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Why do orcas eat only the tongue of whales, liver of sharks, etc.?
I noticed that although killer whales are clearly the top predator living in the present oceans, some of them appear to be very picky with their meals.
After spending hours hunting down a whale, pretty much the only thing they eat is the tongue. I'm not sure how that satisfies their hunger, especially considering how long and arduous the hunt took.
Then there are orcas hunting sharks and eating virtually only the liver. For such a dangerous prey, is such a delicacy worthwhile? I mean, what happens if they're starving after the hunt?
Any relevant comment will be greatly appreciated. Thanks!

Could you add a link to these data. I know, e.g. that grizzlies eat only salmon heads (the fatty brain tissue) when salmon is plenty available. They just sit by the river bed and grab the exhausted, tired salmon straight out of the stream one by one; bite the head off and throw the rest away. They stop doing this when salmon is getting scarce and they start to eat the whole thing. I can imagine the same goes for other predators and humans too. During the "hongerwinter" (literally hunger winter) in '44-'45 during WWII, Dutch folks would eat anything, while now they can be pretty picky :)

Welcome to Biology.SE. Can you please link your sources? That would help

I've got to admit that most of it is memory, but Google gave me these results:
http://www.learner.org/jnorth/tm/gwhale/EnemyOrca.html
http://voices.nationalgeographic.com/2011/11/25/nat-geo-wild-the-whale-that-ate-jaws/
http://www.pbs.org/wnet/nature/killers-in-eden-face-to-face-with-a-killer-whale/1045/
http://knowledgenuts.com/2013/11/19/orcas-can-eat-great-white-sharks/

I really have no idea about this, but consider that orca's are very social and intelligent animals, they may hunt 'just for sport'

Killer whales have a wide range of prey. They hunt in coordinated packs called pods. They are very organized on a hunt and each has a specific job before the kill.
Where the confusion might be coming from is that different pods have different habits. It is true that orcas have been witnessed eating only the tongue, but this is not the norm. They tend to eat the tongue first because it is muscle, rich in protein. In addition, they like the tongue, just as humans may like a good steak. However, in most cases they will consume as much of a whale (typically baleen, or blue whales) as they desire. In fact, whalers hate them because they will follow whaling ships and wait for the fishermen to harvest a whale. They will then rush in and gorge themselves. Another case of their only eating the tongue is when they are well fed. In this case, they can afford to be picky and may only eat the tongue, which on average is the size of an elephant. So, it's no small meal.
As for sharks, it's pretty much the same scenario. However, there are many cases of orcas eating only a great white shark's liver. The reason they target the liver (and they do it with surgical precision) is because it contains large amounts of a compound called squalene. Squalene is important for the synthesis of certain chemicals in the orca's body. They will also target the heart. The attacks on great whites is a more recent trend among killer whale pods. They are quick learners and once they feel the benefits of these organs, they will then focus on the sharks when their bodies tell them they need the squalene. Of course, they don't know that. They just feel better and stronger after consuming GWS organs.
There may be pods that tend to have these habits (outlined above) more than others. Resident pods (staying in one area) seem to be calmer and are not as likely to have the tongue activity, but it is the residents that kill the GWSes for their organs.
Transients are far more aggressive than residents. They are likened to pack wolves and will do some extremely cruel things (by human standards). These are the ones who are far more likely to eat only the tongue of a whale. It could be that since the shark organ habit has not been happening for very long, it's the residents who made the connection between health and these shark organs.
Another factor that could come into play is that scientists/marine biologists tend to believe that there are different species of killer whale. This may play a role in dietary habits as well.
Killer whales are the top (known) predator in the water. While a much larger whale, or GWS could potentially kill one, they are typically no match for a pod and will instead steer clear and only fight if no other alternative presents itself.

Can you cite some of that research?

They eat the tongue and sometimes lower jaw of larger whales because they are the easiest parts to eat. They are soft, unlike the rest of these whales’ bodies. I’ve heard a scientist compare an orca attempting to bite into a grey whale’s body to a human attempting to bite into a whole watermelon. The grey whale’s skin is very hard and thick, and it also has a very thick layer of dense blubber, if an orca tried to take a bite out of, let’s say, the back or side of a grey whale, they would basically only scratch the surface. So the obvious solution is the soft tissue of the lower jaw and tongue. Like someone also said before, the tongues are huge! I’ve heard a scientist say that the tongue of a California Grey Whale calf could feed a family of 5 adult orca!

Can you please add some references to support your answer?

orca have only one set of teeth and i would guess culturally they are aware of the consequences of losing any of them or maybe simply it hurts their teeth to try to eat other parts of the shark -- I mean orca no doubt have nerves in their teeth as we and other mammals do.


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Albinism inheritance problem: what are the father's alleles if he got an albino kid?

Albinism is caused by a recessive gen "c". A normal man marries an
  albino woman. The first son happened to be albino. What are the
  possible phenotypes of the parents? What is the chance that their
  other kids will be albino?

Alright, since "c" is recessive and the woman is albino, then the woman must be "c c" right? And since the son is albino, he must be "c c" too. Hence the father must have at least one "c". But since he is normal, then the other allele must NOT be "c" too (otherwise he would be albino).
My question is, when writing the Mendel table, how do I express that allele of the father (the one that is not "c")?
$$\begin{bmatrix} & c & c\\
? & ?c & ?c\\
c & cc & cc\end{bmatrix}$$
I marked it with $?$ because I'm not sure what to put there. My first thought was "well, it could be a capital C I guess..." - but that doesn't sound right to me. A capital C would mean there is a dominant albinism allele (but I am told that albinism is recessive only...)
I can see clearly that there is a 50-50 chance of having albino kids. I just don't know how to draw that inheritance table.

Super oober short answer: The father is Cc, the mother is cc, there is a 50% chance the children will be albino (as you predicted).

An explination on Mendelian genetics:
First let's look at (what a lot of people consider) the normal Mendel table from here:

Since the dad is normal, that means he has at least one Normal Gene. Which makes him C ? . We also see that mom is normal, so that means she also carries the gene C ? . In this case, they wind up with one child that is affected which means the child has the trait cc. That means both parents had to give the child one little c so that makes both of the parents Cc.
Your answer:
Now, in your problem the mother is albino, which you correctly put as cc.
The dad is normal, which means his C ?. He could eaither be CC (homozygous dominant - an uneffected non-carrier of the affected gene) or he could be Cc (heterozygous - an uneffected carrier of the affected gene). So at this point all we know about the father is that he is C ? . Which means you were on the right path.
Now we look at their first son. We are told he is albino. That makes him cc. That means that the father HAS to have at least one affected gene making him Cc.
So you were correct in thinking that it was Cc. You tripped yourself up by saying that it would make albanism the dominant. As you were told Albanism is a recessive gene. The big C is the normal gene which would hide the albanism trait.
To draw your table, just change all of your ? to big C.

source: Stack Exchange

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E value cutoff for RNASeq search
I am trying to narrow down the possible search criteria from an RNASeq experiment. I already have the cds sequences so I took these and used Blast+ program to blast the data against itself to find sequences that were the same.
From what I have read the E Value is based on the database size. My database only has ~27,000 sequences in it, does this mean that only exceptionally low E values will be relevant to me? Are there any other criteria I should search for before writing the program to eliminate similar sequences?

What are you mapping to the database- RNAseq reads? How long is the query?

Going by an e-value or bitscore cutoff will give you possible homologs, but it sound like you want to remove redundant sequences. If you want to cluster and combine similar sequences to make a smaller database, you could just go via sequence identity using something like CD-HIT. This, for example, is what's done to produce the UniRef set from the UniProt database.

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How can insects survive without an adaptive immune system?
How can insects survive in a world full of pathogens that are able to defeat the innate immune system?

There is not really a definitive explanation for why, although it's important to note that many mammalian pathogens are not adapted to insects and vice-versa. Insects need to survive insect pathogens, and they have a number of defenses for this purpose. Animals and their pathogens co-evolve and exert selection pressures on each other.
Killing the host (or killing the host quickly) is often not in the pathogen's best interest. Pathogens evolve towards their own successful reproduction as much as animals do. Success may ultimately mean evolving towards a less pathogenic state that improves a pathogen's chances of being transmitted.
As animals develop new defenses, they gain an advantage (relative to others of their own species) in surviving various pathogens. Pathogens evolve to escape these defenses, and a new equilibrium is established. An animal lacking this defenses is likely to be more susceptible to dying of infection, as the new equilibrium is dependent on them having these protections.
Here is an interesting paper on this view: http://hedricklab.ucsd.edu/PDF/HEDRICKImmunity113.pdf

I think this is more of a comment than an answer.The question, to me, boils down to "why can insects suffice with an innate immune system (i.e. lacking an acquired immune system)?" This answer, although in itself valid and interesting, poses not more than a general view on  the co-evolution of pathogen and host.

I was debating between posting it as a comment and as an answer. Like most evolutionary questions, I don't think there really is a clear right answer.

