Which inflammatory response with Cytomegalovirus infection? I am thinking about inflammation process with Cytomegalovirus infection.
I first thought it is about chronic inflammation, but then changed my mind because of virus infection.
I think cytokines must be there in activation.

I am thinking which of these is right mechanism for both of these

mononuclear cells and granulocytes (I think this must be chronic inflammation)
granulocytes with scar formation (I think no scar)
cytopathic cytoproliferation inflammation

I think the cytopathic cytoproliferation inflammation is the right one because cytokines are activating the inflammatory response in virus infection.
However, I am not sure if this inflammation is of chronic type.

Which type of inflammation can cytomegalovirus infection lead to?

According to this paper the virus triggers the innate immune system and induces inflammatory cytokines as well as interferon stimulated genes (which is a response to a viral infection).
It seems to be recognized by the cells via the Toll-like receptor 2 and CD14, which subsequently trigger the cytokine production. A schematic view comes from the second paper:

These two articles are interesting in this context, the first addresses CMV in special,
the second is a pretty recent review about how viruses are recognized and how cytokines are involved:

Human cytomegalovirus activates inflammatory cytokine responses via
CD14 and Toll-like receptor 2.
Learning from the messengers: innate sensing of viruses and cytokine
regulation of immunity - clues for treatments and vaccines.


How many times is a single strand of mRNA translated into a protein? In other words, is the mRNA damaged or somehow "marked completed" in the translation process? Or does it pop out the other side of a ribosome ready to be translated again? If the latter, how many copies of a protein result from a single strand of mRNA?
Thank you in advance!

I'm answering my own question for the benefit of anyone else who might be wondering about this. (Please note that I'm just a programmer, not a biologist, but thanks to David's comment, I was able to come to what I think are some correct conclusions.)
A single mRNA strand can be translated more than once, even more than once at the same time. The polysome that David references is a group of two or more ribosomes all attached to the same mRNA strand, all working on translating it simultaneously.
I believe that it may be possible for a single mRNA strand to be translated hundreds or even thousands of times. My reasoning for this is that a virus injects one copy of its RNA into a cell, and from this one copy, new viruses are replicated until the cell bursts. This "burst size" varies by host cell and virus, but it can range from hundreds to tens of thousands or more. While there are still a lot of things I don't understand about the specific steps the RNA goes through (are there intermediary copies made from which multiple mRNA strands are produced?, etc.), it still seems to suggest that a single strand of mRNA can be translated a lot.


How does steroid dependence occur? I have seen on the internet that prolonged steriod treatment can result in the development of steroid drug tolerance leading to decreased hormone secretion. In turn this may lead to drug dependence, as you need to keep taking that drug to keep your body to function normally.

Can steroid treatment lead to drug dependency, and if yes, how?

All classes of drugs react differently in the body. Some bind to receptors, some clean receptors, some drugs cause re-uptake inhibition in the brain, and others destroy viral and bacterial infections. Classifying drugs and how the human body would develop a tolerance to them in a post on this website would take pages upon pages to answer. When you say steroids, i'm assuming you are talking about anabolic steroids. That is the male sex hormone testosterone and its multitudes of derivatives. (DHT and non-DHT). Your body does not in fact develop a "dependance" on the drugs, rather it is a checks and balances system that your endocrine system establishes. Lets say you take a dosage of Testosterone Cypionate at 200mg a week for a 20 week interval from your G.P (common treatment for andropause). In laymans terms, your body senses the increase of testosterone and tells your Leydig Cells in the testes to stop signaling LH (responsible for testosterone production). Because it sees that there is already an abundance of the hormone. Now, once treatment stops, there are a series of protocols one could take to stimulate the natural production of testosterone again. Other forms of AAS are much harder on the HPTA than others however. (Trenbolone Acetate)


If human eyes watch an area, what's the shape of its capturing shape? Rectangular? Half spherical? A normal camera can capture a rectangular image. If human eyes watch an area, what's the shape of the captured region? Rectangular? Half-spherical?

The capture area of the eye is a bit fuzzier and harder to define than that of a camera.

A camera captures consistent, fully detailed data right up to the edge of its sensor, and no data at all beyond it. Captured data is clipped by an ideally uniform sensor, augmented a bit by the lens, and is well-defined during design and manufacturing.

The eye can capture higher "resolution" near the center of its capture area and also has very little information about color near the edges (see also Peripheral Vision); so it's not quite as clean cut depending on your goal of "capture area". The eye also has a bit of a "blind spot" near the middle, which our brains basically Photoshop out. Additionally, it varies from person to person.

The effective capture area would really depend on your application (e.g. the "capture area" for, say, reading text, would be narrower than the area for, say, detecting motion).

Here is a typical diagram for a single eye, showing just the ability to see something in that area (does not show details related to peripheral vision quality):

Here is a typical diagram for both eyes combined, the solid white area is the overlap:

Both of those images are from a 1964 NASA report detailing aspects of the human visual field. If you want the detailed answer to your question and more, you probably want to take a look at that.

Note that our field of vision is very wide, those diagrams may not do it justice. As an experiment, close one eye, stare straight ahead and hold your arms straight out to the sides. Wiggle your fingers and slowly bring your arms forward until you can just see your wiggling fingers in your peripheral vision, and you will get an idea. As an added experiment, hold a piece of paper with text on it, and repeat the same experiment until you can read the text - this region will be extremely narrow and will give you an idea of how the quality of vision changes across the field. Also try with a colored object and bring it in until you can clearly identify the color.

There are also some simplified mentions of it in wikipedia:

http://en.wikipedia.org/wiki/Field_of_view#Humans_and_animals
http://en.wikipedia.org/wiki/Human_eye#Field_of_view
http://en.wikipedia.org/wiki/Visual_field#Normal_limits

A good set of search keywords is "human field of vision". There is also a nice related article entitled The Camera Versus the Human Eye.


Is it possible to establish a newer animal model completely based on Bioinformatics studies? I wanted to know, if it is possible to prove a new organism as an animal model for any human disease by only Bioinformatics methods like NGS and Structural bioinformatics.

For Example, let's say Drosophila is an animal model for Disease X as it have some 60-70% similarity in the gene and protein structure. Can we prove, a newer organism is a better model for X, if it shows a higher similarity, let's say 80-85%, to gene and protein structure of human?

UPDATE
(First I posted it as comment! But I think, this is suited here best!)

@David: Thanks for your answer! Actually, I did looked into it, Large animal models of rare genetic disorders: sheep as phenotypically relevant models of human genetic disease. I am more interested in listing down the problems if we do start this kind of project in our lab. Do NGS is a solution or what part of biology we need to focus so, that we can be more accurate.

It is naïve to think that the extent of protein similarity is sufficient to determine what is the best animal model for a human disease. The physiology of the animal and the question of compensatory genes are all factors that contribute.

Indeed, if the protein is functionally similar, it may be irrelevant if it has diverged in other regions. And, of course, there are ethical and cost considerations — the animals closest to humans are the apes!

I suggest you search for literature on the subject. It’s not my field, but Googling brought up this paper discussing models for kidney disease, and no doubt you could find much more yourself.


A question on glycolysis In the first step of glycolysis, the glucose ring is phosphorylated.
  Phosphorylation is the process of adding a phosphate group to a molecule derived from ATP. As a result, at this point in glycolysis,
  1 molecule of ATP has been consumed.

Is it the phosphate group, or the molecule, that is derived from ATP ?

http://www.sparknotes.com/biology/cellrespiration/glycolysis/section1.rhtml

The question is a bit unclear, it should be reframed as suggested by AliceD. To simply answer the question,

Glucose is the substrate, and in the first step it is converted to Glucose-6-phosphate.

Only the Phosphate group is added which originates from ATP, your notes also are a bit misleading because it tends to suggest that Hydrogen is released, which is not the case, the phostphate group in ATP loses an OH and Glucose loses an H in an SN2 reaction giving rise to Water in the process.

Always remember that ATP is categorized as an energy donor which drives chemical reactions in your body by breaking chemical bonds. ATP or Adenosine Triphosphate has three phosphate groups. The last Phosphate in ATP produces the highest amount of energy in any given chemical reaction where ATP is involved.

This is an ATP molecule.

The first P that you see is the Phosphate which gets released, and the ring that you see is a five member ring called a ribose sugar, while glucose is a six member ring.


Is it Theoretically Possible to Create a Male clone from the donor Cell of a Female? I understand that Dolly the Sheep was created without the presence of a sperm cell. Instead, nucleus DNA from somatic cells of adult sheep were used. Since Dolly was female, i am assuming that the nucleus DNA used came from a female sheep. So, i want to know if the sex of the resulting clone is determined by the sex of the donor animal. Also, in light of the science behind sex determination in clones, would it be theoretically possible to create a male clone where a single woman contributes both the egg and somatic cells used in the cloning process?

So, i want to know if the sex of the resulting clone is determined by
  the sex of the donor animal.

Generally yes for mammals and birds. In animals where the sex is determined by sex chromosomes, the sex of the clone will be dependent by the sex of the donor.

In animals (ie turtles and crocodiles) where the sex is determined by external factors (ie temperature), then the sex of clones will not be dependent on its donor.

  would it be theoretically possible to create a male clone where a
  single woman contributes both the egg and somatic cells used in the
  cloning process?

Short answer is No.

Sex in mammals and thus humans is dependent on presence or absence of the Y chromosome. If the Y Chromosome is present, the mammal is male. If absent the mammal is female.  So a woman does not have the Y chromosome. Hence it is not possible to create a male from her genetic material.

Longer answer... anything is possible. A woman does not have a Y chromosome, so if you added a Y chromosome to one of her ES cells and then used those cells to form the inner cell mass of a blastocyst, then yes you can get a male.


What are the bare minimum nutrients required to survive as a human? I am trying to determine the bare minimum nutritional requirements to survive as a human, ignoring energy (caloric) requirements. Another way to ask this question is: What elements can humans not live without? I am not inquiring solely about what nutrients are needed, but also their approximate amounts.

