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How to judge the distance of nodes in biological evolution tree
I would like to know the method of judging the distance between two nodes in the phylogenetic tree. For example, in the diagram below, is node 299 closer to node 151, or closer to node 201?

Welcome to SE Biology. Please finish reading the [Tour] to find out how this site works, and the Help on asking questions. Generally we like posters to research questions before posting and explain why they were unable to find an answer. Did you?

It depends somewhat what you mean by "closer", but phylogenetic distances are usually judged by "branch length". By this logic, just eyeballing it, node299 is almost certainly closer to node151 than node201.
This means roughly "how far you have to travel up and down the tree to connect 2 nodes". From node299, it looks like you have to actually go back down the tree to pass through node151 to get to node201, so node151 is really in the middle here. Note that branches represent evolutionary time, so that the branch length distance between two descendants of the same ancestor can be expected to be around twice the evolutionary time experienced by each descendant relative to ancestor.
The arrangement of the tree in the left to right axis is arbitrary, for example for any subgroup you can flip it 180º and there is no change in the actual topology of the tree.
This is harder to see in a circular layout like this, but in a standard cladogram it is more obvious:

As one example, you can take the "Dinosauria" clade and flip it so that the chicken is closer to the the crocodile, and there is no difference.
In this specific case, you are noting the "root" of the tree as one of your nodes (node151). The placement of the root is generally the most uncertain/poorly estimated part of the tree, so making arguments based on it is non-ideal, but from the point of view of computation, the answer is unambiguous.

Thanks a lot for your answer. But I have another problem. I want to know why the distance between two nodes evolved from the same ancestor is farther than the distance between the two nodes and the ancestor node.
Is this situation caused by the introduction of genes from other species during the evolution of these two nodes?

@rona not sure that i understand. The distance (ancestor to descendant 1) or (ancestor to descendant 2) is always going to be shorter than the distance (ancestor to descendant 1) + (ancestor to descendant 2), if we're talking about the same ancestor. Negative branch lengths are technically possible but so rare they're not worth considering. Each of those lineages has experienced evolutionary time. Updated answer in bold to be explicit.


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Haldane effect plays more important role in promoting carbon dioxide transport than that of the Bohr's effect in promoting oxygen transport why?
This is the actual question
And the correct option is "A"
But I can't figure out why
Haldane effect plays more important role in promoting carbon dioxide transport than that of the Bohr's effect in promoting oxygen transport because
(a) oxyhaemoglobin is a stronger acid which donates hydrogen ion (H) which in turn displace carbon dioxide from blood
(b) carbaminohaemoglobin is a stronger acid which splits into hydrogen ion (H+) and bicarbonate (HCO) (c) carbon dioxide reacts with to form acid
that lowers the pH in tissue (d) carbon dioxide is less soluble in venous blood than in arterial blood.

Please finish the [Tour] and the help on asking questions, particularly homework question. As with all homework questions you need to show your own attempt to solve the problem. It will help the more general biologist if you state what you think the Bohr Effect and the Haldane Effect are, and it will also be a starting point for you to weigh the merits of the different statements. Also please edit the question so that the four alternatives start on a new line.

I have sympathy for you.  "More important role" is a hard thing to quantify, and the semantics of both honorifics blur out into their inevitable chemical consequences which inevitably overlap.  This one seems better addressed by a process of eliminating the wrong answers than in trying to prove the premise true in an absolute sense.  Nonetheless, (a) is clearly true as written and it does explain why some CO2 is affected that wasn't even stuck to hemoglobin in the first place.

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Is it possible for two fraternal twins to be completely different at the genetic level?
Given that the 46 chromosomes split evenly during meiosis, if the even pairs of the male gametes match with an even pair of the female gametes, the offsprings in theory should be carrying chromosomes the other does not posses, and thus in theory share no genetic material, despite coming from the same parents. This follows the assumption that each chromosome is unique and share no genetic materials with the other chromosomes.

The other answer correctly notes the probability is vanishingly small, equivalent to successfully calling a coin flip many times in a row. I'll also note that due to pedigree collapse, even two "unrelated" members of a population share some ancestor if you go back far enough - both your mother and father carry some small amount of identical DNA inherited from the same individual. For this bit of DNA, it doesn't matter if the offspring inherits from the father or the mother, they're inheriting the exact same DNA which can be traced back to the same ancestor. Fraternal twins can't differ at these otherwise normally variable loci, as the mother and the father don't have distinct DNA to give.

Chromosomal abnormalities aside, every human offspring has 23 chromosomes from mom and 23 from dad.
If chromosomes were inherited as whole units (they are not), the odds of one sibling, fraternal twin or not, having exactly the opposite set of chromosomes would be 0.5^46 = 1.4x10^-14, or about 1 in 70 trillion. That is, the odds of selecting the other chromosome 1 from dad is 0.5, same for chromosome 2, etc, and the same for each chromosome from mom.
Because of crossing over, the odds are even lower.
"Possible" is not very meaningful at these probabilities.

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Is somatic fusion/hybridization off-limits to DIY-ers? ELSE: how can an infertile plant's characteristics be salvaged to a fertile one?
I was amazed to discover plant tissue culture could be performed relatively easily at home.
I have been wondering, what's the likelihood of a DIY-er being able to setup and learn a crude and basic lab setup for somatic hybridization?
I haven't had the chance to ask an actual molecular biologist, but amongst non-specialists I was met with pious contempt for my naivete or told in a very politically correct manner "you're not smart enough to do that".
Now, assuming the worst case (somatic hybridization being 100% off-limits), are there any other possibilities/strategies for achieving gene transfers between an infertile plant and a fertile one of same genus but different species in hopes after due selection and testing a fertile plant could be obtained carrying some desired characteristics from the infertile one?

Not 100% impossible, but highly unlikely (upwards of 99% impossible) for the average home experimenter to be able to do.
Your biggest barriers will be

Cost - you need extensive, very expensive equipment and lots of it to get these sorts of things to work. You also need lots of reagents, many of which are expensive (roughly in the 100's to 1,000's of dollars for a single attempt), temperature sensitive, and unavailable to the average person (i.e. you need to be working at a registered business or research institute before they will sell them to you; you can't just get these off the shelf somewhere). To equip a lab for equipment alone will be in the \$10,000 - \$50,000 range, depending on what you buy and exactly what you need.

Time - this is not something the average person could pick up a book or watch a video on and do, it takes years of training to a post-graduate level before most people attempt this sort of thing.

Regulation - this is an advanced technique for genetic manipulation; you may not have any malicious intent; but there are environmental laws in most countries that regulate the use of genetic manipulation. If you get caught the penalties will be very high.

Assuming you have enough of 1 and 2, you still won't be able to get around 3.
Having said that - techniques/areas you would need to learn: Plant cell culture, sterile technique, preparation of reagents, molecular biology techniques such as PCR (you have to have some way of determining if it worked...), plant physiology (to make sure that it is something feasible biologically and to be able to work out if something is going wrong, and exactly what that is), plant anatomy (where to source the protoplasts).
Scientific method will also be a big one - you would need meticulous attention to detail, recording everything, so that when something goes wrong (and it will; I'm a research scientist writing this) you might have some idea of what went wrong and maybe why and what to do next. Empirical technique (i.e. trying one set of conditions -> didn't work -> alter single factor in the next one) seems to be the way most people do this , but there is a whole field of literature with several hundred scientific papers on somatic hybridization, and what works for one species might not work for another.

It might be appropriate to also mention that it's illegal to propagate a patented plant. I have no idea if the OP has a particular plant in mind.

The plant I was interested in is inferrile as it is found in nature, no patents whatsoever ;)

Thanks @bob1 for your thorough answer. Although utteely disheartening, at least I now have a clear answer. This is very sad indeed. Are there any other methods to cross an infertile plant with another?

@geeheeb not that I know of, but many plants have been brought back from the brink of extinction by simple propagation methods.


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Total number unique chromosome combinations in fertilized egg?
Assume for this calculation no recombinations or crossover .
A male gamete (sperm) is haploid and has 23 chromosomes. These gametes can be selected from the father who has 2 pairs of 23 chromosomes each. So the total number of combinations for the male gamete is 2^23.
The female gamete (ie the egg) which is again haploid has the same number of total combinations 2^23;
These chromosomes are selected from the mother who has 2 pairs with 23 chromosomes per pair.
Thus the inital fertilized egg (ie one sperm plus one egg - ie diploid  ) I believe this means should have (2^23)^2 possible chromosome combinations. Is this correct ? This fertilized item would be diploid with 23 chromosomes in each pair; 23 chromosomes from the male gamete and 23 from the female gamete. Is my calculation for total combinations correct ?
Can one state that all these 46 chromosomes are always different? Ie for example the 2 chromosome #3 have a different DNA sequence ?

No. I suggest that you get a basic biology text book and look up chromosome pairing.

The fertilized egg is also called a zygote-ie the union of the male and female gametes.

Yes, and how does this apply to your question. You have some fundamental flaws in your logic!

@bob1 Seems reasonable to me, what am I missing?

There is no fundamental flaw; there are 2^46 possible chromosome combinations, excluding aneuploidy.

@BryanKrause The maths is right for combinations, but not about the last question, though there's some quibbling to be done there - is OP talking about the coding regions only? non-coding regions?

@bob1 I don't see much to quibble about regarding chromosomes being different; the chances of taking two Chromosome #3s from different people and finding them to be identical are sufficiently miniscule to ignore. Even from the same person it would be unlikely they're actually identical taken from two random cells.


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Can you store 5% BSA, in TBST, in -20C?
I have stock solution of 5% BSA prepared in TBST I use to make primary antibody dilutions for western blot. I'll admit I just assumed -20C, with freezing and thawing as needed, was an acceptable means of storage, but I've found online that people recommend just 4C. Would -20 and freezing harm the potency of BSA? I haven't observed precipitate so I haven't assumed so, but perhaps there are other consequences..

