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Absorption rate of Infrequently eating animals?
Clearly, creatures such as us humans, after vastly increasing the entropy of our food, expel most of the mass that we consume.
Some creatures, however, do NOT get the opportunity to eat nearly as often, even though these creatures are if anything more competitive (and perhaps cannibalistic!) than we are - snakes come to mind here, as do spiders.
Such a lifestyle implies that growing large - or at least to adult form - quickly has a huge advantage evolutionary.
So the awkward question that arises is thus: do such animals have a higher "absorption rate", if you will, then humans and other frequent feeders?
In other words, do such animals maximize their diet by incorporating more of the mass of their food and expelling less of it, or is there some physics/chemistry which makes this difficult?
Thanks!

I'll take a stab at this.
What fraction of your food is absorbed and what fraction is expelled is a function of what kind and how much indigestible material there is in the food, and not related to how often the animal eats.
How often an animal eats is a function of its metabolic demands(how many calories it needs) and how many calories it can get in one meal. Reptiles, as ectotherms, have a lower metabolic demand than endotherms. In addition, snakes can swallow huge amounts(relative to body weight) of high-calorie food in one sitting. As a result, snakes eat infrequently. Pet snakes are fed weekly or biweekly, depending on a number of factors. A reticulated python can swallow and digest something up to its own body weight. Ten weeks of digestion gives 1.4% of its own body weight daily, even without fasting.
Elephants are a migratory large mammal and eat about 4% of their body weight each day, more or less. This takes about 12-18 hours to collect, according to these people.
Elephants eat high-fiber, low-calorie foods, and as a result about 20% of their food mass is turned directly into poop. They feed often, and don't absorb much. Hummingbirds eat constantly, consuming their own body weight in food each day, but poop almost not at all. Their feces contains the indigestible parts of their food, just as the elephant feces does. The different is that large parts of elephant diet is indigestible fiber, while a tiny part of the hummingbird diet is indigestible insect exoskeletons.
All creatures absorb as much nutrition from their food as they can, and expel the remainder. How much remainder there is depends on what kind of food they eat.
Growth rates versus digestion rates and mass intake is a totally different and much more complicated question. Generally speaking, the growth-limiting factor is DNA replication or an essential acid or mineral deficiency and not a raw mass problem.


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Are there any flowers that look like snakes?
In Rio 2, they showed a flower that almost looks like a snake head (with two fangs and a long tongue).

Are there any such flowers in real life too?

Interesting question, but I must say it looks opinion based, as different people may have very different perceptions on the shape of flowers.

The tongue could be the pistil and the fangs could be the stamens. To find such a flower, you need to search for species with two stamen and a bilateral symmetry.

There are quite a few examples of plants which look like snakes. I'll tell about them one at a time.

Darlingtonia californica: or Cobra Lily, is a type of pitcher plant which looks much like a snake. It is native to Northern California and Oregon, growing in bogs and seeps with cold running water. See this image:

Arisaema triphyllum: commonly called Jack-in-the-Pulpit, it is a type of corm which resembles cobra. It is native to eastern North America, occurring in moist woodlands and thickets from Nova Scotia west to Minnesota, and south to southern Florida and Texas. See this:

A similar and closely related plant, Arisaema griffithii, called Griffith's Cobra Lily, resembles even more. See this:

Pogonia ophioglossoides: also called Snakemouth Orchid, whose flowers resemble the face of a snake, pretty much like your image. It is a species of orchid occurring from central Canada to the east-central and eastern United States. See this:

Isotria medeoloides: named Little Five Leaves, its flower also resembles a snake's face. It is a threatened species of terrestrial orchid found in temperate eastern North America. See this:

Malacothrix coulteri (Snake's head) looks like the head of a snake.

It is an annual herb that produces a waxy, upright flowering stem. The inflorescence is an array of flower heads the yellow or white ray florets are about a centimeter long. The bracts are green, often with dark striping or marking.
It is found in sandy and coastal areas, grasslands and deserts.
For more info:
See here, and if you are interested in it's geographical locations, you can visit this page.

source: Stack Exchange

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Can we change the Eye/Hair color by knocking out the OCA2, HERC2 and MC1R genes using CRISPR in an adult human?
This paper seems to describe the use of a plasmid delivered by a gene gun to depigment rat skin;

https://www.nature.com/articles/3302264
Published: 27 May 2004
Seeing the gene therapy: application of gene gun technique to transfect and decolour pigmented rat skin with human agouti signalling protein cDNA

Could a similar technique using CRISPR and chitosan change the eye and hair color of an an adult?

Let's first breakdown this question

What is CRISPR?

CRISPR is a group of DNA sequences that play a key role in the antiviral defense system of prokaryotic organisms such as bacteria and archaea.
They are derived from DNA fragments of bacteriophages that had previously infected the prokaryotes.
These sequences are used to destroy DNA from similar bacteriophages for future infections.

What is CRISPR-Cas?

The CRISPR-Cas system is an immune system seen in prokaryotes that provides resistance to foreign elements such as plasmids and phages. This is a form of acquired immunity.
Some factors allow Cas protein which is an enzyme to recognize and cut foreign pathogenic DNA making them act like a pair of molecular scissors.

What are OCA2, HERC2, and MC1R?

Now we know we can cut a specific part (Gene) of DNA. What do we accomplish by cutting out the genes which Andrew mentioned? To answer this we need to know what those three genes do.

OCA2 (P-gene): Provides instructions for making a protein called the P protein. This protein is located in specialized cells
(melanocytes) that produce a pigment called Melanin.
Melanin is a natural skin pigment. Hair, skin, and eye color in people and animals mostly depends on the type and amount of melanin
they have.
HERC2 (E3 ubiquitin ligase HERC2): Protein ligase which helps in DNA repair regulation, pigmentation, and neurological disorders.
MC1R (Melanocortin 1 receptor): Proteins involved in regulating mammalian skin and hair color.

In short, these Genes affect the Eye and Hair Colour and Andrew is suggesting to us that by removing/modifying them using CRISPR we change the Eye/Hair Colours.

Can we knock out OCA2, HERC2, and MC1R?

Yes, it has been done before and there are sequences available to target these genes within the genome. An example would be the gRNA sequences developed by Sigma-Aldrich and Genscript. I'll provide links of articles which has knocked out the respective gene and links to the gene sequences.

OCA2: (Article: https://pubmed.ncbi.nlm.nih.gov/29555241/ | Sequence:
https://www.genscript.com/gRNA-detail/4948/OCA2-CRISPR-guide-RNA.html)

HERC2: (Article:
https://jmg.bmj.com/content/early/2020/06/22/jmedgenet-2020-106873 |
Sequence: https://www.sigmaaldrich.com/catalog/genes/HERC2)
MC1R: (Article:
https://www.genscript.com/gRNA-detail/4157/MC1R-CRISPR-guide-RNA.html
| Sequence:
https://www.genscript.com/gRNA-detail/4157/MC1R-CRISPR-guide-RNA.html)

Can we change the Eye/Hair Colour by modifying the above genes?

An Interesting article from MIT Technology Review called Engineering the Perfect Baby gives you a nice idea of what I am going to tell you.
In Theory: It's technically possible. We can put up a convincing theory and there is a huge chance that this can be successfully done.
In Reality: Well, Reality kinda sucks cause most of the genetic engineering breakthrough starts from failures. Killing a rat for scientific purposes won't make any big difference but what about killing a fetus? It's almost impossible to get the permissions required to use CRISPR to edit the human genome even if it is to find a cure for a deadly disease that would actually improve the human race significantly. Due to its obvious ethical questions, people always stand against it. I said "almost impossible" cause there are few people who actually got the permissions and there are indeed few ongoing trials experimenting with CRISPR on Human Genome.
A popular Example would be He Jiankui who gave rise to the first-ever gene-modified human babies "Lulu and Nana". He had to forged ethical review documents, misled doctors into unknowingly implanting gene-edited embryos into two women, and many more things which haven't come out yet. What are the consequences? He's bloody missing! May 2022 Update: He's been found.
The point is, there is absolutely no way they would approve the usage of CRISPR for modifying something as silly as Eye/Hair color.
I mean we all like our babies to look like Megan Fox but I totally doubt if anyone would dare to modify a human genome for changing mere appearance cause people would start protesting if they find out someone is putting all those innocent fetuses at unknown and uncalculatable risk for changing external traits.
We want people to use CRISPR for things like this - Scientists edit gene for blood disease in human embryos and not for things like this - The rise of the designer baby: Parents who paid $16,500 to choose the sex of their child.
TL;DR (Too Long; Didn't Read):

What is CRISPR-Cas?

Technique in which we can edit genes relatively more precise than before.

What are OCA2, HERC2, and MC1R?

