What is a subspecies? Within a species there may be subspecies that are named using trinomial nomenclautre. For example the Grizzly Bear, Ursus arctos horribilis is a subspecies of the Brown Bear Ursus arctos.

The dictionary definitions of subspecies seldom expand beyond this:

  A taxonomic category that ranks below species, usually a fairly permanent geographically isolated race.

I'm assuming redefining species into subspecies is not a completely arbitrary process as the definitions would imply, but is based on biology. What are the biological criteria for a group within a species to be "upgraded" to a subspecies?

In practice, subspecies are often fairly loosely-defined, reflecting a degree of uncertainty and ambiguity at this level of taxonomy. There are systematists who take the view that subspecies-level classifications should not be used as they are not rigidly definable.

In general, a subspecies will fulfil the following criteria:

it will occupy a distinct geographic range from other subspecies
within its species,
it will have limited gene flow to other subspecies within its species, while still being capable of interbreeding
it will have some recognizable shared character, used to distinguish it from other subspecies within its species

Subspecies classifications, and their usefulness, are discussed in the Turtle Taxonomy Working Group's 'Turtle Taxonomy: Methodology, Recommendations, and Guidelines', for those interested in further reading.


What is the physiological difference between cortisone and cortisol? There is only hydrogen bond different.
Cortisol is synthesized by our body, while cortisone is given to the patient.

Why you cannot give cortisol directly to the patient?
I think the reason is metabolism that cortisol will break (probably in liver) and not be useful.
Or expansive to produce.
Cortisone however can be given.

What is the physiological difference between cortisone and cortisol?

Cortisol is directly given to the patient - it is then called Hydrocortisone. I don't know why this is done but probably to avoid confusion because both names are too similar.

The difference between both forms is one hydrogen atom at the C11 position of the molecule in Cortisol (or Hydrocortison) (image from here):

Otherwise is Cortisol (or Hydrocortisone) the active version, while Cortisone isn't very active in the human body.
Both forms can enzymatically turned into the other form (from active to inactive and vice versa). Since Cortisone needs to be activated in the liver, it can only be used for oral uptake. Most of the uses which are colloquially called Cortisone in fact contain Hydrocortisone.


How exactly do birds get drunk eating fruit? Fermentation should be anaerobic The Washington Post article Drunk birds are causing havoc in a Minnesota town. Police say they’ll sober up soon. describes birds becoming intoxicated after eating berries:

“The Gilbert Police Department has received several reports of birds that appear to be ‘under the influence’ flying into windows, cars and acting confused,” Police Chief Ty Techar wrote in a statement Tuesday. An early frost meant that berries had fermented earlier than usual, he explained, and birds were eating them and getting drunk.
Incidents around town involving intoxicated birds appear to be more prevalent than in past years, Techar added, because many have not yet migrated south. “It appears that some birds are getting a little more ‘tipsy’ than normal,” he wrote. “Generally, younger birds’ livers cannot handle the toxins as efficiently as more mature birds.”

A few supporting videos:

ABC TV: Drunk birds are flying into windows, cars
TIME: Drunk Birds Are Flying High In Gilbert, Minnesota | TIME

Is the fermentation happening to the berries while on the tree or on the ground as the police suggest, or is it really after being ingested by the birds? How is an anaerobic environment produced for fermentation into alcohol but not subsequent conversion to vinegar?
Humans are a clever species, on par with some birds. They are known to collect the berries and ferment them first before ingesting, and will forage for a trap to let gas escape but keep the oxygen out. Have birds found a better way?
 Source

The insides of fruits are relatively anaerobic environments. Natural fermentation, as in berries that get birds intoxicated, is primarily from yeast, and it seems most likely that humans recognized this process before intentionally encouraging fermentation of anything. Natural fermentation reaching high ethanol concentrations occurs especially when berries high in sugar are frozen and then thawed.

Dudley, R. (2004). Ethanol, fruit ripening, and the historical origins of human alcoholism in primate frugivory. Integrative and comparative biology, 44(4), 315-323.

Fitzgerald, S. D., Sullivan, J. M., & Everson, R. J. (1990). Suspected ethanol toxicosis in two wild cedar waxwings. Avian Diseases, 488-490.


Has any flying creature evolved into a sea creature? I am talking about a creature that has evolved true flight.
Has any such creature evolved into a sea creature, that permanently dwells on water (like fully aquatic fish) and doesn't come out? According to the theory of evolution, many sea creatures of the deep past evolved into land animals and some of them went a step further, evolving flight. I am talking about the reverse process, excluding semi-aquatic or semi-terrestrial animals.

Clarification of the question
The following feedbacks from the OP are his comments below

By creature of course I denote animals
I meant animals that can fly (not glide) and control their flight
By sea creature I mean those animals that either breathe in water with gills (e.g. fish) or the ones that have to surface to breathe (e.g. whales).

Answer
Water beetles are the perfect example.

They live underwater, some of them very rarely (if ever) surface as they capture air under their abdomen and can breathe it for a long time while underwater. Just like dragonflies, butterflies, flies, bees, ants, bugs and many others, beetles are Pterygota and therefore have flying ancestors.

Answer before clarification
It all depends what you mean by "sea creature" and "flying" as well as by you mean by "semi-aquatic" and "semi-terrestrial" and also what you mean by "creature".
Here are examples of eventual interest to you.

Birds that are good swimmers, including those that can't fly anymore such as many penguins. No birds can breathe the air dissolved in the water though.

Insects that evolved a larval stage in the water while the ancestors are fully terrestrial. I don't think any insect can breathe under water however several species can carry quite a lot of air with them underwater (such as water beetles) or many just stick their butt out of the water to breathe (like culex mosquito larvae).

It is unclear whether by the use of the term "creature", but if you accept examples from non-animal forms of life, you'll find examples of seed dispersal through water while ancestors used air, you'll find plenty of examples of parasites too.

If by "creature", you meant "animal" and by "flying", you meant high level of control flight and by "sea creature", you meant animal able to breath air dissolved in the water, then I personally can't think of an example of a flying animal evolving into a sea animal.
None of these examples are as pleasant for you as an example of a big flying bird evolving gills that now live in deep sea though but unfortunately, I can't think of such case.
For fun, you might want to have a look at the post How many times did terrestrial life emerge from the ocean?

Your usage of the term "creatures" as well as the phrase "according to evolution theory" and also the phrase "many sea creatures of the deep past" make it feel like you don't have much knowledge in biodiversity, evolution and evolutionary time scale. You might want to get some intro knowledge on the subject. Understanding Evolution by UC Berkeley is a very introductory and pretty short free online course on evolutionary biology if you are interested in.


What is tissue patterning? This term gets thrown around sometimes in biology articles, and I have a rough idea of what it is: during embryonic development, the tissue differentiates in a certain spatial configuration. Wikipedia also mentions that its two main mechanisms are regional specification and cell differentiation. However, I would really enjoy a thorough definition of the term (either in the form of an answer or a reference).

I would guess that the term "tissue patterning" could be an umbrella term for multiple different developmental processes. In precise (more modern) developmental terms it could be a old synonym or sub-type for "Regional differentiation"
https://en.wikipedia.org/wiki/Regional_differentiation
It also fits to the concept of X-inactivation in female mammals, but this phenomenon can not be observed by the bald eye.
https://en.wikipedia.org/wiki/X-inactivation
It is quite possible the term originated from pigmentation biology an early genetic discipline. The underlying mechanism are the Pibald mutations , which result in dysfunction in dorso-ventral melanoblast migration , a dominant mutation, that is a source of white spots and patches in many mammals.

These mutations are almost omnipresent in domesticated furry mammals (cows, dogs, cats rats,horses) as well as some wild species where it gives an evolutionary advantage.
You can also check out cat coat genetics its a lot of fun and relative easy classical genetics.
https://en.wikipedia.org/wiki/Cat_coat_genetics

Excurse biological definitions:
Many biological terms originated in the first years of biology as a science (<1820 ) when genetics, microbiology, evolution and developmental biology where not discovered as disciplines yet (Mendel, Pasteur, Darwin&Wallace where born later, Boviery, Speemann even later), so people (zoologists, botanists) just named the thing they observed, without knowing what the underlying mechanism was. So since they did not have the concept of mendelian inheritance, nor embryonic development, they just called it in layman's therms: "patterning".
Nowadays with the term "tissue patterning" is not totally clear anymore what an author means, if it has no proper context, in my opinion. We have clearer defined terms.


Why does an electric shock contract the muscle? From what I understand, the electrical impulse in our nerve cells is not made of electrons, but of ions that move from different environments with different concentrations, which is totally not related to the electricity we use, which is made of electrons. The electricity we use makes our muscles contract, why? Does it have to do with the fact, that when we put electrodes with electricity in an electrolyte, ions move?

Nice Question! Lets first introduce ourselves to the topic i.e. Electrical Muscle Stimulation.

  Electrical muscle stimulation (EMS), also known as neuromuscular electrical stimulation (NMES) or electromyostimulation, is the elicitation of muscle contraction using electric impulses...The impulses mimic the action potential coming from the central nervous system, causing the muscles to contract.

Now, lets come to the main point. Its actually not about flow of electrons or ions, but the change in voltage that plays the pivotal role in muscle stimulation. See this:

  Crystallographic structural studies of a potassium channel have shown that, when a potential difference is introduced over the membrane, the associated electric field induces a conformational change in the potassium channel. The conformational change distorts the shape of the channel proteins sufficiently such that the cavity, or channel, opens to allow influx or efflux to occur across the membrane. This movement of ions down their concentration gradients subsequently generates an electric current sufficient to depolarize the cell membrane.

In short, when you touch a wire, you become a part of the circuit i.e. any 2 points on your hand (or your hand and foot, if you're barefeet) act as part of the circuit i.e. there is potential difference between them, which generates an electric field. This electric field causes the voltage-gated channels in neurons/muscles to open which, in turn, generates an action potential and causes the muscle to contract.

