Identifying an Unknown Blood Type The following case study has a student working with blood samples to
  identify their blood types (A, B, AB, and O). Consider the situation
  and answer the questions.

  A student is given eight red blood cell suspensions, which contain
  only red blood cells, and the matching serum from each sample. (Serum
  is blood plasma in which fibrinogen has been removed.)

  She is asked to identify each of the four different blood types
  present. To test these samples, the only materials she has at her
  disposal are a sample of type A red cell suspension and the serum from
  type A blood.

  Describe the step-by-step procedure that she must use to identify the
  four different blood types present. In each step, interpret what it
  means if the cells in the sample clump together, or if they do not
  clump together.

I am mostly confused on what exactly "she has at her disposal are a sample of type A red cell suspension and the serum from type A blood." means..? What is a A red cell suspension?

I already know that:

TYPE A: has anti-B antibodies

TYPE B: has anti-A antibodies

TYPE AB: has neither anti-A nor anti B antibodies

TYPE O: has both anti-A and anti-B antibodies.

The passage:

  To test these samples, the only materials she has at her disposal are
  a sample of type A red cell suspension and the serum from type A
  blood.

means, I take it, that she has available two containers: One has red blood cells from a known blood-type A individual suspended in a neutral fluid such as saline solution.  The other container has blood plasma (without red blood cells or fibrinogen) also from a known blood-type A individual.

These should be enough to determine the blood types of four individuals  from the unknown test tubes (four pairs of test tubes, each pair being one with cell suspensions and one with plasma, coming from four individuals having different blood types).


Small flying insects gathering around the pot flowers Recently I spotted relatively small flying insects gathering around the pots inside my flat.

There are smaller than fruit flies, probably around 1mm - 2mm long, blackish, and fly somewhat erratically. As far as I can tell the insects are active mostly during the day.

I didn't spot any obvious damage to the plants so far, but I might have miss something.

The location is relatively warm (southern window, above heating sink), and excluding the soil in the pots, rather dry.

Geographical location: Central Europe
Time of observation: Late summer, early autumn.

I'd be grateful if someone could help me identify this species.

Looks like some sort of fungus gnat though I won't make any attempt to ID a particular species. Note that fungus gnat describes a very wide range of species over 6 families, though yours looks most like the flies from the family Sciaridae (Wikipedia notes there are ~600 species in Europe).

Fungus gnats feed on organisms decomposing soil, which are most present when the soil is moist, especially if overwatered. The damage you will experience, if any, would be to the roots, rather than visible on the leaves, though you will see wilting if the damage becomes significant.

You say things are dry, however, the important place is the soil. You will deter, though probably not completely eliminate, the fungus gnats if you let the soil dry between waterings (in my personal experience with fungus gnats this approach was sufficient). Some specific parasitic nematodes are also used for pest control of fungus gnats, if they are available in your area.


Are fish roe unicellular? Are roe (fish eggs, caviar, etc.) single cells?

I have tried looking this up on google (sadly, to no avail), and I am guessing they might be multicellular (like bird eggs) or consist of one cell plus corona cells, or indeed unicellular.

Yes; the first division starts at around 45min post fertilization in zebrafish. This picture is stuck in every zebrafish lab.


How do we find antibiotics? So the last class of antibiotics were made in 1984 (I think), which makes it appear as though they are hard to find(/design maybe). How is it then they were discovered? Was it by chance? I know some where accidents, but how are the majority found, testing lots of chemicals on your target?

I imagine now we would have the capability to quickly identify structures and molecules unique to pathogens and be able to model them on a computer, and generate suitable proteins or other compounds that can interfere with their bonding/properties to damage the pathogen?

For something like a 70s ribosome in a pathogen, what is the process of being able to understand its structure, its shape, etc? How much effort does it take to model onto a computer? Or instead a single protein (as a 70s ribosome will be more complex), how long does it take to model a new protein?

Thanks for any help :)

Was it by chance?

Yes, sometimes, Penicillin was discovered by chance (and good observation), see http://www.nobelprize.org/nobel_prizes/medicine/laureates/1945/fleming-bio.html.

  I know some where accidents, but how are the majority found, testing lots of chemicals on your target?

Other important classes, like tetracyclines, were discovered by screening of soil samples for antibacterial activity (The history of the tetracyclines
). At that time it was not known what is the target of tetracycline, it was only observed that it was able to inhibit bacterial growth.
A synthetic antibiotic, nalidixic acid, was discovered as an impurity in the synthesis of another pharmaceutical agent and later became the template for other important antibiotics like ciprofloxacin. (Origins of the Quinolone Class of Antibacterials)

  I imagine now we would have the capability to quickly identify structures and molecules unique to pathogens and be able to model them on a computer, and generate suitable proteins or other compounds that can interfere with their bonding/properties to damage the pathogen?

In theory, yes, but from computer simulation to a drug there is a long, bumpy road. Most bacteria have a cell wall (with either one or two membranes, see here for a detailed discussion), so drugs need to penetrate this barrier before reaching their target. Even if they do so, they must also preferably inhibit bacterial enzymes but leave human enzymes active. This is especially complicated for targets, like DNA replication, protein synthesis, etc. which evolved early in evolution and are common to bacteria and humans. Some antibacterial drugs target tiny differences between humans bacteria, for some like Gentamicin it works well, for others like Chloramphenicol the side effects are dose-limiting. Here is a good blog entry on this topic: Antibiotics not as easy as theysay, look at the blog for other excellent comments on drug discovery and antibiotics).

For something like a 70s ribosome in a pathogen, what is the process of being able to understand its structure, its shape, etc? How much effort does it take to model onto a computer? Or instead a single protein (as a 70s ribosome will be more complex), how long does it take to model a new protein?

To quote Wikipedia:

  "Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. [..] The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins."

To get a computer model of the structure for a single protein where a similar protein is known, it takes a few hours. But to validate this model, i.e. showing that the hypothetical structures matches the real structure, it takes months of human work. You can imagine how much work it is for 31 proteins. In addition tiny deviations in the model, may cause your predictions to give false positive or negative hits (i.e. your computer model predicts that inactive compounds bind to the target or real inhibitors don't do anything to the target).

The traditional approach, finding compounds which kill bacteria or inhibit their growth, is much more promising since one might discover novel targets in bacteria and microorganisms came up with dozens of ways of killing their competition. One new approach is to cultivate bacteria which cannot be cultivated with traditional methods and screen them for antibacterial compounds, e.g. as described in this summary of this research article

Some more good reads on this topic:

The role of serendipity in drug discovery
A Brief History of the Antibiotic Era: Lessons Learned and Challenges for the Future


Why do we grow so much hair on our heads compared to our bodies? I've been wondering about head hair, facial hair in particular. Human males can grow very extensive beards should they choose to not shave - however you do not really see this in our chimpanzee cousins! Yes, they have little pseudo-beards, but the difference being that they do not shave, that is just the length they reach. Whereas in humans we can grow to our hearts content (*this may not be the case, see this question).

I can't really see why this would have been selected, unless it's simply that (evolutionarily speaking) women like men with long beards?

So my question is: why can humans perpetually grow head hair, yet we have lost the majority of our body hair, in comparison to chimpanzees and other ape family members?

Wheeler (1992; and previous) discusses the evolutionary loss of "non-functional" hair in hominids from the perspective of water balance.

Wheeler's hypothesis is that naked, bipedal hominids could have tolerated higher ambient temperatures as well as elevated metabolic heat production. Naked skin would confer higher levels of evaporative cooling, but would have entailed more water loss.

Wheeler argues that bipedalism necessarily would have preceded loss of hair, which seems to agree with Carrier's (1984) hypothesis that early hominids were distinguished not by large brains but by upright, bipedal postures with striding gaits. Humans are unique among similarly sized mammals in their capacity for endurance running.


When do fireflies glow in their lifetime? Does a firefly glow only when adult or larva? Or does it glow during its whole life. By glowing, I mean that they glow only when they require, not all the time.

Is there a reason (evolutionary reasoning) why they glow? Also, if the answer is all the time, then why, or if the answer is specific period in life then why?

Fireflies 'glow' in larval and adult stages but for very different reasons. It is thought that glowing behaviour first evolved in larvae to deter predators(Branham and Wenzel (2003)). This is an example of an aposematic warning, which uses bright colours, smells, sounds, or in this case light, to tell predators they are undesirable as prey. Sometimes a prey animal will use an aposematic warning to tell predators they are poisonous, or simply to mimic a prey that is poisonous. In the case of firefly larvae, they don't taste good to predators because of a steroid compound in their bodies (Branham (2005)).

Adults also glow, but do so in a synchronized pattern of flashes to communicate with mates (Carlson and Copeland (1985)). Mates will time their flashing with physiological fluctuations and even respond directly to another individual's flashing pattern with appropriate delays and timing of responses.

So to answer your first question, fireflies are not continuously glowing, but flash at night as larvae to deter predators, and during active mating as adults.

Your second question can get into a long-winded explanation of how certain traits evolve in response to a pressure, but to simplify, it's likely that fireflies evolved glowing because it relieved predation pressure. This ability then evolved further to communicate the quality of mates more efficiently than phermone signalling.


If evolution is true, how do all organisms have varying amount of chromosomes? I thought genetic mutation changes genes and therefore evolution happens, but it doesn't explain how  chromosomes are created/removed if the first organism had a set amount and now all the organisms have different numbers of chromosomes. How does this happen?

A mutation is a general term referring to any alteration of a nucleotidic sequence. It includes small mutations like indels (insertion or deletion of a single nucleotide) and substitutions, or bigger mutations such as e.g. chromosome fusions, whole chromosome duplications, whole genome duplications and gene deletions. So yes, some mutations do change the number of chromosomes (and ploidy number).

If you are interested in a very short and very introductory course to evolutionary biology, consider having a look at Understanding Evolution by UC Berkeley


Is there evidence to suggest that nutrients in vitamin capsules are not as readily absorbed as the same nutrients in whole foods? I recently fell ill with a cold, and began to take a vitamin C capsule each day to help my immune system. When I noticed no change in my condition, I began to incorporate an abundance of citrus into my diet instead of taking the capsules. When I ate the citrus my condition began to improve markedly.