Genes which control the color of Eyes, Hair, Skin, and has other purposes.

Can we remove OCA2, HERC2, and MC1R genes using CRISPR?

Yes

Has it been done before?

Yes

In Humans?

Nope cause we got all those ethics and stuff.

What are we trying to accomplish by removing those genes?

To change the Colour of the Eyes/Hair of a human being.

Can we change the Colour of the Eyes/Hair of a human being?

In theory, it'll work. In Reality, nobody would allow it. They'd be better off with Hair Dye and Contact Lenses than to risk the lives of innocent fetuses.

https://columbialawreview.org/content/would-you-like-blue-eyes-with-that-a-fundamental-right-to-genetic-modification-of-embryos/
Of clinics that offer PGD [...] 3% have used it to select for a disability common to the parent, like deafness or dwarfism.
Still, there is no outright federal ban on research on human embryos generally, meaning privately funded organizations could still conduct research in this field.

@AndrewM they could, except they don't, because of the enormous ethical implications. The vast, vast majority of biological researchers have very strong ethics, with the occasional exceptions of people like He Jiankui. Real life is not like the movies, with evil corporations conducting mass human experimentation behind closed doors for nefarious purposes.

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Is there anything that tells me how Lichens Grow?
I've done a lot o research about this matter but I could not find anything relevant. So I'm doing a Computer Science project where, using AI and Computer Graphics, we try to predict the growth and aging of lichens on a stone, and at this moment I need some "academic validation", so is there any way like a formula or something that tells me how lichens evolve and grow on stones? Thank you so much!
This image shows what I've accomplished:

In real Life:
https://i.sstatic.net/7S7E5.jpg
So is it possible to predict how are they going to spread along the stone in a period of time? Do they start by growing in small colonies and then tend to get together to create a bigger colony? I don't know if this makes any sense, anyway thank you for your patience!

Welcome to Biology.SE. The questions How do lichens evolve? and How do lichens grow? are both extremely broad and rather undefined. Are you interested in the effect of phosphorus on lichens growth, in whether a logistic model fits lichen population growth, in wether the fungi or the algae is the growth limiting factor in case of low nutrient, in whether this symbiosis first evolve from a parasitic relationship, for what selection pressures exist on genes explaining this symbiosis, in whether there are gene cluster for the symbiosis, etc... You should boil your questions down.

It may help if you could explain exactly what you are modelling with your AI. Also you say I've done a lot o research, if you could link to what you looked for, it may help us to understand which direction you're heading to. Did you find anything of interest to you on the wikipedia article

I edited in the image for the model, but the "in real life" link is not correct.

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How does a cell regulate what leaves its vacuole?
Suppose a plant cell wants to take something out of its central vacuole. Some specific substance. Well if the vacuole is a bit of a soup of water and other dissolved substances, how does the cell get some specific substance out? Without letting any of the water/solution into the vesicle that's budding off? Or do they just let the solution right in?
Clarification: Since a vacuole is full of water and other dissolved substances, wouldn't that solution get into a budding vesicle? How is this prevented? Is it prevented?
When the cell is creating a vesicle, it starts pinching off part of the membrane, correct? My question is how the solution in the vacuole stays out of the vesicle, if it does at all.

could u pls clarify this part:Without letting any of the water/solution into the vesicle that's budding off? perhaps any research done on your part...that would be helpful.

Generally the vesicle budding off will contain the fluid from the organelle it comes from, plus it's cargo. The vesicle can then be modified, e.g. pH changed once it is separated from the original organelle.

Sorry! I'm confusing myself too. So, I was told that a vacuole will form a vesicle (like the Golgi apparatus) when it's transporting substances out of it. I want to know how specific substances are transported out, without any water or other liquid in the vacuole getting into the vesicle. But I was also unsure whether or not the cell cares if this liquid gets in the vesicle in the first place. Does that help at all? Sorry again! Thank you!


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The significance of haplotype blocks
I looked up haplotype blocks in Google Scholar, and the results returned seemed to show that almost all the relevant articles were published between 2001 and 2009, with almost nothing since 2010.
Why has interest in haplotype blocks apparently waned over the last decade? Has the concept been discredited?

Please check out this post at academia stackexchange and maybe edit your question to include representative trend.
The top most articles found by google scholar search are not a random sample of all articles found. I don't know exact google algorithm but my guess is it puts highly cited articles near the top. Older articles had more time to accumulate citations.

can you confirm that the language hasn't just changed? i believe that many people will just write "haplotypes" these days and may omit the word "blocks". Has there been a meaningful decrease in the word "haplotypes"?

also, just posting screenshots of unsorted google scholar hits is not convincing that what you say is true. can you actually quantify the usage of the relevant terms in a time-sorted fashion?

@David yes, I actually would like to ask if the concept of haplotype blocks (or as someone likes to call it, haplotypes) has been discredited

I have edited your question, taking the emphasis away from the Google Scholar Search and towards the validity of the concept. As your inference from the search is clearly wrong, I cut two of your graphics which I hope you will agree are displensible.

Has interest in haplotype blocks waned over the decade?
No.
You can set a time range on Google Scholar, which the screenshot shows was not done. I did that and:

A search for ‘haplotype block’ from 2000 to 2009 gives 22,000 hits.

A search for ‘haplotype block’ from 2000 to 2009 gives 25,700 hits.

(The term haploblock is now often used as an abbreviation, but it turns out that haplotype block is still much more frequent.)
So I have to conclude there must have been something wrong with the approach adopted by the poster. It is worth mentioning, however, that a Google Books ngram analysis of haplotype block shows first usage in 2000, a peak at 2007 dropping to a approx. 30% of the maximum in 2019. This may just reflect an rush to publish books on a new topic that has subsided, although the rate of publication in journals has been more constant.
What are haplotype blocks, why are they interesting, and how do they differ from haplotypes?
This is illustrated by an interesting paper in a recent (2020) issue of Nature that comes from the work of a large consortium addressing the  question of the adaptation of sunflowers to different ecological niches. This involves the evolution of so-called ecotypes, differing in properties such as flowering time and ability to grow on sand dunes.
The problem is that these adaptations involve many different genes (and hence alleles) which means they involve different haplotypes, according to the definition in Wikipedia:

A haplotype (haploid genotype) is a group of alleles in an organism
that are inherited together from a single parent.

However these different sunflower ecotypes are not physically separated from others, so that one would expect hybridization between them to occur, resulting in the loss of the haplotype and the adaptation. As the paper points out, this problem is actually a reformulation of criticisms of Darwin’s theories by his contemporaries:
Romanes, G. J. “Physiological selection; an additional suggestion on the origin of species.” Zool. J. Linn. Soc. 19, 337–411 (1886).
(although I must admit not to have read the original.)
The fact that this does not happen is because the alleles constituting the haplotype exist in non-recombing blocks — haplotype blocks.

A haplotype block is a region of an organism’s genome in which there
is little evidence of a history of genetic recombination, and which
contain only a small number of distinct haplotypes.

What prevents the recombination of such blocks? It appears that the most come explanation is that rearrangement of the regions containing the haplotype blocks occurs, preventing recombination. One of the easiest rearrangement to understand is simple inversion, two large blocks of which were found on chromosome 5.
The studies in the paper started with two haplotype blocks which had been shown to be involved in the ecotypes shown, and which were found to contain genes previously implicated in these processes, such as FLOWERING LOCUS T and HEAT-INTOLERANT 1. By genome-wide association studies they identified a total of 37 haplotype blocks on the basis of linkage disequilibrium. A diagram of some of these blocks in different sunflower species may wet the reader’s appetite:

So, in answer to the poster’s specific query: The concept of haplotype blocks is very much alive!

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Basis of enzyme nomenclature — pyruvate dehydrogenase
In the formation of AcetylCoA from pyruvate, why is the enzyme called “pyruvate dehydrogenase (complex)” when it involves the decarboxylation of pyruvate or the replacement of a carbonyl group by coenzyme A?

The pyruvate dehydrogenase complex catalyses the oxidative decarboxylation of pyruvate. A description of this is easy to find on the web (e.g. Wikipedia), but I would recommend the section in Berg et al. Biochemistry (online), as it is an authoritative book with a high reputation.

