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How did our bodies decide on the right enzymes and where did we get them?
I have read that enzymes act as catalysts to reactions in our bodies and that they are extremely target-specific.
My question is how did our body know that a particular enzyme could act as a catalyst for a particular reaction? How did de we get the perfect combination of reactants and their catalysts?
Note:- I am not a person who is studying biology so I might not know that which is pretty obvious to you people.
Anyways, the least expected answer is that ancient aliens carried out some sort of Worldwide Enzyme Injection Programme ;-)
Edit:- By the knowledge gained after asking this question I've figured out that it might be something like this -
There were species which had a different set of enzymes than us but as these weren't the right match the species perished. Those who had the right enzymes survived. Am I right ?

The problem here is that you've reversed cause and effect.  The body doesn't "decide" to create a new enzyme for some purpose.  Instead, various slightly (or sometimes, but not very often, drastically) modified enzymes happen to be produced by genetic rearrangements.  If those new enzymes happen to do something useful, they're probably conserved in following generations.  Remember that "our body" is the product of a billion or so years of evolution, and that variations on those enzymes are shared by all life.

@jamesqf Do you mean all the catalysts were tried one by one ,by nature, and then the right ones were fixed by evolution ? I had thought of this answer before asking, but the sheer time it would take made me ignore this one. Anyways, I think with references and all you should make this into an answer.

Raghav: Not one by one, but in a very massively parallel process, with each living creature potentially getting to try out slightly different versions, and only the survivors getting to reproduce.

Please check this site out. You seem to have some misconceptions about evolution.

I can understand why your asked this sort of question so I will clear your doubts one by one.
First of all Enzymes are not scattered inside our body, every enzyme is localised in a particular orgenelle or compartment of protoplasm in the cell, where they play their specific role.
Such as the enzymes of glycolysis ( the process by which you create ATP and breakdown glucose to pyruvate) are present in cytoplasm where as the enzymes for TCA ( Oxidative-decarboxylation of AcetylCoA) are present in mitochondria.
Enzymes are very specific.(1) If you have heard of lock and key hypothesis which states that an enzyme binds to the substrate that is complementary to its active site. Enzymes have very high specificity for their substrates the active site where reactions happen are somewhat complementary to the Enzyme substrate complex and thereby it provides the binding energy that lower downs the activation energy of that particular reactions that enzyme is going to catalyse.
I hope that helps!
References: (1) please refer to lehninger principles of biochemistry for further information!

Hi welcome to Biology.StackExchange! Please provide citations to support your claims. We expect and encourage citations or other references to ensure accuracy of responses. "Answers" without citations/references are better off as comments. Thanks!

Hi I am somewhat new to this forum so I just posted an answer without giving any references but thanks will keep in mind for next time!


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Are there more than Five kingdoms?
Is it true that scientists have disregarded their belief that there are five kingdoms and instead, they have theorized that there are multiple kingdoms?

What research have you done to find an answer?

Can you provide a source that led you to ask this question? If you do not provide more information and/or indication that you've researched this yourself, your question will likely be closed and not answered. Please take the time to improve your question. See How do I ask a good question? on our help page.

Taxonomic classification is a large area of controversial debate. See for example Cavalier-Smith's system of classification, they described eight kingdoms, then six, then 7 kingdoms in subsequent publications.
Other (older) theories describe 6 kingdoms, two prokaryotic (Eubacteria and Archeae) and four Eukaryotic (Protista, Plantae, Fungi, Animalia) See image on Wikipedia's "Kingdom" explanation
The three domains Eubacteria, Archeae, and Eukaryota are less disputed.

You shoudn't be answering this until the OP has shown some effort to answer his own question.

I agree in general, in this particular case, however, I shared kind of personal interest

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

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can you identify this plant?
I would like to learn how this plant is called. It grew together with the beans I had planted. The body of the plant grew overnight while the leaves took a couple of days to develop. I decided to keep it in a small pot I had laying around to see if it will develop any further....

These are cotyledons from some species of dicot. However, many species of dicots have very similarly shaped (in this case having a retuse tip) and sized cotyledons. You will almost certainly not be able to ID this plant unless you allow it to grow to the point that its first true leaves (those that have the "normal" morphology characteristic of your species) have grown. These should follow soon after the cotyledons if the plant is properly cared for. DO NOT damage the plant if you want to be able to properly ID this species. Please update us when true leaves have grown.

@theforestecologist - Shucks. I thought I said that...

@anongoodnurse oops sorry missed that. I wasn't going to comment at all and was just going to wait this question out until the OP (hopefully) posted new pictures showing the true leaves. I just saw someone had posted an answer making a guess (I admittedly only read down to your first picture), so I thought it was a good time to clarify in the comments that these cotyledons would make ID difficult.

That was some interesting information. I didn't know that some plans' first leaves do not represent the final ones! I will wait for it to grow and I will post a picture of its real leaves. Thanks again!

@GeorgeTsak Any luck growing true leaves?? :)

@theforestecologist Unfortunately the plant got hit by direct sun and it dried up within a couple of days...

Looks a lot like a radish seedling to me.

However, if I'm not mistaken, it doesn't even have its first true leaves yet, making identification very tenuous.
It can also be any number of brassica species, e.g. mustard (l) or cabbage (r):

If you can't wait to see what it grows into, smash one of the "leaves" between your thumb and a finger. If it's a radish, it will smell like one. If it does, taste the other leaf. If it tastes radishy, you have your answer without waiting. If you want to wait, however, doing that would kill the seedling.
Brassica seedlings will also taste spicy, but not like a radish.
Based on the number of "weeds" in the brassica family, I'd guess it belongs in that group.
I included these diverse possibilities to illustrate how difficult identifying a plant without true leaves is. :)

Good picture examples showing the similarities of plant "seedling" cotyledons. I agree that specific ID is tenuous if not impossible. However, as I commented under the OP's question, I'd recommend NOT crushing the "leaves" and instead waiting for true leaves to grow in order to have a better chance of IDing the species.

I think it's a mustard too. But mustard shoots have whiter and weaker stems, right?

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What is the purpose of ethanol in a DNA extraction experiment?
We were doing a lab experiment in biology class in which we extracted DNA from a banana-detergent solution mixture.(The detergent solution was made of 100ml of detergent, 90ml of water, and 5g of salt.) We then added ethanol to the mixture.
I know detergent breaks down the lipids in cells and salt takes away the moisture from cells but how does ethanol affect cells?

In the case you describe the ethanol is not there to do anything with the cells but to make the DNA precipitate out of solution. DNA is very poorly soluble in 50-70% ethanol and it will precipitate out as a white sticky pellet. It works even better if the alcohol is kept very cold.
Ethanol does kill cells by denaturing proteins and disturbing the lipid bilayers but after you have added the soap, most cells will already have been disrupted.


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How does natural selection process escape from local optima?
How does natural selection process escape from local optima towards global optimum in a fitness landscape during evolution?

Even getting to a local optimum can be difficult and shouldn't just be assumed. See for example this question or this paper.

From your profile, I see that you have some knowledge in computer science so I will try to use some terms from the field of machine learning!
Natural Selection
Natural Selection (NS) can only lead a population toward local optimum. In other words, NS is like a greedy algorithm. Mutations and genetic drift do not behave like a greedy algorithm.
Genetic drift
Genetic drift may allow to go toward the other direction than the heuristic of NS allowing eventually to reach another attractor. This concept is called shifting balance theory.
Mutations
Mutations can allow all sorts of jump! Mutations Causing large jumps are generally called large-effect mutations (see this section of the wikipedia article for more information).
Fitness landscape changes through time
Also note that the fitness landscape is not stable over time. The fitness landscape depends upon the environment the individuals experience. It would therefore be naive to assume that a specific population had to go through a specific fitness valley in the past just because the valley exists today.
Sexual reproduction and recombination
The fitness landscape analogy depicts the genotype - fitness relationship (some fitness landscape depict the phenotype - fitness relationship but I will ignore them here) for a given individual. One can place all individuals of a population over this landscape and may have some feeling of where the population position over the landscape is. However, this may be misleading.
The fitness landscape is highly multidimensional (one dimension for each amino acid and there are billions of them) and therefore through sexual reproduction and recombination, it is possible that an offspring finds itself in a totally different attractor than the rest of the population. As such, in presence of sexual reproduction and recombination, NS only could lead a jump from one attractor to another one (see Bergman and Feldman 1992). This effect is even more considerable in presence of epistasis.

One question came into mind. You mentioned Mutations separately from Natural selection and Genetic drift. Isn't the outcome of a mutation become visible through either of them? Why has Mutation been mentioned separately?

I am not sure what you mean by "outcome of a mutation" and "visible". When a mutation occurs, it needs no further evolutionary process to exist in the population and can be detected straight ahead.

Is it ok: mutation makes the jump for a single, natural selection and genetic drift follows the mutation for whole local population?

Yes, weirdly phrase, but yes. Note that the whole population will not necessarily (it probably won't actually) move toward this single individual that first had a mutation.

My bad english. :(


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Why are successful human rock climbers so dissimilar to Hominidae primates who spend extended time periods climbing?
In rock climbing, the sport considers the Ape Index when evaluating the factors critical for success.
However, the majority of successful climbers are lithe and slim with less than 8% body fat.  As one professional described it

“I feel very pressured to be thinner for climbing. I’m very strong, but I will likely never be thin, and I think that it holds me back…I don’t have that classic thin, long-limbed climber body…”

However, this seems completely at odds with the primates that we see on documentaries and in zoos which appear to be heavy, muscular, powerful and with considerable upper body strength.
Professional human climbers, while strong, rarely have significant quantities of muscle (Bodybuilder-esque) on their skeleton. They seek a power to weight ratio through weight-loss.
What accounts for this difference in development?  How do primates move such heavy masses through the upper canopy and why have they not evolved slimmer, smaller or more lithe frames?