Imagine pills that a person can take that covers all their base nutritional needs and that after taking this pill the person can eat whatever they want to meet their caloric requirements. Hypothetically, this pill could have some amount (how much?) fat, carbohydrates, protein, fiber, minerals, and vitamins, and the person could subsequently eat any other food to meet their caloric requirements knowing their nutritional needs would already be otherwise met. Lets ignore the possibility of the person suffering from health issues due to eating too much of any specific food to meet their caloric requirements (e.g., taking the magic pills and then eating only butter).

A person in this situation could think "Ok I've got most of my bases covered, now I just need to ingest another 1000 calories of (almost) anything I want).

What nutrients are absolutely necessary for humans to survive indefinitely, and how much of these nutrients are required?

I am hoping for a complete list with approximate amounts (e.g., 20g fat, 20g carbohydrates, 1mg Vitamin X, .05mg Vitamin Y, 10mg mineral X).

Essential nutrients include (NutrientsReview):

Water
9 amino acids: histidine, isoleucine, leucine, lysine, methionine,
phenylalanine, tryptophan, threonine, valine
2 fatty acids (alpha linolenic and linoleic acid)
Vitamins: A, B1, B2, B3, B5, B6, folic acid, biotin, B12, C,
D, E and K (and choline, which is considered a vitamin-like substance)
Minerals: calcium, chromium, chloride, copper, iodine, iron,
manganese, molybdenum, phosphorus, potassium, selenium, sodium, zinc

The "bare minimum" intakes of most nutrients needed for survival are not known, because they could be determined only by studies in which participants would be given various low amounts of nutrients and observed for how long they can survive. The following are estimations of the lowest intakes of some nutrients needed to remain healthy.. Note, that this are not "recommended" or "optimal" intakes.

Protein = 35 grams per day (Metabolic Basis of Obesity)

Fat = 20% of total calorie intake, that is 44 g per day in a 2,000 Calorie diet (PubMed, 2017)

Carbohydrates = zero (National Academic Press)

Only 2 fatty acids and 9 amino acids are essential, so theoretically, you could consume only those and would be fine. In foods, these acids usually do not appear individually but as part of fats and proteins, so the recommendation is given for fats and proteins - if you meet that, you will likely consume enough of the essential acids. Theoretically, you can survive without consuming any carbohydrates, because all of them you need can be synthesized in your body. People have survived and remained healthy without consuming carbohydrates for a year or more (National Academic Press).

Sodium = 200 mg per day (Recommended Dietary Allowances: 10th Edition)

Water = 1 liter per day (only in ideal circumstances with minimal sweating; in the table, water requirement = "net water loss") (National Academic Press)

Here's a table with dietary reference intakes for vitamins, minerals, carbohydrates, fats (and separately for the 2 essential fatty acids), proteins and water (Nationalacademics.org), which should be sufficient for most individuals in a given sex/age group to remain healthy long-term. These amounts can be considerably greater than what is needed just for survival.

In Recommended Dietary Allowances: 10th Edition, in the Table 6-1, there are "estimates of amino acid requirements" for all 9 essential amino acids.

There was a man who was fasting for more than a year, drinking only water and getting potassium supplements, and the concentrations of most nutrients in his blood remained normal and he had no health issues (Postgraduate Medical Journal, 1973). This shows how difficult is to find "bare minimal" amounts of nutrients.

Yes, it is possible to make a "pill" with only essential nutrients in required amounts included. Such products already exist, but I don't want to promote them, because there is no evidence of their long-term health benefits and safety.


What accounts for size variation in breeds of dogs? My assumption is that dogs vary so much in size because of artificial selection pressures coming from human breeders, but are there genetic loci that roughly determine approximate size?  Do other feral species of animals exhibit such a wide range in sizes or is this something that only occurs when breeders intervene?

This is a fascinating bit of genetics.

Dogs are especially variable in size and many appearance, behavioral and temperamental phenotypes.  It was long expected that variations in developmental genes were the reason that dog breeds were responsible for the amazing flexibility of dog sizes.  One early locus found was IGF1 (insulin like Growth Factor 1).

This 2011 PLOS paper actually review the specific genotypes of dog breeds and identifying loci that are strongly associated with breed phenotype supports this idea.

  ... (we scanned) the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits.

Emphasis added.

This theory has an intuitive appeal as well - no dog breeds (I think) are larger than the wolf, the stock from which all dog breeds are descended.  All such breeds being derived from earlier developmental stages of the wolf makes an intuitive, if imprecise description of the effect here.

Regardless, dogs remain an important model organism for so many traits because relatively few genomic regions can cause so many important phenotypes, including size, but also behavioral and morphological variations.

In the below figure you can see how few genomic regions are responsible for the 46 breeds Vaysee et al. examined.


Can I use a basic compound microscope to analyze the ploidy of plant chromosomes? So, I'm not really any kind of trained botanist. But I do have two things: some dandelion seeds from France, and, collecting dust in my garage along with related accessories, this thing.

Normally, the dandelions growing in an American yard are apomictic triploids, but in Europe there's both triploids and sexual diploids, the latter getting even more common the further south. I'm assuming that, because these French seeds are a specific common cultivar (Vert de Montmagny), that regular sexual selection was used in breeding it, making it a diploid. But I don't know who to ask to confirm this so I may as well do some testing. If it's a diploid, maybe I can do some breeding of my own?

But I don't even know the first step. Are there some parts of a plant that I'll have an easier time finding chromosomes in? What do I put them in to express their DNA and what do they best stain in? Would I even be able to discern the different chromosome shapes without training? I've heard the standard science project way to extract DNA (dish soap, salt, alcohol) damages the chromosomes so that you wouldn't really find them in a microscope; if true I hope there's another way.

If you want mitotic chromosomes then you want to look at apical meristems — probably the primary root from germinating seedlings will be easiest.  Apical meristems are at the growing tips of roots (and shoots) and contain regions of rapidly dividing cells.  Since you can only see chromosomes as separate bodies when they are condensed for cell division this increases your chances of visualizing chromosomes.

However, you will need to stain the roots to visualize the chromatin (material that makes up chromosomes).

This paper has a protocol for staining dandelion root tips, but I don't know whether you can obtain all the necessary compounds.  However, colchicine and para-dichlorobenzene probably aren't really necessary (they will increase the number of cells in mitosis) and are toxic so best to avoid those steps anyway.

Note, it looks like you would also need a 100x oil immersion lens, which doesn't look like it comes with the microscope you listed.

You may also find this paper useful as a starting point for making "homemade" chromosome stains.

Good luck!


One Gene and many proteins Imagine a gene with  $n$ exons and $m$ introns. How many proteins are possible from that gene? Would all the proteins be isoforms?

I might be wrong, but aren't numbers $n$ and $m$ are connected as $n=m+1$?

Answer seems to be combinatorial: how many combinations of $n$ objects can be assembled under certain restrictions? Namely, how many isoforms certain gene can have.

Restrictions include: how many exon-intron junctions on codon (or precisely between codons), how many exons are actually contain protein-coding sequence of mRNA (some exons are coding untranslated region, 3'- or 5'-UTR, for example), how certain gene processes alternative splicing.

So, as you can see, answer will highly depend on sequence of given gene. As far as I know, maximum number of isoforms is limited by 5, even though there are genes with hundreds of exons.


Genes that exist in old Affymetrix platform but not in the newer one I am using two gene expression datasets from an Affy U95Av2 platform and an Affy U133 Plus 2.0 platform. When I map the Affy probe names to HUGO gene names, there are thousands of genes which exist in the newer Affy U133 Plus 2.0 dataset while not in the old Affy U95Av2 dataset, which is something expected. But there are also 97 genes which exist in the old Affy U95Av2 platform while not in Affy U133 Plus 2.0 platform. I would not expect that because Affy U133 Plus 2.0 is a much newer platform and I would expect it to contain all genes that were measured by Affy U95Av2. What does that mean? Should I understand that those 97 gene measurements in the Affy U95Av2 platform were not reliable and that's why they don't exist in Affy U133 Plus 2.0? Here are those 97 genes:

"ACSL4" "ACSM2A" "AP3S1" "AQP7" "ARPC3" "ATF4" "ATP5H" "BAK1" "BAK1P1" "CBX1" "CCL15" "CELP" "CFHR3" "CHEK2" "CLCNKA" "COL8A1" "CS" "CXorf40B" "CYP2D6" "DDI2" "EIF3F" "EIF3IP1" "EIF5AL1" "FCGR2A" "FCGR3A" "GBX1" "GPX1" "HAVCR1" "HBZ" "HIST1H2AH" "HIST1H2AI" "HIST1H2BC" "HIST1H2BJ" "HIST1H4I" "HOXA9" "HSPB1" "IFNA14" "IGF2" "IL9R" "ITGA1" "KAT7" "KRT33A" "KRTAP26-1" "LDHA" "MAGEA12" "MAP2K4P1" "MIA" "MKRN3" "MROH7" "MSX2P1" "MT1A" "MT1B" "NDUFV2" "OPHN1" "OR7E24" "PARP4" "PCDHA12" "PCDHA13" "PCDHGA12" "PCDHGB4" "PINK1-AS" "PMS2P3" "PSMC6" "PSME2" "RAB13" "RCN1" "RNF216P1" "RNF5" "RPL10A" "RPL18" "RPL27" "RPL35" "RPL37" "RPLP1" "RPS15A" "RPS26" "RPS29" "RPS5" "RPS9" "RSC1A1" "S100A7" "SAA1" "SAA4" "SNX29" "SPRR2D" "TOMM40" "UBC" "UBE2E3" "UBE2S" "UGT2B7" "UQCRFS1" "UQCRH" "VDAC2" "VENTXP7" "VOPP1" "XCL2" "ZNF799"

aI used to work at Affymetrix when most of these arrays were designed.  I was not on the design team itself, but I can maybe talk about this a bit more.