Pyruvate + CoA + NAD+ → acetylCoA + CO2 + NADH

In the overall reaction, shown above, pyruvate is being oxidized (hydrogen removed) by NAD+, which is reduced to NADH. Hence there is nothing surprising in the enzyme having acquired the description, dehydrogenase.
Before asking questions about enzyme nomenclature, one should consider the historical and scientific context in which names arose. This was general scientific ignorance of the overall metabolic pathways in which they occurred or even the direction in which the reaction normally proceeded. There is also the question of focus — here on oxidation of carbohydrates. The working names that arise — trivial names, as they are called — tend to stick: they are in the literature and everyone in the field knows what you are talking about. Eventually, when the dust has settled, scientific commissions assign systematic nomenclature. In this case there are three enzymes involved, so that each has its own systematic name:

Pyruvate dehydrogenase (acetyl-transferring) — EC 1.2.4.1
Dihydrolipoyl transacetylase — EC 2.3.1.12
Dihydrolipoamide dehydrogenase — EC 1.8.1.4

It can be seen that even the systematic name for enzyme E1 (which catalyses the decarboxylation) does not refer to the decarboxylation, but to the transfer of the acetyl group (to thiamine pyrophosphate and then to lipoamide), which is of more interest mechanistically.
Details of the reactions and alternative names corresponding to the EC numbers  (Enzyme Commission numbers) can be found either on the Queen Mary University site or Expasy.


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Interaction of charged triphosphates with the ATP binding region in proteins
DNA-histone interactions involve positively charged amino acid side chains groups neutralizing the negatively charged phosphate of the sugar-phosphate backbone. Is the same true for ATP binding sites on proteins?
In most models I’ve seen, it looks like the base, adenine, is involved in the binding. But the triphosphate seems like it would bind specifically to positively charged side-chains. I Googled a bit, but I couldn’t really find any models depicting this. Does anyone know whether this is so?

Thank you for accepting my answer. I enjoyed answering your question — perhaps in more detail than you required — but the answers to questions on this site are meant to be generally useful, rather than a dialogue with the poster. I had a little spare time in which I improved the illustrations and changed their order. I suspect that the answer was not quite as simple as you expected, which is not unnatural if you are new to the field of proteins. The answer hints at the complex intellectual beauty of this area, which will well repay the further work required to explore it.

a bit low detail actually

Do tell me what you would specifically like more detail of and I'll see if I can help. Some indication of your scientific background might help me pitch things at the right level.

Summary
Many proteins that bind the nucleotide triphosphates ATP and GTP have an evolutionary conserved motif — the P-loop — that binds the phosphate portion of the molecule. This has the sequence, GXXXXGKS/T. Although the conserved basic lysine (K) is interacts with two of the positively charged phosphate moieties, other interactions involve Mg2+ ions (with which NTPs are always complexed) and polar, rather than charged, amino acid residues and the polypeptide backbone.
Detailed Illustration
Although the question asks about ATP, I have chosen the GTP-binding protein H-ras p21 as an illustration because the paper by Pai et al. describing it gives full details of the interactions of the phosphates, which are essentially the same for ATP and GTP. (Many other papers tend to show only ribbon diagrams of the protein.) Note also that the crystal structure was, of necessity, of a complex with the GTP analogue, GppNp. (GppNp is not rapidly hydrolysed, unlike GTP itself.)
In this case the evolutionary conserved P-loop that binds the phosphate has the sequence:
Gly Ala Gly Gly Val Gly Lys Ser

 10  11  12  13  14  15  16  17

A three-dimensional representation of the phosphate-binding region is shown below. The left-hand frame shows the P-loop and residues Thr35 and Asp57 without the nucleotide. The right-hand frame is the same but with GppNp and a magnesium ion included, and only the conserved residues of the P-loop labelled.

[Own work based on Fig.6 of the paper by Pai et al. using Jmol software and Protein Data Bank file 5p21.pdb.]
A two-dimensional schematic of the interactions is shown below. The side-chain interactions (and those from the magnesium ion) are shown as red dotted lines, whereas those from the backbone are shown in black. The conserved residues of the P-loop are indicated by blue text.

[Simplified redrawing of part of Fig.5 of the paper by Pai et al., excluding water interactions and interatomic distances.]
Reflections
Although positively-charged basic amino acid side-chains are involved in neutralizing the negative charges of nucleic acids and nucleotide phosphates, they are not the sole means of doing so, and in the case of the NTPs they are not the main means. Magnesium ions and polar residues (including the protein backbone δ+ve NH groups) can play an important role. To my mind this reflects two things. First, that life is dynamic; so weaker interactions are often favoured in enzymes because they can be easily broken as well as made. (NDP must be released from the enzyme after hydrolysis.) Second, and more speculative, the P-loop is thought to be very ancient as it is found in a wide variety of conserved NTP-binding proteins. A specific backbone conformation has been identified that facilitates this interaction. It could have arisen before all 20(ish) proteins specified by the genetic code had arisen, when the protein backbone could have played a greater role in interacting with small molecules. (This has also been suggested for backbone NH groups binding δ+ve sulphur in iron–sulphur clusters.)


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Do carboxylesterases, arylesterases and acylesterases count to the enzyme class of lipases?
I am currently examining the acyl transfer catalysis activity of several enzymes that I was told are all lipases. Through reading a couple of papers including these enzymes I found out that all of them are hydrolases with promiscuous acyltransfer activity. Specifically one of the enzymes is a carboxyl-esterase, one is an aryl-esterase and the third one is an acyl-esterase. I know that esterases are part of hydrolases and lipases are basically fat-splitting esterases. Lipases also catalyze transesterification = acyl transfer, just like all of the enzymes I am working with do. I just don't understand the classification of all these enzymes as lipases. Can someone explain the connection to me?

Could you clarify. You explain that you understand that the enzymes in question are all "fat-splitting" i.e. lipid-hydrolysing esterases. More specifically they hydrolyse lipids that belong to the class ester (e.g. triglycerides) rather than lipids in general such as free fatty acids or cholesterol. Such enzymes are given the trivial generic name lipase. (They have more specific systematic names.) What is it that you do not understand? Do you want examples of systematic names or what?

The assay we are working with is using para-nitrophenyl butyrate as a substrate. This substrate is usually used for investigating esterase, as well as lipase activity. I read that "Lipases can be distinguished from carboxyl esterases by their substrate spectra, using p-nitrophenyl palmitate (cleaved by lipases) versus p-nitrophenyl butyrate (cleaved by esterases)" (Source: https://www.scielo.br/pdf/cta/v31n3/a09v31n3.pdf). So shouldn't the enzymes I am using be classified as esterases, rather than lipases?

I think your problem is one of the use of trivial names (such as lipase) and systematic EC names, which I have answered here Origin of enzyme names.

This is further to my previous comment which was autogenerated when I voted to close your question as already having an answer. I would stress that "lipase" is not a systematic name but a trivial name, that the names people use for enzymes (as of other things) depends on what they were taught and what interests them. If you are interested in lipids, the name lipase appeals, if you are a chemist, not. See also my answers for other enzymes here and here.


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What mechanism causes the presence of photosensitizers in mitochondria to change membrane ionic currents?
In the original question, the article in question was talking about specifically about this compound, Benzoporphyrin:
Characterization of Perturbing Actions by Verteporfin, a Benzoporphyrin Photosensitizer, on Membrane Ionic Currents
From my original understanding, the addition of a photosensitizer to the mitochondria of a cell and the presence of appropriate light causes a change in the ionic membrane current. Nonetheless, from knowledge of photodynamic therapy, using the benzoporphyrin would create reactive oxygen species, which would wreak havoc on the mitochondria.
Yet this is not the case and it also changes the membrane potential.
I originally wondered what was the mechanism behind this and I still do, however the article goes on to describe a multitude of varying research papers on the similar topic on various types of photosensitizers as if it were common knowledge, yet I could still not find an underlying explanation for this application's.
I will link the other papers which the original article refers to, but this seems to be a wide topic and not reserved solely to this paper. I hope this makes it easier to answer.
-Papers-: 1
2
3

Would the changes in currents show the direction/specificity expected by unspecific damage to mitochondria? Generally there are more ways to break something rather than to improve functionality (https://www.nature.com/articles/nrc.2017.32). Some photosensitizers seem to cause damage to the mitochondria trough reactive oxygen species (https://www.frontiersin.org/articles/10.3389/fphar.2020.557429/full).


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Calculation of final magnification when using a CCD camera
I'm trying to empirically calculate the approx final magnification (mag) of digital images rendered through our confocal microscope. Using a micrometer and the microscopy equipment I have, the following is known:
Objective mag = 63x
Ocular mag =10x
Diameter of field of view when viewing specimen through occular = 320µm
Diameter of field of view when live viewing specimen on the screen = 100µm
What is the final mag of the rendered image on the screen?
This is not a homework question. The manufacturers specification for the degree of magnification that the camera and confocal  (and obviously there is some) provide is unknown.

what is the pixel size? what is sensor size? how many real-life microns fit in one micron of pixels is your magnification

@aaaaaa  live view on the screen is 920 W X 1200 H. No idea the size of the sensor unfortunately.

What is the camera model?