References:

Electrical Muscle Stimulation - Wikipedia
Voltage-gated Ion Channel - Wikipedia


Do homing pigeons fly straight home or follow certain "highways"? Homing pigeons (Columba livia) have been prized for their navigational abilities for thousands of years. They’ve served as messengers during war, as a means of long-distance communication, and as prized athletes in international races. (Source)

Do all homing pigeons just pick a direction, and fly "straight" home, or do they all follow certain "tunnels" or "roads" to get closer to their home area, before heading home? (similar to cars getting on a highway between two regions)

Does any information about that exist? I'd be interested to know if pigeons released in the same area (with different target locations in one common direction) tend to do follow the same paths, or if it's just a chaotic crisscross.

They have mental maps of landmarks, which they use as well as "compass" cues:

  ... experienced birds can accurately complete their memorized routes by using landmarks alone. Nevertheless, we also find that route following is often consistently offset in the expected compass direction, faithfully reproducing the shape of the track, but in parallel.

--Pigeons combine compass and landmark guidance in familiar route navigation

Landmarks are more important than compass cues in general, and pigeons develop their own landmark maps:

  we show that homing pigeons (Columba livia) not only come to rely on highly stereotyped yet surprisingly inefficient routes within the local area but are attracted directly back to their individually preferred routes even when released from novel sites off-route. This precise route loyalty demonstrates a reliance on familiar landmarks throughout the flight, which was unexpected under current models of avian navigation.

--Familiar route loyalty implies visual pilotage in the homing pigeon

That means that different birds do use different routes:

  Here, we demonstrate that birds develop highly stereotyped yet individually distinctive routes over the landscape, which remain substantially inefficient.

--Homing pigeons develop local route stereotypy

In fact the same bird might use different routes over time as it learns new landmarks:

  a wide intraindividual variability was observed in repeated tosses at the same site; some pigeons remained faithful to the first route, whereas other birds tried successive new routes which, in most cases, were significantly shorter than previous ones. This result indicates that pigeons try, and are actually able, to improve their performance in subsequent releases from the same site.

--Pigeon homing: The influence of topographical features in successive releases at the same site


How to feed bacteria out of lab I want to take a sample of skin infection bacteria (I suppose combination of staphylococus, strep, etc) and give it to the doctor for analysis but the appointment is in two weeks. The bacteria will be dead by then, right? Is there any home-made nurturing solution that I can put them in to preserve them until then?

In a lab there are so many ways of doing this. However, at home is a little tricky. This is what I would do:

Keep your bacteria in a liquid media.

Liquid Media: make the media out of NaCl and AS CLEAN AS POSSIBLE (distilled if possible) water (concentration 18g NaCl / L). Place a sample of the bacteria into the solution. Freeze solution with bacteria (-20 degrees C if possible). Take out when wanted.


enzymes that stabilize DNA loops As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops.

I have read that cohesin is one of such enzymes, but works as a transcription factor by binding specific DNA motifs.

My interest is in knowing what other enzymes will create DNA loops with no DNA motif biases from a DNA extraction.

This is a follow-up question to this one, as ultimately I would like to know if there could be any ways of optimizing the process of DNA circularization of very long stretches of human (or mammalian) double-stranded DNA, from several kilobases to megabases, by first creating stable DNA loops that leave two DNA ends close by for a more effective ligation process.

Any ideas?

I have read that cohesin is one of such enzymes, but works as a
  transcription factor by binding specific DNA motifs.

Cohesin binding is not motif dependent (like transcription factors) and is also dynamic. Though sequence may have a role it is, just as in the case of nucleosomes,  mostly the overall composition rather than a sequence based motif:

From this article:

  Cohesin binding peaks correspond closely to peaks of high local AT
  composition, a base composition periodicity of ∼15 kb that is distinct
  from the ∼50 kb periodicity of base composition isochores, consistent
  with axis association of cohesins.

DNA-protein complexes can be crosslinked and subsequently the loops can be pulled down. However, this is tricky. You would need to cut the DNA at the loop ends in order to ligate them together. I don't know how to do that (Perhaps by using an antibody linked to an endonuclease).


How did the Spanish Flu disappear? In 1918 through 1920, an Influenza pandemic colloquially named the "Spanish Flu", ravaged the world. It infected about half a billion people, and killed as many as 50 million people. But my question is - how did the 1918 flu virus disappear in 1920?

One can hardly believe that after infecting half a billion people, the virus was contained in any sense of the word. Why didn't the more than one billion uninfected people get infected? Why didn't we see some small epidemics continue to circulate the globe infecting the yet-uninfected as well as newly born people for many years - potentially until today?

It's didn't disappear.  It's still around today, over 100 years later.  The 1918 influenza virus is the parent virus for all the human seasonal influenza viruses that are around today, as well as for most of the swine influenza viruses out there.

In fact, the presently circulating H1N1 viruses in humans are close enough to the 1918 virus that they probably immunize against each other (Seasonal trivalent inactivated influenza vaccine protects against 1918 Spanish influenza virus infection in ferrets.).

What did happen is that the 1918 virus mutated, becoming less virulent in the process, within a year or so of entering the human population. Why? Presumably because, after infecting virtually the entire human population in its first year, there was so much population immunity that it needed to mutate a little in order to continue to infect. That is, after all, what flu viruses do.

But it continued to circulate for decades, as a very similar H1N1 virus. Also, it almost immediately infected pigs and became endemic in the swine population, only to resurface  after 90 years to cause the 2009 influenza pandemic.

  In 2009, persons who had lived through the first decades of the 1918 pandemic H1N1 era, especially those born before about 1950, were substantially protected from the 2009 pandemic virus by having acquired immunity to the antigenically similar H1 or N1 of the 1918 virus, or both, or to the descendant seasonal H1N1 viruses that circulated over subsequent decades. This is because the 2009 H1 gene was a 1918 viral progeny that had survived for more than 90 years, with minimal antigenic drift, in a domestic pig “time capsule.”

—The Mother of All Pandemics Is 100 Years Old (and Going Strong)! (Am J Public Health. 2018 November; 108(11): 1449–1454)

In 1957 and 1968, the H1N1 virus reassorted with avian viruses to generate first H2N2 and then H3N2 viruses (the great-grandchildren of the H3N2 pandemic still circulate today). But most of the internal genes in those reassortants remained the 1918 versions.

So the 1918 flu never went away. It’s still killing hundreds of thousands of people every year. It’s just that everyone has got used to it, and thinks it’s fine and normal to have hundreds of millions of influenza cases every year.


Can action potential generating ion channels only be understood as assemblies of membrane proteins (and not as single proteins)? I always believed to have roughly understood how voltage-gated ion channels and the creation of action potentials work: as and by single (or non-interacting groups of) membrane proteins, that behave somehow non-linearily by intrinsic means, each by its own. But suddenly I doubt.

Might it be the case that some of the non-linear dynamics of ion channels and the generation of action potentials cannot be understood when looking only at single ion channels as proteins? Or is it like Wikipedia says:

  A voltage-gated ion channel is a cluster of proteins embedded in
  the membrane.

This means, that some of the non-linearities only occur when many membrane proteins (presumably in a fine-tuned mix of different types) interact?

Maybe only then some features of ion channels can be understood:

Action potentials are always of the same size, independent of the voltage (or current) that is applied/injected (which would be hard to understand for single membrane proteins).
Ion channels can exhibit many different firing patterns, which depend on intrinsic emergent mechanisms of assemblies of membrane proteins.

If this is so, one must be very careful when talking or reading about voltage-gated ion channels, because depending on context sometimes single membrane proteins are meant, and sometimes complex assemblies of non-linearily interacting proteins.

Wikipedia's statement

  A voltage-gated ion channel is a cluster of proteins embedded in the membrane.

is most likely referring to the fact that most ion channels (maybe all? I hate to say "all" in biology) are made up of multiple protein subunits; usually these are all considered one protein's quaternary structure, though, so wikipedia's language is not ideal.

I think you are then running with a misunderstanding of this statement to make some conclusions that are not warranted. Of course multiple ion channels come in to play when you are talking about membrane potentials at the cellular level. Of course you need to consider multiple ion channels when considering the overal membrane potential, but it is sufficient to know only a) the gating properties of a given channel and b) the membrane potential to know the contribution of that channel.

Action potentials are only roughly the same 'size' in terms of voltage amplitude - they are certainly not identical, and this size is because of the gating properties of voltage gated channels and the reversal potential for sodium. The membrane potential can never exceed the reversal potential for sodium via sodium-based conductances, so that puts an upper limit on action potential size. In addition, hyperpolarizing potassium-permeable voltage gated channels will open at depolarized potentials, further limiting the maximum amplitude of an action potential.

Ion channels don't exhibit any firing patterns: neurons exhibit firing patterns that depend on all the channels present and the physical morphology of the cell.


How do birds avoid mid-air collision? Across from me there is a large flick of Pigeons and Ravens that like to nest on the roof. They swoop and dive and fly all over. Sometimes the whole flock lifts off at once. My question is, how do they avoid running into each other? Certainly they can't see every bird around them, can they?

They can't see all the birds that are around them as some are hidden behind the others. However, I don't think there is anything so extraordinary; they watch around, have good reflexes and can change direction very abruptly. There is no need for some kind of special sensing abilities to explain bird flocks.

3 simple rules

One can simulate a flock of birds with 3 simples rules:

Adapt your speed on the speed of the other agents

$$\overrightarrow v_{i,1} = \frac{1}{K_L}\sum_j^K\overrightarrow v_j (t) - \overrightarrow v_i(t)$$

, where $K_L$ is the number of birds in the Large area of perception, $\overrightarrow v_j (t)$ is the speed of a given bird in the large area of perception and $\overrightarrow v_i (t)$ is the speed of the focal individual.

Attraction

$$\overrightarrow v_{i,2} = \frac{1}{K_L}\sum_j^K\overrightarrow p_j (t) - \overrightarrow p_i(t)$$

, where $\overrightarrow p_i(t)$ and $\overrightarrow p_j(t)$ are the positions of the focal bird and of a bird present in the large area of perceptio, respectively.

