How fast do different organs turn over cells? It is said that the human body turns over all cells or molecules in 7 year cycles. This is not quite correct, because there are different organs changing at different speeds. My interest is what is the scale of change and especially, is it possible to measure and how fast do:

1) cells change

2) molecules change

3) atoms change

High, medium and max rate organ examples would be appreciated.

1) cell growth

You should look into chemotherapy and cancer medicine in general.  Because chemo is mostly effective because it kills fast dividing cells, this has been worked out reasonably well.  the 7-10 year number is not really correct, some cells are replaced a lot more slowly.

This is why hair often falls out in cancer treatment, because the follicle cells are growing quickly.  Neurons divide very slowly - if at all - and often are never replaced.  Fat cells are in between - probably replaced in the 7-10 year range.  Heart cells are replaced albeit quite slowly - less than 1% per year, which implies that many cells are with you your entire lifetime.

2) atoms/molecules change

The cell itself is in a continuous state of flux, but different parts of the cell, like cells in the body, change at different rates. Some proteins which make up the cell matrix or the DNA in the nucleus are replaced very rarely (through repair or rearrangement of the chromosome for instance) and most of the chromosome DNA is with the cell for the entire life of the cell.

Most proteins are labelled for degradation and are recycled after a few hours of function.  Metabolic compounds such as sugars or salt might drift in and out of the cell continuously, maybe turning over in an hour or so. Fats can be incorporated into the cell and last for years I think.


How useful are vitamin and trace element additions in E. coli culture medium? In protocols for minimal media for growing bacteria I often see that a vitamin mix or a mix of various trace metals is added. But at least for E. coli I know that those are not strictly necessary, they also grow in minimal medium without any of this.

Does it make sense to add vitamins or trace elements when growing common E. coli for protein expression like BL21 (DE3) in minimal medium? Is there some literature data on how this can affect the growth of the bacteria?

Not sure that I have ever come across trace metals in recipes (I assume that you aren't referring to the Ca/Mg salts component of M9), but it is certainly the case that many K12 strains (e.g. C600, DH5α) require thiamine because they are thi mutants. This doesn't apply to BL21 since it is from a different lineage (it is a B strain). In a lab where several strains are being used it will always make sense to standardise on a universal recipe so that the medium available will suit all strains in use.

There is a useful list of E.coli genotypes here.


Difference between sequential and conformational epitope Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

Yes, the difference is "only" in the 3D structure. This makes some differences when proteins change their shape; antibodies which recognize conformational epitopes are usually not well suited for lab work, as proteins are often denatured here.

The different epitopes are also called linear epitopes (for the sequential) and discontinous epitope (for the conformational). Schematically this look like this:


Are MHC Proteins the Most Polymorphic Human Proteins Known? There is a paragraph titled "MHC Proteins Are the Most Polymorphic Human Proteins Known" in the "Molecular Biology of the Cell" by Alberts et al. 6th ed. 2014.

But someone has recently told me that it is not the case making an example of a set of genes helping to identify persons in forensic medicine. (I didn't remember the genes.) Is it true?

Are MHC proteins the most polymorphic human proteins known?

Yes.  There are many MHC (MHC in humans is called HLA) genes.  The classical loci — Class I A, B, and C, and Class II DP, DQ, and DR — are the most polymorphic.

Here's a table from a 2002 article which clearly shows the number of polymorphisms.  It's no contest.

It's worth me pointing out that those numbers are wildly out of date.  The IPD-IMGT/HLA can provide full lists of known HLA alleles, but the exact numbers are in the tens of thousands:

The person you spoke with was probably referring to sequences called microsatellites.  These are small regions that are polymorphic and quite variable between individuals, and using a number of these together can be useful for genetic fingerprinting, but each individual microsatellite will not be as polymorphic as HLA class I A, for example.


What makes some viruses more infectious than others? This week a new strain of the SARS-CoV-2 virus was discovered in the UK, and reports are saying that it's more infectious than the strains we've been dealing with for the past year. Which made me wonder: what is it about different strains (or different viruses in general) that makes them more of less infectious than others?
They've been saying that they don't think the new strain will be any more resistant to the vaccines. Does that mean they're no more able to evade the immune system? Or is it just the immune system that hasn't been primed by a vaccine?

To name a few parameters that can determine the infectiousness of a pathogen:

Transmission pathways used (aerosols, surfaces, vector organisms, feces etc.)
Molecular affinity to bind to host cell (how well does it penetrate the cell)
Strategy within host cell (lysogeny, lysis)
Interaction with the host’s immune system


Is it ok to keep primers at 4 degrees? I reconstitute my primers in nuclease free water ( no sterilised) this morning and I forgot them at 4 degrees, acording to the instructions, they should be storage at -20 after the reconstitution. I am wondering if it will affect to have them overnight at 4 degrees, just for one day.

There is absolutely no problem here. Primers will degrade only very slowly at 4 degrees and even at room temperature leaving them out overnight would not degrade them enough to be of practical consequence. In fact, if you're using them today it's probably better to have stored them at 4 degrees than -20 because repeated freeze/thaw cycles will also degrade primers.


Is there a karyotype database for human cell lines? I'm looking for the karyotype of a specific cell line. Some karyotypes are well known, such as HeLa or some carcinomas, but some are very hard to find, such as LG2 (B cells). Is there a database dedicated to karyotypes of human cell lines?

As far as I know and have found, there is no one master database for karyotypes of all human cell lines. They are usually grouped into subsets either by some commonality (e.g. being cancers) or simply because of who/where they were developed and how they chose to share the line. Some good databases/resources are:

ATCC - A great repository that has cell line datasheets, references, images, and culturing info. I highly recommend using ATCC as your first stop when looking to learn more about a line.
NIGMS Human Genetic Cell Repository - A very robust repository that contains far more than just cell lines. It's good, but the wealth of info can be a bit difficult to sift through.
COSMIC - A great collection of info on cell lines and mutations found within them. Good if you want to look for/understand particular genetic aspects of a line.
Cellosaurus - A fantastic database on cell lines! I particularly like the info Cellosaurus hosts on different names and common misspellings of names for cell lines. It also provides info on hierarchies of cell lines- that is, when multiple cell lines are derived from a parent line. This is super helpful when trying to parse literature with confusing references to similar lines. It also provides references and cross-references. I cannot recommend this one enough.

To get back to your particular cell line, I have only been able to find one reference to a line called 'LG2'- even with the help of the resources listed above and PubMed, so I, unfortunately, can't give you much info on that specifically. If there really is so little info on this line, I would suggest contacting the source (colleague, lab, excel sheet associated with your storage system, etc.) for your cells to see what info they have. If you can't find anything that way, it may be best to just submit a sample for sequencing yourself and get that info out there.


What are the major differences between good study habits for biology vs mathematics? I'm a math prof. But, I've always loved reading about biology (the paleobiology of microbes and some small animals mostly) it's my hobby but I want to learn more maybe take a course. My longer term goal would be to be able to be of better assistance to my online friends who are biologists who are always asking me to help with the statistics in their papers. (I have been able to help, but I feel like I could do better)

When I study math, I aim to be able to identify and prove all major results from memory, state all definitions, and solve new problems and proofs. I have a process it works.

But with biology I often find that there are multiple definitions or there are big differences between textbook content and studies. It's really upsetting. I understand why this is true, that's just the nature of science, but I don't understand how to best navigate when a topic has multiple interpretations that are all possibly true. I get really hung up on not being able to find one definition for some terms.

Should novices and students stick to textbooks and "widely accepted" definitions? Or should one make and effort to keep up with the most recent research and learn to live with the ambiguity?

I can take one course for free at my university each term. Should I start with 101? Or can I do that through self-study and start with something more specialized?

What is a good self-study book?

My only science background is a few newtonian physics courses.
I'm kind of scared to go to the biology department and ask. Biologists are really intimidating when you teach something simple and clear like math.

I started in cell and molecular biology, but moved to applied math and computer science, so perhaps I can give my thoughts.

Personally, I found that biology learning was more about big ideas and visualization. The first is because biology has an extraordinary amount of details (e.g. Molecular signaling pathways, biochemical properties of different molecules, the location of different foramen in certain fossils, etc...), so it is truly impossible to remember them all. You should focus on learning what to look up, not what is actually occurring. Something you work on will be gradually memorized on its own, so don't spend effort memorizing things you can look up (you're not an undergrad :) ). So don't remember that histone acetyltransferases use acetyl-coa to act upon the NH3+ groups of lysines. Just remember that those enzymes modify chromatin in a way that alters transcription, thus changing the cell and its behavior. The second (visualization) is because it is very hard to understand biology without pictures! So use them, not text (no kobayashi and nomizu style). Mathematicians like symbols but (at least in the molecular case) there are too many of them (and they are mostly useless names... e.g. P53). Much of biology is about seeing  visual results (blots, fossils, medical images,...) and interpreting them.

Note that (I think) the first suggestion is harder in biology than in math, because math partitions naturally into theorems, corollaries, lemmas, and their applications (roughly in order of importance of what you need to know :) ). Biology as a field is more of a fast moving chaos of  observations and changing inferences. But of course there is a constantly growing core of the field that is not in flux.

One good thing about biology is that one can be an expert in one area but know little about most others. Math is a little more intertwined. So there's no need to read a "general bio" book. Just read an intro book to your target topic (e.g. Ecology, evolution, cell bio, molecular biophysics, bioinformatics ...). They will cover the relevant parts of other fields, usually. I know genetics experts who know basically nothing about cell trafficking for example. But you will definitely need some background to read the latest literature (i.e. Don't skip straight to Cell papers).

One issue that occurs throughout science, but also in math, is that learning is a process of improving models. In math, we might start with linear algebra, then basic manifolds, and eventually with, say, finsler spaces. In physics, we go from Newton to Einstein. In biology, we start with a basic model and set of rules, but gradually add exceptions and details to it. I think this is where much confusion can arise, because things that were correct in the simplified model might be wrong in the better, more complex one.