The ingredients listed by the vitamin manufacturer are:

Ascorbic Cellulose Gel
Hydroxypropyl Cellulose
Croscarmellose Sodium
Stearic Acid
Magnesium Stearate
Silicon Dioxide

Not excluding the possibility of coincidence, I was was intrigued. Has evidence been published to suggest that nutrients in whole foods like vitamin C in citrus fruits are more readily utilized in the body than nutrients in vitamin capsules?

The answer probably varies for different nutrients.  An informal article by ConsumerLab.com indicates that many vitamins are better absorbed from natural sources, but a few are actually more readily absorbed from supplements.

Looking at Vitamin C specifically, a 2013 review article by Carr and Vissers concluded as follows (emphasis mine):

  Overall, a majority of animal studies have shown differences in the comparative bioavailability of synthetic versus food-derived vitamin C, or vitamin C in the presence of isolated bioflavonoids, although the results varied depending on the animal model, study design and body compartments measured. In contrast, all steady state comparative bioavailability studies in humans have shown no differences between synthetic and natural vitamin C, regardless of the subject population, study design or intervention used. Some pharmacokinetic studies in humans have shown transient and small comparative differences between synthetic and natural vitamin C, although these differences are likely to have minimal physiological impact.

In other words, with vitamin C natural and synthetic sources appear to be equally bioavailable for humans.  The authors do note that "Although synthetic and food-derived vitamin C appear to be equally bioavailable in humans, ingesting vitamin C as part of a whole food is considered preferable because of the concomitant consumption of numerous other macro- and micronutrients and phytochemicals, which will confer additional health benefits."

References:

Carr, Anitra C.; Vissers, Margreet C. M. (2013). "Synthetic or food-derived vitamin C—Are they equally bioavailable?". Nutrients 11 (5). pp. 4284–4304. doi:10.3390/nu5114284. PMC 3847730.


Trying to identify an Ontario bird photographed in Spring in the Don Valley Any help is appreciated! I think this may be a juvenile bird? I thought it might be a brown-headed cowbird, but the plumage and head markings don't seem quite right (compared to examples on the internet)? Any assistance is greatly appreciated.!

Rob aka orbitrob

Based on the location, timing and picture, this bird is a female Red-winged Blackbird (Agelaius phoeniceus)

In the spring in Ontario, it would be unlikely to have juveniles around, as breeding has just begun unless this photo was taken near the end of Spring. Male Red-winged Blackbirds would be in their dark black plumage with the yellow/red wing patch. Here is a photo of a pair with the male on the left and female on the right.

You can find more information about them here


What is the etymology of "moura" in Mourasuchus? Mourasuchus is a unique species of prehistoric crocodile so far discovered. It is a filter-feeder and has shared its habitat with Gryposuchus and the more fearsome Purussaurus in the Miocene Era --  reptilian counterpart of the Whale shark and Basking shark.

The original description of the species was given in 1964 by Llewellyn Ivor Price in:

  Price, L. I. (1964). "Sôbre o crânio de um grande crocodilídeo extinto do alto Rio Juruá, Estado do Acre". An. Acad. Brasileira Ciên. 36 (1): 59–66.

As such, it seems plausible that the name means 'crocodile of Moura', Moura referring to Rio do Moura, a river in the Brazilian state of Acre where the animal's fossils were discovered.


How are Thyroid Stimulating Ab destroying thyroid tissues? I was reading about Graves' disease, which is an autoimmune disorder. I read a few books, including Endocrinology by Hadley and Levine, and websites where they mentioned that the antibody named TSAb (Thyroid stimulating Antibody) binds to TSH receptors and stimulates synthesis and release of thyroid hormones from thyroid gland. This results in the symptoms of Exopthalmic goiter or Graves' disease.

My question is how are these antibodies actually attacking the healthy tissues (which I presume is the tissue of thyroid gland)?

I've so far found no website explaining this part of the autoimmune disorder. I'd appreciate any information or references in this regard.

Thyroid stimulating antibodies (sTRAb) don't destroy thyroid tissue. To the contrary, they have a TSH-like effect on thyrocytes and therefore lead to hyperthyroidism and thyroid growth resulting in goiter. The exception is Graves' disease with Hashimoto component. Here, the thyroid is also affected by cytotoxic T cells and antibodies directed against thyroid peroxidase, which gives rise to destruction of the thyroid. But even in this case, it aren't the sTRAb, which destroy tissue.

Perhaps healthy tissues refers to extrathyroidal tissues. Due to unknown reasons several tissues including skeletal muscle, heart muscle, adipose tissue and skin have TSH receptors, and they are affected by sTRAb, too. Hypertrophy results from cross-talk of TSH receptors with IGF-1 receptors in Graves' disease.

References

Dietrich JW, Landgrafe G, Fotiadou EH. TSH and Thyrotropic Agonists: Key
Actors in Thyroid Homeostasis. J Thyroid Res. 2012;2012:351864. doi:
10.1155/2012/351864. Epub 2012 Dec 30. PMID 23365787.
Krieger CC, Neumann S, Place RF, Marcus-Samuels B, Gershengorn MC.
Bidirectional TSH and IGF-1 receptor cross talk mediates stimulation
of hyaluronan secretion by Graves' disease immunoglobins. J Clin
Endocrinol Metab. 2015 Mar;100(3):1071-7. doi: 10.1210/jc.2014-3566.
Epub 2014 Dec 8. PMID 25485727.
Krieger CC, Place RF, Bevilacqua C, Marcus-Samuels B, Abel BS, Skarulis MC, Kahaly GJ, Neumann S, Gershengorn MC. TSH/IGF-1 Receptor Cross Talk in Graves' Ophthalmopathy Pathogenesis. J Clin Endocrinol    Metab. 2016 Jun;101(6):2340-7. doi: 10.1210/jc.2016-1315. PMID 27043163.
Yoo WS, Chung HK. Recent Advances in Autoimmune Thyroid Diseases. Endocrinol Metab (Seoul). 2016 Aug 26. PMID 27586448.


Why is venom more common in fish and snakes than other vertebrates? Reading this question, I wondered why is it that we associate vertebrate venoms so often with snakes and fish, and more rarely with lizards, amphibians, mammals, and birds (apparently never, in birds?).

Are venoms more advantageous for snakes and fish, or more expensive or dangerous to produce for the other taxa? Or is it connected to evolutionary history – is venom somehow more 'evolvable' for snake and fish lineages?

Or, perhaps, is it just chance?

This write up by Carl Zimmer basically covers anything I could have said.  He links to a number of resources, in particular Casewell et. al. 2013, which at a cursory glance looks utterly fascinating and very well done.  Zimmer recapitulates figure 1, which sums it all up, or to quote Carl:

"Each lineage of venomous animals became deadly on its own, independent of all the others. And yet, in the end, their venoms echo each other... These results show that there are a limited number of ways to kill your victim quickly. No matter what genes you borrow for the evolution of venom, they will end up very similar to other venoms."

Another Zimmer piece specifically points out research purporting to show that snake venom genes are much older than snakes, maybe 200 million years old.  That gets around but doesn't quite answer your question.  An older review tried to coalesce things (as best as he could in '92), spending time focusing on insectivora and dealing with mammals.  The theory is that while venom is an excellent advantage, it requires a significant investment and is often slow-working.  In a world with sharp teeth capable of tearing, venom may not be necessary.  Mammals, for example, might evolve to not use venom, as it may not be suitable for their high daily energy demands.  The pdf linked above briefly touches on the concept of "reverse recruitment," where venom genes may be usefully re-purposed for other biological processes.
Reference:
Nicholas R. Casewell, Wolfgang Wüster, Freek J. Vonk, Robert A. Harrison, Bryan G. Fry. Complex cocktails: the evolutionary novelty of venoms. Trends in Ecology & Evolution
Volume 28, Issue 4, April 2013, Pages 219-229


Significance of lipids in biological membranes...? Membranes are specifically designed by lipids to maintain internal hydrophilic environment in narrow range.There are hydrophobic amino acids among naturally occurring 20 amino acids and as well as there are also number of water insoluble polysaccharides like cellulose. These hydrophobic and water insoluble materials can also be used to build membranes but why not? Why lipids are only choice?

Membranes are built from a specific class of lipids, namely phospholipids, whose key property is that they are amphiphilic and so can self-organise to form bilayers. Not all amphiphiles do this, some prefer to adopt a micellar organisation. A bilayer composed of phospholipids produces the ideal combination of a hydrophobic barrier with a hydrophilic surface.

Although there are clearly amino acids with hydrophobic side chains, it is difficult to conceive of a proteinaceous barrier that would reproduce the properties of a phospholipid bilayer since it would not have a continuous hydrophobic phase.

Cellulose may be insoluble, but is full of polar groups so again would not create a hydrophobic barrier - I'm sure that ions can diffuse through a cellulose structure for example.

added later

@WYSIWYG raises an excellent point in the comments. Archeal membranes are composed of a different class of amphiphile in which the hydrocarbon tails (branched; derived from isoprenoids) are attached to glycerol by an ether linkage. It's instructive to note that the overall design principles are retained however, suggesting that the self-organising properties of these molecules was the key to the "invention" of biological membranes.


Why does carbon dioxide diffuse easier through the bilipid layer than oxygen? When gas exchange occurs during respiration, the pressure of oxygen in alveoli is around 105 mmHg, whereas in the blood vessels in close contact with alveoli is 40 mmHg. For carbon dioxide the values are 40mmHg in alveoli, and 45mmHg in vessels. So the difference in pressure for oxygen is 65 and for carbon dioxide 5.
The fact that the pressure difference required for oxygen diffusion to occur is greater than that of carbon would mean that is diffuses with more difficulty. But how is that possible since the oxygen molecule is smaller and non-polar, so would technically pass easier through a hydrophobic membrane?

After diffusion the partial pressure of both O2 and CO2 in arteries become almost equal to the atmospheric values(100mmHg and 40mmHg), regardless of partial pressures in veins. Rate of diffusion through membrane is roughly the same, it's the solubility that is different, as CO2 is about 22 times more soluble than O2 (it can be stored is water as HCO3-).
  However, oxygen still can easily enter and stay inside the blood vessel because it's bound to hemoglobin inside the erythrocyte. Hence there is no significant difference between the diffusion rates.


Is stereo olfactory ability restricted to humans? Most animals I see around seem to have two nostrils - humans, snakes, birds, fish .. and so on. From reading online I see that 2 nostrils provide a stereo olfactory effect. This stereo effect is caused by the difference in flow of air through the nostrils.