Repulsion

$$\overrightarrow v_{i,3} = -\frac{1}{K_s}\sum_j^K\overrightarrow p_j (t) - \overrightarrow p_i(t)$$

, where $K_s$ is the number of birds present in the Small area of perception.

Then, to update the speed of the birds you just sum up those 3 contributions:

$$\overrightarrow v_i(t+1) =  \overrightarrow v_i(t) + \overrightarrow v_{i,1} + \overrightarrow v_{i,2} + \overrightarrow v_{i,3}$$

see boids for more information.

My point in descrbing this algorithm is that you can get the emergent behaviour of a bird flock out of very simple rules.

Bird Collision

If birds don't often collide each others (what I assume but honestly I don't know much), note that it is estimated that 100 millions birds that die every year after colliding a window (see here). Birds also collide with power lines (ref) and wind turbines (ref).


Can you approximate Cardiac Output by Ohm's law? I found this sentence from my notes which I cannot understand

PR < CO, CO $\uparrow$, PR > CO $\downarrow$

where

\item CO = AP / PR, Cardiac Output = Arterial P / Peripheral Resistance

I cannot understand the first sentence.
I cannot understand how you can deduce by Ohm's law the relationship.

What is the point of the first sentence?

I don't get the first sentence either, since PR and CO in your notation are in fundamentally different units. It's like saying '4 Celsius < 5 meters.' You will have to think about what you are implicitly holding constant and ignoring in that relationship to make it meaningful. I suspect the first sentence is just emphasizing the inverse relationship between CO and PR (PR goes up, CO goes down, etc).

As for Ohm's law, absolutely! You have it written right there. I assume Cardiac output is the flow rate of fluid in a blood vessel, and AP is arterial pressure, and PR is peripheral resistance. Stated another way,

$\textrm{Flow} = \frac{\textrm{Pressure}}{\textrm{Resistance}}$,

which is exactly Ohm's law. Frequently electrical current is described with a Hydraulic analogy, with pressure$\rightarrow$voltage, fluid flow$\rightarrow$current, and flow resistance$\rightarrow$electrical resistance. It makes a lot of sense, since electric current is literally flow of electrons. Poiseuille's Law that makes this analogy rigorous, deriving an Ohmic relationship between those variables. Interestingly enough, Poiseuille derived the law in the context of blood flow, making it particularly applicable.


What is the specific use of a capsule in E.coli? In evolutionary terms, will the capsule cease to exist someday or will it improve ? Does it provide any boost to the organism in any way which harms us ? Can't we remove capsules or engineer E.coli without capsule ?

According to wikipedia, the capsule contains tightly packed polysaccharides that preform several functions including keeping bacteriophages out, blocking recognition by macrophages, and holding water during dessication. Given the wide diversity of bacteria with capsules, it's probably been around for a long time, which implies it isn't going away any time soon.

If the capsule prevents the E. coli from being taken up by macrophages, then yes, it could allow the bacteria to harm us more effectively. This is one form of a virulence factor.

With proper conditions we probably could develop a bacteria with little to no capsule. We have developed L-form bacteria, which don't have peptidoglycan cell walls. It would seem to me that the cell wall is more important than the capsule, but L-form bacteria are very fragile. I don't know what advantage would be gained by producing capsule free bacteria. There would probably be more to gain from making bacteria with different capsules, perhaps carrying proteins that recognize certain substances and produce a signal, allowing the bacteria to be used as a biosensor, or to accumulate toxic compounds for bioremediation.

references: http://en.wikipedia.org/wiki/Bacterial_capsule http://en.wikipedia.org/wiki/L-form_bacteria


What is the largest perennial herbaceous plant? What is the largest perennial herbaceous plant? My guess would be some kind of banana or bamboo.

As mentioned above, the largest perennial herbaceous plant is indeed the banana.  Whilst the main reference to this ("Yes, we have more bananas" - an article in the Royal Horticultural Society Journal from May 2002) has been removed from their website it would be I'm sure possible to order should you need to.

This summary of the banana mentions that the pseudo-stem of the banana plant grows to 6-7.6m in height - I haven't found anything taller when looking around so it doesn't generate any reason to doubt the removed article.

Regarding the comments on Bamboo, there are 7 genera containing bamboo species.  All of these (Arthrostylidium Rupr, Bambusa Schreb, Chusquea Kunth, Dendrocalamus Nees, Phyllostachys Siebold & Zucc., Pseudosasa Makino and Sasa Makino & Shibata) are described as having persistent woody stems so don't meet your herbaceous requirement.


What kind of viruses can be found in sperm? It is well known that the HIV virus can contaminate other people via sperm. But is this the only virus that sperm successfully could contain, or could for example rhinoviruses also be part of sperm?

What causes the difference if there is one?

Those are some viruses that can exist in sperm :

Zika : Zika and Sexual Transmission
Ebola : How Long Does the Ebola Virus Survive in Semen?
Hepatitis C : Hepatitis C virus detection in the semen of infected patients
Human papillomavirus infection (HPV) : Correlation between HPV sperm infection and male infertility
Herpes simplex : Detection of herpes simplex virus DNA in semen of men with genital HSV-2 infection
Hepatitis B : Effects of hepatitis B virus on human semen parameters and sperm DNA integrity


What is the purpose of the viscous gel in the Pacinian corpuscle? I have read that 'when the stimulus (in this case pressure) is constantly applied, the gel repositions itself to prevent the formation of an action potential'. I don't really understand what this means.

Short answer
The adaptation process in Pacianian corpuscles (PCs) is mediated via the outer capsule. This capsule is an onion-like structure that quickly molds itself to pressure stimuli, thereby rapidly desensitizing the receptor.

Background
The Pacinian corpuscles are rapidly adapting (RA) skin receptors, as opposed to the slowly adapting (SA) ones, such as the Merkel cells. RA cells become swiftly unresponsive (i.e., they adapt) when a pressure stimulus is applied, but faithfully transmit rapidly changing stimuli (such as vibrations).

Pacinian corpuscles are specialized vibration receptors. Their dendritic region is shaped as an onion-like structure with layers of stacked lamellae:

Specialized dendritic capsule of the Pacinian corpuscle. Source: Biologymad

These lamellae act as high-pass filters that result in a sharp drop in sensitivity below 150 Hz (Johnson, 2001). If this capsule is dissected from the receptor and a pressure stimulus is directly applied to the sensor element underneath the capsule, the receptor response to a sustained stimulus substantially increases (Mendelson & Loewenstein, 1964). Basically, these elastic lamellae slowly mold their shape to the stimulus and pressure stimuli are only transmitted for a few milliseconds, after which the lamellae absorb the pressure. So only a one or a few spikes are generated at the start of a pressure stimulus.

You can imagine it this way, suppose you have a gel-like substance (say Play-Do) on a weight scale. Now suppose you press the Play-Do quickly and hold your finger steady at a certain point above the scale, within the Play-Do. The weight scale will shortly display a certain weight (equal to the pressure applied in Newtons), after which the Play-Do folds itself around your fingertip, and the pressure is released from the scale.

Upon release of the pressure stimulus another spike or two are generated in the PC. Hence, a continued pressure stimulus is not faithfully reproduced. However, vibratory stimuli generate spikes on the pressure onset as well as offset as well, and this happens on every phase of the vibration. Hence, vibratory stimuli are faithfully transmitted.

Response of Pacinian corpuscle to a sustained pressure stimulus (indentation of the skin) and superimposed vibratory stimuli. Note the vigorous response to vibrations, but the rapid adaptation to the static pressure stimulus. Source: Zavantag

References
- Johnson, Curr Opin Neuobiol 2001;11:455–461
- Mendelson & Loewenstein, Science 1964;3618:554-5


Survival with only water but no food How long can the average, healthy adult human survive with only water?

On average, it has been stated to be about five weeks however it differs from person to person based primarily on physical stats.

The process that would occur :

First food that remains in your stomach is digested
Readily available energy is then absorbed (This includes glucose, carbohydrates, anything that generally doesn't mean fat)
Your body then begins to convert fat into a source of energy. Your body would then begin to lose the resources to make protein and you would experience various effects such as night time blindness due to vitamin deficiencies
As you lose salt and other minerals the water you consume begins to build up in your cells via diffusion
You can either die of not enough energy or lack of protein or too many cells disintegrate from too much water

Source(s) : Biology book, Internet, Knowledge.


What is enantiostasis? I have searched around and read my textbook but I am failing to understand how enantiostasis is different to homeostasis. For reference, Wikipedia definition is as follows:

  Enantiostasis is the ability of an open system, especially a living organism, to maintain and conserve its metabolic and physiological functions in response to variations in an unstable environment. Estuarine organisms typically undergo enantiostasis in order to survive with constantly changing salt concentrations.

Both are ways for an organism to adapt to the environment, but enantiostasis focuses on maintaining functionality while homeostasis focuses on maintaining a stable internal environment.

For example, if the organism has to deal with changing salt concentration in water, it can do it in two ways:

Homeostasis : the organism will adapt itself so that its internal conditions do not change despite the change in the external environment (the focus is on not changing these conditions). This could mean stopping or reducing other activities because of this adaptation, but, in this example, the internal conditions (salt concentration inside the organism) will not change.
Enantiostasis : the organism adapt itself so that its functionality is preserved, at the possible expanse of stable internal conditions. This could mean the salt concentration in the organism will change, but the organism's functions will not stop or be reduced because of it. Enantiostasis can be realized either by avoiding external changes (for example, absorbing more water when the salt concentration is high and less when it's low) or tolerating it with a wide range of possible conditions.

(Source : detailed explanation on this subject as a commentary on a university course)


Red Blood Cell Size Vs White Blood Cell Size I have just found out that white blood cells are larger than red blood cells and now I'm confused due to something I learnt in class. Basically, I was taught that there were spaces between the endothelial cells lining the capillary and these spaces allow white blood cells to escape and enter infected tissues to help clear out the infection. Why don't the red blood cells escape then if they are smaller than white blood cells they should fit through the spaces as well right?

there are several types of white blood cells (at least 4) and they vary greatly in size from type to type.
white blood cells are not rigid, they can squeeze through very small openings. it always buts me in mind of watching a octopus squeeze into a bottle.


