrane than the outside, but some other particle might be more abundant outside, thus creating no diffusional force. However, in the equation this will be taken as if this does indeed generate a force, since it only takes into account the ion more abundant inside.

Welcome to Biology StackExchange. Cross-posting is generally not desired on StackExchange.

Just add up everything of interest. For example, you can include sodium as

which gives you

chlorides, and everything else could be further added in a similar fashion, although likely to diminishing effects. These equations and numbers are from page 107-108 of From Neuron to Brain.


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Enzymes and Digestion
If biological enzymes (protease,amylase,lipase etc.) just speed up the reaction (in the digestion process), then what actually digests the food?? (I'm a secondary student)

Welcome to Bio. The enzymes do, what else?

@Christiaan What do you mean, enzymes actually digest the good?? Like, the definition of a biological enzyme is that its a catalyst made of protein that speeds up the reaction in digestion. That suggests that another substance actually breaks down the food. Am I right, or am I not getting it correct??

Compounds like proteins and nucleic acid have a natural half-life in an aqueous environment, for example in Belle et al: for ~3,700 proteins in a budding yeast proteome, median half-life of proteins was about 43 minutes. Of course they differ and some proteins can last hours.

The enzymes break down the food.

@Christiaan So why it is said that it "speeds up the reaction" rather than "digesting it" ?  (Sorry if i'm not getting it)

In general, catalysts, and hence enzymes, only speed up the process of reaching equilibrium. Proteins inherently have the tendency to degrade through hydrolysis. The only thing an enzyme does is promote the establishment of that equilibrium. No more, no less. Hence, enzymes speed up a reaction that would occur anyway. Admittedly, it's not the whole story, e.g., ATP-powered enzymes can actually shift the equilibrium.

Reminds me of school days when I was fascinated about the exact same thing. My school bio teacher parried away by saying the stomach does it mechanically!! But the actual answer which is given below, I learnt after high school chemistry and thermodynamics. If the free energy change is negative for a reaction, it is spontaneous but not necessarily instantaneous. You need to get the difference. The reaction is possible but just doesn't happen because of the very high activation energy. Such high amount of activation energy can't be delivered in the body by heat, so enzymes do the work.

I suspect that the question reveals an incomplete understanding of enzymic catalysis and could more generally be rephrased as "If enzymes just speed up biological reactions, what makes the reactions proceed in the first place." The simple answer to this is the fact that the thermodynamics of the reaction are favourable, i.e. the reaction involves a negative change in (Gibbs) free energy.
So what is stopping the reaction proceeding at a reasonable rate without catalysis? The fact that the thermodynamic path of reactions involves an activated state with a higher free energy. In most cases this is sufficiently large that it acts as a barrier to spontaneous reaction. You can get over the activation barrier by e.g. supplying heat (i.e. supplying activation energy) but this is not possible in living organisms. Enzymes act by lowering the activation energy (energy barrier) or raising the ground state (which in effect decreases the activation energy).
One should realize that "just speeding up the reaction" is generally increasing the reaction rate from being negligible to biologically sufficient. So what makes the reaction go is a combination of the reactants being there with a favourable chemistry and the enzyme being there in the right place to deal with them.
If you are unfamiliar with this basic reaction chemistry see:
http://www.ncbi.nlm.nih.gov/books/NBK22384/#A1100
and the image below from Wikipedia.


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What is the difference between [Clinical Trials as Topic] category and [Clinical Trial [Publication Type]] category in pubmed?
Dears in biology stackexchange community, I hope that everyone is fine.
I am using pubmed in my current review. My focus is about an application on the scope of Clinical Trial. When I used MeSH for narrowing my research scope on Clinical Trial, I got two different categories which I cannot find any clear difference between them. They are:

Clinical Trials as Topic
Clinical Trial [Publication Type]

However, when I search on the two different categorises, I found very different resulted papers. That means that there are a difference between the two categories where my ignorance is.
Could you please tell me what is the difference?
Possible examples of two queries:
1. ("Clinical Trial" [Publication Type]) AND "Prostatic Neoplasms"[Mesh]
2. ("Clinical Trials as Topic"[Mesh]) AND "Prostatic Neoplasms"[Mesh]
Many thanks to you for your time, in advance.