The question is, if freezing is necessary. I usually made small batches and kept them in the fridge. I also made sure to not store them too long to avoid contamination.

Have you had anomalous or unexpected results from your Western blots?  If you do positive controls and negative controls and they are well-behaved, then I would infer that freezing the blocking agent has not been detrimental.  If the blocking agent is not doing it's intended job, then I would predict higher or unacceptable background on a Western.  You can use many different non-specific proteins, e.g., casein, gelatin, in addition to BSA.


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Induction of IFN-beta in HEK293T
I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta.
I've tried treating HEK293T cells (~60% confluence) with 0, 5, 15, 45, 90, 135ng/ml recombinant IFN-beta for 36 hours.
Based on the (quite vague) protocol we're following (Figure 7B) this should be well more than enough to observe a change in both UBL7 and our positive control ISG15. Instead, UBL7 levels are unchanged from 0ng/ml, and no ISG15 is observed. IFN-beta was added directly to DMEM media in a 6-well plate.
I'm quite new to cell culture so if there's some glaring issue please don't hesitate to call me out, I really don't see how no change at all is occurring :( thanks!
Note: the first figure uses PBMCs, but my figure (7b) uses 293T!

HEK293 cells (whatever the variety) are not an excellent substitute for PBMCs, as they are from a completely different cell lineage and behave very differently in a lot of ways. However, if the paper or protocol you're following uses them, I would also, at first, until you can get your hands on some PBMCs. I don't recall at the moment if 293T cells are sensitive to IFN-$\beta$, but I'll assume for the moment that they are.
I would first test your stock of IFN-$\beta$ to make sure it is active. If ISG-15 is supposed to be upregulated and it isn't, then your IFN treatment isn't working. Get a fresh supply of lyophilized IFN-$\beta$, reconstitute it according to the instructions, aliquot it into single-use portions, store the aliquots at -80, and avoid freeze/thaw cycles. Improper storage can kill cytokine activity. If you must store it at -20, make sure it is a manual defrost freezer (ice forms on the inside over time), as automatic defrost freezers change the temperature and cause the contents to thaw and freeze again. Don't store it at +4 or on wet ice except for during the day while you're using it.
Another line of investigation would be to perform cell counts of the different treatment conditions to ensure that your treatment isn't affecting the cells' growth rate, either positively or negatively. At the same time, determine the protein concentration of your lysates (if you're making them to do your analysis) to ensure they're not different across the conditions.
Finally, while this won't affect your current issue, I would strongly recommend making serial dilutions of your treatment concentrations. 2x, 5x, and 10x are all common dilution schemes. Make your most concentration dilution in one tube, then serially dilute it from that tube into another, then that tube into another, and so on. It helps reduce variability.
Don't worry about things not working the first time. Take a break, think carefully about possible reasons, and correct those issues one at a time so you're not trying to study multiple variables at once. Good luck!


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How to prevent small-protein smearing in SDS-PAGE?
I am doing SDS-PAGE for ubiquitin-6xhis (9.6kDa), and all my hand-cast gels produce a smeared band (see image). I typically use 5% acrylamide for stacking, 15% for resolving gel layers. I don't understand the biophysics of PAGE enough to know what changes to make to mitigate this smearing, any ideas?


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Strange Mitotic phase of oocytes in primary follicles
In the process of learning about the reproductive system, I find  an oocyte enveloped by a single layer of follicular cells appears to be undergoing equal division, resembling a primary follicle located near the ovarian tunica albuginea. This slice is from rabbit ovaries, stained with HE, 40 * 10.
What puzzing me is: It seems that the oocyte should not undergo mitosis at this time, and I am not sure how to explain this phenomenon?
My initial idea is whether it is possible to have multiple oocytes simultaneously in the follicles of rabbits. I tried to searche on PubMed and Google, but found no relevant evidence.

PS: Because the file size is limited to less than 2M, the image here only captures a portion of the field of view. If you need a complete picture, please leave a message.


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What components of a neuron are impermanent during the host organisms's lifespan?
I understand that a neuron's dendrites can die, and new ones can grow. To what extent are other components of a neuron impermanent during the host's lifespan? Do we need to go to the atomic level to find impermanence in the soma and axon?


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Is there any plausible mechanism through which magnetic storms can directly affect the health of people on the ground?
https://ui.adsabs.harvard.edu/abs/2014cosp...40E1114G/abstract#%3A~%3Atext%3DIt%20was%20shown%20statistically%20that%2Ccomparison%20with%20quiet%20geomagnetic%20conditions
This study says that on average, rates of heart attack and brain stroke increased by an average factor of two(!) during geomagnetic disturbances, due to Earth's magnetism.

It was shown statistically that during geomagnetic disturbances the frequency of myocardial infarction and brain stroke cases increased on the average by a factor of two in comparison with quiet geomagnetic conditions.

They offer this mechanism for this observation, and the mechanism involves magnetism:

Our investigations show the red blood cells are very sensitive to electromagnetic forces. Most probable that geomagnetic fluctuations (frequency) acting on blood, brain, adrenals involves the adaptation system. This leads to increasing a level of catecholamines in blood responsible for activation of the clotting system, rise in aggregation and spasm in the afferent vessels of the microcirculatory network. In persons suffering from CHD, the foreground problem is the reversibility of these pathological processes.

On the other hand, USGS, a government domain website, asserts that Earth's magnetism does not affect health. The subject is on the topic of magnetic storms.
https://www.usgs.gov/faqs/does-earths-magnetic-field-affect-human-health

"Does the Earth's magnetic field affect human health? The Earth's
magnetic field does not directly affect human health. Humans evolved
to live on this planet.
High altitude pilots and astronauts can experience higher levels of
radiation during magnetic storms, but the hazard is due to the
radiation, not the magnetic field itself. Geomagnetism can also impact
the electrically based technology that we rely on, but it does not
impact people themselves.
Learn more: USGS Geomagnetism Program"

It says that geomagnetism can affect electrically based technology, but it does not affect people themselves.
Health effects are not listed in their page titled "What are the hazards of magnetic storms?"
https://www.usgs.gov/faqs/what-are-hazards-magnetic-storms
Is it plausible that Earth's magnetic storms causes the rate of heart attacks to double? Is the mechanism suggested by https://ui.adsabs.harvard.edu/abs/2014cosp...40E1114G/abstract#%3A~%3Atext%3DIt%20was%20shown%20statistically%20that%2Ccomparison%20with%20quiet%20geomagnetic%20conditions in any way plausible?

What is the base rate?

The second author has been publishing on these sorts of things for a while Breus T, unfortunately the papers are largely not available or in Russian, so hard to access for me. From abstracts, data seem sketchy at best.

Cross-posted to skeptics here. Please don't clutter the network with duplicates. I suggest confirm the truth of the statement on skeptics, then come here to ask the mechanism by which it happens - once it's been confirmed to be real. Best to delete this here now.


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can you create an offspring from ancient human's DNA?
If a DNA from an ancient human, for example the cheddar man, is still intact, can you make an offspring today using that intact DNA?
https://www.theguardian.com/science/2018/feb/07/first-modern-britons-dark-black-skin-cheddar-man-dna-analysis-reveals

You could, however the DNA is not that intact, there is a steady rate of loss of the genes...
mtDNA is degraded to an average length of 1 base pair after 6,830,000 years at −5 °C (see wiki: ancient dna). that's a speed of 1 base pair every 412 years. The cheddar caves are not frozen, I'd guess that the DNA lost one base pair every 10 or 20 years, so it has lost at least 400 or 800 base pairs. at 5 degrees, it may have lost 2 percent of it's informations, except that they sequenced it many times and reconstructed the original version.
The technology does exist to design synthetic chromosomes. https://www.nature.com/news/synthetic-yeast-chromosomes-help-probe-mysteries-of-evolution-1.21615
https://www.scientificamerican.com/article/scientists-downsize-bold-plan-to-make-human-genome-from-scratch/
I figure that once science has a sure footing on genetic taboos, the do's and dont's, a company will one day try to give birth to neanderthals the cheddar specimen. There is too much scientific value for it to never be realized.

A species is generally defined as a group of organisms that can breed and produce fertile offspring. So, if you are extracting DNA from the an ancient human that is indeed the same species as us (homo sapiens), then by definition, you will be able to combine it with modern human DNA and generate offspring.
This is just stating the theory, the actual biology behind extracting that DNA and using it to fertilize offspring will be... messy.

You don't need to combine with another human, just clone https://www.usatoday.com/story/tech/science/2018/01/24/cloned-monkeys-scientists-china-first/1062649001/

scientifically yes, legally probably not as it would fall under human cloning/experimentation laws in most countries.
Artificial insemination with sperm with inserted genomes or artificial sperm already exists in mammals. Reconstructing genomes is possible and that together is all you really need.

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Genetic modifications in humans to prevent disease
I was reading an article about "designer babies", which was about how before birth the DNA can be modified so to achieve certain features. Can a technique such as this also be used to prevent diseases, such as down syndrome or some others, before the birth of a child? How far into the future are we to achieving something like this?

Regardless of the ethical and philosophical concerns involved, it is theoretically possible to modify a child's DNA to prevent various diseases, with a few caveats.
First of all, many diseases have multiple potential causes, and there is rarely a single method which would work for every case.
Second, the actual modification is not a trivial task in eukaryotes. The more controversial method would be for a mother to be implanted with "petri dish" embryos, who have undergone gene transplantation early enough for all of the embryo's cells to be transformed. The other method involves repeated gene therapy treatments later in the child's development (and even into adulthood) which would not necessarily prevent the disease, but would minimize it's effects.
Technically it could be done right now, but to the best of my knowledge neither procedures are approved for use as of yet. Given the controversy regarding modifying a child's DNA before birth, it may never be approved, but several gene therapies are undergoing clinical trials.

