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Difference between fertilin and fertilizin
I am confused between fertilin and fertilizin.Are these two same or different?
Here are a few sources i referred

Julian Lombardi (auth.) - Comparative Vertebrate Reproduction-Springer US (1998)
Page 210

Richard E. Jones - Human Reproductive Biology, Third Edition-Academic Press (2006)
Page 244

Bioregulators of Reproduction
edited by David Jagiello

google book image link

Please help me know how they are same or different ,specify their functions in detail and thanks for your help in advance !!!

Welcome to Biology SE.
Coming to your question, Fertilin and Fertilizin are different.
Fertilin
Fertilin is a sperm surface protein with an essential role in fertilization. It is required for the migration of spermatozoa through the oviduct, for binding to the zona pellucida, and for efficient binding to the egg plasma membrane. Fertilin consists of two subunits, fertilin alpha and beta, both of which belong to the metalloprotease-disintegrin protein family (ADAMs). Fertilin alpha and beta are made as larger precursors that are processed proteolytically at different stages of sperm maturation in the testis and epididymis. Fertilin alpha is processed first, most likely by a pro-protein convertase in the secretory pathway of testicular cells. Fertilin beta is processed later, while spermatozoa are in transit through the epididymis.(taken from this reference 1) Thus this protein is present in Sperm.
Fertilizin
Fertilizin is sperm-agglutinating substance (glycoproteins) present on Zona pellucida layer of the egg surface. Antifertilizin-fertilizin complex play a key role in sperm penetration. (Have a look at reference 2 &3 ). Thus, Fertilizin is present on egg surface.
Now look back at the images you provided with your question. Role of Ferilizin and fertilin-beta are clearly given.
References:

https://pdfs.semanticscholar.org/0043/f4525b6158d91a00682b86b1b9b15f726125.pdf

https://www.nature.com/articles/169548a0

https://www.journals.uchicago.edu/doi/pdfplus/10.2307/1537786


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What is the role of Cl-, H+ and Malic Acid in stomatal opening and closing?
I understand that K+ influx brings in water making the guard cell turgid. This opens stomata. What is the role of other molecules/ions in this?

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Why do eyes close when we sneeze?
It is a behaviour that is very difficult to control. We can't sneeze with eyes open. Is it a reflex of brain to protect the eye from possible injury in sneezing motion or the neural pathway for sneezing is programmed to do so?

You might be interested in this.

So there is no explanation?

There are lots of things, most of which are indeed quite common like this one, about which we don't know yet. But there are proposed reasons and mechanisms for them. I am busy right now, so somebody will definitely give you a nice answer for this.

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"Treatment" of allergy.
Is there any treatment for allergy? I am not saying about solutions like epi-pen which reduce the symptoms. Is there any way to modify our immunity so that it does not identify the allergens? Can we modify our WBCs to not identify them?

See Allergen immunotherapy and eventually Enzyme potentiated desensitization.

@Remi.b in the article on EPD, there was this in mechanism section:- "The treatment uses dilutions of allergen and enzyme to which T-regulatory lymphocytes are believed to respond by favouring desensitization, or down-regulation, rather than sensitization. Once activated these lymphocytes travel to lymph nodes and reproduce or stimulate similar T-lymphocytes." What does it mean by "are believed to"? How does GIVING allergen desensitise T-lymphocytes?


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Are Na+/K+ active pumps and K+/Na+ "Leak" channels same as given in the figure?
Na+/K+ channels maintain the resting potential with other sodium and potassium channels. Then what are these "Leak" channels? are they the same Na+/K+ pump in a special condition? If so, what is it?
Source of Image: Guyton and Hall- Textbook of Medical Physiology

Pumps are active transporters,  channels are passive. They're different proteins altogether.

@Christiaan my doubt is that the image shows same/similar proteins. What are they? Same or similar?

I agree with @Christiaan because there is a huge difference between a pump and a channel. If you want to check the difference you can simply google it or check what the wiki says about that difference.

Below is the structure of a Na+/K+ ATPase, i.e., the sodium/potassium pump shown on the left in your figure:

(image from here)
Compare to the structure of a potassium leak channel (the type of channel depicted on the right in your question):

(see this publication; image from here)
It's clear they are quite different beasts, without much similarity at all besides both being membrane proteins with several transmembrane domains, which is a characteristic they share with countless other proteins with an incredibly wide range of functions.
The only similarity the pictures from your textbook are meant to convey is that they are both membrane-bound proteins and that they accommodate Na+ and K+; besides that, they are completely different. The figure clearly shows a different mechanism of transport, and the remaining similarity is just from the very abstract way that they are represented.


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Mutation rate in viruses
Mutation rate is a phenotypic trait that evolves. The process of evolution of such kind of traits are often referred to as evolvability. I am wondering about the evolution of the mutation rates in viruses. For the purpose of this question, I'll focus only on viruses that do not possess DNA polymerase. Because the replication of the viral DNA is performed by the molecular machinery of the host cell (eukaryote or not) it seems rather impossible to me for a virus to evolve its mutation rate. Is it correct?

Do we have any evidence of adaptive mutation rate in viruses?
Is there a correlation between the mutation rate of the host and the mutation rate of the virus?
Could the virus evolve some structure (or codon bias) of their DNA/RNA in order to adapt their mutation rate?
Is there another mechanism allowing a virus lineage to adapt their mutation rate?

What do you mean by "adaptive mutation"?