Also, models are being updated at an insane rate in biology. Often that means that previous models were wrong (though the evidence underpinning them is not); hence definitions and results might change over time! Science improves over time, and this is a good thing. Of course, in math, once something has been proved, it will never change. (Although definitions, or at least notation, in math can be very inconsistent too). Of course, if there are inconsistent definitions, you can ask here and see what people think. I will agree that biologists are less concerned about detailed rigor than being correct overall. Generally scientists will either define such things themselves or cite a reference with their chosen definition.

My suggestion for your question is to learn the basic widely accepted definitions first, then go to the literature. Often it is the case that different groups think different things. Most likely, one or both will be proven wrong eventually. Each paper is likely to be internally consistent; the only ambiguity is usually in areas where no one knows the correct answer or interpretation. Two groups in conflict usually have reasonable hypotheses consistent with the evidence, and if they can't decide how to mesh their ideas, probably we can't either. So don't worry about it too much.

So when a topic has multiple interpretations that are possibly true, use your math background and consider it from a Bayesian perspective :) most likely all the interpretations are at least partly true, and have some non zero probability of being true. And as you read more papers, update your posterior. :)

Also, don't worry about talking to biologists (as the other commenter states). In fact, among the sciences and engineering fields, my opinion is that biologists are on average the friendliest and least arrogant :)


Steroid hormones: how do they travel through the cytoplasm (not just the blood plasma) if they're hydrophobic? I get that steroid hormones need hydrophilic plasma protein carriers (eg albumin, TBG) to travel in the plasma because they're not soluble in the plasma. However, I don't see any sources talking about how these hormones can then traverse through the (presumably also hydrophilic) cytoplasm to get to their receptors either in the cytoplasm or nucleoplasm. Anyone have any clarifications on this?

Firstly not all steroid hormones travel inside the cell and regulate the gene expression.
Basically there are two pathways- direct and indirect.
Steroid hormones are lipid-soluble, which allows them to cross the extracellular membrane to the inside of the cell.

Classical models of steroid action suggest that steroid hormones bind to specific nuclear receptor proteins once inside the cell. Reference

Once inside the cell, a steroid hormone binds with receptor proteins in the cytoplasm. The steroid hormone and its receptor form a complex, called a steroid complex, which moves into the nucleus where it influences the expression of genes.
Reference

In the indirect pathway,

The traditional nuclear steroid receptors can also indirectly regulate gene transcription by serving as signal transduction proteins that interact with various signaling pathways in the cytoplasm of a cell. In particular, ER can activate kinases, enzymes that phosphorylate and thereby activate other proteins. This sets in motion a signaling cascade that eventually ends in the nucleus with the induction of gene transcription.
Reference


Why would we overexpress Sir2 by overexpressing its hypomorph (dSir2-EP2300) in C. elegans? Can't we just overexpress regular Sir2 in the paper? Rather than overexpress a reduced-function gene?

The paper is  Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.. 2011. Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila. Nature 477: 482–5.

I have had a little time to look over this paper.

They do overexpress a native sir2 clone in high doses, called sir2.1 OE.  Which seems to be native and also appears in high copy numbers. This strain was found in previous publication to have a high lifespan... that is old news.

This paper sees sir2.1 expression levels as an oversimplification of the causes of longevity.  When they create crosses of the sir2.1 OE strain with wildtype, you can see the Outcross, which is verified to have a high level of sir2 expressed no longer has an extraordinary lifespan.

This can be seen in Figure 1.  http://www.nature.com/nature/journal/v477/n7365/fig_tab/nature10296_F1.html

So this paper is now asking, if sir2 levels do not convey the information that creates an extended lifespan, then what does?  It must be some modulation of some protein that sir2 affects.  They implies that the actual cause of the lifespan increase may have been a mutation somewhere else in the organism.

"However, longevity was not suppressed by sir-2.1 RNA interference (RNAi) ... indicating causation by factors other than sir-2.1, either on mDp4 or elsewhere in the genome."

"This implies that lifespan extension is due to transgene-linked genetic effects other than the overexpression of dSir2."

In the second half of the paper (figure2) the investigators have moved on to drosophila work, where they look at how expressing constructs or inhibiting sir2 protein levels might affect lifespan.  Although the dSir(EP2300) / + construct (drosophila sir2) with a wild type gene promoter did not live quite as long as dSir2(EP2300) with a fancy promoter (dSir2(EP2300) / tub-GAL4), the promoter construct (tub-GAL4/+) alone also had just as long a lifespan.  How can this be?  Not sure, but the expression of sir2 is clearly not the panacea we had hoped.  Note however that the reduced power gene still gave the same boost to lifetime.   This shows dramatically that sir2 activity alone does not drive the longer lifetime.

Lastly, deletion constructs (dSir4.5/1.7) , which should have lower than wild type protein levels for sir2 had completely normal lifetimes.

So the answer to your question; you need to test a hypothesis going in both directions - does increase of the protein really create a strong effect?  Does decreasing it have a negative effect then?  There are lots of other reasons to use knockouts and non functional genes in such an experiment, but those are the broad strokes.


Why must gene entrapping constructs be integrated into introns and not exons? Homework Question:

In enhancer trapping, reporter transgenes are integrated randomly into the fly genome and their expression identifies enhancers and thereby genes expressed in particular patterns. In mice, a similar technique for gene identification is employed called “gene trapping.” In gene trapping, an exon encoding a reporter protein such as GFP (see below) is integrated into random locations in ES cell chromosomes (when DNA constructs are introduced into mouse ES cells, most recombination events are into random sites; homologous recombination is relatively rare). ES cell lines with randomly integrated transgenes are used to generate mice.

Where in the genome must a gene trapping construct integrate in order for ES cells to express GFP?

Answer:

My Question:

Why can't the construct simply be knocked into the coding DNA sequence of the mouse genome? Why does it have to be integrated into an intron?

I don't know that they must integrate into an intron. It seems perfectly reasonable that they could also integrate into an exon, as long as the reporter is in-frame. There is obviously an element of chance in that, and so the advantage of integration within an intron is that splicing will ensure that the reporter is translated correctly. Intragenic regions are also more abundant in the genome and so insertion is more likely. They discuss the advantage of this design in the original paper:
Gossler A, Joyner AL, Rossant J, Skarnes WC. 1989. Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science 244:463-465.

...ES cells permit selection for rare-occurring integration events, which allowed us... to design and use a "gene trap" vector. The vector contains the lacZ gene, lacking a promoter and translation initiation signal, inserted in frame into the homeobox exon of the En-2 gene such that a splice acceptor is placed at the 5' end of lacZ. Integration of the construct into introns of genes in the correct orientation should create a spliced lacZ fusion transcript and a functional fusion protein when the reading frame is maintained. Evidence for this came from experiments in which a construct lacking the 5' En-2 splice acceptor yielded 12-fold fewer lacZ-expressing transformants than the construct carrying the splice acceptor.

Exonal insertions by gene traps have been reported:
Song G, Li Q, Long Y, Gu Q, Hackett PB, Cui Z. 2012. Effective Gene Trapping Mediated by Sleeping Beauty Transposon. PLS One 7.

Insertion of a trapping cassette into an exon or an intron of transcriptional active loci can generate a fusion transcript that contains the upstream exon and the reporter/selectable marker.
...
Eighteen transposition events were obtained from distinct cell colonies. Blasting the human genome in the NCBI and ENSEMBL database... indicated that seventeen of them landed in an intron and one of them integrated in an exon at active genomic loci. These data are in consistence with the fact that exons and introns comprise 1.5% and 24% of human genome, respectively.

See here for further reading.


Quantifying Gene Expression I have found that many studies use the mRNA concentration as a “proxy” for protein activity because there should be correlation between mRNA levels and proteins expression levels. How is protein activity quantified? Which quantity is used? What are protein expression levels?
I am doing some statistical data analysis using this dataset. I would like to understand why they have been interested in measuring mRNA concentration after the cells gamma irradiation (and in general it seems to me that biologists in many experiments are interested in that). I found in this site that discussion about correlation between mRNA concentration (so gene expression level)  and "protein expression level". Therefore I wanted to know what the latter is. Moreover, in the article related to my dataset is written

Very few DNA repair genes displayed significant differential expression in P. furiosus following gamma
irradiation.

And then

the data we reported here suggest that DNA repair proteins in P. furiosus and several other archaea are constitutively expressed and that they may be present in the cell at a level sufficient to maintain the integrity of the cell’s genetic material.

So putting together what the scientists conclude with what MattDMo has answered to me and what is discussed here , I think that I can conclude that "protein expression level" is a measure of the amount of protein actually translated from the mRNA, that then (in this case) will effectively act to repair DNA. Therefore, "protein expression level", as well as "protein activity", indicates the proteins translated from mRNA and that will actively act to repair DNA damages (in this case that we are talking about DNA repair proteins and DNA repair genes).
I have to say that I do not really know well what "DNA repair proteins are constitutively expressed" means, but I think that is that DNA repair proteins have already been translated from the mRNA and therefore they are "present in the cell at a level sufficient to maintain the integrity of the cell’s genetic material" (as they say soon after).
All this makes sense to me if I think about my first objective that was to understand the reason for measuring mRNA concentration. We are interested in it because there should be correlation between mRNA concentration (gene expression level) and the proteins actually translated from mRNA from that specific gene, in order to know which kind of proteins will effectively act in the DNA repair processes (in this case).
I wonder if all this interpretation is correct...

What is Protein Expression Level?
This was the original title of the post, which I edited myself because I regard the answer as trivial, but the question as more substantial. To deal with the trivial first:

‘Level’ is not a scientific unit, and can only be used unambiguously
as a scientific term in its English sense in relation to liquids, e.g. “The level of mercury in the thermometer had
fallen.”, “The land is 10 metres above sea level.”
It is used by some people in informal speech or writing to indicate an
undefined quantitation, and because of its very ambiguity is to be
strongly discouraged in scientific communication.