The actual definitions provided with the MeSH terms look essentially interchangeable:
Clinical Trial as Topic:
Works about pre-planned studies of the safety, efficacy, or optimum dosage schedule (if appropriate) of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects. This concept includes clinical trials conducted both in the U.S. and in other countries.
Clinical Trial [Publication Type]:
A work that reports on the results of a clinical study in which participants are assigned to receive one or more interventions so that researchers can evaluate the interventions on biomedical or health-related outcomes. The assignments are determined by the study protocol. Participants may receive diagnostic, therapeutic, or other types of interventions. While most clinical trials concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans.
But the difference is simple. CT as Topic refers to publications that talk about Clinical Trials in general, as a subject itself. But CT[Publication Type] refers to an article that is actually reporting the results/analysis of one or many clinical trials.
To show you what I mean, these are first PubMed results using the two MeSH heading, when you specifically tell the search engine to not include other branching MeSH terms:
Clinical Trial as Topic:

Clinical Trial[Publication type]:

Dear Maljam, many thanks for your kind, generous and clear answer. You helped me a lot, bless you.


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What has caused my oxeye daisies to mutate?
Some oxeye daisies (Leucanthemum vulgare) in my garden are showing strange mutations. I have a few oxeye daisy plants around my garden in different areas, but only one plant's flowers are showing these mutations. When I search 'oxeye daisy mutation' on Google, this specific mutation does not appear. I will attach three pictures to show this on three different flowers, but there appears to be a new flower growing out of the yellow middle of the daisy. Was this caused by a genetic mutation? Maybe an infection?

This is a known phenotype, including among asters (see also here), known as "doubling" or "double flowering". In the model plant Arabidopsis thaliana, it is well described as a homeotic transformation related to a genetic mutation:

The first documented double-flowered mutant of Arabidopsis, a model organism for plant development and genetics, was recorded in 1873. The mutated gene likely responsible for the phenotype, AGAMOUS, was cloned and characterized in 1990 in Elliot Meyerowitz's lab as part of his study of molecular mechanisms of pattern formation in flowers. [link to Meyerowitz paper]

One paper in a Ranunculus has a very nice figure reproducing the AGAMOUS connection in a doubled ornamental cultivar:

Other work in such species as primrose does show the kind of variable penetrance for sepal-->petal conversions ("Hose-in-hose" phenotype) such as we see here for a homeotic mutation (called "revertant"/"semi-revertant"):

The cause of this variable penetrance appears to be transposon hopping out in the mutant. Unclear whether that could also be true in your case.
The fact that multiple flowers from the same root stock show the same phenotype argues that it is common to the plant, and not just a stochastic event. What actually causes it would take some molecular work to prove, but given the repeated emergence of this heritable phenotype across many different kinds of flowers across centuries, genetic mutation is certainly the leading explanation from available data.
Granted, genetic mutation is not the only cause of this kind of homeotic transformation. At the end of the day, these kinds of mutations are the result of ectopic expression of a gene- and that ectopic expression is, as pointed out in other answers, not necessarily heritable or genetic. This may include viral expression, or even insect galls.
I'd suggest that you could narrow it down to heritable or non heritable by collecting seeds from your plant and sowing them in various locations, and seeing if you get stable inheritance across locations (or stable proportions of inheritance).

Collecting seeds is a great suggestion, and might be the best way to determine the cause of this "abnormal" expression. One question (may not have an answer): why aren't all the flowers affected similarly? (Some have more ray flower expression than others, and some are normal.) Asteraceae and Rosaceae have the highest aphid burdens (of flowering plants) and the viruses they carry spread like they do, kind of contiguously. The plasticity of expression seems to me to be consistent with a virus, but I truly don't know. Purely guessing here.

@anongoodnurse thanks for comment- I added some more examples, including one example of a floral homeotic mutation with variable penetrance driven by transposition. Interesting topic! There seem to be a lot of possible mechanisms.

It is interesting! Lots of research on commercial plants but not so much on ornamentals. Very nice answer. The primrose info is very supportive.