Does this stereo effect apply only to humans? Are there any animals that have a different number of nostrils? Say, more than 2, or less.

Moles and rats also smell in stereo (Catania 2013 and Rajan et al 2006), as do desert ants (link).  The latter is rather interesting, given that ants "smell" using their antennae, which suggests multiple sensory structures, not necessarily nostrils, are required for stereo olfactory ability.

EDIT: Hammerhead sharks have two nares and also stereo olfactory ability (here).  Dolphins have one spiracle, as do a number of other cetaceans.

It's actually not clear whether humans have stereo olfactory ability, (see edit below)  as the "stereo" aspect derives from having nostrils that are sampling from different spatial locations.  However, the research in the eastern mole suggests that this is not so far-fetched an idea, as their nostrils are not so far apart.

EDIT of EDIT: I take that back about humans: we do appear to have stereo olfaction.


Has a primate species ever weighed the average mass of a tonne (1000 kg)? If so, why can't primates weight a metric ton?

There is no specific reason why a primate couldn't weight a metric tonne. You can look at mammals evolution and notice that the primates belong to the clade Euarchontoglires which also contains rodents, treeshrews or rabbits. So basically these species most likely had a common ancestor that was very small.

Primates are currently the biggest animals of that clade. Great apes are the biggest primates. Gorillas at about 150kg on average are the biggest (by weight) currently non-extinct great apes. Chimpanzees, Orangutans and Humans are approximately equals at 75kg. The biggest known primate, now extinct, is the Gigantopithecus which was probably a sort of giant Gorilla twice the size of what you know as Gorillas (200-300kg), so still well short of a tonne. The biggest non-extinct rodent is the Capybara (you can see one at the Cosmocaixa in Barcelona). But the biggest known extinct rodent was the Josephoartigasia and did weight 1000kg.

Euarchontoglires sister clade is Laurasiatheria which does contain many animals bigger than 1000kg, such as Bisons, Rhinos, Girafes, Orcas, Walruses... These 2 clades belong the Boreoeuthenia clade, whose sister clade Atlantogenata also contains many animals heavier than 1000kg (most notably elephants). So evolutionarily primates would have had plenty of time to become as big as rhinos, but it looks like this group found its ecological niche in staying relatively small (although humans and chimps are not that small as compared to rodents or rabbits). Getting big is not always smart as we know from mammals surviving the Cretaceous extinction thanks to their tiny size.

Evans et al. (2012) tried to estimate the maximum rate of evolutionary body mass increase in mammals (through natural selection, it is likely you could force this process to be much much faster). They found that it took about 1.6 millions generations for body mass to increase a 100-fold in terrestrial mammals. So a back-of-the-envelope calculation tells you it would take about 30 million years for current primates to reach 1000kg. They also point out that the aquatic cetaceans grew much faster than any terrestrial mammal, suggesting that being terrestrial strongly limits growth rate. They also point out that macroevolutionary growth rates are far slower than what would be predicted from microevolutionary rates, for reasons still unknown.

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

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

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

Evans, A. R., Jones, D., Boyer, A. G., Brown, J. H., Costa, D. P., Ernest, S. M., ... & Harding, L. E. (2012). The maximum rate of mammal evolution. Proceedings of the National Academy of Sciences, 109(11), 4187-4190. https://www.pnas.org/content/pnas/109/11/4187.full.pdf


What are some examples of non-homologous sequences having similar functions? I am trying to find some proteins that are non-homologous but functionally similar. However, I cannot seem to find concrete examples. Can someone please point out any resources or provide examples?

Serine Protease Catalytic Triad
This is classic example of convergent evolution in catalytic mechanisms. Shown below are chymotrypsin (4CHA, green) and subtilisin (1ST2, blue) aligned on their catalytic triads (Ser/His/Asp, darker colours). There is no obvious sequence or structural similarity.

You can check out the MEROPS database for a list of protease clans ("represents one or more families that show evidence of their evolutionary relationship") and this paper for a discussion on convergent evolution of the catalytic triad:

Although the biophysics of rate acceleration are intricate and sensitive to even minor structural perturbations, evolution has converged on a catalytic triad (or diad) with a reactive Ser, Cys, or Thr nucleophile more than 25 separate times to facilitate central biochemical reactions such as hydrolysis, transacylation, and phosphorylation.


Examples of healthy lifelong asymptomatic carrier of a severe infectious disease? I am curious, is there any known disease/infection that is very severe normally (patient suffers greatly and die easily without medical treatment), but ends up having little to no effect on the lives of asymptomatic carriers? I am asking this as I am thinking whether this means certain disease symptoms are mechanisms resulted from evolution to protect the "greater good", i.e. killing the patient to avoid transmission to another member of the species.

I am curious, is there any known disease/infection that is very severe normally, but ends up having little to no effect on the lives of asymptomatic carriers?

HIV is an obvious example, where so-called "long-term nonprogressors" successfully suppress HIV replication sufficiently that they do not develop AIDS but are unable to clear the infection entirely [1].

  patient suffers greatly and die easily without medical treatment

Since the comments below seem to suggest that HIV does not cause death without medical treatment, I'll point out that this is incorrect.  Over 30 million people have died from HIV infection.

  I am asking this as I am thinking whether this means certain disease symptoms are evolutionarily wired to protect the "greater good"

It does not.  Selection happens on individuals and not whole species, so the greater good is irrelevant.  Asymptomatic infection is a point on the spectrum of possible responses to infection between sterilizing immunity and death. Individuals who are chronically infected mount enough of an immune response to control the infection but not enough to completely clear it.  In the case of HIV, they are typically people who have exceptionally strong immune responses to a normally lethal virus.

Edit

The comments below suggest a deep misunderstanding of evolution. Since I think these are really the core of your question, I'll address them here.

  If traits really evolve only according to how much an individual reproduce sucessfully, it would be a different world today.

Which individuals reproduce is the sole determinant of which genes are passed down to the next generation.  This is because the genetics of each individual are determined at conception, and cannot be changed.  Hence, reproduction alone determines the traits of the next generation.

To quote wikipedia[2]:

  Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or rare within a population

Evolution is the process by which some traits are passed down to the next generation while others are not though the mechanisms of selection (e.g. individuals with harmful traits dying) and genetic drift (e.g. random chance).

  Thank about a hypothetical super fast reproducing bacteria, using up all resources, which means extinction at the end, such traits would not be passed on. In fact some sort of "moderation" mechanism is needed to take care of the "greater good".

This is exactly what happens if you put a lot of fast reproducing bacteria in a closed environment with limited resources.  They will all eventually die.

You seem to be thinking of evolution as something that intelligently looks out for the wellbeing of species.  This is not the case.  Evolution is a random process by which different amounts of reproduction and survival between individuals alters the composition of the succeeding generations. As a random, emergent process it has no goals, no intelligence, and no sense of "good".  Rather, it simply happens as a result of individuals reproducing.  This frequently does lead to extinction, as evidenced by the fact that the vast majority of species no longer exist.

(1) https://academic.oup.com/cid/article/51/2/239/303856
(1) https://en.wikipedia.org/wiki/Evolution


What organism most efficiently converts a given quantity of mass into heat? Question I am trying to answer:

In the popular film The Matrix, heat given off by humans is harvested as an energy source. I wondered, if this were possible, would humans be a good organism to choose? Would any other organism be better?

Question I want to ask:

Many warm-blooded organisms produce heat by metabolism. Do different organisms produce different levels of heat for the same mass of input (food)? Is there any organism that directs energy flux into heat production more than any other organism?

A small hardy warm blooded omnivore that is easily tamed.  I suggest rats.

Small:  You don't want a lot of metabolic effort going into building bone and structure to support structure.
Hardy:  it needs to be survivable with little care.
Warm blooded:  You want to harvest energy from it.
Easily tamed:  The animal shouldn't try to escape its captivity.


How does gene expression work in an adult organism? Is everything encoded everywhere? The color of a person's eyes are genetically predetermined. If I knew how and in which gene(s) colors are encoded, I could change these genes in the ovary and sperm and thus change the eye color of the new human being. I only had to work on one or two cells.

What would I need to do to change the eye color of an adult human? Manipulate the genes in all body cells? Or would a limited number of cells suffice (e.g. those in the eye)?

Eye color is just an example. Your answer does not have to deal with this trait.

With some exceptions (one being red blood cells), all cells in the body contain the complete genome of the individual. The expression of the genes however is, as mentioned in the comments, heavily regulated and different in various tissues. Early efforts at gene therapy have had mixed results, including some fatalities, and the field is still highly experimental.

Depending on the trait you want to change, you might have to manipulate the genes and/or gene expression in just a particular tissue, or in several. The rates of cell death and replenismhent varies between tissues, and will affect the stability of any introduced mutation. Some traits may depend on too many genes to effectively manipulate with current technology, and eye color does depend on several genes. From the Wikipedia page on Eye color:

  Eye color is an inherited trait influenced by more than one gene.
  These genes are sought using associations to small changes in the
  genes themselves and in neighboring genes. These changes are known as
  single-nucleotide polymorphisms or SNPs. (...) There is evidence that
  as many as 16 different genes could be responsible for eye color in
  humans; however, the main two genes associated with eye color
  variation are OCA2 and HERC2, and both are localized in Chromosome 15.

So depending on the original and desired color, you may or may not get away with changing a single gene. However, the pigments that determine eye color are produced in two separate tissues in the eye, making matters a bit more complicated:

  In humans, the pigmentation of the iris varies from light brown to
  black, depending on the concentration of melanin in the iris pigment
  epithelium (located on the back of the iris), the melanin content
  within the iris stroma (located at the front of the iris), and the
  cellular density of the stroma

Note that cellular density also plays a role, and this presents a much harder property to change with gene therapy, if it is at all possible.

Eye diseases have been a popular field for gene therapy research and trials lately, and there seems too have been quite some progress. However, the possiblity of using gene therapy for changing eye color has understandably not received much attention, and so there are few if any papers to consult. What can be said though, is that eye color is a complex trait, with a partially known genetic basis. It is plausible that gene therapy can be used to change pigment production and thus eye color, but even so there would likely to be many limitations. on the changes that can be made.


Can saltwater fishes survive in sugar solution? I know saltwater fishes can't survive in freshwater because of osmosis that water would rush into the body of fishes. How about sugar solution? Does sugar solution provide similar conditions as salt water for saltwater fishes?