I don't understand. Monkeys that are particularly agile at climbing tend to be very thin as well. A famously agile monkey species is the spider monkey.

Orangutan, Gorilla,  Chimpanzee...

Gorillas typically are pretty bad at climbing. I think you make the mistake to put all primates into a single pack and assume they are all alike and are all good climbers and then you make comparison with humans. A human is probably a better climber than a gorilla.

Remi...please dont make uninformed comments.  If you have an academic answer backed up with references then please make it otherwise assumptions benefit no one. http://www.berggorilla.org/en/gorillas/general/everyday-life/do-gorillas-often-climb-trees/ Gorillas can spend 20% of their day climbing

Venture, humans don't have exoskeletons (and you call others uninformed?) Please don't come here and be rude. We like questions, and we like answering good ones, but Remi.b is right that you've grouped a large number of species then compared them to one. You have your answer in your question. Finally, how closely related is climbing rocks to climbing trees? If trees disappear and primates have to resort to living on cliff faces, you'll have your definitive answer in a few million years maybe.

Do gorillas spend their time rock climbing?

@Seeds: Do ANY primates (other than a small subset of H. sapiens) spend much time rock climbing?  Some, but by no means all, of them spend a lot of time climbing trees & other jungle vegetation, but that's rather different from rock climbing.

@jamesqf Aye, that was the point of my question. H Saps do it infrequently, for recreation, all the other apes climb/swing in trees, which is a totally different activity. (closer to some of the things gymnasts do, like the ring thing)

I have specifically said Hominadae @anongoodnurse.  I did call others uninformed to state that gorillas are poor climbers.  I stand by that.  It was uninformed. I made a mistake in using the word exoskeleton but that doesn't make Remi's assumptions and your own any less rude. If you cannot answer, simply don't comment on the question.  I have grouped a large number of species, you are right, they are called the Hominidae family and all display similar traits and characteristics in climbing abilities.

@Venture2099 I don't want to fuel the discussion any more... but I am pretty bad at some things I sometimes spent a lot of time on. The fact that gorillas spend a lot of time climbing does not make them good at it. In fact, maybe if they were better they would have to spend less time doing it and more resting. You were asking for competitive climbers. Just because someone has a better Ape index it does not make them automatically a more avid climber.

And no source has been posted to prove that Gorillas are bad at climbing.  It was merely an assumption by a commenter, like much of this discussion thread.

Of course it varies from one species to the other. The silverback typically don't climb. Few branches would be able to hold their weight anyway. Other gorillas don't climb much in general (although see Western lowland gorillas do climb quite a bit) except for playing and foraging on fruits. They are in any way very bad in comparison with spider monkeys or other monkeys that are thinner and have longer limbs.

No one is comparing them with Monkeys.  Just you.

@Venture2099 Your OP says "primates" in every place except where you mention an "Ape Index". If you want comparisons only to apes, then say apes, don't say primates. You changed your title after the comment thread started talking about monkeys and then wonder why people are still on monkeys.

Actually I said Hominidae

There is an edit history here. You did not say Hominidae in the body of your question, and you added it to the title only after @Remi.b made a comment about monkeys.

After his first comment.  And I clarified in the comments as well but he kept referencing monkeys. shrug

As a rock-climber myself I’ll attempt to answer:  The selection criteria for competitive rock-climbing is exclusively based on sustain non-resting, extremely challenging moves up a rock-face.  The two most challenging aspects are 1) ability to ‘crimp’ (climbing term) on micro-holds without slipping and 2) being able to keep that up without resting throughout the climb.  I personally have a real problem with the later, because of my weight.
Primates selection criteria is not isolated to non-resting climbs.  They don’t get penalized for sitting on the branch.

I have to say, as someone who did a bit of climbing now & then, that the idea of competitive rock climbing just boggles my mind.  It seems to run contrary to everything I enjoyed about climbing...

@Venture2099 If you think this answer answered your question then upvote and accept it instead of posting unnecessary comments.

I will post the comments that I see fit and I will mark the question as answered when I think it is appropriate.


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How does eutrophication yield lower levels of dissolved oxygen?
Where do the oxygen go? Is it consumed by a particular species? Is just not enough being made? Please explain.

This question indicates no prior research by the OP. Even a simple google search provides the answer. For example, see Wikipedia.

@theforestecologist The question keeps its interest. Since algal bloom produces both oxygen and organic matter (whose decay consumes the same amount of oxygen) the question of where has all that oxygen gone and why is there a large net loss of oxygen is not answered by a simple Google search.

From Wikipedia:

Eutrophication arises from the oversupply of nutrients, which leads to over growth of plants and algae. After such organisms die, the bacterial degradation of their biomass consumes the oxygen in the water, thereby creating the state of hypoxia.

The oxygen is used up by bacterial decay of the plants and algae that overgrow when there is too much phosphorus or nitrogen available; the plants grow so quickly that they compete with each other for sunlight.
Any basic source on eutrophication, even Wikipedia, will talk about this extensively.


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Can a human be made with ovum but without sperm?
This article says that scientists were successful in making a mouse using only a sperm and no egg (ovum). The article also states that this procedure could be applicable to humans.
However, I want to know why didn't they try with only an ovum?
Can a human be made only with an ovum, i.e. without sperm?

Nice question! It is actually very difficult to do so because humans, obviously, are far more complex than some animal species which naturally show parthenogenesis. Just to mention, there are female-only animals also present in nature, such as New Mexico whiptail, which reproduce only by parthenogenesis, meaning that it is not as impractical as one might think.
There have been many parthenogenesis tests on mice and monkeys, but they usually result in abnormal development. This is because mammals have imprinted genetic regions, where either the maternal or the paternal chromosome is inactivated in the offspring in order for development to proceed normally. A mammal created by parthenogenesis would have double doses of maternally imprinted genes and lack paternally imprinted genes, leading to developmental abnormalities. It has been suggested that defects in placental folding or interdigitation are one cause of swine parthenote abortive development.
During oocyte development, high metaphase promoting factor (MPF) activity causes it to arrest at the metaphase II stage until a sperm fertilizes it. The fertilization event causes intracellular calcium oscillations, and targeted degradation of cyclin B, a regulatory subunit of MPF, thus permitting the oocyte to proceed through meiosis. The most precise and exact mechanism is not known yet.
But this does not mean that it is not possible. Actually, it has been done quite a few times; once on June 26, 2007 by International Stem Cell Corporation (ISCC), and once (controversially) on August 2, 2007 by Hwang Woo-Suk. Even the procedure for parthenogenesis (in swine though) in lab is available. To initiate parthenogenesis of swine oocytes, various methods exist to induce an artificial activation that mimics sperm entry, such as calcium ionophore treatment, microinjection of calcium ions, or electrical stimulation. Treatment with cycloheximide, a non-specific protein synthesis inhibitor, enhances parthenote development in swine presumably by continual inhibition of MPF/cyclin B As meiosis proceeds, extrusion of the second polar is blocked by exposure to cytochalasin B. This treatment results in a diploid (2 maternal genomes) parthenote Parthenotes can be surgically transferred to a recipient oviduct for further development, but will succumb to developmental failure after ≈30 days of gestation.

The major problem with parthenogenesis in humans is the abnormal development of embryo. This has been accounted by a phenomenon known as genomic imprinting. Genomic imprinting is the epigenetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner. For example, if the allele inherited from the father is imprinted, it is thereby silenced, and only the allele from the mother is expressed. The death of diploid parthenogenetic or androgenetic mammalian embryos is determined by the absence of expression of the genes of imprinted loci of the maternal or paternal genome, which leads to significant defects in development of tissues and organs. How this exactly works is not known yet, but it is supposed that it evolved to prevent parthenogenesis. Bi-parental reproduction is necessary due to parent-specific epigenetic modification of the genome during gametogenesis, which leads to non-equivalent expression of imprinted genes from the maternal and paternal alleles. Thus, genomic imprinting seems to be ineffective during normal reproduction.
As a side note, in the article you refer to, the researchers did not just mix two sperms and produce diploid zygote or something like that. In the procedure, they injected a normal sperm to the above explained abnormal embryo, which later on proved to be viable. They, thus, showed that these kind of embryos can also become viable if they get fertilized by a sperm within time.
References:

Abnormal development of embryonic and extraembryonic cell lineages in parthenogenetic mouse embryos; Karin S. Sturm, Margaret L. Flannery, Roger A. Pedersen
Parthenogenesis - Wikipedia
Patient-Specific Stem Cell Lines Derived from Human Parthenogenetic Blastocysts; E.S. Revazova, N.A. Turovets, O.D. Kochetkova, L.B. Kindarova, L.N. Kuzmichev, J.D. Janus, and M.V. Pryzhkova
Genomic imprinting is a barrier to parthenogenesis in mammals; Kono T.
Genomic Imprinting and Problem of Parthenogenesis in Mammals; E. S. Platonov
Mice produced by mitotic reprogramming of sperm injected into haploid parthenogenotes;
Toru Suzuki, Maki Asami, Martin Hoffmann, Xin Lu, Miodrag Gužvić, Christoph A. Klein & Anthony C. F. Perry
Stem cell fraudster made 'virgin birth' breakthrough; Silver lining for Korean science scandal; 3 Aug 2007, Christopher Williams

"As a side note, in the article you refer to, the researchers did not just mix two sperms and produce diploid zygote or something like that."I asked that whether it can be fulfilled without sperms.Anyway,a beautiful answer

It was just to clear things out, just in case someone might get it that way. Thanks :)

Also, the cloning process that made Dolly the sheep would work on humans as well. That just involved nuclear transfer from one adult cell to an ovum.