Thanks for the question, I though I might have been unclear. I meant "adaptive mutation rate". The trait is the "mutation rate" and I am asking whether this trait has been shown to evolve "in an adaptive manner" or evolve in order to reach some optimum. This might probably also be phrased by: "Do mutation rate in viruses genetically coded" Does it make sense to you?

I think so, yes.

Just as a point of correction, some viruses technically encode viral DNA polymerases.  Reverse transcriptase in retroviruses is a DNA polymerase, and Hepatitis B (https://en.wikipedia.org/wiki/Hepatitis_B_virus_DNA_polymerase) also has a DNA polymerase, although admittedly hepadnaviruses are weird.

@Armory Very good point, thank you! I edited my question in consequence.

Really interesting question.
I am not sure, if the mutation rate is something "actively done" by the virus. I think its more a byproduct of vast replication after taking over the host cell. Mutations with a negative effect are deleted, those with neutral effects will be there, and those with positive mutations will be selected for. This paper looks interesting in this context: "Viral Mutation Rates". Looking for related publications on the site, I found this two:

Rates of evolutionary change in viruses: patterns and determinants.
A short introduction to the origin and molecular evolution of
viruses.

The whole list is here.
Answering your second question: There is obviously no connection between the mutation rate of the virus and the host. I have found this paper ("Rates of Spontaneous Mutation") which gives some pretty interesting numbers. In short: The rate of mutation for DNA viruses is much higher than for eukaryotic cells and for RNA viruses 2-4 orders of magnitude higher than for DNA viruses.
At least RNA viruses encode for some own polymerases, the reverse transcriptase. Depending on which these have a proof-reading (exonuclease) function they induce more or less errors.


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Why is erythropoietin produced in the kidney?
Erythropoietin is a hormone produced in the kidney to stimulate the generation of more red blood cell. It is triggered by low oxygen via HIF transcription factors. Makes sense. Oops, oxygen is low, let's make more erythrocytes to carry more oxygen from the lung to consuming cells.
What doesn't make sense is why evolution would locate the production of EPO in the kidneys. These are organs tasked with excretion via the urine - pump and retrieve. They have very little to do with red blood cell gas exchange (lungs), generation (bone marrow), or removal (spleen).
Can somebody think of a good reason why you would locate the synthesis and release of the primary hormone to trigger red blood cell generation in a seemingly unrelated organ like the kidneys?

There's no reason that an endocrine tissue should be related to the target tissue of the hormone it produces. Think of other examples, e.g. liver glucagon, islets insulin, adrenals epinephrine. The only requirement is that it should be able to detect conditions in which it is appropriate to release the hormone. Your question would be better if you removed the false premise and just asked how the kidney detects a change in oxygen tension.

Evolution adds randomness but function is still selected for. The hunger hormone ghrelin is produced in the stomach when it's not stretched by food and the satiety hormone leptin is produced in adipocytes when fat stores are filled. Insulin and glucagon both come from the pancreatic islets, strategically positioned in the blood stream right after nutrient uptake in the gut and before the liver, the main storage organ.
The question remains is EPO the exception without a good reason?

As I pointed out, it isn't an exeption any more than insulin, glucagon or epinephrine. However, if I were a developmental biologist I might think about the role or developmental stage of tissues in early foetal (and even embryonic) development to consider why the bone marrow might be inappropriate. I'm a more molecular biologist, so I can't, but I suspect the more physiological biologists should be able to discuss this. Seems there aren't any on this list that want to dip their toes in the water. ( Is your 'surprise' partly psychological because of the association of kidneys with urination?)

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Determination of genes to be modified in epigenetics
It seems that during reproduction particular genes are targeted for modification (mutation, deletion, insertion, etc.) given environmental inputs of either or both of the parents.
If a creature was fit given its environment, its seems there is little mutation. However, if the creature becomes less fit (i.e, due to increasingly becoming prey to a predator) it will undergo increased rate of mutation to find a successful adaption to the new environment. But it seems that the mutation is also targeted to particular genes that maybe most beneficial to mutate (i.e, to develop camouflage).
This begs the question - given environmental inputs, is there something that controls gene modification during reproduction? More specifically, is there a process that targets a specific gene or trait?

Before the rants are coming in from the evolutionists and geneticists shooting this question to pieces because evolution is not a teleological thing - isn't it indeed so that certain loci are hot spots for mutations while others are conserved thereby allowing evolution in certain directions? +1

@Christiaan Doesn't it has some connection with Epigenetics?

@Christiaan Then that should be the question and not the question as is.

@Christiaan I think you're right; there is a good question and premise here. But it needs an edit to make that clearer. It's not clear as it stands.

@TalhaIrfan I came across Epigenetics again for a quick refresher. It seems I wasn't completely off-base with my premise.

Mutations are not performed targeting a specific new phenotype. There is no way an organism can "know" the impact of a specific future mutation anyway. A mutation is just a mistake in the replication process. As a consequence the majority of mutations are deleterious and only a handful of mutations are beneficial.
It is true though that the mutation rate can be affected by the environment or the stress induced by an individual (Agrawal 2002). It seems more intuitive that these are just a consequences of the cost of the DNA replication machinery and DNA repair machinery but it is not impossible that such changes in mutation rate could eventually evolve as a bet-hedging strategy. In the extreme case where the same types of environmental change happen over and over again, it is not impossible that a lineage could evolve the ability to modify the mutation rate at a particular locus. However, to my knowledge this has never been found.
You might want to follow an introductory course to evolutionary biology. You might also want to read this post too that gives a mixture of related information

It turns out there is some level of targeted mutation, but not direct mutation of genes. Without mutating any of the underlying DNA, environmental inputs can affect the repressors of a gene, resulting in altered gene expression in reproduction.