No, the chloride cells in the gills rely on the relationship  between chloride and sodium to remove salts out of the body against the gradient. Switching the environment to sugar would cause the chloride cells to not be able to maintain ionic regulation. See the below link for basic info on chloride cells: https://en.m.wikipedia.org/wiki/Chloride_cell


What happens to an ant colony when the queen dies? Does the colony collapse? Do workers keep following the last orders? Or can future queens replace the dead one? I'm guessing this might also depend on each specific sub-species.

Not really my field, but I can point to this review which discusses a couple of different ways in which ants organize their communities:
Heinze. 2008. The demise of the standard ant (Hymenoptera: Formicidae)

I know that in some species there can be several queens per colony (so more robust to queen deaths). In many species, workers can start laying eggs if the queen dies, but these will develop as males (since they are unfertilized). However, in some species (e.g. Platythyrea punctata) the workers can reproduce by parthenogenesis which can stabilize the colony to some extent after the queen dies.


Genotype to phenotype map and the G-matrix Suppose I have a genotype-phenotype map defined by the matrix $\mathbf{Z}$:

The scalars $G,P$ represent the number of genotypes and traits, respectively. The map assigns a set of phenotypic traits (the columns) to a set of genotypes (the rows), where $z_{ij}$ is the quantitative measure of an individual of genotype $i$ with respect to a trait $j$. I want to know how the average value of each of the phenotypic traits changes over time, suggesting I should use quantitative genetics theory and formulate the equation

$\Delta \bar{\boldsymbol{z}} = \mathbf{G}\mathbf{P}^{-1}\mathbf{s}$,

where, $\mathbf{G}$ is the additive genetic variance covariance matrix, $\mathbf{P}$ is the phenotypic variance covariance matrix, and $\mathbf{s}$ is a vector of covariances of each trait with fitness. Assume that I know the frequencies of the different genotypes in the population.

Question 1 Can I formulate the additive genetic variance-covariance matrix from the genotype-phenotype map alone (and pop freq)? Note, I don't know anything about the underlying genetic model - number of loci representing each genotype, dominance structure, epistatic interactions, etc.

Question 2 If I assume the genotypes represent haploid individuals, does this change things? Is the additive genetic variance always equal to the phenotypic variance (assuming no environmental effects) in a haploid model? In other words does $\mathbf{G}\mathbf{P}^{-1} = \mathbf{I}$? What I'm thinking is that epistatic variance might affect things, but it shouldn't affect heritability in a haploid model, which is what $\mathbf{G}\mathbf{P}^{-1}$ is a measure of.

From the pheno-geno map and the genotypes frequencies, you have the whole distribution of phenotypes in your population. The mean of the phenoype $n$, $P_n$ is the

$$\bar P_n = \sum f_{G_i} P_{G_i}$$

, where $f_{G_i}$ is the proportions of individuals having genotype $G_i$ and $P_{G_i}$ is the phenotype of the individuals with genotype $G_i$. Therefore, the variance of $P_n$ is

$$var(P_n) = \sum f_{G_i} (P_{G_i} - \bar P_n)^2$$.

The covariance between the phenotypic traits $n$ and $m$ is

$$cov(P_n,P_m) = \sum f_{G_i} (P_{G_i} - \bar P_n)(P_{G_i} - \bar P_m)$$

The only assumptions you need is that there is no environmental variance. I don't think the above calculations required any other assumption. $G$ can be defined at the haploid or diploid stage, it doesn't change anything.

The above calculations however give you the genetic variance and covariance but not the additive genetic variance covariance. I think (but I might be mistaken) that the additive genetic variance would be equal to

$$\sigma_D^2 = \sum_i f_i^2(1-f_i)^2(2 \cdot P_{n,i,12} - P_{n,i,11} - P_{n,i,22})^2$$

$$\sigma_A^2 = \sum_i 2f_i(1-f_i)(f_iP_{n,i,11}+(1-2f_i)P_{n,i,12} - (1-f_i)P_{n,i,22})^2$$

, where $f_i$ is the frequency of the allele $A$ at the locus $i$ (you should get those data by reformatting your geno-pheno map matrix) and $P_{n,i,11}$, $P_{n,i,12}$ and

$$P_{n,i,22} =\frac{1}{l-1} \sum_j P_{n,i,j,22}$$

is the $n^{th}$ phenotypic trait for the genotype $22$ and locus $i$ averaged over all other genotypes. There are $l$ genotypes in total. Of course, this works only for biallelic loci. I don't know what it would look like for more alleles.


Correlating Ki values of pesticides to bacterial growth Four pesticides P1 to P4 are reversible inhibitors of an enzyme E that
  is essential for the growth of a bacterium B. Their Ki values are
  given in the table below. Each of these four pesticides is used in
  four geographically different regions R1 to R4. The residual
  concentrations of these four pesticides in the respective regions are
  also shown in the table below:

  Which pesticides will be able to inhibit bacteria ?

My question : I know that Ki shows the binding affinity. So, how is that related to residual concentration ? How can I deduce whether it will kill the bacteria or not ?

Unrelated question : Is it acceptable to use the word pesticide here ?!

Ki is the equilibration dissociation constant. The smaller this constant is, the stronger (more specific) is the binding between the inhibitor and the enzyme.

If the residual concentration is now higher than the Ki, for each molecule from the inhibitor which dissociates from the enzyme a new will bind (simply because of the concentration). If the concentration is lower (or much lower), this will not be sufficient to inhibit the enzyme. This assumes that the relation between enzyme, inhibitor and substrate are linear (and we are not getting some kind of saturation here).

Under the conditions mentioned above, P1 and P4 will inhibit the enzyme. For P2 and P3 the concentration is to low.


Cytoskeleton made of only actin? I am aware that the cytoskeleton has three structural components: actin, microtubules and intermediate filaments. I was wondering if any cell could possess a cytoskeleton made only of actin. Or made only of microtubules, for that matter. Is it possible for actin to perform the functions that microtubules ordinarily perform in a cell? Or vice versa?

1) Can cells survive without any of the different cytoskeletal components?

Yes, most certainly. At least for actin and microtubules (MTs) there are plenty of eukaryotic cell types that can survive without them. MTs can be disrupted by cold-shock (see for example here https://www.ncbi.nlm.nih.gov/pubmed/16505977). How well the cell survives depends on the type of cell, but the ability to survive without MTs can range from minutes to hours as far as I'm aware. Once the temperature goes back to normal, the MTs just grow back. Of course, the cells won't behave normally in the meantime, because many processes do depend on MTs. Actin can be disrupted using various drugs or genetic constructs, or they can be cut using femtosecond lasers (see for example https://www.ncbi.nlm.nih.gov/pubmed/28324605). Again, many processes are disrupted, particularly cell motility, but most cells can survive without actin for a while.

I'm not aware whether any eukaryotic cells exist that have no intermediate filaments or can survive at least for some time without them.

2) Could a cell function normally while lacking one type of cytoskeletal component?

First, to my awareness there is no eukaryotic cell without MTs or actin. We do commonly use actin and tubulin promoters for transgenes and assume that all cells will express them. So I'm taking this question hypothetically.

As with every hypothetical question, the answer then purely depends on the restrictions that you define. Can the cell possess arbitrary new proteins that currently don't exist? Then yes, definitely you could get eukaryotic cells with just MTs or just actin or just intermediate filaments. You just have to bend all the other things the cell does to fit with that filament type, and then enjoy arguing whether that's still a eukaryotic cell or not.

But I think actin would find it easier to take over the other filaments' jobs compared to the other way round.

MTs are large and rigid. They can't operate on scales below 25nm like actin can, and the individual tubulin dimers can't do anything useful until a tube of some minimal length has been formed out of many dimers. Intermediate filament monomers are pretty thin, but very long. Actin monomers are small and globular, and a supershort actin filament made of a handful of monomers can already function as a filament, branch out, form networks, pull on things etc. Actin-mediated endocytosis crucially depends on this (https://www.ncbi.nlm.nih.gov/pubmed/25675087 for example). It would be difficult to find workarounds for these small-scale functions of actin if MTs or IFs were to replace it. On the other hand, actin filaments can very easily be made into large, thick, rigid rods like microtubules. Many cell types do this constantly when they form filopodia. Actin meshworks can also provide similar mechanical support (both stable and flexible) as IF meshes. With minor shifts in the regulation of where, when and how to organise filaments, actin could probably take over the other cytoskeletons' functions. It would probably require a quite sophisticated regulatory system though to perform all the different functions at the same time in one cell.


Is it possible to re-align of SAM/BAM files? I am carrying out some metagenomic comparison using whole genome sequencing approach. I would like to filter out reads from my files in a sequential manner, thus I would like to align to a first reference genome, then use the generated SAM/BAM file to extract the mapped reads with samtols view -F4, re-generate fastq files and align those to another reference genome. This decreases the size of the input and speeds the procedure.
Using BWA, though, I get an error of file synchronization when doing the second alignment:

[mem_sam_pe] paired reads have different names:
"HISEQ:90:C3UNJACXX:1:1107:16388:61141",
"HISEQ:90:C3UNJACXX:3:1303:2008:58095"
[mem_sam_pe] [mem_sam_pe] paired reads have different names:
"HWI-ST1437:64:C3UM1ACXX:4:1214:3833:62731",
"HWI-ST1437:64:C3UM1ACXX:4:1202:18519:45906"

This is weird since the fastq files were generated by the filtered BAM file, samtools should have known how to keep the synchronization of the files.
My question is: is it possible to realign a BAM file? maybe not with BWA, at least with another tool?

Thank you.

The procedure I carried out is:

# align
bwa mem -R <read_group1> <ref.fa> <file1_1.fq> <file1_2.fq> -o <file_aln.sam>
# convert
samtools view -Sb <file_aln.sam> > <file_aln.bam> # sort samtools sort <file_aln.bam> -o <file_alnSRT.bam>
# select mapped
samtools view -h -F 4 <file_alnSRT.bam> -o <file_alnMAP.bam>
# convert to fastq
samtools fastq -1 <filemap_1.fq.gz> -2 <filemap_1.fq.gz> <file_alnMAP.bam>
# re-align
bwa mem -R <read_group> <ref2.fa> <filemap_1.fq.gz> <filemap_1.fq.gz> | samtools sort -o <file_realign.bam>

Looks like I solved it by using PICARD: extracting the aligned reads but without sorting, I used

java -jar picard.jar SamToFastq I=<file_alnMAP.bam> FASTQ=<filemap_1.fq> SECOND_END_FASTQ=<filemap_2.fq>
bwa mem -R <read_group> <ref2.fa> <filemap_1.fq> <filemap_1.fq>

From samtools flagstat the output looks fine.


