Why do redheads tend to sunburn more easily? Reading Marion Roach's book on redheads she mentions visiting Rees lab where he shines UV light on her skin. Apparently this is an ongoing experiment of his regarding the propensity of redheads to sunburn more easily, but the book doesn't adequately explain why.

Why do redheads sunburn more easily?

You should have a look at wikipedia > melanin.

  Melanin is a broad term for a group of natural pigments found in most organisms. [..] Melanin is an effective absorber of light; the pigment is able to dissipate over 99.9% of absorbed UV radiation.1 Because of this property, melanin is thought to protect skin cells from UVB radiation damage, reducing the risk of cancer. Furthermore, though exposure to UV radiation is associated with increased risk of malignant melanoma, a cancer of the melanocytes, studies have shown a lower incidence for skin cancer in individuals with more concentrated melanin, i.e. darker skin tone. Nonetheless, the relationship between skin pigmentation and photoprotection is still being clarified.

Most of the variation in skin color among humans is caused by differential levels of melanism. People with red hair have a low level of melanism (almost by definition) and therefore suffers more from sunburn than people with more pigmented skin.


Mammalian advantage at filling large-animal niches after the KT extinction? Larger animals are more prone to extinction due in part to smaller numbers. The asteroid that impacted 65 million years ago killed off the larger mammals and dinosaurs but spared some of the smaller ones. The smaller niches were refilled by both mammals and Theropods (as birds), but there is a paucity of large bird species. Is there a reason mammals were better at refilling these large-animal niches?

Birds have to feed and guard there eggs for 30-40 days, against the elements and against predators, whereas mammals can bear larger offspring in exposed environments. That's especially an advantage for swimming mammal megafauna, because the birds can't lay eggs in water, and also for predator-intensive environments and for forests.
Birds lack hands and teeth and four sets of claws for manipulating leaves and prey and defense. Birds can only have a hooked bill to peel up prey, and less sophisticated molars for herbivory. The sheer range of mammal teeth shapes appears to be an advantage compared to beaks.
Quadrupeds have some advantage for running and turning without falling over, whereas birds mostly have long necks which are a bit of an easy target for horns and claws and teeth.
It's interesting to think about a pack of wolves attacking an ostritch, and a pack of predator ostritches attacking a springbok... The wolves and the springbok have a wider range of attacks and defenses to use for survival.


Do we find protein not of cellular origin in nature? I read once that we have two sources for proteins:

Protein that is made in cells
Protein that is made in labs

However, based on Miller–Urey experiment, it's argued that amino acids can be made from initial Earth's condition, and from this link, it seems that protein-first world is a hypothesis.
Yet if we accept that proteins could be made before cells, then the process that made proteins in the first place is still out there. This means that we should be able to find proteins outside cells or labs in nature.
Do we find protein not of cellular origin in nature?

On our planet, there is such an incredibly massive amount of protein creation by biological organisms (as well as smaller peptide constructs) that it would be essentially impossible to identify any that was created by a natural non-biological process.
Moreover, now that there is life, any location with the right conditions for non-biological creation of protein would likely also be a good place for modern microbes  to take advantage of those same resources to grow themselves, diverting the necessary inputs or quickly eating the outputs.
It is for this reason that we search for precursors of life in space, and have long ago found the basic building blocks. This is also why probes to other planets are carefully sterilized, because otherwise we will never know if life found on Mars is just hardy colonist organisms transplanted from Earth.
To the best of my knowledge, however, no non-Earth molecule has yet been found that has the full complexity of a protein, as opposed to just isolated amino acids.


If rabies always kills its hosts, must there be some animal that is an asymptomatic carrier? I searched a lot on the Internet, but I am not clear about the spread of the rabies virus. As I understand, rabies kills any animal it infects—cats, dogs, foxes, bats, humans. If it kills all of its hosts, then where does it stay?

So, if all rabies-infected animals die, but in order to transmit the virus, every rabid animal has to bite some other animal or have rabies without symptoms, must there be some animal that is an asymptomatic carrier?

This is an interesting question, and it's been subject to a fair amount of research. From an epidemiological perspective, most rabies outbreaks have been studied in dogs. Among domestic dogs, the R0, or basic reproduction number, of rabies is usually quite low—estimated to be around 1.2 in rural sub-Saharan Africa, and <2 in most historically observed cases [1] (though a particularly bad epidemic in Osaka had an R0 of ~2.42 [2]). This implies that, among dogs, it's quite possible for rabies to spread faster than it kills its hosts, but can be entirely eliminated in dogs by mass vaccinations (see [1] and [2]).

But your question is still valid—if, say, the virus infects all the dogs in an area, and they all die, shouldn't rabies disappear from that area? There's some debate as to where the virus keeps hanging out. For one, there is some circumstantial evidence [3] that the fatality rate in dogs is not 100%, but actually closer to 85%. However, this doesn't necessarily explain the reemergence of epidemics, since for the virus to spread, it needs to get to the dog's saliva, by which point the dog is likely exhibiting lethal symptoms [4][5]. Dogs sometimes being asymptomatic carriers is a tempting explanation, but remains a "highly speculative" possibility [6].

To answer your question, let's look at a place where rabies outbreaks can cause severe economic losses—the livestock farms of South America and sub-Saharan Africa. Vampire bats, the hematophagic suckers, can bite over half of the animals in at-risk zones [7], which house some 70 million head of cattle. Since bats are very well-known sources of infectious disease—in fact, they're known to be hosts of 10 out of 11 recognized Lyssavirus species, including the rabies virus [8]—they've been a tempting explanation since 1911, when a bat-borne rabies outbreak in Brazil was first diagnosed [9]. [9] continues to say this:

  An idea that vampire bats may be asymptomatic rabies carriers, shedding the virus in their saliva for months, was popular during initial studies of vampire bat rabies (16). However, in a well-documented experimental study by Moreno and Baer (17), the disease in vampire bats was similar to rabies observed in other mammals. The bats that developed signs of disease and excreted the virus via saliva soon died, whereas those that survived the inoculation without clinical signs never excreted the virus or had it in the brain as demonstrated upon euthanasia. More recently, the asymptomatic excretion of RABV in the saliva of experimentally infected vampire bats, which survived the challenge during at least 2 years of observation, was documented again (18). Clearly, this phenomenon requires additional investigation.

This is all I've been able to find so far. If I had to bet, I'd put my money on bats being the asymptomatic carrier that you're looking for, with a solid $n=14$ paper to back it up [13]. However, when it comes to established scientific consensus—well, I'm not sure there is one.


What does this graph explain? I find this graph incredibly confusing. Is it saying that when there is a decreased affinity (of hemoglobin to oxygen, I think?), the partial pressure of oxygen increases with the same percent saturation of hemoglobin? What does that even mean if that's the case?

A graph is generally meant to be interpreted as y being a response to a change in x. This graph highlights that as the partial pressure of oxygen $P_{O2}$ increases, so does the percentage of hemoglobin that are saturated in oxygen. The relationship is not linear (unlike you seem to suggest) but is logistic.

The graph also highlights how three different level of affinity would affect the relationship between $P_{O2}$ and the fraction of hemoglobin that is saturated and highlights side consequences of such affinity variation.

Finally, with vertical dotted lines, the graph indicates what the $P_{O2}$ is in the lungs and in the other tissues.

  why a decreased affinity is a shift to the right and an increased affinity is a shift to the left?

Consider a single point in the x axis such as $P_{O2} = 40$ for example. If affinity is increased you would expect that the percent saturation of Hb would increase, right? This causes a shift of the left.


Can the immune system stop plasmodium from being active? Suppose a female Anopheles infected with Plasmodium bites someone and transmits Plasmodium to their body.

Can that person's immune system be strong enough that it can kill the Plasmodium before it starts entering into red blood cells to rupture them?

The experience of a former adviser of mine was that some people who are not taking anti-malarial medication can still resist infection with Plasmodium falciparum, one of the parasites responsible for malaria. The parasite's life cycle includes stages inside the Anopheles sp. mosquito, and they are transmitted to human host via the female mosquito's saliva when she bites to have a blood meal:

(from Wikimedia)

There is currently a great deal of research going on to understand the biology of the parasite and how it typically evades the immune system so well. Proteins expressed by the parasite can undergo antigenic variation, meaning that different forms are expressed at different stages of the life cycle, and just as the immune system may be forming a response to one version, it is down-regulated and another takes its place. This is one reason why making a vaccine has proved to be so difficult, as unlike the influenza virus, for example, a single strain of Plasmodium can alter its immunogenic appearance and escape antigen-specific immune responses.

While malaria is responsible for a high degree of morbidity - sickness - it is not necessarily fatal except in some cases, frequently when the victims are young, already ill, or are otherwise immune-compromised, or when the infection moves to the central nervous system and the brain. I can't speak from personal experience (fortunately!), but I have been told by numerous friends that malaria is something you want to avoid at all costs. The sickness can last for weeks in some cases, and apparently is quite debilitating at its worst. Brain fever can be deadly, and in many third-world countries and among the poor the lack of good medical care can lead to complications. There is the additional factor that the family has to care for the sick, and if the ill person is a wage-earner that can mean the difference between food on the table and going hungry.

So, your friends are not going to die (probably) if they don't take their tablets, but there is no reason not to take them unless you have strong side-effects, and in that case the doctor may be able to find you another one. Other common-sense measures include always sleeping with a bed net, putting screens in windows, covering exposed skin during active mosquito hours, wearing repellant if available, and eliminating places where standing water can collect, stagnate, and provide a breeding area for mosquitoes.


Are fatty acids and glycerol lipids? As far as I know, lipids are defined as biomolecules which are hydrophobic.

Triglycerides are composed of fatty acids and glycerol and are considered lipids but, are fatty acids alone or glycerol alone considered as lipids ?

From IUPAC Goldbook:

  A loosely defined term for substances of biological origin that are
  soluble in nonpolar solvents. They consist of saponifiable lipids,
  such as glycerides (fats and oils) and phospholipids, as well as
  nonsaponifiable lipids, principally steroids.

That means that lipid does not mean any hydrophobic molecule.
Lipids can be amphipathic as you already know about fatty acids.

Glycerol is not a lipid; neither is it hydrophobic. Glycerol, if to be classified into one of biomolecular classes, it would be that of monosaccharides (in the form of sugar alcohol like sorbitol and xylitol).