Predicting the protein interactions based on a DNA change, let alone overall organism traits and impacts, is far beyond the processing power of any system except reality itself. You can think of evolution as brute forcing problems with a vulnerability to partial solving. Obligatory: https://xkcd.com/1605/


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What's the name of this bug?

A friend of mine found this bug in Germany. He sent the picture and asked if anyone knew what kind of bug it is. Since no one knew and I didn't find anything similar via google search, I decided to ask it here. Since he only sent me the image I can't really give good information regarding size.
So can anyone identify what type of bug this is?

It's the Jedi bug. Do you see the green laser sword?

I would put it in the family of Curculionidae (true weevils or snout beetles). The problem with that is it comprises about 86,000 species worldwide and about 900 in germany. Maybe someone else can narrow it down

@timbernasley that's at least a start and definitely better than nothing.

Do you know if it had fully developed wings? It looks like the head is on the right, and the abdomen is on the left, like Sudachi mentions in his answer below. It looks to me like this might an immature nymph form of a species that undergoes incomplete metamorphosis. That would help narrow down the order of insect.

I'm quite sure that it didn't have fully developed wings. But it's definitely possible that it had some sort of wings.

It looks like it's the other way around to me. More likely a member of Auchenorrhyncha, which includes cicadas and leafhoppers. I say this judging from the leg structure, abdomen shape, and the eyes. It is however missing wings... perhaps they were removed by another organism?
It somewhat looks like Philaenus spumarius, the "meadow froghopper" which is found in Germany. As for the green tail bit, I am not all that sure.


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Multiple start and stop codons in mRNA and pre-mRNA
I have a main question that will lead to further questions depending upon the answer.
In the process of transcription, will there be multiple start and stop codons in one sequence of pre-mRNA?  If there is, do they remain in the mRNA after splicing?  If they do, does that mean one mRNA has the coding sequence for the synthesis of multiple different proteins?
One last question: assuming a single mRNA has the sequence for synthesis of a single protein, is the stop codon always the final sequence before the poly-A tail?
Thanks in advance for your help and sorry for the mini rabbit hole.

I've changed the title to reflect what seems to me the particular essence of the question: the concern with multiple start and stop codons. For this reason it doesn't really appear to be a duplicate.

In reviewing some of my older answers in order to update them, I find this has been marked as a duplicate of a question that, at least in its current form it is certainly not a duplicate of. This question asks "does that mean one mRNA has the coding sequence for the synthesis of multiple different proteins?" The one it is a duplicate of only asks about stop codons. Is there a mechanism for rescinding this sort of incorrect decision?

Whether or not there are multiple start and stop codons depends on what you mean by "start codon" and "stop codon".
The start codon has the sequence "AUG", and the stop codon has the sequence "UAG", "UAA", or "UGA". Both the pre-mRNA and the mature-mRNA can, and usually do, contain multiple instances of all of these sequences. However, only one "AUG" instance serves as the translational start site, and only one instance of the stop codon sequence serves as the translational stop site.
The translational start site is usually the first (5' most) AUG. However, for reasons that are still not entirely understood, in about 5% of genes the first AUG is skipped, and translation starts at one of the other AUG sequences.
The translational stop site is always the first stop codon to occur in-frame with the translational start site in the mature mRNA.
The stop codon is usually not (I'm tempted to say never) the final sequence before the poly-A-tail. The coding sequence (the RNA region that codes for the protein) occurs in the middle. There is a 5' untranslated region (UTR) before the protein coding region, and a 3' UTR after the protein coding region. The UTR sequences vary among genes and can have different functions depending on the sequence.