Keep in mind that not all unusual forms come from mutations.  In addition to the previous answer that MadaboutMonarchs suggested, it may be just a developmental glitch, maybe due to insect damage or other injury (unless it appears on more than one flower,... then likely genetic).

Re the parenthetical at the end of the answer, the original question states that the unusual flower form appears on multiple flowers (of a single plant).

It's likely not a mutation, but rather a change in gene expression. Other asterids (like Chrysanthemums) like your daisies, have two different types of florets, rays and discs. The rays are the white florets and the yellow are the discs. Environmental factors can effect whether a floret expresses as a disc or ray, even if it typically expresses as the other.
https://link.springer.com/article/10.1186/s12864-016-2733-z

Your reference notes difference in expression between the tissues, but it does not seem to support a model in which only gene expression would lead to the observed homeotic transformation. Do you have other evidence for such a regulatory change underlying a homeotic transformation/morphological change in the floral body plan?

Hi and welcome (apologies if this comment seems unwelcoming.) On any science site, being able to interpret the literature you use as a source accurately is paramount. The source you cited does discuss differences in expression of appropriate disc flower and ray flower tissue, but states nothing about abnormal expression. As @MaximilianPress asked, please back up your answer about abnormal expression with a better source. Thanks. ...

...Clearly it's about a change in expression (there's no other way to get such an anomaly), but what caused this change? A virus/bacteria/fungus/injury/mutation/other?


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Doubt regarding the existence of a life form unrelated to all the other life forms
Primitive life on earth began from a mixture of complex organic compounds which were formed millions of years ago which evolved and gave rise to all the current species. So is it possible that another form of life may have evolved in the past or may be evolving currently from a different mixture of organic compounds leading to organisms simple or complex totally different from the organisms we know having no common ancestry?

Welcome to SE Biology. Please finish reading the [Tour] to find out how this site works, and the Help on asking questions. One thing you should check before posting is whether a similar question has been asked before, by using the search facility. If you had done this you would find that there are several variants on your question. Also note that the Indian English “doubt” is not British or International English. Use “question”.


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What is this huge mosquito looking insect?
This is on top of a refrigerator on my porch in North Carolina about 45 minutes from the coast. I’ve never seen anything like it!

A moskote obviously

Related: https://biology.stackexchange.com/questions/95599/what-is-this-giant-mosquito-like-insect

Looks like a Diogmites robber fly, but I'm not great at robber flies so it could be a different species.

See more images at Genus Diogmites - Hanging Thieves


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Extracting amino acid sequence from WGS data
I would like to know, given a dataset of WGS data, what tools can I use to identify the coding regions within the DNA sequence and then convert them into amino acid sequences?

Welcome to the Biology Stack Exchange. Please take a [tour] and visit the [help] for more information on this site and how it works. Please note the homework policy. Because this is a very basic bioinformatics question it is something that your supervisor or other person in your lab, or any basic text should be able to answer.


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Why certain COGs appears more often in Humans Bacteria but not in plants Bacteria
I'm doing a Bioinformatic project from the university where I  got a DB of COGS from Human & Plants Bacteria genomes and I need to find distinguishing sets in this DB and explain the biological reason behind these results. Unfurtinly my Biologi knowledge is very basic and I do not know how to explain the results so maybe someone here could help me.
Here are some of the distinguishing COGs I found and the known info about them:
Results for FreqItem: ['0049', '4465']
IG of FreqItem:  0.6682341035127484
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG4465;K;INFORMATION STORAGE AND PROCESSING;Transcription;GTP-sensing pleiotropic transcriptional regulator CodY;
Number of occurrences in Human Bacteria genomes: 63
percentage of genomes that carry it in Human Bacteria genomes: 25.0%
Number of occurrences in Plant Bacteria genomes: 4
percentage of genomes that carry it in Plant Bacteria genomes: 5.56%