RNA Array designs were built to cover anything that might possibly be real transcript in the mix of EST collections, cDNA, in silico gene detections and miscellaneous entries in public databases.  There were a lot of different people trying to find genes as quickly as possible and a good deal of it was not real gene naturally. I'm sure there was a reasonable amount of contamination in the millions of transcripts we took in as well.

The team would find a good number of errors in the sequence database.  There is no way to submit this in a meaningful way to most bioinformatics databases by the way.  Just a note:)

When a new design came out the team would do auditing to see if any of the transcripts had fallen out of favor with the evidence and some of those 'genes' would be pared from the content.

This is useful because DNA hybridization tech is very high throughput for the dollar but it has a background noise and even a probeset with no correspondence in the RNA sample will give numbers that are non-zero.

RNAseq has similar issues from assemblies and sensitivity from limits of reads on the sample BTW.  There's no perfect solution as of yet.

BTW sometimes genes get renamed. I didn't get into your methods to see if this is a case, but something to keep in mind.


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

Background information

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

So when this happens, many protein molecules will aggregate like soap micelles (because hydrophobic interactions are favored). This will lower the total surface area of hydrophobic amino acids in contact with the water, thus lower disturbance in H-bonding in water molecules.

Here's my self-made depiction of effect of organics molecule on H-bonding in water (its quite rough, so don't care about fine details).

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


Does atrophy of the thymus not effect T-cell selection and tolerance? The thymus atrophies as age progresses. Does the T cell selection (which happens in the thymus) continue to take place? This doubt came into my mind because in the cadaver we dissected, the thymus was hardly more than scanty fibrous tissue. This definitely should have some effect on immune tolerance right? Is this the reason why the elderly are more prone to autoimmune diseases?

Or is it that selection happens only in children? This line of thought would pose a problem since T-cells are short lived and they continuously need to be produced. Or is it that the site of selection is shifted to some other place?

P.S. I am asking these questions assuming that selection is necessary every time new T cells are made. Correct me if this primary assumption is wrong.

T cells have a long half life (both naive and memory cells have halflives measured in years), especially when taking into account the fact that memory cells in particular can slowly proliferate and renew themselves.  An adult human therefore has 20-50 years' worth of accumulated T cells by the time they grow old, and those include both memory cells and naive cells that are potentially able to recognize new antigens. The thymus does continue to produce some new cells at a slow rate, but the backlog of previously produced cells are also able to monitor for pathogens.


Differences on biological classification? Why we use the term phylum for kingdom animali but for kingdom planti ,fungi and prokaryota we use them division?                         What difference between phylum and division ?

Phylum and division are both listed under the same taxonomic ranks. The wikipedia page for phylum states that

  Traditionally, in botany the term division was used instead of
  "phylum", although from 1993 the International Code of Nomenclature
  for algae, fungi, and plants accepted the designation "phylum".

What you have to keep in mind is that the scientists categorizing plants and animals worked in isolation for a long time and only recently have they come together to build a tree of life for all organisms (rather than just working separately on plants / animals / bacteria)


Does there exist a reagent that can only be precipitated by Haemoglobin and nothing else? I recently read Sherlock Holmes and in the book A Study In Scarlet, Holmes says to Watson that he has discovered a reagent that can only be precipitated by Haemoglobin and nothing else. I know about the Guiacum test but is there any other test like I have discussed above as the Sherlock Holmes test.

This very point is well addressed by Laura J Snyder in Sherlock Homes: Scientific Detective (a great read) where the author challenges the view that Conan Doyle is the 'father of scientific crime detection' and argues that the new science of forensics actually influenced Conan Doyles' writing, rather than his novels being the inspiration for the new emerging discipline.

Furthermore, not all his claims were scientifically valid, and the 'infallible test for bloodstains' is a good example.

The relevant passage is as follows:

  Let us examine, for example, the ‘infallible’ test for bloodstains Holmes is presented as having ‘invented’. By1887, when A  Study  in  Scarlet was published, many researchers already shared the desire for such a test; this desire was not satisfied until the turn of the 20th century,when the spectroscopic method was developed.

  A modern chemist has noted that the method Holmes describes – one which would precipitate a brownish dust and change the color of blood in water to mahogany – would need an acid to increase the oxidation rate, as well as a material to be oxidized. By examining the possibilities for the ‘few white crystals’ and the ‘drop of transparent fluid’ that Holmes uses, this chemist suggests that the ‘Sherlock Holmes test’ would probably have had a sensitivity similar to the guaiacum test that Holmes derides as being ‘clumsy and uncertain’[15].

  Moreover, Holmes’ test does not distinguish between human blood and the blood of animals– a problem that, by 1887, was considered an even larger concern than the sensitivity of the blood tests currently in use. A solution to this problem did not arise until the work of Paul Uhlenhuth in 1901 [16].

The two references quoted in the above passage are:

[15] Gerber, S.M. (1983) A study in scarlet: blood identification in 1875. In Chemistry and Crime: From Sherlock Holmes to Today’s Courtroom (Gerber, S.M. ed.), pp. 31–35, American Chemical Society (Columbus,OH, USA)

[16] Thorwald, J. (1965) The  Century  of  the  Detective (Winston, R. and Winston, C. trans.), Harcourt, Brace and World


Is it theoretically possible to treat filaggrin deficiency with a dietary supplement? http://f1000.com/prime/reports/m/3/2/

  "Filaggrin is a highly abundant protein expressed in the uppermost part of the epidermis that is critical to the formation and hydration of the stratum corneum—the outermost dead cell layers responsible for the barrier function of the skin. Filaggrin deficiency leads to a 'leaky' skin barrier that allows higher than normal water loss (explaining the dry, scaly skin), as well as allowing entry of allergens through the epidermis where they trigger inflammatory and allergic immune responses (atopic eczema and allergies)."

Not that such a supplement exists, but is it biologically possible to treat filaggrin deficiency with something taken orally?

I highly doubt it. Filaggrin is a human protein which is expressed in the skin and stored as profilaggrin. The profilaggrin has a molecular weight of about 350 kDa (which is rather big) and is cut into smaller units of filaggrin, which then crosslinks kreatin fibers of the epidermal keratinocytes. This enhances the durability of the skin. Mutations in the filaggrin gene have been associated with dry skin and excema. See here for more information:"Filaggrin - revisited."

To supplement the profilaggrin, you would have to bring this rather large protein into the skin. You could think about making a cream with the smaller filaggrin in it to promote crosslinking of the upper skin. The question here would be how effective such a treatment ist and how deep the crosslinking would be.


Can forensic DNA analysis be used to generate a visual approximation of a suspect? In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I realize the term reasonable is subjective, so characteristics, such as skin color, hair color/texture, approx height, eye color, freckles, etc. I came across this article a few years ago, but the company that made the test went bust in 2009. It could detect race (how accurately?). I seem to recall reading an article a few years ago stating that "soon" we'd be able to get an approximation of appearance from a DNA sample that was better than a sketch artist could provide, though I can't recall now where I read it.

In theory it's possible to have an approximation, but not to know with certainty. Identical twins have the same genomes and look very much alike. Whether it can be done in practice depends on how well we can model the relationship between genes and looks and on how much information is necessary for a judge to permit arresting and questioning a suspect.

Scientists know relatively little about how genes influence physical appearance yet. The height of the suspect is controlled by hundreds of genes with complicated interplay between them, so I don't think it's possible to estimate it just yet. Eye color is more simple: it's controlled by only 3 genes. We know weight is partially controlled by genetics but exactly which genes are responsible is not clear. Age is impossible to tell by DNA alone. Skin color should be predictable, since it's caused by melanin production, and we know which genes are responsible.

So to sum up, DNA analysis can tell the gender, skin color, and eye color of the suspect, but very little about height and weight, and virtually nothing about age. That's not enough information to identify a suspect, although perhaps someone with legal knowledge could comment on this.

But let's say in the future we know enough to determine all these traits. Then DNA analysis would be helpful but never enough to identify a suspect. The problem is that different cells in your body undergo different mutations in their DNA with time. That's how one gets cancer. Let's say there's a mutation in the eye color gene in skill cells from a murderer found on a victim's body. It won't affect the murderer's eye color but it will affect the forensic analysis. So it's impossible to know for sure what the suspect's appearance will be.


Reliability of SARS-CoV-2 tests - false negatives This is about the entire process from sample collection through transportation to lab processing and assessment. In Canada, we are seeing about one COVID-19 test in 10 produce a positive result. Can we be confident that the number of false negatives is negligible? There have been reports of issues potentially occurring at every step which could result in a false negative, from failed collection of the sample to degradation of the sample in transit, to perhaps process or reagent issues in the lab.

Also, is there any possibility of the virus mutating in such a way that what makes it COVID-19 from a public health point of view remains the same but its genetic identity changes enough to no longer be recognized by the existing tests?

Is the testing process from end to end reliable enough that we can trust the reported result be it positive or negative?

Also, is there any possibility of the virus mutating in such a way that what makes it COVID-19 from a public health point of view remains the same but its genetic identity changes enough to no longer be recognized by the existing tests?