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Henry Fingerprint Classification System Disrepency Among Articles
I know that the formula for fingerprint primary classifications is [1+(even finger value sum)]/[1+(odd finger value sum)]. So according to this formula and the Henry Classification System finger values, if a person has whorls on all ten fingers, then the classification ratio would be (1+31)/(1+31), which is 32/32. But some of the articles I have read say that it is actually 31/31 for a person with whorls on all ten fingers. Here are two articles that say that: article 1 and article 2 while other articles such as article 3 say 32/32. To me, the first two articles did not add the +1 to the numerator and denominator. Which is correct?


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Is newly produced sperm healthy if there was previous DNA damage?
I read that sperm cannot repair DNA damage. So does this mean that if your sperm has DNA damage, then all of your sperm (whether present or future) has DNA damage? Or does it just mean that the present sperm has DNA damage, but new sperm will be healthy?

Male gametes (aka sperm) is produced by meiosis of numerous germ cells (gametes precursors). It is unlikely that all germ cells have damaged DNA so the newly produced gametes should be healthy. This also implies that if the DNA inside the gametes was damaged after they were produced, then again, the new gametes will be healthy.
As a disclaimer, I am talking exclusively about damages to the DNA, it could very well be that gametes are unviable for other reasons than just spurious DNA (e.g. low mobility). In this case, viable gametes are unlikely to be produced unless the reason underlying the original production of unviable gametes is fixed (e.g. via medication).


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what's the difference between traditional genetic engineering and and CRISPR?
While at school, I learnt about restriction enzymes and how you could insert foreign DNA into an organism.
When I first heard about CRISPR I thought it was very similar except much more precise/targeted.
It seems however that CRISPR only allows editing (substituting nucleotides)
What are the differences, advantages, etc?

In what organism? In yeast for example you don't need restriction enzymes nor CRISPR for precise engineering only PCR products.

Bacteria and archaea evolved CRISPR as part of their adaptive immune system to protect themselves from invading viruses and foreign plasmids. The defence system relies on small, non-coding RNA molecules (CRISPR RNAs/guide RNA) that in association with a CRISPR associated (Cas) protein silence foreign sequences by means of cleavage. Twenty nucleotides at the 5’ end of the CRISPR RNA, corresponding to the protospacer region, direct the Cas9 protein to a specific sequence within the DNA using predictable Watson and Crick base pairing between the target DNA and the guide RNA, triggering enzymatic cleavage of the foreign DNA. Essential for cleavage is the presence of a sequence motif immediately downstream of the target region, known as the protospacer-adjacent motif (PAM),the PAM sequence in S. pyogenes (the most widely used system) is NGG. Because a sequence match also exists between the guide RNA and the host’s DNA that encodes it, it is vital that the guide RNA identifies bona fide targets without attacking the host chromosome. Discrimination between the target and host protospacer is achieved by the Cas effector recognition of a PAM sequence that initiates binding and cleavage of the foreign DNA. Changing the DNA target site that is specified by the 20 nucleotides at the 5’ end of the guide RNA redirects the system to target a different DNA sequence, making it a highly versatile and programmable tool. In 2012, the CRISPR system was  programmed to cleave specific DNA sites in vitro and since then, the system has been widely used in many gene modification applications.
CRISPR allow so much more than just substituting nucletodies. Like you say, CRISPR is a much more precise system than restriction enzymes, the guide RNA for CRISPR systems is typically around 20 nucleotides long so it can theoretically be used to target a unique site in the genome (4^20 = 10^12, so only the recognition site is expected to feature once 1 in 10^12 bases, N.B. the human genome is only 3x10^9 base pairs in size).
There are several options using the CRISPR with an active Cas9 protein, the first is to create a gene knockout, which removes the function of a gene. Gene knockouts can be performed by targeting the CRISPR-Cas9 system to the start of the gene and cleaving both strands of the DNA to generate a double stranded break which will be repaired most likely by the cellular repair pathway non homologous end joining (NHEJ). NHEJ results in insertions or deletions and so will most likely result in a frameshift mutation which alters a large amount of the amino acid sequence in the gene or introduces an early stop codon, so the protein produced is non functional. Alternatively a conserved residue (e.g. a catalytically important residue) in the protein can be targeted and mutation of this can remove the catalytic function or recognition domain in an enzyme or protein. NHEJ can also be used to mutate DNA that codes for RNA products. Additionally, the CRISPR system can be targeted to regions outside of the coding sequence such as the promoter or enhancers and silencers/operators (depending on whether prokaryotic or eukaryotic), which can also remove the functionality of the gene.
The CRISPR system can also be introduced to the cell  together with a single-stranded or double-stranded DNA template to make very small and precise changes to the DNA (e.g. single base mutations), or insert DNA sequences up to thousands of bases in length so that entire genes can be incorporated into the target region. This more precise editing method also involves the double stranded break formation by the cas9 protein, but relies on different cellular repair pathways: homology directed repair, the most common form of which is homologous recombination. Importantly, the template DNA must have homologous sequences to the DNA flanking either side of the double stranded break. In the presence of the correct exogenous DNA template, homology directed repair can occur in which the exogenous template DNA is incorporated into the target DNA in exchange for the damaged DNA.
Other use of CRIPSR include using a catalytically inactive cas9 protein (dead Cas9). This system is unable to cleave DNA, but is still able to target specific sites in the DNA. dead Cas9 can be fused to or recruit effector proteins for regulating gene expression at the transcriptional level, as well as guiding enzymes capable of precise base editing without introducing double stranded breaks. The dead cas9 system can be fused to transcription repressor domains such as the Krüppel-associated box (KRAB) or transcriptional acitvators such as VP64 for effective and specific repression or activation of gene expression at sites that don't contain recongion sequences for these effectors. dead Cas9 can also be used to recruit epigenetic modifitying enzymes such as methylases and acetylases to regulate gene expression this way. Additionally, this system can be fused to DNA base editors, which are enzymes created by directed evolution that are capable of causing efficient and specific point mutations in DNA and RNA (this is much more specific and effective than point mutations using homology directed repair), although RNA editing required using cas13.
Gene editing can be used to repair disease causing mutations, introduce new genes with novel functions into organisms' genomes, transiently alter gene expression to treat diseases; create knockout, knockdown and knock in strains for studying the effects of genetic factors on phenotype and even more.
In contrast, restriction enzymes typically have recognition site of 6 nucleotides and so they will cut at many orders of magnitude more sites than CRISPR will (4^6 = 4096, so 1 in 4096 nucleotides are expected to be a cut site for restriction enzymes) so they are not suitable for specific editing of genomes as they will cause non specific fragmentation of genomic DNA, which will kill the organism, so CRISPR is a much better enzyme for editing genomes. Instead, restriction enzymes are used in molecular cloning to generate sticky overhangs (or blunt ends) for the assembly of DNA molecules to generate recombinant DNA.
Although the PAM appears to limit the number of target sites that the CRISPR system can be targeted to (around 1 in every 16), through directed evolution, a Cas9 variant with increased PAM compatibility has been developed. This new Cas9 is capable of recognizing PAM sequences including NG, GAA, and GAT, this makes it  more versatile and greatly expands the number of targets available for site-sensitive genome editing applications.
Whilst CRISPR based gene editing is very exciting, a lot of work is still needed to: increase the specificity of the system as it causes numerous off site mutations, which can be lethal to cells; to increase the effectiveness of delivery of the system in vivo to large organisms such as humans; to reduce the immunogenicity of the system (it can trigger an immune response in humans) so that it is safe to use; as well as increase our understanding of the affect of making specific mutations in humans (e.g. which mutations can treat diseases safely).
References/further reading:
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (80-. ). 337, 816–821 (2012).
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell 152, 1173–1183 (2013).
Liu, X. S. et al. Editing DNA Methylation in the Mammalian Genome. Cell 167, 233–247.e17 (2016).
Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339–50 (2015).
Hu, J. H. et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature (2018). doi:10.1038/nature26155
Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science (80-. ). 358, 1019–1027 (2017).

so use of CRISR is limited by the presence of PAM sequence in the target DNA?I mean say Cas9 recognize NGG,so I can only edit the sequence near to NGG?

I left that out at the time because there has been a lot of work done to reduce the requirement of Cas9 proteins for recognising a PAM sequence, but I have edited the answer to include a note on it.

As a note about this: "increase the specificity of the system as it causes numerous off site mutations", J. Doudna and E. Charpentier both said that CRISPR-Cas9 was very specific and that was far from the major concern at that point. Also discussed here: https://biology.stackexchange.com/questions/49106/how-specific-are-crispr-cas9-cuts

I would strongly disagree with you, there has been masses of evidence showing that CRISPR is not yet specific enough for targeted therapeutic applications:https://science.sciencemag.org/content/364/6437/289
"The technology requires further development to limit off-target editing." A quote from a paper written by Jennifer Doudna - DOI: 10.1126/science.aat5011.
Look at the recent mess up with gene editing cows, the technology is far from where we want it to be in terms of specificity - https://www.technologyreview.com/s/614235/recombinetics-gene-edited-hornless-cattle-major-dna-screwup/

CRISPR is a gene system used by bacteria to resist virus invasion/avoid mammalian immune response. Scientists use RNA to guide cas9 nuclease to cut and modify specific genomic sites in a variety of cells, including IPS. The Rudolf jaenisch team injected cas9, te1 and tet2 specific sgRNA into the fertilized eggs of mice, and successfully obtained the homozygous mice with double gene knockout, with the efficiency up to 80%. They co injected cas9/sgRNA with primers with mutated sequences, which can accurately introduce the required point mutations into two genes of mice. In ES cells, they successfully knock out five genes at a time. Compared with ZFN/talen, CRISPR/Cas is easier to operate, more efficient, and easier to obtain homozygous mutants, and can introduce multiple mutations at different sites at the same time. But whether the system has Miss target effect needs further study.
The traditional transgenic and gene targeting technology, due to its stable and mature technology, can modify the genome sequence of mice and rats, and will still be the main technology of model animal construction. If ZFN/talen, especially CRISPR/Cas, can solve the Miss effect, it may be widely used in the preparation and research of mice, rats and other model animals, and become an important supplement to the traditional transgenic and gene targeting technology.