Can pheromones be received other than by odor? I'm trying to understand how deodorants affect pheromones in humans.

Wiki states:

Axilla

  In humans, the formation of body odor happens mostly in the axillary
  region. These odorant substances serve as pheromones which play a role
  related to mating.

Deodorant

  A deodorant is a substance applied to the body to prevent body odor caused by the bacterial breakdown of perspiration in armpits, feet, and other areas of the body.

Can the opposite sex receive pheromones if a person uses crystal deodorant (doesn't have a fragrance; doesn't block sweating; prevents body odor by creating an invisible, protective barrier against odor-causing bacteria)?

We have only 5 senses, a 6th sense has been controversial, and some 6th senses are sometimes reported in new research in newspapers, but none have been conclusively been added to the clearly known 5. There is a second olfactory organ that deals with social signals in other animals, that we possess, the vomeronasal organ.

Pheromones are only olfactory molecules, so you can't get them other than by catching molecules and analysing them, i.e. smelling.

Humans react very strongly by attraction to some perfumes other than pheremones, and you arent supposed to block all your smells, only make them containable, a bit is probably a good thing.

Scientists did publish a study claiming that people can tell if they make a good immune response / metabolic genetic combo with a partner from smelling a potential partner's t-shirt.


What signals a ribosome to stop production when the cell is out of available amino acids? In the production of a protein molecule, there have to be a ready supply of free-floating amino acids. When a given codon for adjoining, say, serine comes up, how are the serine molecules found out of a soup of 20 different types of amino acids?

For example,

Meleagris gallopavo (turkey) small muscular protein
NCBI Reference Sequence: XP_010724014.1  88aa GI: 733873411

 1 mskqpashvk aiqaninipm gafrpgaghp hkrkevtpee veesvpatee ekdkkhlpga
61 iklpgpavnl seiqniksel kfvpkaeq

has 9 alanines, 1 aspartate, 11 glutamates, 2 phenylalanines, 5 glycines, 4 histidines, 6 isoleucines, 11 lysines, 4 leucines, 2 methionines, 4 asparagines, 10 prolines, 4 glutamines, 2 arginines, 5 serines, 2 threonines, 6 valines, 0 tryptophans, 0 cysteines, 0 tyrosines.

So the cell would deplete glutamates much faster than aspartates and obviously infinitely faster than tryptophans. So, as the concentration of glutamates drops drastically with the production of each new turkey muscle polypeptide strand, getting diluted by the nonreactants tryptophan, cysteine, tyrosine, wouldn't the reaction rate get exponentially slow?

And when the last available glutamate residue gets attached, and if it happens before the polypeptide is complete, yet it needs one more glutamate to complete the chain, what signals the ribosome to "stop looking for more glutamates"?

When cells run out of amino acids, more and more of their tRNAs remain uncharged. This elevated ratio of uncharged/charged tRNAs trigger complex signalling pathways that control amino acid biosynthesis, general reduction of translation, halting ribosome biosynthesis, autophagy (includes ribophagy - digestion of ribosomes) to recycle cells' components, etc. This can be clubbed into general amino acid control (GAAC) and involves the super important regulatory kinase protein called as Target of Rapamycin (TOR) and other transcription factors. The regulation of amino acids level is one of the most basic and important features of cellular metabolism and can be found conserved from yeast to humans. In addition to GAAC, there can be pathways for some specific amino acids as well.

There is not shortage of scientific literature. To start with you can read following article:

http://www.cell.com/trends/cell-biology/abstract/S0962-8924(14)00036-1
http://jcb.rupress.org/content/206/2/173.full


How are the first mammary glands thought to have functioned? I happened upon a book (not about biology) containing this text:

  A life-changing birth occurred on the planet about 190 million years ago [...] the first tiny shrew like creature brought forth an infant and began suckling her young. [...] this furry little mammal embodied a huge leap in biological evolution

The description is nicely dramatic, but it doesn't ring true for me. While I know that evolution likely wasn't as gradual as high school books represent it, the thought that a non-mammal bore a daughter with fully functional mammary glands who actively suckled her young is a bit too much for me to swallow. For other body systems, I have read stories how they emerged gradually, for example the oldest species having a few nerve cells, then new ones having a whole nervous "network" with a few ganglions, before actual brains emerged. Or similarly, worms having a patch of photosensitive cells on the skin evolved into animals with eyes. I know that platypuses have mammary glands without nipples, but presumably even they are already much more sophisticated than the first mammary glands.

So what are proto-mammary glands thought to have been like? Did they evolve de novo especially for feeding babies, or were they maybe repurposed sweat glands or something like that? What are they supposed to have functioned like?

the production of liquids to nourish offspring has evolved separately in several lineages, mammals have simply taken it further than any other group. it is pretty easy to see how it could evolve, any way of providing even trace nutrients or nourishment to young will have an advantage in organisms that are already engaged in child rearing. it means exposing the young to predators less often.

Mammary glands are modified sweat glands.

Monotremes do not have nipples what they have is a cluster of mammary glands on a patch of skin. the young have to suck the milk of the a cluster of hair.

The exact sequence of how lactation evolved is not well known since lactation leaves no fossil evidence.

Sources:

Lefèvre, C.M., Sharp, J.A. and Nicholas, K.R., 2010. Evolution of lactation: ancient origin and extreme adaptations of the lactation system. Annual review of genomics and human genetics, 11, pp.219-238.

Capuco, A.V. and Akers, R.M., 2009. The origin and evolution of lactation. Journal of Biology, 8(4), p.37.


Is the ringing sound in the ears caused by dying ear cells? I was recently watching the movie "Children of Men" (great movie) by Alfonso Cuarón. Now in a certain scene, the lead actor happens to be nearby a loud explosion. Later, when he complains about the 'ringing-sound' in his ears due to the explosion, a co-actor replies:

  Julian: You know that ringing in your ears? That 'eeeeeeeeee'?    That's the sound of the ear cells dying, like their swan song. Once it's gone you'll never hear that frequency again. Enjoy it while it lasts.

How true is that statement?
Do the ear-cells really die after such an incident?Can you really never hear that frequency of the ringing-sound again?

Short answer:

That MAY be the sound of the damaged hairs dying. You MAY not hear that frequency again but that's unlikely.

Long answer:

Okay, so tinnitus, or ringing in the ears, can happen because of many reasons. There are three real kinds:
1) Spontaneous tinnitus can happen because of slight shifts in the acoustic systems of the ears, some of the hairs in the cochlea may amplify wrong and create a tiny feedback loop and ring for no reason. see this article about that kind of tinnitus here

However, that's not the kind of tinnitus you're referencing. That kind, post acoustic trauma, is more serious.  This kind (which can result in hearing loss) results from either 2) one really loud noise OR 3) prolonged repetitive exposure to certain frequencies (like how your mom told you to turn your headphones down or you'd go deaf. Lower frequencies move a lot of air and can indeed be dangerous to your hearing.) Just how serious the damage from a single acoustic trauma event like the explosion from Children of Man would be to you would depend on just how loud the noise was you were exposed to, the frequencies of it, and how close you were.

So now that we've gone over the different kinds of ringing-in-the-ears (tinnitus), we can talk about how it works in this situation.

This is a great article on acoustic trauma tinnitus.

So these characters didn't rupture their eardrums or they'd be in a lot of pain and unable to hear at all in one side. Instead what happened was the tiny hairs that send electrical signals to the brain were probably bent and crushed (see awesome images on the article above of before, at, and ten days after acoustic trauma.) Three possibilities from here: either the hairs recover, they partially recover, or they don't recover at all. The most likely situation is that they do recover in a matter of days, leaving the characters with undamaged hearing. Some of the hairs (usually lower frequencies) may be more damaged that others. Those may dim or cut out frequency ranges in hearing. Multiple hairs cover the same range, so some of them may be out of commission while others survive, leaving you with diminished hearing of that frequency. However, that is not likely to be related to the buzzing/ringing frequency we first hear after acoustic trama, which is the sound of all damaged hairs freaking out and sending signals at once.

Great article on how we hear frequencies

source: Sound engineer. Protect your ears, guys!


In what two ways is ATP used in coupled reactions? I already have down "A coupled reaction is when leftover energy from a reaction fuels a reaction that needs more energy. ATP can break apart to transform into something new and use the energy created by breaking a bond to fuel a reaction in need of more energy" I think that is one use but I am not sure and I still need another

A coupled reaction is where a catabolic reaction drives an anabolic reaction, usually with ATP as an intermediary. The energy released from the first reaction allows for the formation of ATP from ADP and P. The second reaction is then driven by the hydrolysis (breakdown) of ATP, which releases energy.

So the answer to your question is: In a coupled reaction, ATP is first used to store energy from a catabolic reaction and then used to release energy for an anabolic reaction.


Help reading gene markers I'm sorry if "gene markers" is not the correct word. An edit could be appreciated but I don't study in an English speaking country unfortunately.

Question overview:

In a family, there is a genetic, dominant disease. The father and a son is sick.
A gene marker analysis is performed with markers close to the assumed mutated gene on chromosome 11.

Marker D11S4088

Marker D11S1344

How do I read these and "What sort of markers are these"? I'm not sure what is going on here and I'm not sure what to search either due to language problems.

Thanks!

Just googling, they are SSLPs.  You do PCR, and the different alleles make different length amplicons.  Looks like there is some kind of artifact that causes some of the amplicons to have peaks that look 2, or 4, or 6 letters shorter than the true length.

So for the top marker, the 211 bp long allele is linked to the disease, and for the other one, the 118 bp allele is linked to the disease.


Insect ID Montreal, Qc Canada I found this bug in my kitchen, in front of my oven.
It has wings and moves quite slowly on the ground.

I can provide additional pictures if required.

Can somebody tell me what it is?