Results for FreqItem: ['0049', '3833']
IG of FreqItem:  0.6952252521930348
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG3833;G;METABOLISM;Carbohydrate transport and metabolism;ABC-type maltose transport system, permease component;
Number of occurrences in Human Bacteria genomes: 109
percentage of genomes that carry it in Human Bacteria genomes: 43.25%
Number of occurrences in Plant Bacteria genomes: 8
percentage of genomes that carry it in Plant Bacteria genomes: 11.11%

Results for FreqItem: ['0049', '1847']
IG of FreqItem:  0.7334916442185917
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1847;R;POORLY CHARACTERIZED;General function prediction only;Predicted RNA-binding protein Jag, conains KH and R3H domains;
Number of occurrences in Human Bacteria genomes: 122
percentage of genomes that carry it in Human Bacteria genomes: 48.41%
Number of occurrences in Plant Bacteria genomes: 9
percentage of genomes that carry it in Plant Bacteria genomes: 12.5%

Results for FreqItem: ['0049', '1115']
IG of FreqItem:  0.6323046964671385
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1115;E;METABOLISM;Amino acid transport and metabolism;Na+/alanine symporter;
Number of occurrences in Human Bacteria genomes: 161
percentage of genomes that carry it in Human Bacteria genomes: 63.89%
Number of occurrences in Plant Bacteria genomes: 15
percentage of genomes that carry it in Plant Bacteria genomes: 20.83%

Results for FreqItem: ['4585']
IG of FreqItem:  0.3643909812004458
COG_INFO semantic description per each COG in the itemSet if exist:
COG4585;T;CELLULAR PROCESSES AND SIGNALING;Signal transduction mechanisms;Signal transduction histidine kinase;
Number of occurrences in Human Bacteria genomes: 118
percentage of genomes that carry it in Human Bacteria genomes: 46.83%
Number of occurrences in Plant Bacteria genomes: 49
percentage of genomes that carry it in Plant Bacteria genomes: 68.06%

Results for FreqItem: ['0049', '1006']
IG of FreqItem:  0.8034282332952798
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1006;P;METABOLISM;Inorganic ion transport and metabolism;Multisubunit Na+/H+ antiporter, MnhC subunit;
Number of occurrences in Human Bacteria genomes: 50
percentage of genomes that carry it in Human Bacteria genomes: 19.84%
Number of occurrences in Plant Bacteria genomes: 23
percentage of genomes that carry it in Plant Bacteria genomes: 31.94%

Thank you for your time!

Bacteria in human and plants are adapted to different life conditions: different food and different environment. E.g., human gut bacteria are more likely to be anaerobic and adapted to processing organic food. So I would search in this direction (disclosure - I am not a biologist either.)

The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Unresearched questions may be subject to down-voting and closure. Please see our homework policy for more information.


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When was peptidoglycan discovered?
I've searched for some time now, but I can't find a definitive answer. The closest I have gotten is "knowledge about peptidoglycan structures dates back to the 1970s–80s" from this paper.

This is a not really a good question for this site — and if you ask better questions please put them in the question rather than the assume we remember the title. The reasons are 1. The purpose of this site is not to construct a chronology of the discovery of every biological compound, 2. Nobody on this site knows the answer to that sort of question without doing a search, 3. You can easily find it yourself — search “dictionary peptidoglycan” — and choose a reputable primary dictionary from the results. I chose Merriam Webster and it gave me 1966. For a citation you might need to look further.

@David not sure what your qualm is with the question. If people have this question, they can look at it, otherwise they can just as easily not open this thread. This site even provides a history tag, so it seems that this falls within the meta. Additionally, Merriam Webster does give 1966 but it’s very vague and unconvincing (and I had looked at this before posting). I asked simply because the answer seemed complicated, and would probably be best answered by someone with knowledge of the topic.