So neither I nor anyone else can say what ‘protein expression level’ is without finding out what the originator of the phrase intended (if indeed he knew) in any individual instance: quantity or concentration of protein, or the rate of its synthesis.
Quantitation
Let us consider some general aspects of a cellular molecule that may require quantitation: Amount, Rate of Synthesis, Rate of Degradation and, where relevant, Biological Activity.
The quantitation of molecules at its most basic is the number species,  or, more practically, their total mass (grams), where possible related to their molecular mass (i.e. moles). The rate of their synthesis or degradation is expressed in terms of the change of their amount in unit time.
In order to compare different systems a reference is needed for the quantitation. This may be per unit volume, per cell, per g cellular protein, per g DNA etc. (However for comparison of similar systems or within one system the reference is often omitted.)
The biological activity of molecules only has meaning if the molecules are, indeed, biologically active (e.g. enzymes). It is expressed in units related to that activity.
Examples of Quantitation for Proteins
The actual units used in quantitation are determined by how one is able to measure the parameter of interest.
Relative amount of protein: You might detect a protein by the intensity of staining of a band on a gel, or by the extent of precipitation using a corresponding antibody. These would have to be calibrated against standards in order to convert raw experimental measurements to g or mole protein. Typical units of relative amount are g/g total protein, g/g DNA.
Rate of synthesis or degradation of protein. You might detect the synthesis of protein by the rate of incorporation of radioactive amino acids into non-radioactive protein, and the rate of degradation by the liberation of radioactive amino acids from pre-labelled protein. Typical units of synthesis would be mg amino acid incorporated per min per mg total protein. (This can be converted to molecules synthesized or degraded per minute, if necessary.)
‘Protein Activity’: The use of this term is not recommended. In chemical terms the activity of a molecule is a measure of its “effective concentration”, and in relation to proteins would only be the concern of biophysicists and the like. Other biologists would associate the term with the biological activity a protein such as an enzyme might have, but as many proteins are structural the term ‘activity’ cannot be applied to proteins generally. Where it is of interest it would be quantified in terms of the nature of the activity, e.g. an enzyme is quantified in units related to the amount of substrate converted to product in a given time.

Quantitation of Gene Expression using Oligonucleotide Microarrays
The two extremes in quantifying gene expression are the detailed study of the expression of one particular gene encoding a protein for which information and tools are available; and general study of the expression of many genes using modern methods that allow the study of many molecules simultaneously. Such methods included mass spectrometry (for small metabolites), two-dimensional gel electrophoresis (for proteins) and microarrays or RNAseq (for mRNA). In general in the latter case one would examine the effect of some agent or condition on the whole spectrum of gene expression.
Let us examine microarray technology as that is the main concern of the poster.

Microarray technology measures the relative amounts of mRNA.

The methodology involves amplifying a mixture mRNA species by reverse transcription to cDNAs, which are labelling with a fluorescent dye. The cDNA is hybridized to immobilized oligonucleotides based on the sequences of the genes in the organism, and the strength of the fluorescence signal is assumed to be proportional to the amount of individual mRNA species in the sample. However the data supplied to the user is the relative image intensity within the experiment, rather than units that allow one to calculate the actual amount of mRNA.
How does these relative amounts of mRNA relate to gene expression?

The relative amounts of mRNA are a relative measure of the rate of synthesis of proteins (3 in dig.), if one assumes that the rate of synthesis of each protein is similarly proportional to the amount of its mRNA (a in dig.) which would be limiting. This is a reasonable assumption in most cases given mRNA is degraded more rapidly than protein. (They are not a measure of the amount of protein — b in dig.)

The relative amounts of mRNA cannot be taken as a measure of the rate of transcription of a mRNA from its gene (1 in dig.) because of the relatively greater effect of mRNA degradation (2 in dig.) on the steady state concentration of mRNAs, and the fact that different mRNAs have different half-lives.

Postscript for the Poster
I have tried to make this answer general, to be of use to more people. As the poster is not a biologist she may still have difficulty in understanding the background to the biological experiments that generated the data she is analysing.
The biological system of interest is gene expression, which encompasses the whole series of events from transcription of genes to mRNA and their translation into protein. The background to this is that there are some genes that are (almost) always expressed, irrespective of physiological circumstances because they are needed to maintain the structure and everyday functions of the cell. This is termed constitutive expression, examples being expression of the genes for cytoskeletal actins or ribosomal proteins. Other genes are expressed (‘switched on’) only when needed (and may be termed inducible). The question here would appear to be whether the genes for the enzymes involved in DNA repair are expressed all the time (constitutively) to deal with normal ‘wear and tear’ of DNA, or whether their expression only occurs in response to some insult knwn to damage DNA, such as gamma irradiation.
As I mentioned, as an experimental scientist, one approach that can be adopted here is to look at the expression of one or two well characterized proteins that are known to be involved in DNA repair. However, there may be proteins involved in this process that you are unaware of, so the modern methods of looking at the expression of all the genes in an organism (if the DNA sequence is known) — oligonucleotide microarrays or, better, RNASeq. These methods measure relative quantities of mRNA in a cell. This is not a proxy for amount of protein or rate of  its synthesis (the term ‘protein activity’ is meaningless and is not and should not be used), it is what it is, but is also a reflection of the expression of the genes that encode the mRNAs. No expression, no mRNA.
You can think of the microarray and RNASeq approaches as a fishing expeditions. If you find mRNAs that are only present after the cell receives a stimulus or an insult, expression of the mRNA has occurred (whether or not the amounts are directly proportional to the rate of synthesis). If the mRNA is synthesised you can assume it is translated into the protein it encodes. In the case of gamma irradiation you might assume any mRNA that shows a large increase in quantity encodes a protein that involved in protecting the cell from the radiation. This will be of scientific interest, especially if it is not what one anticipated.


Is it possible to grow a fertilized human egg entirely outside the woman's womb? Many science-fiction movies (for example, The Island) show the possibility of growing a fertilized human egg cell (from the beginning to the end) outside the womb of the woman.

This means that you have to create the exact circumstances for the fertilized egg cell to develop into a human being. These exact circumstances coincide, obviously, with the womb of a woman.

Doesn't this require a woman, where those circumstances are exact, which means the only place where a fertilized egg cell can grow is the woman itself? So basically I'm saying that you need a woman (the womb is connected to the entire body) to let the single fertilized egg cell into a fully grown 9 months baby.

Well, this isn't exactly true: after development for 5 months or so in the womb, an artificial environment can take over, which is possible with current technology. But to devolop the fertilized egg right from the start is another story? Can it be done, or is it impossible (of which I'm certain, but nevertheless I ask this question)?

I believe what you're describing is referred to as ectogenesis which is essentially developing a fertilized egg inside an artificial womb until it’s able to survive outside the controlled environment. So is this possible outside of science fiction? To answer this we have to compare the stages of human reproduction and how close today's science and technology can come replicating/sustaining them.

We'll begin by dividing these stages into two groups: fertilization and development of embryo to fetus.

When it comes to answering the question of whether fertilization can be replicated in vitro or not, the answer is yes it can be done! In fact in vitro artificial fertilization (IVF) has been possible for several decades. In most cases when IVF is performed the egg is then placed inside the mother's uterus where it goes onto to develop into an embryo and then fetus. In regards to "ectogenesis" the IVF egg would be placed into an artificial womb.

In order to form a zygote (fertilized egg) to develop properly into a fetus it has to be an environment to meet it needs. In a female uterus all these needs are met but replicating them might be difficult. An artificial womb would have to be able to provide nutrients, oxygen, and channels for the development process of a fetus as well as system to expel (birth) the fetus once its development is complete. So can today's technology and science do all this? In theory yes, if resources and time where dedicated (and red tape cut) it would be possible to develop a fertilized egg in an artificial environment within the foreseeable future. There have been multiple experiment where artificial wombs were implanted with fertilized eggs and began to grow but were stopped due to legality.

I encourage you to read the following Wikipedia and motherboard articles regarding artificial wombs and ectogenesis.

https://en.wikipedia.org/wiki/Artificial_uterus

http://motherboard.vice.com/read/artificial-wombs-are-coming-and-the-controversys-already-here

*Note there is a lot of biology I did not mention regarding zygote to fetus development which is the biggest question/obstacle that ectogenesis might face


Why is it difficult to bend the waist while keeping the knees straight? It's easy to keep your legs straight when you're standing up or laying flat on your back, but as soon as you try to sit up or bend down, you need to bend your knees as well as your waist.  (Try it.  Lay down flat on the floor, then try to sit up straight while keeping the backs of your knees pressed against the ground.  You'll have trouble long before you reach 90 degrees.)

Why is this?

First off, I would be careful generalizing people's experiences with this exercise (..."Try it...You'll have trouble long before you reach 90 degrees"...):

Source: Yoga Tune Up

The muscles you are feeling at 90o, and the lady pictured above perhaps not even at 180o are the hamstrings. They run along the back of your thigh, attaching at both the hip and the knee. They flex the knee and extend (straighten) the hips.

Source: Precision Nutrition

When you do the exercise you are describing, the pelvis starts pulling on the hamstrings from the top because your knees are staying in place. Bending the knees releases the stretch.


Grapefruits and CYP3A4 Grapefruit juice contains furanocoumarins, which irreversibly inhibit CYP3A4.  For this reason, when one is taking certain medications it is necessary to not eat grapefruits because the inhibition of CYP3A4 can reduce how much of the drug is metabolized before it can get used, resulting in an overdose.   It apparently takes 24 hours after eating a grapefruit before the enzyme level is 50% and up to 72 hours for it to be completely normal.  So, it seems that eating one grapefruit a day would substantially impair one's CYP3A4 levels indefinitely.