Welcome to Biology.SE! It isn't clear that this adds anything to the very thorough existing answer and seems to incorrectly imply that CRISPR isn't already widely used. In addition, answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. ——— Thank you for taking the [tour], but please also consult the help pages for additional advice on [Answer] effectively on this site. Thanks!


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Why don't we hear all the processes in our body and what prevents us from doing so?
Why don't we hear all the processes in our body (like the rushing of our bloodcells through our arteries, the pumping of our heart, the electricity of neurotransmitters or our brain cells, etc.)
Is it only because the sound is too low for us to hear?

The issue here is with the definition of the word "hear". We do hear most of this, that is our ears actually pick up and transmit this sound. But we don't hear it in the sense that our brain ignores it and filters it out of what we are aware of. Only a very small fraction of all the sensory data that comes into the brain ever gets processed. The brain does something called sensory modulation it filters through all the sensory data and decides what is worth paying attention too.
This happens at several levels, not surprising since we see these same levels of filtering in animals, as soon as you evolve sensory organs the ability to filter sensory information is an advantage. Some happens directly at the sensory organ, many have a threshold before a signal is sent. In the brain the reticular formation is responsible for much of it. But each sensory processing area also does some of its own filtering. Basically each portion of the brain contributes in some way. Attention and how it is controlled is greatly studied as it is central to how consciousness functions. A complete rundown of all sensory processing is tricky since some senses (like smell) skip some parts of the process, and there are so many ways it can be filtered. you can find a more detailed breakdown here.

It's still very mysterious how Allah made us hear like we consider as normal and how did He make us not here the processes. And what part of the brain regulates that specific task? The auditory cortex in the temporal lobe? I'd prefer medical terms, I'm used to remembering Latin names. So go ahead please ;)

The sound is mostly drowned out by all the other sounds in your environment. The environment is just too noisy. However you can hear it if you are place in sensory deprivation chamber. You can hear stuff like your heart beat, the eyelids moving, joints creaking, muscles tensing and even the movement of blood in the arteries within your ear.
You cannot hear neurotransmitter diffusion because it is a movement of chemicals, which do not generate a pressure wave and is thus soundless.
But there are sounds that you hear. You can hear yourself breathing and chewing your food.


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Are women smaller to optimize cloth needs during pregnancy?
Current life events made me wonder: Is it possible that female humans evolved to be on average smaller than males, so that they can reuse their partner's cloth during pregnancy?
At least in my culture, males prefer smaller females, which would suggest some selective pressure, but I'm unsure whether this is cultural or actually makes biological sense.

For how long do we wear clothes and possibly recycle them to partners? I would say this is not longer than for one generation. So it is quite unlikely that evolution plays a role here.

No.  Making of cloth is only perhaps 30,000 to 40,000 year old (History of clothing and textiles), and body coverings of any form, e.g. animal skins, only around 100,000 years old (based on body lice).
Females being smaller than males is much, much older than this. Chimpanzees, our closest relatives, similarly have smaller females (and don't dress in cloth); their line and our line separated around 4 million years ago.  Our next closest relatives, the gorillas, have an even greater difference between the sexes, the females being half the size of the males.  They separated from our line perhaps 6 to 8 million years ago.  Further back, most all our anthropoid primate relatives also show smaller female size (but the most distant primates, like lemurs, do not).  For more information see Sexual dimorphism in non-human primates.


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What is a centrosome?
I know that a centrosme is composed of two perpendicular centrioles, but the following sentences of Wikipedia confuse me:

Interestingly, centrioles are not required for the progression of mitosis.
Many cells can completely undergo interphase without centrioles.
Unlike centrioles, centrosomes are required for survival of the organism.

If centrosomes are essential then does this doesn't imply that centrioles too are necessary since centrosome is made of two centrioles, if not then what is it made of?

Reading the specified Wikipedia article about Centrosome, actually explains why centrioles are NOT IMPORTANT for the PROGRESSION OF MITOSIS.
To better understand what wiki meant, let us look at both centrioles & centrosomes.
According to Biology Pages for Centrioles and Centrosomes >>

Centrioles are built from a cylindrical array of 9 microtubules, each of which has attached to 2 partial microtubules.
The Centrosome

is located in the cytoplasm usually close to the nucleus.
It consists of two centrioles — oriented at right angles to each
other — embedded in a mass of amorphous material containing more than
100 different proteins.
It is duplicated during S phase of the cell    cycle.
Just before    mitosis, the two centrosomes move apart until    they
are on opposite    sides of the nucleus.
As mitosis proceeds,       microtubules grow out    from each
centrosome with their plus ends       growing toward the    metaphase
plate. These clusters of microtubules    are called spindle
fibers.

So, now we know that during mitosis, the nuclear membrane separates and the centrosome nucleated microtubules (parts of the cytoskeleton) can associate with the chromosomes to fabricate the mitotic spindle.
Understanding the conceptual working of centrosome, the Wikipedia article states >>

Interestingly, centrioles are not required for the progression of
  mitosis.
When the centrioles are irradiated by a laser, mitosis
  proceeds normally with a morphologically normal spindle.
In the absence of the centrioles, the microtubules of the spindle are
  focused by motors allowing the formation of a bipolar spindle. Many
  cells can completely undergo interphase without centrioles.

Therefore, even in the absence of centriole, centrosomes develop Astral microtubules which just exist amid and quickly before mitosis. Astral microtubules are characterized as any microtubule beginning from the centrosome which does not interface with a kinetochore.
Astral microtubules are not required for the movement of mitosis, but rather they are required to guarantee the devotion of the procedure. The capacity of astral microtubules can be by and large considered as assurance of cell geometry. They are totally required for right situating and introduction of the mitotic spindle assembly, and are in this way required in deciding the cell division site in light of the geometry and extremity of the cells.
An important note from the the Wikipedia article >>

Unlike centrioles, centrosomes are required for survival of the
  organism. Acentrosomal cells (i.e. cells without centrosomes) lack
  radial arrays of astral microtubules.
They are also defective in spindle positioning and in ability to
  establish a central localization site in cytokinesis.

so if we irradiate the centrioles then, what is left to be called as centrosome? The only constituents of centrosome are 2 centrioles , if we destroy them with laser,  then directly we are destroying the whole centrosome too.

@JM97 that is not entirely correct. If you read the answer, it says centrosome includes 2 centrioles PLUS 100 different proteins. The only constituents of centrosomes are not centrioles.


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Effect of forced breathing on RBC size

Microcytosis, i.e. decrease in the size of RBCs occurs:
– In iron deficiency anaemia,
– During prolonged forced breathing and
– When osmotic pressure of the blood is increased.

I am unable to understand how forced breathing results in microcytosis.

My attempt: I think prolonged forced breathing results in low CO2 concentration in blood which would lead to low H+ ion concentration , but this would lead to hypo-osmic plasma, which would certainly produce macrocytosis.

Source:Textbook of physiology

I thought H+ concentrations cause pH changes in blood and protein concentrations cause osmotic changes.

Co2 in the blood will be in the form of H2CO3, which will dissociate into H+ and HCO3- , if the rate of respiration is increased then, this is lost from the blood, so some amount of osmotically active species is lost from plasma. You are right in that osmotic changes, are mostly due to proteins, and it was  just a guess to solve the original problem.

I am hypothising too here:for maintaining constant blood viscosity->reverse of hamburgers->decreases swelling of RBC->makes the RBCs comparatvly irregular->viscosity rises.feedback occurs decreases the no. of such RBCs thus viscosity is controld.If I findrefrences I would post it as an answr later.


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Number of regulators required for specify the total state of genes
My course notes make the following claim:
If the regulation of each gene could include all transcription regulators
available, then in principle the total state of all genes could be specified with only $log_2(N)$ regulators.
It then gives this explanation:
To see this, imagine that one had 10 regulators that can be on or off. Then one can, in principle, specify $2^{10}$
different states, and thus specify all possible states for up to N = $2^{10}$ genes.
I don't understand the explanation given. For n genes, each of which can be turned on or off, there should be $2^{n}$ states. This would then mean N regulators would be required to regulate N genes.
Could anyone explain why this is incorrect?

Not sure what this means. what does "total state of all genes could be specified" mean? "Specified" like once we observe log2(N) regulators as on/off we can make a good guess about the state of any given gene, or we can make a statement about some overall state of the network, or something? Or like if we were god we could completely control the network by turning on/off only log2(N) regulators? What is "total state"?

@MaximilianPress I think it means that all the possible states for N genes could be specified using log2(N) regulators.

Have you asked your course instructor?

@jore1 I'm still not sure what a state is, or what it means for regulators to specify states for genes. In what context? why? I suspect that this is a description of a mathematical/graphical model of gene regulation, but the terms and structure of the model are not specified in your question, so it's hard for me to evaluate standalone statements about the behavior of the model.


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Pupae in sheoak tree
Can you identify this pupa? We found it when trimming our sheoak. It had bored into the wood. We are at Cape Jervis in South Australia.


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Can anybody identify what insect laid these eggs? Find in my backyard in N. Texas
I happened to turn over this leaf in my backyard and found these eggs.  Would really like to know what they're from. I'm in North Texas.

Maybe https://springfieldmn.blogspot.com/2018/11/fuzz-on-kale.html


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What wavelength of light should I use to measure the absorbance of an anabaena population?
I am trying to use a spectrophotometer/colorimeter to measure the relative amounts of anabaena (cyanobacteria) in different samples.
What wavelength should I use to get the maximum absorbance?

Welcome to the Biology Stack. Please take the [tour] and visit the [help] for more information on this site and how it works. Please also note the homework page - so what have you found in the literature about measurements of Anabaena cell density using spectrophotometry? I can find the result within the first few papers on PubMed.