You are probably right, but I thought it might be possible to answer this one without an evolutionary perspective. After all, evolution is not mentioned in the question, although it may implicity be tied to it. One way or another, fine enough. Downvote retracted :) [had to make a slight edit to do so - feel free  to roll back]

As mentioned by InactionPotential, organisms and their parasites are caught in an arms race. When an organism develops a new defense, the parasites with traits that allow them to survive those defenses excel and vice versa. Parasites must balance their survival and reproduction with that of their hosts or go extinct. Over time they may become commensal/symbiotic, transfer to another species, and/or eradicate its host species.
Invertebrates' immune systems (including insects) as a whole are quite complicated. Because of the diversity of these systems we may not have anywhere near a complete understanding of them for decades. Some species intentionally upregulate their immune systems in anticipation of events that may expose them to pathogens. Social insect species, like ants, have evolved specialized immunities that take advantage of individual sacrifice, situational recognition, and colony health. Fruit flies possess radically expressive immunoglobulin receptors (IgSF), similar in some ways to the vertebrate major histocompatibility complex.
This diversity is key: the world is full of pathogens capable of defeating certain innate immune systems to some degree. However, the variety of challenges presented by even two different species usually prevents a pathogen from killing all of either species. As a pathogen becomes adapted to one species, it may lose its fitness for the other. If a pathogen is limited to one species, it has to make do with what it has or it will disappear with its host.
References and further reading

The Evolution of Adaptive Immune Systems
Social Immunity
Extensive Diversity of Ig-Superfamily Proteins in the Immune System of Insects
Biology of the Bed Bugs
Immunoglobulin superfamily members play an important role in the mosquito immune system

In the innate immune reponse, pathogens are recognized by a fixed repetoire of cell-surface receptors and soluble effector molecules. These receptors have evolved to recognize pathogens over hundreds of millions of years and provide a formidable defense against a wide range of pathogens.
Adaptive immunity has evolved only in vertebrates and complements the innate system with a very different strategy that allows for an almost infinite number of adaptations in the production of B and T cells.
That lower life forms survive without this adaptation is probably just a testimony to the efficiency of the innate system. Much of this answer must be credited to Peter Parham's text,The Immune System.

Insects have generally shorter life spans than many vertebrates, and since they are smaller they also have a lesser amounted of invested energy in the generation of individual members of the species.  A large number of animals have nervous systems and are capable of movement, and can thus actively avoid environments that might be harmful to them and have predators that are either orders of magnitude greater or smaller in size than the organism in question.
If they have variation among individuals for self recognition and complement, then a greater ability to reproduce more different individuals quickly with a lesser amount of food may help fill the relative deficit in disease resistance from not having adaptive immunity.
For vertebrates that is generally not an option due to the longer life cycles of each individual organism in comparison with either insects or bacteria or viruses.

Please add some references


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BSA for trouble shooting failed PCRs?
I am using PCR to amplify a 1000bp region of the CytB mt gene. Some of the samples had not amplified and I wish to change the reaction components (or use additives like BSA) to attempt at getting amplification. The DNA was extracted from liver/muscle samples, so I am not expecting many inhibitors present, but I am eluting samples in AE  buffer.
I used the following combinations of PCR mixture but the reactions still failed (reaction volume 20ul)
Combination1 : MasterMix (10ul), Primer 1 (1ul), Primer 2 (1ul), BSA 2mg/ml (2ul), water (4ul), DNA (2ul)
Combination2 : MasterMix (10ul), Primer 1 (1ul), Primer 2 (1ul), BSA 2mg/ml (4ul), water (3ul), DNA (1ul) : Tried to increase BSA concentration and reduce DNA to decrease the volume of inhibitors (if any) going into the reaction mixture.
Someone who has previously used BSA to successfully troubleshoot PCRs, am I going about this in the right way ? If I need to take a different approach please help me out.
Thanks!

The albumin shouldn't be what your trouble shooting I don't think. It's something I've always kept constant if required by the enzyme. Since your inconsistency is across different samples and I assume you are creating a 'mastermix' containing the taq, ntp's, primer etc I would troubleshoot the purification steps. If that's not possible, there are other parameters of The pcr (especially annealing temp and primer concentration) that will have more apparent results. MtDNA usually requires a more stringent extraction protocol like using guanadine.

There are other samples from the same extraction batch that are working fine, so I'm assuming the problem is not with the extraction or with the PCR temperature settings ? And I use a mastermix, yes.


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How did zootoxins evolve?
I've always wondered how toxins in certain organisms have evolved. Particularly, organisms that produce toxins as a deterrent to predators as opposed to organisms that use it to paralyze their prey.
Where did this toxicity come from? How did it develop to what it is today?
There must've been a drawn out period where evolution 'tested' and 'fine-tuned' the toxin. Presumably until it was somewhat efficacious to the target.
What are the current popular theories on this?

Anything and everything is toxic in the right concentration, so there really is no first toxin.

@John There are some compounds that are exceptionally damaging to other organisms in low concentrations but do seemingly no harm to the toxic/poisonous organism. That is what we mean by a toxin here. Furthermore to your point, there is such a diverse range of toxic/poisonous organisms that there were probably many toxic substance evolutionary origin events.

if I exposed your brain to your own digestive enzymes or bile either would destroy it. both would be incredibly destructive to any other part of your body. It would be a toxin anywhere else in the body, indeed that is how many venoms start. Other toxinsjust don't matter to the host. Capsaicin is the oil  that makes peppers spicy but it only works on mammals (binds a unique to mammals receptor), it does nothing to birds much less plants so of course the plants can make it with no problem.

Basically there is no one way to get a toxin, each toxin is different and evolved from diffrent things in different ways. Toxins have evolved many separate times. That's why your question is confusing, there is no one single toxin precursor and no single way to evolve a toxin.

General overview.
Each toxin and poison probably have their own evolutionary "arms race". Generally, an organism contains a compound that is a bit harmful to other species. As a predator or prey species becomes tolerant to low doses of this compound through natural selection, the compound efficacy could be increased (again by natural selection) on a molecular level, or at a dosage or concentration level.
Below are a few examples of where this has become the case, and some more general examples of how venom evolved in the first place.
Examples.
California Newt.
These newts contain tetrodotoxin (you may be familiar with this from the fugu fish). It is preyed on by a species of garter snake. This is a textbook arms race as the garter snake is naturally selected to have beneficial alleles that are tolerant to the toxin.
Dart Frogs.
The golden dart frog Phyllobates terribilis contains enough batrachotoxin to kill 10 people. That is apparently overkilling for any predator it would surely have to face especially given that the only animal alive that is immune to the poison is the frog itself. However, the snake Liophis epinephelus can tolerate massive doses of batrachotoxin (although I've heard it gets pretty poorly after eating a frog, rather understandably). These two species are locked in an arms race that drives the frogs to produce an unbelievably fatal cocktail and the snakes to become ever more tolerant.
Snakes.
Modified sweat glands evolved to damage the prey as much as possible for immobilisation, partial digestion, or defence. There are textbooks about snake venom and toxins. Here is a neat article I found with a cursory search or if you want to sink your teeth into the topic (heh.) check out this article.
Long story short: venom sacks are modified saliva glands from non-venomous snake ancestors. The diagram shows generally just how modified these apparatus have become!

Platypus
Let's not forget the weird and wonderful monotremes. It's hard to pinpoint exactly what drove the platypus to develop venomous barbs on its elbow (last time I looked into it, it was still disputed if they were for defence or hunting).

But what we can learn from this is that venom can independently evolve. Although the venom producing proteins are different, they produce the same venom as some snakes.

Sortof. Just as every adaptation is the product of a small change in something the species already expressed, all toxins start out as something the organism just happens to produce as part of its life. Then there are two evolutionary paths for useful toxins:

Poisons - "If you eat me, you will be sorry." These typically begin as metabolites that happen to confer an advantage to an organism's siblings, work as an aid to escape, or are just mildly irritating to predators or parasites.
Venoms - "If I bite you, you will be sorry." These typically begin as digestive assistants - mucous or saliva.

Once there is some advantage to expressing a chemical in a certain way it can be considered to be "locked in" - organisms with that trait stand a better chance of surviving to reproduce and will therefore multiply. As the organisms that exhibit that toxin multiply, mutations in their descendants that improve the utility or effectiveness of the toxin allow those organisms to better survive, and so on. So, a saliva gland that once caused mild irritation in a certain species of prey becomes a descendant's vertebrate-paralyzing-venom gland.
References

Venomous Marine Fish: Evolution of the Venoms. Chondrichthyes (Cartilaginous Fish)
The defensive role of alkaloids in insects and plants
Molecular genetics of ecological diversification: Duplication and rapid evolution of toxin genes of the venomous gastropod Conus


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What is the distribution of the expected number of lineages in a birth-death tree after time T?
I've been looking at The reconstructed evolutionary process by Nee et al. 1994 and they provide a number of equations dealing with the birth-death process, specifically the "reconstructed" birth-death process where you only have information about lineages that currently exist today.
I am interested in this equation for the likelihood of observing N lineages after time T:

What I want is the distribution of the expected number of lineages N after time T given per-lineage birth and death rates lambda and mu. I've looked around and haven't found anything providing such an equation.

You are actually asking the explanation of the entire paper. There are 20 equations that precede this one. Have you understood them all?

@CactusWoman I reread your post and got confused. What do you mean by distribution of the expected number? Distribution over what parameter(s)? Expected value of which distribution?

Maybe it is more strategic to direct your question more in reaction to the content of the paper. Pick a particular step you don't understand and ask what it means.

@Remi.b I was beginning to write an answer but figured out that even the first equation relies on many assumptions which are not really defined in this paper. The equation in the question follows equation(3)  which is from a 1948 paper by Kendall. That's why I asked the OP if they have understood the previous equations.