Wikipedia says, the purpose of CYP3A4 is "to oxidize small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they can be removed from the body."   It seems like inhibiting CYP3A4, from a biological standpoint, would reduce one's immune system or at least the ability to tolerate and eliminate certain toxins.   Are there other enzymes that take up the slack, or is there something in grapefruit itself which does the job instead, or is a daily grapefruit just a bad idea?  What are the effects of extended inhibition of CYP3A4?  Will the body perhaps build up a tolerance or immunity, or (perhaps with negative effects) pump out more CYP3A4 to try to compensate?

In general, xenobiotic biotransformation (i.e. processing the xenobiotics aka drugs - detoxing the body) is accomplished by a limited number of enzymes with broad substrate speciﬁcities. In humans, for example, two cytochrome P450 enzymes— namely,CYP2D6 and CYP3A4 — metabolise over half the orally administered drugs currently used. (Gonzalez and Tukey,2006).

The various different CYP enzymes can act on various different foreign organic compounds with varying levels of efficiency. The CYP enzymes oxidise these organic molecules adding on -OH groups to make them more solube and thus more easily excreted.

Grapefruit contains compounds known as furanocoumarins that block the CYP3A4 enzymes. These compounds do this by irreversibly binding to the CYP3A4 enzymes, putting them out of commission. Like the wikipedia article says it takes about 24 hours for the CYP3A4 enzymes to return to normal levels after the average glass of grapefruit juice is consumed. During this time your body’s ability to process drugs for elimination is decreased because CYP3A4 is the main CYP enzyme for processing many drugs and toxins.

You might think that this could be used to reduce the dose for a drug, but the amount of furanocoumarin in your blood would vary widely (grapefruit isn't uniform in it's concentrations) and CYP3A4 levels vary between individuals.
 If you tried using grapefruit juice or another source of furanocoumarins to do this you'd be reduced to guessing how much of your prescribed drug is safe to take. Blood levels of the drug may rise, resulting in the risk for new or worsened side effects. it can essentially cause the normal, dose of a therapeutic drug to act like an overdose by increasing the bioavailabilty of the drug in your body. Better not to risk it.

Sources:

Gonzalez FJ, Tukey RH: Drug metabolism, in Goodman LS, Gilman A, Brunton LL, Lazo JS, Parker KL (eds.): Goodman & Gilman’s the Pharmacological Basis of Therapeutics. New York: McGraw-Hill, 2006, pp. 71–91. [I'm afraid I unable link you directly to it]

Textbook - Toxicology - the basic science of poisons, Cassarett & Doull (A PDF version of the textbook can be found here: https://ilmufarmasis.files.wordpress.com/2011/07/casarett-and-doulls-toxicology-the-basic-science-of-poisons7th-ed.pdf)
Half-remembered undergraduate lectures.


The distance the electromagnetic field of the heart can be detected A very smart friend of mine seems to get taken in by junk science. He started telling me last night that the electromagnetic field of the heart can be detected beyond 30 feet. What is the actual distance? Thank you.

The electomagnetic field of the heart actually changes with emotions so there is no fixed range as such (reference). It could also change with temperature and other external magnetic disturbances (reference). The heart generates the largest electromagnetic field in the body which is up to 50 mV/m, and that of the brain and other vital organs up to 5 mV/m. Here is a paper on the exposure of human beings to electromagnetic waves (reference). This paper details some of the current medical treatments focusing on the electromagnetic fields (reference).


Why do more complex DNA strands take longer to anneal? My textbook and several websites told me that more complex DNA strands take longer to anneal because it is harder to find the correct sequence. A simpler, repeating sequence like ATATATATA would be faster to anneal since it would be really easy to find a spot to reanneal.
I kind of get the logic here. Yet, this wouldn't always produce the exact complement strand. Consider the following:

The point is to illustrate that there could be matching of strands without correctly pairing the whole thing (i.e. there is a shift of the strands).
This means that if you want to fully anneal the strands, you need to find the correct spot in the second strand to begin annealing - which is no better than if these were completely random strands.
So then, why is annealing more complex strands slower? I've tried searching it up on the internet but all I get are people telling me it is true, and without much of an explanation.

What is meant by complexity?
This is the crux of the matter. As is often the case, confusion arises from not defining one’s terms. In this case the three possibilities we have to deal with are:

The extent to which a sequence is not homogenous. e.g. ATATATAT is more complex than AAAAAAAA; ATGCATGC is more complex than ATATATAT; ATGCTCAG is more complex than ATGCATGC. This would seem to be the definition assumed by the questioner (and also in another answer).
The length of the sequence. This is the definition given in the article quoted in the question: “Complexity - the total length of different sequences”. However it is not one that would have occurred to me on encountering the expression.
The extent to which a length of DNA (especially a chromosome) has regions present in multiple copies. This seems not to have been considered in the question, but is historically what was meant be genome complexity deduced from annealing experiments. This is shown in these extracts from a venerable text on nucleic acids, long out of print:

In human cells unique DNA has a Cot1/2 value of 1000 (moles nucleotide seconds litre–1)…Repetitive DNA includes all of the rest of the DNA. Among the repetitive DNA is a fraction which reanneals with a Cot1/2 value of between 100 and 1000…thought to be those [genes] coding for proteins which form major structural components of the cell… [some examples given of multi-copy genes like tRNA]…At the other extreme DNA with a Cot1/2 value as low as 10–3 consists largely of satellite DNA.

Explanation for Case 3 (complex because of multiple copies)
As the article quoted in the question correctly states, “Renaturation, or duplex formation requires random collisions between two single-stranded molecules”. However such experiments are performed with fragmented DNA in solution, not whole chromosomes, so the two molecules that must collide are gene-size or smaller in length. The more copies of geneX or sequenceX there are in the DNA, the greater the number of targets there will be containing geneX or sequenceX, hence the faster fragments containing such genes will anneal.
Explanation for Case 1 (complex because less homogeneous)
Assuming that one is comparing single-copy genes of different degrees of homogeneity, one can imagine that for something like ATATATAT there will be more ‘hits’ that give partial overlaps that may be detected as double-stranded:
A T A T A T A T A T A T A T A T
        T A T A T A T A T A T A T A T A

Alternatively, once bound imperfectly, there may be a greater chance of perfect binding after dissociation because of proximity.
However, it is also possible that writers are confusing or amalgamating this with Case 3, as simpler DNA may actually be present in more copies in a genome.
Explanation for Case 2 (complex because longer)
The explanation here is trivial. If you perform reannealing experiments with two geneomes — E.coli (4.6 Mbp, c. 4000 protein-coding genes) and Carsonella ruddii (0.16 Mbp, 182 protein-coding genes) — employing the same amounts of DNA as 300bp fragments, the fragments from the smaller genome will be approximately 20x more likely to make a random collision with a complementary fragment.


What is the role of tracrRNA in CRISPR-cas9? From what I understand, in a CRISPR cas9 complex, gRNA is comprised of tracrRNA and crRNA.  I've read that crRNA is the part which is matched to the DNA which is targeted, but what role does tracrRNA play in the process?  That I'm not clear about.  Also, unless this should be its own question; how is gRNA prepared with cas9 protein?  Does the protein automatically bind to certain RNA strands?

Your two questions are related and you are correct in your supposition that the Cas9 protein associates to a specific RNA sequence. That of the tracrRNA processed with the crRNA into a gRNA. This is achieved without any other aid so could be considered to  do so automatically. How specific the tracrRNA sequence needs to be is an interesting and often overlooked question.

When comparing tracrRNA from different species it is clear that there is not a lot of sequence conservation but they are predicted to be contain similar secondary structures.

Matching tracrRNA and Cas9 from closely related species does result in in vitro DNA cleavage but this does not work with more distantly related species. Nevertheless they are remarkably versatile and this has been exploited in a number of exciting genome engineering applications where additional structures are added without compromising the binding of the RNA to the Cas9.

The tracrRNA and the crRNA together form the gRNA which targets the Cas9 protein to the location of cleavage. In the endogenous bacterial systems the gRNA takes the form of a processed RNA duplex but in the genome editing implementations this takes the form of a single chimeric RNA with the two components already fused together.

When it comes to actual cleavage of DNA it is important that the Cas9 is in the correct conformation and changes in this are known to occur when binding to the target DNA. Recent work suggests the tracrRNA plays a role in maintaining the Cas9 protein in an active form allowing it to be able to target DNA.

It likely also contributes to the overall stability (and thus efficiency) of the CRISPR-Cas9 complex.

Ultimately the tracrRNA is an essential component of the CRISPR-Cas9 system via it's role in both guiding the Cas9 protein to its target and aiding it's function.

The following references might be of interest to you:

The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems

Guide RNA engineering for versatile Cas9 functionality

Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease


How do Mockingbirds find each other during mating season? Since mockingbirds imitate songs of other birds, how do they find each other during mating season? How can they tell it's a mockingbird singing, instead of other birds? Is there something in their imitations that still identifies them as a Mockingbird?

Wildlife biologist Daniel Edelstein implies as much here: he says that there are in fact variations in tone and context that distinguish mockingbirds from other birds they imitate. (He was writing about the possibility of mockingbirds attracting the birds they are imitating, which doesn't happen. I can't find much about what specifically attracts female mockingbirds, except for the variety he alludes to.)


The difference between "Hunger" and "Appetite" When I am "hungry", I need something to eat physically. But what about "appetite"? I think it is a psychological phenomenon. Is that correct?

According to the website "Appetite vs. hunger", the difference is very similar to what you were saying:

  Hunger is the need to eat.

Hunger is instinctive, it is the body's way of letting you know it needs sustenance.

and

  Appetite is the desire to eat.

It is a coordination between the brain and the stomach, this is learned behaviour.