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Can a school of 'suction cup' fish block the gills of a predator as a defence mechanism?
(This is about a FICTIONAL FISH - I MADE UP THE FISH. To my knowledge, this concept is not based on any real principles or precedents.)
Now, this fish has a strong capability for suction, and very little in the way of offensive capabilites. As such, I had the idea that a swarm of these fish could use their suction to attach themselves to the gills of predators (i.e. sort of 'stapling' themselves to the space around the gill using suction, although I can include gripping teeth if necessary), thereby starving the predator of oxygen and either
My fish is about 25cm/10 inches long. It is based on the extinct Sacabambaspis (see picture below), and I imagine the small mouth would make effective suction easier.

Is this realistic or possible?
Sorry if this doesn't fit Biology Stack Exchange, I can put it up on Worldbuilding SE if it's not suited. I couldn't find anything about made up creatures in the rules.

Since you're not asking about something in the world, perhaps your fictional creature might find a better home on Worldbuilding as you suggest. We don't do hypotheticals so much here.

If you look at the “rules” they exclude questions that can only be answered by opinions, rather than facts. Indeed this is one option in the close vote form, which you will probably be unaware of. It should, however be obvious from the examples in the [Tour].

Surely a hypothetical question can have a definitive, non-opinion answer (not sure if this one does, though).

I will give you some ideas to think about. I think your hypothetical is plausible enough.

Most fish gills are protected by an operculum (bony gill cover). This might make attaching directly to the gill filaments difficult.
If they rely solely on suction, the water flow could dislodge them, especially if the fish can thrash. Tooth-like structures may be a good idea.

The question asks if this is realistic or possible. I think so. I see no obvious reasons why this would be impossible. Though, in reality, the prey of these suction fish would eventually evolve defense mechanisms.


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Why does sunburn cause fever?
Today I found out that sunburns can cause fever.
What I don't understand is how/why? In my understanding fever is the side effect of an immune reaction against an intruder, mainly bacteria (though I admit I can be wrong).
Google searches like "can sunburn cause fever" only bring up that it is possible, but not why.

Please don't comment I should see a doctor. I know. Also I had a hard time finding appropriate tags, feel free to edit.

Here is a good article on the topic.
https://www.nlm.nih.gov/medlineplus/ency/article/003227.htm
But it's most likely due to the fact that a sun burn is an actual burn on the skin that can cause inflammation, inflammation can in turn cause fever. Also having a really bad sunburn can open you up more to the possibilities of skin infections. If this happens then once again you might get a fever due to infection. If you really want to find out more on the cause of fever after sunburn you need to examine the pathophysiology of fever and why fever happens. I bet my money on fever due to skin inflammation after a sunburn, I guess the real question would be why does inflammation cause fever since sunburn = skin inflammation
Here is a good article
http://antranik.org/inflammation-and-the-pathophysiology-of-fever/

Mr Hons, you are right on the money; no need to guess. Here's a reference backing up your answer: Ultraviolet Light Induces Increased Circulating Interleukin-6 in Humans.


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Any references contradicting Hormesis from low dose studies?
I've recently read some papers on Hormesis (the stimulatory effect of low doses of substances toxic at high doses). The papers are all published in respected peer-reviewed journals, here, here, and here for example, but they're pretty much all by one person, Edward Calabrese. I'm struggling to make sense of an issue which is clearly an acceptable enough possibility to appear in peer-reviewed journals, but which seems to have garnered absolutely no further interest beyond the one man. I naturally presumed that the concept had been dismissed by some later study, but I cannot seem to track such a study down.
To be clear, I'm not interested in policy, as the use of linear no threshold models vs Hormetic models for public policy is so highly politicized a topic with unscientific approaches on both sides (the vested interests of polluting industry vs an easily panicked population urging it's legislators). I'm just looking to fill the gap in my reading of the science. Papers showing demonstrable low dose responses which match a LNT model would be good, papers showing contrary results to Calabrese's for the same toxins would be ideal.

Hormesis Defined Nesbitts paradox resolved? Nicotine physiological response changes with dosage I think in general it's accepted that decreasing pollutant concentration is better than increasing it.

He is not the only person. I have come across papers on hormetic effects of heat stress on C. elegans. https://www.nature.com/articles/ncomms14337, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847401/. See this review for more references.

I'm voting to close this question as off-topic because: 1. it is based on a wrong assumption that the "theory" in question is propagated by just one person 2. it is asking for literature mining for evidences "contradicting" an established phenomenon.


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How does residual chlorine in tap water work?
As I understand it, residual chlorine levels in tap water are below 1mg/l in the UK. Most chlorine based cleaning products suggest at least 1% solution to be effective (quite a long way off 0.5mg/l by my maths).
Given that chlorine has a very slight disadvantage to health (albeit a tiny one), if 0.5mg/l is not enough to kill harmful bacteria, why is it there at all? If it is enough to kill bacteria, how does it do it when cleaning products require what seems to be several thousand times greater concentrations to do the same job?

Actually, I think that to qualify this statment, you should use about a 3.33% solution of household (5%) bleach for disinfecting. So that's actually, 0.15% sodium hypochlorite solution.
Also, time and pH are factors. A 0.15% bleach solution will kill many bacteria within 5 minutes. But after a few days, a more dilute solution will also have killed many bacteria.
Also, given that household bleach has a pH of around 11, a 1% solution will have a pH of about 9. The optimal pH is about 6, where all of the -OCl is converted to HOCl which is roughly 80x more effective as a germicide.
So, I realize that 0.5mg/L is still about 3000 times less than 1.5g/L (= 0.15%), and that's the real question. The real answer is that the place where the bleach is added (in a municipal supply) is at the filter, where bacteria collect. Once the old filter has been bleached the fresh water supply is allowed to resume which flushes the bleach along (at tolerable levels). Also, they often use other oxidizing agent which are synergistic with HOCl, so that they can reduce their cost and improve the function.

Great, thanks. Just a couple of things 1. Are you saying that residual chlorine is really just a by-product of the main cleaning process and it's not deliberately put in at all? 2. Is the time/dilution effect roughly equivalent. i.e would tap water have the same disinfection effect as a bleach solution after 3000x5=15,000 minutes (10-11 days)?

@Isaacson it's not so simple. With antibiotics there's a threshold or minimum inhibitory concentraton. But there are many different kinds of bacteria, each with their own MIC. But at the filter, they are not using 0.15% bleach. They can use much less and wait a few hours. I don't suppose that 0.5mg/L Would be germicidal, but that's really just an average. sometimes it's higher or lower. I avoid using tap water for growing bacteria, because it does make a little difference though.

I've marked the answer because I think it's the best I'm going to get, but still a little confused. You say "I don't suppose 0.5mg/l would be germicidal", this pretty much still leaves open the question of what's it there for then? If it does not kill germs, why don't the water companies just remove all the chlorine before piping the water out, is it that the "little difference" you mention is enough to justify it from a public health perspective?

Well, bleach isn't that bad for you. It's kind of like oxidized salt. Compared with the amount of salt we need and actually ingest, there's no way it is making any difference, health-wise. Every thing can kill you, if you have too much... too much water and you destroy your kidneys or simply drown. Too much air, too much light, too much heat, too much anything will kill. But we need all these things (in the right amount). Chlorine is an oxidizer. It breaks down into common salt.

@Isaacson it's at 0.5mg/L after the water has resumed. In the filter area I'm sure it's probably way higher, like around 0.001% bleach which reacts with germs and turns into salt. They will use just enough to kill the germs probably within 24 hours. Then they resume water flow through the filter and the residual chlorine gets diluted. Now I'm not very familiar with municipal supplies. They are all built and operated a little differently. I'm just saying this is one probable scenario.

From the Drinking Water Inspectorate's own leaflet on Chlorine "the trace of chlorine is there only to preserve the high quality of the water as it passes through the miles of pipes used to convey water to homes and workplaces". So the question remains, how does it achieve this at doses too low to be germicidal? What is this 'quality' that it is 'preserving'?

If someone could explain this to me we'd have the answer. From the WHO recommendations for drinking water safety it says under residual chlorine that to achieve a log2 reduction in bacteria you need "Ct99 = 0.04–0.08 min·mg/l; 5 °C; pH 6-7)" By my understanding at 0.5mg/l you would need less than 1 tenth of a minute contact (0.5 x 0.1 = 0.05). That can't be right, it would make tap water an effective disinfectant within minutes, can anyone explain why?

As WHO says in that report, Bacillus, Clostridium, Mycobacterium and Nocardia can be resistant to chlorine disinfection. Different bacteria have different MICs. Also, a reduction never reaches zero unless you have a digital world... luckily, cells are digital so you can achieve complete sterility. But suppose you have 10^6 bacteria per ml. Using WHO's numbers, with e. coli, 0.04mg/min L^-1 for the hypoclorous acid (pH 7) or 0.92mg/min L^-1 for the hypochlorite ion (pH 8.5). Which means 0.5 at low pH will probably kill 99% of E. coli in a minute. So after 3 minutes you should have 1 cfu left.

Please see page 46 the report from WHO.


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How does latency in carcinogenisis differ from the effect of chance?
Most chemically induced cancers seem to have a long latency between exposure to the carcinogen and expression of the disease. Mesothelioma typically 30-40 years, bladder cancer about 20 years, for example.
Most carcinogens also seem to have a dose-response relationship, with both tumour formation andlatency.
The only way I've ever heard latency explained, however, is the number of cell activities in the presence of the mutagen which are required to give reasonable accumulation of errors, but this seems like the same level of variation as dose. The higher the dose the more likely an error so the fewer iterations required before such an error might reasonably occur.
Yet this doesn't seem to be how latency manifests in epidemiology at all. For a start it seem an absolute value - no one no matter how unlucky, gets cancer five minutes after exposure to the carcinogen, it's seems to take some absolute length of time no matter what. Also, whilst latency is dose dependent it seems much less so. Risk can vary between 1 in a few hundred at high exposures, to 1 in a few million at low exposures, yet latency varies hardly at all despite massive variation in dose.
So basically, what causes latency in carcinogenisis, what is happening in the body for those decades, and how does this differ from the randomness of simple dose-response carcinogenicity?