Can anyone identify this plant? We found this seemingly ornamental plant somewhere in the midwestern United States; does anyone know what it is?

It's fairly low to the ground.  Thanks!

From the general appearance, and from the opposite leaves (seen if you look carefully in the enlarged photo) I think this is Euoynmous europaeus (Wikipedia entry).  Specimens I've seen can grow like a ground cover, similar to your picture, but they also get shrubby/woody.  It is not native to the US.  We'd need more details/pictures to be sure, but I'm guessing from how you worded the question these might not be available.


What bug is this? Manchester, UK The creature appears to have a green body with 5 legs of the same size, and one longer than the rest. It moved this long leg around, and it looked like it was using it to sense it’s surroundings.

Location: Manchester, United Kingdom

That looks like what I would call a "daddy long legs", also known as harvestmen. These are arachnids of the order Opilones. There are some 30 species of harvestmen found in the UK. The webpage https://harvestmen.fscbiodiversity.uk/ has a very useful identification tool and based on it, I believe your photograph shows a Leiobunum sp. A:

Please visit the site itself for more details as it doesn't allow copying.


How does cold water help to overcome high fever? Why cold water helps to overcome from high fever in body? As fever is inside the body and we're applying cold water over the body!

Fever is triggered when pyrogens cause release of prostaglandin that acts on hypothalamus (which is the center of thermoregulation).

Fever assists in the healing process by:

enhancing phagocytosis
decreasing negative effects of endotoxins
stimulates proliferation of lymphocytes

Although is a good reaction, when the temperature gets too high it could determine negative effects, like convulsions at children. Brain damage appears when the temperature rises as much as 42 degrees Celsius, and most febrile conditions go up to 40.6 degrees Celsius.

So fever must be kept under control, and cold water helps lowering body temperature. Lowering the temperature will prevent negative effects of fever. Cold water is a symptomatic treatment for fever. Most important is to determine cause of fever and do an ethiological treatment.

Source: Wikipedia contributors, "Fever," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Fever&oldid=614212619 (accessed June 27, 2014).


What determines whether a regulatory T cell suppresses a naive T cell binding the same antigen-presenting cell? Here's what I learned about how regulatory T cells work:

There is a self-recognising naive T cell around.

A regulatory T cell that recognises the same self-antigen binds the same antigen-presenting cell as one of these T cells.

It suppresses activation of the naive T cell.

However, let's say the antigen-presenting cell is presenting foreign antigen on some of its MHC molecules. The naive T cell binds the  antigen and there happens to be a regulatory T cell nearby binding a self-antigen on the same antigen-presenting cell.

Does the regulatory T cell suppress the naive T cell? Is it just do with proximity, or do both cells have to bind the exact same antigen?

There a strong implication for a feedback loop mechanism for IL-2.

If a Treg is bound to an APC, it downregulates IL-2. It will then require exogenous IL-2 to be maintained. This IL-2 comes from a nearby naive T cell which is also binding a self-antigen. When that happens it upregulated IL-2. When it upregulates IL-2 and dumps it to all nearby cells which are then taken up by the nearby Treg. That causes Treg to continue its normal function by suppressing all nearby cells. It's an IL-2 negative feedback loop. It's all about proximity. What you are suggesting is not feasible since T cells recognise APC cells by MHC class II which are loaded by phagocytosis, meaning that the self-antigen has to be taken from outside of the cell. That means the APC would have to engulf two different self-antigens and displayed them on separate MHC class II which I guess is probably possible...

Check out this paper and figure 2:

http://www.cell.com/cell/pdf/S0092-8674(08)00624-7.pdf


Can acetylcholine leak away from the synapse and cause spasms? I am currently studying Pharmacology and a question came to mind. We know that Acetylcholine is used as a neurotransmitter in the neuromuscular junction, both Sympathetic as Parasympathetic, but as I understand, correct me if I am wrong, they don't interfere with each other because of their locations being physically separated. My question is, could somehow occur the incomplete absorption of Acetylcholine in the receptor of the organ, let's say for a Parasympathetic response and it "leaked" to a nearby muscle or even into a Sympathetic receptor and create a involuntary movement for example?

The enzyme responsible for the breakdown of acetylcholine (Ach), i.e., acetylcholinesterase, rapidly degrades, and inactivates Ach in the synaptic cleft after release. This process is particularly fast, as the synapse has to be cleared of neurotransmitter for a next action potential to occur (Čolović et al., 2013). So no, Ach does not leak away under physiologiocal conditions (Fig. 1).

In fact, common cholinesterase inhibitors that lead to Ach buildup by inhibiting its degradation, do not cause involuntary muscle twitches (spasms) as side effect. However, they do evoke muscle cramps, but that is easily explained by the increased retention of Ach in the synaptic cleft, leading to prolonged muscle contraction.

Fig. 1. Cholinesterase is active in the synaptic cleft. source: Health & Fitness.

Reference
- Čolović et al., Curr Neuropharmacol (2013); 11(3): 315–35


Why do fruit flies go so close to large reservoirs of liquid when they are likely to fall in due to surface tension? I had accidentally left out half a glass of red wine by the windowsill when I went to sleep. As anyone knows, if you do this with a window cracked you will get quite a few fruit flies near it in that time(region dependent obviously).

I noticed that many of them had simply fallen in as there was nearly nothing on the sides of the glass. What causes this behavior in a likely death scenario? Is it only exhibited during extreme hunger? Would this also not likely be an evolutionary cost or is that outweighed?

Although this is from  a popsci article, a biologist says that fruit flies can normally land on liquids and take off from them thereafter:

However, simply leaving a shot glass full of fruit-vinegar will only serve to feed the flies. The surface tension of the liquid [Ed. note: You remember surface tension, right?] allows fruit flies to land on liquids but not drown.
To break the surface tension you’ll need a tiny bit of dish soap. Dish soaps contain surfactants, which are molecules with a head that likes water, and a tail that doesn’t. Because of this property, the surfactants tend to situate at the interface of air and water, forming molecular “cliques” that disrupt the surface tension of water.
By putting a tiny bit of dish soap on your finger, and touching it to the surface of the vinegar in the shot glass, you will add enough surfactant to break the surface tension. (Add too much and the molecules in the dish soap will alert the fruit flies to danger).
Now fruit flies will unknowingly attempt to land on the vinegar for a little sip, then, before they can react, will break through the surface tension and begin to drown.

So if this is true/confirmed, then they do have enough of an evolutionary adaptation to the [surface tension of the] usual liquids of their diet. Just not to [trace] dish-soap contaminated liquids.
And I can confirm from a peer-reviewed paper that dish soap is indeed used even in science trapping experiments:

The cup trap (figured by Beers et al. 2010) is a 946-ml clear plastic
drinking cup with a clear plastic lid (Solo, Urbana,
IL), with four 1-cm-diameter holes in the sides of the
cup near the top. A drowning solution or drowning
solution plus bait was placed within the cup. Forty
grams of boric acid and 0.5-ml liquid dishwashing
soap (Palmolive Pure and Clean Spring Fresh Dishwashing Soap; Colgate-Palmolive Company, New York, NY, USA) were added to a batch of 3.8 l of
water or aqueous bait to make a drowning solution
used in all traps. Boric acid served to inhibit microbial
activity of baits and captured insects, and soap
reduced surface tension to promote capture and submersion of trapped insects. For both types of traps
and all treatments in all experiments, each trap contained either 300 ml of drowning solution or 300 ml
of bait in drowning solution

0.5ml of soap to 3.8l of water is very little, but that's all it takes to drown the little flies. It seems entirely plausible to me to have this level of trace contamination on glasses that have been dishwashed.
And as a complementary survival mechanism, fruit flies can apparently survive 12 hours of drowning at room temperature (or more in lower temperature):

Flies submerged at 23°C did not survive after a submersion time of 12 h whereas flies submerged at 3°C survived up to 72 h of submersion.

@Frieke may be on to something, namely that ethanol lowers the surface tension of the solution (with water) by itself, significantly. At 20-25 degrees C, pure water has a tension of about 72 mN/m. Adding 10-15% ethanol lowers that to about 47-42 mN/m. Also, the trapping science paper does mention that

Very few flies were captured in traps baited with 10% ethanol in water.  Traps baited with a combination of acetic acid and ethanol in water captured more SWD flies than traps baited with acetic acid or ethanol solutions alone.  These results indicate a synergy of the two materials, and of the two chemicals, as lures for SWD.

Interestingly wine has substantially higher attractive effect than an equivalent ethanol solution though:

Wine is about half as effective a vinegar and about a quarter as effective as a combination of wine and vinegar. On the other hand, a 10% ethanol solution was 20-50 times less effective than alcohol 10% plus acetic acid 2%. So there's more to wine than ethanol that attracts the flies.
So the flies probably do avoid the higher alcohol concentrations... unless there's also vinegar.
Another paper finds that wine's surface tension is mostly determined by its alcohol content.

So it does look like:

Fruit flies are fairly strongly attracted to wine (on the same order of magnitude as to vinegar).
The surface tension of wine is substantially lower than that of water.

I'm still not sure what the surface tension of (2%) vinegar might be, in comparison. Pure acetic acid has substantially lower surface tension compared to water, about 27 mN/m at room temperature. And if Wikipedia is correct, 10% acetic acid solution has about 55mN/m around temperature. So acetic acid lower the surface tension less than ethanol, but not by much less. On the other hand, fruit flies are much more attracted to acetic acid than to ethanol (alone). So perhaps that's enough to explain why they drown easier in wine.
Actually it look like Wikipedia is wrong here. From an authoritative source, acetic acid has nearly the same effect as wine on surface tension; at 11.4% it has 43.5 mN/m; just 3.2% is enough to lower the tension to 55.6mN/m; at 1.6% it's 61.7mN/m.

So probably just the fact that acetic acid is much more attractive to flies than ethanol is the only factor (other surfactants excluded). Perhaps they "confuse" a higher concentration of ethanol to a lower concentration of acetic acid, which they would be able to handle as far as surface tension goes.
Yet another source (actually quoted in the previous one, on the next page) gives even lower values for ethanol surface tension.