Would a spinal injury decrease human height? A woman I know has been losing height at a rate of few cm a year following a severe spinal injury. How is this possible? What kind of injury could cause such progressive loss of height? Could this be a genetic defect? Are there any disorders that cause this type of shrinking?

In case it could be relevant, her brothers are very tall.

As @WYSIWYG pointed, muscular atrophy is the main cause for height decrease.

A spine injury leads to neural impairment and paresis / paralysis. This affects directly muscular trophism. It also limits physical activity, this being another favoring factor for muscular atrophy and overweight issues [1]. Association of bone degenerative processes (osteoporosis, osteopathy, osteolysis) is also a factor and it is dangerous because it promotes spinal cord injuries if vertebral height reduction amount is notable [2].

Focusing on muscular atrophy, here is how it can decrease height: by increasing vertebral column curvatures mostly on the upper region with articulating vertebrae. The vertebral column tends to gain a spring-like, spiral shape, associating accentuated cervical lordosis, accentuated thoracic  kyphosis and thoracic scoliosis.

Image source: Scoliosis Treatment Alternatives. Chiropractic for Scoliosis Treatment Review (2014). Accessed 21.07.2014

While reading the comments to the question I found something interesting:

  we know that the brain tells the body to grow, would a shock or something make the brain tell your body to shrink instead of growing?

Yes, the brain (hypotalamus) initiates a neuroendocrine response that leads to growth hormone secretion. The secretion is about 700 micrograms/day in a young adolescent, while in a healthy adult it is about 400 micrograms/day [3]. The deficiency in an adult person leads to a tendency of fat mass increase and a relative decrease in muscle mass and, in many instances, decreased energy and quality of life [4]. The brain can't "tell your body to shrink", but the lack of "communication" between the brain and organs leads to less to absolutely no use of that organ, thus inducing atrophy. The lack of both external and internal stimuli leads to atrophy (in general) [5].

References:

Gupta N, White KT, Sandford PR. Body mass index in spinal cord injury -- a retrospective study. Spinal Cord. 2006 Feb;44(2):92-4. doi: 10.1038/sj.sc.3101790. PubMed PMID: 16030513.
Ji L, Dang XQ, Lan BS, Wang KZ, Huang YJ, Wen B, Duan HH, Ren F. Study on the safe range of shortening of the spinal cord in canine models. Spinal Cord. 2013 Feb;51(2):134-8. doi: 10.1038/sc.2012.99. PubMed PMID: 22945745.
Wikipedia contributors, "Growth hormone," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Growth_hormone&oldid=616959802 (accessed July 21, 2014).
Molitch ME, Clemmons DR, Malozowski S, Merriam GR, Shalet SM, Vance ML, Stephens PA. Evaluation and treatment of adult growth hormone deficiency: an Endocrine Society Clinical Practice Guideline. J. Clin. Endocrinol. Metab. 2006 May;91(5):1621-34. doi: 10.1210/jc.2005-2227. PubMed PMID: 16636129.
Wikipedia contributors, "Atrophy," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Atrophy&oldid=611770442 (accessed July 21, 2014).


What is meant by [protein name]+/- (ie "Myod+" and "Myod-") I have read a paper where this notation for protein names is used:

Myod+ and Myod-

(or another example, Myog+, Myog-).
What does this indicate?  In the paper I'm reading, and some brief googling, it seems that Myog is itself a protein, and not that there are two kinds called Myog+ and Myog-.
Examples are here (the one I'm reading) (Figure 6c), or here (page 3, pdf page (journal page 958)).

The Stem Cell Reports paper linked in the question is open-access, so anyone can download it freely. Unfortunately the Nature paper is not.
There are two different abbreviation conventions being used in the open paper – MyoD+/MyoD- and MyoD+/MyoD-. The italicized version indicates the genotype of the cell, tissue, or individual being referenced, so for example MyoD- indicates the MyoD knockout they made. This convention is very widely used to refer to genes or mRNA.
Examples where the gene name is not italicized refer to the protein product of that particular gene and its presence or absence. So, MyoD+ cells express the wild-type protein, while MyoD- cells do not. This convention is also very widely used to refer to the presence or absence of the indicated protein.


Questions in Regards to Isolating Promotor Region for Recombinant DNA Techniques For a while now I have been trying to isolate the promotor region of this Protein.

Using sticky end PCR, I need to isolate this promotor region so it has paticular sticky ends for the purpose of placing it into a plasmid. However, I have a couple of questions on how to do this:

A. For inserting it into a plasmid, how precise does the sequence have to be? It is nearly impossible to find a restriction enzyme which lines up exactly to the start codon. How far can I deviate away, while still allowing the protein to be transcribed properly (on the plasmid)?

Thanks.

If you are performing sticky end PCR you do not need any restriction enzymes at all.

Design primers for your acceptor plasmid to 'linearize' it at the ATG and add a unique 4 nucleotide on the full length forward and another unique on on the full reverse primer. Design your promoter fragment primers to have compatible overhangs to that of the vector. And to answer your question: you will have very very poor yields if both are not perfectly complementary.

You will need to phosphorylate the full length primers for the promoter because primers are usually not phosphorylated at the 5' end. Do your PCR, anneal and ligation as per normal.

But if I were you I would switch over to Golden Gate cloning, our lab did a year ago and I have not regretted it one moment.

Edit:
I have added a diagram below. There was one thing which I overlooked in my original answer: You can get a direct repeat of the overhangs when the two longest products of each annealing reaction combine in a blunt end ligation but that should not affect your expression too much. However I still think that sticky end PCR is not the best way out of this. Blunt end ligation, gibson or my favourite: Golden Gate are all much more powerful techniques


How is vitamin B12 stored in the body although it is water-soluble? Vitamin B12 is stored in the liver for a long time.

How is it stored?

Vitamin B12 (cobalamin) is a cofactor required by the enzymes methionine synthase (MTR) and methylmalonyl-CoA mutase (MUT). These are the only known enzymes that use B12 in humans, and are abundant in the liver. Since it is a cofactor, B12 is not consumed by any reactions, and hence there is no need to store large amounts of B12 beyond that bound to MTR and MUT. (In contrast to major nutrients like glucose and fats, which are stored in large amounts.)

Early biochemical studies showed that B12 isolated from cells was bound to an unknown large protein complex, called the intracellular cobalamin binding protein (ICB). It was later found that ICB actually consisted two separate proteins, and that these were identical to MTR and MUT.

So B12 is "stored" by simply being attached to the enzymes that require it. But, as @jzx also pointed out, perhaps "storage" is not an accurate description --- cobalamin is an integral part of these enzymes; it is not present in excess, and not kept in some storage compartment from where it can be mobilized (like glycogen, for example).


Why is active transport needed in repolarization? During the repolarization phase of an action potential, the potassium ions diffuse out of the cell, and active transport begins.

What I do not understand is why active transport is needed when the movement of ions is not against their concentration gradient?

Since the potassium ions have diffused out in repolarization, only the sodium ions are left in the intracellular space.

The sodium/potassium pump is used to pump 3 sodium ions out and 2 potassium ions in. However, isn't there a concentration gradient as the sodium ions are moving out of the cell, where there are no sodium ions, and thus from a high concentration to a low concentration?

Is it because the active transport allows the imbalance to occur (3 out and 2 in)?

...when the movement of ions is not against their concentration gradient...

This assumption is incorrect: Na+ has to be pumped out of the cell against its chemical gradient (table 1) and against its electrical gradient, given that the inside of the cell is negative (Fig. 1).

  ...potassium ions have diffused out in repolarization, only the sodium ions are left in the intracellular space

This is incorrect: There are heaps of K+ ions in the cell, also after repolarization. A tiny fraction exits the cell during repolarization.

  ...moving out of the cell where there are no sodium ions...

This is incorrect; there are Na+ ions out of the cell, heaps in fact. You should be aware that the flux of ions is not an all-or-nothing phenomenon. It is a flux of relatively few ions out of a pool of them. Action potential formation and ion gradients are membrane-bound phenomena. While Na+ may enter the cell during an action potential, there is still a nearly infinite large amount of Na+ left in the intercellular space.

Table 1. approximate ion concentrations in and out of the cell. source: Med Quarterly

Fig. 1. Action potential. source: UC Davis


Where to find the corrected BLOSUM matrices? I was looking at this paper which talks about the miscalculations in the BLOSUM matrices and how the "wrong" BLOSUM62 matrix performs better than the corrected version. I was trying to find the corrected version they talk about to experiment with, but the link they list in the paper appears dead.

Does anyone know where I can find the corrected matrix that the authors talk about?  (preferably a version listing frequencies rather than scores)

Okay, I emailed Dr. Mark Styczynsk (one of the authors) to ask about a link to the matrix. Here are the links he gave me:

http://web.mit.edu/bamel/blosum/revised_blosum.c

http://web.mit.edu/bamel/blosum/original_blosum.c

http://web.mit.edu/bamel/blosum/RBLOSUM64 (isentropic with BLOSUM62)

http://web.mit.edu/bamel/blosum/RBLOSUM62 (not isentropic, but it's 62)

The first link is to the c code to generate the corrected BLOSUM. According to Mark, just replacing the original c file in the original BLOSUM tarball with the revised c file can generate the corrected matrix for any of the BLOSUMs (30, 50, 92). Haven't yet tried that myself.


How does one calculate how to dilute a solution to working strength? If I'm loading a 3.5ul PCR onto an agarose gel, how do I calculate how much of the 6x loading dye to add?

Since its 6x (6 times concentrated), you have to dilute it 1:6, so you add 1ul of 6x dye for every 5ul of reaction.

5 +1=6ul final volume

6ul final volume / 6x concentrated = 1x working concentration

Now the dye is diluted down to a 1x(working) strength.