Some further information can be found in the article preview "The Biological Nature of Appetite" (Stellar, 1992)


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

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

Question:

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

I would assume that as a result of the lengths of the tendons and the arrangements of the various flexor + extensor muscles, the slightly folded positions (curved) fingers, hands, legs, etc. are the "default" positions, in which both antagonistic muscles are in their relaxed state (thus without neural stimulation)
The evolutionary benefit of the slightly curved fingers, hands, legs, etc. may have been more relevant in our primate ancestors than it is today


Why is thymidine incorporation (DPM) normalized to per mg protein content while testing for cell proliferation? Sorry for this naive question. After performing the thymidine incorporation assay to test proliferation, many papers report normalization of disintegrations per minute (DPM) to per mg protein content? What does this normalization or ratio of DPM to cellular protein content exactly signify?
Thanks in advance.

I'm not sure that there is a strongly disciplined reason for the mg protein content as the normalization, but there is obviously a need for some normalization for different amounts of tissue- if you use 10X as much tissue, you should expect DPM to be 10X as high!
For example, in this somewhat old paper, They normalize not to protein content but to wet tissue mass or to intestinal crypt count (as they are looking at incorporation in intestinal crypts). So the normalization that you observe is not universal (or more likely, is a more recent innovation). They observe that the cruder measure of wet mass provides a poor normalization:

Instead there was a positive intercept of dpm/mg tissue which represented about
25-30% of the maximal tritium content of the intestine. (abstract)

That is a good reason to use a more precise normalization! They find that the more precise normalization of dpm/crypt works better, presumably because the crypt is the incorporating tissue.
I would suspect that the dpm/mg protein is simply a more precise method for normalization.
A yet more precise method would be the one used in this 1987 paper, in which thymidine incorporation is estimated as dpm / microgram DNA- here, you are actually directly comparing to the mass of the DNA, which is where thymidine is incorporated. That is a more obvious normalization than protein content.
However, for crude tissue extracts I suspect that it is more straightforward to estimate protein content than DNA content. So protein content is used as a "good enough" normalization.


Do all plant hormones of one group show the same qualitative effect with respect to their target pathway(s) and the biological response? I wonder, terms like "Auxin", "Cytokinin", "Gibberellin" etc means NOT a single compound; but a class of compound.

For example "Auxin" does-not mean a single compound, but several compounds such as : natural auxin (IAA in all plants*, 4-Cl-IAA in pea*, IBA in mustards*) and their synthetic analogs like NAA, 2,4-D, 2,4,5-T, dicamba ( * ), etc.

Similarly there are more-than one natural compounds under the group "Gibberellin" (such as GA1, GA3, GA4, GA7 etc),

and similarly more-than one compounds under cytokinins: natural: cis-Zeatin, 9RiP ( * ) etc. and their artificial analogs such as kinetin ( * ), 6-BAP , etc

Now, my question is, would all the auxins work in exactly the same way? or would there be slightest difference (qualitatively) between their actions? and similarly, Would all the cytokinins work the same way? and would all the gibberellins work in the same way?

(So far I heard that they have difference in their 'strength' i.e. in which concentrations they are undetectable/optimal/toxic to a cell. (i.e. quantitative difference), but don't have any references for this.)

But beside that;  my question is, would there be ay qualitative difference?

So far I haven't found anything clear-cut about this in any book or on the web.

Any help welcome

  (  *  )  (ref.  Plant Physiology/ Taiz and Zeiger, ed3; chapter 19, fig. 19.3, fig. 19.4)

Update:

In one source, Plant Tissue Culture: Theory and Practice/ Bhojwani and Razdan, (edition= ? ) 3.2.3. Growth hormones; , it is told that "IBA and IAA are widely used for rooting, and with a interaction with a cytokinin, for shoot proliferation.  2,4-D and 2,4,5-T are very effective for the induction and growth  2,4-D and 2,4,5-T are very effective for the induction and growth of callus. 2,4-D is also an important factor for the induction of somatic embryogenesis."

However there I could not found,  is this difference is really due to a difference in biological (signaling-path) process, or due to some-other superficial difference (solubility, binding with same receptors, etc) of these applied molecules.

Preface: As @David says, the question is very broad. So, here, I'll take up the most common plant growth factors i.e. auxins to give you an idea.

Short Answer: We don't definitely know yet whether the pathways of two auxins (I take indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) here) are exactly same or not.

Background: We know that auxins have very similar functions1:

  Auxins are a class of plant hormones (or plant growth substances) with some morphogen-like characteristics. Auxins have a cardinal role in coordination of many growth and behavioral processes in the plant's life cycle and are essential for plant body development.

So much similar that2:

  genetic evidence has been found that suggests that IBA may be converted into IAA through a similar process to $\beta$-oxidation of fatty acids.

Now, when it comes to whether the exact mechanisms of how IAA and IBA work are similar or not then, as I said, we don't know yet.

When we talk about IAA, there is a theory known as Acid Growth Theory3 (though there are evidences against it):

  Plant cells elongate irreversibly only when load-bearing bonds in the walls are cleaved. Auxin causes the elongation of stem and coleoptile cells by promoting wall loosening via cleavage of these bonds. This process may be coupled with the intercalation of new cell wall polymers. Because the primary site of auxin action appears to be the plasma membrane or some intracellular site, and wall loosening is extracellular, there must be communication between the protoplast and the wall. Some "wall-loosening factor" must be exported from auxin-impacted cells, which sets into motion the wall loosening events. About 20 years ago, it was suggested that the wall-loosening factor is hydrogen ions. This idea and subsequent supporting data gave rise to the Acid Growth Theory, which states that when exposed to auxin, susceptible cells excrete protons into the wall (apoplast) at an enhanced rate, resulting in a decrease in apoplastic pH. The lowered wall pH then activates wall-loosening processes, the precise nature of which is unknown. Because exogenous acid causes a transient (1-4 h) increase in growth rate, auxin must also mediate events in addition to wall acidification for growth to continue for an extended period of time. These events may include osmoregulation, cell wall synthesis, and maintenance of the capacity of walls to undergo acid-induced wall loosening. At present, we do not know if these phenomena are tightly coupled to wall acidification or if they are the products of multiple independent signal transduction pathways.

However, there are evidences supporting this hypothesis, like this one4:

  When auxin stimulates rapid cell elongation growth of cereal coleoptiles, it causes a degradation of 1,3:1,4-$\beta$-glucan in hemicellulosic polysaccharides. We examined gene expressions of endo-1,3:1,4-$\beta$-glucanase (EI) and exo-$\beta$-glucanase (ExoII), of which optimum pH are about 5, and molecular distribution of hemicellulosic polysaccharides in barley (Hordeum vulgare L.) coleoptile segments treated with or without IAA. IAA (10–5 M) stimulated the gene expression of EI, while it did not affect that of ExoII. IAA induced gene expression of EI after 4 h and increased wall-bound glucanase activity after 8 h. The molecular weight distribution of hemicellulosic polysaccharides from coleoptile cell walls was shifted to lower molecular weight region by 2 h of IAA treatment. Fusicoccin (10–6 M) mimicked IAA-induced elongation growth and the decrease in molecular weight of hemicellulosic 1,3:1,4-$\beta$-glucan of coleoptiles in the first 4 h, but it did not promote elongation growth thereafter. These facts suggest that acidification of barley cell walls by IAA action enhances pre-existing cell wall-bound glucanase activity in the early first phase of IAA-induced growth and the late second phase involves the gene expression of EI by IAA.

But when it comes to IBA, all we have is this2:

  Although the exact method of how IBA works is still largely unknown, genetic evidence has been found that suggests that IBA may be converted into IAA through a similar process to $\beta$-oxidation of fatty acids. The conversion of IBA to IAA then suggests that IBA works as a storage sink for IAA in plants. There is other evidence that suggests that IBA is not converted to IAA but acts as an auxin on its own.

So, if IBA is converted to IAA before use then, obviously, it works the same way. But the article below suggests that either the mechanism or effectiveness of IAA and IBA is different5:

  We have examined in vitro rooting of apple ‘Jork 9‘ shoots exposed for three weeks to each of the three auxins commonly used for ex vitro rooting: indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and $\alpha$-naphthaleneacetic acid (NAA). During the initial five days of the rooting treatment, the cultures were incubated in darkness. In this period, the root initials are formed. Then, the cultures were moved to the light. NAA resulted in a low (ca. 8 roots), and IAA or IBA in a high (ca. 15 roots) maximal root number. The maximal root number was reached at a wide range of IAA concentrations (10-100 $\mu$M) but at only one concentration of IBA (10 $\mu$M) or NAA (3 $\mu$M). With NAA and IBA, growth of roots and shoots was much more inhibited than with IAA. For these reasons, IAA is the preferable auxin for in vitro rooting of apple ‘Jork 9’ shoots.

This suggests that IAA and IBA use different mechanisms or that IBA can't use the same mechanism as effectively as IAA.

References:

Auxin - Wikipedia
Indole-3-Butyric Acid - Wikipedia
The Acid Growth Theory of auxin-induced cell elongation is alive and well
Auxin-Induced Elongation Growth and Expressions of Cell Wall-Bound Exo- and Endo-$\beta$-Glucanases in Barley Coleoptiles
Effectiveness of indoleacetic acid, indolebutyric acid and naphthaleneacetic acid during adventitious root formation in vitro in Malus ‘Jork 9’


What is a subgenomic promotor? I am looking for a good definition of the term "subgenomic promotor". Can someone help me out?

A subgenomic promoter is a promoter added to a virus for a specific heterologous gene, resulting in the formation of mRNA for that gene alone. Many positive-sense RNA viruses produce these subgenomic mRNAs (sgRNA) as one of the common infection techniques used by these viruses and generally transcribe late viral genes. From doi:10.1128/jvi.74.13.5988-5996.2000
So it seems to be an added promoter that helps express certain genes. Often useful in viral engineering.