Apparently determining surface tension is a hard problem, both experimentally and theoretically. So I'm not sure we can properly compare figures reported in different sources. Alas no single experimenter has done both ethanol and acetic acid in the same paper/setup. But what was observed about their relative attractiveness to flies is probably sufficient...
And for ballpark comparisons, a similarly or lower surface tension as that of 10% ethanol (or acetic acid) i.e around 30-40mN/m can be obtained by a adding a few ppm (parts per million) of a surfactant, such as LAS or AE.


Can I sterilize the equipment for experiments without an autoclave? If I don't have access to an autoclave, can I sterilize my equipment in a regular pot. If so, what time is needed at about 110°C (I measured inside) for a proper sterilization?

It certainly can be done. Tyndallisation may as discussed on labmate may work well for your situation. If not, there are many other viable alternatives suggested.

  **Tyndallisation:
  **
  Developed partway through the 19th century by English physicist, John Tyndall, the eponymous Tyndallisation was a commonly used
  technique by the microbiologists of the 1800s. Tyndall experimented
  with boiling beef broths to develop a method to sterilise liquids in a
  safe and comprehensive manner.

  His research led him to the basic principles for Tyndallisation, a process by which medias are subjected to relatively short boils at a
  regular atmospheric pressure. This relatively straightforward method
  is still suitable for small labs, or research facilities which only
  require sterilised equipment part of the time.

  It is not recommended to attempt to sterilise closed glass containers using this method, without lining them with cotton and
  capping them with foil – allowing for air to escape without being
  subjected to contaminants.

  The process involves boiling fluids for 10-15 minutes before leaving to cool to room temperature and leaving it to sit for 24
  hours. Repeat this process another three or four times, by which time
  sterilisation should have occurred.

  Naturally this method has reduced in popularity due to the requirement to continue the process for up to five days to achieve
  sterilisation.


Extinction of non-mammal Synapsida I am following M.J. Benton's Vertebrate Palaeontology, which explains how many groups of Synapsida were already extinct in the Mesozoic Era, with one obvious exception being the group of Cynodontia, which includes modern day Mammalia.

Nevertheless, I cannot find when the last non-mammal synapsids got extinct and I would be very grateful to anybody giving more information about the topic.

OK, I don't know how I did it but I misread your question as being why all the non-mammalian Synapsids went extinct. I answered your question at the end, but I'm leaving the rest as-is until I figure out how to rewrite it (it was rather too much work to delete).

According to The Wikipedia page for Synapsids, the answer really depends on the Synapsis since there are quite a gap between the start of the Synapsid clade and the appearance of Cynodonts.

The first big "culling" of Synapsids (i.e. the extinction of all groups except one clade that led to mammals - Therapsids in this case) seems to occurred over the Permian era. Some groups went extinct in the early Permian but most groups went extinct at various points during the Middle Permian. No clear reason is given for these various extinctions (though the page for Dinocephalia suggests "disease, sudden climatic change, or other factors of environmental stress may have brought about their end"... which basically covers all possible extinction reasons so that's helpful); it's probably various reasons specific to each. Most species do go extinct after all.

Among Therapsids, the only clade that survived the Middle Permian, most seem to have been wiped out in the Permian-Triassic extinction, the largest extinction event in Earth's history, of which only three Therapsid clades survived: Therocephalians, which went extinct soon after, Dicynodonts, which were extinct by the Early Cretaceous, and Cynodonts. Aside from the usual environmental factors, a reason for the extinction of those two clades could have been competition from the then-ascendant Dinosaurs, and Cynodonts themselves.

As for when the last non-mammal Synapsid when extinct, it appears to have been a member of the Tritylodonts, which survived into the Cretaceous (and arguably having a representative after the K/Pg extinction, emphasis on "arguably"). Mind you these are very close cousins to Mammals indeed:

  Tritylodontids ("three knob teeth", named after the shape of animal's teeth) were small to medium-sized, highly specialized and extremely mammal-like cynodonts, bearing several mammalian hallmarks like erect limbs, endothermy and lactation. They were the last known family of the non-mammalian synapsids.


Why do some protocols require prewarming a liquid medium before inoculating? For example, in this protocol for E. coli competent cell preparation, it says:

  Plate 10 uL E. coli BL21(DE3) cells on a LB-agar plate; incubate overnight (12 hours).

  Prepare 500 mL SOB medium so it can be pre-warmed in the 37 degrees Celsius incubator the day before.

  Pick a single selected colony and inoculate in 5 mL of SOB medium and grow for 16 hours at 37 degrees Celsius and 250 rpm in a shaker.

  Inoculate 500 mL of prewarmed SOB medium with 5 mL of the fresh overnight culture.

and then in the protocol for overexpressing proteins after transformation of these cells, I basically follow similar steps as above but this time, without prewarming the large-scale inoculation lqiuid medium. Why is that?

It's because E.coli BL21(DE3) are competent cells. The competent is the key here as the cells were chemically treated so the transfection can be performed by heat-shock with high efficiency.

This means these bacteria are quite fragile, due to the chemical treatment, and therefore are very sensitive to both mechanical and thermal shocks.

Pre-heating the media simply avoids damaging the cells and maximizes the growth rate.


What is the genetic reason that this flower has petals of two different colors? I have two different varieties of the flower, portulaca: one is bright pink, the other is pure white with pink specks at the centre. Recently a flower bloomed which had 50% of the former and 50% of the latter: both traits in the same flower. Is this an example of co-dominance or is there some other reason for it?

This can be a result of a somatic mutation, especially if the other flowers on the same plant don't have the same color pattern. Somatic mutations are not inherited for parent organisms but occur spontaneously in one of the cells in the body. If that cell then proliferates all of its descendants will have the mutation and new phenotype associated with it.

Look for example at Fig. 1 (c, d) in this article. Those peach flowers have similar coloration to the one on your photo.


How to classify equilibrium points I have the two differential equations:

$$\frac{dN_1}{dt} = N_1(2 - N_1 - 2N_2)$$
$$\frac{dN_2}{dt} = N_2(3 - N_2 - 3N_1).$$

I worked out the equilibrium points to be at $N_1 = 0, \frac{4}{5}$ and $N_2 = 0, \frac{3}{5}$. I then calculated all the Jacobi matrices and worked out the eigenvalues (and eigenvectors). I now have to classify these equilibria. How do I do that? Is there a set of rules I follow to classify them?

Also, the next part says:

  Sketch the phase portrait of this system in the biologically sensible region: draw the the null- clines of the system and determine the crude directions of trajectories in parts of the phase plane cut by the null clines, designate the equilibria in the phase plane, and sketch a few typical trajectories.

I can do the null - clines and I think once I have found out the stability of the equilibria, I can determine the directions of trajectories of the bits cut by the null -cline, but how would I sketch the trajectories of the equilibria?

Classification of equilibrium points is done on the basis of the eigenvalues.

If the two eigenvalues have no real parts, it is a hyperbolic fixed point and represents undamped oscillation.
If both have a negative real part, it is a stable fixed point. If any of the eigenvalues has an imaginary part then it represents damped oscillations (in that case the equilibrium point is called a focus).
If one or both eigenvalue have a positive real part, it is an unstable fixed point.
If one eigenvalue has a positive real part and the other a negative real part, it is a saddle point.*

You sketch the trajectories of the equilibria by starting a tiny distance away from the point (where it is not in equilibrium) and trace the quiver plot. Drawing trajectories around unstable points is tricky and you have to plot the function in negative time i.e. instead of plotting f(x1,x2,t), you plot -f(x1,x2,t).  This page has representative trajectories for the different types of equilibrium points.  This page has a more thorough explanation, generalized to multiple dimensions.

*This classification appears to be slightly variable (more or less categories), on the basis of the two links I found.  I think the one I list is the simplest version, but any classification should suffice.  They are all based on the same principles. You can refer to some books on non-linear dynamics:

Nonlinear Systems by Hassan Khalil
Nonlinear Dynamics and Chaos by Steven Strogatz


How do sarcomeres coordinate contraction? As can be seen from the figure

if myosins from both sides apply equal force then how does muscle contract? And also how do actins resist tearing?
Is there any kind of  coordination between different sarcomeres? How does they achieve it? I know that acetylcholine is released in response to action potential so does the release of acetylcholine controlled in each individual sarcomere?
Or simply there is an increase in the number of myosins as the distance of each sarcomere increases from the neuromuscular junction?

I'm answering question 1, I think it'd be better to post these questions separately.

Consider action and reaction: myosins (thick) filament is experiencing force F towards Z line.

If the muscle is acting on something that is movable (e.g. you're pulling on a drawer which isn't locked), the force F towards Z line is greater than the force that maintains your thick filaments in place, and they'll slide towards Z line. The speed at which they slide is limited by the rate at which myosin heads can detach once they have performed power-stroke.

If the drawer is locked, then force F cannot overcome the external force. This force however is normally lower than the force required to tear actin or z-line, it is limited by two molecular factors: myosin will stall and not effectuate power stroke under too strong an opposing force, and myosin heads  will detach after some time and relax the tension they have built up. This is how you get the maximum force under clamped conditions.


What is this structure in human brain? Scientists made a new image of brain.

I wonder, what is this arc (denoted by blue)?

Is it the caudate nucleus?

Short answer
Based on shape and approximate position, I think it is the corpus callosum.

Background
I think it is the corpus callosum (Fig. 1). The corpus callosum is approximately 10 cm in length and is C-shaped. It becomes thicker posteriorly, as is also evident in your image. The corpus callosum is a structure consisting of white-matter, containing about 200 million axons.

Fig. 1. Mid-saggital section of the brain showing the corpus callosum. source: University of Central Florida

I think it is not the caudate nucleus, alhough it has also the curved shape. The caudate is positioned more laterally than the corpus callosum and by the looks of it your picture shows a mid-sagittal section of the brain. The caudate seems to be positioned too far laterally in the brain as far as I can see (Fig. 2).

Fig.2. Nucleus caudatus. source: Brain Notes


Is trembling an advantageous response during periods of anxiety? I originally had planned to ask about whether there was any biological truth in the popular phrase "shivering with fright".  However, after doing a fair bit of googling it seems that there is a lot more medical reference to trembling as a result of anxiety (1) (though I would imagine the distinction to be fairly minor).