That's unlikely. These assays look for several specific regions of the viral genome under high selection pressure (i.e., highly conserved) to make a clinical diagnosis (such as orf1ab, N, and S genes, ref. https://www.thermofisher.com/us/en/home/clinical/clinical-genomics/pathogen-detection-solutions/coronavirus-2019-ncov/genetic-analysis/taqpath-rt-pcr-covid-19-kit.html and https://www.fda.gov/media/136286/download for examples), with the aim to minimize test error from off-target effects (varieties of genomic mutations, ref. https://en.m.wikipedia.org/wiki/Off-target_genome_editing) and misidentification with other respiratory viruses.
I can't speak to the other questions in your question with numerical error rates of tests, except to say that controls, procedures, and better PCR primers can be used to increase sensitivity, to get a true positive (ref. https://en.m.wikipedia.org/wiki/Sensitivity_and_specificity). Sensitivity is a real issue for test kits in Russia, where one must have high viral counts (and likely be very ill) in order for a test to give a positive diagnosis (ref. https://abcnews.go.com/International/russia-reporting-covid-19-cases-cover/story?id=69717763)

According to PCR News, the Russian test is based on the same method used by other countries.
But the Russian test, PCR News wrote, only detects the virus when there are over 100,000 copies of it per milliliter in a sample. That is far more than in other countries’ tests. A test in use in the U.S., for example, will pick up the virus with just 6,250 copies.
“That would mean it’s about 10-16 times less sensitive than what’s available in the U.S.,” Carmen Wiley, president of the American Association of Clinical Chemistry, told ABC News by a phone. At such a level, she said there was a risk the Russians were missing cases, in particular where people were asymptomatic.

From a public health standpoint, I suspect diagnosis of sick people is less useful than diagnosis of asymptomatic carriers who feel fine but are shedding virus everywhere. You want a test to let you quickly tell positive people to self-quarantine, before spreading it around.


What makes a wet dog so stinky? Similarly, what makes a wet down comforter so stinky? Why do they make no smell except when liquid is added?

From this source,

  We answered this question on the show...

  We posed this question to Dr David williams from the Veterinary School
  at the University of Cambridge... David -  First of all, what actually
  makes something smell?   Molecules have to leave the smelly objects
  and get to your nose through the air and that means that these
  molecules must be very small and volatile.  That's to say they must be
  easily evaporated.  The chemicals that make dogs smell are mostly what
  we call volatile organic acids and they are produced by bacteria from
  the fats that are breaking down from sweat; and that's maybe why we
  find these body odours unpleasant.  They signal a presence of bacteria
  and decay and death to us.

  Their [dogs] skins mostly have
  Staphylococcal bacteria, which don't produce much in the way of a
  smell at all, but they've also got some yeasts too which are really
  pongy.   But why does the smell seem worse when the dog is wet?  Here,
  I think we have to go into some physics.  The amount of evaporation of
  a substance is related to the concentration of the compound on a
  surface it’s evaporating from and the amount of compound that's in the
  air, just above the surface.

  So how might that change when it’s wet?

  Well, if the organic acids are dissolved in water on the fur of the
  wet dog, as the water evaporates, the concentration of those smelly
  acids increases, so they'll evaporate more, so there are more
  molecules in the air for us to smell.  Diana -   A bit of evaporation
  can effectively amplify the amount of volatile chemicals that emanate
  from a dog’s skin, and Dr. Williams thinks it’s the same effect that
  causes that damp earth smell when it rains.  It may also alter how
  dogs interact with each other when they're wet.  So, if you have a
  dog, watch to see if it sniffs differently at other dogs on a dry day
  versus a wet one...

There's a start, sounds legitimate to me...


Is it in principle possible to revive an extinct species having no living relatives? Is it, in principle, possible to revive an extinct species having no living close relatives but whose DNA and other tissues have been preserved?

What about the case where there are no living individuals of a species but there are some living somatic cells?

What about the case where only individuals of only one sex are alive?

This may absolutely be possible. Check this for some info. But really it appears that using somatic nuclear transfer, using the same principle used to generate Dolly, we may be able to recreate an extinct species by swapping in the genetic material into a new cell. One current problem that we face with this is that while the genetics should be fine in nuclear transfer, controlling proper epigenetic programming is difficult.


How should I put a large phylogeny into a scientific paper? I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is crucial to show the whole tree on which the among-species distribution of a characteristic is indicated. I have looked up some journal issues but so far haven't found any similarly large phylogeny in one article. How do people usually treat this kind of situation in scientific papers? Could anybody tell me how to do it, or show me examples? Thank you so much.

The simplest way of course is to add it to the supplementary materials. However, 220 species are not that many, you should be able to fit that into a page. You have not shown us your tree so it is kind of hard to give specific advice but I am guessing that you have a linear rather than circular tree. If you convert it to a circular tree you should be able to fit it on a single page.

Here are a few random examples of large circular trees I found on the internet:

If you update your question to show us the actual tree I might be able to give you more specific advice. For example, you could split the tree into smaller ones, each showing a specific order or class or whatever resolution you are working on. There are various tricks you can try but they all depend on the details.


What would be the conduction speed of A-alpha fibers, were they unmyelinated? It's known (Hursh 1939) that myelinated axons exhibit the behavior $v = 6d$, where $v$ is the propagation speed [m/s] and $d$ is the axon diameter [μm].

A related relation for unmyelinated axons is (Malmivuo & Plonsey, eq. 2.1):

$$v = \sqrt{\frac{i_\text{Na max}}{r_i c_m^2 V_\mathrm{th}}}$$

I want to approximate the propagation speed that A-alpha nerve fibers would exhibit, if they were unmyelinated. How could I find values for the constants in the above equation? Is there an easier way to conduct these calculations, or has there already been a study done on this?

For the (myelinated) A-alpha fibers, d = 13-20 μm and v = 80-120 m/s according to Wikipedia.

The provided relation for unmyelinated axons only holds up to certain diameter value of the axon and is valid only as long as the sodium conductance iNa is uniformly distributed along the cross-section of the axon. This explains why non-myelinated fibers are so thin, being only 0.2-1.5 μm in diameter.

In axons having a larger diameter the axon potential can only move between Ranvier nodes. If this fiber gets unmyelinated the axon potential just stops propagating, due to several reasons:

Sodium concentration through the complete axon surface is too high so that it diffuses internally along the axon and reduces the concentration gradient in the direction of AP propagation.
AP is propagated not only along the length of axon but also laterally, that leads to its flatenning over the axon surface, decreasing its amplitude etc.

Unfortunately I couldn't find the reprint of the original publication in Biofizika referenced by the webpage you provide the link to, so I cannot investigate the constraints of their model for AP propagation.

In order to estimate the propagation velocity in unmyelinated axons of large diameter I would take some theoretical papers investigating the properties of nerve fibers undergoing demyelination. Z. J. Koles and M. Rasminsky "A computer simulation of conduction in demyelinated nerve fibres", J Physiol. 1972 December; 227(2): 351–364. seems to be one of the earliest publications on this topic and it is freely available online.

In this paper the authors tried to simulate the conductance of demyelinated motor axon with diameter of 10μm and 5μm myelin sheath. They gradually decreases the amount of myelin width until 2.7% of the initial value where they saw the abolishment of AP propagation. The propagation time was 12.5 times higher than in normally myelinated fibers (for the distance where AP could travel). If we consider the initial propagation velocity being 80-120 m/s then after demyelination it is reduced down to 6-10 m/s and fade after a short travel.


What is this sea shell? Found in Belgrade, possibly carried back from the Mediterranean or Aegean coast.

It is not /Bolma rugosa/, but in fact /Angaria delphinus/, from the Indo-Pacific.

Listing on gastropods.com


Temperature to kill virus Why do I see only high temperature advice to kill microorganism, and not low temperature?

Why isn't there any low temperature which kills virus? Are they more resistant to low temperature?

High temperatures means that lots of energy is available in the environment. This energy speeds up chemical reactions, and make possible some reactions that wouldn't happen at all at lower temperatures. In particular, proteins can adopt new shapes as temperatures get higher. It's the misshapen proteins rather than the temperature per se that kills the microorganisms.

Low temperatures mean there is relatively less energy available in the environment. This slows down or stops chemical reactions, including the ones that result in mis-shaped proteins. Extremely low temperatures may slow down a microorganism's metabolism and stop it from reproducing. That's why we keep perishable foods in refrigerators. However, if you warm the microorganisms back to a normal temperature, most of them will pick right where they left off. A few may be killed by the formation of ice crystals inside the cells that mechanically break the cell membrane.

If you walk into a microbiology lab you'll often see a wall of refrigerators, used to preserve microorganisms for later revival and use.


How are fragments isolated during shotgun Sanger sequencing? For a large genome (say millions of base pairs) -- we split the genome into fragments < 1000bp that are sequenced and can then be put back together computationally.

My understanding is you use some sort of shearing technique to get the DNA into fragments as in: https://en.wikipedia.org/wiki/DNA_fragmentation

Now you have a vat full of random fragments -- how do you sanger sequence these?

From what I can tell if you took the solution with the sheared DNA and ran sanger sequencing you'd get a bunch mixed of fragments mixed together resulting in a lot of noise ... you'd basically get all the runs averaged together. Don't you need to isolate each fragment before running Sanger sequencing?

How is this done?

In the original method, one would clone all of the resulting fragments into a suitable vector, and transform the collection into a bacterial host, to create a so-called library.  By plating the library clones under appropriate conditions you would have a collection of so-called clones, and each clone would be randomly selected and sequenced using the Sanger technique.


Is identifying the genus of a fungus (mushroom specifically) enough? Does the genus of a mushroom have enough information about it, without the species?

Let's say I wanted to identify a mushroom (when picking) to see if I can safely pick and later eat it. Let's say I successfully identified the mushroom's genus (using an identification key guide book such as this one). Is this enough to determine whether or not the mushroom is edible? Is it enough to determine other general information about it? Furthermore, is it enough to determine whether it is good-to-eat (as in not bitter)? For example, I know that some edible mushrooms have other mushrooms very similar to them that are not edible or that are bitter and difficult to cook.

In other words, are there any genuses of mushrooms that generally are recognized as edible but in reality contain both edible and inedible species of mushrooms in them?

Again, I would say: no, genus is not enough.

Another example: boletes (specifically, genus Boletus).

According to Wilderness College:

  One of the most common and well-known groups of edible wild mushrooms are the boletes or boletus species (Boletaceae) ...

But

  Many species in this group are edible, with only a handful being poisonous. The poisonous boletus species have red or deep orange pores. Outside of the few toxic species, some species of boletus are bitter or inedible.