Usually the software that comes with the camera has the option of adding a scale bar. For all compound microscopes the final magnification = eyepiece magnification × objective magnification. The camera itself doesn't have any lens (AFAIK) and the image is not further magnified. However there are some settings that ensure that the digital image preserves all the optical information: the pixel size must be smaller than the inverse of 2.3-times the cut-off frequency [source].

@WYSIWYG if the image on the screen as compared to what your seeing through the occular is mag by a factor of 3,2, then the mag is different correct?

Assuming that the FOV that is captured by the CCD on the screen is 100µm wide as determined by the micrometer, and you are viewing the 920 pixel wide image on a standard 96 ppi monitor, the zoom would be approximately 2434 times.
$$\frac{920p}{96p/in}/100µm \approx 2434$$
Additionally, you should ensure that the minimum resolution on the micrometer is at least twice as large as each pixel on your microscope CCD.
The reason that the pixel size must be at least 2 times smaller than the minimum resolution present in the image is due to the Nyquist-Shannon sampling theorem.
This being said, all microscopes (and arguably all measurement devices) should be calibrated against a standard. This paper explains the usage of a standard to calibrate confocal microscopes.

A similar technique used to calibrate normal optical microscopes using a stage micrometer standard can be used if you do not possess such a standard. First calibrate the normal microscope, then image an identical sample using both microscopes in order to obtain the size of the field of view.

This is great info but doesn't answer ?, I already did this. The fov is above.

@rhill45 Sorry for initially misreading. Added my interpretation of the digital zoom.


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Cationic lipid mediated transfection optimization for 150mm dishes
I need to optimize a transfection protocol to transiently express a plasmid encoding a chimera of  eyfp attached to the c term of a Golgi apparatus signaling molecule) in hela cells and hepg2 cells and get as high expression as I can get.
I need enough protein for about 100 wb's. I've seeded hela cells to 12 150mm dishes. And the same with the hepg2. I've prepped mg's of plasmid.
I'm using invitrogens original lipofectamine reagent; not the 2000, or ltx or any of that stuff.
Any suggestions on a protocol here for hela and hepg2 plasmid dna and lipofectamine mediated transfection on such a large plate size.
I figure just scaling up should work but there's some pitfalls here. Look at this table for example when you go from 60 to 100 mm you about double the area, so you also about double the culture volume. However when you go from 100 to 150mm you triple the area, but only increase the culture volume two fold about. This is making my scale-up calculations for transfection look really off:

Despite what the numbers look like, across all values going from 100mm to 150mm you're scaling up by a factor of ~2.76: (a) 152/55 = 2.76, (b) 1.52e7/5.5e6 = 2.76, (c) |avg(30.4-45.6)/avg(11-16.5)| = 2.76.

Ahhh! I should have crunched the numbers cause you R correct. It's a weird concept because when you scale up in vessel size you want all parameters, ideally I would think, to increase at the same rate. However the depth of media can reach a certain point where I believe it hinders growth. When the volume gets to be too much it can take too long for those needed soluble factors to build up in the environment. Also increase in medium depth can delay delivery of soluble oxygen to the cells.  Thank you for seeing through

All my nonsense to make that comment. I think this ? Is a little scatter I'm going to reword it to focus it on the ratio, area and volume if you want to post an answer its yours. I'll post a seperate ? On the hela optimization

@Kendall please post your comment as an answer to close this question. Thanks!

So, for every row on the dish protocol, the entire process is scaled up a discrete value. In the case of 100mm to 150mm, the values are scaled up by about 2.76 across all values:
(a) 152/55 = 2.76, (b) 1.52e7/5.5e6 = 2.76, (c) |avg(30.4-45.6)/avg(11-16.5)| = 2.76
(as answered in comments)


text:
Testing CO₂ for cell culture
I'm am refurbishing some old CO2 incubators. I would like to test the precision of the CO2 sensor. There is a sample port on this incubator.
What sorts of  methods are commonly used to measure CO2 in these incubators?
Strangely, the manufacturer of the incubator makes no recommendations.
I need to be able to report the measurement as a percentage.

I would presume calibrating it with a known gas concentrations is what they do at the factory. In my lab, the calibration is done by the servicing company.

Chemistry SE might be able to come up with a simple way get some known concentrations.

Found this:
http://www.mybacharach.com/fyrite-gas-analyzers.htm
Probably what I need


text:
Why would a plant evolve to produce an addictive chemical?
It seems kind of anti-productive in terms of survival for a plant to produce an addictive chemical as that plant will constantly be sought after by animals that ingest it. In this instance, I'm looking for a possible general & inclusive answer here that would describe most plants that make this. Not a specific instance (although if provided as an example would be a plus).
To appreciate the scope of this is terms of number of plants producing potentially addictive compounds - see this compendium:
compendium of botanicals reported to produce toxic, physchoactive or addictive compounds

Which addictive chemical?.. Can you add some examples and references?

Compounds like nicotine and caffeine are poisonous, especially to insects.

@WYSIWYG I'm trying to keep this general, but I know this question is borderline-maybe a little too open ended.

The supposed addictive properties easily could be random side effects, unrelated to whatever function the chemical performs in the plant.  Remember that evolution does not plan ahead.

@canadianer There was an article in science magazine some months back which said that bees develop a stronger memory of flowers that contain caffeine in their nectars.

@WYSIWYG That's quite interesting. I was also thinking that such compounds, being addicting, could aid in seed dispersal by higher animals.

@canadianer Found the article... I added that as an answer..

Well, see. Coca or tobacco plantages house billions and billions of plants. That's a huge success in terms of Darwin!

They didn't really "Evolve the trait of addictiveness"

@WYSIWYG didn't think about seed dispersal! You come up with that yourself? Nice one

Besides smoking a truck load of banana peels what fruits have addictive compounds? Interesting.

Good compendium http://www.efsa.europa.eu/en/scdocs/doc/280rax1.pdf

@WYSIWYG: Which suggests that caffeine is good for bees - as it is for humans.  I suspect bees would also have better memories for flowers with more/more nutritious nectars, while the plants would have pressure to evolve (through selection of random variations, not intent) nectars that "taste good" but are not so energy-intensive to produce.

How do you define "addictiveness" in the general case (i.e. not only for humans)? Would you e.g. consider nectar an addictive compound for nectar-feeding insects? How do you separate addictive compounds from simply preferred compounds, substrates or foods. Does the compound have to be detrimental or toxic to some extent for the species feeding on it (many examples normally labelled as "addictive chemicals" in humans are considered detrimental)?

Just this morning I've read about a caterpillar that produce a sugary substance addictive for ant. The ants will spend the rest of their lives acting as bodyguards for the caterpillar. Plants could develop a similar defence mechanism, doping other organism to act as its defence.

@algiogia symbiotic relationship

It's a matter of perspective. Most of the chemicals that are addictive to us humans (particularly alkaloids), and may be addictive for some other animals as well, are also insecticides. Lots of plants that we consider poisonous are good food for other species, and lots of plants that insects would consider poisonous are treats for us.
This is a great example of the aimless nature of evolution. The plants that could successfully defend themselves against insects stabilize on a solution that happens to be bad for them in certain ways. Although, you would be hard pressed to find a better way to guarantee reproduction than being addictive to humans.
Background reference

Plant-insect coevolution and inhibition of acetylcholinesterase
The defensive role of alkaloids in insects and plants
Exploration of nature's chemodiversity: the role of secondary metabolites as leads in drug development

Also of interest

Bees prefer foods containing neonicotinoid pesticides

Good answer, gonna keep this open for a couple more but I like this

No addictive products produced by plants can be found to have exclusively detrimental effects on the plant, they all have mostly positive effects, and plants can minimize or maximize a single chemical at their disposal, over some dozens of generations, because it's only a single chemical. Chemical changes are the most usefual and evolutionarily cheap method for plants to ward off or attract animals, easier to adjust than color, shape, hairiness, stinging cells, size, and so on.

Indeed. Even if they are generally toxic to the plant's system, they simply store them in vacuoles.

1 for "Although, you would be hard pressed to find a better way to guarantee reproduction than being addictive to humans."

Add to that most plants are not nearly so addictive in their natural forms as they are when processed.  So, the problem probably self regulates to an extent until such time as we decide to break out of the natural system and cultivate it.

Being attractive to humans may promote distribution, but "good for us" hardly matches "good for the species" (our plantains (bananas) would die quickly if care ceased), and we are careless (Silphium was possibly harvested into extinction).

As someone commented earlier, chemicals such as nicotine and morphine were products of evolution meant to repel animals. It is explained in more details in this article here.

Evolutionary biologists studying plant–herbivore interactions have convincingly argued that many plant secondary metabolites, including alkaloids such as nicotine, morphine and cocaine, are potent neurotoxins that evolved to deter consumption by herbivores.