Do all parts of a plant contain the same type of cell? I have only learned about the plant cell which is shown below. But plant stems alone are made up of different parts like xylem, phloem, parenchymatous cells, sclerenchymatous cells etc.

Are all the parts of a plant made up of cells like the one in this diagram or is the cell diagram changed for different parts of a plant?

The diagram shows an exemplary plant cell . Except for the raphide/druse crystals, which I do not know, all of these components are definitely present in every plant cell. Do note that this diagram is only an example and while it describes the basic components present in the cells, details can vary, since plants can have highly specialised vacuoles or plastids (like chloroplasts) in special cell types.

As @AlanBoyd pointed out, there are some specialised cases like the Sieve Tube cells, that do not have a nucleus. But in your average cell, you should find all of the components described in the diagram.

The differences between cell types are typically caused by the expression of different genes, that change the behaviour of each cell, and not directly by a change of how the cell is build up.


Does CoA always bind to organic molecules through a thiol bond? Does CoA always bind to organic molecules through a thiol bond? Sometimes I see it written as SCoA in textbooks but sometimes it's just written as CoA, are those actually chemically different, or just laziness on the part of the author?

This is coenzyme A (CoA). As you can see, it has an -SH group at its end. So when it interacts with other reagents, it forms thiolesters. CoA is just shorter.


What is this species of asphodel from Morocco? It grew about 2 metres high. Photographed in spring. It has 6 tepals and 6 stamens.

It appears to be Asphodelus aestivus, but there is similarity with Asphodelus ramosus, both of which have strap like leaves and highly branched stems. They have some overlapping ranges as well in southern Mediterranean/north Africa.

https://en.wikipedia.org/wiki/Asphodelus_aestivus

https://en.wikipedia.org/wiki/Asphodelus#Systematics


Genomic distribution of tRNAs in eukaryotes The title says it all. I'm doing a literature search trying to see what is widely known and/or well established. I've found a couple of mentions that tRNAs are dispersed throughout the entire nuclear genome. Does this mean they are isolated from each other? Or do they occur in clusters? Is this true across eukaryotes? Or is any of this even well studied?

In Drosophila, at least, some are clustered (e.g. these), but there are many tRNA genes in eukaryotes, so overall they are dispersed. You might find the Genomic tRNA Database useful, and the paper describing it.


Effect on fitness of mutations What is the distribution/probability density function (PDF) of impacts on fitness of new mutations?

I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution. Information of the kind: "If we consider only beneficial mutations, then the PDF is $P(X=x) = f(x)$" are also welcome.

When I say mutations, one might have want to reduce the concept of mutations only to indels and point mutations.

Of course the answer will depend on the species under consideration and from population to population but I welcome any answer that could give some insights. Eventually, some information according to what is generally assumed to be the PDF of effects on fitness of new mutations might be useful.

Here is a related question

Here is an article that assumes an exponential distribution of effects on fitness of beneficial mutations.

To a good first approximation $\overline{\Delta f} = 0$. Where $\overline{\Delta f}$ is the mean change in fitness down to any point or indel mutation. The reasons for this are as follows:

In the genome of higher organisms, most of the genome is non-functional ("junk") so most mutations will not have any effect regardless of the change made.
A substantial proportion of in-frame point mutations will be synonymous mutations that result in the same amino acid being coded for (actually this can have an effect on protein expression but I don't believe anyone has - yet - shown a fitness difference?)
Even where a mutation does alter an amino acid many amino acid changes have no measurable effect on the protein produced. Especially where the new amino acid has similar properties to the one it has replaced.
Even when a mutation does alter the protein function, or render the product non-functional, in many cases this will not impact fitness since fitness is conditional on the environment in which it is measured and not all genes impact all environments.

So the distribution, whatever it is, will have a large spike at 0. Probably this spike is several orders of magnitude higher than the next highest value. Further, we can be reasonably certain that $\overline{\Delta f} < 0$ since there are more possible ways to break a Gene through a point or indel mutation than there are to improve it. If this is the case, so that there is a large excess of mutations with a negative effect on fitness, we can conclude that the distribution of mutational changes in fitness will be non-normal (negative skew and spike at zero), and that the normal distribution will be a poor approximation.


What is the minimum caloric intake for a truly starving adult What is the minimum caloric intake for an adult?  I'm not talking about a healthy diet.  There's plenty of advice on that.  I'm wondering what the absolute limits of H. sapiens are.  When there's a multi-year famine, and the body is willing to shut down as much of its capacity as possible without actually failing to function for years at a time, how much energy is it consuming?

I know the Basal Metabolic Rate is a key factor to this, but the numbers I have seen for it are all "healthy" BMRs.  I'm interested in the unhealthy numbers.  For example, I'd consider maintenance of temperature optional for these circumstances (assume we have a temperate enough climate), and I presume heart rate and breathing will go down, decreasing those loads.  Obviously there's limits as to how many environmental constraints can be addressed (if I knew what environments this was studied in, I'd likely know which studies to look for!).  And obviously not everyone is the same, but that's an issue in every human study ever completed.

A better example is the stories of tibetan monks who wrote accounts of their experience to survive for months or years on faith alone, and watch their hair and nails fall out in the search for wisdom. they could tell you how fast a coma arrives from eating just 300 calories per day.

There isn't a minimum amount though, because it's all subjective for time until, temperature, survival chores, time until coma, time until difficulty moving... you can probably keep someone in an emaciated coma with intravenous injections, or someone could stay awake with high exposure risk to illness, hair loss, nail loss. The question is vague, and there are 100 scientific studies about calorie restriction, so you are hoping someone will read 10-20 pages until they find some information for you.

It also depends how many watts the human needs to use in that situation to stay alive.

In 30'C you probably need 30 watts to stay warm, and 20 degrees about 60 watts, so the value can double based on temperature, you must change your question a bit.

60 watts basal metabolic rate body temperature would use 70 calories per hour, about a slice of bread, so 1400 calories per day without bedcovers. It depends a lot on ambient temperature and exercise, for example 1 mile of walking uses 100 calories. At less than 1000 calories per day, exercise becomes difficult and the person gets thin. Jogging uses about 250 watts. Extreme athletes and triathletes peak at about 650 watts for sprinting.

There are 100ds of citations on caloric defficiency and restriction, with values around 350 - 700 per day, which change metabolism considerably:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014770/

https://www.ncbi.nlm.nih.gov/pubmed/2718912


Why are cells affected by time? We as individuals die when we get old. But why are cells affected by time? We are constantly providing energy to the cells through food, but the cells die after a certain time. Why does this happen?

Individual cells don't live forever because they are damaged by their environment, for example by chemicals, radiation and mechanical wear and tear, or by other organisms (see this review). In multicellular organisms, such "worn out" cells are typically dismantled by programmed cell death and new cells are generated to take their place.

The life span of animal cells varies widely depending on their location and function. For example, epithelial cells lining the skin and intestines are exposed to a harsh environment, and consequently live only a couple of days. At the other extreme, neurons, which are safely lodged in the protected brain tissue, can live as long as the individual (or even longer).

Note that the life span of a given cell is very different from replicative age, which refers to the number of divisions a cell lineage has undergone, measured from some progenitor cell. Most animal cells are allowed only a limited number of cell divisions (known as the Hayflick limit) and thus their lineage is "mortal", while that of microorganisms are not.


What is this fruit / nut? These were found in a park in Pittsburgh, PA. From a distance they looked almost like plums, but they're actually hollow, paper-like covers that contain a hard pea-sized seed.

Most likely a member of the genus Staphylea. Since you are in Pittsburgh, PA, it's most likely Staphylea trifolia L., or an introduced species.


Do we know if dogs are asymptomatic transmiters of sars-cov-2? Dogs do not use mask when going for a walk nor they observe the security distance. On the contrary, they frequently join their noses, and put their noses where other dogs had put them before or had urinated. So, as they are our pets, it is important to know if they can be asymptomatic transmiters of sars-cov-2. Do we know it? At least, have we tested asymtomatic pets of people infected with sars-cov-2?

It may be too early to tell.

Testing of dogs in Wuhan found no infected dogs
"487 dogs including 90 beagle dogs, 147 pet dogs and 250 street dogs during the outbreak of SARS‐CoV‐2 were also tested serological negative."
from https://onlinelibrary.wiley.com/doi/full/10.1111/tbed.13577

This article mentions deliberate infection of five dogs. on this very small sample they suggest that dogs are not likely to become carriers.

"Coronavirus can infect cats - dogs, not so much."
https://www.nature.com/articles/d41586-020-00984-8

found by searching "dog" on LitCovid at https://www.ncbi.nlm.nih.gov/research/coronavirus/


Why are children more active than adults? I have observed that children are usually more active than adults. For example, in the morning they get up and start playing, they have their lunch and get up and start running, while as adults they are relatively lazy.
Why is this so or is it that my observations are somehow errenous?
Thank you.

This is a great question!
As I see you are new and you have explained within the comments above that you haven't studied biology much I will keep the explanation short and sweet.
Young children have fatigue resistant muscles and they also recover faster from high intensity workouts when compared to adults. Children have also been found to use more aerobic respiration when compared to adults during high intensity workouts. This means the child will feel less fatigue and so can continue exercising for longer. As the muscles also recover faster, the child is able to get up and start exercising again much faster than the adult as they will still be recovering.
Aerobic fitness at the muscle level decreases however once the child reaches adulthood and this explains why children have more energy and can play/exercise for much longer. They experience less fatigue and recover faster.
I hope this answers your question.
References:
https://www.frontiersin.org/articles/10.3389/fphys.2018.00387/full


What makes the electrical charge inside the neuron more positive at the end of action potential and returns it to resting potential? When a neuron's stimulated by something, electric potential difference changes immediately and inside of the neuron, becomes more potentially positive than the outside of it.

I've read that sodium-pottasiom pump returns membrane potential back to its resting potential at the end of action potential's process.