I was, after about an hour of fruitless searching, beginning to wonder if it was a phenomenon created only in literature (such as being 'frozen by fright') rather than genuine human physiology, however then a website described how many people often have minor trembling before exams, interviews or other high pressure situations - something I can attest to myself!

This hasn't really changed the biological purpose behind the question however - is there any advantage to shivering in a fight or flight situation or is it more a side effect of the release of adrenaline or another chemical response? I am struggling because I can only imagine it being a real disadvantage (consider for example an organism hiding from a predator - uncontrolled movement in a stressed situation can not be beneficial) so the only way that I can see is that the shivering must be linked to something that is a definite advantage in a high stress situation.  What would that be?

Some assumptions made in the question.

There is an implicit assumption in your question which I don't think to be correct: you assume that any reaction of the human organism to stress (let's substitute "fright" by "stress" in your question) is a physiological reaction, meaning that this reaction somehow helps the organism to overcome the stressful situation. From medical viewpoint the reaction to any external action can be:

physiological one (i.e. the one that is expected and is considered "good", helping the organism to adapt to this action).
pathophysiological:

as a side-effect of physiological reaction
as a result of nervous/humoral system overlast and depletion
as a reaction to unknown action
as a reaction to something mistaken for known action that is indeed something else

Mechanisms of tremor.

From mechanical viewpoint our body consists of dozens joints that are absolutely not fixed and have from two (moving in one plane) to three (for free movement in 3D, for example coxofemoral joint), thus giving our extremities an incredibly high number of degrees of freedom.

In order to sustain a certain posture our joints are equipped with antagonistic muscles: muscles that move the joint into opposite direction. The muscles, again, by design are very badly adapted for isotonic action. That basically means they cannot keep the same pressure for long time and the only way to get a fix posture for the whole body is to keep sending repetitive pulses to antagonistic muscles so that none of them actually wins.

Normally the impulses are very short and frequent. They also have to come synchronously and out-of-phase, meaning that whenever one muscles contracts its antagonist should dilate and vise versa, so that no muscle rupture takes place because of the simultaneous contraction of two opposite muscles. This synchrony accounts for very subtle trembling of the body, almost not seen by a naked eye in healthy humans. This trembling is also called physiological tremor to designate its being normal, e.g. physiological.

There are two ways how this trembling can increase so that it becomes visible and sensible:

Due to impaired synchronisation between the pulses sent to the antagonistic muscles. Since these pulses are generated in brainstem nervous centers, the impairment of those (in case of Parkinson's desease) or some inhibiting input into them (as in case of cerebellar deseases) leads to desync of these pulses, the frequency goes down whereas the amplitude might increase, making the trembling visible.
Due to attenuated cell sensitivity to the incoming impulses. This happens if the muscle cells start to overreact to the normal impulses and respond with prolonged contraction (followed by longer refractory period when they are unable to respond any impulse, thereby missing frequent pulses and reducing the effective frequency). These is mainly caused due to special metabolic changes within and in the vicinity of the muscle cells.

The most common metabolic change within the cell is either the increased Calcium concentration within muscle cells, leading to much stronger contraction, or increased sensitivity for Calcium (via Ca and ryanodin receptors), that leads to much abrupter Calcium concentration rise in cells and results in the same.

The reason for Ca to increase within the cells might be the intake of some known Calcium liberators, like caffein, increased concentration of the humoral factors that use Ca as second messenger, like adrenaline, insuline, thyroid factors etc. Those, again, can be released during some stress conditions, during artificial or temporal low sugar level and other factors.

Shivering as a reaction to stress.

The shivering, or in medical terms tremor might appear due to the following mechanisms:

Massive release of adrenaline during the stress: both directly via the adrenaline receptors and indirectly by causing temporal hyperglycemia via the metabolic adrenaline receptors. The action of adrenaline is also increased due to concomitant release of corticosteroids.
(muss less probable in case of fright, however might be common in many other cases) Overlast of the hypothalamic/amygdalic/brainstem structures responsible for stress reaction with probable weakening of deep nuclei controls over the posture and muscle contraction.

Conclusion.

So, as you see, the tremor is rather a pathophysiological reaction when it appears as response to stress, a side-effect manifestation due to acute temporal increase in adrenaline concentration in blood. Funny enough, but exactly this tremor is referenced to as "physiological tremor" in medical literature, because this type of tremor is not indicative for any CNS or endocrine disorder, that is very common for other types of tremor (postural, intentional etc.).


Gel electrophoresis question Leena is a molecular biology student. She purifies two fragments of DNA, 800 and 300 base pairs long. These were obtained from a plasmid after digesting it with HindIII. Each of these fragments has a single EcoRI recognition site.
Leena wants to join these two fragments to get a 1.1kb gene as shown in Figure 7.1. She suspects that this gene has a unique protein-coding sequence.

She, therefore, mixes the two fragments in the presence of excess DNA ligase in an appropriate buffer and incubates the mixture. She removes an aliquot (a small part of the reaction mixture) after 30 minutes and loads it on an agarose gel to check the results. She is surprised to find many bands along with the expected 1.1kb band  in the gel.

FIG 7.1

Leena is interested in the 1.1kb fragment shown in Figure 7.1. Hence, she elutes the 1.1kb fragment from the gel shown in Figure 7.2 and subjects part of this sample to HindIII digestion. She obtains the expected pattern with two bands, 800 and 300 base pairs long. To confirm its restriction map, she subjects the remaining sample to complete EcoRI digestion. Which pattern of bands would she obtain?

The answer given is this and I understand why this is the answer and other options given in the question(not posted here) are definitely not the answer but I do not understand why there are no 0.4kb fragments, 1.1kb fragments here.

You are being too smart for this question ;) If you assume that the enzyme is perfect, you've optimized the amount of template, and you leave the reaction for a really long time then there will be complete digestion. If you assume complete digestion, then there won't be any 1.1kb fragments. Furthermore, if you work out all the possible orientations of the 800bp and 300bp that were ligated together (each piece can be in the orientation shown and the opposite orientation) and you force an EcoRI cut at every available EcoRI site, then you won't have any 0.4 kb fragments from imcomplete digestion, either.

In reality, I've never been able to optimize my reaction conditions to get complete digestion of my template, and I always have some residual template around, so it's good your thinking that way for "real-world" preparation.

If you do not assume incomplete digestion, in addition to the 1.1kb and 0.4kb bands missing from this gel, I calculate that there should be a 1kb band as well.

Edit: I goofed up the last paragraph. It should read: "If you do not assume complete digestion, in addition to the 1.1kb and 0.4kb bands missing from the complete digestion gel, I calculate that there should be a 1kb band as well.


Is there a correlation between B12 deficiency and cardiovascular disease? I've read in several health sites that state that high blood homocysteine, as well as low B12 intake, is not only correlated, but actually causes cardiovascular diseases. In order to verify those claims, I've looked for related studies and found controversial results. This one, for example, observed no positive effects from B12 supplementation:

  In this randomized double-blind trial, high-dose vitamin therapy had no effect on the outcome measures of stroke, CHD events, or death.

The author speculates several possibilities for the negative results, including that high homocysteine levels could be merely correlated, but not actually causing the problem.

I wonder if there have been advancements on that matter. Is it known whether low B12 causes cardiovascular diseases, or is merely correlated? If it is just a correlation, then what is causing both low B12, high homocysteine and increased cardiovascular disease? In particular, have any study observed if a diet rich in red meat, for example, has the positive effects that pure supplementation failed to show?

Is it known whether low B12 causes cardiovascular diseases?

Yes, it is known. B12 deficiency does not directly cause cardiovascular disease, and I would be suspicious of any health site that says it does. B12 deficiency causes hematologic and neurologic problems.

  Why is low B12 correlated with high homocysteine:

Low B12 is correlated with high homocysteine because it is a cofactor for the conversion of homocysteine to methionine by homocysteine methyl transferase. Low folate will do the same thing (cause an elevation in homocysteine).

These cofactors and metabolites are involved in methyl donor reactions that are particularly important in the production of blood cells and myelin. Strict nutritional B12 deficiency (reduced intake) often occurs along with other nutritional deficiencies.

The primary hematologic problem is anemia, with associated changes in the morphology of certain white blood cells. The anemia, if severe and prolonged can contribute to cardiac problems of other causes. You also see paresthesias (often symmetric), a shuffling gait, and other odd neurological problems including depression and psychosis.  B12 supplementation does not always reverse the neurological problems.

You can read about B12 deficiencies in Cecil medicine Chapter 225 and 167, Harrison's Chapter 74, and in this review.


What is the difference between a cytokine, a hormone and a protein hormone? I'm trying to figure out the difference between hormone, cytokine and protein hormone. It's clear to me that all three are biological messengers, but there seems to some ambiguity and overlap between terms and I'm trying to understand the nuances.

In brief:

What do each of these three terms mean and how are they different?
Do any of the three terms represent a superset of the others? e.g are all cytokines, hormones? Are protein hormones just a subset of hormones?
Are the terms context specific at all? For example, cytokines are referenced in the context of immunology below, but are they actually fundamentally different from hormones?

If there is context-dependence, under which contexts should each word be used?
Are there any canonical examples of each? e.g Prolactin is given as an example of a protein hormone below, how about for cytokines and ordinary hormones?

  In June 1905, Ernest Starling, a professor of physiology at University College London, UK, first used the word 'hormone' in one of four Croonian Lectures—'On the chemical correlation of the functions of the body'—delivered at the Royal College of Physicians in London. Starling defined the word, derived from the Greek meaning 'to arouse or excite', as “the chemical messengers which speeding from cell to cell along the blood stream, may coordinate the activities and growth of different parts of the body” [1]

  Cytokines and chemoattractant cytokines known as chemokines are highly localized soluble signaling proteins produced by many cells of the immune system (neutrophils, monocytes, macrophages, B-cells, and T-cells) to regulate immune responses [2]

  A great deal of evidence has accumulated and confirmed that hormones secreted by the neuroendocrine system play an important role in communication and regulation of the cells of the immune system. Among protein hormones, this has been most clearly documented for prolactin (PRL), growth hormone (GH), and insulin-like growth factor-1 (IGF-I), but significant influences on immunity by thyroid stimulating hormone (TSH) have also been demonstrated. [3]

References

[1]: Tata JR. One hundred years of hormones. EMBO Reports. 2005;6(6):490-496. doi:10.1038/sj.embor.7400444.