But it seems that those same chemicals produce adverse effects to what they were originally intended for:

For example, one or more plant alkaloids have been identified that interfere with nearly every step in neural signalling. Targets include neurotransmitter synthesis, storage, release, binding, deactivation and reuptake, ion channel activation and function, and key enzymes involved in signal transduction.
Paradoxically, the same properties invoked to explain why common drugs like caffeine, nicotine and cocaine are toxic are also those invoked to explain why these compounds are rewarding. It is therefore important to stress that these and other addictive drugs appear to have evolved only because they successfully deterred, not rewarded or reinforced, plant consumption.

For example, let's take a closer look at nicotine. This compound is not present at all times in the plant, instead it is produced as a reaction to a trigger.

Nicotiana attenuata is an important model species for the analysis of plant–herbivore interactions involving nicotine. It is a domesticated North American tobacco plant that is attacked by over 20 different herbivores, ranging from mammalian browsers to intracellular-feeding insects. These attacks elicit a battery of defensive responses, including nicotine production.
Nicotiana has therefore evolved to allocate chemical defences strategically by concentrating them in the most valuable parts of the plant, such as young leaves, stems and reproductive organs, and by modulating its production according to the type of herbivore and extent of leaf damage.

This last example concentrates on nicotine, but it makes it easier to grasp how plants might use the production of such a chemical as a mean of protection.
Also, depending on the substance and the creature which consumes the plant, one might witness different outcomes. I found interesting information in this less detailed text here:

Defensive compounds from plants, like nicotine and cocaine, usually target nervous system components in insects. These components include proteins that have important roles on the insect’s physiology, which may include specific receptors, ion channels, enzymes, etc. In most cases, the defensive chemical kills the insect by interfering with one or more of these proteins; in other cases, the chemicals just make the plant distasteful for the insect, and therefore, the bug will leave the plant alone.

I am providing an example which somewhat contradicts the points mentioned in the other answers regarding toxicity of alkaloids to insects.
Caffeine is a stimulant and is toxic at high doses (also for humans) but at low doses it has a stimulating pharmacological effect on the organism. The same principle applies to insects as well. A study by Wright et. al (2013) has revealed that caffeine in the nectar of some flowers, enhances the bee's memory of that flower (a reward, in general).
They have also mentioned that:

Two caffeine-producing plant genera, Citrus and Coffea, have large
floral displays with strong scents and produce more fruits and seeds
when pollinated by bees (8, 9)

However, caffeine tastes bitter and bees would reject nectar (sugar solutions) containing high levels of caffeine (>1mM).

Arguably, caffeine acts as a stimulant at all doses, which is why it is toxic at high doses.

It's also arguable that everything is toxic at high doses - including oxygen and water.

Caffeine has an overall positive effect? That's not what I heard:  New research from Johns Hopkins Medical School shows that performance increases due to caffeine intake are the result of caffeine drinkers experiencing a short-term reversal of caffeine withdrawal. By controlling for caffeine use in study participants, John Hopkins researchers found that caffeine-related performance improvement is nonexistent without caffeine withdrawal. (found at https://www.linkedin.com/pulse/20140908162020-50578967-caffeine-the-silent-killer-of-success )

As for bees developing a preference for addictive drugs, that's actually turning into one of the great tragedies of our age: part of the reason honeybees are dying off so catastrophically in the last few years is because of the introduction of new pesticides derived from nicotine, which, in addition to being highly toxic to bees, is also highly addictive, so they just keep on coming back for more until it kills them.  Entire colonies worth of them.

@MasonWheeler Caffeine and Nicotine has been existing for several thousands of years.

@WYSIWYG: Sure, but what does that have to do with what I wrote in comments?

@MasonWheeler That question was asked on Cognitive Sciences if you're interested.

I don't think this contradicts the other answers, just adds a potential second reason why plants might have evolved to produce certain drugs.

Short answer
The appearance of psychoactive compounds in plants has nothing to do with their addictiveness in man.
Background
Psychoactive plants were there long before humans. The question therefore should be: "Why would humans evolve brains that exhibit addictive propensity to poisonous compounds abundantly available in nature"? The answer is: because our brain evolved in the absence of addictive substances.
One has to realize that addictive compounds are grown and processed. When humanoids evolved over millions of years, for the larger part there were no means to grow, harvest and process coffee beans, tobacco and coca leaves. Moreover, the most addictive drugs like injectable heroin and smokable cocaine (crack) are chemically purified. Methamphetamine and many addictive opiates are purely synthetic. In their native form, coca leaves and poppies are far less addictive, because in the raw form they lack the dopamine rush. Instead, the chewing of raw plant materials like coca leaves produces a mild high with a slow onset, and a mild offset. The sudden dopamine rush is what evokes the blissful euphoric state chased by heroin, crack and meth addicts, while the dreadful crash associated by these purified drugs is one of the strong motivators to seek for another hit. Also note that tobacco is heavily processed through a curing process before it is sold. The raw, woody tobacco products are far less likely to cause addiction.
Moreover, note that many of the addictive stuff originates from the Americas (coca) and Asia (opiates). Humans came from Africa. Africa is one of the continents with very, very few drug containing plants (Qat being the exception - a mild drug).

It's a good response but not what I'm looking into. It's pretty obvious that purifying cocaine and heroine make a much more addictive version. And the disease model of addiction...another topic. I was trying to question a natural selective process in which these compounds have apparently developed a survival niche in a sense

@rhill45 - and that line of thought is exactly what I counter here. I understand it is not what you want to hear, but I deemed it appropriate to share my view. Others have explained why plants produce drugs, I explain why the appearance of those plant-based drugs have nothing to with addictiveness in man.


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Regulation in plants bearing cleistogamous and chasmogamous flowers
In most plants bearing cleistogamous flowers, chasmogamous flowers are also borne by the plants. For example, Viola, Oxalis and Commelina contain both these kinds of flowers.( I am unaware of a species which bears only cleistogamous flowers, which would be very unfavourable for evolutionary success)
The Cleistogamous flowers help in reproduction with minimal energy and resource expenditure. It also maximises the chance of reproduction, which is an important factor where the agents of pollination are scarce. On the other hand Chasmogamous flowers provide variablity, hybrid vigour and generate better genotypes through recombination. Both of these strategies are useful in different environment. In adverse (less pollinators, energy stress) cleistogamy would be favourable, and in other cases where no energy stress prevails, chsmogamy is advantageous.

My question is, How can plants, if they can, regulate which strategy
  is supported? Is the ratio of cleistogamous to chasmogamous flowers
  constant irrespective of the environment, or does the prevailing
  environment have a say in deciding which of these two kinds of flowers
  will be preferred over the other? If it does, what is the regulatory
  mechanism underlying this control of flowering startegies?

One other related question is whether there are any species which bear only cleistogamous flowers? That would seem very unfavourable for evolution to act on.

+1 interesting question. I am sure there are some articles presenting more or less complex (depending on the number of parameters that we authorize to vary) mathematical models to explain to frequency of cleistogamous and chasmogamous flowers. Eric Charnov's book The Theory of Sex Allocation is a classical book in this kind of discussion and it maybe addresses your question.

This book from Stuart West might also address the question

did you check this article

This is a very good question, but I think the reason that it's not being answered is because it is in a sense too broad: different plant groups maintain balances of cleistogamous and chasmogamous flowers, and they modulate that balance through different mechanisms. Many of these mechanisms (genes involved, environmental cues, developmental pathways) may not be fully understood.
Culley and Klooster (2007) categorize cleistogamy depending on the degree to which "the prevailing environment has a say":

In dimorphic cleistogamy CL and CH flower differ in the time or place
of production, with CL flowers produced in conditions (underground,
low light levels, early in the season) that are potentially
unfavorable for outcrossing.
In induced cleistogamy potentially CH flowers that experience conditions such as drought or low temperatures fail to open and self-pollinate, becoming, in effect, CL flowers.

You should check out the Culley and Klooster (available online if you make a jstor login) – they discuss complete cleistogamy which addresses your last question. They report several completely CL species in their Table 1, and give references.
More generally, many different plant groups maintain balances of self-pollination and outcrossing (i.e. "real sex"), through an even more diverse set of mechanisms.
Even more generally, many plants and some animals maintain balances of sexual reproduction and clonal reproduction, through an even more diverse set of mechanisms. For instance, vegetative reproduction (e.g., strawberry runners) is very common in many plant groups; facultative and obligate parthenogenesis in animals also occurs.