How sodium-pottasiom pump returns membrane potential back to its resting potential and makes inside of the neuron more potentially possitive when three sodium ions are transported to the out of the cell and just two potassiom ions are transported back into the cell?

I mean, in this condition, it is expected that inside of the cell is gonna be more potentially negative, not more positive.

(Sodium-pottasiom pump ➡ puts 3 Na+ outside - brings 2 K+ inside ➡ 1 negative charge inside...!??)

The issue is the permeability of the membrane to Potassium and how membrane potential is created in the first place. The resting membrane potential of the neuron is very close to the equilibrium potential of Potassium. Large fixed anions (proteins) in the cytosol are represented in the image below by [An-]:

If Potassium and cytosolic proteins were the only thing inside the cell and the outside were water (ignoring osmotic effects), then in Figure 1 there is an outward K+ concentration gradient.
In Figure 2, we allow the membrane to become permeable to Potassium (as it is in the cell). The Potassium begins to leave [green arrow], but as it does, it begins to create a charge separation that sets up a negative voltage in the cell that pulls the Potassium cation back in [red arrow].
In Figure 3, we see that enough K+ has left the cell to the point that the membrane potential has grown negative enough that the rates of K+ leaving and entering are equal, so no net change in K+ concentration occurs. This is the definition of chemical equilibrium, and so we call this voltage the equilibrium potential of this single-ion system (~-80mV for biologic concentrations of K+).

We could do a similar experiment with Na+ starting high outside in Figure 1, with the arrows reversed, and the equilibrium potential of the Sodium-only system would be ~+60mV.

So, if a real cell has both K+ and Na+ concentration gradients in opposite directions, why don't they just cancel each other out? Why is the resting membrane potential negative, and in fact, much closer to the equilibrium potential for Potassium alone? The answer is: permeability. Imagine if you had Figure 1 again, with [K+] high inside, and [Na+] high outside, as it is in the cell, but in Figure 2 you ONLY made the membrane permeable to K+. Would the Na+ gradient change at all? No, because there would be no pathway for it to move. Thus, if ALL the permeability is for K+, then K+ has all the influence on the membrane potential. If both are equally permeable, it would be their average (-10 mV, or about neutral).

However, the permeability for K+ AT REST is about 20 times the permeability for Na+, so we'd expect the cell's resting potential to be 1/20th of the 140mV "distance" between the equilibrium potentials for K+-only and Na+-only systems, or: -80mV + 1/20(140mV) = -73mV. The fact that it's not exactly -73mV is explained by the existence of a small amount of Cl- and other ion permeability. But, in essence, Potassium determines the resting potential, with a little offset due to sodium permeability.

Now that you understand that, understanding the action potential graph should be easy:

Rising Phase: major increase in Na+ permeability, voltage rises almost to the equilibrium potential of Sodium.
Falling Phase/Undershoot: Na+ permeability shuts down, major increase in K+ permeability, voltage drops back down to equilibrium potential of K+.
Restoration: K+ permeability drops back to normal (not completely shut down), and the Na+/K+ pump just restores the concentration gradients that allow the resting potential in the first place.

So, really, your initial confusion about the electrical work done by the Na+/K+ pump existed because you didn't take it in context with the permeability. Yes, the pump by itself makes the voltage more negative, but some of the potassium it stuffs back into the cell immediately turns around and leaks right back out until it's 95% of the way to its own equilibrium point again, as determined by the membrane permeability.


In which organs is water that we drink absorbed into the blood? From biology classes I remember that water from food we eat is mostly 'sucked in' (absorbed into blood) in the colon. I guess the same is true for water we drink. But if I eat something, it will reach the  colon after say 4 hours, and if I drink a lot of water, I'd want to go to bathroom earlier than in 4 hours.

So is water absorbed not only in colon?

If it's absorbed in other organs, what % of it would be absorbed in each organ?

Role of the stomach in water absorption:
The absorption of much of the ingested water from a hypotonic food already starts in the stomach due to osmotic reasons.
If we study the mechanism of secretion of HCl by the oxyntic cells of the stomach, HCl secretion favours water osmosis from the blood to the lumen both for protective reasons as well as to maintain the osmotic balance of the gastric juice. This is predominantly the phenomenon in a filled stomach.
However, in the empty stomach, absorption of water is relatively more perceptible in the reverse direction upon water consumption.
Furthermore, the pyloric sphincter is usually open to the passage of water and electrolytes to empty to the duodenum. Thus, they may travel to the large intestine for absorption even before chyle. But this too is dependent on the empty or filled condition of the stomach, in which an empty stomach would pass the water and electrolytes in 5-6 minutes whereas in the filled stomach it could take 15 minutes or even more. Thus these factors may cause the early micturition to ensue.
Role of the small intestine in water absorption:
The small intestine, besides the transcellular pathway (through the cells), also facilitates water transport via the paracellular pathway. Thus it is more permeable to water osmosis than the stomach. Furthermore, the small intestinal segments duodenum, jejunum and ileum are differentially permeable to the absorption of different solutes. This facilitates the simultaneous absorption of water according to the osmotic gradient resulting from this differential absorption of the solutes, maintaining isosmoticity with the blood plasma.
However, this also has the implication that, when the digested products from the stomach (chyme) are hyperosmotic, water may flow from the blood in the villus to the intestinal lumen rather in the opposite direction until chyme is rendered isosmotic to the plasma.
Role of the large intestine in water absorption:
The large intestine is the key centre for water reabsorption rather than the stomach and the small intestine because of the following reasons:
a) It prevents most of the paracellular flow of water and electrolytes because of tight junctions, unlike in the small intestine. This prevents the back flow of electrolytes and water from the chyle to the blood.
b) The proximal colon is where most of the water reabsorption occurs as a consequence of major electrolyte intake. This region is highly active in the reabsorption of Na+ and Cl-.
c) It is mainly involved in concentrating the fecal matter, so reabsorption of water and electrolytes becomes its principle function.
For reference:
Textbook of Medical Physiology by Guyton and Hall


How does evolution explain the apparation of different group like: mammals, insects etc When I am learning about evolution I barely see any source that explains how insects, mammals, reptiles and fish came to be. Can someone show me a source where I can learn about this? Especially insects and mammals - I want to know how those 2 distinct group came to be.

And I have a related question: can a fly evolve into a rabbit given enough time with the necessary condition? (I know the question sound stupid but please can someone explain me that)

I have a layman understanding of evolution. So please can any of your source or explanation be simple? Thank you.

Insects and mammals diverged from one-another over 500 million years ago. For most of Earths 4.5 billion year history, life was single-celled, or organized into colonies of single-celled organisms. Likely sometime shortly before the Cambrian, multicellular animals evolved. The first multi-celled animals were likely a kind of colony that was not differentiated into tissues. It didn't have a head, or tail, or look much like an animal. From these simple undifferentiated, multi-celled building blocks, came most of our animal phyla, during a burst of innovation called the "Cambrian explosion". At this time, one lineage headed down a path that would lead to insects, and another lineage, toward mammals. Although theoretically, it is possible, given enough time (as in billions of years) for a fly to evolve into a rabbit, this is highly unlikely. Evolution works with what it starts with and modifies it under natural selection to favor fitness. So having six legs and wings works pretty well for flies, and having 4 legs and fur works pretty well for rabbits. The hurdles to go from one form to another, given that these lineages are already well adapted, would be enormous. It was much easier, 500+million years ago, to go from one colonial lump of cells to a rabbit, and another lump to a fly. As an example of how evolution works with what it starts with, virtually all tetrapods (amphibians, reptiles, and mammals) have 5 digits on their limbs. This is because they share a common ancestor that did. Not because 5 is somehow special. Another example, humans choke to death because we share a common ancestor with fish, and fish share a tube that connects both the mouth with their swim bladders and their gut. Swim bladders were modified into lungs, but the common connection from our fish ancestors remains (a really bad design, but we are stuck with it).


The concepts of relatedness - Hamilton's rule and kin selection Here is a quotation from this wikipedia page

  The relatedness parameter (r) in Hamilton's rule was introduced in
  1922 by Sewall Wright as a coefficient of relationship that gives the
  probability that at a random locus, the alleles there will be
  identical by descent.[14] Subsequent authors, including Hamilton,
  sometimes reformulate this with a regression, which, unlike
  probabilities, can be negative.

Here is my question:

What are all the different definitions of relatedness in biology?

how do we calculate them?
what do they mean?

Is that really trying to imply that there are significantly different definitions?  It seems to me the intent was just to put it in terms of an equation with more useful numbers.  This terrifying paper from 1964 gives some of the follow-up works, in particular works from Cockerham in 1954 and a number of papers by Kempthorne, in particular this from 1955 and this from 1963.  There is also Malecot's method of coancestry from 1948. (WorldCat.org link)  The idea was mainly to look relatedness outside of the specific limitations present in Wright's work.  Some of the math in those are more accessible than others...


Plant identification and toxicity What type of plant this is and is it poisonous (and, if so, in what quantities)?
The pictures were taken at Gullane Bay, Scotland. The plant is widely present in that region.

This is common sea buckthorn, Hippophae rhamnoides. The blueish leaves and the orange berries are unmistakable.

It occurs mainly in coastal regions, but is also cultivated throughout the world. The berries are processed to all kinds of food.
In their natural habitat in Northwestern Europe, the berries serve as a food source for migrating birds that fly from Scandinavia to the UK or the Netherlands. However, because the berries are often rotting and contain alcohol in september, sometimes drunk birds can be observed.


Reconstituting genomes of archaic tribes of humans Will it be logically possible for genome studies to reconstitute the genomes of our local human populations as they were 2000 and 4000 years ago? What is the mathematical precision and science for that kind of thing?

I am fascinated by human facial features and i wonder what our archaic tribes looked like regionally when they were isolated, a few thousand years ago, before mixing into the melting pot that they are today.