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How could one calculate the gene flow between two populations?
Imagine there are two populations X and Y, and for each population you have the genotypes of each individual in that population (e.g. Aa, AA, aa, etc.), but for multiple loci (e.g. AABb).
How could one calculate the gene flow between population X and population Y?
An answer would ideally recommend either or:

An R/Python/C++ library, or any other software tool
the breakdown of the maths, for which I would be much obliged, but not entirely necessary in the answer

Background reading

Indirect measures of gene flow and migration: FST≠$\frac{1}{4Nm+1}$

Related questions

Variance in Fst in the infinite island model (by Remi.b)

@Remi.b here's the question in case you are interested in finding out the answer (great hearing from you too by the way)

Theoretical Background
From Slatkin 1991, at equilibrium
$$F_{ST} = \frac{1}{1+4Nm\left( \frac {d}{d-1} \right) ^2}$$
, where $N$ is the per island population size, $m$ is the migration rate and $d$ is the number of islands ($d$ stands for "deme"). As $d \rightarrow \infty$, $\left( \frac {d}{d-1} \right) ^2 \rightarrow 1$ and Slatkin equation becomes the standard Wright's equation $F_{ST} = \frac{1}{1+4Nm}$.
From the above, it is easy to show that
$$m = -\frac{(d-1)^2(F_{ST}-1)}{4 d^2 F_{ST} N}$$
For 2 islands, it becomes
$$m = -\frac{9}{16} \frac{(F_{ST}-1)}{F_{ST} N}$$
In consequence, in a 2 island model the expected $F_{ST}$ is almost twice as low $\left(\frac{9}{16} = 0.5625\right)$ than in the infinite island model.
The above equation is an approximation that assumes...

low mutation rate (would not apply to microsatellite data)
relatively low migration rate (there is a $m^2$ term that is dropped)
symmetric migration rate (backward and forward migration rates are equal)
equal population size per island
equilibrium!

Further Reading
I recommend reading this paper (Slatkin 1991), it is IMO one of the best on the study of $F_{ST}$. I would also recommend Nei 1973, Slatkin 1985 and Whitlock and McCauley 1998.
The specific software to use depends on the kind of data you have. In any case, if you average $F_{ST}$ over a number of loci, make sure to use Weir and Cockerham 1984 method.
Bioinformatics
The first step for you is to calculate your $F_{ST}$. Assuming you have a number of SNPs, you will want to use Weir-Cockerham estimate of $F_{ST}$. There are a number of solutions to compute such estimates. One solution to calculate this is vcftools. The following (Bash) will do the job
./vcftools --vcf MyFile.vcf --weir-fst-pop individual_list_1.txt
--weir-fst-pop individual_list_2.txt --fst-window-size 800 --fst-window-step 100

, where MyFile.vcf are your data in vcf format (you might eventually want to use PGDspider to reformat your data). individual_list_1.txt and individual_list_2.txt are files containing the list of individual names (seperated by \n) belonging to the first and second population, respectively. The options --fst-window-size and --fst-window-step allows you to compute the estimate over a sliding window. I chose arbitrary numbers above. EggLib is another good alternative.


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Why do sneezes come out the mouth?
As anyone who's ever sneezed can tell you, it's caused by irritation in the nose.  And the answer to a question on this very SE attests that "sneezing is a reflex, partially autonomous, to clear the nasal cavity of particles that don't belong there."
That being true, the sneeze mechanism is a little bit strange: if you hold your hand up in front of your face when you sneeze, you'll feel that all of the rapidly-expelled air that ought to be cleaning out your nasal cavity is coming out your mouth, not your nose.  In fact I don't think I've ever felt air coming out my nose when I sneeze.
So what's going on there?

Your premise is wrong: http://si.wsj.net/public/resources/images/PJ-AT748_respor_F_20100222143757.jpg

@kmm: Is it? I see a huge spray of droplet-stuff coming out of the mouth and a tiny bit of barely anything coming from the nose.

To say that "all of the rapidly-expelled air" comes out of hte mouth is not accurate. Maybe the amount that comes out of the nose is sufficient.

If you keep your mouth closed, the sneeze will come out of your nose.  From an evolutionary perspective, the mouth being open might help to reduce pressure which is good for preventing an aneurysm.

I've pondered this question too.  It's very clear that when we sneeze, the expelled air comes mostly from our mouths.  However, at least as far as my own sneezes are concerned, some of the air comes from my nose as well.  I know that if I pinch my nose closed as I sneeze, my ears hurt and pop.  If my nose is sniffly, I usually notice mucus come out.  Our soft palate partially lowers and our tongue rises as we sneeze, in order to divert a portion of the air up into our noses.  That position of our tongue is why our sneezes make a CHHH sound. If people intentionally keep their mouths wide open as they sneeze, that could explain why nothing comes from their nose, as there's nothing to divert the air.

A good book to learn as background is called 'Why We Get Sick: The New Science of Darwinian Medicine'.
In a sense you can consider us vectors for some microorganisms. When you cough you spread germs to other individuals (other vectors). Thus, it would be evolutionarily advantageous for a microorganism's genes if they were to infect more vectors.
How many germs are spread from the nose rather than the mouth? I don't know. However, expulsion of germs from your mouth will reach further than from your nose. It might be that there is a greater density of germs coming out of your nose, but that they don't travel as far in the air.
The above is slightly speculative, though, and I could speculate more but from what I can tell that is to be kept to the comments. (I can't comment due to <50 rep).
TL;DR More germs being spread from the mouth due to increased capacity for infected droplets and increased potency in terms of expulsion - advantageous evolutionary mechanism for spreading germ's genes.

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Insect identification: white spotted beetle

3 pairs of legs, a pair of antenna, wings absent, compound eye, 4-6 centimeter approx. in size.
I found this beetle at my door, in Pune, India.

Whitespotted Sawyer in Assam, india. It killed many plants in my home. I don't know how to deal with this

It is a longhorn beetle (Cerambycidae), most certainly from the subfamily Lamiinae (flat-faced longhorns). The overall apparence with a downward-pointing face, partially divided eyes, robust build and spined pronotum fits well with Lamiinae.
The beetle in you picture is very similar to species in the genus
Batocera, for instance Batocera rufomaculata (also called Mango trunk/stem borer), and the red spots on the elytra fit relatively well. This species is considered a pest on mango plantations in India and Nepal (Hill, 2008 and Insects in Indian Agrosystems), so it's probably not all that uncommon.

(picture from Insects in Indian Agrosystems, from the National Bureau of Agricultural Insect Resources.)
However, there are probably hundreds of species in Lamiinae found in India, and I cannot give you a certain answer.
The striped elytra with raised lines doesn't fit with the species I've seen in Monochamus (suggested in the other answers), so I don't think that is the correct genus.
References:

Hill. 2008. Pests of Crops in Warmer Climates and Their Control

I think it is from  Cerambycidae family,
Batocera parryi -

I don't think this is correct. First, Monochamus scutellatus is a North American species. Second, species in Monochamus usually don't have a striped elytra with raised lines, so I don't think that the genus is correct. It is probably a species from Lamiinae though.

I think that your insect is a White-spotted sawyer. For more information check this: Monochamus scutellatus, commonly known as the white-spotted sawyer or spruce sawyer,is a common wood-boring beetle found throughout North America. Adults are large-bodied and black, with very long antennae; in males, they can be up to twice the body length, but in females they are only slightly longer than body length. Both sexes have a white spot on the base of the wings, and may have white spots covering the wings. Both males and females also have a spine on the side of the prothorax. Most research done on M. scutellatus focuses on their relationship with burned forests and the logging industry,with interest also being shown in their mating behaviours.

I don't think this is correct. First, Monochamus scutellatus is a North American species. Second, Monochamus usually don't have a striped elytra with raised lines, so I don't think that the genus is correct. It is probably a species from Lamiinae though.


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Jurkat single cell clonal expansion
I'm hoping to do a clonal expansion of Jurkat, expressing my construct which is currently transduced virally. From the FACS data I currently have roughly 30-40% expression in my culture but I need it to be close to 100% as the effect I'm looking for I believe to get diluted by the reduced presence of my molecule of interest in the total culture. I can do cell sorting but usually what happens is that the 5% cell population that do not express the construct eventually take over after a few passages.
I'm planning to do a 96 well plate format single cell seeding and expansion of Jurkats but it has been done before by another member of our lab and the person suggests that single cell Jurkats (unlike CHO cells) do not survive a single cell state although they are suspension cells and do not necessarily require contact to survive although they clump. Hence I'm wondering if anyone has any protocols they could suggest such as contents of the media (e.g. conditioned media) or any other recommendations for Jurkat single cell clonal expansion.
P.S. I am fully aware that there might not be a single right answer to this and the answer requires a degree of experience/opinion on the working method but I would fully appreciate any helpful suggestions/responses.
Many thanks

Is there a chance to use a selection marker like G418 to kill all the cells which do not express your construct?

I will look to see if the vector has this otherwise a fresh co-transduction or a new vector containing antibiotic resistance selection marker containing something like G418 might be required. I think people are unsure as to exactly what backbone the construct is in so that could be tricky and require month of cloning and sub-cloning. Are Jurkats tend to be difficult with clonal expansion?

Jurkats shouldn't be difficult to clonally expand. If you're having problems, get a fresh culture from ATCC. You really also should know what kind of vector you're using - if you don't know what your reagents are, there is no way to independently verify your results. Therefore, they are invalid.