Culley, Theresa M. and Matthew R. Klooster (2007). The Cleistogamous Breeding System: A Review of Its Frequency, Evolution, and Ecology in Angiosperms. Botanical Review. Vol. 73, No. 1, pp. 1-30


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Confusion about Photosystem 2 with regards to lysis of water
I am slightly confused about the role of $\ce{H2O}$ lysis in PII. I know that this releases $\ce{H+}$ ions, which I think are important because they drive the production of $\ce{ATP}$ through F-Atpase across the thylakoid membrane. But I don't understand how else this is important? With my current understanding, I would think that it is perfectly sufficient for PII to receive photons to excite an electron in the primary pigment reaction centre, which goes along the electron transport chain to PI. Is the water lysis there to replace electrons lost by photosystem 2? If so, how is it controlled that the correct number of $\ce{H2O}$ molecules are lysed so that excess electrons aren't generated?

Generation of ATP via photons is the primary aim of the photosynthesis pathway, which is accomplished by the generation of a chemiosmotic gradient of $\ce{H+}$, which then drives the ATPase pump. All the other enzymatic setups are designed to just let this process run in the most efficient way.

I would think that it is perfectly sufficient for PII to receive photons to excite an electron in the primary pigment reaction centre

While you are partially correct in assuming this, since the ETC also participates in creation of a chemiosmotic gradient (Plastoquinone), such a mecahinsm would not be able to run repeatedly. Without the replenishment of the electrons of the PSII, it will not be able to initiate another round of electron transport. Hence, the oxidation of water is crucial in providing PSII the electrons it passed onto plastoquinone, so as to allow another round of photon-absorption and continuation of the photosynthetic process.

how is it controlled that the correct number of H2O molecules are lysed so that excess electrons aren't generated?

This is achieved by a complicated interplay of the enzymatic components within the PSII. In summary, utilizing the four stable oxidation states of manganese core in the redox center ($\ce{Mn}^{(2-5)+}$, four separate states of the center ($S1\rightarrow 4$) are formed. These states cyclically shunt one electron during each step, until a water molecule is bound to $S4$ which is then directly converted to $\ce{O2}$ by $P680+$, formed in PSII due to photon absorption, which is a strong reducing agent. Since the final step occurs only with water molecule bound to $S4$, which in turn is formed only by the cyclical transition between the various states of the redox center with systematic sequential loss of electrons, the overall process is very tightly constrained to extract only the limited number of electrons preventing any troublesome redox intermediates.
See here for some basic treatment of photosynthesis.

Thank you for your answer. Your answer and some additional reading allowed me to understand the role of water lysis! However there is one question that has come up for me which I cannot seem to find the answer to: so quinone B, after accepting electrons and hydrogen, transfers electrons to cytochrome b6f as plastoquinone/quinol. These electron are accepted by cytochrome b6f, to re-form quinone B, which is not lipid soluble. How is the quinone B replaced in PSII? It cannot diffuse back in the phospholipid bilayer as it came?


text:
Relative abundance and action of 5p and 3p microRNAs
I am a beginner in genetic research and am currently conducting a project concerning microRNAs. Let's say we have miR-1-5p. If miR-1-5p is upregulated in a disease, will miR-1-3p always be downregulated in the same disease? Or will it also be upregulated?
In addition, will miR-1-5p and miR-1-3p have any difference in functions? Or will they always target the same target genes and induce the same cascades with the same resulting effects?
I have been reading some sources but keep getting confused.

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

The reason I think you have not received any answer to your question yet is that it is unclear. What precisely is your research project? When you talk about mir-5p being upregulated, are you describing actual RNAseq results or are you just considering a  hypothetical situation with increased transcription of the precursor? You talk about targetting genes, but it is the mRNA that is targetted, answering your second question. See also here.

It's best to think of miRNAs on a case-by-case basis. Canonically, miRNAs are thought of as negative regulators of their mRNA targets via the RISC complex, but some miRNAs can have a protective effect on their targets in some contexts.  As with much of biology, there aren't any hard-and-fast rules concerning miRNA function relative to their target site.


text:
Solubility of Amylopectin and Glycogen in water
The only difference between the structures of Amylopectin and Glycogen is that Glycogen is more highly branched than Amylopectin. How this difference between their structures makes difference between their solubilities in water?

The answer is relatively simple: Amylopectin is watersoluble, and this seems to be a classical textbook error, which has been propagated now for decades. As you say yourself, the only difference is the number of 1,6-glycosidic branches, which occur every 8-12 glucose monomers in glycogen and every 15-30 monomers in amylopectin.
There are even scientific articles which show that amylopectin is watersoluble, see the references below:

Green et al., Journal of Chemical Education vol 52, p.729 (1975) Which  Starch Fraction  is  Water-soluble,  Amylose  or
Amylopectin?
J. Robyt, Encyclopedia of Life Sciences (2001) “Polysaccharides: Energy Storage”

The question is incorrect in asserting that the only difference between amylopectin and glycogen is their extent of branching. This is only an incidental difference.
As I explain in more detail in the answer to another post, the key difference is in the topography of their branching.

This leads to spherical size-limited globules, in the case of glycogen, and large semi-crystalline extended structures, in the case of amylopectin.
This is the basis for their different chemical and physical properties within the cell (glycogen is soluble, starch is in a semi-insoluble form), which is all that is of biological interest to me. I cannot adjudicate on, nor am I concerned with, the properties chemists observe when extracts are manipulated in vitro.


text:
Introductory book on cell biology
I am studying the human circulatory and respiratory systems to develop tools for automated diagnosis of disease.
During the past year, I have read basic books about respiratory physiology, electrocardiography, etc.
At the moment, I feel that my lack of understanding of basic cell biology is prohibiting any further progress. I would like to find a very introductory book on cell biology, which would teach me

what kind of cells there are in humans, what are they made of, and what are their main components
basics of cell cycles, how cells are studied, how they look under the (various kinds of) microscopes
etc

The ideal text would probably be on the undergraduate level and not be much longer than 300 pages. Any suggestions? So I just want to find something to start with.

I would like to suggest the classic: Molecular Biology of the Cell, 5th Edition , ISBN-10: 0815341059

@LuizRobertoMeier MBOC now has a 6th edition, however, as Dexter pointed out, the 4th edition is available for search on the NCBI book shelf. I would almost suggest to the OP that you start by reading the relevant chapters of a recent edition of Campbell Biology, and then tackle MBOC. MBOC is a comprehensive and fantastic book, but if you don't have a basic understanding of the concepts it can be easy to struggle if you are trying to self-learn.

I just saw your final caveat... about 300 pages, MBOC clocks in around 1100... Start with the relevant chapters in Campbell. I believe that if you go to the Pearson website you are able to order by the chapter, which will make the book less expensive and leave out many of the sections you may not be interested in.

The Cell by Cooper is another option which I forgot to add in original list.

Lot of classic books available, most famous (at least in India) are

Molecular Biology of the Cell by Alberts et al [ Free Online | Amazon ] -- Simple language, good figures and my personal favorite
Molecular Cell Biology by Lodish et al [ Free Online | Amazon ] -- Very detailed with good examples
Gene IX by B Lewin [ Amazon ] -- Nice examples and figures. Lessons are in different order than most cell biology books.

If you want to just learn quick concepts, use online resources like Scitable by Nature. Pretty nice information with references and recommended reading.

Gene is far too advanced for an introduction to cell biology. MBOC is excellent.

All of these books are excellent about molecular biology and genetics. But that is not what the question asks for. They are completely inappropriate.


text:
What forms a mutation hotspot?
From https://en.wikipedia.org/wiki/Recombination_hotspot#:~:text=Recombination%20hotspots%20are%20regions%20in,that%20of%20the%20surrounding%20region.
I understand that hotspots may arise when certain regions are enriched with particular repeats, or if certain loci are located in chromosome regions that facilitate recombination.
But I'm not sure I understand this paragraph and the implications it may have:
"Recombination hotspots do not seem to be solely caused by DNA sequence arrangements or chromosome structure. Alternatively, initiation sites of recombination hotspots can be coded for in the genome. Through the comparison of recombination between different mouse strains, locus Dsbc1 was identified as a locus that contributes to the specification of initiation sites in the genome in at least two recombination hotspot locations. Additional crossing over mapping located the Dsbc1 locus to the 12.2 to 16.7-Mb region of mouse chromosome 17, which contains the PRDM9 gene. The PRDM9 gene encodes a histone methyltransferase in the Dsbc1 region, providing evidence of a non-random, genetic basis for recombination initiation sites in mice. Rapid evolution of the PRDM9 gene explains the observation that human and chimpanzees share few recombination hotspots, despite a high level of sequence identity."
I interpret this as there is a locus "Dsbc1" that plays a role in determining which place in the genome gets to have a recombination site (or makes that site more prone to recombination), and that the PRDM9 gene difference between chimps and humans causes our recombination sites to be different to those of chimpanzees. If I'm correct here, does that mean mutations to this or similar genes can have downstream effects on the mutation rate and thus how conserved another gene is?