I have found an article on a local website that seems to say this is a carpet beetle even though it's written bedbug right bellow it.

http://www.exterminationmontrealbedbugs.com/insects/

Dermestidae, Reesa vespulae; wasp nest dermestid
http://pestcontrolcanada.com/5965-2/


Why is beta thalassemia major not lethal while alpha thalassemia with loss of all 4 genes lethal? So why is beta thalassemia major with two B0 alleles not fatal in utero (despite the hemoglobin not having any B chains), while alpha thalassemia with deletion of all 4 genes encoding for the alpha chain fatal? Is the alpha chain more important than the beta chain?

This has to do with the fact that fetal hemoglobin (HbF) isn't made of the same chains as adult hemoglobin. The latter comes with 2 alpha chains and 2 beta chains while the main fetal hemoglobin is made of 2 alpha chains and 2 gamma chains. Hence any disease affecting the quality or quantity of beta chains won't have nearly as much impact on a fetus as it does on an adult.

Reference: https://www.uptodate.com/contents/fetal-hemoglobin-hemoglobin-f-in-health-and-disease


How to get a list of kinases that phosphorylated a particular protein? I am analysing the protein SF2 (also named as SRSF1). In the database, it is shown that this protein is often phosphorylated at the 189th tyrosine residue.

I want to know which proteins could have phosphorylated the protein at this site. Is there a way to figure this out using databases? What about getting a list of proteins that phosphorylated SF2 at any site?

I use PhosphoSitePlus too. I use it in combination with ELM as it finds linear motifs and generally gives a good generic candidate.

The literature if not. Checking all close homologues sometimes pays off.

Checking protein protein iteraction databases such as StringDB or IntAct may help too, but that gets very iffy —XL-MS (a smoking gun) is rare and does not pick up low concentration enzymes like kinases.

(A note: this question ought to have been asked in bioinformatics SO)


Will gene mutations give rise to a protein that is shorter than the full length protein? What is the relationship between deletion or insertion of nucleotide in the gene sequence and the protein's length that is coded out from the mutated gene?

It depends on the nature of the insertion or deletion.

Many mutations are point mutations, where one single nucleotide is changed:

ATGACTACGCTATTCAGT
M  T  T  L  F  S

ATGTCTACGCTATTCAGT
M  S  T  L  F  S

Notice that changing the fourth A to a T caused a T->S change in the final protein, and didn't change its length. However, an insertion/deletion is different. Starting with this sequence:

ATGTCTATTGACGCTATTCAG
M  S  I  D  A  I  Q

Let's have an insertion, an A after the A in position 7:

ATGTCTAATTGACGCTATTCAG
M  S  N  STOP

Notice we now have a stop codon (TGA). This means the protein will be truncated, and will be much smaller. That isn't always the case. Rather than adding an A at position 7, let's add it after position 9:

ATGTCTATTAGACGCTATTCA
M  S  I  R  R  Y  S

The protein is about the same length, but the AAs are completely different than the original version after the insertion:

M  S  I  D  A  I  Q
M  S  I  R  R  Y  S

This is called a frameshift mutation. Biologically, these mutations are harmful because they change all the amino acids after the mutation, the protein is often not functional and can end up being different sizes (if a stop codon is now in frame or out of frame) and the protein can even end up being unstable and rapidly degraded.

So, to answer your question about the length of the protein, it'll increase/decrease by one AA every time 3 nucleotides are added/removed, but can increase or decrease drastically if a stop codon is added or removed by a frameshift mutation.


Risk of autosomal dominant disorder What can you conclude about the risk (with each pregnancy) that a couple could have a child affected with an autosomal dominant disorder if...

One parent is affected (heterozygous) and the other parent is unaffected.

I did a punnet square and concluded it was 50 percent because half were Aa and half were aa.

But a classmate told me to line up Aa and aa and conclude that there is only a 25 percent chance that a child is affected because there is only one capital or dominant A and three are "a".  Which do I do?

Your classmate is forgetting that the child will have to inherit one allele (A or a) from each parent. Suppose the dad is affected---so his genotype is Aa. He has a 50% chance of passing the A on to his kid. That means the kid has a 50% chance of being affected.

If your classmate was right, then it would be possible for both the kid's alleles to come from just one parent. You have to pick one allele from each parent.


How to get the correct RefSeq Protein transcript for a given RefSeq Nucleotide transcript? How to get versioned Protein Accession Number for a Refseq Accession Number?

I have some versioned RefSeq Accession numbers and I would like to know their corresponding Protein Accession Numbers.

According to the RefSeqFAQ   http://www.ncbi.nlm.nih.gov/books/NBK50679/#RefSeqFAQ.what_causes_the_version_number there is not a 1-to-1 mapping between these numbers.

  Also, nucleotide (NM_, XM_) and protein (NP_, XP) records for the same
  transcript may not have the same version number after an update. For
  example, an update to the 5’ UTR of a RefSeq nucleotide record would cause a version number change for the updated nucleotide record but not for the corresponding protein record. Conversely, a change in the annotated start site of the coding sequence without a change in the underlying nucleotide sequence would cause a version number update for the NP_ but not for the NM_.

I have tried this, but it gives me a huge

>>> from Bio import Entrez
>>> Entrez.email='email@example.com'
>>> f = file('entrez_NM_005529.5.txt', 'w')
>>> print >>f,  Entrez.efetch(
...     db="protein",id="NM_005529.5", rettype="native", retmode="xml").read()

The XML results contain the Protein Acc No, <Textseq-id_accession>NP_005520</Textseq-id_accession> but there is no version specified. Is there a simple way to get obtain the matching protein transcript version?

There is another simple way for human sequences.

Go to RefSeq FTP and download the LRG_RefSeqGene file. This file contains updated mappings between the gene, mRNA and protein sequences (latest versions).

From README:

    Tab-delimited file reporting, for each Gene, the accession.version
      of the genomic and RNA and protein RefSeqs the RefSeqGene/LRG
      project treats as reference standards.

    The columns are:
      NCBI taxonomy id (all 9606)
      GeneID
      Symbol of the gene (official from HGNC when available)
      Accession.version of the standard RefSeq
      Term describing the RefSeq
         RefSeqGene              genomic sequence
         Ref Std, nucleotide     RNA sequence
         Ref Std, protein        protein sequence

      The LRG equivalent of the RefSeq standard
         LRG:                    genomic sequence
         t1                      locations for transcript 1
         p1                      CDS from transcript 1

         NOTE: t values can be > 1 ,  the integer assigned to t
               is matched by the integer assigned to p

Some few lines from the file:

9606    3329    HSPD1   NG_008915.1     NM_199440.1     NP_955472.1     reference standard
9606    3329    HSPD1   NG_008915.1     NM_002156.4     NP_002147.2     aligned: Selected
9606    3336    HSPE1   NG_008914.1     NM_002157.2     NP_002148.1     reference standard
9606    3339    HSPG2   NG_016740.1     NM_005529.6     NP_005520.4     reference standard

It is not that easy for other organisms. For them, you should either parse the mRNA page to find the RefSeq protein id or go to their specific designated databases (such as FlyBase for Drosophila) and obtain information on the gene to protein mapping.

For obtaining RefSeq records from NCBI using parsing you should first obtain the GI accession number corresponding to the mRNA.

Example: NM_007393 (mouse beta-actin)

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=NM_007393

which would give the GI accession number: 930945786.

Then fetch the protein GI using this accession number:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nucleotide&db=protein&id=930945786

which gives the GI accession number: 6671509

Finally get the RefSeq id (if available) corresponding to this GI accession. You can download the feature table and look for the RefSeq i.d:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nucleotide&db=protein&id=930945786&rettype=ft

For more information on how to use Entrez E-Utilities see here.


What insect is this? I saw it in my house in Kolkata on 2 April 2018, at 8:00 p.m I saw this insect in my house in Kolkata (India) on 2 April, 2018 after a storm at around 8:00 p.m.  I would like to know what insect it is.  Thanks in advance.

I would concur with user22542 --> order Diptera: family Dolichopodidae

Supporting evidence outside of wikipedia is on an Australian website. http://www.bowerbird.org.au/observations/35021

I don't suggest them to be the same species, however potentially related as they seem to live in grassy places across the globe.


How high is the energy yield of photovoltaics compared to photosynthesis? I'm not an expert in plant physiology. I was wondering if, per square centimeter, leaves are converting more or less energy than photovoltaic systems. Can this be estimated? How?

According to wikipedia, plants typically convert around 5% of the energy of the sunlight that hit the leaves into energy usable by the plant.  Sugarcane seems to be the best, it converts up to 8% of the energy into actual biomass.

The best solar panels on the market, according to the Independent, convert 21% of energy from sunlight into usable electricity.  Experimental prototypes do much better, and there are some that get over 40%.  Wikipedia has a nice graph of the most efficient solar cell prototypes.


Is there a normal human melatonin concentration to light level curve? I'm looking for a graph or a curve that would show the typical concentration of melatonin in blood or saliva for humans over 24 hours. It would be good to know the photoperiod for the same human as well.

I know that melatonin release is inhibited by blue light, perceived through the retina, with melanopsin being the photopigment that signals suprachiasmic nucleus to suppress melatonin release. This is why it would be great to see melatonin data alongside light exposure data.

Thank you for any hints on where I can find such information!

Found a few samples here: http://ars.els-cdn.com/content/image/1-s2.0-S0024320503008142-gr2.gif this shows the nocturnal melatonin peak, which is apparently very important for well being


mutant down but not out I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from WT with siRNA or other molecular methods without virus vectors? I'm not interested in a medillian solution but an inducible molecular way.
Thank you

I would like to generate a heterozygous Sod2+/- like they do in this paper in mice and possibly human:
http://physiolgenomics.physiology.org/content/16/1/29.full.pdf+html

Antisense, promoter replacement and when possible tetracycline allows one to titrate of gene expression
http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-321-9_20#


Double use of ATP in relaxing myosin & active transportation of calcium? Is the ATP molecule which is bound to the myosin head for relaxation of the muscle (i.e., to break the cross bridge) also utilized for active transport of calcium to the sarcoplasmic reticulum during muscle relaxation?

ATP is used (hydrolyzed) by ion pumps to transport ions such as calcium against their concentration gradient.

Molecular motors (such as myosin and kinesin) also couple ATP hydrolysis with movement.

However both these processes are separate and just because calcium flux changes happen during muscle contraction doesn't mean that it is the same ATP that drives some kind of a bifuntional enzyme to perform both tasks.