As this question is a first post it is probably just a basic question about protein synthesis, which @Sean Johnson has answered adequately. However I’m not quite sure. And as I used to work in protein synthesis (but am a rather out of touch now) I decided to look at the recent literature a little to address some more esoteric or obscure questions it raised in my mind. I’ve set out the results below, and divided my answer into mature mRNA (which Sean covered primarily) but have also considered pre-mRNA. If the answer is not very useful to the questioner it may still be of interest to others.
Start and Stop Codons in Mature mRNA
The general picture of initiation and termination of protein biosynthesis in eukaryotes (bacteria and archea are different) has been described by Sean and can be found in standard texts1. In most cases the first AUG from the 5'-end of the mRNA is the one recognized as the ‘start’ signal for protein synthesis by the ribosomal-subunit initiation complex that scans along from the cap, according to the Kozak model2; and any one of the three termination codons encountered in the reading frame is recognized as ‘stop’ and (almost) invariably lead to termination of the polypeptide chain.
START EXCEPTION 1
As mentioned, in some 5% of mRNAs certain aspects of the environment of the first AUG from the 5'-end results in it being ignored by the complex, and the insertion of methionine and start protein synthesis occurs at the second (or perhaps even a subsequent) AUG.2
START EXCEPTION 2
Certain eukaryotic viruses were found to initiate the translation of the mRNAs internally, by a mechanism distinct from the 5'-scanning method. This involves an ‘internal ribosomal entry site’ — IRES. It subsequently transpired that a small subset of host mRNAs posses an IRES and can initiate translation internally. These include some growth factors, transcription factors and translation factors.3 Such (rare) mRNAs can therefore have several AUGs in their 5'-untranslated region.
Although it is possible to envisage an mRNA with several IRESs, and thus encoding several different proteins (analogous to a bacterial polycistronic mRNA), this does not appear to happen. It is striking, for example, that poliovirus RNA has just a single IRES for the start of the synthesis of single a large polyprotein, from which it generates multiple proteins by proteolysis. It would seem that the main purpose of this alternative initiation is to allow protein synthesis to proceed in the absence of a 5'-cap.
STOP EXCEPTION 1
There are some AGU codons that are recognized by a specific tRNA that inserts selenocysteine into the polypeptide chain. Some aspect of the environment of these codons causes them to be ignored by the protein termination system, and the ribosome continues translating, eventually terminating at a subsequent stop codon4.
STOP EXCEPTION 2
It has long been known that certain bacterial and eukaryotic viral mRNAs can increase their genetic repertoire by what is known as ‘read-through’ of ‘leaky’ stop codons. This is a ‘percentage’ effect, rather than all or nothing, and results in a mixture of ‘normal-length’ and extended products. It is now clear that the same phenomenon can occur in some eukaryotic mRNAs: quite frequently in Drosophila5, but also in mammals6.
STOP CODONS & THE 3'-UTR
I’m not clear what the questioner means by “is the stop codon always the final sequence before the poly-A tail?”. If the question is whether there can be additional stop codons in the 3'-UTR between the functional termination codon and the AATAAA polyadenylation signal (purple in Sean’s diagram) the answer is yes. Looking at the sequences of some muscle protein cDNAs done years ago, I found several stop codons in this region in each that I looked at. Of course they are without any function as the ribosome has already departed, but there is no reason for them not to be there on a random basis (and at apparently random positions).
Start and Stop Codons in pre-mRNA
By pre-mRNA I assume is meant the initial RNA transcript before splicing. There is no reason why an intron that is spliced out so that it does not appear in the final mRNA should not contain start or stop codons, which if not removed would have altered the reading frame. Many do.
A more interesting situation is where there is alternative splicing to produce different mRNA transcripts that encode different proteins. Pertinent to the question is the situation with start codons where the proteins differ in their N-termini, and stop codons where the proteins differ in their C-termini. The latter are quite common, but the former also occur, particularly were there are alternative forms of a protein, with and without a signal peptide7. In these cases the start or stop codons will be present in both of two exons, one of which is spliced out in each case. Examples of this from a couple of Drosophila genes are illustrated:

In both cases the coding regions are in orange, and the untranslated regions in grey. The thin lines represent the position of introns that have been spliced out. The arrowhead represents the direction of transcription and is at the C-terminal side of the protein. (i) Different N-termini for alternative products of gene vha14-2; (ii) Different C-termini for alternative products of gene vhaSFD.9


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Why do we take antibiotics if our immune system already produces them?
Why do we take antibiotics if our immune system already produces them? Is it because our body doesnt make enough or the specific complementary antibody to fit with the antigen?

Perhaps you could respond to the answers — or this comment — to clarify whether you were really confusing antibiotics and antibodies, or whether you were interested in "innate immunity".

Since people and animals routinely get sick, it is obvious that our immune system (which includes but isn't limited to antibodies) doesn't always protect against pathogens.  There are many reasons for this, far too many to summarize here, but one common reason is that it takes several days for the adaptive part of the immune system (which includes antibodies, among other things) to gear up and control an infection. Therefore, early treatment with antibiotics can help limit an infection before the immune system is fully engaged.
Pathogenic bacteria are often resistant to immunity in many ways as well; that's one of the adaptations that makes them pathogenic. That means that even later in an infection, antibiotics can supplement the immune response and help eliminate bacteria.  Note that many antibiotics require a functional immune system to be completely effective.

We take antibiotics when our own immune system is insufficient to control infections. We do make antibiotics as localized defence systems

Defensins and cathelicidins belong to antimicrobial peptides (AMP), called also the natural antibiotics. They are found in Prokaryotes and Eukaryotes, also are synthesized in plants. These molecules were described in bacteria, invertebrates, vertebrates, also in mammals including humans.

But clearly these  can be overwhelmed by bacteria resistant to their action, or by overwhelming rates of reproduction of invading bacteria
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487008/
Our mammalian physiology has further evolved the innate immune system, and the adaptive immune system to cope with invasions that bypass these simple non-adaptive molecular defenses.

Please provide a citation for your quote.

I assume from your question (and your pseudonym) that you are confused by terminology. Our adaptive immune system does not make antibiotics, it makes antibodies. Antibiotics are small molecules that interfere with bacterial metabolism. Antibodies are proteins that recognise foreign macromolecules. (You could regard both as “anti-bacterials” — perhaps this is what you were thinking of — but the immune system is not restricted to recognizing bacteria.)
We take antibiotics when we have an infection from bacteria that have evaded the immune system.

This isn't true. We do make antimicrobial peptides, which are essentially antibiotics.

@MattDMo The immune system makes antibiotics? I answered the question at the level it was asked. We are dealing with a first poster who is unfamiliar with scientific terms. We do not help him or anyone else by muddying our answers with esotericism.

Questions are simply a vehicle for producing answers. Remember, the point of Stack Exchange is not to answer an OP's specific question just for the OP, it is to produce a lasting repository of knowledge. If you're going to make an answer, make it an accurate, complete answer. Besides, antimicrobial peptides (AMPs) are not "esoteric" - they're a vital part of the innate immune system.