For example, see here for a list of edible boletus mushrooms (e.g., B. edulis), while some examples of Boletus species to avoid include: B. huronensis and B. satanas

An additional issue to classifying all species in a genus as "safe to eat," is that our classifications are not always reflective of real taxonomic associations. In other words, some groups are not monophyletic and their evolutionary (and therefore physiological/nutritional) characteristics should not be assumed to originate from the same common ancestor .

This is apparently true of the boletes. From Wikipedia:

  Boletus has been found to be massively polyphyletic, with only a small percentage of the over 300 species that have been assigned to Boletus actually belonging there and necessitating the description and resurrection of many more genera

See for example: Nuhn et al. (2013)1

1: Nuhn, M.E., Binder, M., Taylor, A.F., Halling, R.E. and Hibbett, D.S., 2013. Phylogenetic overview of the Boletineae. Fungal Biology, 117(7-8), pp.479-511.


Why is there complementary base pairing for DNA? Why is there complementary base pairing for DNA? Why can't A pair with C given that they can all form hydrogen bond?

It's to do with the physical space the base molecules occupy. There are 2 classes of molecules in DNA bases, purines and pyramidines.  One of each always pair together as there will be a total of 3 ring moieties present.

E.g., Adenine (a purine) pairs with Thymine (a pyrimidine).

If you were to pair 2 pyrimidenes together, you would induce a kink in the DNA backbone and destabilise it.

That said, there is no chemical reason 2 purines or 2 pyrimidines can't hydrogen bond, and they do. This causes mismatches and DNA mismatch repair enzymes recognise the torsion it induces in the DNA backbone and they replace the mismatched base in the proofreading process. If the enzymes miss one mispairing, which can happen as it occurrs often (but the enzymes are very effective), then you end up with a mutation.


Do two hormones have the same effect on a cell if the second messenger is the same? There are so many hormones/cytokines/neurotransmitters and receptors, all of which act through about 4-5 second-messenger systems. So if one particular cell has receptors for say, two different hormones which act via the same second messenger, is there any way that the cell can distinguish the two stimuli? I’m guessing there must be some distinguish between the two, otherwise, wouldn’t the effect of both the hormones be the same?

For example, in a hepatocyte, beta-adrenergic receptors and glucagon receptors both act via Gs-coupled receptors, downstream of which, cAMP is increased. Since the cAMP is the same, the changes it would make are also the same. So does it to the hepatocyte, make no difference if the first messenger was epinephrine or glucagon?

I’m assuming the receptors would make a difference, but aren’t the coupled G-proteins (Gs) also the same? Is there a difference of amplitude?

Note: I understand that it is not necessary for the hormones to produce an exclusively different effect. I also understand that systemic effects can be different because of differential distribution of receptors. My question pertains to the effects on a single cell.

Secondary signaling molecules like cAMP, Calcium, and Ras-Raf are common in many pathways and I think its a way of integrating different signals.We cannot say that at a moment only one pathway operates in a cell or a single pathway will be enough for a process to happen.I think common second messengers is a resource and time-saving method adapted by our system to coordinate different response efficiently.https://www.nature.com/scitable/topicpage/cell-signaling-14047077

Then how a cell can identify which pathway and process should go on? I think that each time this second messenger will make a small change in choosing down stream effectors.Like Calcium binds to calmodulin which in turn choose next binding partner.Maybe the number of second messengers like concentration and affinity decide which downstream effector will be appropriate for the required stimuli.You can see in this link about how different secondary messengers make different results https://www.ncbi.nlm.nih.gov/books/NBK9870/

About GPCR, more than 800 GPCR are there and you can see from this link http://jcs.biologists.org/content/116/24/4867

So, Do two hormones have the same effect on a cell if the second messenger is the same?
I think yes, see this table (https://www.ncbi.nlm.nih.gov/books/NBK21705/)

Here, from the table, you can see adrenaline and glucagon are having the same effect in the liver cell and both have cAMP as a second messenger.But in cardiac muscle and intestine, adrenaline is having a different function. So I think it depends on the cell also.


Is glycolysis the beginning part of fermentation, or does fermentation follow glycolysis? Is glycolysis the beginning part of fermentation, or does fermentation follow glycolysis?

I see conflicting information from different sources

https://honchemistry.wikispaces.com/Lactic+Acid+and+Alcohol+Fermentation+in+Humans

  "..Alcohol fermentation follows glycolysis, just like lactic acid
  fermentation..."  <-- So glycolysis is preceding fermentation, not part of fermentation

and

  " The Actual Fermentation Part

  Glycolysis and fermentation are two separate processes. Glycolysis was
  explained briefly to give the reader an idea of the events leading up
  to fermentation and the starting conditions in terms of molecules
  available for reaction.....Going into the fermentation, the molecules NADH and pyruvic acid are present. "  <---  so glycolysis is preceding fermentation, not part of fermentation.

Whereas these two links put glycolysis as part of fermentation, not a preceding stage before fermentation.

https://www.khanacademy.org/science/biology/cellular-respiration-and-fermentation/variations-on-cellular-respiration/a/fermentation-and-anaerobic-respiration

  "Fermentation and cellular respiration begin the same way, with
  glycolysis" <-- glycolysis is part of fermentation, not preceding it.

and

http://study.com/academy/lesson/anaerobic-respiration-lactic-acid-alcoholic-fermentation.html

  "fermentation, which is a process that anaerobically generates ATP by
  performing glycolysis..." <-- fermentation includes glycolysis,  so glycolysis is part of fermentation, not preceding it.

So, which is it?

Is it a)like khanacademy and study.com,  or b)like honchemistry.wikispaces.com

I have heard the idea that glycolysis is independent, in that it can produce some (not much, but some), energy on its own, and it can happen without fermentation or cellular respiration following. Though when would glycolysis occur without fermentation or respiration following? And even if glycolysis is that independent, it may still be at the beginning of respiration and fermentation and not preceding it.

Wikipedia speaks in a contrary way..

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

  "Before fermentation takes place, one glucose molecule is broken down
  into two pyruvate molecules. This is known as glycolysis." <-- so glycolysis is preceding fermentation, not part of it.

so the above quote from wikipedia suggests that glycolysis is not the beginning part of fermentation, but a step preceding it

whereas still on the fermentation wikipedia page, it says

  "Fermentation is a metabolic process that converts sugar to acids,
  gases, or alcohol....The first step, glycolysis" <-- so glycolysis is part of fermentation.

Links on respiration are more unambiguous that glycolysis is part of respiration.. the links on fermentation vary a bit on whether glycolysis precedes fermentation or is part of it.

As @bpedit indicates in his comment, this is a semantic question — i.e. one regarding the meaning and usage of words. I will explain how I and others use these words and why. If you are convinced by my logic you will wish to use them in the same way, if not you are free to use them differently. However there is no ‘universal truth’ here, and if you are student I have no idea what your instructor thinks.

The problem is that ‘fermentation’ and ‘ferment’ (both as a noun and a verb) are old words, predating any understanding of the processes involved. Thus the Oxford English Dictionary quotes a relevant early example of the use of ‘ferment’ as a verb as follows:

  1663 Cowley Verses, to Royal Society iv, All their juyce did .. Ferment into a .. refreshing Wine.

From this, it is clear that the idea of the fermentation process is the conversion of some initial compound (the sugar in the ‘juyce’) to some final compound (the alcohol in the wine). This usage is still current in referring to the process of fermentation, for example a Google search brings up a BBC Science educational page which states:

  Beer and wine are alcoholic drinks made by fermentation reactions that use yeast to convert sugars into ethanol.

You may or may not be aware that term ‘ferment’ was historically used to mean what we now term yeast, and ‘Zwischenferment’, the obsolete German term for certain enzymes in yeast, is derived from this. So the original concept was merely of some biological conversion effected by yeast, although this has later been extended to bacteria and the idea changed to indicate metabolic processes capable of generating ATP anaerobically.

Part of the discrepancy in definition may be the emphasis on the end-product of the fermentation — ethanol fermentation, lactic acid fermentation etc. However, it seems clear to me that the fermentation is the whole chain of metabolic events from sugar (or whatever) to alcohol (or whatever); and if glycolysis is part of that process (which it is in this example) then glycolysis is part of the fermentation. (Of course, glycolysis can occur in other circumstances where the product, pyruvate, is oxidised in the tricarboxylic acid cycle, which is not a fermentation process.)

Footnote

The extent to which one can tie oneself in knots with trying to define fermentation is illustrated in the best-selling and well-respected text book, originally written by Lubert Streyer and subsequently maintained by Berg et al. I mention this text both because an older edition is available on-line, and because a book of such value to the publishers is carefully vetted by referees. In the chapter on Glycolysis there is an attempt to define Fermentation:

  Fermentation: An ATP-generating process in which organic compounds act as both donors and acceptors of electrons. Fermentation can take place in the absence of O2. Discovered by Louis Pasteur, who described fermentation as “la vie sans l’air” (“life without air”).

So the biochemical lawyers have produced a definition that very few readers will be able to take in at first sight. What is this business about electron donors and acceptors? Well what it means in relation to the fermentation process in which lactic acid is produced (note my legalistic choice of words) is that one organic compound is reduced (glyceraldehyde 3-phosphate) — by NAD+ — and one organic compound is oxidized (pyruvate) — by NADH. And as the production of ATP is included in the definition this means that Berg et al. include glycolysis in this definition of fermentation.

…except that on the same page there is the following statement:

  pyruvate is converted, or fermented, into lactic acid in lactic acid fermentation or into ethanol in alcoholic fermentation

So here it seems that the word is being used for the conversion of pyruvate to lactate or ethanol, i.e. it excludes glycolysis.

Pasteur managed to talk about fermentation without being aware of glycolysis or ATP, and it is clear to me that you can write whatever carefully phrased definitions you like, but people are going to continue to use venerable terms like fermentation in whatever way seems natual to them.