Moreover calcium is released during the contraction phase from the sarcoplasmic reticulum (SR); pumping back the calcium to the SR happens during the repolarization (there is no myosin movement at this stage).


How long does a spiking signal last? It is surprisingly hard to find information about the timing of neurons, in particular how long an action potential can contribute to the summation of a neuron. Is it on the order of milliseconds or rather seconds, i.e. for a neuron to fire, do many of the presynaptic neurons fire about at the same time?

Effective integration time of a typical neuron is in the order of 10-100 ms. You might want to look into this classic paper (read it with a critical mindset):

Shadlen, M. N. and Newsome, W. T. (1994). Noise, neural codes and cortical organization. Curr. Opin. Neurobiol., 4:569-579.

Or some biophysics book like:

Biophysics of Computation by Christof Koch


Can ovulation and menstruation occur simultaneously? Is that possible that ovulation happens in the time of actual menstrual haemorrhage in human females - let say in a case that woman has 21 day cycle and her menstrual period is 7 days?

If yes, does it means that in this particular case the woman has lower chances to conceive?

Ovulation and menstruation don’t happen in normally cycling women at the same time. A basic outline of the hormonal cycle that triggers these events will make this clear.

Proliferative (a.k.a follicular*) phase
Beginning after menses (when the endometrium is thinned), the hypothalamus produces GnRH which stimulates the anterior pituitary to produce LH and FSH. These in turn stimulate ovarian follicles to develop. A dominant follicle produces estradiol which causes the endometrium to thicken (proliferate).

At a certain level of estrogen (actually estrogen/progesterone ratio), the feedback on the hypothalamus flips from a negative to a positive feedback loop. Thus, there is a GnRH followed by a LH surge. The latter triggers ovulation. Note that at this time the endometrium is stable due to relatively high estrogen levels.

Secretory (a.k.a. luteal*) phase
After ovulation, the high levels of LH trigger formation of a corpus luteum from the tissues left behind after ovulation. The corpus luteum makes progesterone. This hormone triggers a change in the endometrium from a proliferative to a secretory state. Progesterone also provides negative feedback to the hypothalamus and anterior pituitary, maintaining low levels of GnRH, LH, and FSH, so no new dominant follicles develop at this time.

If pregnancy does not occur, the corpus luteum will eventually (10-12 days) degenerate and stop producing progesterone. It is this abrupt drop in progesterone that triggers the sloughing of the endometrial lining. You can see these hormone shifts in an illustration like this:

The decline of the corpus luteum is correlated with a decline in serum levels of ovarian hormones including progesterone, estradiol, and inhibin A. Release from negative feedback provided by these hormones at the level of the hypothalamus and pituitary permits FSH to rise, and the cycle begins again.

You should now be able to see that:

Around the time of ovulation, the uterine lining is not fully developed and is stable due to the hormonal milieu. Menstruation does not occur.
Around the time of menstruation, FSH and LH are suppressed in a way that is not conducive to ovulation.

In theory, yes, of course there would be a lower chance of initiating a viable pregnancy (implantation rather than conception is the most obvious problem) were the endometrial lining to be unstable at the time of ovulation. The problem of luteal phase deficiency is along these lines. In this condition, the corpus luteum does not produce adequate progesterone during the luteal phase to develop the endometrial lining in such a way as to support a healthy pregnancy. However, ovulation and menstruation are still time-separated events for the reasons outlined above.

*Note that the first term is with respect to the endometrium; the second is with respect to the ovary.

Abbreviations:

GnRH - Gonadotropin Releasing Hormone; LH - Luteinizing Hormone; FSH - Follicule Stimulating Hormone

References

1. Anatomy & Physiology, Connexions Web site. Illustration is also from here.

2. Jerome Strauss, Robert Barbieri. Yen & Jaffe's Reproductive Endocrinology. September,  2013. Saunders.


Are alleles equally sized? If alleles occur at the same locus on a chromosome, does that mean they are of the same size? I was under the impression that they were, but I saw a gel electrophoresis testing different alleles of the same gene and saw them separate. I don’t understand how they could separate if they are of the same size, but if they aren’t, then how can they be housed in the exact same locus?

In general, alleles don't have to be the same size. Two major examples which come to mind are the Huntingtin gene and FMR1.

Huntingtin is the causative gene of Huntington's disease. In people with Huntington's, a sequence of three nucleotides is repeated. The number of repeats varies, from a low of 9 in unaffected individuals, to more than 60 in severely affected ones. So depending on how many repeats you have, each of your Huntingtin alleles may have a different nucleotide size.

FMR1 is the causitive agent of Fragile X syndrome. Like Huntingtons, the gene varies in the number of trinucleotide repeats, but for FMR1, affected individuals can have over 1000 repeasts, meaning an extra 3 kilobases of genetic material versus the alleles of an unaffected individual.

Other genetic disorders are also related to the difference in allele size. You can have a deletion of a region of DNA (or an insertion) which is normally silent (recessive). The normal-length allele compensates for the defective allele, but the differently-sized disease allele is still present in the population, and counts as an allele of the gene.

It's not just disease-prone alleles which exhibit length polymorphism. A number of other genes will show variation on both the DNA and on the protein level. If the insertion/deletion is a multiple of three nucleotides and occurs in a loop region of the protein or on an intrinsically disordered domain, the insertion has a reasonable chance of minimal structural effect on the expressed protein. For one (completely arbitrary) example, PER3 has two major length variants in the population, with a 54 base pair difference between the two. Different populations have vastly different prevalence for each, with a range of 20-90% for the shorter version.

One thing to keep in mind is that "locus" points are just a human convention to help us map DNA. To the cell, DNA is just a single long molecule. (Or multiple molecules, for different chromosomes.) There isn't any labels for absolute position in the cell, so inserting or deleting a chunk of DNA mainly affects just the local environment. There isn't any sort of long-range indexing that gets messed up by the insertion.


Reproductive isolation causing evolution My course book says about reproductive isolation that it does not allow the interbreeding among the individuals of different species. It also says that it is a cause of evolution.

How is this cause of evolution?

Reproductive isolation isn't exactly a cause of evolution, but rather a cause of speciation. Reproductive isolation allows for two cohorts of one species to be reproductively separated. In this case, evolution via random mutation or mechanisms like genetic drift allows for the differentiation of the two groups, up to the point that the two cohorts and their respective gene pools have evolved to be completely different species.

Truly defining a species is still debatable (via the Biological species definition, Morphological, etc) but reproductive isolation is definitely a mechanism involved in speciation.


What is a "mechanistic study"? I believe a "mechanistic study" means a study where a medicinal product is being used but the purpose of the study is to investigate the patient or disease, not the medicinal product.

How does this differ from any other type of study?  What is the purpose of this study?  Why would we not be interested in the medicinal product?

Please provide a very simple example that a non-scientist could understand.

A mechanistic study aims to uncover a mechanism. It can be a mechanism of the disease (exactly how does the disease do damage to the body), or a mechanism of a drug (exactly how does the drug prevent or repair the damage) that is being investigated.

Understanding mechanism, be it mechanism of disease or mechanism of the drug, is very important toward targeted improvements of treatments, as opposed to trying lots and lots of compounds, hoping that someday we'll find one that's better.

Non-mechanistic studies involving drugs aim to show that the drug provides a clinically relevant health benefit over competing treatments, or to determine the safe dosage of a drug. At that point, the mechanism of action of a drug is known to a reasonably large extent.

In short, there are many different things that need to be known for drugs to reach the market. Mechanism is one of them.


What is the purpose of the incus? The three bones in the middle ear -- the malleus, the incus, and the stapes-- play a role in transmitting sound waves to the inner ear (the cochlea). I understand that the malleus is the bone closest to the tympanic membrane (and therefore the primary receiver of information) and I understand that the stapes is responsible for transmitting the information to the cochlea... so why even have an incus bone?

The incus is there in humans because it is there in our mammalian ancestors, and it is there in our ancestors because the mammalian three-bone ossicle system was inherited from early amniotes.

The synapsid ancestors of mammals had the ancestral jaw articulation between the articular (later called malleus) and quadrate (later called incus). This is the bottom image below. There are fossil species with a transitional form in which there are two jaw joints (e.g., Pachygenelus). In extant mammals, the jaw joint lies between the dentary and squamosal (part of the temporal bone), while the old articular and quadrate are part of the ossicle system (top image below).

There is a lot of material on the web about this:

http://crompton.oeb.harvard.edu/publications/transformation-quadrate-incus-through-transition-nonmammalian-cynodonts
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552421/
http://www.zoology.ubc.ca/~millen/vertebrate/bio204_labs/Lab_3__Skull.html

So in short, the incus is there because there was no other way for the mammalian ear to evolve from the ancestral system. It doesn't have a purpose per se, except that it's always (at least going back to jawed fishes) been attached to the stapes and articular (malleus).


What can give rocket salad (Eruca Sativa) a fish smell? I bought an 'already washed' plastic tray of rocket salad (arugula, or Eruca Sativa) enclosed in a sealed plastic bag. It has been kept in the refrigerator for four days. When I opened it, some 12 days before the "best before" date,  I noticed a strong smell of fish.

I am a regular consumer of this sort of vegetable, I also have some in my garden, so I know how it smells. Yet, by searching on the net I realized that other people have lamented this fish smell in their pre-washed arugula salads.

I am wondering now where does this fish odor come from? Can it come from the plant itself, or is it a side-effect of industrial washing? What exactly is giving this smell? Bacteria, molds, natural decomposition of the plant's essences, or something else?

(Following my instinct I threw the salad away, but I did taste a few leaves and it did not taste 'bad' or 'foul'. It was just the smell that was off.)

Complete guess - the arugula could contain or be decomposing into amine-containing compounds (known to have a fishy smell).

https://en.wikipedia.org/wiki/Amine#Physical_properties


What is the relationship between Homocysteine and Norepinephrine metabolic cycles? I've been researching neuromodulators and have taken a look at the Norepinephrine/Noradrenaline  system.

The diagram of biosynthesis of Norepinephrine is presented in the wikipedia article:

Catecholamines_biosynthesis

The diagram appears to state that Dopamine gets converted to Norepinephrine , which gets converted to Epinephrine, and as a side effect, Homocysteine cycle gets advanced too (or is it involved?).

This article describes the homocysteine biosynthesis

I would like to understand what this means when two biosynthesis cycles are related like that. If I envision two cycles as connected gears, then turning one would turn the other, and if one is malfunctioning, so will the other. Is this a correct analogy?