There are many examples of genes that impact DNA processing and thus mutation rate globally. See pol delta (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2169052/), mutS (https://elifesciences.org/articles/22939), etc.

@MaximilianPress Yes, I'm guessing genes encoding DNA repair proteins may have the same effect, but I was thinking more about genes that determine hotspots (or make an existing spot hotter), and how this may impact the "conservativeness" of gene regions.

Yes, there are such cases. Another example would be homology-directed repair
(HDR) genes, where HDR targets rejoining of DNA breaks to regions sharing homology with each other. https://www.nature.com/articles/s41467-019-11105-z. This is one of the reasons why pericentromeric and other repetitive regions have high structural variability.

Latin -us singular, -i plural (for the particular declension to which locus belongs).


text:
Stability of helical strands of DNA?
The DNA molecules contain phosphate groups involved in $3'\rightarrow 5'$phosphodiester linkages. These groups, in the bonded state with deoxyribose, contain 1 negative charges ($\ce{3'-PO4^{-}-5'}$). This means that the two strands are very highly negatively charged. What than stabilizes the double helix, preventing the natural electrostatic repulsion between the two strands?
[I am assuming that the phosphate groups are dissociated under physiological pH, correct me if I am wrong.]

There is indeed a repulsive force between the phosphates in the DNA backbone. (The pK of the phosphate is very low so it will be ionised at all physiologically-relevant pH.) This is why DNA behaves like a stiff rod over short distances. However cations in solution will help to shield some of this repulsion. This is why DNA melting temperature decreases as the ionic strength of the buffer is reduced (by increasing the repulsive force relative to the favourable energy term coming from the base-pairing).
When DNA is condensed these repulsive forces are masked by cations like spermine, and of course by histones.

Careless typo.Corrected in the question. :)


text:
Formation of disulfide bonds in protein expressed after transduction
Say I transduce a nucleic acid sequence using a viral vector that encodes a protein having at least one disulfide linkage. For simplicity, let’s assume that there are only two cysteines in the protein and the side chains of these cysteines are close together when the protein is folded with the cysteines unlinked (reduced/thiol). Also assume that the cell being transduced is a eukaryotic cell (mouse or human). What is the chance that this disulfide will be linked (oxidized) when expressed by the cell? Does this happen pretty reliably? What might it depend on?

Could you please clarify. 1. By the use of the word transduce I assume you mean by a viral vector. Is that correct?If so, what vector? 2. By cell I assume you mean a eukaryotic cell rather than a bacterial cell. Perhaps you could edit your answer and also change the title to something more precisely descriptive like "Formation of disulphide bonds in proteins expressed after transduction".

In the protein intracellular or secreted?

@canadianer The sequence includes a secretion signal and meant to be secreted. These comments are giving me some ideas about what the formation of disulfides might depend on.

A lot depends on the nature of the disulfide; it may form in the ER during folding. It could also form in the oxidizing extracellular environment.  I don’t have any experience with expressing exogenous proteins in eukaryotic cells so I can’t be of much help.

I am not an expert on expression of genes from viral vectors, but as I requested the poster to clarify his question I feel an obligation to provide at least a partial answer.
The first question to address is whether the mRNA for the protein of interest is expressed in the same way as normal cell proteins. In the case of the lentovirus vectors which are integrated into the genome there is no reason to think otherwise.
In this case the factors determining the formation of disulphide bonds would be the same as for any similar normal cell protein translated from mRNA.
In summary:

Only secreted proteins have disulphide bonds.
In eukaryotes these protein are synthesised on ribosomes on the endoplasmic reticulum, which obviously must be present in the cell in which one is trying to express the protein (i.e. it must be capable of secreting proteins). One assumes that if one is restoring a function found in normal cells this will be so.
Oxidation of sulphydryl groups occurs in the intercisternal space before secretion. It involves a number of proteins and there are reduction and chaperone systems to deal with inappropriate oxidation, which occurs to a greater or lesser extent. A recent freely-accessible account of this topic can be found in a Cold Spring Harbor perspective by Neil Bulleid in 2012.
The (small?) proportion of incorrectly oxidised proteins that are not recycled are presumably removed by the cellular mechanisms that degrade aberrant proteins.

It would not seem possible to answer in a literal manner the question what the numerical ‘chance’ is of correct oxidation, but this would not seem to be pertinent. The question of interest is whether the protein would be oxidised to the correct native structure with the same efficiency as in normal circumstances. There seems no reason to think it would not.

This answer gives me ideas about how to start understanding my problem and what issues might be involved (the viral vector, the secretory pathway, protein disulfide isomerases).

I know you said you are not an expert on gene expression from viral vectors, but you mention "whether the mRNA for the protein of interest is expressed in the same way as normal cell proteins." This implies that there might be vectors that don't express proteins in the normal way. Did you have a particular example in mind?

@WaterMolecule — The way you phrased your question suggested an assumption that the insertion into the viral vector and it’s incorporation into the host genome were done correctly and that the gene would be transcribed normally. Thus your main concern was disulphide bond formation. I was able to answer the latter. However the former is not necessarily straightforward, and if that is a concern you would need to read specialist reviews of that area.


text:
How does human body deal with inert solid material in the bloodstream?
How does human body deal with inert solid material in the bloodstream? For example, if there is a powder of glass injected into our bloodstream, will the white blood cells do anything or will kidney excrete these materials? Thanks.

I once read a crime story (fictional), where injecting solid material like glass powder into the bloodstream was used as a means of deliberately murdering the patient :-). That would imply, that the body would not deal with such a condition very well. My mother is a medical doctor, read the same story, and did not say it was nonsense, recommended the book.

in some cases it will form scar tissue around it and even try to expel it by moving through the tissue.  in many cases it won't actually go anywhere, but form lump in the tissue.

As @shigeta points out, it would matter where the insult occurs and also what "inert" real means.  Glass could easily not be inert, and even if it were, you could easily kill someone with fine glass in a central line, just from the damage that would produce.  You want to look into inert foreign bodies.

Non-opsonized particles (Particles that can't be coated with opsonins like antibodies or complement proteins) can be engulfed by macrophages which could end up, for example, in the lung secretions and be coughed up one day. Note that a cell can only engulf a particle so large, so you'll not feel yourself coughing up anything out of the ordinary. Only tiny particles can be dealt with like this. Bigger particles can become trapped in fine vasculature (small veins; venules, and small arteries;arterioles). This can lead to abscess formation necessitating amputation of the affected limb.

It will not lead to abscess formation (that's a bacterial problem), but will lead to ischemia. Remember, most likely it will be injected into the venous side, which gets progressively larger until the pulmonary system is reached, so obstruction can occur in arterioles and capillaries of the lung.


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Birds and Dinosaurs
This came up in an argument with some friends. I know that birds are direct descendants of dinosaurs, shown pretty clearly through the fossil record. However, is it proper to say that birds are dinosaurs, or is there an actual distinction?

Do you know the concept of monophyly?

To comment on common scientific usage, I definitely hear paleontologists refer to "non-avian dinosaurs" when they want to exclude birds. Which implies that they would refer to birds as dinosaurs.

I bet you'll be interested about the concept monophyly. Any human-made group of species (or taxon) like birds dinosaurs, primate, bacteria, angiosperm, reptiles, … are either monophyletic, polyphyletic or paraphyletic. This picture explain the concept When the taxon is monophyletic it is called a clade.

Monophyletic taxon are those groups of species that can be considered to be objective in the sense that it represents a group of species where each species in the taxon is more related (in terms of time to common ancestor, not according to their genetic similarity) to any other species within the same taxon than to any other species outside this taxon. This is obviously not the case for paraphyletic or polyphyletic taxon.
Typically, we do not consider a parrot or a deer to be reptiles. Therefore, the ususal understanding of "reptiles" makes this taxon paraphyletic. Now, one should not confound the common understanding (what is a reptile in our everyday life) with the strict definition of the taxon Reptilia, which is a monophyletic taxon (or a clade in other words). Probably the best source for exploring the tree of life is tolweb.org. Here, you will find the clade Reptilia (who include birds, snakes, turtles and lizards). Note: Mammals are within the Reptiliomorpha, not the Reptilia.
It is exactly the same issue with the dinosaurs. When we talk about dinosaurs in our everyday life we do not mean birds. But there is a clade called Dinosauria, which include both dinosaurs and birds.
In short, I would say that a bird is a Dinosauria (monophyletic taxon) but is not a dinosaur (paraphyletic taxon). But this little play on word is not a scientific issue but an issue of english usage.
You will also find in this post an introduction to phylogeny

Some comments: 1) "paraphyletic clade" is an oxymoron; 2) "Monophyletic clades are those clades": again, clades can be only monophyletic by definition; 3) "clades ... can be considered to be objective": clades exist or do not exist irrespective of our considerations; 4) "more related" is very dubious term in this context, which could be here incorrectly understood as "more (genetically) similar"; 5) Reptilia doesn't include mammals on tolweb.