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How much salt [NaCl] is too much in DNA precipitation?
In DNA extractions, how much is too much salt in a CTAB extraction buffer? Protocols hover around 2.5 molar; if you go over this (e.g. 25 molar), will you saturate your solution, and precipitate the DNA too early?
Background:
  Most DNA extraction protocols approximate the following:

~Physical lysis
~Chemical (detergent) lysis
Phase separation (dreaded phenol-chloroform-isoamyl step)
Precipitate, dry

Variants are plentiful, but a common feature of steps 1\2 is inclusion of CTAB and NaCl in the extraction buffer - detergents and salts help to rupture the cell membrane, but (maybe more importantly) CTAB 'selectively'  complexes and precipitates out organic impurities (saccharides, proteins...) while DNA/RNA are left in solution.
For this to work, the net-negative charge of the DNA phosphate (PO4-) backbone needs to be neutralised allowing the DNA to stay in solution: sodium (Na+) ions are attracted to the regular (PO4-) groups, while more irregularly spaced charges*  in proteins etc. associate tightly with CTAB, and 'fall' out of solution: you keep your DNA in the liquid phase and purify, with excess salt washed out at the end using repeated 70% EtOH washes.
Would excess Na+/Cl- effectively level the 'selective' properties of CTAB? 'Salting-Out' the DNA from solution (disrupting the solvation shell) is used in step 4, most often with sodium acetate and 2-propanol: how much salt can be used in Steps 1\2 before the DNA is precipitated out with other organic materials? Are there other considerations (e.g. salts and organic solvents in Step 3)?
First description I've found for this is Zhou (1996), but a really good protocol on it is Wilson (2001).
*: presumably?

What are you afraid of? Did you follow the published protocol? If not, just repeat it and follow the protocol. Ffrom the standpoint of biochemical purification, a cell contains four types of molecules: proteins, lipids, carbohydrates, and nucleic acids.  These last two co-purify through most fractionation steps. As I recall, the CTAB binds to the denatured proteins. and the denatured protein-detergent complex is highly insoluble in the presence of high concentrations of monovalent cations--voila.  RNA can be precipitated by monovalent cations alone, but I don't think DNA can.

Saturated sodium chloride is approximately 6M, making 25M impossible to achieve in water.

@ mdperry my belief was that the Na+ is (also) used to 'cloak' the negative DNA phosphate-group backbone from complexing with CTAB, keeping the DNA in a soluble 'sweet spot': my worry is that too much Na+(Cl-/AcO- etc) will totally disrupt the H-bonding between the solvent and solute, and precipitate the DNA early, at the same stage as the CTAB-protein complexes, though not necessarily for the same reason. Also think you can salt out DNA, but it needs to be cleaned up afterwards.
@MarchHo - Hah, thanks! Challenge accepted.

@incertae_sedis final NaCl concentration in the extraction was increased from 0.5-2M to a dramatic 5M following advice from a colleague and greatly improved DNA yield. Not an answer as such, but suggests not enough NaCl is more likely than too much.


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Proteins and Blood Acidification
Is there evidence to suggest that excessive consumption of Whey, or similar proteins will lead to acidification of the blood?

Can you provide a source for this claim?

Found a study on cows


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Please explain what a gene isoform is in lay terms?
I am a physicist by training, however I am now doing computational biology research. I know what genes, DNA, proteins, enzymes, introns and exons are.  I sort of understand how DNA is used to create RNA, which is used by ribosomes to manufacture proteins.  That is the extent of my biology and genetics knowledge.
So, could someone explain what a gene isoform is in lay terms?  There is a related question here and wikipedia has an explanation.  However, there is a significant jargon barrier for me.

Gene isoforms are all the different RNAs that can be synthesised from a single gene. You may be referring to splice variants, which are systems of getting different mRNAs from the same sequence using different combinations of introns and exons.

(source: riken.jp)
Translating your wikipedia article:
Gene isoforms are the different RNA products obtainable from a gene that can vary on the place where the translation starts (protein synthesis), that have different sequences in the coding region (thus giving different proteins, sometimes with different functions) or by having different untranslated regions, UTR (the overhangs of the sequence that are not translated in the mRNA). This last difference, the UTR, normally gives rise to different stability within the cell as UTR secondary structures usually control the speed of degradation of an RNA.
Hope it helps


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How do signal transduction pathways utilize transcription factors to express a specific gene?
I have an inquiry regarding the regulation of genes via extracellular signaling.
To my knowledge, in autocrine, paracrine, and endocrine cellular communication, large protein ligands that cannot directly diffuse through the plasma membrane of the target cell(s) use surface receptors to perform their desired action on the target cell(s).
I have learned that some of these ligands activate signal transduction pathways such as the MAPK/ERK and JAK/STAT pathway and drive the expression of specific genes by utilizing transcription factors (of course, in eukaryots). A simple example of this would be the action of epinephrine (adrenaline) on hepatocytes (liver cells), where the amino acid-based hormone uses the transcription factor CREB to express the gene coding for Glycogen Phosphorylase to engage in glycogenolysis.
Here I have two questions:

How does the transcription factor chemically indicate which gene to express? (Is there a gene indexing system like a computer filesystem?)
How does the transcription factor locate and bind to the promoter of the gene it is trying to express?

Thank you.

1: by recognizing the promotor sequence. 2: trial and error. TFs don't have eyes nor a brain or ways to propel themselves. Somehow the answers are in the question it seems, as 2 answers 1, while 2 is basically chemistry in a way.

@AliceD But don't most genes have similar promoter sequence patterns? How could we specify a set of transcription factors to express a specific gene? If trial and error was used, signal transduction pathways that involve gene expression would pitifully fail most of the time.

Subquestion 2 does not have "specificity" included. As of now, it looks like you wish to know how it gets to its target. maybe refine your question a bit and perhaps the whole story on signal transduction is not really relevant?

Most genes have a similar core promoter but varying proximal and distal promoters which contain specific TF binding sites. Signalling pathways are integrated with other signals and the status of the cell in order to correctly express genes.

This is a combination of multiple regulatory systems. Most genes are not regulated by a single factor, but by many. Moreover in eukaryotic organisms there is also epigenetic, which "inactivates" permanently certain areas of the genome by compacting these zones forming heterochromatin.
Moreover, even when we are interested in a single function a TF might have, that does not mean that it only has this function in the cell. We view it as humans, and maybe for us it is logical that a response to a high metabolite in the environment simply leads to expressing the protein that metabolizes it. However, probably it is interesting for the cell to also activate other pathways and gene networks (i.e. anabolic pathways that feed off this metabolite, compensatory pathways to mantain homeostasis...). Because that normally TFs affect more than one gene naturally.
The mechanisms of action of the TFs are multiple, but they tend to simply allow or deny the access to the adequate RNA polymerase. For more information about this check the wikipedia article on TF structure
In this image we see a typical mechanism of action, DNA bending
Different domains interact in activating a gene, enhancers which are usually long distance, promoters which tend to be in the upstream region, though they can be downstream or in the gene sequence, and epigenetic factors that change the compaction of DNA, making it inaccessible to proteins.
Just as a last thing to point out, you should acknowledge that the biological systems are far from exact and yes, a single TF might activate 200 genes, even when its main objective in that moment is to activate one, but it won't really matter as long as the those 199 activated genes express at a very low rate (for example by not having the right RNA polymerase subunit accessible, being marked as inactive by epigenetic systems or having their own inhibitors).

Thank you so much!! You just clarified my understanding of gene regulation!

I'd also like to add with respect to many text figures, that while the coactivating complex Mediator isn't necessarily required in all instances of gene regulation, it does give the transcription a level of robustness you wouldn't otherwise get without it. More on mediator here.


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How can we determine the polarity of fat molecules?
I'm trying to solve a question in a biochemistry quiz, which is asking for classifying a set of lipidic derivatives, by increasing polarity. Unfortunately, we didn't cover the classification of different liposoluble molecules by polarity in Biochemistry class. I find myself buried in details every time I use google seeking a good explanation. So:
How can we determine either if one molecule is more/less polar than other ?

For example, classifying Cholesterol, Triglyceride, Phosphatidylcholine, Phosphatidylserine, by increasing polarity.

PS : I'm not searching for the answer of that example too. I just need the exact method for determining how strong a polar fat molecule is. I'm sorry for my bad english.

Please read our homework policy, then [edit] your question to include what you've learned so far, what your thinking is regarding the polarity of the different molecules, and where exactly you're stuck. We're not here to do your homework for you, but we are here to help you learn.

This is not homework. I'm just practising some random exercises from the internet in order to develop my knowledge and skills in Biochemistry. I asked for the method, not the answer to the exercice. And this example I provided is not the set provided in the exercise. :)

You determine polarity, generally, by looking at the composition and the functional groups on the molecule, and the geometry of the molecule. Do you expect a separation of charge, or something uniform? Water is polar because the draw on the net electrons for the molecule is to the oxygen atom, resulting in a more negative charge in that region. Carbon dioxide is nonpolar because of it's linear geometry, even though there are two oxygen atoms.

Not that. For example, a fatty acid have a hydrophilic region and a hydrophobic region right? and a phospholipid also do. But, they differ in composition of the polar head (Hydrophilic part). So, I want to classify these two molecules, by their hydrophilic part polarity. Which one is more polar and can interact with water more than other. Got it ?

http://chemistry.stackexchange.com/questions/18589/how-do-i-figure-out-the-relative-polarity-of-organic-compounds
I managed to find a good answer in the chem stack exchange. Otherwise you'd use column liquid chromatography and a gradient elution technique to determine experimentally which one is more polar.