If we can one day image facial construction from DNA using some thousands of facial genes, it will be cool if we can also find what local dna pools were like precisely a few hundred generations ago. Is it possible?

The answer is basically 'No.'.

Too much mixing has happened since then. Fortunately, in most of the world we had scientists 2000 years ago describing facial features, and in part of the world (i.e. China) we had scientists describing facial features 4000 years ago.

We do occasionally recover viable DNA samples from both 2000 and 4000 year old corpses, also actual corpses that still retain significant vestiges of their facial features, but expecting to recover even general facial features over hundreds of generations from present DNA is quite frankly unrealistic.

The good news is that human facial features aren't actually super variable; humans are just super good at spotting small differences (which comes with the territory as social animals). The bad news is that as a modern reader of latin or chinese texts on phylogeny (if you can find them, which I won't guarantee) the subtle differences in what they mean when they describe a nose as, let's say hooked, will probably be lost on you, or me, or any of us.

Your best chance is probably sequencing corpses from the relevant era and matching them up with phylogenisists' descriptions to form an idea of what they were talking about; and you might end up with a general sense of what people looked like.

I expect it will lead to severely underwhelming results, but I suppose it's worth a shot.


The fastest vaccine developed is a mumps vaccine, which took 4 years. Where is the hope that we will find a COVID vaccine in less time? I understand that doctors and scientists are working hard to find a vaccine, but is there a reasonable chance that we will find one in the time that scientists and politicians are suggesting?
I also understand that we have no choice but to socially distance and bithe our time to find a vaccine if COVID is anything like the flu, but what if it proves to be as hard as finding a vaccine for HIV? The first HIV outbreak occurred in the 1980s, and if I'm correct we still don't have a vaccine for it yet (even though we do have treatment for it so people could just live their life with it).
So my question is with all this in mind, how could there be a chance that we will find a COVID vaccine in less time? Is it just optimism, or is there actually reason to believe the vaccine will be produced say by the beginning of 2022.

Expectations for accelerated vaccine development are based on two main points.

Groups have been working on vaccines for SARS-CoV-1 since 2003, and much of that work is applicable to SARS-CoV-2 (the COVID-19 virus). Here is a review article discussing work on SARS-2 vaccines based on work on SARS and MERS. One example, transgenic mice are available that express the human version of ACE2, the host receptor protein that allows SARS coronaviruses to enter a cell. These mice allow vaccine testing that is much more informative than cell culture tests, and weren't developed until 2006-2007. SARS was eliminated in 2004, so we can estimate it would take at least two years to develop an animal model for COVID if it wasn't already available.

Here is a diagram from the linked review showing timelines for traditional vaccine development and the accelerated SARS-CoV-2 vaccine development:

Several pharma companies have developed "plug and play" vaccine platforms which allow rapid manufacture of vaccine candidates once a molecular target is known. In this case, the target is the 'S' glycoprotein. Once the sequence that encodes for this target is known, it can be inserted into the platform and produced quickly.

Here is another diagram from the same review describing some of these platforms:

EDIT - I wanted to emphasize a third point: If you notice the "Production (at risk)" text in the accelerated development diagram, it means that pharma companies are producing large amounts of their vaccine candidate before testing is complete, and therefore running the risk that their warehouses full of product will be rendered worthless by bad outcomes in the clinical trials. Moderna had started production of their mRNA vaccine candidate by July 15 2020, so this gives them a several month head start if the trials turn out well.


What are the white dots on the tree in this photo? Today in Kongens Have, I noticed a lot of white dots on bark of trees. There are plenty of them, and they were usually on 'bottom' side of branches. Does anyone know what this could be?

I took a photo:

I suspect some pupa of insects, but it is just a quess.

I'm not 100% sure, but I think they look like scale insects (Coccoidea). In particular it looks at bit like a hermaphrodite cottony cushion scale insect (Icerya purchasi)...

The white fluffy thing underneath the insects is the ootheca (egg case). The mature insect migrates to the main trunk of its host tree and attaches to the bark. It then secretes the cottony sack between itself and the bark. Hundreds of eggs are laid into the case, which eventually hatches and the nymphs disperse to the tips of branches where they feed on leaves. As they get older they gradually move first to twigs, then to branches and finally back to the main trunk to breed again.


Squirrel nest construction I've often wondered how squirrels -- specifically, eastern grey squirrels (Sciurus carolinensis) make their nests. Specifically, I've been curious about how they "weave" everything together to make these so called "dreys" stay together (and stay in the tree).

According to this site:

  [squirrel nests are] constructed from various twigs, leaves, moss and other material. To start, twigs are loosely woven together to make up the floor of the nest. Next, squirrels create more stability by packing damp leaves and moss on top of the twig platform to reinforce the structure. Then a spherical frame is woven around the base, which creates the outer shell. The final touches include stuffing in leaves, moss, twigs and sometimes even paper to build up the outer shell of the new home.

I've tried finding a video (preferably time-lapse) of a squirrel nest being built to better understand/appreciate this animal home. However, I've thus far been unable to find such a video on the internet.

Does anybody have such footage or know where I can find some?

Ideally, close-up and even internal shots would be included.
Additional notes about tree-branch drey construction would be appreciated, too!

Check for:

https://www.youtube.com/watch?v=6uKDpHM-OsI
https://www.youtube.com/watch?v=3jPtZByr740
https://www.youtube.com/watch?v=Kh1HnMFolgw
https://www.youtube.com/watch?v=M5dduAX8iuI

The third one was filmed by BBC. The fourth one is a closer look of the nest complemented with a fairly good analysis.
The first two are reasonably good, but the third one is just awesome for your purpose!


Why do we have no enzyme to digest cellulose? As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have an enzyme to digest cellulose?

While it's true that cellulose is full of calories, it's very difficult to get the calories out.

Symbiotic bacteria take ages to digest cellulose, and as a result animals that digest cellulose with specialized symbiotic bacteria have a huge gut to house them in.

It's likely that the reason humans can't digest cellulose is because mammals generally can't. And mammals generally can't because it's way too much work, and we don't need to.


Can you increase the microbiota in an insect? I know you can suppress the microbiota of an insect with antibiotics, but I´m am looking for a way to increase it. For example, can I feed an insect with something that helps boost the bacteria like agar or something.

The answer is absolutely yes.
There are 3 main ways:

Faecal transplant: faecal sample from other insect could be
transplanted in order to colonize the gastro-intestinal tract
Injection of bacterial culture into the desired tissue
Use of functional foods to increase the abundance of specific bacterial
genus.

See this review for more detail


Lac operon: How can lactose enter the cell in the absence of lactose permease? My textbook states that

  lactose permease...transports lactose into the cell

and

  When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor protein

My question is, how can lactose enter the cell to bind to the repressor protein to allow beta galactosidase and lactose permease to be synthesised if there is no lactose permease present to transport the lactose into the cell?

Introductory textbooks will not get into the details of the lac operon.

Basically, the operon is expressed constitutively at a low level that means that Beta Galactosidase and Lactose Permease are expressed at low levels by the bacterium. This is because it takes a little bit of time to build up the concentration of LacI in the cell before it can start to bind the operator.

The LacI repressor only binds the operator in the absence of Lactose in the cell's environment due to the fact that allolactose allosterically binds the LacI repressor and affects that molecule's ability to bind the operator. So RNA polymerase can bind the promoter of the Lac operon at some low rate and continue to produce the protein.

When the cell no longer has glucose, it generates cyclic AMP, which induces the CAP protein to bind to the CAP site, just upstream of the promoter of the Lac Operon. CAP associates with RNA Polymerase, and this makes the promoter very active. Beta Galactosidase and Lactose Permease levels increase rapidly.

Where you see the full effects of the LacI repressor is when neither Glucose nor Lactose are present in the environment of the cell. At this point the repressor binds to the operator and blocks transcription by DNA Polymerase.

I hope this helps. I have an entire book that covers the Lac Operon, so even though this is a bit expanded of an explanation from a basic textbook, it is still a summary.


How can cancer preventing genes from animals be transferred to humans? I recently read this non-peer reviewed article that states that the prevalence of cancer in crocodiles or elephants is really low, much lower than humans.  It is said below

A team of researchers in the US looked closer, and found an abundance of a gene called TP53. This gene is known for its ability to repair damaged DNA and thus halt the spread of cancer, and it's some 20 times more common in elephants than it is in human beings. It appears elephants have developed more of these genes as they've evolved, in part to protect calves born to older mothers
"These findings, if replicated, could represent an evolutionary-based approach for understanding mechanisms related to cancer suppression," says the report, published in the Journal of the American Medical Association.
Naked mole rats are even more miraculous - they never develop cancer, even when scientists try and induce it artificially. What appears to be happening, at least according to a recent study, is that the mole rats are using natural mechanisms to clamp down on the spread of cancer and fight back against the mutation.

Question
So why is it that these genes cannot be transferred from animals to humans? Maybe when the baby is at fetus stage?  What are the current problems/limitations and if possible, how would scientists transfer these genes?
My logic is that since mice and elephants are both mammals,  it should not be too hard to achieve this.

While this research is interesting and might help curing cancer at some point, it's not a ground breaking revelation.

The gene in question here is TP53, coding for the very-well known tumor supressor protein p53. Humans do have this gene, but apparently elephants hav acquired multiple copies of it (~20) during evolution and that might explain why they don't get cancer so easily.

The problem of testing this is not a technical one. Using modern genetic engineering methods it should be fairly easy to multiply the gene in human or mice embryos, or introduce the additional variants from the elephants. Someone might already be planning to do that in mice.

For use on humans however, this is highly unethical. Without proof that these gene copies actually prevent cancer (and one observational study is not a proof), you can't just use a new medical treatment. Secondly this treatment would require genetic modification of an embryo (because its actually cancer prevention, not acute treatment) and that is illegal almost everywhere on earth (even genetic modification of somatic tissue for cancer treatment is just now becoming an experimental therapy).