[2]: Stenken JA, Poschenrieder AJ. Bioanalytical Chemistry of Cytokines-A Review. Analytica chimica acta. 2015;853:95-115. doi:10.1016/j.aca.2014.10.009.

[3]: Kelley KW, Weigent DA, Kooijman R. Protein Hormones and Immunity. Brain, behavior, and immunity. 2007;21(4):384-392. doi:10.1016/j.bbi.2006.11.010.

Parts of the answer are in the text that you provide yourself. But I shall try to add where i can.

What do each of these three terms [hormone, cytokine and protein hormone] mean  and how are they different?

Both cytokines and hormones are a class of signalling molecules that are secreted by cells.

Cytokines are a group of small protein that  have a fundamental role in the immune system. They are typically short lived and typically have local effects and are specific cytokines are often produced by multiple cell types.

For example they cause local cells to generate heat and cause blood vessels to become wider and more permeable to blood cells. parham (2015) Some cytokines can act over longer distances, IL-6 for example cause local inflammation and regulates fever by targeting the  hypothalamus causing it to increase body temperature overall. For more information check this link.

Hormones are secreted into the blood by dedicated endocrine cells so the can regulate other cells across the body.(alberts, 2008)

Do any of the three terms represent a superset of the others?

Protein hormones are a subset of hormones. An other important subset are steroid hormones.

It can be argued that cytokines function as hormones in some situations. For example: in the case of an infection high concentrations of cytokines can regulate body temperature causing fever. IL-1α, IL-1β and IL-6 are good examples here

Are the terms context specific at all?

In some situations it can be argued that cytokines act as hormones. But the feature that groups them is that the are an actor in the immune response. This wiki discusses some differences.

Classical hormones are produced by a gland and excreted in the blood. This is not context depended.

Are cytokines actually fundamentally different from hormones?

All Cytokines are proteins and don't act fundamentally different from protein hormones. Both have to act through membrane bound receptors since proteins can not pass the cell membrane on their own. Steroid Hormones can pass the membrane and typically have intracellular receptors.

Are there any canonical examples of each?

Interferons and Interleukins are a large classes of cytokines. IFN-γ and IL-6 a well known examples.
Androgens are steroid Hormones . Testosterone is one of them.


Why does cucumber skin kill ants? I recently read that cucumber skin is an effective repellent for some ants:

Set out cucumber peels or slices in the kitchen or at the ants' point of entry. Many ants have a natural aversion to cucumber. Bitter cucumbers work best.
Source: Natural Insect Pest Control

See also: How to Use Cucumbers to Prevent Ants from Entering the Home
But when I tried it out they died instead. What made this happen?

Cucumber contains a compound called trans-2-nonenal (reference 1 and reference 2) that repels insects. This particular compound (reference) has can also be used in insecticide foams for repelling ants (reference)


RNA-Polymerase III transcribed genes I have a list of differentially regulated genes from a high-throughput experiment of the human genome. I would like to find out which of these genes are transcribed by a RNA polymerase III and which of them (probably most) are transcribed by the RNA polymerase II.

I have downloaded some Chip-Seq tracks for polymerase II and III and some GO categories which apply for the RNA polymerase III transcription.

I have also tried the biomaRt repository to search for these mentioned GO categories, but I can't really find substantial results.
For example I have the gene RN7SL1 which according to the literature is transcribed by PolIII, but I'm not able to find any repository which also says so.

Is there any (better) way to search for this kind of data/annotations?

thanks a lot
Assa

PS.
I am not sure, if I have found the correct GO categories (e.g. GO:0006383 - transcription from RNA polymerase III promoter). So are there any better one?

GO is based on experimental evidences; biomart is quite good. GO:0006383 seems to be the right tag.

If you want to use the ChIPseq data then you can do this:

Map the ChIPseq reads to the genome. If you already have the tracks
then you need not do the mapping. You would have the position of the
reads in the genome.
Now count the number of reads mapping to each geneic region. The gene boundaries can be obtained from a GTF file.
Optional: Normalize the reads with the length of the gene.
Find the difference between the number of Pol-II and Pol-III reads for each gene.

By doing this you still won't be able to say that "gene-x is transcribed by pol-III". All you can say is that "pol-III binds to that geneic region". If there is an even distribution of the ChIPseq reads along the gene then you can assume that there is an active transcription and the polymerase is not merely stalled. You can also do a CLIP (Crosslink-Immunoprecipitation) of Pol-III followed by a RNAseq. This will enable you to find RNAs transcribed by pol-III (this is a better way than ChIPseq but I don't think anyone has done it yet; so no ready data).


Are there autotrophic fungi? Are there any completely autotrophic species of fungus?

If so, what species are they? What ecosystem do they live in? Some answers from Quora state that a fungus can never be autotrophic, but why is that?

Thanks for your time!

no none of the fungi in the nature is  autotrophic.
they are dependent mostly upon dead and decayed matter.
the reason that they are not autotrophic is that they lack any type of photopigment to carry out photosynthesis.
photopigments are necessary because the are the only components that can trap the solar energy and use it to extract the electrons from the inorganic source such as h2s or h2o by splitting them which are further used to prepare ATP and NADPHH+. these 2 are the assimilatory powers for the further dark reaction. so if these are not there then the processes of photosynthesis would not be there and therefore the organism will not be able to produce its own food in turn it would depend on other autotorphs for food (in case of fungi dead and decade matter).


Are there viruses that show definite enzymatic activity? Perhaps due to outer coat protein individually or collectively.

As some of the comments mention, this question could use some clarification.

First, assuming you're asking in general about enzymatic activity in viruses:

A few classes of "non-autonomous" viruses (particularly endogenous retrotransposons) don't encode any enzymatic functions and sometimes don't even encode their own structural proteins - they rely on the structural proteins and/or enzymatic functions of the "autonomous" viruses.

With the exception of those non-autonomous viruses, all retroviruses encode the reverse transcriptase and integrase functions, while many non-retroviruses (those which don't have a step in their lifecycle where they convert RNA into DNA) also have RNA-dependent RNA polymerase activities.

Now, assuming you meant to limit your question to the viral coat (AKA capsid) proteins of an intact virus-like particle (VLP):

Most do not have any "enzymatic" activity per se - they do not catalyze the formation or breakage of any covalent bonds. However, many viral coat proteins have membrane associated domains which undergo conformational changes essential for uncoating and trafficking of the virus across the membrane:

Gao, D., Lin, X., Zhang, Z., Li, W., Men, D., Zhang, X., & Cui, Z. (2016). Original Article: Intracellular cargo delivery by virus capsid protein-based vehicles: From nano to micro. Nanomedicine: Nanotechnology, Biology, And Medicine, 12365-376. doi:10.1016/j.nano.2015.10.023

This membrane translocating (aka cell penetrating) activity sometimes does depend on the "collective" action of oligomeric complexes of capsid proteins, but it is not an enzymatic activity.

However, the parvoviruses do encode a phospholipase enzymatic activity in their coat proteins which serves to disrupt cellular membranes and allow viral entry:

Kobiler, O., Drayman, N., Butin-Israeli, V., & Oppenheim, A. (n.d). Virus strategies for passing the nuclear envelope barrier. Nucleus-Austin, 3(6), 526-539.

I don't know of any other classes of coat proteins with bona fide enzymatic activity, but I wouldn't be surprised if some exist, and I've only touched on a few of the multitude of enzymatic activities exhibited by other viral components.


How are cells of the cornea transparent? We know that cells have mitochondria, chromosomes and other organelles so that's why they are opaque but can you say how the cells present in the eye cornea are transparent and allow light to pass through?

Most cells are transparent, which is why we can see cells using bright-field microscopy, where the light travels through the cells before you see it. That's how we can see inside onion cells and see structures like onion cell nucleii, moss cells, human epithelial cells and animal mast cells.

The human cornea is made up of five layers, each of which have different structures allowing them to be transparent: the outer and inner epithelial layers are very thin and naturally pretty transparent, and the middle layers have collagen fibres; based on that Wikipedia article, it sounds like there are several hypotheses for why these layers are transparent, but it doesn't look like there's a definitive answer yet.


How do I reverse my insert within a plasmid? I have a plasmid with:

...T7pro. -- RBS -- XBa1 cut site -- ProDpro. -- RBS -- AmilCP -- T -- Spe1 cut site -- T...

How do I design primers to reverse the portion in bold, such that the T7 and ProD promoters are on opposite sides of AmilCP? I am finding it difficult to understand how to design the appropriate primers.

Design your 5' primer upstream of ProDpro. with a Spe1 cut site added to the end (plus a few extra random bases to allow for better cutting). Add an Xba1 cut site to the end of the 3' primer, again with a few extra random bases on the end to allow for better cutting.

Amplify the insert, PCR cleanup, digest, cleanup again, and you should be able to easily clone into the Xba1/Spe1 digested vector that has been gel purified.


How does Celiac's Disease cause people to stop growing? In all of the sites I've looked on, one of the symptoms of Celiac's Disease is the failure to grow in children. Why would an immune attack against gluten cause stunted growth?

Celiac.org states:

  When people with celiac disease eat gluten (a protein found in wheat,
  rye and barley), their body mounts an immune response that attacks the
  small intestine. These attacks lead to damage on the villi, small
  fingerlike projections that line the small intestine, that promote
  nutrient absorption. When the villi get damaged, nutrients cannot be
  absorbed properly into the body

Journal of Pediatric Gastroenterology & Nutrition published a study on catch-up growth in children diagnosed with Celiac's before the age of nine.

Is the lack of nutrients what causes the impaired growth, or is there more to it than that?

The "proper" term to use in a case of growth retardation in children is "failure to thrive", abbreviated as FTT.

Celiac disease is one of the most common Organic endogenous (genetically based) FTT syndromes.

The main cause of FTT in pediatric celiac patients is malabsorption. In a case of insufficient vitamins and nutrients absorption the child will (have) FTT.


Sephadex column for alpha-amylase I want to purify crude alpha-amylase with column chromatography. I am using a spehadex 75, But for some reason I can't find any information on how to make the slurry.