As mentioned in the chemistry-SE post, dipole moment can be empirically calculated based on electronegativities of different atoms. I guess there are other ways to calculate the net dipole moment (perhaps by spectroscopic techniques or subjecting the molecule to electric fields). I cannot comment further on this question would be suitable for physics or chemistry SE. I suggest that you edit your question such that it is about experimental techniques to calculate dipole moment. You can also narrow down your question by describing the kind of "fat" molecules you are interested in.


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Why didn't humans evolve to reproduce identical twins all the time?
According to the selfish gene theory, it seems like because identical twins sometimes get produced, a mutation to a gene that says, "if you have an identical twin, be fully altruistic towards them" would get selected for when ever it happens to arise in an identical twin. After humans evolve to be fully altruistic towards identical twins, wouldn't a mutation to a gene that makes a woman more likely to produce identical twins also be selected for because if it happens to appear in a a child who has a non-identical sibling, that gene might be discontinued from reproduction by the partial selfishness of the sibling but if it appears in an identical twin, the other identical twin will preserve that gene with their altruism.

Can we even assume that it's possible for a gene to say "be altruistic to your twin"?  Certainly we don't see any sort of exclusive altruism between siblings.

One issue is twin baby's are difficult to carry to full term. So it's not a good idea for a twin birth to be preferential over a single birth

What you describe could have happened under the right conditions. However, there are a few things you haven't considered.

Because humans are especially altricial, always having twins would double the cost of children on parents.
The benefit of sexual reproduction is immune diversity. So a population like this could be far more vulnerable to disease.

So as far as this thought experiment goes, genes can't be too selfish or they dramatically reduce their own fitness. It's something worth simulating computationally to see what happens.
References

Sexual reproduction as an adaptation to resist parasites (a review)

Although I didn't want to making the question very long to explain it, what I meant was that should be an evolutionary advantage for a mother to reproduce 2 identical twins only once than to get pregnant and reproduce one kid then get pregnant again and reproduce another kid when she only has enough food to feed 2 kids. I'm assuming the tendency for a mother to choose not to reproduce once she already has 2 kids means having identical twins won't cause her to reproduce more than 2 children.

2 children require twice the resources of one, during gestation those resources come directly from the mother, twins are more likely to have complications because of this higher demand on the mother's body. Twins are often underweight or premature and have higher occurrence of birth defects. https://www.ncbi.nlm.nih.gov/pubmed/11321243

Maybe it was an evolutionary disadvantage to produce two kids at the same time because when two kids get produced at the same time, by the time they're nearly finished getting reared, two children both have a high energy demand at the same time and the parents can't keep up with providing both of them such a high energy demand. Maybe the parents also were unable to simultaneously defend two babies against predators.

From jzx's answer, I thought of a possible answer to my own question. Maybe not producing identical twins all the time is a paradoxical evolutionary stable strategy for the following reason:
Until recently in evolutionary history, the population remained constant when parents only had enough food to feed 2 children. Siblings didn't evolve to be fully altruistic towards each other so if a parent had 3 children in case of the small chance of having enough food to feed 3, none of them would willing let themself starve to make sure the others survive, risking making only one survive, so the parents would have had an evolutionary advantage in only producing 2 children in the first place. Although definitely producing identical twins is an evolutionary advantage, a mutation that makes the chance of producing identical twins slightly higher than it already is is an evolutionary disadvantage because a woman with an increased chance of producing identical twins might have produced 1 child on her first pregnancy and identical twins on her second pregnancy, giving a total of 3 children and increasing the risk of only rearing 1.

If we produced identical twins all the time then we'd completely lose genetic diversity which would, I assume, overwhelmingly compromise our adaptive capabilities. Don't forget, those identical twins then need to reproduce with other identical twins of others families. Moreover, and this is the more obvious explanation, as a consequence deleterious recessive disorders would rapidly increase in rate.
For more, see
https://en.wikipedia.org/wiki/Inbreeding_depression
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109585
You might also like to study frequency dependent selection for why it is sometimes advantageous to have identical twins, albeit at a low rate.

I think that you may be confusing identical twinning with reproductively closed populations. Also, with the mix and match of chromosomes and crossover events during Meiosis, there will still be a good deal of diversity, even in populations that are relatively isolated. Even if two identical twin males mated with two identical twin females and produced the same number of offspring, it is highly unlikely that any of the offspring of different births would have an identical genetic make up.

I don't see a reason we'd lose genetic diversity because the identical twin of the spouse of somebody wouldn't be the same person as the spouse of their identical twin.

But by definition you restrict the diversity by at least a factor of 2. i.e. imagine you had two non-identical twins v two identical twins.


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Can anyone ID this flower plant by the photo?
Can someone identify this plant? It has big red flowers when it flowers! Not sure if it is native, but it is in my grandmothers garden in Vancouver, British Columbia, Canada.

It seems like it's either a Paeonia brownii or Paeonia californicus.  According to Wikipedia, these are the only peony trees native to North America, but there aren't any that are native to Canada specifically.  I guess these are the closest you can get.  I added some images to hopefully help you out a bit.
https://en.wikipedia.org/wiki/Paeonia_brownii
https://en.wikipedia.org/wiki/Paeonia_californica

That'd be a peony tree. I'd say they're a pretty common occurrence!
https://en.wikipedia.org/wiki/Peony
I'm afraid I'm unfamiliar with identifying the individual species, however, if anyone is more knowledgeable here than me.


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What is the mechanism by which bactericides kill bacteria?
"Bactericides kill bacteria". What is the meaning of "killing" in this context, and how exactly is this "killing" happening chemically?

This is rather broad. Each bactericidal agent has a different mechanism of action. For example, alcohol denatures proteins necessary for function and the lipids in the plasma membrane dissolve into the alcohol. "Iodine can penetrate the cell wall of microorganisms quickly, and the lethal effects are believed to result from disruption of protein and nucleic acid structure and synthesis." [CDC]

Each bactericidal agent has a different mechanism of action. For example:

Alcohol denatures proteins necessary for function and the lipids in the plasma membrane dissolve into the alcohol.
"Iodine can penetrate the cell wall of micro-organisms quickly, and the lethal effects are believed to result from disruption of protein and nucleic acid structure and synthesis." [CDC]
other mechanisms include tampering cell metabolics, tampering DNA replication, and more.

See also:

The 2008 CDC guidelines for sterilization and the such for healthcare settings. Each method will contain a comprehensive description along with a statement of "mode of action," i.e. how the method actually kills the bacterium.
Another good link here from the CDC examines factors affecting the efficacy of sterilization.

Otherwise, it would be best therein to split the specific mechanisms you perhaps don't understand into separate questions. But an important take-home message in the efficacy link above just adds to just how broad this question is:

Microorganisms vary greatly in their resistance to chemical germicides and sterilization processes.

Could you please also give a few examples of what's going on from a pure chemical point of view?

@Sparkler this question is far too broad. From What types of questions should I avoid asking? "If you can imagine an entire book that answers your question, you’re asking too much."


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Why do almost all SNPs have two alleles?
Reading the Wikipedia page for SNPs I find the sentence "Almost all common SNPs have only two alleles." This is consistent with terminology elsewhere, such as the therm "Minor allele frequency", which references the least common allele, which implies there are generally only two alleles for a given SNP.
But there are 4 common nucleotides, A, T, C, and G. Why wouldn't it be common to have 3 or 4 alleles at a certain location? The only way this seems possible to me is if strand is ignored, and so at any given location "A" and "T" are considered the same allele and "C" and "G" are considered the same allele. Is this the case, or am I misunderstanding things.

Well, though it is possible to have SNPs of more than two alleles, and some exist, due to the low probability of having a basepair change twice in the same base-pair (there are aproximately 3.000 Mb in the human genome) and have it in more than 1% of the population (remember we are talking about single nucleotide polymorphism) to classify as a polymorphism is a very rare phenomenon.
I can check the maths for it if you need it, but it's just matter of probability.

To be sure I understand, the idea is that say 100% of a population has an "A" at some loci at some point in time. Then say a mutation causes a member, call her Alice, of the population to have the loci at that base replaced with a "C", and they pass that mutation on to their offspring. After some time, that loci would be considered a SNP if enough of Alice's descendants survived such that they make up 1% of the population. The only way for another allele to exist is is if someone else at some other point in time ALSO has a mutation at that loci that switches away from "A" or "C", which is rare

The percentage varies between definitions of polymorphisms, some say 1%, some say 5%, but you got the idea. You have to think that is not a loci, but rather a single position of a loci. Even if all locis accumulated 1 single base mutation each generation with a 2.5 kb length (that is the average loci if i remember correctly) it would still be 1/2500 probability of affecting the aame letter and times 2/3 (as one of the mutations would be a reversion to the original). So yeah, it is highly improbable.


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How did the tendency to perform death rituals evolve?
Both elephants and humans perform rituals when deaths occur.
However, I do not see any evolutionary benefit of this. The rituals take time, which apparently could be better spent hunting, foraging, traveling, mating, or grazing.
I am interested to know if these behaviours have any significance and whether they confer any kind of survival advantage.
A cursory google revealed nothing about this.

Good read: http://www.bbc.com/future/story/20120919-respect-the-dead

I'm voting to close this question as off-topic because it is more the realm of anthropology. No, there is no Anthropology.SE and yes there is "evolution" in the question, but those two statements are not a reason to believe that all anthropologists are hiding at Biology.SE and that every question about evolution is on-topic here.

@AliceD It's not just about anthropology, because elephants have death rituals as well. Would it be best if I only ask how elephant death rituals originated?