First, tags do not define what's on topic and whether a question is satisfactorily presented. That is explained in the [Tour] and the Help. (Not sure what you mean by "falls within the meta".) There are circumstances where a question about the history of biology is on topic, but, as is clear from the Help on Asking Questions you need to make it generally relevant and provide context. As you had not done this I explained how to find the answer. The aim of the site is to build a library of questions about biology that are of general use.

https://pubs.acs.org/doi/pdf/10.1021/bi00879a016?casa_token=L-dTOhCAdyUAAAAA%3AMkJotlvSnQXk9gL1gkdl7DkOgSi25bNmMWO-OOxffK3qFFEo_mdXfmRHOk4PbItEf5ZYnIa7N5mtISw&

The discovery of peptidoglycan, as present in the bacterium cell wall took many years.
“The terms mucopeptide, glycopeptide, or murein, used by some authors, are all synonymous with peptidoglycan.” [Ghuysen, J.M. (1968) Bacteriol. Rev. 32:425-64] Among those, Weidel and Pelzer previously coined the term murein [Weidel, W. and Pelzer, H. (1964) Adv. Enzymol. Rel. Areas Mol. Biol. 26:193].
Regarding the organized, higher structure of the peptidoglycan as found in the Gram-negative cell envelope, Salton [Salton, M.R.J. (1994) New Compr. Biochem. 27:1-22] mentioned the following:
“The exact nature of comparable ‘wall’ fractions obtained from Gram-negative bacteria remained a matter of uncertainty until the advent of electron microscopy of ultra-thin sections of bacterial cells as demonstrated by Ryter and Kellenberger [Ryter, A. and Kellenberger, E. (1958) J. Biophys. Biochem. Cytol. 4:671-678.]. The response of cells to the Gram stain procedure and the early chemical analysis of ‘cell wall’ preparations clearly pointed to some basic differences in the properties of the envelopes of Gram-positive and Gram-negative bacteria and the greater chemical complexity of the isolated fractions from the latter organisms [Salton, M.R.J. (1953) Biochim. Biophys. Acta 10:512-523.]. The structural complexity of the Gram-negative cell envelope was clearly resolved in the thin sections of Ryter and Kellenberger [Ryter, A. and Kellenberger, E. (1958) J. Biophys. Biochem. Cytol. 4:671-678.] and established the presence of an outer membrane as a characteristic feature of the cell envelope. The mysteries of the structure of the Gram-negative cell envelope were finally solved with the demonstration of the thin layer (peptidoglycan) between the outer and inner (cytoplasmic) membranes by use of lanthanum-stained thin sections by Murray et al. [Murray, R.G.E. et al. (1965) Can. J. Microbiol. 11:547-560.], and the isolation and demonstration of the thin murein sacculus of E. coli by Weidel et al. [Weidel, W. et al. (1960) J. Gen. Microbiol. 22:158-166.]. Thus, the complex cell envelopes of Gram-negative bacteria were resolved as consisting of an outer membrane anchored to the underlying rigid, thin, peptidoglycan layer or sacculus.”


text:
How do humans detect temperature differentials on the skin?
I just read this question on Physics SE about how the body detects cold or warm surfaces. As someone who already understands how heat flux devices like thin film gauges and thermocouples work (by exploiting the known relationship between temperature gradients and electrical/thermal properties of the relevant materials), I was actually more interested in how the nerve endings in my body actually implement this.
When I touch something warm or cold, what is the nervous mechanism that causes the correct signal to be sent to my brain, causing me to perceive a hot or cold surface?
How is the "thermocouple", which tells me whether a surface is hotter or colder than my finger, implemented?

Related: https://biology.stackexchange.com/questions/28520/do-humans-perceive-temperature-or-heat-flux-or-both

Sensory neurons in the skin express TRP channels such as TRPV1 channels, TRPM8, and others (see Voets et al 2004 for more information on how these channels work). Different sensory neurons express different combinations of TRP channels .
Changes in temperature shift the probability of whether these channels are open or closed. Opening or closing of ion channels changes the membrane potential of the sensory neuron, which changes the rate of action potentials which informs the rest of the nervous system about the temperature.
The TRP channels can have other ligands, as well, such as capsaicin or menthol. The activity of these ligands at temperature-sensitive receptors is why we perceive chilis or mustard to taste "hot" and menthol to feel "cold".
More generally, the nervous system typically responds to changes better than constant stimuli through adaptation. Therefore, if your hand is fairly cold and you touch something warm or hot, you will perceive a hotter stimulus than if your hand started out already warm.
There isn't really a thermocouple or temperature difference detector in the skin, just these two mechanisms: channels whose open probability is a function of temperature, and sensory adaptation which heightens perceptual sensitivity to changes in temperature.