Reference to hypothesis about breast sexual attractiveness? Some time ago there was a hypothesis published,suggesting evolution made breasts mimic buttocks for either primitive men being attracted to women when they started to walk on two legs, or to discourage sexual intercourse from behind for other reasons I can’t remember. I can find many posts about this online, but I can’t find any reference to the original idea. Can anyone provide information about this?

Eventually, I found it, here it is:

  In considering the human animal, zoologists proposed that the human
  female is the only primate that possesses permanent, full-form breasts
  when not pregnant. Other mammal females develop full breasts only when
  pregnant. The zoologist Desmond Morris proposed that the rounded shape
  of a woman's breasts evolved as frontal, secondary sex characteristic
  that is a sexual-attraction counterpart to the buttocks, and so
  encouraged frontal copulation, the reason being that while other
  primates mate by means of the rear-entry position, the upright,
  bipedal human being was likelier to successfully copulate face to face
  in the missionary position.

https://www.reddit.com/r/askscience/comments/uflgy/why_are_breasts_so_attractive_after_all_theyre/


Can we harvest energy from plants? This is a cross-cutting question but I think its core is about biology. Our society's need for energy is dramatically growing and we are messing up with our environment to answer them. Maybe another way to proceed would be to use the primary energy source that is the sun in the same way as it has been used throughout the ages: photosynthesis.

I know the energy effiency is not as good as a solar panel's but it could clearly be compensated by volume. I found surprisingly little information about harvesting energy from photosynthesis which is why I began to wonder where we are at today.

Thanks!

Edit
I meant transforming the chemical energy generated by photosynthesis into electrical energy. For instance, the first algae powered building was unveiled at the International Building Exhibition hosted in Hamburg. This is a whole different approach.
The most basic example of what I would like to talk about seems to be the algae powered lamp that has (apparently) been developped. In other words, it seems that some sort of plant solar panels are under development and I don't understand how it's done.

It is not possible to do this directly. Indirectly, it is possible, this is actually done by harvesting fruits - they contain the energy of the sunlight conserved in chemical compounds like sugars or starch and their cellular structures. The basic process for this is photosynthesis.

The products from the fields are used technically to produce gas by fermentation, which then can be burned to produce electricity. Read reference 1 for more details.
What is also done is the use of sugar cane (done widely in Brazil) or corn to produce ethanol which is then used in the fuel of cars. See references 2-4.

Besides these technical processes, there is of course still the possibility to simply burn whole plants or the wood of trees, which is also the result of the fixation of sun energy.

References:

Biogas Production from Maize Grains and Maize Silage
Ethanol Production Using Corn, Switchgrass, and Wood; Biodiesel
Production Using Soybean and Sunflower
Ethanol fuel in Brazil
Corn ethanol


Plasmid Expression Vector If I am going to transform a plasmid into a bacterium, which will then be fed to a C. elegans, the expression vector needs to be bacterial correct? The other option is to have a worm expression vector, but I just wanted to make sure that I was correct in my thinking. Thank you.

You are trying to express the plasmid in C. elegans, so it should be a worm expression vector and promoter. Otherwise, it will be expressed in the host bacteria, but not in the worm, so you won't get the phenotype you're looking for.

One thing you can do is add a bacterial origin of replication to the vector (if one isn't already present) so the bacteria produce multiple copies of the plasmid after transformation. Otherwise, the amount of plasmid consumed by the worms will be rather low.


How to solve these kinds of problems? 16% of people in a population can not roll their tongue .what is the frequency of people which are heterozygous of this character? Please ,any one help and guide me to solve these kind of problems.
 I tried to solve it using punnet square but i failed .

So i tried my best please help me to solve this.

I deffinitly recomment to look at your calculations. But the abbility of cannot rolling tongue is recessive not dominant. And after all look at the Hardy-Weinberg equision p^2 + 2pq + q^2 = 1 (p*p=p^2). Try to extract the root of q^2 and you will get right sollution (because the 0.16 is squareroot).


Is there any reason the common housefly continues to return to an area? This might come off as a really silly question. But I'm wondering (especially in the case of food) if there is any reason a fly would continue to try and sit on top of a piece of food even after swatting it away. I assume (it could be misconception) that it is instinctive that animals and insects would leave an area if it is harmful / dangerous to their existence after having close encounters more than once. Is this not the same for the fly?

I have this question mainly because I recall waving a fly away several times while eating lunch, and I couldn't understand why the fly wouldn't just find another place where there is food or somewhere safer.

I don't think it's a silly question, but it is a common error to anthropomorphise animals.

Insects respond to cues which they have evolved to respond to, and this is how they 'make decisions'. They do not have free will or any more complex decision-making process like common sense. This is evident is lots of insect behaviour: flying repeatedly at a closed window; landing on brightly coloured clothes instead of flowers; and returning to a food source when they are in real danger of being swatted!

When a fly senses the food (often by olfactory receptors), they are 'programmed' to fly towards it in response to some chemical they sense depending on the species and food. They may not have adapted a response to swatting, or perhaps the food cue overrides others. In nature swatting is not so much of a threat to a fly. Some animals may brush them away, but since they are not really doing any harm in feeding from another animal's food, they are mostly ignored.

CO2 traps are used to entice and kill mosquitoes. The mosquitoes are attracted to CO2 (as it is dispelled from the animals from which they blood feed), they will only evolve to avoid the traps if there is another cue which they could eventually associate with a negative effect.

Another thing to remember when thinking about insect behaviour is that their life strategy is very different to ours. Insects are more r-selected than humans, meaning that each individual life has not had so much energy put into it as a more K-selected animal (such as humans), and to compensate for this, many more young are produced. This often results in more risks being taken by individuals since there will still be a viable population even after many deaths.

Chapter 4 of 'The Insects' by Gullan & Cranston gives a good introduction to the sensory responses of insect behaviour. There are other books on the subject, 'Introduction to insect behaviour' by Atkins looks like a good starting point, but I have not read it yet.


What do we use as baseline to determine what genetic segments are "mutations" (and what are not) In order to determine whether a particular segment of the genome is a mutation, there must first be a baseline code on which that code looks somehow different.

How has the baseline genome been determined? Did someone dig up a _very_old_ human skeleton which was subsequently DNA-analyzed to be used as the baseline?

Or do mutations contain some kind of fingerprint that tells researchers that "it is not the original genome"? If so, how does that fingerprint look like?

It may help to think about the genealogy of the sequences in question. In general, we suppose that all DNA sequences from organisms are related by a set of processes. A particularly important process relating DNA sequences is replication. This establishes a parent-child relationship between DNA sequences in one round of replication or an ancestor-descendent relationship when we view more than one round of replication.

For simplicity, consider a single bacterial cell, which replicates its genome and divides, yielding a descendent cell. This process continues for each cell and produces a population of cells over time. This population of cells (and their genomes) are related to each other by this process of replication and division. The structure of this relationship is a tree (in the mathematical sense). The vertices of the tree are the DNA sequences (or cells) and a directed edge from vertex i to vertex j exists if and only if the sequence represented by vertex j is the result of a replication of the sequence represented by vertex i.

In addition to the replication process which makes this tree structure relating sequences, there are mutational processes that lead to sequence differences.

There are many ways for mutations to arise before or during DNA replication. The important thing to note is that these mutations are passed on to descendants. So, a cell is either genetically identical to its parent cell, or it contains some number of mutations (insertions, deletions, or polymorphisms in the DNA) with respect to its parent.

These mutations (sequence differences) are inherited during replication, and you can think of them as "occurring" along a given edge in the tree from a parent cell to a child cell.

Now, if you consider any two DNA sequences, as well as the model just given, these two sequences are related through the replication-mutation process (the tree). If the DNA sequences are not identical, you have many ways to interpret this question of what is a mutation. It is useful to consider the most recent common ancestor of the two DNA sequences in making sense of the differences observed in the DNA. If you think of the genealogy as a tree, and you're considering two vertices in the tree, then tracing backwards towards the root of the tree from each vertex, these traces will eventually meet at another vertex. The first vertex at which they meet is the most recent common ancestor.

It is possible that mutations have occurred along both paths from the (most recent) common ancestor to the descendent sequences you're investigating. If you're investigating N sequences, there are N paths from the common ancestor on which mutations may have occurred.

All of this is to say that mutations occur with respect to this genealogical process. If you just consider 2, or N, sequences without regard to the process that generated them, then it can be meaningless or confusing to consider a particular sequence difference as a mutation with respect to another sequence under consideration. For example, if you observe a single nucleotide polymorphism between two sequences, how would you know which sequence was the result of the mutation? It is possible that one or both sequences carries a mutation event in its genealogical history since the common ancestor of both sequences.


Identification: Stinging walking/flying skin cells Here I was, sitting in the veranda, minding my own business. Kids were playing outside, and I wasn't in charge of watching them. While browsing my stack overflow feed, I felt a pinch in my left arm. Like a very tiny needle just fell from the sky and decided to 'bug' me in my free time.

I looked at the spot where it hurt and saw a minuscule insect. It looked like two shedded skin cells crawling around slowly. Just very flat and small. What surprised me is that it kept hurting for approx 30 seconds afterward.

Not knowing what it was, I decided to get the camera. But how to photograph such a tiny creature, if you do not have the proper gear. Thankfully my wife remembered a trick where you can turn around the lens of the camera (if it's detachable), and take a picture while holding the lens firmly against the body. This way you get a sort of macro. Very difficult to hold it steady and to focus, because the focus field is extremely shallow.

Nevertheless, I managed to take some shots, and now my question is.. what is this stingy little buggy? I obviously let it live after the photoshoot and most likely it's a very common insect, but I've just never seen it in my life. Especially not something that stings like that.

Ah yes, apparently it can fly. Little bugger (literally) tried to flee the scene a couple times.

Additional info:

Origin: Romania, Targoviste (DB)

Date/time: 06 July 2018, 18:30, sunset

Warm sunny but windy day, still warm, 25 degrees Celcius

That is a Lace bug (Hemiptera). Family Tingidae. https://en.wikipedia.org/wiki/Tingidae.
From Wikipedia: "Lace bugs sometimes fall out of trees, land on people, and bite, which, although painful, is a minor nuisance. No medical treatment is necessary."