@Kyth'Py1k I would suggest that you modify your question such that it is about animal behaviour. Please try adding details and if possible some more examples/references to support the point.

@WYSIWYG In what way is it not about animal behavior? The question is about death rituals, which is an animal behavior. Also, what point are you talking about? I am not trying to make a point in the question; I'm just asking a question.

@Kyth'Py1k I meant that you add more emphasis on the animal behaviour part and defocus from the human aspect so that it is not interpreted as a question about anthropology. Gosh! I am trying to help you here; this question can be edited a little bit so that it can be on-topic. Why are you getting defensive?

@WYSIWYG My apologies; I did not intend to come across as defensive. I was just trying to better understand what was wrong with the question so I could improve it. What exactly made me seem like I was being defensive. Anyways, do you think asking only about elephant death rituals would be a good idea?

This question is not different enough from the original question. If anything the original question is more on topic because it builds a strong case of showing that habitual social ceremony exists without anthropomorphism, whereas in this question it appears that you're trying to ask why it would benefit elephants to have human-like death rituals.


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How does the brain regulate its temperature?
I recently ran into a bio-physical paradox while trying to solve an engineering problem, using nature's way as a guide; namely the brain.

I'm working on designing a totally new system of liquid/gas cooling for a project. In Normal systems, the coolant is first cooled at a point, then sent along to the target areas; however, the coolant gets too hot along the way and cannot meet my target at one of the end components. Additional external cooling fins along the path still do not compensate.
I took biology classes in college and recall some mechanisms of the brain and pictures too (usually depicting the brain as all white internally). So, I theorized that maybe the coolant (blood) was not in direct contact with the brain in a substantial volume; however that was debunked: Why is the brain white?
From what I gather from the major answer, the brain's way of achieving homeostasis might present the answer to my problems. There is a lot of blood in the brain. This blood comes from the carotid arteries, which means it comes from the main circulation, and is hence at body temperature {considering homeostasis of all the body organs i.e. the lungs in this case}. By connotation, the brain should be the hottest organ in the body!
Considering the volume of blood in the brain, how does it regulate its temperature?

Great question, thanks for posting it as a new question. +1

Well, blood is highly toxic to the brain, which is why there is a blood brain barrier and there are astrocytes and glial cells that interface between blood vessels and the central nervous system. Homeostasis is maintained chemically much more than mechanically and it is more the task of the glial cells to maintain homeostasis in the CNS. As for heat dissipation, the majority of that happens through the enormous surface area of the skin. Basically the entire body acts as a radiator. And no, core body temperature is 37°C, barring an infection or inflammation. There is no hotter or colder organ.

What you saw in the post that you linked to is the amount of vasculature that is circulating around the cranium, but that is hardly any different from the amount of vasculature in the rest of the body. Yes the body is able to shunt blood flow to different areas under different conditions using hormones, but the network of blood vessels is still there. If you really want to compare that to a cooling system then calculate the volume and surface area of of all of those blood vessels to the volume and surface area of the brain, then compare that to the cooling components in your project,...

... and if you had a 1000th of the amount of cooling capacity running through your device as compared to the brain, or any part of the body for that matter I would be very surprised... the average human has 96 thousand kilometers of blood vessels in them. Cells are usually never more than 50 micrometers from a blood vessel, and the entire environment is aqueous which dissipates heat much better than air. Either you need to go really cold, N2(l), or you will need better tolerances for the downstream components. Or do like the body does, lots of pipes close together running for short distances.

Amazing! I believe I just got my answer. The chemical cooling you mentioned. All I need is to find an intermediate coolant fluid whose volume at any component along the path will regulate the amount of heat removed along that path before the end component. Though that is easier said than done. Thanks.

@AMR -  blood is highly toxic to the brain? If I would pump demineralized water around it would readily die :)

@AliceD Yes it absolutely is. Just think of the effects the Complement proteins would have if the got anywhere near the tissue of the brain.

@AMR - Agreed, it's just that OP's distant knowledge about Bio may make him interpret it as whether blood's a bad thing in the brain. It's not.

@AliceD. Blood flow through highly specialized vessels is not. There are two types of strokes. One is obstructive, the other is hemorrhagic. Both can cause severe disability and both can be fatal. His question says the "(blood) was not in direct contact with the brain in a substantial volume; however that was debunked," but it is not in direct contact. You have extremely tight endothelial cells of the blood vessels of the brain. You have astrocytes that surround the blood vessels and glial cells that protect the neurons. The architecture of the brain has evolved to keep blood out.

@AMR oh yes definitely. Blood's kept confined anywhere in the body, only a bit more in the brain via BBB. I am not arguing against, just the tone of the statement.

@AliceD. The use of homeostasis in their question is also problematic, as it is much more than just temperature regulation, but I let it slide. And the BBB is a lot more than a bit more when compared to the rest of the body. It is like the access point to a top secret military installation to the screen door on a porch, or to use an example from Biology, a BSL 3 or 4 facility to a freshman lab. And as far as tone, spend a day on a Neuro ICU and see what they think of blood and brain coming in contact with each other.

The gaming sector and data centers have done a lot of work on using liquid cooling. Also if you look at Texas Advanced Computing Center or CERN, they will likely have published plenty of material on component cooling.

There is an assumption that the OP is making that is problematic and that is that biological systems and man-made systems operate under the same principals. Man-made systems tend to be run a maximum efficiency or we push the envelop, over-clocking a CPU, afterburners on a jet engines, etc. and we then develop robust cooling systems to try to keep the components at the threshold of failure without exceeding it. Biological systems almost never do this, and metabolic activity is tightly control with enzymes that catalyzes chemical reactions in a controlled manner and with negative-feedback loops.

It is only in rare occasions that a biological system pushes the envelop, and that usually has to do with survival mechanisms that are for organism preservation, even if some deleterious effects are endured... Fight or Flight signals, inflammatory response to infection, chasing prey, etc. That is why these things happen in short bursts for short periods of time, because failure in a biological system leads to severe disability or death.

From what I can make up from your question is that you assume the blood in the brain is a bad thing in terms of temperature control. It is not. On the contrary, blood circulation is crucial in maintaining brain temperature.
Under conditions where the brain is heating up, which seems the focus of your question, there are mechanisms in place to extract this heat and dissipate it. Ambient temperature is often lower than body temperature, and even in hot climates, transpiration and water evaporation may cool the skin nonetheless.
Indeed, during hyperthermia, venous blood flow from the skin of the face and scalp fed to the dura mater (the brain's membranes) is enhanced and cools the brain (Brinnel et al., 1989). Moreover, blood from the nasal and paranasal mucous membranes flowing to the dura mater cools the brain due to the evaporative cooling of sweat or mucus. The dura mater may also transmit temperature changes to the cerebrospinal fluid compartment (Zenker & Kubik, 1996).
References
- Brinnel et al., Arch Dermatol Res (1989); 281(1): 66-72
- Zenker & Kubik, Anatomy Embryol (1996); 193(1): 1-13


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Why do feces vary so little in color?
Why do feces vary in color so much less than the food they are results of? E.g. you may eat food of all kinds of different colors but the resulting feces will almost always be some shade of brown.

Answer the questions what is the cause of variations of colors in living organisms, such as plants and what happens to molecules during digestion, and you will have an answer. Maybe look at an Organic Chemistry and Biochem text book.

The reverse can also be true - products of newborns in their first weeks range from tar black, to green, yellow and brown, all on amniotic fluid and mother's milk :)

The colors in feces can vary tremendously - the bilirubin answer posted below explains the brown tinge that's always present, but other colors can also be present, depending on the type of food and the presence of dyes or other chromagenic molecules.

feces color can vary with the food you eat. ever tried beets or eaten too much broccoli?

The main reason for the color of our stool (or feces) is the presence of bilirubin, a breakdown product of the hemoglobin. The amount of it causes different variations from yellow to dark brown. When the passage time of the food in the intestine and the amount of bilirubin is constant, the color changes very little. Illnesses like diarrhea, which cause a lower passage time have therefore a ligher color because a lower amount of bilirubin can accumulate.
The color of the stool can also indicate illnesses of the internal organs, white stool (or pale clay like colored) can for example indicate problems with the biliary system (drainage system of the gallbladder, liver and pancreas).
You can find some more information here and here.


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Why is the DNA helix anti-parallel?
Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.

How could they run parallel instead of anti-parallel when they need to be complementary to each other, and at the same time have the same structure? Having them parallel and complementary would need them to be enantiomers, and that's biochemically a huge mess. I'm not posting it as answer because I can't really justify it

This is a similar question in Biology SE http://biology.stackexchange.com/questions/27839/why-is-dna-antiparallel-can-it-be-parallel

Parallel nucleic acid double strand is possible but it is not as stable as the antiparallel form (Szabat and Kierzek, 2017). This is because the nucleobases are not aligned in a way that is conducive for the Watson-Crick (WC) type base pairing. In parallel conformation, the bases can form Hoogsteen (HS) and reverse Watson-Crick (RWC) type base pairing (see below).

You can see that these base pairs are not as strong as that in WC base pairing:

No triple bond between G and C in RWC base pairing
GC pair occurs in HS base pairing only when C is protonated at low pH

Formation of parallel helices, therefore depends on the sequence.

In general, the formation of duplexes with parallel strand orientation
  is determined mostly by the sequence context and pH conditions.
  Fragments of RNA or DNA capable of forming a parallel duplex are often
  rich in A and C, which is related to their ability to become
  protonated, in middle acidic conditions.