I can quickly find tons of information on how to pack and store a column, but what i really want to know is how much powder and buffer do I mix together?

The '75' of Sephadex G-75 refers to the water regain value, which is defined as the grams of water absorbed upon hydration of 1g dry powder, multiplied by 10 (see Reiland). Thus the water-regain value of Sephadex G-75 is about 7.5ml. This value refers only to the water contained
within the gel particles and not to the water trapped outside of the particles in a packed gel (Reiland). As a rule-of-thumb, the latter figure can be estimated to 50%.

So ... 1g of dry Sephadex will give about 15 ml of packed gel

From here: 1 g swells to 12-15 mL gel

Just a thought ...
Does alpha-amylase interact with Sephadex?  Maybe 'thinking' it resembles a substrate, and (reversibly) binding to it or otherwise interacting to cause effects in addition to gel-filtration ?


Before Evolution was proposed by Charles Darwin, what were the leading secular theories to explain how life developed? Outside of evolution, what were the leading scientific schools of thought that Charles Darwin contented with when he published his evolution theory as way of natural selection in 1859?

There were many (more or less) non-theological theories of how life had developed before Darwin, starting at the ancient greeks. Many theories included spontaneous generation but also aspects of modification by descent of existing species (i.e. evolutionary change), but most were not that well developed and complete thought. However, one of the more complete evolutionary theories that pre-dated Darwin was Lamarckism, which claimed that individuals pass on traits that they have acquired during their life time. So the basic idea was that individuals respond and adapt to the environmental conditions they experience, and that these traits are then transferred to their offspring. This is one example of a non-theological theory that pre-dated Darwin, but I cannot really say if it was the leading one. I do know that Lamarck's ideas were relatively ignored during his own lifetime.

Darwin included some aspects of these ideas in his "Origin of Species", but challanged Lamarckism when it came to the main processes of evolution. A weak interpretation of Lamarckism has actually seen a revival after the discovery that epigenetics can be transferred from parents to offspring, see e.g. Heard & Martienssen (2014) and Szyf (2014).


Stable and strong promoter? I need a mammalian promoter that will maintain stable expression through differentiation.

I was originally planning to employ UbC for this specific project, however new information from a different experiment has come to light and now I need a promoter that has both extreme stability and high strength (as you know, UbC is renowned for it's very low expression rates).

Do any of you have suggestions? Perhaps I should look into a hybrid promoter of sorts...

Thank you,

CDB

There seems to be quite an amount of resources to help OP.

Addgene has a page on topic with list and description of common promoters usable in variety of organisms: Plasmids 101: The Promoter Region

Experimental biophysics textbook mentions some useful promoters as well, or this review.

Surprisingly, there has been some quantitative analysis of promoter strength: Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter, as well as effort toward stronger synthetic (version of CMV) Synthetic design of strong promoters

My conclusion is that either viral, or CAG (based on chicken actin) promoters might be useful candidates. But one cannot expect ubiquitous and even expression in various tissues/cells types without fine-tuning expression cassette.


What is this? Is it harmful? Anyone find out what this is? Looks like A Caterpillar with a home it made from surrounding items, this was found in VA in the moutians on our home.! It went back inside its home after attempting to touch it with my phone. It's the size of an adult female pinky.♀

That appears to be what is known as a bagworm:

According to the University of Maryland extension Home & Garden Information Center, they can cause significant damage to ornamental plants especially conifers.


What is the leaf venation of a scuppernong vine leaf? I googled around and I didn't find anything that says its leaf veination. Anyone know?

Using the link, it's netted veination, though it doesn't say if it's palmate or pinnate. So I relied on using my own judgement on looking at my scuppernong leaf and it looks decidedly palmate. It would be better if I had confirmation from some site or such, but as it has main veins and smaller veins sprouting from those main veins, I think it's palmate.

Additionally, for all other botany question confusion, I finally found this website which may be useful: http://rampages.us/fieldbotany/2014/05/23/grape-vine-3/


Why in the Electron Transport Chain does PS2 go before PS1? Why in ETC does PS2 go before PS1?

If your question is related to numbering, the photosystems were named in the order of their discoveries not participation.
In cyclic ETS PS-II doesn't participate at all.

PS-I would have gone first if PS-II was named PS-I.


Finding the number of chromosomes of an organism For a school project I need to find the number of chromosomes of an organism (specifically the adelie penguin, Pygoscelis adeliae). After several internet searches and a look through the encyclopedia at school, I am unable to find a definite answer to this question. Sources on the internet claim anything from 38 to 96 for diploid cells (with none of them citing a trustable study).

Is there any database that records the chromosome number for organisms?

Also, if this information is unavailable, what is the best way to estimate this value? On the Wikipedia article for number of chromosomes for various organisms, it listed the value for some birds, most of them in the 70-80 range. Is it safe then to assume that the number for penguins in general would be somewhere in this range?

Thanks.

Answer

An comprehensive online database of the chromosome numbers of all living species most likely doesn't exist. This Wikipedia article is the best and most complete reference comprising animals that I can personally find on the internet.

This source in Spanish, which I've translated with Google Translate reads:

  Canedo Delgado (1999) performed the karyotype description of the three species of the genus Pygoscelis , noting that there is a high homology both numerically and morphologically: Pygoscelis antarctica presented 2n = 92, Pygoscelis papua 2n = 94 and Pygoscelis adeliae 2n = 95 in females and 2n = 96 in males.

Also, note that chromosome number cannot be "guessed" or "assumed" for closely-related species. As shown above, the three Pygoscelis species have a high homology, but have very different chromosome numbers.

The other chromosome number you found for the species (38) is actually that of the Emperor penguin, as a simple Google search shows.

References

Ledesma, Mario A., T. R. O. Freitas, J. Da Silva, Fernanda Da Silva, and R. J. Gunski. “Descripción Cariotípica De Spheniscus Magellanicus (Spheniscidae).” El Hornero 18, no. 1 (August 2003): 61–64.


What is the optimum length of abstinence for maximum ejaculation volume in humans? There have been papers discussing this, and whether the abstinence period should be 1 week, 2 weeks or other [1, 2]. Some think the time to maximum ejaculation volume is even longer than this.

doi: 10.1530/jrf.0.0570391
PMID: 7114956

There don't appear to be many robust studies on this, but this study by De Longe et al in 2004 suggests that, whilst the volume of the ejaculate is increased after 5-days of abstinence (in most participants), for many this did not increase further after 8-days [1].

Here are the 11 participant included (along the x-axis), and for each participant there are four coloured boxes:  dark blue, day 1 (corresponds to 24 hours' abstinence); red, day 3 (corresponds to 3 days' abstinence); yellow, day 5 (corresponds to 5 days' abstinence); light blue, day 8 (corresponds to 8 days' abstinence).

This study has a very small sample size, and really shows how the variability between people is massive. There could be many other factors affecting individuals, from smoking and drinking behaviours, to exercise and stress.

What seems much clearer is that sperm concentration increases with abstinence [2]. This study included 27 men and did not specifically ask them to remain abstinent for periods of time, but asked them how long. The average abstinence is about 2-days.

I could not find any study which investigated abstinence for longer periods - but there are undoubtedly more that I did not see.

De Longe, at al. 2004. Influence of the abstinence period on human sperm quality. Fertility and Sterility (http://dx.doi.org/10.1016/j.fertnstert.2004.03.014)
Carlsen, et al, 2004. Effects of ejaculatory frequency and season on variations in semen quality. Fertility and Sterility (http://dx.doi.org/10.1016/j.fertnstert.2004.01.039)


Why isn't phosphorus or nitrogen a limiting nutrient for animals? Nitrogen and Phosphorus are usually the limiting nutrient for plants, especially for algae.  Phosphorus is used for DNA, ATP and phospholipids, and Nitrogen is used for pretty much every protein a cell might want to produce.  That is, their need for biological processes is not tied specifically to photosynthesis: anything that lives is going to need them, pretty much for anything it might want to do.  It would make sense for them to be a limiting nutrient for almost anything that's trying to grow, plant or animal.

Yet for animals the limiting "nutrient" seems to always be energy, ie: food.  Why aren't animals limited by lack of nutrients in the same way that plants are?  Obviously animals need these nutrients, too.  Or to reverse the question, why do plants need so much more phosphorus/nitrogen than animals do?

My best guess is that an animal's digestion of plant material is relatively inefficient energy-wise but relatively efficient nutrient-wise.  So for an animal to eat enough food to have sufficient energy to survive, it's probably eaten more than enough Nitrogen and Phosphorus for its needs.  But I'm just guessing and I can't find any data that would back up that guess.

Phosphorus

Your suggestion that if we are meeting our calorific requirement we will be getting enough is true for phosphorus.
Most foods contain lots of phosphorus. The maximum dietary requirement occurs during adolescent growth, estimated at 1250 mg per day. Assuming a calorie intake of 2500 kcal we can calculate a 2500 kcal equivalent phosphorus content for various foods:

skimmed milk contains 7,400 mg phosphorus per 2500 kcal

roasted chicken breast contains 7,500 mg phosphorus per 2500 kcal

cooked white rice contains 3840 mg per 2500 kcal

(Calculations are based upon values obtained via this site.)

Nitrogen

Our requirement for nitrogen is met by our protein intake: inadequate protein intake manifests as kwashiorkor which is essentially due to a dietary deficiency of essential amino acids. In other words, the only way to achieve a nitrogen-deficient diet is to not eat protein, and this would not be alleviated by any inorganic source of nitrogen, even if we could consume enough of such a N source.


About validation process of phenological study I have recently done a phenological study using remote sensing techniques. Now I need to validate my results and my methods, that is, to determine if the phenology estimated from remote sensing is suitable to describe phenological events or not. However, I don't have empirical phenological data from the ground to do validation.

Are there any other ways to validate the phenological signal from remote sensing, that do not require empirical data from the ground?

Thank a lot

idea 1) It's possible that some subset of your area has higher-scale / better resolution aerial photographs available. Could you find these and use them to test your model?

idea 2) What geographical area / timescale are you looking at? For certain areas/times, you can get a bit of data on phenology from dated herbarium specimens (ie pressed plant collections). So, for instance, you might select a few plant species that you think are good indicators of whatever phenology you're modelling, search for them on GBIF, consider only those specimens that match your geographical area, and look at what time of year the collections have been made. Then you could look at the first, or last, or various quantiles of phenology. It's not ideal data, but each specimen represents a very direct data point (that is, you know there was at least one individual that had flowered / leafed / whatever at that exact date and georeference), and it's available without getting your feet dirty.

idea 3) Again depending on your geographical area and what measure of phenology you're interested in, you might even be able to use non-aerial photographs, if they're dated.