Water snake with a yellow criss-cross on a black background? I saw a 60 cm long, very skinny (~15 mm diameter), black with yellow diagonal criss-cross patterned snake swimming in a pond this afternoon in northern Taiwan.
It was swimming near the top of the water and I could see it very clearly, but as soon as it noticed me it dropped most of its body to the bottom of this shallow pond and just kept part of its head above water, so the photos are not very clear.
I tried to wait for it to continue but something else disturbed it and it took off.
Is it possible to identify this snake or at least narrow down the options?
First image is cropped from the large image. I have played with contrast, color and sharpness to make the pattern and color look most like what I remember before it dropped its body lower into the murky water.

sketch of pattern as I remember it

The useful relevant facts are:
Present in freshwater
Active in daytime
Yellow patterning
(photos from wikipedia)
I used the site
www.snakesoftaiwan.com/
This gives most likely candidates of:
Rhabdophis tigrinis subspecies formosanus, the Tiger Keelback.
Grows to 0.6 to 1.0 metres long.

more photos (cannot embed due to copyright) at http://m.blog.sina.com.tw/d100vs/article.php?pbgid=30839&entryid=404413
and
Fowlea piscator  the Checkered Keelback or Asiatic Water Snake. growing 1-2 metres long.

more photos at http://m.blog.sina.com.tw/d100vs/article.php?pbgid=30839&entryid=342476


What is the importance of alkaline condition in biuret test? Biuret test aims to quantify the amount of protein in a given unknown sample. Biuret agent contains copper sulphate, sodium potassium tartrate and Sodium hydroxide. Coppper ions form the complex of purple colour. Sodium hydroxide is added to make the solution alkaline. Why is it needed to make the solution alkaline?

In the Biuret reaction, copper forms a complex with the nitrogen of the peptide bond, that looks like this (Structure 61 from the paper below):

A strong base is necessary to provide the conditions for deprotonating these nitrogen atoms and have the conditions to form the complex. If you want to read this in detail, have a look at this publication:

Coordinating properties of the amide bond. Stability and structure of
metal ion complexes of peptides and related ligands


Crick’s Central Dogma — Counter Cases I was recently reading about non-coding RNAs being a counter example to Central Dogma of Biology. Can someone add more cases which violate the Central Dogma? Thanks!

UPDATE - Reference of lncRNAs violating Central Dogma:

  Although the central dogma remains a core tenet of cellular and
   molecular biology, the appreciation of lncRNAs as functional genomic
   elements that defy the central dogma may be essential for fully under-
   standing biology and disease. [Iyer et al. Nature, 2015]

Crick’s Central Dogma was actually:

  The Central Dogma
  This states that once ‘information’ has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of basesin the nucleic acid or of amino acid residues in the protein.

So, although in my comment I stated that the discovery of reverse transcriptase was the first violation of this — as was generally regarded — this turns out not to be the case.

I remember that the case of reverse transcriptase was felt to be different from the existence of RNA viruses because it involved the flow of information from RNA to genomic DNA, which were generally represented by a unidirectional arrow in the opposite direction in diagrams of the dogma. The following is a typical illustration of that, taken from some University lecture notes that I found on-line and which are described as:

  These diagrams ..., created originally by Crick, summarize the basic processes of information transfer within cells.

But the NCBI collection of facimilies of Crick’s documents include a 1956 diagram that is quite different and much more sophisticated:

And, so the central dogma has not been violated (certainly not by lncRNAs), unless you consider that it has by prions, where information of sorts is transfered from protein to protein.

Morals

It’s amazing what you can find on the internet.
Never believe what you find on the internet.

Footnote

I’ve seen the DNA → Protein arrow repeated as if it were fact in diagrams, although Crick only said ‘may’. I know of no example of this.


What governs the distribution of blood vessels? Whenever someone is sick, doctor places 2 fingers on wrist & observes the heart-beat-rate by feeling pulses of a certain artery.

To me it seems the distribution of blood vessels are pretty standard across all variations of humans (I mean identical blood vessel positioning seen across Caucasians, Africans, etc. members)

So when someone is born with extra finger or joined skull - which rule/gene/algorithm decides the distribution of network-of-blood-vessels in those special parts?

PS: I am definitely / apparently not a biology student, so pardon my ignorance

Is positioning of blood capillaries random or they too are identically positioned among all humans, although we can't see them.

The growth of blood vessels is called angiogenesis. This process occures during embrional development, tissue repair, and even tumor formation (in fact this is a crucial step for tumors to survive). This Nature review ("Molecular regulation of angiogenesis and lymphangiogenesis")provides great overview of the process, I'll try and briefly summarize things:

In general large arteries grow circumferential  to keep up with increased blood transfer, while capillaries branch to a more complex network in order to be able to supply blood to every cell. The circulation system starts as a

  primitive
  and uniform vascular structures, known as primary capil-
  lary plexi,

that later develop into a hiearchical system of arteries, capillaries and veins. Main regulator of the morphogenesis of blood-vessels is the

  vascular endothelial growth factor A (VEGFA; also known as vascular
  permeability factor (VPF)).

This needed for the chemotaxis (the movement of an organism in response to a chemical stimulus. from: http://en.wikipedia.org/wiki/Chemotaxis) and differentiation of endothelial precursor cells (EPCs; angioblasts), endothelial cells (ECs) and the assembly of ECs to vascular structures (termed vasculogenesis), as shown in the figure taken from the article I linked. EPCs themselves differentiate from mesodermal cells during early embryo development and aggregate to form blood islands that later form the  vasculogenic formation of honeycomb-shaped primary capillary plexi.

Also it is important to note that :

  alternative splicing of VEGFA can generate several variants of the growth factor, including the so-called b isoforms that differ in the last six C-terminal amino-acid residues and have anti-angiogenic properties. The balance between the different VEGFA isoforms can regulate blood-vessel
  growth and patterning.

Also local composition of extracellular matrix (ECM) and the interaction between ECM and cells can affect angiogenesis. For example release of matrix bound VEGF is important in the regulation of the level of available VEGF. Also:

  Furthermore, the physical contact between ECs and pericytes is thought to induce a quiescent, non-sprouting phenotype.

Sprouting itself carried out by the selection of some ECs in the capillary wall to lead the growth of the new sprout. See next figure also from the linked article:

Notch receptors and Delta-like 4 (DLL4) ligands play key role in this process. In tip cell(s) DLL4 expression is induced (in response to VEGFA), while the Notch signaling in neighboring cells (activated by the DLL4) represses sprouting (by down regulating VEGFR2 - VEGF receptor 2) . This is important, because otherwise excess sprouting would lead to a dense network of capillaries and blood would just spread out too thin and would be unable to supply the organs with oxygen and nutrients.

In order to tip ECs be able to grow new capillaries they ahve to undergo some changes. Mobility is most likely gained by activated secreted or cell-surface bound proteases, to locally degrade the basal membrane. Interaction with other ECs have to be changed, without completely disrputing cell-cell junctions and the integrity of the vessel-wall. Also the apical-basal (apical side - faces the lumen of the vessel) polarity of the cells have to be reversed in order to be able to grow outwards (from the basal side of the endothelium. In order for the new capillary vessel to grow, the elongation of the new sprout has to be polarized and directional. This is achieved by spatial concentration gradient of ECM bound VEGFA isoforms along with prominent expression of VEGFR2 in the tips of sprouts.
For blood functional blood vessels to be formed the tips must cease growing and exploratory phenotype when they find their target, and string EC-EC junctions need to be formed. Also the generation of the lumen of the newly formed vessel is required.

As you can see forming of new blood vessels is a complex process that is controlled by local signals, yet it is part of a bigger process - the development of the embryo and organs that is regulated by many many genes and processes. Since our general architecture is the same it is logical that or circulatory system is similar. As for the abnormal structure of a body I think perfusion of that extra body part depends on the local environment.

The review linked at the beginning of this post has extra info on arterio-venosus differention and many other things.


Free software for measuring parts of an image? Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? Would the software be able to export these data to a spreadsheet?

ImageJ is all you need. Particularly see the documentation sections on setting the image scale and measuring.


Could transfusion of a different blood type cure blood-based cancers? Different antigen detection triggers an immune system response that could perhaps stimulate mitochondria and such in killing cancer cells - something like chemo without the hair-loss?

No. When a different blood type is introduced in the body, the host immune system recognizes the foreign blood as non-self and attacks it. The transfused blood becomes useless, and the potentially massive immune reaction can cause shock, which itself can be fatal.

More details in the book Blood Groups and Red Cell Antigens, which can be found at the NCBI library.


What is the current molecular explanation of Mendel's pea cross? With reference to the simplest Punnet square for Mendel's pea plant experiments it occurred to me that I could not connect the little I know about genetics to the little I know about molecules.

The mathematical model assumes that there are two factors (alleles) involved. With respect to Mendel's pea flower colors, to what do those alleles correspond at the molecular level? Genes--minimally it might be two codons, each with binary states so that a protein involved in the manufacture of color molecules changes at two specific amino acids.

Of course it is not so simple. But it must be true that there are two physical objects which in the aggregate have two binary states for this particular case. Do we know what they are, exactly, for Mendel's peas?

Thanks for any insight.

The article you have linked to does explain everything thoroughly, though in a somewhat complex way. I did not know how much genetics you actually know, so I tried to answer very thoroughly.

So the article states that the gene Mendel studied and that was responsible for the white color of the pea flower is ANTHOCYANIN1 (in the article it is also called - bHLH, that is the name of the protein family that ANTHOCYANIN1 belongs to). So, ANTHOCYANIN1 is a transcription factor - a molecule that activates the transcription (making of mRNA) of other genes, basically it activates other genes.