@swbarnes2 maybe it could work, but I couldn't find any scientific paper related to its testing on humans. Also, I'd speculate that it would also lead to some kind of abnormal development of resulting embryo; you never know where complications might arise.


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What Makes an Afrothere an Afrothere?
The mole-like golden moles.
The hedgehog-like tenrecs.
The shrew-like sengis.
The rodent-like hyraxes.
The anteater-like aardvarks.
The whale-seal-hybrid-like sirens.
The tapir-like proboscideans.
All these mammals, diverse in appearance, actually belong to one superorder, called Afrotheria.  Which raises the question — what are the anatomical characteristics common to all afrotheres?

your question is confusing as it is worded/structured. It's fine that you rolled-back my attempted edits, but I suggest that you provide some context at the beginning of your question to help reduce the confusing structure of your question.

I did.  It can't have been any more straightforward.

The word "Afrothere" comes from Latin Afer (referring to Africa) and Ancient Greek θηρίον (thēríon, meaning “beast”). In other words, "Afrothere" etymologically refers to animals with origins in Africa.
So really, Afrotheria and it's members are referred to based on their origins and not their physical characteristics. In other words, they needn't share morphological characteristics, but rather they all evolved from the same common ancestor from Africa.
From the Afrotheria Wikipedia page:

Afrotheria is a clade of mammals, the living members of which belong to groups that are either currently living in Africa or [are] of African origin...
They share few anatomical features but many are partly or entirely African in their distribution

These animals are all chordates of the class Mammalia, and therefore do share the common "basal" characteristics shared among all members of these higher taxanomic levels -- for example, a notochord (and backbone), hair, three middle ear bones, mammary glands, etc.

Emphasize on the "few anatomical features".  A little clarification is required.

@JohnWDailey The few characteristics they share are those shared with common ancestors. I've listed some of these in my final paragraph.

And what are those "few characteristics"?  That last paragraph answers what makes a mammal a mammal, not what makes an afrothere an afrothere.  And location is very circumstantial.

@JohnWDailey that's right. Because the only characteristics that afrotheres consistently share are those characteristics shared basally by all mammals.

There grouping is based purely on genetics not morphology, although there are a few of those. vertibral count http://www.tandfonline.com/doi/abs/10.1017/S1477200006002258  and placental membranes http://onlinelibrary.wiley.com/doi/10.1002/jez.b.21079/abstract;jsessionid=D30EE1D51D29755F7736702616AB0930.f04t04

@theforestecologist is right, there are very few anatomical synapomorphies (shared derived traits) if any of Afrotheria, and the few there are almost all exhibit homoplasy. But if you want obscure putative anatomical synapomorphies that may not strictly hold:
"
presence of a naviculocalcaneal facet
scattered vomeronasal organ blood vessels, placement of the internal carotid lateral to the anterior pole of pars cochlearis
 four allantoic vessel chambers
 Presence of a small P3 protocone
 presence of well-developed buccal cingula rather than stylar shelves
 increase in lumbar vertebra number from 6 to 8 testicondy (intrabdominal testes)"
Are listed by Seiffert 2007 as possibilities-- but only under certain phylogenetic constructions.
Ref: Seiffert 2007 A new estimate of Afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence. BBC Evolutionary Biology. https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-224


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How to read from flow chart
So I got the following picture and question:
a) Assume that F1 = 10 mmol h$^{-1}$ and the flow is not negative (ie f$_i$ ≥ 0,
i = 1, ..., 8). What is the most you can produce of the polymer DCDE (i.e.  determine F$_{obj}$).?
b) What can be said about the upper and lower limits of the flow values F2, ..., F8 when F$_{obj}$ is maximized?
I thought that you would want everything to flow through F4 and there onto F$_{obj}$ (where mmol h$^{-1}$ would double). However if this was true I don't understand question b, since in that case there would only be one possible flow value for F2,...,F8.


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What kind of fish is this? Spotted or largemouth?
I don't know if this is a weird looking largemouth bass or a spotted bass. It was caught in southern Oklahoma. Please help! Thanks.

Where did you catch this? (state, body of water, type of water, etc.). If you can, please provide a map showing the general location of the body of water. Adding as much info as possible to a species identification question is a must.

Thank for the tips, I'll keep them in mind next time I need help identifying a species and thanks for your answer!

This looks like a spotted bass (Micropterus punctulatus).
Here's an image showing some quick differences between some common bass species:

Using the above photo and this source to guide our judgment we can see your specimen appears to:

Have a jaw that does not go posterior to the eye (as it otherwise would in a largemouth).
Have rows of pigment towards its ventral side (below the "lateral line").
Not have the typical darker horizontal line of scales characteristic of the largemouth bass .
Have smaller-sized cranial scales (those around the eye) characteristic of the spotted bass.

If you can provide additional pictures of the following, I can provide a more definitive ID:

Both dorsal fins -- if the 2 dorsal fins are connected, it would further suggest a spotted bass (as largemouth bass dorsal fins are not typically connected)
Tongue -- evidence of a tooth patch is more likely on the spotted bass.

According to the International Game Fish Association:

Spotted bass can be found throughout the central and lower Mississippi basin to the Gulf of Mexico (from Texas to the Florida panhandle), including Georgia, Alabama, Tennessee, Kentucky and other nearby states where it occurs naturally or has been introduced.

It was caught in southern Oklahoma

And I remember checking the tongue and it was rough, I just wasn't aware that this lake had spotted bass. Thanks for answering my question this is a new species for me!


text:
If a particular protein contains 178 amino acids, and there are 367 nucleotides that make up the introns in this gene,
what is the number of nucleotides that make up the coding and noncoding regions of the gene including the start and stop codons

where is this question from? is this for homework? can you give any rationale for what you think the answer is?

178 amino acids => 178 codons =>178 *3 nucleotides => 534 nucleotides for the coding region. Plus 3 nucleotides each for start and stop codon. So the grand total will be (534+367 +6= ) 907 nucleotides


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Where did the nondisjunction occur?

A father with gene AC has a child with gene ACC. Where did the nondisjunction occur? (Meiosis I, Meiosis II, none of the above)

I do not know because both Meiosis I and II have the possibility of producing gametes with n+1. Is there something I'm missing here?

It can happen during any of the two Anaphases.

There are three forms of nondisjunction: failure of a pair of homologous chromosomes to separate in meiosis I, failure of sister chromatids to separate during meiosis II, and failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).

@zainabrija That's nice and all, but it doesn't really help me answer the question

Think about what gametes the father could have given the child. If the mother contributed an "A", then the father gave two "C"s, if the mother contributed a "C" then the father contributed an "A" and a "C".
In meiosis I, the father's chromosomes duplicate, so he has AA and CC - normally, at the end of meiosis I, these would be pulled into separate cells, so one of the resulting cells would be AA (and then in meiosis II, split into two further cells both with one "A") and CC (which in meiosis II splits into two further cells both with one "C"). The final result would be four gametes (sperm cells), two with "A"s and two with "C"s.
Since this is tagged "homework" I'm not going to give the final answer - but think about what phase of meiosis would have to go wrong to create an "AC" sperm, and what phase of meiosis would have to go wrong to create a "CC" sperm.

AC - Meiosis 1 and CC - Meiosis 2?

You got it! (Or I suppose to go with your username, I could also say "!ti tog uoY")


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How does the bladder transition from releasing urine at night to being able to hold urine at night?
I wonder about this.  What's the biology of the transition from wetting the bed at night to holding urine at night?  Is there a chemical change with how the bladder muscles contract?

When I first read the question, I thought the question deals with the difference between bladder activity during the day and during the night.
A second read two days later makes me think you are actually asking about maturation of the bladder, or in other words, what is the process by which children "learn" to control the bladder during the night when they are off diapers. It seems the answer you accepted deals with the former interpretation, but your phrasing points to the latter. Can you please clarify your intention?

I'm not sure how much the bladder has a role in this. Mostly, the reduced frequency of urination during the night is the result of less urine production by the kidneys. This is in response to a hormone called ADH, antidiretic hormone (it has other names as well). ADH acts on the distal convoluted tubules of the nephrons in the kidney to fine-tune the reabsorbtion of water in the tubule bringing it back into the circulatory system. This hormone is released in reponse to a few factors including blood volume. But it's release is also cyclic over a 24 hour cycle. https://www.ncbi.nlm.nih.gov/pubmed/202988
It can happen that this daily cycle of ADH release intensity gets out of adjustment and you urinate more frequently at night, perhaps more than in the day. This has happened to me. Also, according to my GP, it is a frequent cause of bed wetting in children.

The bladder is controlled by both the autonomic and somatic nervous systems. This means that part of the bladder activity is voluntary and another part is involuntary - more precisely, the detrusor (which is the smooth muscle in the bladder wall) is controlled involuntarily, while the external sphincter (the muscle around the bladder neck) is controlled voluntarily (see picture, this is the female bladder).
I found all kinds of references that describe the maturation process of the bladder during infancy. This paper, from Pheonix Children's Hospital, is about voiding disorders in children. It notes in the first paragraph three conditions that make up the bladder's maturation process (the rest of the paper discusses voiding disorders):

The bladder capacity must increase.
The child must develop voluntary control over the sphincter muscle in order to start and stop voiding.
the child must develop voluntary control
over the infantile voiding reflex which allows the child to stop involuntary bladder contractions.

This article discusses the topic of bladder maturation in greater detail (see the first section titled: MATURATION OF BLADDER CONTINENCE). From the article: "As bladder urine increases, a critical volume is reached (functional bladder capacity), which initiates a spontaneous reflex contraction that is mediated by the sacrospinal ganglia. As the bladder contraction ensues, the increased bladder pressure overcomes the detrusor muscles at the bladder neck and spontaneous emptying occurs. As the infant grows and matures, control centres in the pons and medulla initiate inhibitory signals that slowly dampen this reflex over a period of years ... Nighttime continence is achieved in association with the abolition of spontaneous bladder contractions, mediated by the pons and medulla; a nocturnal bladder volume less than the nocturnal functional bladder capacity (NFBC), which is ADH-dependent; and the achievement of prolonged rapid eye movement (REM) sleep and attainment of sleep arousal."