@har-wradim Indeed there were many corrections to do. I hope I fixed the problems. I confused the words taxon and clade. Thank you for your comments. Please feel free to edit the answer yourself in order to improve it.

English usage is definitely evolving on this one. I'd say "Birds are dinosaurs" is the new "spiders aren't insects" - it's getting into the repertoire of the annoying know-it-all who has learned cool scientific facts and insists on sharing them with the world. Some references : https://xkcd.com/1211/, https://en.wikipedia.org/wiki/Origin_of_birds (notice "birds are a group of theropod dinosaurs"...)

@RozennKeribin Except that insects (not counting spiders) are a monophyletic group. Dinosaurs (not counting birds) are not monophyletic (as your xkcd comic indicates).

@RozennKeribin I strongly disagree - the distinction between birds and dinosaurs is much muddier (@Remi.b's mono/paraphyletic distinction is excellently described) than the distinction between spiders and insects.

@Remi.b but dinosaurs (counting birds, and excluding pterosaurs and other dinosaur-like reptiles, which many paleontologists and nerds who employ this usage do) are monophyletic.

@BryanKrause I wasn't comparing birds/dinosaurs to spiders/insects from a biological standpoint, but from a meme/English usage standpoint. My point being that while the vernacular "dinosaur" usually represents a different group from the clade "Dinosauria", the usage is evolving in certain circles at least to make them coincide (and that group are those that will tell you that birds are dinosaurs and pterodactyls aren't).

Spider + insects (+ crustaceans and other things): monophyletic. spider: monophyletic. insects: monophyletic. birds+dinosaurs: monophyletic. brids: monophyletic. dinosaurs: not monophyletic. Dinosaurs is not a stand-alone mnonophyletic group unlike spider and insects are. In other words, spiders and insects are sister(-ish) taxa while dinosaurs contain birds. This is why I think your comment is misleading.

You are begging the question. Dinosaurs: not monophyletic if "Dinosaurs" is defined so as to exclude birds. And what I am saying is that in modern English usage, that definition is no longer so clear-cut as to exclude birds; there is an increasing number of people who use the vernacular "dinosaur" to mean "belongs to the clade Dinosauria", and to explicitly include birds. I'm not talking biology here, I'm talking an evolution in the English language.


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Why plants (eg. parsley) can keep vitamin C despite all the sun?
I have read that vitamin C is highly sensitive to light. So, how could parsley, for instance keep its vitamin C as it's flooded with sunlight?

UV light promotes the photo-oxidation of ascorbic acid (AsA) to dehydroascorbic acid (DHA).

DHA can be reduced to AsA by a specific dehydrogenase using reduced glutathione as reductant. I'm pretty sure that all cells are able to carry out this recycling of ascorbate.
Interestingly, in plants it appears that ascorbate acts as an electron donor to photosystem II (which is equivalent to it being oxidised).

Thanks a lot for that! So would it be correct to say that parsley only contains DHA? (Or most of it) (AsA should logically have been already reduced just after the DHA syntheses)


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Why only water in liquid form is essential to live?
My question is:-
Only liquid water supports almost every living organism's metabolism, neither the vapour nor the condensed form of water does so. What is the chemical & the biological reason behind this fact?

Because we depend on dissolved molecules, nutrients, minerals and so on. This is neither possible in solid (frozen) nor in gaseous water. Besides that, the temperatures necessary to have water either frozen or liquid are not really life promoting.

@Chris Just a minor correction, dissolved solutes may be present in solid form, forming a solid solution. Otherwise, the arguments are perfectly valid.

Ok, I wasn't thinking about this, but I think this doesn't play a role for life.

@SatwikPasani.. There is no fluidity in solid "solutions". Reactions that happen in a solid state will be extremely local and all the diffusion effects (including morphogenesis) will not occur. Rigid solid microdomains are important to maintain structure but there should be an appropriate solvent that can sustain the multitude of biochemical reactions.

Organisms evolve to fit the environment they are in and all of earths organisms have a typical body temperature of above 0C and 100C, the freezing and boiling points of water respectively. So water at this temperature is liquid and we have evolved to carry out reactions at this temperature and use water as the solution for many reactions.
But why couldn't we have just done the same for water as a gas or a solid. Well as a gas it takes up a much larger volume, phenomenally higher and therefore we would either need to be massive or use high pressures. Additionally, containing reactions that carried out at this temperature with probably huge releases of energy is incredibly difficult. As a solid it is difficult to mobilise. As we dissolve essentially all of our bodies nutrients in water, or use the hydrophobic properties of fats to mobilise lipid soluble things, it would be incompatible with life. We rely very strongly on the ability of water to flow. Solids can't.
An interesting question is why water and not another liquid?

This is because of the physico-chemical properties of water. It can form hydrogen bonds with itself, making sure it will not be gaseous before reaching 100°C (under normal pressure). H2S for example, which is relatively similar when looking at the atoms from which it is build, melts at -85.7°C and boils at -60.2°C. Water is also capable of dissolving a lot of other substances, it is not acidic or reactive (though it can take part in reactions), which makes it the perfect substance for the basis of life.

What about alcohols?

Lower alcohols could work, but we have the same problems here with melting/boiling points and the solubility of substances. An alcohol based life form would of course rely on other molecules, but it would still be difficult.

A layman's view of the problem :
Let's assume that water in liquid form was not necessary and organisms could survive on solid or gaseous water. What would some of the difficulties be to sustain such a life form?
Solid Form of water

How would the organism move without breaking or tearing itself apart? How would essential substances be transported from one part to another of the organism body?

Gaseous form

What would be the size of the organism? Gas has a much bigger volume than water.
In order to transport nutrient molecules within the a gaseous body, a huge air pressure needs to be generated. Also, how will gravity be overcome while transporting these molecules? A lot of energy will be required to maintain such pressures.

I guess nature (which always takes an optimal path) asked such questions and found that water in it's liquid form was the most suited to support life on Earth.
It need not be water alone. Other liquids may be able to support life as well. Only, we haven't discovered them yet. But whatever the substance, it's liquid form would seem to be an optimal solution for life.


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How are viruses weakened to be suitable for vaccination?
I understand there are two kinds of active vaccination

Injecting complete viruses that are weakened to not cause the disease being vaccinated against
Injecting only antigen particles of viruses that the body creates antibodies for. So the disease can't arise, not even in a weakened form.

I am wondering how the viruses for vaccination are weakened. Is this simply a process where randomly parts of the virus DNA/RNA are taken out and tested on animals, and as soon as it is sufficiently weakened, it is considered suitable? Or is this an analytical and systematic process?
I am wondering because some popular vaccinations (including that against measles) can still (very rarely) cause fatal complications. Which made me think whether it's systematic or just "accelerated mutation and selection".
I'm interested in an answer for layman, if that is possible at all.

There is a Wikipedia page on the topic of attenuated vaccines.
Basically the idea is that the virus is grown on some sort of foreign host such as cells in culture, eggs or an animal. This selects for mutant viruses, present in the original population, which are pre-adapted to the new host (so that they grow better). By repeating this process several times it is possible to develop a new variant of the virus which grows poorly in the original host (i.e. humans) but is still able to stimulate an immune response. The resulting antibodies, will recognise a subsequent infection by the original disease-causing virus as long as the viral component responsible for the immune response is still present in the attenuated virus that is used for vaccination.

So simply the fact that the virus now replicates in a foreign host is enough to ensure that it no longer affects humans? I would have expected that there needs to be some sort of selection for strands which do not make humans sick, but obviously the only way to do that would be to try the mutation on humans which is not possible for ethical reasons.

There are basically three classical possibilies:

Using an attenuated virus as Alan described in his answer
use only parts of viruses (here mostly proteins, which are displayed
on the surface of the virus and which can be recognized by the immune
system)
inactivated viruses (here often formaldehyde is used, which changes
parts of the proteins, the formaldehyde is then cleaned away to have
the vaccine free of it)

The part you describe about using DNA from a virus is done these days. It is called "reverse vaccinology" and uses conservation analysis between different strains (this is also used for bacteria) to get a vaccine which covers as much different strains as possible. For the vaccine, proteins are selected which are conserved as good as possible and which show no similarities to human proteins (you don't want to induce autoimmunity). Candidate proteins for a vaccine are then expressed biotechnically and tested if they work.
Complications in vaccinations (which are really rare, for measles the chance for complications is 3-4 orders of magnitude lower than when actually get the disease) are usually due to allergic reactions.