However, it is not as simple as RNA/DNA base pairing with its complement. Parallel helices would not follow the WC base pairing rules and therefore predicting whether they will form is not that straightforward. However, parallel helices can form in vivo (see references 23–25 of Szabat and Kierzek, 2017).
You can also check out this article by Leontis et al. (2002) for hydrogen bond patterns in parallel and antiparallel helices.

This is more chemistry than Biology.
Both strands of DNA are 5' to 3' direction. Why so? because the direction is determined in terms of the direction in which purine or pyrimidine bases are added.
The four bases that exist in DNA are Adenine, Guanine, Thymine and Cytosine. They are referenced under Purine and Pyrimidine links posted above.
This molecule is added to the end of a new DNA molecule.
It will be added to the 3' end of a new growing DNA molecule.
"Adenosintriphosphat protoniert" by NEUROtiker - Own work. Licensed under Public Domain via Commons.
What is the 3' and 5' end?

The ribose sugar at position two will lose the OH, the 5' position is the one where the long chain of phosphates are added in the top image and this phosphate at position 5' will be bonded to the OH at position 3' seen in the deoxyribose molecule, this reaction will generate a phosphodiester bond.
"Phosphodiester Bond Diagram" by File:Enlace fosfodiéster.png, File:PhosphodiesterBondDiagram.png: User:G3pro (talk)
Original uploader was User:G3pro at en.wikipedia.org
Derivative work: User:Merops (talk)
Derivative work: User:Deneapol (talk)
Derivative work: User:KES47 (talk)
Text tweaks: Incnis Mrsi (talk)
Text tweaks: DMacks (talk)) - File:Enlace fosfodiéster.png. Licensed under CC BY-SA 3.0 via Commons.
And here's the complete reaction

If you have noticed the negative charge on the Oxygen, then you will notice that Oxygen has one more electron to donate for a covalent linkage. So this electron attacks the O-H bond at the 3' OH of the deoxy-ribose sugar to generate the phosphodiester bond.
So the 3' OH is always a requirement for addition of new bases to a DNA strand. The 5' refers to the dangling 5' end of the first Phosphate, while the 3' refers to the 3' OH of the Ribose sugar at the last base of the DNA. The entire reaction is catalysed by DNA Polymerase
P.S. They are not really free, there are many modifications which make them inert.
So that is why DNA is anti-parallel.

This answers why DNA strand have polarity but not why they form anti-parallel helices.

Is there any other way in which DNA polymerase can polymerize the polymerization reaction?

Nucleic acids must be added to the 3' OH forming the phosphodiester bond, which is the basis for 5' to 3' direction of DNA, there must always be a 3' OH to add more bases to which is why a Primer is added during replication, or else DNA will not have been replicated, so is that not reason enough for anti-parallelism?


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Normalise protein database domain-wise
Suppose we've collected a big (hundreds of thousands) library of different protein sequences with certain features. Then we want to use this data base to train a classifier. And for several statistical reasons we want different functional domains to have somewhat equal frequencies in the data base to reduce domain-specific bias. The straightforward way to achieve this is to use structural information from UniProt and the like, but many proteins don't have any verified structures and de-novo structure prediction might take ages to compute. Alternatively we can perform sequence clustering and pick an even number of sequences out of each cluster. We can either apply a local-alignment based clustering algorithm with ~35% identity threshold or use some sort of hidden Markov model to cluster by profile. What do you think? How biologically relevant this might be? Can this simple clustering based approach help normalise the library to some extent?

Biologically relevant for what? If you told us what are the "statistical reasons" or why would you want that we might be able to help. I understand the question but I have no idea what would you want to get rid of some data just to have a "non-biased database".

@Athe We are working on a prediction tool that can get biased due to overrepresentation of specific functional domains in the data set. I'm sorry, but that is as much as I can tell due to information policies in my lab. The sole question can be put in a single sentence: "Is sequence clustering sufficient to normalise the library domain-wise?"

Any bias you will get will be the result of a deeper knowledge on certain structures or domains, rather than because of your database. Anyway, if you had a biased database that wouldn't mean you identified wrongly the proteins, but rather that your ability to identify proteins would greater when dealing with certain stuff.

@Athe basically, we want to compare the performance of biased and unbiased classifiers. It's likely that an unbiased classifier will fare better with new data on poorly studied proteins.

@EliKorvigo If I have understood your question: I am wrestling with a similar problem, and this is why clustering is useful. Generally, clustering reduces over-representation of a group. What it cannot do is increase underrepresented elements, which in databases is a big problem. Over/under-representation is likely due to the element being over/under-studied (often because of "fashionable" subject area, or experimental difficulty) rather than biological significance.

@James good to hear from you. I've been working on this ever since. Regretfully, clustering based on sequence alignment is of little use for complicated/modular objects such as proteins.


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How to model missing residues on a protein from multiple PDB files?
I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as possible. Is there a tool (web-server, software) available to do this?
In a particular application, I have one additional requirement. One of the PDB files is special (call it the template), in the sense that I only want to add missing residues to it. That is, the resulting model should contain the special pdb file, and align perfectly to it, the only difference being that the resulting model has some additional residues that were completed from the information in the other pdb files. Okay, the resulting model should not align "perfectly" to the template. I'll allow some relaxation in the connecting points. But still, the idea is that the template PDB should carry a "larger weight".
So, those are the two problems: 1) How to reconstruct a more complete model from a bunch of PDB files of the same protein? 2) How to complete missing residues in one PDB file using information from other PDB files of the same protein?

I'm not an expert on this, but the technical term you're looking for is "loop modeling", e.g. https://en.wikipedia.org/wiki/Loop_modeling -- I hope this gives you some leads

@MichaelKuhn That's the appropriate term if the missing residues are located on a loop (which they usually are).

I suggest you to use modeller - advance modelling (https://salilab.org/modeller/tutorial/advanced.html), Where you can use multiple template PDB to get final model structure.
All the best..:)

Please add some explanation. This looks more like a comment.


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Can anyone identify this plant from Bangladesh?
I have taken the picture from an agriculture university in Bangladesh.

Lantana, likely Lantana camara. family Verbenaceae.  Famous for widespread distribution from hot regions to cool regions. Leaves contain strong fragrance.

The genus is Lantana, of Verbenaceae. That particular one could perhaps be L. camara. There's a number of papers that exist which study L. camara in Bangladesh, just some examples:
http://link.springer.com/article/10.1007%2Fs11676-007-0060-6
http://www.banglajol.info/index.php/BJB/article/view/1513


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Cancer in myogenic heart cells?
Why cancer does not occur in myogenic heart cells? Is there any special ability in heart cells to resist cancer ?

Could you provide a reference to the article that you read that in? I want to look at what was said before answering.

I was just reading about cancers in my book trueman..and also searched how many types of cancer were there but no heart cancer was found so I asked

@Pi5 just to let you know, the answer you marked as correct is, in fact, not. You can see my comment below it for more info.

What do you mean by "myogenic heart cells" precisely? As I understand it, "myogenic" refers to a precursor cell (myoblast, myotube etc), as opposed to a fully developed cardiomyocyte. Such myogenic cells are mainly present during early development --- are you thinking of a childhood cancer of the heart?

Related question: http://biology.stackexchange.com/questions/10809/extremely-rare-occurence-of-heart-cancer

@roland If something is Myogenic, it performs independently. I believe that the OP is referring to the Myoctyte cells in the heart. I.e. a Myogenic contraction is initiated from within the myocyte cell itself not, by the innervation of the nerves (stimulus), for example. This can be shown if you carefully remove a heart from the body - it will continue beat until it runs out of essential ATP stores. That type of Myogenic ;)

@user19679, I don't think myogenic contraction is relevant in this case. Here we're talking about myogenic cells, that normally means a precursor cell -- question is which one. This is relevant since heart cancers, when they occur, do not arise from mature (contracting) myocytes but from precursors or supporting cell types (fibroblasts etc).

@Roland I'm not sure if OP knows either ;) From the looks of it, I thought he/she was asking about "the myocardial cells that function by themself" (myogenic cells) so, I was just giving an example of one (I wasn't trying to undermine/insult you at all, either) :( You could suggest a slight edit?

@user19679 Absolutely no problem. Anyway I'll write a short answer even if I think the question is unclear.

As a preface, this isn't a comprehensive answer for everything. As MattDMo points out, some of the original answer was poor in it's presentation. In my update there's some supporting information to some expert testimonial, but this is mainly targeted at adult cases rather than pediatric cases, i.e. why would cardiac cancer be rare in an adult with no prior history of cancer. There's a reference #5 at the bottom which goes into some of the genetic conditions that result in rhabdomyocarcoma.
Cardiac muscle cells do not divide particularly often (though they may divide: Evidence for cardiomyocyte renewal in humans). This would be a good mechanism of resistance of heart tissue to a more typical or rapid cancer development, compared to say, the endothelium of a vessel or an interstitial/connective tissue cell. Not to say heart tumors are impossible, either, as rhabdomyocarcoma is a good example of a cardiac tumor. Moreover, here's an excerpt from this article on heart cancer:

“There’s not a lot of fatty tissue [in the heart],” Gaynor said. Even more, “the heart’s enclosed in a membrane,” he explained. Known as the pericardium, this fluid-filled sac may itself become engulfed by cancer, with tumors metastasizing to the outside of it, but still it does its job of protecting our precious hearts.
So, even though cancer can happen anywhere there are cells, your heart remains virtually immune due to its muscular nature and the assistance of the pericardium. Smart heart.