A mathematician's confusion regarding parametric $t$ tests for gene expression data I'm a mathematician trying to test some things on gene expression data, and I'm thus skimming over various articles such as Sotiriou et. al. to understand what is typically done with such data sets. Several things confuse me; in particular, a paragraph in Sotiriou et. al. reads:

"Clinical parameters such as ER status, [...] affect the behavior of breast
cancers. We asked whether these clinical/pathologic characteristics were
associated with differential gene expression. Parametric t tests identified 606
probe elements of 7,650 elements represented in our array that could segregate
ER+ and ER- breast tumors (P < 0.001)."

As segregation of ER+/- based on gene expressions is one of several things I'm
interested in attempting to achieve through novel methods, I have been trying
to understand what precisely is meant with the above paragrah. To recap the
article, there are 99 patients with 7,650 probe expression values, and one
ER+/- value each. The article sets out to determine which of those 7,650
probes successfully segregate the dataset into ER+ and ER-.

I've run the above paragraph by a nearby statistician, and he could not for
the life of him figure out what was done, and had not even heard of such a
thing as a "parametric t test". This leads me to suspect that the term is
specific to biology, so I ask: what is meant?  It is also unclear to me (and
him) what the P-value means in this context.

I hope the scope of this question isn't too broad. Of course I want to avoid
asking "explain this article to me, the outsider, please"; I do believe the
paragraph above is relatively self-contained in the context of gene
expression.

References:

Sotiriou et. al., Breast cancer classification and prognosis based on gene
expression profiles from a population-based study.

I understand this in the following way:

For each probe you have two sets of measurements, one for ER+ and one for ER-. What you do is a T-test (to my understanding is that the "parametric" just emphasizes that T-test is a parametric test) on these two sets, testing if their mean is significantly different (they refer to this as "separated"). You repeat this test for all 7650 probes, and you get a set of 7650 p-values. You then do some multiple testing correction, such as a Bonferroni correction (I haven't checked in the paper if they did it, but they obviously should). Finally, they find that 606 of the p-values are significant (for some choice of threshold), suggesting that they can "separate" ER+ from ER-.

As a computational biologist I would advise you to look specifically at bioinformatics papers if you are looking into developing new methods, since the analysis in "pure biology" papers can often be lacking and would not give you a good perspective of state-of-the-art analysis methods. Specifically for the question of separating groups from gene expression you should look into the field of Machine Learning, as it had been widely applied to this problem.


Somatic Mutations in meristem tissue in plants In angiosperm, in which layer of the meristem does a new mitotic mutation occurring has chance to be found in a pollen grain or in an ovule?

I also welcome some insights about non-angiosperm plants.

You can see the wikipedia article on meristem.

The apical meristem differentiates into floral meristem that gives rise to flowers.
From this the cells specifically expressing APETALA3 (AP3), PISTILLATA (PI), AGAMOUS (AG) and SEPALLATA (SEP) would give rise to the stamen [ref].

CRC gene is essential for female development and plants lacking this will not produce pistils. So cells expressing this gene will give rise to female parts[ref].

Nonetheless mutation happening at any stage of the development of floral meristem can be transmitted to the pollens/ovules if the mutated cells stochastically give rise to that lineage.


Help analyzing SDS-Page gel In this experiment, we transformed a truncation of the NFAT protein sequence into a plasmid vector to be expressed in E.Coli as a fusion protein with GST.  We also attempted to transform the normal plasmid without NFAT so that we could get GST alone.  After growing up these colonies and selecting positive colonies, we lysed the e.coli.  We collected some of this lysate for SDS-PAGE.  We then put the lysed GST and GST-NFAT solutions in separate columns with glutathione beads.  GST binds glutathione.  We washed the column and collected some of the wash for SDS-PAGE.  Finally, we eluted the GST and GST-NFAT off the column and saved some for SDS-PAGE.

I have attached a picture of a successful version of the SDS-PAGE.

You want to direct your attention to the first lane, the Molecular Weight Marker (MWM).  The rest of the lanes should be interpreted in sets of 3.  The first of the three is the crude lysate, the second of the three is the first wash, and the last is the eluted protein of interest.  The important lanes for my analysis are 8-10 and 11-13.

I will explain what I know from this SDS-PAGE gel so far.  I know the weights of the different bands in the molecular weight marker because I was given a copy of the different proteins in the marker.  From this information, I was able to confirm that I isolated my protein of interest in lane 13 and isolated GST-alone in lane 10.  I also understand the reason why the lysate lanes are darkest, followed by the wash lanes, and then very clean protein of interest lanes.  Also, note that the marker and the elution lanes were loaded with 10 microliters while the other lanes were 2 microliters each. However, there are some things that I do not understand from the gel.
(1) Why are the bands so diffuse/low resolution.  I imagine it may be overloading the wells, but I am not convinced because I followed a set procedure.
(2) Why is there large amounts of streaking, especially in lanes 5, 8, 9, 10, and 11.
(3) I isolated my protein of interest because it was a fusion protein with GST (or just GST alone), and then eluted the protein off the glutathione beads via excess glutathione wash.  Theoretically, the lanes for the elutions should be free of everything except the protein of interest and glutathione then.  This mostly holds true for lanes 4 and 9, which should only have GST and glutathione.  However, lanes 7 and 13 should only have GST-NFAT and glutathione.  The lanes are not as clear however and seem to have stained numerous other proteins.  What is going on?
(4) I was told by a professor that the second band in lane 13 (the GST-NFAT lane) was a degredation product.  How can this be?  The band does not correspond to the weights of NFAT alone or GST alone.  Also, if the NFAT-GST was degraded, wouldn't there be two bands of degredation product?
(5)  Why do the GST-alone lanes have what looks like doublet-bands?  (Lanes 4, 10).
(6)  If we eluted the proteins of interest with excess glutathione, which has a very low molecular weight, why doesn't it show up on the gel?  Is it possible that it ran off before everything else?
(7)  I have a list of the weights of the bands of the molecular marker.  Yet, there is an extra band at the bottom that does not show up on my list.  Is it possible my list is incomplete, or is there something else happening?

Finally, I have attached a picture of a failed SDS-PAGE gel.

The only thing that I definitively know was a source of error is the fact that my buffer level fell during the run (due to a leak).  The results of this gel are accurate (Lanes 2-7 correspond to lanes 8-13 on the above gel, and the results are almost identical) yet the gel turned out horribly.  How can the buffer falling cause this result?  Or is there something else that may have contributed to this weird pattern?  Finally, the lanes are not as distinct in this gel as the first gel, yet the same comb, and thus the same size and spaced wells were used.  So why was there so much bleed between lanes/ lack of space between the lanes?

Thanks in advance for any help.

Here are some thoughts based on my own experiences purifying many proteins and running many SDS-PAGE gels:

(1) Resolution--how fast did you run this gel? Often if you run at higher than say 150V or so you can get bands that look like this. The resolution could also be related to..

(2) I would bet the streaking is due to salt in the sample--a lot of the time lysis/wash/elution buffers can have upwards of 500 mM or 1 M salt, and this invariably causes streaking. Load less sample in these lanes and keep the total volume the same to dilute the salt below 250 mM at least. Other things in your buffers could be causing the streaking, but salt is the most common (let us know the composition of your lysis/wash/elution buffers).

(3) Your purification of GST alone looks very good--often your preps will look much more like the lanes you have indicated, which are not entirely clean. This is quite common for a one step purification--often you need 2-3 for certain proteins to completely remove contaminants. There are several possible sources of these bands:

Endogenous proteins: Many bacterial proteins will non-specifically stick to the beads (this is why we wash), but even thorough washing can still leave some contaminants. These proteins also could be bound to your protein of interest and are co-eluted off of the resin.
Truncation products: Depending where your tag is (let's sat it is on the N-terminus), you can sometimes get incomplete translation products--they have the tag, but they are not full length proteins. These will still bind and elute from the beads because they have retained the tag. Ignore this point if you tag is on the C-terminus, as in that case the tag will only be on full-length protein.
Degradation products: This is related to your later questions--often during the purification your protein will be degraded by bacterial proteases. Did you include a variety of protease inhibitors in your lysis buffer? Keeping all of your samples on ice is also important for this reason.

(4) Understand that degradation products do not mean you get only your protein and the fused GST--they can be a variety of truncations due to degradation by proteases.

(5) I would bet this is just due to your running conditions or the salt in your samples. I think this is probably actually your single GST band.

(6) Glutathione will not show up on the gel--it's formula weight is about 300 g/mol if I recall meaning it's about 300 Daltons, so much smaller than anything that you'll retain on the gel. Further, remember than your stain is for proteins--Coomassie blue binds basic residues on proteins.

(7) I'm not sure which band you are referring to, but I think the very bottom band in your marker lane is simply the dye front. It could also be a degradation product of a protein in your ladder.

As far as the second gel goes--it is all due to the buffer level falling during the run. Without buffer covering the top of the gel there is no current flowing. Probably as the leak was occurring you had uneven distribution of the buffer. Strange things can happen when this occurs (unscientific, I know).


Is there any evidence for sperm parameters being connected to fitness of the offspring produced by that sperm? In most (if not all) sexually procreating species the amount of offsprings a male can produce is limited not by the amount of sperm he can produce, but by the amount of eggs his sperm can fertilize (with rare individual exceptions).
Because of that the optimal strategy would be to fertilize eggs with the best sperm.
Therefore it is reasonable to assume that there would be adaptations making sperm with deficient genes less likely to fertilize an egg.
But is there any evidence of this happening? E.g. would fertilizing eggs with less motile sperm (potentially with IVF) produce a less genetically fit offspring or result in a miscarriage?

The only way that natural selection can act on genes is when they're expressed, there's no mechanism for reading and assessing the "quality" of a gene in a sperm. Obviously the genes that effect the quality of the sperm will be selected for/against.