Is narrow sense heritability heritable? I was wondering if narrow sense heritability $(h^2 = \frac{V_A}{V_p})$ was heritable itself. $(h^{2'} = \frac{V_A}{V_{h^2}})$

Heritability of heritability

Heritability is a property of a population (see here for more info), not of an individual. One can only calculate heritability for a trait if this trait can take a value for every given individual because you need variance among those individuals (as it is made clear from your equations). In other words, the trait you want to calculate the heritability from has to vary from individual to individual.

As we are looking for the heritability of heritability, then heritability would need to be defined at the individual level in order to calculate its heritability. But heritability is not defined at the individual level.

It makes no sense to talk about the heritability of heritability. Just like it makes no sense to talk about the heritability of the fitness variance or heritability of the species geographic range.

Phylogenetic signal for heritability

You might be interested of whether related lineages tend to share similar heritability (for a specific chosen trait). I do not know of any study on the subject, but it seems likely that related species are more likely to experience similar population size and structure and similar selective pressure on a given trait than more distantly related lineages. Per consequence, I would expect that heritability shows a phylogenetic signal. It would be wrong to say that heritability is heritable though.


Why are there so many different humans yet chimpanzees are just chimpanzees? There are two species belonging to the Pan genus (Pan troglodytes and Pan paniscus). That's just two.

I mean, humans have changed radically since we split from chimpanzees, we have Australopithecus afarensis, africanus, anamensis, Paranthropus robustus and boisei, Homo erectus, habillis and so on.

A chimpanzee fossil that is 2 millions years old should be pretty different from a modern one, why aren't they considered another species?

For fossils the answer is simple chimps live in forests and forest are really bad at preserving fossils, we lived in savannah which include some floodplains which are really good at preserving fossils. Thus we find a lot more human fossils than chimp fossils.

Otherwise Chimps exhibit far more genetic diversity than humans. humans are just a weird branch of chimp.consider the genetic diversity below. If we were not so  morphologically biased we sould easily conclude all hominids as just one species based on genetics.Chimps actually have quite a wide morphological variation its just we as humans are far better at noticing human variation.


What is the name of this plant I found in ROAD HIGHWAY? Location of the plant is South India,

Plant stem looks like Banana.

It is Fishtail Palm, Example picture look like this:


Why placental progesterone suppressed or drop before onset of labour? As we know during pregnancy predominant hormone is progesterone which is at early pregnancy about first 3-4 months produce by corpus luteum  of pregnancy together with estrogen after that placenta can make its own progesterone with estrogen till birth but for initiation of labour estrogen go up and progesterone should go down because it prevents uterine contraction. Does anyone know mechanism of suppressing of progesterone and rising of estrogen before onset of labour ?
In other word mechanism of initiation of labour ?

Pregnenolone -the precursor of progesterone is principally converted to estradiol instead of progesterone.Thus the oestrogen:progesterone ratio increases prior to parturition.

  Fetal cortisol stimulates activity of placental 17 α hydroxylase/17, 20 lyase (CYP 17) enzyme, which catalyzes the conversion of pregnenolone to estradiol.

Confinement of the foetus in the uterus stimulates the stress responses.

  Stress leads to a rise in foetalACTH. The rise in ACTH causes production of cortisol from the foetal adrenal glands. The rise in foetal cortisol leads to an increased oestrogen:progesterone ratio by upregulating aromatase enzymes, which convert androgens to oestrogens. Cortisol also reduces progesterone production.


Correlation between genetic distance and birth defects It is folk knowledge that in-breeding causes birth defects due to similarity of genetics between parents. Consequently, is there a similar correlation between genetic distance of parents and probability of birth defects?

The best reference I can find of this is this handout by the Australian Centre for Genetics Education which says:

  If parents are unrelated, their chance of having a child with a birth
  defect or disability is between 2% and 3%.

  If parents are first cousins, the chance is a little higher at 5% to
  6%. This is due to the increased chance that they will both carry the
  same autosomal recessive mutation, passed down through the family.

However this doesn't talk about genetic distance in particular.

This question is really just a more specific version focused on a single metric (genetic distance) and outcome (birth defects) of two previously answered questions:

Genetic pros or consequences of children born to parents of mixed nationalities?
Does it make sense to classify all humans in a single species?

For humans the closest argument may come from observational studies (since experiments aren't possible due to ethical reasons).

One example for the correlation of genetic distance and "defects" comes from a recent study of Chagnon et al. PNAS, 2017 http://www.pnas.org/content/114/13/E2590.full . Rather than asking for birth defects directly they however survey the number of children, and survival of children to age 15 (which would be one example of the term "inbreeding depression" that is more general than "birth defects")

Note that their study also sheds some light on the underlying big question, why certain types of kin relationships can be common despite their effect on the creation of healthy offspring - and why certain types of cousin relations are different from others.


Insect Identification - Ecuador I took a picture of this bug while I was in Chucchilán Ecuador in June. I am wondering what type of insect this is?

It was about 1-inch long.

This was the only good photo I was able to take, sorry for the poor angle.

This is a phasmid (Order Phasmatodea) from the Genus Monticomorpha. Its common name in Spanish is (insecto) ututo.

Here is an image of it:

Source: http://www.projectnoah.org/spottings/1847685515

They are found in Colombia, Ecuador and Peru. You can see that the distribution matches your place:

Source: http://phasmida.speciesfile.org/Common/editTaxon/Distribution/ShowDistribution.aspx?TaxonNameID=1199515

Identifying the species may be a bit more complicated. The Phasmida Species File page I linked above lists 8 species of ututos (with pictures), 5 of them occurring in Ecuador.


Toronto spider identification I found it in Toronto, Ontario, during early June, 2015.

When prodded it seemed to jump around, or at least to move very fast.

I can also post a short video of it if needed.

That jumping spider is a Jumping Spider! (That is, family Salticidae, commonly called Jumping Spiders).

There's a lot of diversity in the family, but your pictures look similar to the Zebra Jumping Spider.


Species ID from Hungary I found it on the wall, it was calm for 15 minutes. Central Europe, Hungary. Never seen anything like this. I have two more pictures.

This appears to be a Gastropacha Quercifolia, the Lappet Moth.

    It is found in Europe and Northern and Eastern Asia.

    The wingspan is 50–90 mm. The females are larger than the males. The moth flies from June to July depending on the location. Source


When do plasmids replicate relative to its host cell cycle? For plasmids is so much shorter than their host cell's genome (about 1/1000 in my case), it will take only 1/1000 time for it to replicate.

With respect to cell cycle, when will that replication occur?

Description of the situation I'm facing:

I have a low copy number plasmids (pSC101) in E.coli, and I'm measuring a fluorescence protein expression level. The problem is, even if the plasmid copy number is known (N), depending on when it is replicated, the number of plasmid in my cell can vary. Therefore, I cannot directly infer expression level per plasmid. Higher expression level might just result from higher number of plasmids.

For instance, if it is replicated right after cell division, I will have 2N plasmids for the most of my cell cycle.

If on the other hand, it gets replicated right before cell division (and partitioning machinery delivers exactly half the number to each daughter cell), I will have N plasmids per cell for the most my my cell cycle.

So, when do plasmids get replicated?

I could not find a similar question here with search.
Thank you very much in advance.

I've found a nice review that has many details on plasmid replication in general, and several papers about pSC101 in detail, and I'll try to extract the key information from these papers.

First of all your plasmid as an ori region that contains so called iteron:

  In many cases, the origin of replication contains directly repeated sequences, termed iterons, which are the binding sites for the plasmid-encoded Rep proteins and which have control properties. (...)iterons have been described for several replicons like P1, F, pSC101 (...).

pSC101 plasmid has three of these iterons present, along with a protein called rep that is necessary for replication. Besides these there are sequences that provide binding sites for host proteins such as DnaA and integration host factor (IHF).

Details of these can be found in this and this paper, both provides details on replication and the function of ori region in your plasmid.

As stated in this other paper, plasmid copy number is controlled by the plasmids themselves, that may vary on host type and growth conditions but:

  At steady state, the 1 number of replications per plasmid copy is exactly
  one per cell generation. This defines the steady state as shown in Figure 1. It should be stressed that while this is true for the population, it is not for individual plasmids-these are selected randomly for replication.

So not all plasmid copies are replicated once per cell cycle rather random ones are selected and they replicate to maintain the desired number.
When your plasmid has reached its target copy number it will adjust its replication frequency to maintain this number. This is achieved by negative control loops. There are many ways to do this (repressor proteins, anti-sense RNA) or in your case iterons. These sequence along with the rep protein may inhibit replication if too much plasmid is present by a phenomenon called  “steric hindrance" or “handcuffing”. This happens because the rep protein is capable to bind two iteron, simultaneously.
At low copy numbers saturation of iteron sequences by rep proteins initiate replication, but at high copy number rep proteins tend to interact with each other and plasmids pair up through rep-rep interactions therefore cannot replicate. See figure below:

So, long story short: plasmid replication in part depends on host factors but plasmids have means to control their copy number, and once target has been reached they maintain this number in a stable form. I know this answer does not provide solution to the when part of your question, but it provides an answer to the practical part of your problem namely: plasmid numbers are quite stable after the target number has been reached. I hope this helps

EDIT: I've found this article http://www.ncbi.nlm.nih.gov/pmc/articles/PMC210920/pdf/jbacter00181-0364.pdf that says:

  In all experiments, plasmids pSG21 (oriS only), F'lac (oriS oriV),pBR322,
  and pSC101 were capable of replicating at all stages of the division cycle,
  with no detectable differences in the patterns.

So bad news for you, because according to the paper above you cannot tell when your plasmid actually replicates. Yet still as the average copy number is quite stable due to reasons described above this may not pose a big problem. Keep in mind even if you have an extra plasmid for a short time that may still not cause problem, because transcription of your riporter gene, folding, etc takes time under which previously synthesized proteins might degrade.