@mattdmo To be strictly fair, David is correct since the original definition of an antibiotic was that it was s substance made by bacteria and fungi. But the internet and non scientific use, progress, and synthetic antibacterial agents has invalidated the original definition.

So sulfonamides were not initially called antibiotics, but antibacterial agents because they were synthetic.

Methinks thou dost protest too much. But if I am wrong, retitle the question  something like immunity and antibiotics, rewrite it, and supply your answer. Because if you don't nobody will benefit from your contribution as they'll assume that it's a naive question that really should be pulled.

The op isn't involved in the discussion

@GrahamChiu  Op?

I give a short straightforward answer to an obvious misunderstanding and someone marks it down. OK.I'll make it less comprehensible by qualifying it, then will that person mark me up again. In my dreams! What's wrong with you guys?


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Is there a term for a procedure in which the chromatography column is washed with 20% alcohol
From a method description in a Russian document:

After the chromatographic analysis is complete, the column is flushed with at least 2-3 volumes of water at a rate of 0.4 ml/min. The column is then mothballed (?) by washing it with at least 10-15 volumes of 20% alcohol at a rate slowly declining from 0.4 ml/min to 0 ml/min.

The word I translated as "mothballed" is konservirovat (консервировать колонку) in Russian. It has the general meaning of "preparing something for storage" (for instance, "preparing vegetables for storage by pickling").
In an effort to determine the correct terminology, I would like to know the reason why a chromatography column would be washed with 20% ethanol. Any recommendation on the standard biochemical terminology for this procedure, if it exists, would also be welcome.

You have accepted an answer (which alternative?) that allows you to do what I consider the wrong thing. The right thing would be not to try to translate but to explain what it is the 20% alcohol does. What does it do? Remove uneluted protein, prevent bacterial growth, or what? If you know, say, followed by "before storage".

@David thank you for the good advice, but I don't always have time to investigate the issue that deep when translating a large text. I write questions to the authors, but that takes some time too.

@tomd Perhaps you can add this as an answer.

Prepared or conditioned for storage would probably be perfectly acceptable.
If you're looking for a single-word equivalent, in this case, I would translate as stabilized. From dictionary.com:

stabilize
[stey-buh-lahyz]
verb (used with object), stabilized, stabilizing.

to make or hold stable, firm, or steadfast.

This seems appropriate, since one wants to ensure maintenance of the proper condition of the column for later usage, when taken out of storage.

I don't like "stabilize" because it implies that the column is unstable otherwise, which it isn't.

@David , I'm not familiar with the technique in detail, so I'm poorly equipped to evaluate it from that perspective. Is it stable in storage without the ethanol washout procedure?

I suspect it will either get clogged up or bacteria may grow on it, but I'm not sure. I don't think the beads will disintegrate though.

The ethanol is indeed to prevent microbial growth.

@canadianer Hmm, so preserve might be better than stabilize?

Possibly. I don't think information about how the columns are stored is really very necessary when describing methods.

This is a routine procedure in FPLC to prepare columns for storage. 20% ethanol is used to prevent microbial growth. See this technical note:

All SEC columns are delivered in 20% ethanol to prevent microbial growth.

I have always found it strange that we only use 20% ethanol, why not add 0.05% sodium azide for further protection as some microorganism will grow in 20% ethanol alone.

@JeppeNielsen It's an interesting point which I don't have an answer to. I store gravity flow columns in sodium azide.


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What type of snake is this?

We came across this snake when were on a hike in a typical dense forest in the Philippines. . Been wondering if this snake is venomous or not.

Where did you see this?  There are many countries with many "dense forests".

Definitely venomous. It's a viper but you should tell the exact geographical location for correct identification.

My guess is that it is a juvenile temple pit viper (Tropidolaemus subannulatus).

It's in Asia. Thanks for the info!

@Jay Asia is a huge continent with diverse ecosystems. Can you be more precise with the geographical location?

It's in the Philippines.

Can you please [edit] your question to include all the necessary information?

It is a green tree python (Morelia viridis)

I think that's accurate. A young one, perhaps 10 months old.

Green tree pythons are limited to Australia: https://animaldiversity.org/accounts/Morelia_viridis/

Please add some references to support your answer. I guess your answer is also incorrect. The snake looks very much like a viper. Can you add some explanation on why you think it is a green tree python?

Thank you. I would agree. This one is close to a viper.

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text:
Predatory insect - what kind?
I've seen several of these insects near my house in southeast Michigan this summer, including the one seen here feeding on a green bottle fly. What are they?

Probably Efferia or Promachus but I can't know for sure without knowing the size. How big was it?

@Praearcturus IIRC 2-3cm, but not positive. Feels like forever ago :)

That looks like a type of "robber fly" — compare with this image:

BugGuide is a great resource for identification of insects, spiders and their ilk.

Definitely correct! Thanks

You're welcome, glad I could help!


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How to find which genetic pattern is responsible for structure of a cell
I studied that DNA are blueprints that describes an organism.
How do I learn more specifically about DNA regions responsible for storing structure of a cell.
By Structure of a cell I meant to ask which genes are responsible to store the 3-d structure of cell, sub units of a cell and its structure, number of layers a cell should contain and how thick it should be etc.
What I have researched to find answers: Looking at bacteriophage, it has 6 legs and they fold and lock. I did a recent study and learnt that genes are same throughout the organism and epigenitic modification turns on/off a particular gene based on the cell group it belongs to by a process called methylation. I signed up in coursera for a curriculum course, but yet to choose one.
What I am looking for: Is there a reference educational material that teaches gene in below format.