The white flowered peas have a mutation (Guanine to Adenine transition) in the sixed intron of the gene ANTHOCYANIN1. Introns are sequences of non-coding DNA, that does not encode amino acids, and is removed from the RNA transcript by a process called splicing. The mutation occurs at a binding site for the Spliceosome (a protein and RNA molecule) that splices the RNA, because of this the RNA transcript is not spliced correctly. The faulty RNA transcript for the gene ANTHOCYANIN1 contains 8 extra nucleotides and because the genetic code is a triplet, a frame shift occurs. When a frame shift occurs all of the codons bellow the frame shift sight get changed. In this case, this leads to a premature stop codon. The translation of the ANTHOCYANIN1 RNA get stopped before a full protein can get synthesized and a non-functional protein is made.

If ANTHOCYANIN1 does not function, no genes are activated and no pigment is synthesized.

To summarize - the white pea flower color is a consequence of a nucleotide mutation (Guanine to Adenine) in a intron sequence of the gene ANTHOCYANIN1, this leads to incorrect splicing of the ANTHOCYANIN1 RNA (a frame shift) and to the production of a shorter protein that is non-functional.


Is there a standard way of measuring culture nutrient levels in real time? I am working on optimizing growth rates for a culture, and one thing I'm trying to monitor is nutrient consumption rates to pinpoint any bottlenecks, i.e. the culture goes through all the calcium in a few hours and then stops growing.

Short of manually taking samples every few minutes and running individual tests for wide arrays of nutrients (minerals, amino acids, nitrogen compounds, etc.), is there a standard way of monitoring nutrient levels automatically in real-time? This is a personal research project, so unfortunately I don't have access to industrial bioreactors and the like.

Enzyme-based sensors for taking real-time measurements of growth substrates do exist. In brief: an enzyme degrades the substrate and thus changes the local redox state which is detected electronically (example glucose sensor). There's no guarantee that the substrates that you want to measure can be measured using such sensors. Also I think those sensors are fairly expensive and are tailored to specific conditions (ie it's not as simple as dipping the sensor into your culture medium). Practically speaking I think systems using these sensors are limited to monitoring just a small number of substrates.

LCMS or GCMS is the standard method for measuring concentrations of substrates. LC or GC  (without the MS) may be possible, but probably not since there are are many components to culture media and so lots of overlapping peaks. Using this method is labor intensive (lots of samples), likely to be low resolution (temporally), and the equipment is pretty pricey, but if you have access to an LCMS and are willing to put the time in to become an LCMS expert then this is a good option.

Culture based methods using minimal media supplemented with substrates is an option, these experiments may achieve the same thing as real-time monitoring of substrate concentrations. If you have access to a plate reader this will be so much easier. The speed at which different substrates are consumed, and the order in which they are consumed can be inferred by measuring the growth rate of the bacteria and the final population size/dry weight of the culture.

I mention this culture-based method because, although it's not exactly what your question was about, it's much cheaper than the other options and much more established (and in my opinion more fun: you get a great feel for how the bacteria grow and what media they like, and the graphs look great).


Techniques to find out which species are endangered Most countries have a list of endangered species and international organisations too issue such lists of vulnerable and endangered species.
What mathematical or statistical models are those estimates based on?
Regardless of which techniques the lists use, what are some of the most popular mathematical models to find out whether a certain species is endangered or vulnerable given the population and/or other environmental data in the academic literature? What is the state of the art currently?
Especially, if I want to learn the models at an intermediate and then advanced level (I already have training as an Economics student on mathematical and econometric modelling), what are some books/ other sources you would recommend?

Based on the IUCN Criteria for endangered status there are two broad categories of models to help in determining endangered status. Note that no one methodology is used to determine the status of any species. Rather, a panel of experts consider all available evidence (including numerous modelling studies) and essentially make a determination based on their own judgement.

Range Estimates
Estimating the range of a species uses two primary techniques. The first is an expert range maps drawn by people very familiar with the species distribution, which involves essentially no modelling. The 2nd is ecological niche modelling, aka. species distribution modelling. See 1 and 2 for introductions on the latter. Note that the IUCN guidelines have criteria based on total range size, and well as the amount of fragmentation and patchiness of the range.

Population Size Estimates
Since it is usually impossible to count all individuals of a species, models are used to estimate total populations. These usually fall in the realm of mark-recapture models. There are numerous variations on the basic model form which account for things like an open population, varying birth and death rates, and varying capture probabilities.

1: Elith, Jane, and John R. Leathwick. "Species distribution models: ecological explanation and prediction across space and time." Annual review of ecology, evolution, and systematics 40 (2009): 677-697. https://doi.org/10.1146/annurev.ecolsys.110308.120159
2: Araújo, Miguel B., et al. "Standards for distribution models in biodiversity assessments." Science Advances 5.1 (2019): https://doi.org/10.1126/sciadv.aat4858.


Any good website/book to understand protein folding and enzymes? I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes.

I understand that the protein is a polypeptidic chain, I know its composition, but the part that I really can't figure out is "the folding of proteins", I mean "How a straight polypeptid chain turns into a complex folded structure?"

Okay, so for introduction the 4 levels of protein structure (each level influences the levels after it):

primary (1st): the order of amino acids.
secondary (2nd): alpha-helicies and beta-sheets
tertiary (3rd): complex 3d structure
quaternary (4th) : 3rd+ non-protein elements (ions, co-factors etc)
and / or multple subunits interact. Not every protein has this kind
of structure.

I think the first does not need any explanation.

The secondary structure is where amino acids form 2D structures: alpha-helices or beta sheets. From wikipedia on a-helix and b-sheet

  The alpha helix (α-helix) is a common secondary structure of proteins and is a righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier (i+4 \rightarrow i hydrogen bonding)

  The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins. It is less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet.

Pictures are from here, that is a great site that explains basic protein strucutre in a quite understandable way.

These secondary structures are important because they can from motifs with specific functions like DNA binding, interaction surface with other proteins. The aforementioned wiki sites have detailed info. These secondary structures and motifs serve as building block for higher order functions. Between motifs "loose" non-structured parts can be found to allow for flexibility.

Tertiary structure:
This is the level where complex 3D geometric structure is defined. The aforementioned 2D structures are packed into domains - a single functional element of a protein. A single protein can have multiple domains and the relative position of these domains result in the tertiary structure. The domains themselves are connected with loose regions that do not show any high order structure and provide flexibility between the domains. Flexibility is necessary for conformational changes.

The quaternary structure is where non protein elements and / or multple subunits are involved. For example the positioning of the heme group in hemoglobin. Or when monomers from dimers, trimers etc. so in general when mature proteins get together to form a larger complex.

Here is a great image about the different structure levels:

source: https://dopeahmeanbio.files.wordpress.com/2013/03/333.gif

So now onto the "how" part :)

As I mentioned in the beginning all levels influence the levels after it. So the amino acid sequence predestines the 2D structures to be formed. The secondary structures themselves are formed by amino acid forming hydrogen bonds with each other. This process occurs "naturrally", so by the inherent properties of the amino acids. At the third level disulfide bonds stabilize the structure. This is also a naturally occuring event. Also binding ions, co-factors, etc also stabilizes the protein strucutre.

The folding process can also be supported by chaperon proteins, These proteins can actively "twist" the polypetide chain using ATP as energy source. They can "sense" if there are hidrophobic amino acid chains facing the outer surface of the protein, a thing usually avoided because these amino acids need to face inner surface of the protein where they can avoid water - this is energetically better. This signal (outward facing hidofobic AAs) indicate that either the protein is un/misfolded or it is damaged because of for example heat - that denatures ("unwinds") proteins.

Finally the wiki page on protein folding if you need more. I hope this helps.


What percentage of a Neanderthal's DNA could be in a Denisovan? My questions arose from an online course video at 3:11-19

The professor mentioned that the Neanderthals were inbred with their cousins breeding together but the Denisovans were very diverse , with 70% Neanderthal's DNA, there was found mixing between Denisovans and an even earlier mysterious species.
The followings are my questions:

Did he mean that most of Neanderthals were prone to inbreeding? Why?
I'm not sure if that was exectly what he meant by 70% Neanderthal's DNA could exist in a Denisovan. If that were true, why not just called it Neanderthal if only 30% is not Neanderthal?

You should be very careful trying to conclude something from what is known about Neandertal genetics.

To answer question 1: NO! This is probably not what he meant. To date, we have only two high-quality full genomes of archaich humans, one being the (Neandertal from Denisova cave, called Altai Neandertal (Prüfer et al., 2014)) and one being the (Denisovan from Denisova cave (Meyer et. al., 2012)). From this sample (which is exactly one Neandertal) you cannot draw conclusion for the whole population. It seems, however, that this Neandertal individual from the Altai Mountains was indeed inbreed (high runs of homozygosity in the genome) - it does, however, not even tell us in what way her parents were related. Prüfer et al. (2014) write

  We conclude that the parents of this Neandertal individual were either half-siblings who had a mother in common, double first cousins, an uncle and a niece, an aunt and a nephew, a grandfather and a granddaughter, or a grandmother and a grandson.

You cannot say more. You also cannot say if this was due to preference in mate choice, or caused by the fact that this group was very isolated, or  that this population had an extreme small effective population size (note that it is debated whether the last two effects are actually equivalent).
To make a long story short: based on the available data it is not wise to draw general conlcusions about Neandertal mating behaviour. Altai is the only example where direct inbreeding could be shown, all other genetic data from Neandertals suggest that genetic diversity was just low.

To answer question 2: I do not really know what this means, 70% Neandertal DNA in Densiovans. I can just generally tell you something about Densiovan-Neandertal differences. The Densiovan might be the only (at least mammal) species that was defined based on genetic information alone. Alle that was found were a few teeth and a pinky bone. People thought this was another Neandertal. After sequencing the DNA from that bones to high coverage (vaguely, a measure of qualtiy), one found that the DNA falls both outside the variation of modern humans - showing that this was not a Homo sapiens, but interestingly it also clearly falls outside the variation of known Neandertal sequences - showing that this was not a Neandertal. It also became clear that Densiovans are more closely related to Neandertals than to modern humans (you might now ask yourself how this is possible with just one genome. In fact, there are more genetic data availabe: low coverage genomes, exome sequences, mtDNA and all of them show the same thing: Neandertals and Densiovans are different but more closely related to each other than to modern humans). Overall, Denisovans also seem to have had rather low genetic diversity (which by the way is also a characteristic of modern humans).
Long story short: There seem to have been admixture events between Denisovans and Neandertals but I do not know how to relate this to the 70%. Prüfer et al. (2014) detected about 0.5% contribution from Neandertals in Denisovans.