However this paper says the F+ plasmid replication is cell-cycle specific, you may wan to give it a try.


growth stages of Maize I am reading about growth stages in Maize and found this image.

I downloaded a brochure of a maize variety grown in Brazil.

On the right column, it says male flowering 63 days after planting (947 degree days) and female flowering 63.5 days after planting (955 degree days).

When stage does the male and female flowering happens in the first image?

In the first image, flowering occurs in the stage labeled "Pollination", which is when the male releases pollen and the female accepts pollen.  It give the time as 56-63 days after emergence, but note the asterisk ("*"); the footnote for it says their given times vary by "growth class" (such as "early" or "late"), indicating that these numbers are just a guide and actual times will vary by the cultivar (breeding strain) selected.


Is this formula describing the loss of unfixed genes from a population accurate? In the 1954 science fiction novel Search the Sky by Frederick Pohl and Cyril M. Kornbluth, a formula is featured that "quantitatively describes the loss of unfixed genes from a population".

$$L_T=L_0 e^{-T/2N}$$

  "A final word. There has been much loose talk among the troops about the slogan of the Joneses, which goes $L_T=L_0 e^{-T/2N}$. Some uninformed people actually believe it is an invocation which gives the Joneses supernatural power and invulnerability. It is not. It is merely an ancient and well-known formula in genetics which quantitatively describes the loss of unfixed genes from a population. By mouthing this formula, the Joneses are simply expressing in a compact way their ruthless determination that all genes except theirs shall disappear from the planet and the Joneses alone survive. In the formula $L_T$ means the number of genes after the lapse of $T$ years, $L_0$ means the original number of genes, $e$ means the base of the natural system of logarithms and $N$ means number of generations."

Is this formula indeed an accurate description?

Or was it made up by the authors? I find it suspicious that it contains two different measures of time, years and number of generations, while they seem related to me.

An earlier version of this question omitted the minus sign in the equation. I noticed it when finding it again on Google Books.

The expression is based on a real one, but missing a minus sign (EDIT: not anymore! See updated question), and the explanation is garbled. For the actual equation, see "eigenvalue effective population size" in, e.g., WJ Ewens, Mathematical Population Genetics. There should be a negative sign in the exponent: $L_T = L_0 e^{-T/2N}$. Note that you need this minus sign so that "genes" (actually heterozygosity) are lost with time rather than growing exponentially in number!

As for the errors in the explanation: $T$ should be measured in generations rather than years, and $N$ should be the number of individuals (or rather the "eigenvalue effective number") instead of the number of generations.


Structure of mitochondrial ribosomes Is the ribosome found in mitochondrion and choloroplast formed of 30S and 50S subunits as in prokaryotes. I couldn't find any information on internet concerning it.
The general wikipedia page has no information about it though it says

  The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 70S particle.[9] These organelles are believed to be descendants of bacteria (see Endosymbiotic theory) and, as such, their ribosomes are similar to those of bacteria.

The wording of the question suggests that it may be useful to clarify the meaning of the numbers in the designations 70S, 50S, 30S etc. These are sedimentation coefficients in Svedberg units as determined in the analytical ultracentrifuge, and are an indication of size.

All ribosomes have two subunits. The reference eubacterial ribosomes from E.coli are 70S with a large subunit of 50S and a small one of 30S. The reference eukaryotic cytoplasmic ribosomes (rat liver, say) are 80S, with large and small subunits of 60S and 40S respectively. The actually sizes (S-values) of the subunits in other eubacteria (say mycoplasma)  and different eukaryotes (say yeast) may differ, but the eubacterial ribosomes share an antibiotic sensitivity (e.g. to streptomycin, erythromycin) which differs from that of eukaryotic cytoplasmic ribosomes (e.g. to cycloheximide) and so it is often convenient to refer to 70S-type ribosomes or 80S-type ribosomes, despite the size difference.

Mitochondrial and plastid ribosomes share some of the antibiotic susceptibility of eubacterial ribosomes (e.g. sensitive to streptomycin, but not to erythromycin) and their rRNA is more closely related to the latter. So they have 70S-type ribosomes with 50S-type and 30S-type subunits. However they vary greatly in size. For example, pig mitochondrial ribosomes are smaller at 55S, with large and small subunits of 39S and 28S, respectively. In contrast, yeast mitochondrial ribosomes are larger at 74S, with large and small subunits of 54S and 37S, respectively. More important, they differ from eubacteria in their ratio of RNA to protein, unlike chloroplast ribosomes, which workers in the field have classified as bacteria-like. This is shown in the table:
 [Adapted from Supplementary Table S1 in Science (2014) vol 343, 1485–1489]

The striking thing about most mitochondrial ribosomes is, whether or not they have undergone a decrease in their rRNA, they have additional proteins with no analogues in bacterial ribosomes. Structural work on both mammalian and yeast mitochondrial large ribosomal subunits show that these additional proteins are associated with an altered exit tunnel for the growing polypeptides, which appears to be tailored to conduct the latter directly to the mitochondrial membrane.

Answers (depending on intent of question)

Yes, mitochondrial and plastid ribosomes have large and small subunits.
No, their sizes are not 50S and 30S, but vary greatly.
Yes, mitochondria and plastids have 70S-like ribosomes, rather than 80S-like ribosomes, but these have evolved considerably from their eubacterial precursors.

Sources

Some of my assertions are based on recent papers and earlier work referenced in them. Also access to them may not be free outside university libraries. Apologies for that — if I find more accessible sources I will add them later.

Mammalian mitochondrial ribosomes: Nature (2014) vol 505, pp. 515–521.
Yeast mitochondrial ribosomes: Science (2014) vol 343, 1485–1489.
Spinach Chloroplast ribosomes: Proc.Nat.Acad.Sci. (2007) vol 104, pp. 19315–19320.
Antibiotics and ribosomes (review): EMBO Reports (2001) vol 2, pp. 318–323.


ADCs: by what mechanism are antibodies internalised I read that ADCs (Antibody-Drug Conjugates) act by a -mab for a particular target being bonded to a cytotoxic compound. From my high-school-with-crayons knowledge of antibodies, however, one part of the mechanism stands out as being strange: the internalisaiton of the complex into the cell.

In my head, antibodies are either free in plasma or expressed bound to the surface of cells. How and why (mechanistically/evolutionarily/functionally) does this antibody internalisation take place? Is it a natural process in most organisms, or a backdoor which must be engineered into the ADC?

The usual sources for neophytes are quiet in this area, and the advanced material is bewildering.

What we're basically looking at with ADC internalization

Courtesy of Bayer

So the way an ADC works: The antibody-drug conugate binds to a target antigen like a transmembrane receptor, the cell in response engulfs the entire complex and send it to an endosome. What the cell can do with the endosome depends on the cargo. Digressing, the ADC internalization mechanism is often attributed to receptor-mediated endocytosis, where the most prominent mechanism of receptor internalization is the clathrin-mediated pathway. We're going to be referring here most of the time.

  Clathrin-mediated endocytosis commences with the recruitment of adaptor proteins, accessory proteins and a clathrin polymeric lattice to phosphatidylinositol-4,5-bisphosphate-enriched plasma membrane regions

A common adaptor protein here is AP2 that's capable of binding to motifs present on the cytoplasmic tails of membrane receptors. What it's doing is selecting which receptors are the cargo. Then the clathrin mobilizes to the now-enriched membrane regions, and the polymerization of clathrin causes the membrane to displace and curve. Dynamins, large helical GTPase proteins capable of stretching the invagination in the membrane to a vesicle, bind the phosphatidylinositol-4,5-bisphosphates in the membrane, and may work in concert with BAR domain-containing proteins and actin tension to stretch the membrane into a vesicle and cut it away (Doherty & McMahon, 2009).

Obviously there's some missing information, as we don't fully understand it. I think reading the first reference, published in mAbs in 2013, is a really good place to start however!


What is the surface area of the human heart? I heard that the human heart had a surface area of 1000 square feet, and I thought that that cannot be true. So what is the surface area of the human heart and what are the different ways it can be measured?

The number you are looking for might be quite large depending on the level of detail you demand for the measurement.  There is no single number for the area of most objects in fact.

The importance of fractals is much related to the question of what is the perimeter or surface area of something.  The classic example is trying to determine the length of Britain's coastline.  If you took a surveyors sight and set a point every 500 ft you would get a certain number, if you paced it out in strides you would end up taking more curves and turns and you would get a longer number.  If you took out a ruler and measured down to the inch you would get a still larger number.  In these two wikipedia pictures you would get a perimeter of 2400 km and 3400 km for points set every 200 and 50 km respectively:

As you can see that makes a big difference.  So in the same thought organs also need to be measured using fractal sorts of measurements- depending on the level of detail desired. For a heart, if you were to cover the organ with a tight stretch of Saran wrap, you'd have maybe 1-2 square feet, but if you estimate the surface area for not only the inner chambers, but the blood vessels and capillaries, it would be much larger.  The latter is probably relevant if you are a physiologist and want to know how much oxygen the heart is taking in as it beats.

I can't find a reference for a human heart, but fractal calculations for the human lungs tell me that 1000 sq ft seems reasonable.  If you take the oxygen accessible area of lungs, including every bronchial passage and aveoli, the answer is 50-100 m^2. This is about 538- 1,076 sq feet.

The heart does not need to have as much surface area as the lung, but the capillaries and arteries that feed the heart need to be spaced a few millimeters apart to keep the tissue oxygen saturated.  1000 sq feet seems a possible range for the heart compared to the lung's surface area, maybe on the high end...


Why is the GULO pseudo gene expressed in humans? The GULO pseudo gene is being expressed in humans according to Genecards.

Why is this still taking place after tens of millions of years since then gene lost the capacity to encode for a functional enzyme?

I suggest thinking about this from a different direction — something like: "What selection pressure is there for loss of expression of the GULO pseudogene?"