And then from Cancer Prognosis: Role of BMI and Fat Tissue,

Many prospective clinical trials have linked excess body weight—typically represented as a BMI of 25kg/m2 of body surface area or greater—with a higher risk of development of cancers, including postmenopausal breast cancer in women and esophageal, colon, pancreatic, endometrial, and kidney cancers in both sexes. The number of obese Americans will increase by an estimated 65 million by 2030, increasing cancer diagnoses by 500,000 (Lancet 2011;378:815–25).

So fat content has it's role in progressing cancers, determinately. Let's explore this part. The adipocyte isn't simply a storage for fat, it has it's own host of proteins it produces and secretes. In obesity, the adipose tissue becomes dysregulated in it's secretion of adipokines [1]. The book Adipose Tissue and Cancer by M. Kolonin, the author notes that two major adipokines, leptin and adiponectin, play a major role in tumorigenesis by induction of cell survival and proliferation pathways [2]. Also duly noted, increased circulating insulin and insulin-like growth factors due to insulin resistance results in mitogenic effects on tumor cells.
White adipose tissue has been shown by Pedro et al. to increase bioavailability of sex hormones such as estradiol, through increased aromatase activity and  "increased insulin and bioactive IGF-1 levels which downregulate the concentration of the circulating sex hormone-binding globulin, resulting in an increased fraction of bioavailable estradiol, but decreased testosterone production." The same study has a section on inflammation induced by adipose tissue in section 3.2, the entire article is rather long but they sum up some of the information into a figure,

Source: Pedro et al.
Generally speaking, and in reference to the expert testimonial above from Dr. Gaynor, the heart isn't a very fatty organ, and it's protected from the surrounding adipose tissue by the pericardium. You could also argue that the fast flow of blood through the heart would leave a smaller fraction of circulating tumorigenic molecules for ready uptake by cardiac cells.
Being said, and while I haven't any data for the molecular pathogenesis for cardiac tumors, nondividing epidermal cells have been shown to enter a proliferative state in response to inflammation [3]. We also see that adipokines have been implicated in heart disease due to pro-inflammatory effects [4]. My concession here is that the rarity of cancers in adult cardiac muscle cells is because this process is very slow, and it's aided in part by the sort of environment the heart finds itself in. We often see cases of cardiac tumors in children due to errors in development [5].

Yeah the first part is a good point, cardiac cancers are rare but they do occur. And lack of replication may play a big role in this. I would point out though that there are plenty of nervous system cancers that affect cells that do not divide much if at all either (so we do have to be careful about assigning causation with division rate)

That was my exact thought as well. I did want to make the distinction, though, that for the cardiac muscle cells themselves primary tumors are quite rare; More so than those of endothelial cells or interstitial cells that are part of the heart, and progress into cancer of the heart, like an angiosarcoma.

This doesn't really answer the question. Your second sentence is incorrect - cells do not have to be dividing to accumulate mutations. You then go on to say that this is your "opinion", which does not by any means constitute proof. The BMI part is irrelevant to the question - it's been well-established that excess weight can lead to all sorts of health risks, including cardiovascular disease and cancer of various body parts, but it has nothing to do with heart cancer. Please answer the question factually and support your reasoning with relevant citations from the scientific literature.

It looked good at the time, but I've tried to make something more acceptable in the little time I had.


text:
dominance coefficient, why (1+k)?
I'm trying to get a better understanding of quantitative genetics by reading Lynch and Hill 1986. I'm getting stuck with some notation that's used right at the beginning referring to the mutant and WT alleles at a given loci.
2ai is the genotypic value for WT homozygous
(k+1)ai is the genotypic value of the F1 heterozygous
 0 genotypic value for the non-existent "mutant" homozygous
From my understanding, a is the additive genetic effect and k is the dominance coefficient. I understand that 2ai is the additive genetic effect at this particular loci which moves this trait away from the population mean for this trait.
Can someone explain the (1+k)? I understand that there could be dominance between the new and old allele, but I don't understand why 1 needs to be added to the dominance coefficient.

Without digging into the paper to be sure, it seems to just be a definitional thing.  Including the "+1"  would allow the dominance coefficient (k) to scale between -1 for perfectly recessive to +1 for perfectly dominant.


text:
What is the difference between Ostracodermi and Placodermi
I looked the word origin and found Placodermi is PLATE SKINNED while Ostracodermi is Shell Skinned.
Can someone please explain the difference between being Plate skinned and Shell skinned?

If in reference to the prehistoric groups of fish of the respective classifications, ostracoderms would have had a bony head much like a shell, and placoderms had articulated plates covering the head/thoracic area. The differences are relatively straightforward, see the wikipedia pages for each:
https://en.wikipedia.org/wiki/Ostracoderm
https://en.wikipedia.org/wiki/Placodermi


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Does pH affect Michaelis constant?
I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in the 21.5. According to this paper, Fig. 2C, the normalized specific activity of the enzyme is about 70% at pH 6.3 and about 47% at pH 7. If I divide 34 mM at pH 6.3 by 0.7 (which should get me the optimum Km at the optimum pH of 5.5) and then multiply by 0.48, then I get 23 mM. However, the paper says Km is between 30 - 38 mM, so if I divide 30 and 38 separately by 0.7 and multiply by 0.47, I get 20 and 25.6 mM respectively. Because my value falls within this range, this then must mean that I have the right enzyme and the same result as the paper.
So my questions are:

When the paper says Km is "34 +/- 4 mM", can I assume that means the Km can be anywhere between 30 - 38 mM? I'm surprised to see how wide the range is. I assumed Km is usually just one value with a deviation of at most 0.1.
Do pH change Km values? I understand that pH changes the shape(s) of the enzyme and/or substrate. Therefore that must affect how much it wants to bind to the substrate. If the enzyme's desire to bind to a substrate decreases due to increase in pH, for example, that would mean more substrates are needed to surround the enzyme, thus increasing Km.
If pH does change Km, is this how I determine the Km value of a different pH value if the Km value at another pH is already known? I know that specific activity and Michaelis constant are different, but how much product can be converted per minute depends on how much the enzyme likes to bind to a substrate, which is represented by the Michaelis constant. Did my reasoning and calculation arrive at the right conclusion? If not, how is the calculation done?

A very brief answer is yes, pH levels almost always effect enzyme efficiency. An example is lysosomal enzymes which are optimally active in the acidic environment of the lysosome, but are ineffective in the near neutral pH of the cytosol. This protects the cell should a lysosome rupture; the enzymes will not digest the cell itself. From the wikipedia article "The value of K_\mathrm{M} is dependent on both the enzyme and the substrate, as well as conditions such as temperature and pH.". And try not to forget Maud Menten.

Thanks for your reply. But is there an equation or method to calculate the relationship between Km and pH? If there isn't, was my calculation valid? I want to verify that if pH = 6.3 and Km =34, then Km must equal twenty-something at pH 7.

@wswr No that assumption is not valid because the relationship between Km and pH can be non-linear and vary between different enzymes.

Actually now that I think about it: I was confusing Michaelis-Menten constant with specific activity. My calculation was invalid. At pH 6.3, the specific activity is high, and the Km value is 34. The Km I got at pH is 21.5, but according to the paper, at pH 7, the specific activity is lower, which mean the Km should be higher. Can it can be assumed that the higher the Km, the lower the specific activity, and vice versa?

This paper might help you: Current IUBMB recommendations on enzyme
nomenclature and kinetics

From the derivation of Michaelis-Menten kinetics you can see that:
$$K_m=\frac{k_f + k_{cat}}{k_r}$$
Where $k_f$ and $k_r$ are binding and unbinding rate constants (for Enzyme-Substrate binding), respectively, and $k_{cat}$ is the turnover number. This is for the Quasi-Steady-State approximation (QSSA). For the equilibrium approximation:
$$K_m=\frac{k_f}{k_r}$$ which is same as the association constant.
In both the cases pH can affect the rate of binding and unbinding by affecting the affinity between the enzyme and the substrate. For example lets assume that the substrate binding site is negatively charged. Low pH would increase the electrostatic potential of the substrate binding site towards zero by affecting the ionization of the functional groups.
pH can also have indirect effects on the substrate binding site because it can modify the overall structure of the protein.
Many enzyme catalysed reactions involve acid-base catalysis i.e. there is a transfer of proton. In reactions like these, pH can affect $k_{cat}$.

If pH does change Km, is this how I determine the Km value of a
  different pH value if the Km value at another pH is already known?

You can do that by making a Lineweaver-Burk plot for the changed pH.

I did make a Lineweaver-burk plot to get the Km of 21.5 at pH 7. But because the only Km value I can compare to verify the enzyme activity is at the different pH value of 6.3, I want to know if there is another way to see if my result is correct.

@wswr Make a LB plot for pH 6.3 and then compare. If your measurements are done accurately, your result should be correct. Result is what you observe; so there is no question of correct or incorrect. Unfortunately, there is no simple relationship between Km and pH. You can perform LB analysis at different pH and try to find a relationship by regression. But this would be applicable only for your enzyme.

In a pedantic tone, "unbinding" would idiomatically be described as dissociation.

I just noticed, isn't Km = (kr + kcat)/kf  = dissociation rate constants:association rate constant?

@wswr kr is dissociation rate constant. kcat is the turnover number or the rate constant of product formation. Both these reduce the concentration of the [ES] complex.