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How to annotate the SwitchGear gene models?
According to this page(http://switchgeargenomics.com/wp-content/uploads/2009/02/switchdb_technote1.pdf), the SwitchGear gene models can be annotated by the NCBI annotation associated with Refseq accession numbers, but I couldn't find such information in this page(https://www.ncbi.nlm.nih.gov/refseq/), which is indicated in the above pdf page...
How can I annotate the SwitchGear gene models?


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Cellular respiration — How is the water expelled?
The equation of cellular respiration is as follows:
6 O2 (g)  +  C6H12O6 (aq) $\rightarrow$ 6 CO2 (aq)  +  6 H2O (aq)  +  ATP
How is the water produced expelled from the body (of course, after some of it is used)? Is it expelled in urine? Or is the water vapour we breath out actually the by-product of respiration? Or, is it expelled in both methods/ways?

Homework is an appropriate tag for this question. Take a look at this to learn what fall under homework.

Sure. I misconstrued homework questions to be relating to questions that come in your assignments/projects/etc. Good that I read it. Thanks.

there is complex interchange of substance between different metabolic pathways.

@SanjuktaGhosh. As one who taught this for 24 years, I doubt this is a homework question, I think it's curiosity.

It appeared trivial to me because the water produced as byproduct in a reaction becomes part of the cytoplasm's water and it can be used up either in any other metabolisms where it is needed or by simple diffusion end up in blood from where it might get excreted out or recycled back to the cells. The water can even be excreted as sweat or end up in any other body secretions. As such though it is curiosity but is eligible for homework tag. @bpedit

Edited: I was wrong, the balance varies quite a bit by species. Reptiles and birds are far more water efficient than large mammals becasue they do not lose water through sweat or urine. There are animals that are metabolically water neutral, but humans are not one of them. In humans the water produced metabolically does far exceed the water used metabolically. I should have realized that reptile also produce less water. source 1source 2
In humans there are three main ways water is take in, drinking, injection (food), and a net metabolic production. There are four major losses, urine, sweat, respiration, and feces. so it is through one of these four methods.

This doesn't sound right. Metabolically, the human body is a net producer of water, as the respiration equation suggests. We require water because of respiration, sweat and urination, but this is a matter of using ingested water as a solvent to "flush out" other waste products. Water is not consumed by the body for metabolic purposes.

it can't be only urine and sweat , becasue organisms that use uric acid and don't sweat still need to drink.

I did a major edit, I am so used to dealing with birds and reptiles I hadn't considered how much it might vary.


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How to anaesthetise mosquitoes during a mass-trapping field study?
Do any of you have experience in anaesthetising mosquitoes during a mass-trapping field study?
Normally, mosquito traps have a little net in which you catch the mosquitoes. The nets can, after collection, be placed in a freezer to knock out the mosquitoes. However, the trap used for my study doesn't have a net, so mosquitoes will fly around inside the trap.
I thought about using Ethyl Acetate to knock out the mosquitoes, however, the trap needs to stay clean of odours, so that's not an option. I think using CO2 would be most convenient, but I will not be able to drag a big CO2 cylinder to all my trapping locations.
Is it maybe possible to use CO2 tablets which can be dissolved in water? I could then use a plastic bottle where the cap is connected to a tube, which I can place in the trap. Would this be efficient? What do you think?
Thanks a lot!

What type of trap are you using?

It's a new prototype from Biogents. Not sure if I'm allowed to give more information on that. I've already started the study and used a big freezer back at the lab where the trap fits as a whole, but that's not very convenient since the traps need to be placed back in the field on the same day.


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Why do humans sneeze out mucus if it's a good thing?
The Wikipedia article on mucus says that mucus acts as protection from bacteria and other microorganisms.
Given that mucus plays this positive role, why do humans sneeze out mucus?

used mucus contains dirt and pathogens trapped in it, which should be removed for replacement by fresh mucus.

Indeed, mucus is essential for in this case protecting the respiratory pathways, which includes the nasal cavity and the pharynx, against different threats, such as microbes. Sneezing, which is initiated by virtue of the activation of mechanoreceptors in the upper parts of the respiratory system, leads to a buildup of intrathoracic pressure, due to the contraction of expiratory muscles against a closed glottis. The pressure gradient, when the glottis opens, will then lead to the rapid flux of air from the lungs, through the respiratory tract and out through the mouth and the nose, whereas mucus containing the initial irritant will follow, merely due to the forces at play.
Note that the epithelia in the resp. tract normally transport the mucus containing everything from microbes which have been breathed in, and different particles, to the oropharynx, so as to allow you to swallow and take it to the GI tract instead.
For further reading, I recommend Boron Boulpaeps Medical Physiology chapter 32 on the "Control of Ventilation" (2012).


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"Air sac" and "air cell" in a chicken embryo
I need to translate the Russian term "воздушный мешок". It is part of the chicken embryo, marked by number 5 in the figure below.

I found the expression air cell but also found the expression air sac in English. On one site, "air sac" is described as a synonym to the "allantoic sac":

Just to make sure: is air cell the only correct translation for the structure marked by number 5?
My sentence goes roughly like this:

...  the injections are made from the direction of the naturally-occuring air cell (?) so as to apply the material onto the chorioallantoic membrane (CAM).

air sac can also mean the air spaces created by outgrowth of the lung into the bones, which are part of the bird breathing mechanism. Air cell would this be less confusing.

According to Atlas of Chick Development by Ruth Bellairs and Mark Osmond, a book I'm using for my developmental biology course :

Air space  is the space between the two shell membranes at the blunt end of the egg. The chick pushes its beak into this space shortly before hatching and takes its first breathe of air.

Besides allantois is the extra embryonic membrane and the space enclosed by it is allantoic cavity.
Here label 2 is Allantoic cavity.

Thank you, Sanjukta! So "air cell" is also a miss, or it will be okay?

I can't assure you but from a google search the term air cell appears to be in use too.


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Query for gene upregulation in cBioPortal
there! Could anyone help me with some biostatistical problems using cBioPortal.
We are looking for cell lines with upregulation of certain genes on cBioPortal. My supervisor is teaching me to use this website because I have no prior experience. She is using EXP >= 0.5 to define upregulation. Although I am of no bioinformatics background, my opinion is that 0.5SD away from the average is not strong enough to define an upregulation. I think it better to use EXP >= 2 or 1.5. I have discussed this with my supervisor but she insists using EXP >= 0.5.
Does anyone have any experience with this issue since I am still not convinced by what I was told. Thanks a lot!

Well, I have worked with expression patterns. Unfortunately there is no clear cut or magical numbers for cutoffs . I agree with you that 0.5 is not stringent. However, to explore data usually one can parse it using lower cutoffs and later on you can rise the bar to see what happens.

Many thanks Andrei! I also asked a friend of mine about this and she has similar opinions with yours. I will do queries with different criteria and compare the results! Thanks a lot!


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What is the right definition of 'Sex Linkage'?
I am confused about definition of "sex linkage". I have found different definitions but they do no match.
From P.S Verma, V.K Agarwal cell biology, genetics, molecular biology, evolution and ecology:

If the genes are situated in the same chromosome and are fairly close to each other, they tend to be inherited together. This type of coexistence of two or more gene in the same chromosome is known as linkage.

From: Anthony J.F Griffith "Introduction to genetic analysis

In general, genes in the differential regions are said to show inheritance patterns called sex linkage.

From: Wikipedia

Sex linkage is phenotypic expression of an allele related to the allosome (sex chromosome) of the individual.

Related post.

This question is being bumped often(4 times from your post history). If any of the entries below have answered your question, please consider accepting an answer or asking a follow up question instead. Bumping of a post that has a good but unupvoted answer removes a post that deserves attention off the main page.

Linkage is the tendency of two genes present on the same chromosome to be inherited together. The degree of linkage depends on the distance between the two genes, i.e two genes that are physically close are less likely to be separated onto two different chromosomes during recombination/crossover.
So this is what your first definition trying to convey.
Sex linkage simply means that a gene is to be found on the differential region of a sex chromosome (and not an autosome). See it as (gene) Linked to sex chromosome.
Note: Linkage and sex linkage are not the same.
An Introduction to Genetic Analysis, 7th edition makes it a bit easier:

Sex linkage is the location of a gene on a sex chromosome.

So to sum up the definition:

Sex linkage is the location of a gene on the differential region of a sex chromosome. (this is applicable to human beings because we have PARs)

For animals in general having sex chromosomes the definition from Genetic analysis is alright.
Note: Sex chromosomes are chromosomes that have genes that have roles in determining the sex of an individual of a species.

Good answer. +1. Why are is the PAR important in order to be allowed to talk about sex linkage? Note your answer make it feel like only animals have sexual chromosomes which would be wrong. Also, I am not sure that a sex chromosome is solely defined by the presence of loci explaining variance for sex. If I am not mistaken, there are GSD species that are not considered to have sex chromosomes (typically when sex is a polygenic trait).