What are the implications of the Homocysteine and Norepinephrine cycles touching each other? As far as I understand, Epinephrine(Adrenaline) is a stress related hormone, does this mean that stress also results in elevating the levels of Homocysteine ?

Thank you for your clarification!

Norepinephrine is converted to epinephrine by phenylethanolamine N-methyltransferase (PNMT). In mammals PNMT is just one member of a large family of methyltransferases which use S-adenosylmethionine (AdoMet) as a cofactor to provide a methyl group. These methyltransferases are involved in a very diverse set of pathways including the synthesis of nucleic acids and of certain phospholipids, as well as the methylation of DNA and histones.

As you point out, these reactions generate homocysteine via S-adenosylhomocysteine. However, because AdoMet is such a critically important cofactor it is thought that cellular levels are tightly regulated. As part of this regulation, homocysteine is re-methylated to methionine via two different routes requiring either methionine synthase or betaine-homocysteine methyltransferase. Methionine synthase obtains the required methyl group from 5-methyltetrahydrofolate in a vitamin B12 (actually methylcobalamin)-dependent reaction. This latter reaction links the AdoMet-based methyl transfer system to the other part of the cellular one-carbon economy, the folate pool. This is why vitamin B12 deficiency leads to hyperhomocysteinemia.

This Figure is reproduced from Luka et al. (2009) Glycine N-methyltransferase and regulation of S-adenosylmethionine levels. J. Biol. Chem. 284:22507–22511. I show it here just to illustrate the point that there are, in fact, many gears interacting in this system. The minireview is interesting and I recommend it to you.

In conclusion, my answer to your question is that it is unlikely that stress leads to elevated levels of homocysteine as long as all of the relevant regulatory machinery is functioning correctly. If there is a problem with homocysteine recycling then yes, homocysteine levels would rise, but given that there so many AdoMet-dependent methylation reactions it is unclear how big a contribution PNMT would make to the overall homocysteine load.


Question about equilibrium potential formula My biology book says, that the equilibrium potential for an ion with a charge of +1 is: $$E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)$$

Where does the 62 mV come from? How was this value derived? I understand that it's the equilibrium voltage of $\ce{Na+}$.

That quasi-travesty is the Nernst equation in $\log_{10}$ for a positive monovalent ion at physiological temperatures (37 degrees celsius), but they've hidden all that from you. Shame on them.

The canonical form of the Nernst equation, for an ion $S$ is

$$
E_{S} = \frac{RT}{z_{S}F}\ln{\frac{[S]_{out}}{[S]_{in}}}
$$

where $R$ is the gas constant, $T$ is temperature expressed in Kelvin, $F$ is Faraday's constant, and $z_S$ is the charge of ion $S$. This is the actually useful form of the equation that can be used for any ion for any temperature.

The Nernst equation is a limiting case of the Goldman-Hodgkin-Katz equation for a single ion. The Nernst equation is useful for directly determining the equilibrium potential of a single ionic species. The GHK equation is used for determining the reversal potential of a membrane or channel in multi-ion cases.

Note that the terms "reversal potential" and "equilibrium potential" are not synonymous, except in the case of a single ion system. The reversal potential is where the direction of current switches. An equilibrium is when net ion flux is zero (although, in a living cell, it is more appropriate to call even this situation a steady state). If membrane were only permeable to one ion, the reversal potential will be at the equilibrium potential (given by Nernst) for that single ion. However, when there are several permeant ions, usually none of the ions will be in equilibrium at the reversal potential--that is, all the ions will have a measurable flux across the membrane even though the sum of those fluxes (weighted by permeabilities) is zero at the reversal potential.

Converting natural log to log base 10, you can use the identity $\log_b{a} = \frac{\log_{10}{a}}{\log_{10}{b}}$, which gives

$$
E_{S} = \frac{1}{\log_{10}{e}} \cdot \frac{RT}{z_{S}F}\log_{10}{\frac{[S]_{out}}{[S]_{in}}}
$$

In the case of sodium ions (Na+) at 37 degrees (physiological temperature), $T$ is 310 and $z_S$ is +1. Substituting in these values, we have

$$
E_{S} = 2.303 \cdot \frac{(8.3145) (310)}{(+1) (96485) }\log_{10}{\frac{[S]_{out}}{[S]_{in}}} \\
E_{S} = 61.5 \text{ mV} \cdot\log_{10}{\frac{[S]_{out}}{[S]_{in}}}
$$

YAK uses a less common form of the Nernst equation in membrane physiology which uses the Boltzmann constant directly and deals with elementary charges instead of moles ($R = N_A k_B$). It is a wonderful exercise to derive the Nernst equation from the Boltzmann equation,

$$
\frac{p_2}{p_1} = \exp{(-\frac{u_2 - u_1}{k_BT})}
$$

where $p_i$ is the probability of a particle being in state $i$, and $u_i$ is the energy of state $i$. All it takes is some rearranging and keeping careful track of the units.


What is protein secondary structure? Could someone please clarify what is protein secondary structure:
https://en.wikipedia.org/wiki/Protein_secondary_structure

I believe I understand the primary structure, I am not sure what's the difference between secondary and tertiary structure. Tertiary structure seems to be 3d structure of a polypeptide but I am not at all clear about the secondary structure.

Proteins are made up of long chains of amino acids covalently joined together. The order of amino acids is the primary structure of a protein. In physiologic conditions, these long chains of amino acids fold into three dimensional shapes. The terms secondary and tertiary structure are used to refer to specific aspects of the three dimensional shape.
tl;dr what's the difference?
Both secondary and tertiary structure refer to the three-dimensional shape of a protein. Secondary structure is the regular repeating patterns, generally stabilized by hydrogen bonds between the NH and CO groups of the peptide backbone. Tertiary structure can be thought of as the way secondary structural elements fold together to create the overall shape of the protein.
Secondary structure
Secondary structure refers to regular repeating patterns stabilized by hydrogen bonding between the NH and CO groups of the peptide bond. Typically textbooks will focus on the $\alpha$-helix and the $\beta$-sheet.
Berg biochemistry has some useful diagrams demonstrating these secondary structures. The first is an $\alpha$-helix. The side-chains are represented by green balls here. Notice the orientation of the NH and CO groups, which stabilize this structure:

The $\beta$-sheet forms a very different secondary structure, but it's also stabilized by hydrogen bonding between NH and CO groups of the peptide bond.

Tertiary structure
Tertiary structure is the larger three-dimensional structure of a protein in its environment. It can be useful to think of tertiary structure as the way different secondary structural elements fold together to form the full, active protein. Notice in this figure, also from Berg, the way the elements of secondary structure (the $\alpha$-helices) fold into an overall three dimensional shape that can nicely cradle the heme group.


On which amino-acids residue is the SDS acting on? I would like to know exactly what is the mechanisme of the SDS, and I would like to know on which amino-acids residue the SDS is acting on.

Can you help me please ?

Thank you in advance !

If your talking about Sodium Dodecyl Sulfate(a detergent) it has a two main functions:

(1) It disrupts all non-covalents bonds in proteins i.e hydrogen bonds from the main chain, or hydrogen bonds between residues which are dependent on protein shape.

(2) It coats the proteins with a negative charge which is useful for laboratory techniques such as gel electrophoresis.

Your question states "what amino acid residues does it act on?". You can be safe to assume that the SDS will coat the entire protein. About 0.1% SDS solution is enough to sature the polypetide chains of protein molcules with about one SDS molecule per two amino acid residues.


ATP to disassembly of nucleotide ratio DNA Helicase, the enzyme that is responsible for tearing apart the strands before DNA replication, requires ATP to rip apart nucleotides. I have asked this question to several professors and they couldn't give me a clear answer. My question: What is the ATP:nucleotide bond breakage ratio? In other words, how many nucleotide  bonds can be broken from a single ATP through helicase.

The answer to this is perhaps not as simple as you may think, in part because there are many different helicases in the human body. There is also some passive activity of a helicase that does not require ATP.

It is not clear exactly whether ATP is just involved in the translocation of the helicase or the actual unwinding.

For a RecQ helicase in E. coli, one study found that "The determined tight mechanochemical coupling of 1.1 ± 0.2 ATP consumed per nucleotide traveled indicates an inchworm-type mechanism." For more information see Sarlós et al. (2012).

Another study (Donmez and Patel, 2008) notes that "As compared with non-ring-shaped helicases such as PcrA (Dillingham et al, 2000) and UvrD (Tomko et al, 2007) that move on an average 1 nt for every ATP hydrolysed, the ring-shaped T7 helicase is three times more fuel efficient." This shows how there can be quite a bit of variation.

Bottom line - you can count on your fingers the number of nucleotides unwound by a helicase per ATP.


Can I grow unlimited stem cells from limited embryonic stem cells? If I theoretically extract a few embryonic stem cells from the embryo and cultured in vitro with enough nutrient to grow more cells. How many maximum of stem cells can I get?  Do I need to add any compound to inhibit the differentiation progress?

Like I said in my comment stem cell culture is a very difficult process, and while people have been doing research on this for about two decades there is still a lot we don't know about stem cells. Additionally working with (human) stem cells can cause a lot of ethic problems and is therefore under strict regulations in most countries.

In principle stem cells will continue to divide until they get a signal o differentiate. In normal embryo development some cells start producing these signals at different stages, and the complete interaction of different signals allows the formation of the organism.
In cell culture one has to make sure that exactly the right signals (which are mostly growth factors) are present in the culture medium, since stem cells can easily die if they do not get any signals.

I don't have any detailed experience or knowledge in working stem cells, but a quick literature search turned up these two papers, which should provide you a good starting point. There's likely a lot more research out there you can look for.


Does the term "upper extremity" include hands? I see on http://en.wikipedia.org/wiki/Upper_limb that the term "upper extremity" seem to include hands. However, in many hospitals, there is a "Hand & Upper Extremity Service", which would tend to indicate that the term "upper extremity" does not include hands.

Does the term "upper extremity" include hands?

As far as I know, and the same is written on Farlex Free Dictionary, the upper extremity or superior limb includes:

the shoulder girdle
the arm
the forearm
the hand

Again, on this Dartmouth Medical School page, the upper limb bones are described and the article includes the bones of the hand.

So, anatomically speaking, the upper limb includes the hand.