I am not sure if I understand your question. To clarify, are you asking why doesn't a higher dose of the mutagen lead to a faster initiation of a tumor. Also, many times, as I understand, these cancers are due to a prolonged exposure to the carcinogen. Take smoking as an example.  Correct me if I am wrong, but that what I understand...


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Is autoimmune disease associated with self-reactive B cells?
I'm a bit of an amateur, so excuse what may be a very naive question, but I somewhat understand how B cells that are self-reactive (bind to endogenous epitopes) are selected out during development. I also know that autoimmune disease is caused by the immune system persistently attacking specific components of the body, which sounds a lot like self-reactive B cells.
Is autoimmune disease associated with (dare I say caused by?) errors in this self-reactive B cell selection process? Any useful references so I can hopefully become less amateurish?


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Why it seems that principles of chemistry are not being applied in this biochemical process?
According to an answer in this question, my concept used below does not apply:
In the non-cyclic photophosphorylation, consider splitting of two water molecules, then 4 e- (electrons) and 4 H+ (protons) are generated in the lumen of the thylakoid. Due to quinone cycle 8 H+ are transferred from stroma to lumen. 4 e- will reduce 2 NADP+ to 2 NADPH, these H+ are taken from stroma so there is a net decrease of 8 + 2 = 10 H+ and a net increase of 4 + 8 = 12 H+ in the lumen. So if we apply principles of chemistry then to attain equilibrium there should be equal number of H+ on both side. Therefore 11 H+ must be transferred from lumen of thylakoid to stroma. Now there is 1 H+ on each side at equilibrium. We know that F0-F1 ATPase will produce 1 ATP for 3 H+ being transferred so in this process 11/3 ATP should produce but in books it is given that all 12 H+ are transported which is violating the principle of chemical equilibrium and produces 12/3=4 ATP.
So I basically want to ask: Why does it seem that in this process the principles of chemistry are violated?

About which principles of chemistry are you talking?

@chris According to books all 12p will get transferred but we know from chemistry point of view that only 11p could get transferred as per the gradient created

@Chris the principle is that at equilibrium there must equal number of protons on both sides

A schematic of the reactions involved would help. It's kind of a narrative.

You should just write down the equation. Here is an explanation on how to write chemistry expression. Then, you'll probably want to use the term stoichiometry somewhere in your post. Finally, note that your question would be a better fit for Chemistry.SE than for Biology.SE but I would predict that the level of knowledge in chemistry needed to answer the question will be simple enough for us, biologists.

http://www.ncbi.nlm.nih.gov/books/NBK22519/ I think this answers the question, but let me know.

From the link given by @Kendall

Such a gradient can be maintained because the thylakoid membrane is essentially impermeable to protons.

I think this solves your dilemma of 'why not maintaining equilibrium' totally.

The reason for this difference is that the thylakoid membrane is quite permeable to Cl- and Mg2+. The light-induced transfer of H+ into the thylakoid space is accompanied by the transfer of either Cl- in the same direction or Mg2+ (1 Mg2+ per 2 H+) in the opposite direction. Consequently, electrical neutrality is maintained and no membrane potential is generated.

It precisely shows why electrical equilibrium is not disturbed due to pH disturbance.
Finally:

2 H2O + 2 NADP+ + 10 H+stroma => O2 + 2NADPH + 12 H+lumen
12 H+lumen + 4 ADP + 4 Pi => 4 ATP + 12 H+stroma


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How are primary monoclonal antibodies for screening mutant cells made, physically?
I'm working with a fairly common protein expressed in a large numbers of organisms, let's say a keratin-associated beta-protein. I'm trying to develop a process which requires primary-secondary antibody screening for the keratin-associated beta-protein. Trouble is, it's expensive. Very much so.
I can't find the antibody for any less than $778/mL, and after accounting for dilution and volume required for the recommended protocol, I can't imagine I'll be able to finish designing the process with any less than 20mL. The protein can't change as a design constraint, so there's no reason I'd ever need to change my antibody, but if I need so much... is there any way I can make it myself?
How are these antibodies actually manufactured? Would I need to get ahold of actual B cells and use those, or could I isolate the cellular machinery that produces the antibodies and use that?

If it is not that difficult in your organism, then you can create a transgenic with your protein of interest with a HA or a FLAG tag. The anti-HA and anti-FLAG antibodies are cheap.

Monoclonal antibodies are typically manufactured from a hybridoma cell line. If you are able to obtain hybridomas already made for your antibody (not very likely), or another antibody against your protein, then it's quite easy to produce the antibody yourself. The hybridomas secrete the antibodies into the media, so after growing a bunch of cells, you can purify the antibody from the media with a protein G column.
However, there are not very many hybridoma cell lines available. It's a lengthy and expensive process to make your own (several months and thousands of dollars), even with the help of a core facility/company. You would provide the facility with several milligrams of your protein, they would use it to immunize mice, then after 1-3 rounds of screening, you could obtain hybridoma clones.
There are some banks with hybridomas available for research, for example:
http://dshb.biology.uiowa.edu/
http://www.cellbankaustralia.com/ecacc-hybridoma/


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Is synthesizing DNA in-house feasible?
I've been reading up about DNA writing, and it seems there are machines available around the five-figure US dollar mark for DNA synthesis, and I'm considering picking one up for my lab.
We normally order our DNA/oligos from IDT and similar companies, and for cutting down cycle time from a few days with next-day shipping to a few hours with in-house printing, as well as potentially saving on cost with enough scale (how much is enough scale?), this seems really promising for our lab.
Is this a reasonable thing to do?

Have you looked at how much reagents cost?

@Cell Is that the concern?

I'm not sure. My ex-supervisor purchased a DNA sequencer and the consumables were so pricey it was actually cheaper to send samples to a dedicated facility. The only reason we would use it was if we wanted results in a few days and not weeks. I would look into it if I were you.

it would be helpful to know more about the scale of oligos, etc. Definitely look at the consumables price. I know that for the opposite approach, DNA sequencing, the technology advances so quickly that it really doesn't make sense for independent (small-medium) groups to buy their own sequencing instruments, as they're pretty finicky, so most people just send their libraries to a dedicated provider like genewiz or a university core facility.

So far as I'm aware, the big distinction right now is whether you want dsDNA or oligos.
If you often want lots of oligos, then getting your own synthesizer likely makes sense. Run the numbers and see what the time for return on investment will be and you'll see if it works for you financially.
If you want gene-scale dsDNA, you're currently generally better off getting a specialist company involved (or a foundry, if you've got one that you can access). Not only do they have economies of scale, but they have a lot of experience figuring out how to handle difficult sequences and assemblies.  If you take it all in house you might appear to save money but actually end up losing significant money and time when you count in the time and frustration that your lab ends up spending to go from oligos to genes.
If you've got particular expertise or highly specialized needs, it's a whole different story, but that doesn't sound like the case based on your question.
Note that there are a number of desktop synthesis companies that are working to make this answer obsolete right now, and it may well change quickly in the future.


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What vitamins exist for other animals but not humans?
As you probably know, humans are among the minority of animals that require Vitamin C and don't produce it ourselves. For whatever reason (multiple theories exist), we lost the ability. Meanwhile, the vast majority of animals out there that require Vitamin C simply produce it internally, so they have no need for food choices that contain it. Had it not been for the discovery of scurvy as Vitamin C deficiency, we likely wouldn't have ever known that Vitamin C exists at all as a requirement for human health.
Are there known to be cases in other animals of dependence on food containing vitamins that we humans produce ourselves?

what a cool question!

The best example I can think of is taurine, which is a non-proteinogenic amino acid.
Taurine is "conditionally essential" for humans1, but essential for cats2,3.
References:
1: Stapleton, P. P., Charles, R. P., Redmond, H. P., & Bouchier-Hayes, D. J. (1997). Taurine and human nutrition. Clinical nutrition, 16(3), 103-108.
2: Knopf, K., Sturman, J. A., Armstrong, M., & Hayes, K. C. (1978). Taurine: an essential nutrient for the cat. The Journal of nutrition, 108(5), 773-778.
3: Markwell, P. J., & Earle, K. E. (1995). Taurine: an essential nutrient for the cat. A brief review of the biochemistry of its requirement and the clinical consequences of deficiency. Nutrition research, 15(1), 53-58.

@user1136 — Yes and No. Depends on there being a formal accepted definition of vitamin that would exclude taurine. Can you supply one?

@user1136 —  No. There is an obvious difference between "essential amino acids", which are needed in stoichiometric amounts as components of proteins, and taurine, which although chemically an amino acid is not a constituent of proteins. I don't actually know what taurine is needed for in the body, and a quick glance at the summaries of the papers cited doesn't make this clear, but it does not appear to be an energy factor in nutrition. A key criterion would be the quantities needed in the diet. My impression is that the definition of vitamin is something of a post hoc fudge.

Could you flesh out your answer a little to address the points made by @user1136. I imagine you have a strong case, but it would be good to have it in the open.