Voets, T., Droogmans, G., Wissenbach, U., Janssens, A., Flockerzi, V., & Nilius, B. (2004). The principle of temperature-dependent gating in cold-and heat-sensitive TRP channels. Nature, 430(7001), 748-754.

Is it then correct to say that the proteins responsible for detecting temperature (the TRP channels) respond to absolute temperatures, but the nervous system itself causes us only to perceive differentials?

@quant That would be a reasonable birds-eye summary, though it's not precisely true that only differentials are perceived (they are just emphasized), there are ways that the sensitivity of the channels themselves can be altered by endogenous agonists and antagonists such that absolute temperature isn't the only thing they respond to, and the channel gating itself is complex, non-linear, and voltage-dependent (the Voets reference would be a good place to start). Even seemingly simple things in biology are much more complex the more regulation you start to consider.

I also found it interesting that TRP channels play a role in spices being perceived as hot or cold. I had always thought this perception was cultural/linguistic.


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Why do some enzymes have giant structures around the active site?
As a part of my inorganic chem. course (it's a required course at my college), we have a module called Introduction to Bioinorganic Chemistry. There, the prof. showed examples of enzymes like Cytochrome P450 and the drug erythromycin, and circled the active portions.
From what I can see, the active portions are a tiny portion of the actual drug/enzyme, so my question is: why do enzymes (and drugs, for that matter) have huge structures surrounding them?
I tried Googling my question but couldn't find anything relevant to what I was looking for. I suspect that I wasn't using the correct terminology, so the search engine had no idea what I wanted to know.
Simple explanations are preferred, preferably from the high-school level biochemistry side. I've never taken a biology course in school or college. I am a math major and this inorganic chemistry course is a required one. However, I still want to know why the amino acid chains are required, as they don't seem to be doing anything (that's what the active site is for.)
Picture for reference:


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What specific molecules cause the difference in spectral sensitivity in the cones?

What causes the difference in their spectral sensitivity of the S, M and L cones. I'm guessing that the opsin or photopigments are different, but haven't been able figure out conclusively from my web searches. Would you happen to know what opsins or photopigments each of cones have?

In Protanopia, the L cones are absent, or their spectral sensitivity has shifted. In the latter case, is it that the molecular structure of the opsin in this cone is different than normally expected, or is it that the opsin is using a different photopigment than normally expected?

Welcome to Biology.SE. This is not simply an answer site, but instead a site that promotes self-learning with some expert help. Consequently, questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] to a single question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please take the [tour] and consult the [help] starting with [ask] for details.

When we talk about spectral sensitivity, we talk about the spectral sensitivity of light-responsive complexes which are composed of

non-protein chromophore moieties that combine with
photosensitive chromoproteins.

In cones, you find a specific kind of opsin (photopsin) which combines with a non-protein photopigment that reacts to light via photoisomerization or photoreduction. Long story short: with light, you change the shape of the protein, and this initiates or boosts signal transduction cascades.
This study on Drosophila photoreceptors and spectral sensitivity-modulating factors is a great place to start, with supporting empirical data.
You'll find that both protein component and chromophore affect spectral sensitivity. For instance, difference between Rh1 and Rh2 opsin are responsible for different spectral sensitivities, as well as differences between the same opsin (say, where amino acid subsititutions are made to recapitulate other photoreceptors' structures and sensitivities, see this example). Likewise, the chromophore affects the overall sensitivity to light spectrum too:

The apparent lack of reduction in sensitivity of the UV-sensitive Rh3 and Rh4 rescue flies may be explained by the simultaneous reduction in UV-sensitising pigment associated with Rh1, which strongly absorbs UV wavelengths in the outer receptors.

This answers your title question.
Protanopia is characterized by missing or malfunctioning L-cone (red) cells. The cells are absent/malfunctioning, so the pigment genes specific to the L-cone have no 'place' to function, or are themselves absent from the retina (no expression).