When thinking about that question note that the expression level is very low (less than 1 transcript in a million in the tissue with the highest level of expression.

In general, evolution is messy and I think your null hypothesis should be that this as a vestigial trait.

In other words, unless you can show that there is a significant cost for the low level of expression seen from this pseudogene there is nothing to explain.


Can Phosphogycolate buildup in a plant kill it? I'm trying to think of some things for the science fair, for part of my experiment I need to know if Phosphogycolate build up in a plant can kill it. Also, are there any chemicals that may disrupt the enzymes which break down phosphogycolate. Thanks!

Phosphogycolate can break down enzymes needed in the Calvin Cycle along with other enzymes in a plant so that is a yes.l.


Why can I raise my left eyebrow independently from the other but not the right? I've seen the same question on other forums, but have not come across any definitive explanation.  The non-cited answers seem to fit into three categories:

It is due to greater muscle dexterity on one side of the face.
It is a result of being either left/right brained.
It is genetic.

Perhaps it has to do with a combination of these three, or none of them at all.  Some have even said that with practice they have been able to raise both independently from the other.  Why is this so?

The muscle responsible for being able to raise both eyebrows is one and the same (m. occipitofrontalis). You can not raise one eyebrow because the whole muscle is connected to both eyes. It is possible that one side is not connected or less connected but that's usually not the case and such a person would not be able to raise both eyebrows at will.

What happens in almost all people is that they are not raising one eyebrow, but instead keeping one eyebrow down and raising both at the same time thus giving the impression of only raising one. There are various muscles that are able to lower the eyebrows.

So if one person is "not able" to raise one eyebrow, it actually means that they are not able to keep the other side down.


Examples of virus originated from a living system Do you know some examples of virus or a viroid (or a prion) that originated from a known living organism? How does the virus/viroid/prion lives? Does it paratize the organism from which the virus originated?

UPDATE

Thanks to the first answers I have examples of newly originated prions. Does someone know such an example about viruses?

Prion diseases are still very poorly understood, but one of the dominant theories is that they are misfolded proteins that cause disease by catalyzing the misfolding of more proteins of the same type.  If that is the case, then they arise from the organism that they affect simply by protein misfolding.  In the case of bovine spongiform encephalopathy (mad cow disease) being transmitted to humans and resulting in new variant Creutzfeldt-Jakob disease, it seems like it might be transmissible between species, but it probably needs to infect a closely related species so that the protein has a homolog it can act upon.

Can't say I know of any examples where people have shown the de novo creation of a virus from a living organism.  There are definitely virus protein homologs in the genomes of organisms, but directionality is hard to argue since its common for viruses to pick up host genes, or leave behind viruses genes.


How to calculate Oxygen consumption? I am looking into Glycolysis and TCA cycle.
I have learnt that oxygen is the final electron acceptor.

So, let's say we know the amount of NADH and FADH2 produced under some circumstance related to the Glycolysis and TCA cycle.

How would we calculate the amount of oxygen consumption level?

Assuming that you know the amount of NADH and FADH$_2$ produced by glycolysis and TCA cycle, you can determine the reducing equivalent produced: for each NADH or FADH$_2$ produced, two reducing equivalents are produced. It means that the re-oxidation of NADH and FADH$_2$ will release 2 electrons. Here are the corresponding half-reactions:

$\textrm{NADH} = \textrm{NAD}^+ + \textrm{H}^+ + 2~\textrm{e}^-$

$\textrm{FADH}_2 = \textrm{FAD} + 2~\textrm{H}^+ + 2~\textrm{e}^-$

Knowing the total reducing equivalent produced, divide it by four in order to obtain dioxygen consumption: O$_2$ is reduced into 2 H$_2$O by accepting four electrons. Here is the corresponding half-reaction:

$\textrm{O}_2 + 4~\textrm{e}^- + 4~\textrm{H}^+ =  2~\textrm{H}_2\textrm{O}$

Of course this only applies to aerobic organisms: some microbes are able to use other electron acceptors than O2.


Are scientist able to correct mutiple gene defect in our body by using CRISPR Are scientist able to correct mutiple gene defect in whole body by using CRISPR recently?

AS i know, it is in a beginning stage

Certainly not yet - there is not yet any evidence that this can be used to correct specific deficiencies in an adult, though the in vivo applications are growing.

In particular, an exciting recent advance is the opportunity to better understand carcinogenesis by 'editing in' certain known mutations into a mouse, say, that should cause a cancer, and watching for when the cancer actually arises...


How would ecology be affected if 100km² of an ocean surface was covered by a floating object? Assume that we planted floating solar cells on the ocean surfaces. Assume a 100km² solar cell field in the middle of the Pacific Ocean. All of the sunlight will be blocked by them. How would that affect the life in oceans?

The vast majority of light only penetrates the top 200 metres of the ocean, the euphotic zone, so your answer is roughly "what ever lives in the euphotic zone which requires light." In all likelihood I would expect this to cause:

anything  which is not highly mobile but, is dependent on sunlight (phytoplankton etc.), would die.

the more mobile ("free swimming") which rely on either sunlight or the (now dead) slower resources would move out of the area.

reduced flow of nutrients in to the lower parts of the ocean - biomass from the upper regions dies and sinks to the lower levels, if it no longer grows in the upper 200m then there will be less down flow after time.

Overall, the impact would be low because the area of the pacific is >165,000,000 km2 so the density of biota would only increase marginally in the top 200 metres of the pacific (the sunlit water volume decreases from 33,040,000,000,000 cubic metres to 33,039,080,000,000 cub. metres). Also, if we assume that the platform is free floating that means it would drift thus only causing short term loss of sunlight for the less mobile organisms.
EDIT:
Upon reading @Kotatsu's answer I feel they have made a very good point and I should add the following:
By providing a solid surface it could also benefit oceanic life by increasing area available to live for sessile organisms (just like shipwrecks, oil rigs etc.). Further if the panels were broken up (I assume this would be the likely design because sitting a huge sheet across the ocean will leave it prone to twisting by wave motion) light would be able to pass between the gaps. I agree with @Kotatsu, and this "floating panel" could even be beneficial to the ocean ecosystem.

note: I am not an expert on this so it is purely an application of logic and my best guess


Do mitochondria simply automatically convert glucose to ATP? I wonder whether there is any intelligent decision-making in mitochondria in the timing of their operation.

Do they simply begin ATP production as soon as the correct reactants are present?

Or, because they have their own DNA, do they have more complex strategies that vary to benefit the mutual cooperation with the host cell? This assumes that the simple circular DNA is performing higher level decisions in switching.

Mitochondria are comprised of ~3000 proteins. However, the mitochondrial genome has only 13-14 protein-encoding genes. The remaining 99.6% of mitochondrial proteins are encoded by genes in the nuclear genome. (Wikipedia) Chloroplast genomes are only slightly larger (~100 genes).

Gene regulation and signaling between the nucleus and mitochondria (and between nucleus & chloroplast in plants/algae) occurs in both directions. Anterograde regulation is the signalling from nucleus to mitochondria and was once thought to be the only method of regulating organelle function. We now also know that Retrograde regulation occurs, in which the mitochondria sends signals to the nucleus.

To answer your question directly (but not thoroughly), both the mitochondria and the nucleus are sensing the environment and needs of the cell and signaling to each other to regulate ATP production.

If you want to learn more about retrograde signaling, googling "retrograde regulation" will bring up lots of papers on this topic in different organisms. This paper also has some diagrams of signalling pathways.


Purpose of Fc Region Could someone explain to me the role played by the Fc region of an antibody as well as the purpose of isotype switching? According to Wikipedia, it's to allow the antibody to be usable by different Fc receptors, but I don't get what Fc receptors are for.

For context,

I'm reading about affinity maturation and learning about how ecological and evolutionary processes --- division, selection, and mutation --- drive the maturation of B cells leading to high-affinity plasmocytes that can better target a foreign antigen. Because all this happens on the Fab fragment, it makes sense to me why the Fab region is important in the antibody.
I'm not trained in cell biology.
My goal is to understand the general purpose of the Fc region and how isotype switching may be a major determinant for specific immunological or physiological outcomes, although I'd love to hear anything interesting!

Thanks in advance!

Preamble

From the point of view of understanding I think it is better to talk about the constant and variable regions of antibodies, rather than Fab and Fc, as these are historical designations for fragments of the molecules that were useful in research, but do not exist as separate entities.

Cartoon representation

It is possible to represent the immunoglobulin molecule diagrammatically as shown below. In the left-hand diagram V = variable and C = constant, and the suffixes H and L refer to the heavy and light chains. The right-hand diagram, which purports to be more three-dimensional, shows how the variable regions are responsible for binding the antigen — different manifestations of the variable region have different antigen-specificity.

The different iotypes for an immunoglobulin with a particular antigen-specificity are shown next, with a pre-colour scheme that focuses on the difference between the constant regions of each isotype.

Functions of the constant region of different isotypes

The variable region of an immunoglobulin does the exciting stuff — it binds an antigen, but that is not sufficient for its action. As well as the specific discriminatory action of the variable region, there are roles in presentation and disposal that are the same for all antibodies of a class, but may differ between classes. That is what the constant regions do.

I am not an immunologist (although had to teach the biochemistry at one time in my life — hence the diagrams) so the examples I present are simplistic and incomplete. However here are a few:

IgM is made early in the immune response and hence is not very abundant. In order to enhance its response it forms pentamers in which the constant region of the heavy chain interacts with an additional J chain.
IgA is involved in immune protection in mucous regions of the body exposed to the exterior. It is directed there by interaction with a receptor on the appropriate epithelial cells, which binds the constant regions of an IgA dimer attached to a J chain.
IgE stimulates mast cells to produce histamine. These mast cells have receptors for the constant region of the heavy chains of IgE.

There are many sources on line dealing with this topic, including a section in Berg et al. that has a similar structural approach to that presented here.