The first definition is a definition of linkage as in "linkage disequilibrium" - that one has nothing to do with sex linkage.
Sex linked means that the gene or genes involved in a trait are inherited on one of the sex chromosomes (X or Y) and that, as a result, the disease may occur at different rates in different sexes. A good example of this is color blindness caused by a recessive genetic variant found on the X chromosome. Men only have one X chromosome, so if they inherit the variant, they will be colorblind. Women have two X chromosomes, so they will not be colorblind unless both of their X chromosomes have this problem.
In addition to saying "sex-linked", you can also be more specific and say that color-blindness is "X-linked". There are also Y-linked disorders, although they are much rarer since they usually cause infertility and don't get passed on. The term "sex-linked" seems to be gradually dying off as people adopt these more specific terms.
There are also some other terms you may come across, which sound similar but mean different things:
Sex-limited trait: This has nothing to do with genetics and instead refers to whether a person is biologically capable of manifesting a disease. For example, prostate cancer would be sex-limited because only men have prostates.
Sex-influenced trait: A genetically-influenced trait where, although the genes influencing the trait are not on a sex chromosome, a person's sex may still influence whether/how a trait manifests. An example of this would be breast cancer - certain variations in the BRCA genes increase risk of breast cancer in both women and men, but women with a BRCA mutation are still much more likely to get breast cancer then men with a BRCA mutation are.
Unfortunately, some people use the term "sex-linked" to refer to sex-limited or sex-influenced traits, which can make things very confusing.
To read more about these three categories, see: http://www.eplantscience.com/index/genetics/sex_linked_sex_influenced_and_sex_limited_traits/sex_linked_sex_influenced_and_sex_limited_traits.php

can you add some references so others can read about your answer, etc?

The first definition is a definition of "linkage (physical linkage)", not "linkage disequilibrium"


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How does human body keep track of its age?
How does the human body knows that it's time for a event that happens around a certain age like puberty or something that's periodic like menstruation or gestation time of 9 months?
Please note I'm NOT talking about day-night biological clock .

It's not clear what do you mean by 'how does the body know'.

this is still a very active are of study, the field is called chronobiology.
Epigenetic clocks which may be longest, there are several Horvaths being the most famous and is based on the DNA methylation. I don't know the details of how it functions however.

This is an interesting question, but as written now is broad and shows none of your own research. If you can edit to narrow down (e.g. only menstruation) and include some of your own research (what you found when reading about it), I'd happily remove my close vote and take a stab at the answer. Thanks!

@SanjuktaGhosh it's quite clear that it means how does human body triggers certain functions at certain age or period

@anongoodnurse I did search but nearly all result ended up on biological clock that regulates sleep. And that's not what I am searching for so I ended up posting a targeted question on SE

@anongoodnurse same here, also voting to close.

@user1062760 Please do not post such accusatory comments. What is there to be political about? There is no logic in favouring a certain user/group of users and discriminating against others. We don't even know anyone here in person. Posts are voted upon, not the users. Instead of taking things personally, why don't you consider the advice of experienced users and edit your post accordingly. Your question is interesting and others have said it too. However, it is also very broad. One can write a book or a big review on this topic. SE is not designed to handle questions like this. Pls understand

It doesn't always. Some people have an undistorted slown down aging. Jyoti Amge is over 18 and looks like an undistorted little girl. Yesterday, I saw a TV show that showed a 22 year old who looked like an undistorted 8 year old girl. There are also people who have distorted aging. People with progeria look like a distorted older person. I think nodoby has an undistorted sped up aging. Gabby Williams looked like a distorted toddler when she was 12. Nicky freeman from https://thewest.com.au/news/australia/forty-year-old-trapped-in-childs-body-ng-ya-220462 has a distorted bone structure of a ten year old boy and is all wrinkly. The girl in the YouTube video at https://www.youtube.com/watch?v=xoBetcKAxII&t=96s has the undistorted bond structure of a 13 year old girl and is all wrinkly.


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Changes in spongy urethra during tumescence
How does the columnar cells of spongy urethra expand during tumescence(erection of penis)?
If we assume that the urethra has the length, long enough to sustain tumescence without expansion of cells, then will it form wrinkles on retraction just like skin? Probably latter should not be the case, since accumulation of urine would then take place in the grooves of those wrinkles.


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Activation of Glycogen Synthesis by Insulin - mechanism and cellular location?
My textbook states the following...
Insulin activates enzymes that convert glucose to glycogen.
Does this conversion occur inside or outside the liver and muscle cells?
If it is inside, does the Insulin act as the primary messenger and activate an enzyme cascade that activates glycogen synthase?

What research have you done to try to find an answer to this question? Have you checked Wikipedia or Berg on NCBI Bookshelf online?

@David I researched Wikipedia and Wikibooks on the synthesis of Glycogen Synthase. It provided no results. I then did the same for Insulin and no results were produed either of significance :)

You didn't look at Berg, though, did you? Anyway, I've given a short answer to your question, leaving you to read further if necessary.

Insulin, like glucagon, binds to receptors on the surface of muscle cells and illicits a response that is transduced to produce changes of phosphorylation in the enzymes controlling glycogen turnover. Unlike glucagon it does not initiate an enzyme phosphorylation cascade, but its binding to the receptor causes autophosphorylation on tyrosine residues, resulting in protein–protein interactions which lead to the activation of various enzymes through subsequent phosphorylations.
I would recommend you go to Berg et al. in NCBI Bookshelf online — rather than Wikipedia — for this kind of thing. It is a best-selling biochemistry textbook which is produced with great care (even if the edition online is out of date). Thus in Section 21.5.2 you will find:

How is glycogen synthesis stimulated? As stated earlier, the presence of glucagon signifies the starved state and initiates glycogen breakdown while inhibiting glycogen synthesis. When blood-glucose levels are high, insulin stimulates the synthesis of glycogen by triggering a pathway that activates protein phosphatase 1 (Figure 21.20). The first step in the action of insulin is its binding to a receptor tyrosine kinase in the plasma membrane. Multiple phosphorylations again serve as the instigation for a regulatory wave of dephosphorylations. The binding of insulin to its receptor leads to the activation of an insulin-sensitive protein kinase that phosphorylates the RGl subunit of PP1 at a site different from that modified by protein kinase A. This phosphorylation leads to the association of the RGl subunit with PP1 and the glycogen molecule. The consequent dephosphorylation of glycogen synthase, phosphorylase kinase, and phosphorylase promotes glycogen synthesis and blocks its degradation.

I am assuming that you are familiar with the pathways of glycogen synthesis and breakdown. (If not, search for this in Berg et al.) At the risk of violating copyright, I reproduce Figure 21.20 below:

You can read more about the insulin receptor in Section 15.4.1 of Berg et al.
Addendum
Insulin also affects glycogen synthesis indirectly by stimulating/activating the glucose transporter, GLUT4. The mechanism by which this is accomplished is less well established than that described above.


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How can sequence analysis establish whether a genomic sequence is a functional gene or a pseudogene?
BLASTX of a query gene shows 5 hits in my subject, how can I find out which of these are expressed and which are pseudogenes (using DNA sequence or by sequence analysis)??

Perhaps search the EST or TSA database?

Think for yourself. What types of pseudogene exist? How do they differ from functional genes? If you do not know the answer to this search on the web. When you understand what pseudogenes are some of the answers to your question will be apparent.

There is no good single answer genes which long have been though to be pseudogenes may have function in a very narrow set of cells.
That being said, some of the best indicators are; destruction of the ORF, accumulation of C->T and G->A mutations (methylation/deamination in mammals).
Expression is probably not a good indicator, because once you start including long non-coding RNA, pseudogenes may be transcribed, but may not have a protein-encoding function (if any).
You can also measure loss of introns and a poly-A tail in the DNA sequence which is consistent with a retro-pseudogene, but that doesn't mean that the 'pseudogene' doesn't have it's own function.
Overall, evolutionary conservation is the fastest and most reliable indicator, but ultimately genetic knock-out would be required.
If you have more information about the pseudogene, there may be other useful information which could help distinguish the two.


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Do neural axons extend around connections like this?
I was wondering if axons sometimes connect like this:

Note that I'm not referring to situations where the path of that network is curved and the 3rd / 4th neuron is just as close to the 1st neuron as the 2nd is, I'm talking about situations where the 3rd / 4th neuron is physically 2-3x as far from the first than the second neuron, or more. This is relevant to neural simulation.

Yes, all the time, but there isn't much meaning to the conceptualization of "1st, 2nd, 3rd" neuron. Real, biological neurons in the CNS aren't connected in simple feedforward loops, recurrent connections are common, and individual cells can have both local and distant projections.

@BryanKrause You answered my question but I'd point out that I wasn't suggesting that the system is as simple as a 1-2-3-4 feed forward connection, I'm just referring to the physical location of 4 specific neurons in a much more complex network.

Got it - you might be surprised that many people who come at neuroscience from a background in artificial neural networks take all sorts of biologically goofy assumptions away from it. I will say that in the neocortex, where most of my expertise is, the pure number of contacts between cells is definitely a function of distance, falling off over 200-400um, but there are also projections that go for many mm, even in a small brain like a rodent.

@BryanKrause interesting. This may be too complex for a comment question, but I'll try: Could localization (axon "length" limit) to some extent be beneficial to a neural system, or would a system likely benefit from infinite axon length potential?

I would search for some literature on "small world networks" if I were you - I think this will interest you a lot. Doesn't directly answer the questions you are answering but it will tell you a bit about the types of optimization that are possible.


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What is "enzymatic activity"?
I should be grateful if anyone would send me a link to an article or an encyclopedia/handbook contaning an explanation of the concept of enzymatic activity. Surprisingly, I did not manage to find anything else but a brief definition.

Are you asking how enzymes work in general (which is a broad question, and covered in any basic biochem text), or are you wondering how to precisely define and measure "activity"?

I'm not sure why people have voted this off-topic. As far as I can see the poster is unclear about the term activity, which for someone coming from a more physical science (like chemistry) — as I did myself — can appear a little puzzling. My own answer takes a much broader look at the meaning of enzyme activity in a biological context than the quantitative definitions provided by some, and seems to me on-topic. Perhaps the poster could clarify his question.

An Introduction to Enzymes (pdf) can be found here.