Cheapest way to measure S. aureus and Rhinoviruses density at home I would like to measure the surface density of Staphylococcus bacteria and Rhinoviruses (only those two, to be specific) within my home.  What's the cheapest way?

The textbook procedure is to:

rub a clean wet cotton swab on the surface in a controlled way
dip the swab into a clean agar (or some living media to detect viruses?) dish
incubate the dish
"look for genetic patterns from special enzyme reactions".

Is it possible to do the last step at home?  Or, is there some easier way if I only care about Staphylococcus bacteria or Rhinoviruses?

For anyone getting ideas

S. aureus and Rhinovirus are risk class 2 infectious substances that should only be handled in a BSL or containment level 2 environment. Your only feasible step here is swab, seal, and send to a lab that can handle it.


How can an infection of lower respiratory tract lead to a skin infection? I am interested in the multifactorial process about infectious diseases of the lower respiratory system and their progression to a skin infection.
Possible agens are zwitterions, viruses, fungi, amoebas, bacteria and/or parasites.

Zwitterions

Small protein segments, much unknown but their importance is much greater than known.

Viruses

Parvovirus B19

Example of a case: 5 children develop a bright red rash on the face and turns violet after a few days and then disappears. Then maculopapular rash appears on the trunk, buttocks and extremities. It soon fades from the trunk but persists on the thights and forearms. Two children have also had a slight fever and a sore throat, but all were not terribly sick. What is the genetic material of the most likely causative agent?
It is a skin infection. Not so severe. Little upper respiratory infection but not necessary caused by the agent. Infects many so spread probably by respiratory droplets. **But how a respiratory infection can lead to a skin infection?*

Bacteria

....

Amoebas

...

Fungi

....

Parasites

...

One might argue that since replication takes place in erythroblasts (Brown, Anderson, & Young, 1993), that it's not actually a respiratory infection either.  Fluids are simply more hospitable to the virus and more transmissible.

As for the rash, perhaps it is because the P antigen receptor that erythrovirus uses to infect erythroblasts is also expressed on endothelial cells, like those in skin (and alveolar) capillaries .


Can the heart generate its own rhythm independent to the SAN? My textbook and a revision guide, which I believe is a reinterpretation of the textbook, state that:

  The SAN initiates waves of excitation that usually override the myogenic action of the cardiac muscle.
  From the textbook

The revision guide is more direct in its interpretation of the textbook:

  The heart muscle is myogenic, which means that it can generates its own rhythm. However, this rhythm is overriden by the sinoatrial node (SAN).

I wonder whether the textbook was interpreted incorrectly, or if in fact the heart can contract independent to the SAN?

Your textbook and review guide are correct, but the missing details may be a little confusing. Yes, the heart has the property of automaticity, meaning action potentials fire on their own at a certain rate, without input from the nervous system. Yes, the SA node typically controls the overall rhythm of the heart because it overrides the rhythm of the rest of the heart.  However, not all cardiac muscle cells have automaticity. Cells in the SA node, the AV node, and to a certain extent, the conducting system all exhibit a physiologic automaticity, that is, they have ion channels that carry what is called a pacemaker current (or sometimes "funny current"), that slowly depolarizes their membranes after each action potential. When this slow depolarization reaches the threshold voltage, another action potential fires. The SA node drives the rate of the heart because an action potential reaches these other automaticity centers, or latent pacemakers, before they would fire on their own. Normal, non-conducting atrial and ventricular myocytes do not exhibit a pacemaker current (except in certain pathological situations), so do not contract independently. So, while the heart muscle is, as your textbook describes it, "myogenic", normal cardiac myocytes (in an intact organ) are not.

This becomes important in cases where the SA node is unable to generate an action potential, is suppressed (is generating an action potential at a slower rate), or other cells with a pacemaker current have increased their rate of firing. In these cases, you can experience an escape beat (a single action potential from a latent pacemaker propagates through the conducting system to cause a heart beat), or an escape rhythm (a series of escape beats).

These are general textbook level principles. You can refer to the wikipedia entry linked above. They are discussed, perhaps more authoritatively, in Lilly's pathophysiology of heart disease. Chapter 1, under electrophysiology, discusses the general principles of automaticity, pacemakers, and latent pacemakers. Chapter 11, under native and latent pacemakers, alterations in sinus node automaticity, and escape rhythms, goes into more detail about the circumstances in which latent pacemakers drive the heart.


How to convert a genus name to a noun or adjective Consider the crayfish family Cambaridae.  As I understand it, this familial name can be turned into an English noun or adjective by changing the first letter to lower case and dropping the "ae." An example use is "Responses of cambarid crayfish to predator odor" (adjective). Similar conversions from generic names are widely used as well.  For example, for the crayfish genus Procambarus, the english conversion "procambarid" is widely used, primarily as an adjective, but also as a noun. A google scholar search for this word turns up hundreds of uses.  A search for "id" conversions for other generics names for hermit crabs, and snake genera turn up uses of them as well. I cannot find any information that actually describes this conversion and it's rules.  Can someone point me to a reference, or otherwise help clarify the issue?

I think that it boils down to taking a Latin name and removing the case ending to get an acceptable English adjective. Given that it might be a purely linguistic situation, it's possible another SE site would be better (English language?), but this topic is definitely relevant to biologists, as they're probably the ones who run into it most frequently.
We can look at IAPT article 60.10 and it suggests a systematic way to do this, albeit for an unrelated reason. I don't see that they directly address the anglicized Latin adjective form:

A noun or adjective in a non-final position appears as a compounding form generally obtained by
(a) removing the case ending of the genitive singular (Latin ‑ae, ‑i, ‑us, ‑is; transcribed Greek ‑ou, ‑os, ‑es, ‑as, ‑ous and its equivalent ‑eos) and
(b) before a consonant, adding a connecting vowel (‑i- for Latin elements, ‑o- for Greek elements).

I think that we want to apply step (A) but not step (B) here, as their goal is the formation of compound names, and step A alone will get us -id, which is an anglicized adjectival ending (-idus --> -id).
Taking your examples:

Cambaridae --> remove Latin genitive suffix -ae --> cambarid.
Procambarus --> make Latin noun into the adjective procambaridus --> remove suffix -us --> procambarid.

Unfortunately, it looks like there are a ton of possible Latin adjectival endings- the -id examples seem pretty straightforward because you can get an English adjectival ending directly, but other taxonomic names don't resolve so neatly. For example, if I want to use "Lachnospiraceae" as an adjective, I could imagine the following (applying only step A above doesn't seem to work well: "lachnospirace"):

lachnospiraceid
lachnospiraceal
lachnospiraceous

and I don't really know how to pick among them!
I have left a comment on a blog post from Stephen Heard on a related subject (comment above), perhaps he'll see fit to weigh in here.


What is the reason behind the subphylum name "Urochordata" for tunicates? There are two major invertebrate subphyla of the chordates (phylum Chordata):

Cephalochordata (the lancelets)
Urochordata, aka Tunicata (the tunicates)

My understanding is that the cephalochordates are named as such (meaning “head chords”) because the notochord reaches into the head. From Wiktionary:

  Any of the primitive fishlike creatures, of the subphylum Cephalochordata, including the lancelets, that lack a true spine but have a notochord which, in the case of cephalochordates, reaches into the head, contrary to the Urochordata.

Urochordata, by contrast, means "tail chord", though I cannot find a reputable source (or any, really) that describes or details why this is the case.

I can surmise it's simply because the notochord doesn't reach the head of a tunicate embryo -- as is corroborated by an image from Lemaire 20111 copied below.

 Image D' shows notochord in red. Credit: Lemaire 2011

However, I would prefer a quotable, reputable source that indicates explicitly that the Urochordates are in fact named as such due to their notochord not reaching their head.

If this is not the case, then my question more broadly stands at: Why are the Urochordates named the way they are?

 1: Lemaire, P., 2011. Evolutionary crossroads in developmental biology: the tunicates. Development, 138(11), pp.2143-2152.

In 1877, Lankester proposed in "Notes on the Embryology and Classification of the
Animal Kingdom" division of the group we now call Chordata into three parts:

Urochorda
Cephalochorda
Craniata

which is more or less the accepted division today, with Urochorda being called Urochordata now.

In this essay, Lankester says:

  The evidence of degeneration is admitted as conclusive in the case of the parasitic Crustacea and Cirrhipedes. It is equally incontestable in that very large and varied group of non-parasitic organisms, the Tunicata (Urochordate Vertebrata).2

(in the above 'Vertebrata' is what we call 'Chordata').  He adds this footnote:

  2The whole argument as to the Tunicates of course rests on the view- supported by many arguments, that the larval urochord, which many of
  them possess, is not a larval organ acquired by larval adaptation, but is hereditary and transmitted from adult ancestors.

The term 'urochord' seems to be established and used without comment there, and probably is taken as simple neo-Latin for 'tail chord', although that may be somewhat loose, perhaps meaning the notochord is present but does not extend into the head.  A 1913 Webster's Dictionary defines urochord as:

  (Zool.) The central axis or cord in the tail of larval ascidians and of certain adult tunicates.

In 1882, Lankester futher discussed the anatomy of the tunicates in the context of the division of the chordata in a paper called "The Vertebration of the Tail of Appendiculariæ".  This paper includes an illustration of a larval tunicate with the "notochord (urochord)" indicated.


Text/resource with information on all skeletal muscles and their motor units Something analogous to an encyclopedia on baseball players with a list of all thier stats would be ideal.

I'm not looking for just generic muscle names, locations and illustrations.

Good answers would include links to resources, textbooks etc. which include stats for most or all of the following of every skeletal muscle in the human anatomy:

Language of origin/LOO definition
Labeled by ? shape, location, size etc.
Type of Shape (i.e., fusiform, pennate, bipennate, multipennate, convergent, parrellel etc)
Angle(s) of pennation (if applicable)
# of motor neuron innervations
# of proprioceptors in muscle
# of fibers
Length of muscle
Length of fibers
Typical fuel system reliance (determined off of biomechanical placement and architecture..CPr, oxidative, etc.)
Biomechanical function (structure of corresponding bone/tendon anchors and corresponding movement manipulation)

You can try Biomechanical models used in software frameworks such as OpenSim.

Here is an example of a combined upper and lower body model in XML: ULB_Project.