Movements of a cell always stay in this region.
Shape of the cell is defined by head region of DNA.

To put in a question, How do I learn how to map which region of gene is applicable for which characteristics of a cell?
Why am I looking for this answer: I want to build a simulator that can take in an organism's DNA and simulate its growth and cell structure. I am looking for precise sub field in genetics that will educate me for my need.
PS: Thanks for providing feedback on the question. I'll pickup asking the right questions gradually once I get a grip on the subject.

Welcome to Biology.SE!  Please clarify what you mean by structure.  Do you mean the three dimensional shape of a cell? —— It is expected that you will demonstrate that you have done research on your own before asking questions here — to do this please outline what you already know (ideally with references) about this subject. ——— Please also take the time to take the tour and then the help pages starting with How to Ask questions on this site. Thanks!

As an additional note this a very broad question about a very complex topic - even with additional clarification there will still be whole textbooks on the answer.

I am going to post an answer that is maybe not helpful for the exact goals, but which will maybe help restate the problem to be easier. As commenters noted it is super big and complex, many whole careers have been devoted to solving very small parts of this problem.
Possible problems with premise
I think that this question starts from this statement as a premise:

DNA are blueprints that describes an organism

This premise is not correct. Or rather, it is a way of explaining what DNA is doing in very simple terms. I do not think that you will be able to simulate with any precision cell structure based on DNA sequence. But at the end of the answer I suggest some things that are a little more focused that I know you can do.
More specifically, DNA is not a blueprint because DNA does not have instructions for how to build a cell. DNA is more like instructions for how to maintain and repair a cell. A manual for a car may tell you how to keep your car in good working order and how to replace every piece of the car, but it does not tell you how to build a car.
A quick example: cells are enveloped in the plasma membrane, which has as its fundamental component a bunch of phospholipids. DNA has instructions for these steps:

how to make new phospholipids
how to insert phospholipids into an existing plasma membrane

DNA does not have instructions for this step:

how to make a new plasma membrane de novo

DNA is always assuming the pre-existence of a cell. Cells won't work without DNA, but DNA is useless without an existing cell.
Some things you might be able to do

There are specific genes that are related to some cell compartments, like e.g. endoplasmic reticulum (ER). Eukaryotic cells have ER and prokaryotic cells do not. If you see genes for ER, you can guess that your cell should have ER. You would need to infer the presence of such genes, but there are existing tools that do this gene prediction from DNA sequence, e.g. https://en.wikipedia.org/wiki/List_of_gene_prediction_software
For your bacteriophage example, it seems like you are interested in macromolecular structure of a phage particle. (Note, bacteriophage are not cells). There do exist a lot of programs for predicting protein structures from protein sequence. You can often infer protein sequence from the DNA sequences of genes. Proteins are important building blocks of cells, and there is a lot of work on figuring out their structure (field is called "structural biology", loosely). I would recommend looking at some of the existing software in this field, e.g. https://www.rosettacommons.org/software.
I would recommend looking into existing cell simulators, which exist. For example: https://en.wikipedia.org/wiki/Virtual_Cell, https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005991. I am sure there are more that you will be able to find.

Hope that helps.
UPDATE
I realized afterwards that when I say that that DNA doesn't tell you how to make a cell that could be considered confusing, because cells divide to make more cells. However, The process of cell division is not making a new cell "de novo" (out of nothing)- rather it's taking an existing cell and reforming it into 2 cells.
In other words DNA does this:
1 cell --> 2 cells
But DNA does not do this:
materials of a cell --> a functional cell


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What is the difference between transpiration and evapotranspiration?
According to my point of view transpiration and evapotranspiration are different things, but i am confused about this topic. After great effort, I found a major difference between it.
Transpiration: The loss of water in the form of vapour from plants surface is called transpiration.
Evapotranspiration: The loss of water from any surface in the form of vapour is called evapotranspiration. Such as water surface, soil and any body surface.
By educationspot
Is it correct? Please explain.

Essentially, evapotranspiration is the sum of evaporation and plant transpiration from the Earth's land and ocean surface to the atmosphere.

Here are some links to articles about transpiration: https://biolympiads.com/plant-anatomy-and-physiology/


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Do housekeeping genes vary between tissues
I am working on an RNA-Seq project, and I am aware that some researchers use housekeeping genes as a method of normalization.  My project has several different tissues, and I was wondering if housekeeping gene expression is generally invariant across tissue type?

There is no such thing as a universal housekeeping gene.

It depends on the definition of housekeeping genes.
ENCODE recently released RNA-seq of 17 tissues at 8 developmental stages.
A list of housekeeping genes was also provided.
They are not exactly constant. They just are less variable than other genes.

Your answer sounds as if it may be correct, however in order for the reader to find out he needs to go to an external site. It would be more useful, and more in keeping with our model if you could flesh out your statement "They are not exactly constant" with some representative examples, which would enable us to upvote your answer. The interested reader (the poster has presumably finished his project now) can follow your link for full details.