Excerpted from a very popular Worthington publication which was
  originally published in 1972 as the Manual of Clinical Enzyme Measurements. While some of the presentation may seem somewhat dated, the basic concepts are still helpful for researchers who must use enzymes but who have little background in enzymology.

Source: Worthington Biochemical Corporation.
The quantity or concentration of an enzyme can be expressed in terms of activity in enzyme units. See Wikipedia:

Enzyme activity = moles of substrate converted per unit time = rate × reaction volume. Enzyme activity is a measure of the quantity of active enzyme present and is thus dependent on conditions, which should be specified. The SI unit is the katal, 1 katal = 1 mol s−1, but this is an excessively large unit. A more practical and commonly used value is enzyme unit (U) = 1 μmol min−1. 1 U corresponds to 16.67 nanokatals.

Here are some additional useful, simple videos explaining enzyme activity:

How Enzymes Work
Explain factors affecting enzyme activity

The entry for Enzymes in Wikipedia contains 28 instances of the word ‘activity’. I can only assume, therefore, that it is the fact that this term is not explicitly defined that is the problem — one for which a novice to the field need make no apology. I shall answer it in elementary — but not self-evident — terms.
Enzymes are biological catalysts, so catalysis is their fundamental property or quality. In this context my definition is:

Enzyme activity is the manifestation of the catalytic ability of an enzyme

My use of the word ‘manifestation’ is deliberate and important: the essence of enzyme activity is the action or functioning of the enzyme, because this is the way that we are aware of its presence and, hence, how we draw quantitative or qualitative conclusions about its behaviour or function.
Detection of enzyme activity
Enzyme activity is detected by observing a reaction which it catalyses, i.e. by observing — and usually measuring — the conversion of  some chemical reactant (termed the substrate of the enzyme) to a product. This allows certain questions to be answered:
1. Is the enzyme present or not,  or, if present, is it able to manifest its potential?
The most basic question that measurement of enzyme activity is used to answer is whether or not there is enzyme present, e.g. in a tissue. In fact, the absence of enzyme activity can have other interpretations besides the absence of enzyme protein: the enzyme could be present but denatured or poisoned, or it could be present in a inactive form because of the absence of some secondary agent (cofactor, regulatory molecule) required for it to function.
2. How much enzyme is there?
In experimental work where one wishes to compare amounts of an enzyme in different tissues, monitor its purification from other proteins, or study the effects of agents and conditions upon its functioning, one needs not just to detect it (e.g. by observing that a coloured substance is formed) but to measure how much enzyme or functioning enzyme there is. To quantify enzyme activity we measure the amount of substrate converted to product in a given time under suitable conditions.
Explanation of the units used and the suitable conditions are available in standard texts and on the web. My own self-teaching material on this topic can be found  found here.
3. What is the nature of the reaction  catalysed or is there more than one enzyme there?
These are other questions that measurement of the activity of an enzyme or impure preparation can answer. What is important here is what precise reaction is being catalysed. If an enzyme can catalyse the phosphorylation of D-glucose to glucose 6-phosphate, can it also catalyse the phosphorylation of L-glucose — i.e. is it specific for one rotamer? If the preparation can also phosphorylate fructose (for example), are there actually two different enzymes present in the preparation? If it phosphorylates some other sugar 50 times better than glucose, perhaps its function within the cell is different from that previously assumed.
Activity as a general concept in science and biology
The measurement of activity rather than quantity is not restricted to enzymes. One is also concerned with the activity of hormones, drugs, neurotransmitters etc. (e.g. to determine what tissues they affect and what their effects are). And more generally in science, we deduce the existence of things by their ability to do something — gravity is an example from physics.

@tomd — I think this refers to another answer than mine which is totally non-quantative.

I have revised my answer considerably, because the questioner seems to me to be asking about the concept of enzyme activity — not how to assay enzymes and what their units are and definitely not what their kinetic constants are. (If he meant that he has not expressed himself very well.) So I have extended my answer to address the question of enzyme activity more generally than with respect to quantitation, and so that it gives a broader explanation of why measurement of enzyme activity is important. Coming from chemistry myself, I think this may help others.

Enzyme activity refers to the dynamic process of an enzyme catalyzing a reaction and is a measure of the quantity of catalytically competent enzyme present in a preparation.
We measure enzyme activity by making a trial of the enzyme reaction, that is we assay the enzyme. The trial, or assay, is done first and foremost under conditions where the enzyme works.  The pH, for example, may be critically important, as may the presence or absence of inhibitors or activators. In addition, the assay is conducted under conditions where the experimenter can directly or indirectly detect the catalytic transformation, perhaps by monitoring the production of a product or the consumption of a substrate.
For example, if I want to measure the activity of a dehydrogenase, I could measure the decrease in absorbance at 340nm, where NADH but not NAD(+) absorbs strongly. In a spectrophotometer, this may be done continuously with time and is an example of a continuous assay.
However, there may be no convenient change in absorbance but we might have a radioactive substrate. In this case we might conduct our trial under conditions where we would expect the enzyme to work for, say, 30 min, stop the reaction (by denaturing the enzyme with acid, for example) and isolate a radioactive product.  This would be an example of a discontinuous assay.
In both cases we are observing a change due to the enzyme catalyzing a specific reaction, that is we are measuring enzyme activity.
We now come to an important distinction.  An enzyme assay is a measure of catalytic activity, which may or may not be related to the total amount of enzyme protein present.  Consider a genetic disease that results in a particular enzyme activity being totally absent from an organ. We assay a liver sample for lactate dehydrogenase, for example, and find none present (to take a trivial example). This could mean that the  enzyme is not being produced: there is no enzyme there.  But is also could mean that the enzyme is present but is being produced in an inactive state.  Maybe the 'normal' enzyme has an essential tyrosine at the active site, but a genetic mutation has changed this to a phenylalanine in the case under study.
If we have an antibody directed against the enzyme under study, we could develop an enzyme-linked immunoassay (ELISA) which will (if it is any good) specifically measure the total amount of protein present whether active or not, even in a crude liver extract. (A Western blot, of course, might also detect the presence of inactive protein). That is, an enzyme assay gives an estimate of the amount of enzyme present based on enzyme activity, whereas an ELISA gives an estimate of the total amount of enzyme protein present.
Enzyme activity is usually reported in terms of amount of substrate or product transformed per minute or per second: in micromoles/min, for example.  It is also usual to measure the total amount of protein present and report the enzyme activity in terms of micromoles/min per milligram of (total) protein.  This is the specific activity and allows for ease of comparison. Almost invariably, the 'per milligram' part of a specific activity measurement refers to the total amount of protein present (measured with the Lowry protein assay or the like).
(If, for example, Lab A reports that 20 microlitres of their liver extract has a-dehydrogenase activity of 5 micromoles/min and Lab B reports that 20 microlitres of their liver extract has a-dehydrogenase activity of 50 micromoles/min, these measurements may well be identical when compared on a protein basis (micromol/min per mg) and that the only difference is that liver A was extracted in 100 volumes of buffer but that liver B was extracted in 10 volumes of buffer).
Units of enzyme activity invariably refer to specific assay conditions, and this may be a very important consideration when designing an experiment. In addition, enzyme are labile and the activity may decrease with time (on prolonged storage for example).  If, for example, a protocol requires you to add 10mg of of an enzyme preparation with a specific activity of 100 Units/mg (100 micromoles/min per mg), but freezing the enzyme preparation has resulted in denaturation, you are adding 10mg of enzyme protein but no enzyme activity. This may also be important.
Finally, a great reference:
Principles of enzyme assay and kinetic studies by K. F. Tipton in Enzyme Assays: A practical approach


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Squirrel nest construction
I've often wondered how squirrels -- specifically, eastern grey squirrels (Sciurus carolinensis) make their nests. Specifically, I've been curious about how they "weave" everything together to make these so called "dreys" stay together (and stay in the tree).

According to this site:

[squirrel nests are] constructed from various twigs, leaves, moss and other material. To start, twigs are loosely woven together to make up the floor of the nest. Next, squirrels create more stability by packing damp leaves and moss on top of the twig platform to reinforce the structure. Then a spherical frame is woven around the base, which creates the outer shell. The final touches include stuffing in leaves, moss, twigs and sometimes even paper to build up the outer shell of the new home.

I've tried finding a video (preferably time-lapse) of a squirrel nest being built to better understand/appreciate this animal home. However, I've thus far been unable to find such a video on the internet.
Does anybody have such footage or know where I can find some?

Ideally, close-up and even internal shots would be included.
Additional notes about tree-branch drey construction would be appreciated, too!

Check for:

https://www.youtube.com/watch?v=6uKDpHM-OsI
https://www.youtube.com/watch?v=3jPtZByr740
https://www.youtube.com/watch?v=Kh1HnMFolgw
https://www.youtube.com/watch?v=M5dduAX8iuI

The third one was filmed by BBC. The fourth one is a closer look of the nest complemented with a fairly good analysis.
The first two are reasonably good, but the third one is just awesome for your purpose!

https://www.youtube.com/watch?v=BcTweYHQ-II
It seems like they just pile the leaves on.

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If a person has a specific mutation in a gene, is it more likely he has other mutations in that gene?
If a person has a specific mutation in a gene (2281 del/ins in a single copy of the Bloom BLM gene), is he more likely than the general population to have other types of mutations in the same gene?