One last comment about this mysterious species (nobody says it but most people think of Homo erectus): again, Prüfer et al. (2014) found some interesting patterns of derived allele sharing between present-day Africans, Denisovans and Neandertals (this should be equal for African-Denisovan and African-Neandertal comparisons, but present-day Africans share about 7% more derived alleles with Neandertals than with Densiovans - even 13-16% in alleles fixed in present-day Africans). This is either ancient population structure (however, with very deep lineages) or, as suggested in the paper, due to gene flow from a (genetically) unknown archaic hominin into Denisovans.

I hope this clears things up a bit. Feel free to ask in the comment and I will edit the post as it might be a bit unstructured.


Does the DNA stick to surfaces we touch? In case of robbery, the police visit the robbery scene and collect some samples like foot print or any item suspected to have been touched by the robber. The sample is then taken to laboratory for DNA analysis. Does that mean whatever we hold or touch, our DNA sticks or drops on it?

Yes, we leave DNA on everything we come in contact with. Even simply standing, we shed skin cells and hair (although only the follicle has DNA) etc. DNA may also be transferred from clothes to clothes.

You might be interested to read this article :) http://www.forensicsciencesimplified.org/dna/how.html


Why should the pharyngeal cavity be essential for articulated speech? In a lecture, I've been told that one of the signs that homo habilis and homo erectus couldn't speak was that they probably lacked the distinction between oral and pharyngeal cavity. But do we really use it, apart from the nasal consonants?

This bit of the book Developmental Neuropsychiatry: Fundamentals describes the difference between the oral cavity in humans and other animals. It doesn't refer to Homo habilis in this context, but it says:

  As a result of this anatomical pattern, the range of sounds that an animal can make is limited because of the pharyngeal cavity, which is necessary of sound amplification, is small.

and:

  Still, this lower position of the larynx produces a larger pharyngeal space above the vocal chords, which makes possible a greater range of sound modification and becomes the key to the production of articulare speech.

Which suggests that the pharyngeal cavity has a more general use in speech than just making nasal consonants.

This article goes into some detail about Human speech anatomy and its evolution; what it says about the pharyngeal cavity is less about the cavity itself than about the position of the tongue, which allows the separation of that cavity into different sections, leading to different wavelengths being produced. They further say that apes have their tongue entirely in their oral cavity, and are as a result unable to make vowels other than schwas (the basic vowel you make when you're making no effort whatsoever) (they do mention one exception but that species apparently doesn't use its pharynx to make vowels like we do).

The article makes another very interesting point that is relevant to your question, I quote:

  Speech communication would be possible without quantal vowels [note from me: the sounds it was talking about that we can make but monkeys can't]. Indeed, there would have been no selective advantage for retaining whatever mutations led to the evolution of the human supralaryngeal vocal tract unless some form of speech had already been part of hominid culture.

That is an excellent point, which is that we need to separate the concept of "speech" from "fully modern speech". Things evolve gradually, and there will have been a continuum from simple communication and vocalizations that our latest common ancestor with other apes likely did, to modern speech with its sounds, grammar, and anatomical and cognitive abilities it implies. And since we no longer have examples of anything on that continuum, we don't know which parts of it we'd be more or less likely to think of as "speech".


a biochemical pathway for evaluating the effect of 3' to 5' exonuclease on the proofreading activity of DNA synthesis Can the following oversimplified biochemical pathway for DNA synthesis serve as a model for evaluating the degree of the effect that the 3' to 5' exonuclease affinity for mismatched base pairs can have on the degree of the fidelity of dsDNA synthesis? Is this idea basically correct to model the relationship?

Thank you for your attention

well I tried to implement this pathway in MATLAB and it seems to me that it makes some sense. Here are two versions of the reaction progress simulation, one with low and the other with high affinity of the 3' to 5' exonuclease domain for the mismatches. The violet curve of the simulation corresponds the amount of synthesized dsDNA and the green curve corresponds to the error-free amount of that dsDNA.
The next figure shows that with low affinity of the exonuclease for the mismatches, the error rate is high (12%).

The figure below shows that the dsDNA synthesis error rate decreased with the increase of the affinity of the exonuclease for the mismatches.

The MATLAB code of this simulation is provided
https://matlab.mathworks.com/users/mwa0000016879211/Published/x551/x551.html
Your comments and suggestions are most appreciated.
Thanks,


Origin of enzyme names Sometimes I get confused about why this or that enzyme was named in this or that particular way.

1) TCA: Why was not isocitrate dehydrogenase named isocitrate decarboxylase?

Wouldn't it have been at least as accurate to name the enzyme in question isocitrate decarboxylase as to call it isocitrate dehydrogenase? It does remove the -COOH, doesn't it?

2) Glycolysis: PEP (phosphoenolpyruvate) carboxykinase. Why isn't it oxaloacetate carboxykinase? Isn't it agreed upon that enzyme substrate be used in the name of enzyme?

3) Why name enzymes by reverse reactions (especially when the reaction is irreversible)? Pyruvatekinase makes pyruvate from PEP. Why not use another name, PEP phosphatase, for example?

I understand that this is the way the enzymes were named and I just have to accept it. But I would also like to understand the logic behind these names.

As @Chris commented, when assayed in vitro with a single substrate (which may not even be the physiological one) most enzymes can catalyse a reaction in either direction. And enzymes such as pyruvate kinase were discovered before the pathways they are constituents of were worked out in full. Furthermore, the ways of naming enzymes only became more sophisticated as more were discovered and characterized. (Try googling for ‘old yellow enzyme’.)

Let us take pyruvate kinase as an example. The name kinase is clearly not chemically descriptive but was applied to any reaction using ATP. But, never mind, go to the Wikipedia page for pyruvate kinase and click on the EC (Enzyme Commission) number — 2.7.1.40 — in the box on the right. You will come to a page where you will see that, like TS Eliot’s cat, the enzyme has three different names:

Accepted Name: pyruvate kinase
(because that’s what everyone uses and is in all the text books)

Other names: phosphoenolpyruvate kinase; phosphoenol transphosphorylase
pyruvate kinase (phosphorylating); fluorokinase; fluorokinase (phosphorylating); pyruvic kinase; pyruvate phosphotransferase
(note these include naming it for the reverse reaction)

Systematic name  ATP:pyruvate 2-O-phosphotransferase

So why is that the systematic name? If you click back from this page to the group EC 2.7.1 to which this belongs, you will find that this group is of ‘Phosphotransferases with an Alcohol Group as Acceptor’, itself a subgroup of phosphotransferases.

So, to summarize, there is a systematic name that have been arrived at after long and careful deliberation and appears in the introductory paragraphs of scientific publications. Thereafter the common name is used, which although sometimes now recognized as a misnomer, seemed most appropriate at the time.


Regarding signalling pathways Do all signalling pathways have something that can inhibit them? If the signal pathway is benefitial  and it is inhibited would the inhibitor be caused by a biological problem?  Are all inhibitors controlled by some subcellular  mechanism?

There are some inhibitors in the cell, which have specific effects on signal transduction. These are mostly second messengers (like cAMP, cGMP, calcium ions,  inositol 1,4,5-trisphosphate and others), which are then able to diffuse relative fast to other proteins. There they can either amplify a signal or cause inhibiting processes to start which then terminate the activation of the signal transduction cascade.
The problem is that these inhibitors that they work unspecific in their inhibition and termination. Signal transduction is tightly controlled as they directly influence the expression of various genes.

A lot of the proteins in these cascades are kinases which are activated upon phosphorylation and then carry on by phosphorylating the next step of the cascade. The activity is stopped by phosphatases which remove the phosphorylations from the kinases and thus inactivate them until the next signal is passed down the cascade. It works like in this figure (from here):

Specific inhibitors for single proteins in the signalling cascades are available as drugs against cancer. Since these signalling cascades regulate gene expression including cell cycle control, they are important targets for dysregulation in cancer. A numer of kinases in the MAP kinase pathway for example are mutated there and constantly active. The so called small molecule inhibitors bind to the protein and inhibit the kinase activity, preventing a permanent signal. See this article for more information:

Targeting cancer with small molecule kinase inhibitors


Determining and Differentiating specific ATPases In respects to this certain ATPase transporter. What do i look for in respects to determining what specific kind it is out of:

F-ATPases
V-ATPases
A-ATPases
P-ATPases
E-ATPases

Im assuming that analyzation of the gradients dealt with will guide me to the answer. With that logic, i can assume that this is an F-ATPase since i know this membrane protein can synthesize ATP using a H+ gradient, and work in the reverse to create a H+ gradient using the energy gained from the hydrolysis of ATP.( I see 2H+ cations being expelled) Is this a correct method in differentiating ATPases ?

First of all, I think you need to research the subunit structures of the various ATPase classes in the list because I am pretty sure that several of them are not as complex as this.

Although this superficially looks like the F-ATPase responsible for synthesising ATP by using the proton gradient generated by the electron chain, there is a clue in that diagram that this may actually be a V-ATPase. The V-ATPases use ATP hydrolysis to move protons from the cytoplasm into the lumen of acidic organelles like lysosomes. The diagram in the question depicts a process like that (ATP is being hydrolysed). Now, you can drive the F ATPase in reverse to achieve this situation, so that isn't definitive.

The labelling of the two compartments is also consistent with the idea that it is a V-ATPase since 'lumen' isn't a word that is usually used in the context of the mitochondrion (it would normally be 'matrix').

So I would suggest that you find out if the subunit labelling is like that used in F-ATPase or V-ATPase (or both). A Google image search will help you to find cartoons of ATPases.

My guess, before doing the suggested research, is that this is a V-ATPAse.