Historically, the vitamin concept arose out of nutritional studies that demonstrated the dietary requirements of additional factors not supplied by a diet of protein, carbohydrate and fats. These substances are 'specific in function' and are required by the body in very small amounts, and were termed vitamins by Casimir Funk (see Hopkins' Nobel Lecture).
One substance that comes very close to being a vitamin for another organism but not for humans is biopterin, although I suspect that the term  'essential growth factor' is more appropriate than 'vitamin', given the current state of biochemical knowledge.
The organism is the protozoan Crithidia fasciculata, which requires the unconjugated pteridine biopterin as growth factor (Patterson et al).
Despite this requirement, and despite the fact that this metabolic need is the basis of an assay for unconjugated pteridines (Dewer and Kidder), no one knows the molecular basis (although there are some suggestions that is it required in pyrimidine biosynthesis) (see Kaufman)
Dewer and Kidder go further and state that "the only organisms at present known to have a dietary requirement for an unconjugated pteridine are members of the flagellate order Kinetoplastida (trypanosomids)" although personally I have never been able to confirm this except for Crithidia. Trypanosomes (the causative agent of sleeping sickness), for example, have never been shown, as far as I am aware, to require an unconjugated pteridine.
Humans, of course, do require an unconjugated pteridine (in the form of tetrahydrobiopterin, or BH4): it is the cofactor for phenylalanine hydroxylase, tyrosine hydroxylase, trytophan hydroxylase, for an enzyme involved in the oxidation of glyceryl ethers, and for nitric oxide synthase (among other roles).
However, it is not a vitamin! We can synthesis it (from GTP, as it so happens). This aspect is discussed in detail by Kaufman, as is the essential role of BH4 in neurotransmitter biosynthesis.
None of the above enzymic systems are known to occur in Crithidia  (Kaufman). This organism, for example, cannot convert Phe to Tyr: the only enzymic system, or enzymic systems, capable of converting Phe to Tyr require an unconjugated pteridine (no cytochrome P450 system, for example, is capable of this transformation).
Both plants and E.coli are also of interest.
The evidence for any BH4-requireing enzyme in plants is scant. Plants can synthesise Phe and Tyr (they have the enzymes of the shikimate pathway) but they cannot convert Phe to Tyr. Phenylalanine hydroxylase, for example, has never been isolated from a plant source.
The same applies to E.coli.  This organism has no requirement for an unconjugated pteridine and cannot convert Phe to Tyr (see Miller and Simmonds and Kaufman).
But this is not the case for all bacteria. Those, such as Chromobacterium species (ref), that are capable of using Phe as a carbon source have phenylalanine hydroxylase, which requires BH4 (or a closely related pteridine) as cofactor.  In these cases, too, the pteridine (BH4?) is not a vitamin but is synthesized de novo from GTP.
Thus, to summarize.  The only organism known to require an unconjugated pteridine as a dietary growth factor is Crithidia fasciculata but no one knows why. You and I (as humans) require BH4 as cofactor for key hydroxylation reactions, including the conversion of Phe to Tyr, but it is not a vitamin: we synthesis it.  Plants and E.coli have no known requirement for biopterin (or any unconjugated pteridine) and cannot convert Phe to Tyr. Some bacteria, however, do require BH4 (or a closely related pteridine) as cofactor for hydroxylation reactions but these organisms also synthesis it.

Could you clarify? Is your answer “none”, or just “not pteridine”?

OK. That is interesting. I have no specialist knowledge in this area, only a wish to clarify and improve answers to help raise the standard of this site. I feel that we should give a fair consideration to the answer given by @tyresome. It may need expanding, but I don’t think it should be dismissed in a perfunctory manner.

This is exactly the type of thing I was looking for! How fascinating that a single species requires a "vitamin" (essential growth factor? tomato, potato) which is either synthesized or unnecessary in every other known organism. Good argument as well


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Why is it possible to render fat if it's in cells?
To the casual onlooker, fat seems like a mass of yellow-white material, composed of lipids. Biologically speaking however, rather than being a large mass, it's actually divided among countless cells, each of which is composed chiefly of lipids stored in vacuoles, in addition to a few other organelles. In essence, while it looks like a giant mass, akin to a big pile of coconut oil, it's practically more like a big pile of sandwich baggies, each filled with coconut oil, and a small amount of rice for good measure.
Yet when rendered, fat melts as if the cells and structure didn't exist, and many food animals are bred to have fat that melts at slightly above body temperature. These two models, the pile of coconut oil, and the pile of baggies of coconut oil, seem to conflict when it comes to expected behavior. For the latter to act like the former, the cells would have to be broken down, but I wouldn't expect cell membranes to rupture at just above body temperature.
So my mental model is badly predicting reality. Where is it wrong?

"many food animals are bred to have fat that melts at slightly above body temperature" - can you cite this?

Melting point of the fat is not the same as rendering temperature.

@bryankrause Apparently rather than being just above body temperature, it’s below, and now I’m even more confused

Interesting question connecting biology and industrial processes! Re: " it's practically more like a big pile of sandwich baggies, each filled with coconut oil," I think a better analogy would be soap bubbles rather than baggies. The phospholipid membranes (which also contain a lot of lipids) are not physically robust. The general descriptions of the rendering process indicate a main goal is to remove the water; the remaining material is fats and a proteinaceous meal. Without water, the membranes should all go away as you won't be able to maintain the bilayer anymore.

@TheEnvironmentalist I would say Armand's comment just before yours should explain the confusion.


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How would infection of mosquitos with sterilizing bacteria have any effect?
According to this article from the New York Post, the US just approved the mass release of male mosquitos infected with a bacteria that sterilizes them. The idea, according to the article and some inference, is that they'll mate with female mosquitos and impregnate them with non-viable eggs, causing a missing generation of mosquitos. Brilliant, right?
Well, no. Male mosquitos, from what I can gather, typically live less than a week in their adult phase, mating perhaps once while females will live for a few weeks mating, feeding, laying eggs and repeating until they die. Even if males and females both only manage to mate once, for every female you want to not produce viable young, you'd need to release one infected male. With a very conservative estimate of 10 trillion mosquitos in the United States, one generation per year, and current separation of male from female mosquitos in the lab by hand according to the article, you'd need to manually infect 10 trillion male mosquitos per year, for at least a few years, to make a serious dent in the mosquito population.
How does anyone think this is a practical idea?

I'm not an expert on this, but I think you're right that they have to release many infected mosquitoes, and repeatedly. Instead of spraying a pesticide, which might target other insects or have negative consequences for people, I think they're releasing infected mosquiotos. So you have to continue doing it, and in large numbers. But you don't need to kill all mosquitoes in country, just where people are. Furthermore, ultimately goal is to limit transmission of diseases like Zika, not to kill all mosquitoes. Having fewer mosquitoes might limit spread of things like Zika among the mosquito pops.

@rbatt Well even if you're just targeting the urban 0.1% of the country, and you're only trying to decrease the mosquito population by 10%, that's 0.01% of the 10 trillion mosquitos per year above, or one billion mosquitos, hand-separated, per year needing to be released to have the desired effect, every year. That's just as impractical as 10 trillion

Well, there are a few extra things to consider. 1) it's not 1 infected = 1 dead. If you had 50% of the population infected, then the entire pop would die in 1 generation (because 50% of pop would be ~100% of males, then 100% females dead). 2) On the other hand, they also aren't replacing wild males with infected males ... it's a dilution. That makes it even harder. 3) As you start to decrease the population size, the problem becomes more tractable with each successive generation. If you go from 10 tril to 1 tril, that 1 tril is 10x easier to dilute the next time you try


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How didn't large, highly active dinosaurs overheat?
The cube-square law seems to be the deciding factor when it comes to biological heat management. Small organisms with large surface areas relative to their volumes, like mice, need fast heartbeats and huge energy consumption relative to their size to keep themselves warm. Large organisms like elephants with small surface areas relative to their volumes need slow metabolisms and fairly little energy consumption relative to their size to keep from overheating.
But, dinosaurs. Most research seems to indicate they were basically warm-blooded (yes, that wording really bothers me too, but research as recent as 2015 states that they seem to lean decidedly toward warm-bloodedness, though they are technically somewhere in between). Modern-day creatures of that size tend to divide neatly depending on whether they live on land or in water, with the former being fairly inactive and herbivorous and the latter sometimes able to support the metabolic needs of predation by having water to help disperse the heat.
Dinosaurs, though, are an exception. Many of the fiercer predators were large, highly-active land-dwellers, three conditions that are mutually exclusive in modern organisms. How was this possible?

There has been a long debate whether dinosaurs were ectotherms or endotherms but  most of the recent studies (hypotheses)1 show that they were endotherms. In one of the most promising recent studies (in 2011), a technique called clumped-isotope thermometry2 (which is based on a reaction involving the bond between carbon and oxygen; and used in paleoclimate reconstruction) is applied to bioapatite (a form of calcium phosphate in bones and teeth) which acts like a thermometer.

The nature of the physiology and thermal regulation of the nonavian dinosaurs is the subject of debate. Previously, arguments have been made for both endothermic and ectothermic metabolisms based on differing methodologies. Here, we used clumped isotope thermometry to determine body temperatures from the fossilized teeth of large Jurassic sauropods. Our data indicate body temperatures of 36 to 38°C, which are similar to most modern mammals. This temperature range is 4 to 7°C lower than predicted by a model that showed scaling of dinosaur body temperature with mass, which could indicate that sauropods had mechanisms to prevent excessively high body temperatures being reached due to their gigantic size.
Dinosaur Body Temperatures Determined from Isotopic (13C-18O) Ordering in Fossil Biominerals
Robert A. Eagle, Thomas Tütken, Taylor S. Martin, Aradhna K. Tripati, Henry C. Fricke, Melissa Connely, Richard L. Cifelli, John M. Eiler
http://science.sciencemag.org/content/early/2011/06/22/science.1206196
(emphasis mine)

However, a study as of 2014 claims that dinosaurs were mesothermic3 (meaning the blood runs neither hot nor cold, a thermoregulatory strategy intermediate to cold-blooded ectotherms and warm-blooded endotherms) based on the metabolic rates of dinosaurs by looking at changes in body size as animals grew from birth to adults.