A priori, no! Why would it? Do you have any specific hypothesis in mind you would like to discuss?
Below are some expectations from a simple model and possible reasons for why this expectation may break down under more complicated models.
Simple model
Under a simple model (panmictic population and a few other simple assumptions), the number of mutations a given individual has in any sequence considered follows a poisson distribution. Assuming that all mutations occuring have a constance selection coefficient $s$, a constant dominance coefficient $h$ and that the mutation rate for the sequence of interest is $U$, then the number of mutations an individual carry comes from a Poisson distribution with mean $\frac{U}{2hs}$ (Crow 1970).
This model is simple but is probably a pretty good approximation to reality. Below are three assumptions that are not necessarily true and that would yield to a higher variance in the number of mutations (that is a higher probability for an individual that already carry a mutation to get a second mutation).
Population structure
In reality, populations are often not panmictic. As the genetic load depends upon the population size. More specifically, the smaller the population, the higher the genetic load (or the higher the number of mutants alleles present in the population) (Kimura et al. 1963).
Past evolutionary and demographic history
Populations are not stable through time. Some population have recently gone through a bottleneck, others a quickly expanding, some are shrinking, some have recently suffered from a plague, etc... Such processes can all cause populations to differ in the number of mutations they carry and therefore would increase the variance in the distribution of number of mutations individuals carry.
Within a specific short enough sequence, physical linkage associated with specific past evolutionary process will create a relatively long lasting linkage disequilibrium.
Condition-dependent mutation rate
It has been shown in Drosophila melanogaster that individuals with poor genotype tend to have a higher mutation rate causing their lineage to accumulate even more mutations (Sharp and Agrawal 2012).

I would add that there are mutations in certain genes that increase the likelyhood of mutations in general or genomic instability. But i agree that mutation in one gene is not likely to increase mutations in that gene. https://www.ncbi.nlm.nih.gov/pubmed/16020738

I agree theoretically it's unlikely, I wonder though if there is empirical data to support this from the 1000 genomes project.

thanks! so, correct me if I'm wrong, but all 3 arguments are supporting higher variance in the total number of mutations for an individual, NOT for a higher variance in the number of mutations of the SAME gene, correct?

Yes, you are right. However, higher variance in the total number of mutations also increases the variance in the number of mutations for any sequence of interest, including a specific gene.

I think you're missing the most important factor: variation in coalescence time across the genome. The fact that the individual has one polymorphism in the gene means that the coalescence time of their two copies is not very short, and so they are more likely than average to have additional polymorphisms in the gene.

@DanielWeissman This is exactly the same as "Past evolutionary and demographic history", isn't it? Demographic (population bottleneck) and evolutionary (high background selection) is what is affecting coalescent time.

@Remi.b I think the last sentence of that section is going in the right direction. Let's be clear though: the effect I'm talking about is present in completely stable, completely neutral populations. (In fact, bottlenecks can decrease the strength of the effect.)

Bear in mind that the average mutation rate of DNA polymerase is about 1 error for every 1 x 10^6 bases.  So the probability of mutation is independent at each base pair, but low - there's nothing that would prevent another mutation, but there also is nothing that says it is demanded.
There is, however, a phenomenon known as compensating mutations - a second mutation that compensates for a detrimental effect of an earlier mutation.  For example, if I have a mutation in a gene that codes for a protein, and that mutation changes an amino acid that is a contact point for protein folding (or a similar structural component), the protein may not fold correctly until there is a compensating mutation in the region of sequence coding for the residue that interacts with that first amino acid.  Compensating mutations would tend to be positively selected if the protein function is significantly affected....

Any sources you could add?

The answer of course depends some on the details (e.g., whether or not the mutation is neutral), but in general, yes, polymorphisms should cluster along the genome. Roughly speaking, the presence of one polymorphism indicates that the most recent common ancestor of this individual's two copies of the gene probably lived pretty far in the past, so there's been a lot of time for them to accumulate additional mutations.
I'm being a little sloppy here about polymorphisms within an individual vs differences from the reference genome, but the logic is the same.


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How can I evaluate the hydrophobicity and/or surface charge of a protein?
How should I evaluate protein surfaces in terms of hydrophobicity and surface charge properties of the surface.
Particularly I am looking to compare hydrophobic patches or surface charge between two proteins, from .pdb or Fasta sequences for example.
The goal is to study protein adsorption mechanism in the context of protein purification.

Have you used pymol?

Yes, but does pymol shows a numeric value for total surface hydrophobicity percentage for example?

Yes. You can calculate solvent accessible surface as a fraction of the total surface. Although I'm not exactly sure what "total surface hydrophobicity percentage" is.

I've made some edits to your question to make it more about the biological concepts rather than "what tool is best".

Since you have the structures the best option, in my opinion, is Pymol.
Hydrophobicity
Open Pymol. Load up your protein of choice. Download color_h.py which is a script from the University of Osaka that colours the residues according to Eisenberg's scale of hydrophobicity. Load this into Pymol by File->Run->PATH/TO/color_h.py. Then in Pymol run the following commands

show surface
color_h

Note that the script can be edited to use whatever scales you like. @mimat points you toward protscale and I would suggest the same. The Eisenberg scale is a rather old consensus scale. More up to date scales might be more appropriate in your case.
To start quantifying this, Pymol has tools for calculating solvent accessibility for example.

Additionally PDBSum and PDBe-PISA can estimate solvent accesible surface area.
Surface charge
Vacuum electrostatics
The quickest and easiest way to generate electrostatics is with the inbuilt vacuum electrostatics tools. In Pymol, select the action button (A)->generate->vacuum electrostatics->protein contact potential.

ABPS
Since the Pymol inbuilt electrostatics make a lot of assumptions, for publication it is best to get a much more accurately quantified surface map. However, ABPS is a bit more involved. Read the wiki if this sounds more like what you need.

I think you are after protscale. It gives you a whole bunch of options to predict how your protein will be 'behave' for HPLC purification and hydrophobicity, buried residues, etc.

Protscale is a great tool for sequence analysis. Since we have the structures I think there are more reliable ways to look for biochemically interesting surface patches that take advantage of the 3D knowledge we have.

I agree with you completely, your answer will definitely give a more reliable and complete picture of hydrophobicity. Then again it also depends on the volume of proteins you need to analyse, since the poster was asking about purification you often want something quick and dirty for a lot of different targets.

I see. Good point!


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Why does ATP contain ribose rather than deoxyribose?
I read in a textbook that ATP is made from ribose and not deoxyribose. Originally, I thought that the pentose sugar didn’t have functional importance.
Is there a functional reason why the ATP used in metabolism has to be made from ribose?

I have edited your question, in particular changing the reference to ATP being used in respiration to being used in metabolism, and making it clear that your concern is the lack of a functional role of the sugar ring in ATP hydrolysis. If this is not what you meant, do revert the question, clarifying.

Can I ask for a clarification of your question. Are you asking why dATP does not function in contemporary energy metabolism, whereas rATP does? (i.e. why the enzymes will not use it). Or are you asking why organisms evolved to use rATP rather than dATP?

Mainly why rATP is used in metabolism and dATP is not, I assume it may be to do with the fact dATP is used in DNA but I was wondering if there was a specific biochemical reason

Short answer:
The pentose ring does not participate chemically in the energy transfer reactions involving hydrolysis of ATP to ADP.
Enzymes that catalyse these reactions would tend to be specific for ATP (rather than dATP) because they bind the whole molecule and this would most likely include the 2'-OH of the ribose ring. dATP would therefore bind less well or not at all. (There may also be an advantage for evolving such specifity so that dATP could not compete for the active sites.)
The reason that evolution produced ATP as the energy transfer molecule rather than dATP is purely a matter for speculation. One might argue that it is an extra energy expense to reduce the ribose ring, although I prefer a more mundane answer. That is that if one assume RNA genomes (and enzymes) predated DNA genomes evolutionarily, then molecules involved in energy metabolism that contain ribose — not just ATP, but NAD and coenzyme A — arose at that time. When the genomes switched to DNA there was no selective advantage in changing ATP (and NAD) as well, and such an advantage would have been required as the enzyme systems that used these small molecules would by then have been already established.


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Plant identification — Phuket, Thailand
Found in Phuket, Thailand. White flower, five petals, 5 stamens. Strings of flowers hanging down from red stems. Buds white, tear-drop shape.
RHA, Here are the leaves. The flowers hang from a bush about 6 foot (2 metres Tall)
Bli, thanks, but not honeysuckle. No scent.

Nice pictures of the flowers! Do these flowers hang from a tree? Any idea what the leaves look like?

This vaguely reminds me of Lonicera, but is clearly not the species I know.

This is Clerodendrum schmitii similar to C. wallichii (Bridal Veil). It is commonly called Chains of Glory and is native to Thailand.
It belongs to Verbenaceae family.

Chains of Glory is a shrub to small tree, multi-stemmed, with hanging branches. Each winter it grows long, pendent, dark red racemes, 1.5 ft long, of delicate white flowers. The cascading white fragrant flowers are held in loose hanging clusters, similar to Bridal Veil. The white flowers on long dark red flower stalks look very attractive against the dark green leaves. Chains of Glory is native to Thailand.

(from flowersofindia)

The genus is native  to tropical and warm temperate regions of the world, with most of the species occurring in tropical Africa and southern Asia, but with a few in the tropical Americas and northern Australasia, and a few extending north into the temperate zone in eastern Asia.

(from wikipedia)
Picture reference:
 Chains of Glory $^1$
 Bridal Veil $^2$
$^1$ (Source: tuoitre.vn)
$^2$ (Source: Cebuano wiki)

Excellent find! It would be nice to include a picture or at least a link to a picture; your wikipedia only points to the genus.

@RHA Updated the answer.


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Manual Primer Design for a gene on the reverse strand
My question might sound very naive and stupid but I am hopeless now. I read so many websites and pages but could not figure out this PCR primer design thing completely.
Some genes are on the reverse strand of the DNA as we can see on the certain databases. Like this:

Source: http://www.wormbase.org/species/c_elegans/gene/WBGene00019616#0de1-9g4356caf-3
So when I click and get the sequence data of that gene, it also says it's on (-) strand. My most potentially silly question is: Do I just copy paste that sequence and try to find my primers manually or do I need to get a reverse complement of that sequence to make it (+) strand so I can design my primers? This minus, plus stand and reverse complement thing confuses me a lot! And I also do not get why do we get the reverse complement of the reverse primer sequence once we design it.
Thanks for the help in advance!