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CDRs and antigen-binding sites
Are complementarity determining regions (CDRs) not the same thing as antigen-binding sites?
If not, what is the difference?
An old exam question states:

"Clarify how CDRs are related to the antigen binding sites"

To answer this I would simply say that CDRs provide a binding surface that is complementary to that of the antigen. Is that what is meant by the question or am I missing something?
All help is appreciated!

Each antigen binding site (also known as paratope) is made up of six complementarity-determining regions (CDRs) - three from each of the light and heavy chains.


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Role of the CD3 proteins and ζ chain
Could someone please explain which of the following is correct and why?

The role of the CD3 proteins and ζ chain on the surface of the cell is to:
a) transduce signals to the interior of the T cell
b) bind to antigen associated with MHC molecules
c) bind to MHC molecules
d) bind to CD4 or CD8 molecules
e) facilitate antigen processing of antigens that bind to the surface of T cells

From what I have read I believe a) to be the correct answer but I am unsure if I have understood it correctly. This is based on this paragraph in the book "The Immune System 4th Edt":

"By inducing this organization of molecules in the T-cell membrane, the interactions
of MHC ligands with T-cell receptors activate cytoplasmic protein
tyrosine kinases, which phosphorylate particular tyrosine residues in the cytoplasmic
tails of the CD3 cell-surface proteins and the associated ζ chain
(CD247), a purely cytoplasmic protein (see Figure 5.6, p. 118). The tyrosine residues
that become phosphorylated are part of short amino-acid sequence
motifs called immunoreceptor tyrosine-based activation motifs (ITAMs).
Enzymes and other signaling molecules bind to the phosphorylated tyrosine
residues and thus also become activated. In this way, the extracellular binding
of antigen to the T-cell receptor initiates pathways of intracellular signaling
that lead to alterations in gene expression and end with T-cell differentiation."

The quote from the textbook is incorrect in that $\zeta$ has both transmembrane and extracellular domains, so it is not "purely cytoplasmic". The ECD is small, but not non-existent.

A is most likely the answer they're looking for. However, CD3$\epsilon$ and either CD3$\delta$ or CD3$\gamma$ associate with CD4 or CD8 (depending on cell type) in the TCR complex, bringing in kinases like Lck to phosphorylate the ITAMs on the CD3 chains' intracellular domains, leading to further downstream signaling. So, CD3 does associate/"bind" CD4/CD8, making D correct as well, at least in my opinion.


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What is the significance of an adjuvant to traffic vaccine antigen directly to draining lymph nodes without diffusing into the systemic circulation?
I found the following sentence in the this paper- Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBV152: a double-blind, randomised, phase 1 trial

An imidazoquinoline molecule, which is a toll-like receptor (TLR) 7/8 agonist, has been used to stimulate cell-mediated responses. Algel-IMDG (an imidazoquinoline molecule chemisorbed on alum [Algel]) has been designed to traffic vaccine antigen directly to draining lymph nodes without diffusing into the systemic circulation.

My question is- what is the significance of trafficking vaccine antigen to draining lymph nodes? What will be the consequence if the vaccine diffuses into systemic circulation?

This paper, Controlling timing and location in vaccines, explains the concept in detail. The TL:DR version is that immune response is affected by the amount of antigen that reaches lymphatic tissue, that is, the tissue where the cells ultimately determining antibody production reside.
With a "non-lymph node-targeting adjuvant" vaccine given intramuscularly, the antigen in the vaccine must diffuse through more tissue, essentially with less reaching lymphatic tissue. With a targeted vaccine, more antigen goes directly where it's most effective, thus hopefully improving immune response.

As antigen availability plays a deterministic role in the strength and type of B cell and T cell responses induced by immunization, optimizing targeting of vaccines to lymph nodes and prolonging antigen availability over an optimal temporal window become key parameters shaping the immune response. As illustrated by recent studies, these are not just “nice to have” features, but can determine the difference between a vaccine inducing neutralizing antibodies or not.

Another theoretical benefit of targeted vaccines is that lower levels of antigen are required to produce the same response, meaning more vaccines can be made from the same amount of antigenic material.
The paper also nicely describes the benefits of nucleic acid vaccines (e.g. the mRNA vaccine).