My experience is: Yes they can vary quite a lot (according to differences in the genetic profile of the cells) and you have to test this. As a primer I can recommend reading the articles listed below. These are mostly looking into this in the context of realtime PCR, but this should be valid for RNAseq as well. For some applications it is also a good idea to use more than one gene for normalization.
References:

Accurate normalization of real-time quantitative RT-PCR data by
geometric averaging of multiple internal control genes.
Selection of housekeeping genes for gene expression studies in human
reticulocytes using real-time PCR
Reference Genes / Housekeeping Genes
Gene Ontology Based Housekeeping Gene Selection for RNA-seq
Normalization


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What is the function of human Trypsin Inhibitor if trypsin is secreted in the inactive form of Trypsinogen?
I was reading about pancreatic digestive enzymes in a Textbook of Medical Physiology and I came across Trypsin Inhibitor. The text stated that:

It is important that the proteolytic enzymes of the pancreatic juice not become activated until after they have been secreted into the
intestine because the trypsin and the other enzymes would digest the
pancreas itself....  ....substance called trypsin inhibitor. This
substance is formed in the cytoplasm of the glandular cells, and it
prevents activation of trypsin both inside the secretory cells and in
the acini and ducts of the pancreas.

It also states that:

When first synthesized in the pancreatic cells, the proteolytic
digestive enzymes are in the inactive forms trypsinogen,
chymotrypsinogen, and procarboxypolypeptidase, which are all inactive
enzymatically. They become activated only after they are secreted into
the intestinal tract.

My question is, why is Trypsin Inhibitor secreted if trypsin is already secreted as trypsinogen which can only be activated in the intestine?

I think this is a pertinent question, which deserves more attention. My own brief survey suggests that there is no simple answer. If nobody else answers I'll summarize what I can find when I have a moment.

@David As you say, it is not an easy answer. It's a matter of time.

@Chris I’m not blaming anyone. Just trying to draw attention and let the poster know that he might have to wait for a proper answer.

I’m voting to close this question because it is cross-posted with an answer at: https://medicalsciences.stackexchange.com/questions/24834/why-is-trypsin-inhibitor-present-if-trypsin-is-already-secreted-in-form-of-tryps Please see https://meta.stackexchange.com/questions/64068/is-cross-posting-a-question-on-multiple-stack-exchange-sites-permitted-if-the-qu

@BryanKrause — Thanks for noticing that, and saving me spending my time duplicating someone else’s work. Which is one good reason why cross-posting is anti-social.


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What is the limiting factor for algal growth in the oceans?
As far as I can tell, pelagic algae require four main things to live: sunlight, carbon dioxide, trace minerals and physical space. What is the limiting factor?
Note this is kind of a deceptive question, because although it might seem straightforward, it can be tricky to figure out the limiting factor. So, in fact, there may be no definitive answer, but nevertheless I am sure there are people out there who know more about this than me, and I am hoping to get some expert insight.

Sunlight varies by the depth and lattitude so it can be the limiting factor.

Maybe other animals eating it?

According to Liebig's Law of the Minimum, such organisms as algae will grow until they are limited by anything that they need. So unless we start from the absurd position that all marine environments are effectively identical, the limiting factor must vary from microenvironment to microenvironment.
A trivial example would be sunlight, as suggested in the comments. The photic zone of the ocean is only 200m deep, such that when you get deeper than that is is nearly impossible for algae to grow, due to the lack of sunlight. This is only one such limiting factor.
Another limiting nutrient that has gotten a lot of press is iron. In fact, there are people who think (or have thought) that we could reverse trends in atmospheric carbon dioxide concentrations and thus global warming through iron fertilization of the oceans. (I have not been following the literature on this but I believe there is reasonable to be skeptical of the claim.)
In other cases it appears that the limiting nutrient is phosphorus, or nitrogen, etc. There are obvious correlates to the problems of algae blooms, eutrophication, marine dead zones, etc.
There is a significant amount of academic work on this that I would recommend reviewing, to see if you can figure out the answer to your underlying question:

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1988.33.4part2.0796
https://www.jstor.org/stable/1352354
https://www.srs.fs.usda.gov/pubs/chap/chap_2019_grace_001.pdf


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Why are there few quail any more in the Northeast of the US?
I currently live in southeast New Hampshire and was reading a history of my town and it describes the landscape as having a lot of quail and even partridges. The book said children going to school around 1920 would see lots of quail. The town itself has not changed much from 1920 except that there are fewer farms. The population is about the same. In fact, the population is probably lower now than it was in 1920.
I have never seen a single quail here, and certainly never seen a partridge. I have seen a pheasant on rare occasion. There are a lot of turkeys.
Is this like a Silent Spring thing, they all got killed off by DDT or something? Or is it because of insecticides killing all the crickets, maybe? I almost never hear crickets at night.

I don't recall ever seeing quail growing up in the rural northeast, yet partridges and pheasnts were fairly common.  Yet quail are very common where I live (just east of the Sierra Nevada).  I can see a dozen or so running around my yard most evenings.

Work in the early 1990s (https://pubs.er.usgs.gov/publication/5210546) (https://www.nwf.org/en/Magazines/National-Wildlife/1993/The-Case-of-the-Disappearing-Quail) suggests development (curtailing habitat), climate crisis (and associated water loss), and decline in insect populations (reducing food supply) as possible causal factors.
Insects are an important energy source for birds, generally. They help pollinate plants, which help feed birds, and they are also a food source, themselves. Their loss (https://en.m.wikipedia.org/wiki/Decline_in_insect_populations) particularly hits bird populations hard. Unless we change our agricultural practices, it is predicted that most insects may be extinct within a century. This would decimate many forms of life (ourselves, included with quail and other birds) that depend on them.