Not a stupid question at all. I was just as confused by this as a beginner in molecular biology. You get the hang of it after a while. :)
I find it much more difficult to design primers from just one strand, especially the minus strand, so I always try to get both to work with. If you don't feel like doing that, just one strand is sufficient (plus or minus), but I would recommend at least getting the reverse complement in your case because plus strands are much easier to work with.
For a quick example, let's say I have a ten bp sequence I want to design primers for and this is my plus sequence:
5' ATAACTTCGT 3'
Now let's say I want a three bp primer. So the forward primer would simply be 5' ATA 3', that's easy. The reverse primer, if I just take it from there without flipping it, would be 5' CGT 3'. But if I put that into my PCR reaction, it will not do anything because DNA binds to it's complement strand, meaning that primer would only bind to 3' ACG 5', or 5' GCA 3'. So instead, I'm going to want 3' ACG 5' because it will bind to its compliment, the 5' CGT 3' part of my sequence. (Technical issue here, suppliers usually only give the option to write in 5' to 3', which makes sense, but you must remember to flip your reverse primer before giving it to them because it will be in 3' to 5' originally. In this case, I would ask for 5' GCA 3'.)
This is easier to visualize if I have both the plus and minus strand though, which would look like this:
5' ATAACTTCGT 3'
3' TATTGAAGCA 5'
If you have both strands like the example above, you can find both the forward and reverse primer without much difficulty.
I could give a more comprehensive answer of how this all works out during DNA replication that would involve illustrations, allegories, and maybe a few mildly humorous jokes, but I would hate to bore you unnecessarily, so let me know if you understand now or if you need more. ;)
Edit: Exactly (to your third comment I mean)! Remember, DNA is always read and replicated 5' to 3', so the forward primer will bind to the minus strand and be replicated 5' to 3', so will extend the sequence to the right. The reverse primer is the opposite, 3' to 5', so it will extend the plus strand to the left. After both of those happen, you will end up with two full strands. As promised, here is an illustration:

Now, to your question about Primer-BLAST. You do not have to enter a plus strand, but the tool is assuming that you are entering the plus strand, so you will get the right primers, it will just call them the wrong names (i.e. with the example above, it would give you 5' GCA 3' as your forward primer and 5' ATA 3' as your reverse). The forward and reverse primers are treated exactly the same, so this wouldn't throw off your PCR, but it would be incorrect nonetheless. To avoid confusion, I suggest utilizing a tool to reverse-compliment your minus sequence into plus before running it. It's rather easy to get the reverse compliment of any sequence; here is a good tool for that.
I hope this helps. :)

Thank you very much for the answer with a positive attitude. :) It indeed helped me to establish some concepts in my head. If you feel like elaborating your answer and have time for it, feel free to do so, I would read it with pleasure :)
However, some confusion continues. When we design a forward primer, it is to bind to + strand, and reverse binds to the - strand, no? So if I am correct, wouldn't the fwd primer: 5'-TAT so it binds to 5'-ATA? And rev: 5'CGT so it binds to 5'-ACG on - strand? Or am I completely wrong now?

And another thing: If I decide to use primer-BLAST to design primers, do I still need to reverse complement the sequence or it does not matter anymore it is + or - strand as the program will calculate the possible primers?

Oh no, ok now I got it. Fwd primer extends the - strand and rev is the other way around. So what you say definitely makes sense now. But my BLAST question is still on :)

Thank you very much :) Finally I can design some primers! Have a great day.

My pleasure. :) Good luck!


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Odds of finding superbug in soil?
There are tons of soil, rock, etc. being dug up, dug into, and moved all around the world each day. Paleontologists likewise regularly excavate fossils and both buried and frozen specimens, and biologists take samples of permafrost, soil and underground bodies of water.
Given all of the upheaval of these ancient and underground substrates and specimens, I'm wondering what the odds are that we unearth a superbug?

by superbug, I mean an otherwise unknown microorganism that modern medicine does not have a way to kill.

I understand that this is likely too broad of a question to be answered here (but feel free to try!), so I will break this down into a more relevant set of questions to inform my research.

How many microbes (# of species and/or density) typically exist in a cubic meter of soil? (or some other volume)

This article seems to be a good start.

Do these microbe abundances and diversity change with depth?
What is the deepest place in the crust that has been found to harbor life?

This article from 2010 suggests almost 1400 meters. Have we found deeper?

What is the deepest place in the crust that has been found to harbor life?

The deepest living animal:

That award goes to the "Devil Worm" (Halicephalobus mephisto), a nematode that has been found living at 3.6 km below the surface!!

Halicephalobus mephisto is tiny (only 0.5mm long), and represents the deepest multicellular organism ever found.

The original paper can be found here: Borgonie et al. (2011)

I should note, that the paper found definitive Halicephalobus mephisto at 1.3km depth, but found rRNA gene sequence belonging to a specimen of Monhysteridae at the deep 3.6km depth.

Do these microbe abundances and diversity change with depth?
According to  Inagaki et al (2015), microbe density is very low at low depths:

By counting the cells of these microbes, they also conclude that it is a small community, with just one cell in a cubic centimetre of sediment in some sections of the sediment

It's an interesting question and I hope this answer doesn't seem flippant, because that is not my intention. The odds of finding a microorganism that has never encountered humans (or any mammal) but has evolved the ability to infect them seem rather low, in my opinion. For an organism to be pathogenic it must have the means evade the host immune system. This is an adaptive trait requiring co-evolution with the host. You can find a textbook discussion of pathogens in Molecular Biology of the Cell. Importantly, there's a section titled Pathogens Have Evolved Specific Mechanisms for Interacting with Their Hosts which answers your question rather well:

In contrast [to the normal microbial flora], dedicated pathogens do not require that the host be immunocompromised or injured [to cause an infection]. They have developed highly specialized mechanisms for crossing cellular and biochemical barriers and for eliciting specific responses from the host organism that contribute to the survival and multiplication of the pathogen.
In order to survive and multiply in a host, a successful pathogen must be able to: (1) colonize the host; (2) find a nutritionally compatible niche in the host body; (3) avoid, subvert, or circumvent the host innate and adaptive immune responses; (4) replicate, using host resources; and (5) exit and spread to a new host. Under severe selective pressure to induce only the correct host cell responses to accomplish this complex set of tasks, pathogens have evolved mechanisms that maximally exploit the biology of their host organisms.

Also keep in mind that the appearance of superbugs is due to intense selective pressure by the use of antibiotics. Such a scenario is not applicable to organisms we've never encountered before.

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How does Vibrio cholerae benefit from infecting its host?
As far as I know, V. cholerae secretes a toxin called choleragen into the intestinal lumen which affects the intestinal epithelial cells causing release of Na+ and Cl- ions into the lumen and reducing the lumen's water potential which causes water to flow into the intestinal lumen resulting in diarrhea. How does this benefit V. cholera in any way?

Related http://biology.stackexchange.com/q/45099/3340

After V.cholerae gets into the human intestine it starts to multiply its numbers, and then becomes virulent after sufficiently expanding its numbers. This virulence drives the diarrhea which in part causes the bacteria to slough off into the intestinal lumen, and then into the external environment again.
So in short it uses the human intestine to increase cell numbers.
See work by Bonnie Bassler for a really fascinating understanding of the complexity of this infection.

How does the human intestine help V. cholera multiply? I mean, why cannot it multiply in the external environment?

@Taimur Perhaps it is better to look at this as an empty niche. If the bacteria can expand both in the intestines and in the ocean than it would be advantageous to do both. I don't believe that there is any requirement that that bacteria must infect a host in order to expand.

Okay, wait, I actually did some research and found that only humans get cholera. This means that V. cholerae secrete choleragen only to grow and escape human intestines and not of other mammals. Why so? Also, if they can grow in water bodies, why have they developed a specific human-affecting toxin and not a general mammal-affecting toxin?


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Where can I find a list of medical conditions and their incidence rates?
Where can I find a list of diseases and their incidence rates? I'm giving a presentation on Long QT Syndrome, which affects 1 in 2000 people, or 50 per 100,000. I'm trying to find other, more well-known diseases with a similar incidence to give my audience a frame of reference.
(Note: This is not a duplicate of this question. That question is asking about very rare diseases, and the answers to that question reflect that)

Welcome to Biology.SE. The question would be a better fit on Health.SE.

The WHO probably have this kind of data. Consider this document for example.

Thanks. Didn't realize there was a Health.SE, I'll ask there if I can't find it from the WHO


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Where do I find the CO2 clearance rate for various plants?
I'm trying to get enough plants to bring my office from ~1k ppm of CO2 to ~300ppm of CO2. (If I can't get below the ambient 450ppm, that's fine too.) It'd be nice to know before I start buying plants if I can expect to reach that target without, say, having to turn a conference room into a greenhouse.
But I can't easily find a table that lists the rate at which various kinds of plants remove CO2 from the local atmosphere. I'm aware of the NASA Clean Air Study, which looked like it was mostly focused on other pollutants, and Kamal Meattle's conclusion that it takes 4 Areca Palms per person. But I want to know where that number of Areca Palms came from. Or, more importantly, be able to calculate it for other plant varieties. (He might have been optimizing for something different than I would want to.)
So where can I find this information?


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Why do we use klenow fragment in pyrosequencing?
Why do we use klenow fragment in pyrosequencing instead of polymerase

The Klenow fragment is a polymerase. Are you asking why the fragment is used instead of the full polymerase?

Yes exactly right