In early depictions, dinosaurs lumbered slowly, dragging their tails. More recently, we have imagined them lifting their tails and running. The question boils down to whether dinosaurs had energetic systems closer to those of rapidly metabolizing mammals and birds, or to those of slower reptiles that do not internally regulate their body temperature. However, determining the metabolic rate of extinct organisms is no easy task. Grady et al. analyzed a huge data set on growth rate in both extinct and living species, using a method that considers body temperature and body size. Dinosaur metabolism seems to have been neither fast nor slow, but somewhere in the middle—so, dinosaurs did not fully regulate their internal temperature but they were also not entirely at the whim of the environment; neither slow goliaths nor supercharged reptiles.
Evidence for mesothermy in dinosaurs
John M. Grady1,*, Brian J. Enquist2,3, Eva Dettweiler-Robinson1, Natalie A. Wright1, Felisa A. Smith1
http://science.sciencemag.org/content/344/6189/1268
(emphasis mine)

As we covered the thermoregulation system of dinosaurs, we can start with the question "How didn't large dinosaurs overheat?". As explained above, whether they were endothermic or mesothermic, dinosaurs had mechanisms to regulate their internal temperature not to overheat. There are theories that say that some larger dinosaurs relied on shade and dense flora to keep cool or they might have migrated due to seasonal changes. Other theories claim that they used large surface area organs (like long necks and tails) as a heat radiator4.
One of the most plausible explanations is that large dinosaurs displayed tachymetabolism. Tachymetabolic animals have high resting metabolic rates, usually resulting in endothermy and homeothermy. Further explanation of how big tachymetabolic dinosaurs coped with high heat loads5:

BIG TACHYMETABOLIC DINOSAURS WOULD HAVE COOKED IN THE HEAT
Myth: Because tachymetabolic rates scale to W0.75, while surface area scales to W0.67, it is almost universally believed that big endotherms suffer serious heat stress in tropical climes. Big dinosaurs, sauropods especially, should have had low metabolic rates to avoid this dire fate (Martin, 1979; Regal and Gans, 1980; Spotila, 1980; Reid, 1984; Schmidt-Nielsen, 1984; Carroll. 1988; Alexander. 1989; Prothero, 1989: Russell, 1989). Alternately. tachymetabolic sauropods needed well developed cooling systems (Bakker. 1980, 1986).

Figure 5 This plot shows the time it takes high level endotherms to overheat if they store all internal heat production and exclude external heat by allowing their body temperature to rise to maximum tolerable levels. The mass range approximates that of adult dinosaurs (including lagosuchians), with the highest masses of mammals also indicated: note that giant endothermic dinosaurs would have been more resistant to overheating than giant mammals! Energy storage capacity is in kcal assuming a 6-8°C rise in body temperature (up to 46.5°C), with 0.83 kcal/kg stored for each 1°C rise in body temperature; total active metabolic rates are either 2.0 times endothermic standard energy production/bout, or only 1.3 times normal standard metabolic rates due to suppressed levels of activity and/or standard metabolic rates. The results are in good agreement with thermal tolerances observed among large tropical endotherms.

  Reality: This is a major misconception (Costanzo and Paul. 1978; Paul, 1988a. 1990a). Many tropical mammals have reached from 1 to 20 tonnes, but no classic reptiles have done so, exactly opposite the predicted pattern. Elephants lack well developed evaporative cooling systems. Elephants living in treeless habitats do not drop dead from heat stroke, even in the most dangerous conditions of an extremely hot drought when it is not possible to dump excess heat by radiation or evaporative cooling in the first place, and shade is not available. Instead, large bull elephants have the highest survival rates under such circumstances, again opposite the predicted pattern (Owen-Smith, 1988). Field biologists have long known that endotherms from 100 kg on up use a classic thermal strategy in which their great mass is used to store a relatively low rate of internal heat production for most or all of the day, body temperatures are allowed to rise 3-10°C, and water loss is kept to a minimum (Schmidt-Nielsen et al., 1957; Taylor. 1969, 1970. 1972: Gordon. 1972; Finch and Rohertshaw, 1979: Schmidt-Nielsen. 1984). The built up heat is then unloaded into the cool night sky. This makes large endotherms practically invulnerable to over-heating under the harshest conditions, small endotherms must seek refuge or quickly die from heat stroke or dehydration. The large size of dinosaurs may have been an adaptation for better coping with high heat loads with a tachymetabolic level of heat production (Figure 5).

References:
1. The Evidence for Endothermy in Dinosaurs -
 Top Ten Hypotheses http://www.ucmp.berkeley.edu/diapsids/endothermy.html
2. Paleoclimate reconstruction using carbonate clumped isotope thermometry
(John M.Eiler) https://www.sciencedirect.com/science/article/pii/S027737911100268X
3. Why Dinosaurs Were Like Tuna, Great Whites, and Echidnas http://phenomena.nationalgeographic.com/2014/06/12/dinosaurs-tuna-great-whites-echidnas/
4. Sauropod Necks: Are They Really for Heat Loss?
(Donald M. Henderson)
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077108
5. Dinosaur Studies - Commemorating the 150th Anniversary of Richard Owen's Dinosauria (By L. B. Halstead)

Further readings (supporting above theories or with different theories):

GEOL 104 Dinosaurs: A Natural History - University of Maryland -
Department of Geology -
https://www.geol.umd.edu/~tholtz/G104/lectures/104endo.html
Body Temperatures in Dinosaurs: What Can Growth Curves Tell Us?
(Eva Maria Griebeler)
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074317
Ecology and Behaviour of Mesozoic Reptiles (by John L. Cloudsley-Thompson)
Dinosaur Paleobiology (by Stephen L. Brusatte)
The Dinosauria (edited by David B. Weishampel, Peter Dodson, Halszka Osmólska)
The Complete Dinosaur (edited by James Orville Farlow, M. K. Brett-Surman)
Encyclopedia of Dinosaurs (edited by Philip J. Currie, Kevin Padian)
Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution (Phil R. Bell, Nicolás E. Campione, W. Scott Persons IV, Philip J. Currie, Peter L. Larson, Darren H. Tanke, Robert T. Bakker) - http://rsbl.royalsocietypublishing.org/content/13/6/20170092
Dinosaurs used nasal passages to keep brains cool - https://phys.org/news/2015-10-dinosaurs-nasal-passages-brains-cool.html


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Is there a standard way of measuring culture nutrient levels in real time?
I am working on optimizing growth rates for a culture, and one thing I'm trying to monitor is nutrient consumption rates to pinpoint any bottlenecks, i.e. the culture goes through all the calcium in a few hours and then stops growing.
Short of manually taking samples every few minutes and running individual tests for wide arrays of nutrients (minerals, amino acids, nitrogen compounds, etc.), is there a standard way of monitoring nutrient levels automatically in real-time? This is a personal research project, so unfortunately I don't have access to industrial bioreactors and the like.

I assume LCMS is out of the picture?

@canadianer Unless it can be conducted by a self-contained sensor that doesn't require my intervention for measurements, obviously a bit of a stretch

Enzyme-based sensors for taking real-time measurements of growth substrates do exist. In brief: an enzyme degrades the substrate and thus changes the local redox state which is detected electronically (example glucose sensor). There's no guarantee that the substrates that you want to measure can be measured using such sensors. Also I think those sensors are fairly expensive and are tailored to specific conditions (ie it's not as simple as dipping the sensor into your culture medium). Practically speaking I think systems using these sensors are limited to monitoring just a small number of substrates.
LCMS or GCMS is the standard method for measuring concentrations of substrates. LC or GC  (without the MS) may be possible, but probably not since there are are many components to culture media and so lots of overlapping peaks. Using this method is labor intensive (lots of samples), likely to be low resolution (temporally), and the equipment is pretty pricey, but if you have access to an LCMS and are willing to put the time in to become an LCMS expert then this is a good option.
Culture based methods using minimal media supplemented with substrates is an option, these experiments may achieve the same thing as real-time monitoring of substrate concentrations. If you have access to a plate reader this will be so much easier. The speed at which different substrates are consumed, and the order in which they are consumed can be inferred by measuring the growth rate of the bacteria and the final population size/dry weight of the culture.
I mention this culture-based method because, although it's not exactly what your question was about, it's much cheaper than the other options and much more established (and in my opinion more fun: you get a great feel for how the bacteria grow and what media they like, and the graphs look great).

The whole purpose of this is to identify bottlenecks in growth and factors which increase growth rates. If I only measured the bacteria themselves, I'd know the effects but not the causes. How is there not a real-time way of measuring this stuff considering the same factors can be used to optimize plant growth in the industry that feeds the world? Do realtime nutrient sensors not exist?

@TheEnvironmentalist As I said, they do exist, but they are expensive and not as convenient as say a temperature sensor. And about the culture based method: you can match effects to causes if you are causing the causes. So if you compare [M9 (minimal media) + glucose] to [M9 + glucose + acetate], any difference in growth will be due to the acetate.


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How does human life expectancy change with age?
Human life expectancy tends to be given as a single number reflecting age at death from birth.
But life expectancy should really grow the longer you live, because, for example, once you hit your fifth birthday your chances of dying before age five drop to zero, so the contribution to the average life expectancy of all the people who died before age five shouldn't apply.
To put it another way, once you hit age ninety, your life expectancy calculated then and there should be at least ninety years even though that exceeds the life expectancy in every country on the planet, simply because you've clearly already made it that far.
Does life expectancy as a function of current age have a name, and what shape does this function typically take? Perhaps more interestingly, does this function take a significantly different shape in humans than in other animals (I'd expect infant mortality to significantly affect this for example)?

Maybe a survivorship curve describes what you are looking for, https://en.wikipedia.org/wiki/Survivorship_curve.

I think you might be looking for period life tables

A period life table is based on the mortality experience of a population during a relatively short period of time. Here we present the 2014 period life table for the Social Security area population. For this table, the period life expectancy at a given age is the average remaining number of years expected prior to death for a person at that exact age, born on January 1, using the mortality rates for 2014 over the course of his or her remaining life.

I read a paper once - but have not been able to find it since - that said that every (age) milestone in our life extends our life expectancy statistically and biologically. General life expectancy averages people who die of diseases that affect us at different ages: infant, child, young adults, middle-aged adults and the elderly. When you live beyond each phase in your life, you beat the statistics and at the same time show that your biological make-up has more resilience than those who succumbed during previous phases. Something that I just read reminded me of this and prompted this internet search. It said that though the average life expectancy in America is 78, when you hit your 70th birthday, you can - on average - expect to live 14 more years.

Is this the article you are referring to? Relatively new, but it is similar to what you say.

That looks like the same information. I think I was reading something like a research report. I would guess that the article you linked was written from the paper I read.