But that would not explain why they have apparently declined in the northeast, but are plentiful here in the west.  Might it be a change in land use?  Quail tend to inhabit open grasslands (and sagebrush scrub, hereabouts).  If the small fields & pastures of agricultural New England in the 1920s largely reverted to forest, there would not be as much quail habitat.


text:
Are microRNAs transcribed from the same DNA strand as their parent messenger RNAs?
I am new to micro RNAs. I have been trying to find the answer to the question if microRNAs are transcribed from the same DNA strand as the messenger RNAs encoded by the encompassing gene?
From the scientific articles I have read so far, I infer that it is the same strand. If so, does the transcription of microRNA and mRNA occur simultaneously?
Finally, does the strand from which the microRNA is transcribed have any implications for its interaction with its mRNA target?

What do you mean by "the same gene as mRNAs"? What scientific article makes you think that? Try searching for microRNA promoters, e.g. In Drosophila.

@David What I meant was if the miRNA is created from the complementary DNA strand from where the mRNA is created.

The following bear on the question of the relationship of the transcription of microRNAs to that of the pre-mRNAs of protein-coding genes:

Some microRNAs (termed ‘intergenic’) do not reside in a protein-coding gene (e.g. Drosophila mir-31a). Here the question does not arise.

Many (although not all) of those that do reside within a protein-coding gene are found exclusively in introns (termed ‘intronic’) — e.g. mir-11 and mir-998 in Drosophila gene E2f1.

For those microRNAs that reside in a parent gene, the direction of transcription is generally, although not exclusively, the same as that of the transcript (ca. 70%, according to this review).
The question arises whether the intronic microRNAs are generated from the spliced introns of transcripts of their parent genes. One of many papers which consider this is by Ramalingam et al. (2014). It appears that in some cases this may be so, but in other cases this appears to be ruled out by a disparity between the expression profiles of parent genes and microRNAs, and between different microRNAs encoded in the same intron.
The co-directionality or otherwise of transcription of ‘parent’ mRNA and microRNA has no implications for the interaction of microRNAs with their, often numerous, ‘target’ mRNAs. This is because (1) there is no genetic relationship between parent mRNA and target mRNAs — the parent mRNA, lacking the intron that gave rise to the microRNA, is not the target; (2) the hairpin loop of the microRNA precursor (imperfect though it may be) in effect represents both strands, from which may be generated either the 5ʹ portion, the 3ʹ portion, or both, depending on the microRNA. The miRBase site contains information on relative abundance of 5ʹ- or 3ʹ-fragments for individual microRNAs, and the microrna.org resource lists potential target mRNAs.

Thank you, David. That is really what I was looking for. By the way, even if a miRNA is not from the same DNA strand, it can form the miRNA-mRNA complex right?

I have added a line to your question to include this concern, and have addressed it in my answer, which I have modified somewhat to improve it. The Ramalingam paper may be of interest.

That is very helpful. Thank you very much once again.


text:
After a bacterial infection is dealt with, do any of that colony of bacteria remain?
Suppose that I get a bacterial infection, which my immune system deals with. Are there any remnant bacteria, or are they all gone? Now consider the same scenario, but having been treated with a full course of antibiotics - are there any bacteria left alive? Now suppose I take a partial course of the antibiotics - enough to reduce the bacterial population to a level that my own immune system can deal with by itself. In this last case, if I beat the infection, is there any chance of bacteria having evolved resistance to those antibiotics, or are they all dead?
I ask having recently read an article claiming that conventional wisdom on antibiotics might not be as useful as once thought.

Have you read anything on resistant bacteria?

@rg255 yes; what are you getting at?

I think @rg255 is on the generation of resistance by not finishing antibiotical treatments...

Which is exactly what I'm interested in, but am questioning the 'accepted' wisdom of the matter.

Can you point out exactly where the article states "a full dose of antibiotics is somewhat arbitrarily determined and based on a single case study"? (It did state recommended "antibiotic courses are often arbitrary; they may reflect long-standing convention or be based on a manufacturer’s decision during an initial drug trial." Note that an initial drug trial is light years from a single case study. (cont.)

Furthermore, the paper states that "Recent clinical trials show that even for some serious infections, shorter antibiotic courses can be as effective as conventional, longer ones," which directly contradicts your assertion that duration of antibiotic treatment is arbitrarily determined. The article has a lot of correct information, but can be easily misinterpreted, which I believe you have done.

@anongoodnurse fair call; which is why I'm asking the question here.


text:
Examples of biological turing machines
Are there any examples of biological Turing machines? And what can they do?

Take a look at: https://www.quora.com/Is-DNA-a-Turing-machine or http://www.nature.com/nrg/journal/v13/n7/full/nrg3197.html.

Welcome to BiologySE and thanks for your question! It always helps by adding references and some background information so that others can understand what you're asking - and it will strengthen your question.

Are you asking for "natural" Turing machines or artificially created ones?

Hm interesting question. I think natural Turing machines would be way more interesting. But both are interesting.

There have been several Turing machines constructed using DNA computing. One of these machines has been used to solve the boolean satisfiability problem, another was used to solve the bounded post correspondence problem, both NP-hard combinatorial problems which are difficult for conventional computers to solve.
Also, a DNA computer was constructed that plays the optimal strategy in tic-tac-toe.
DNA computers store information in DNA sequences and perform calculations by DNA baseparing and other molecular biology strategies. In principle, DNA stores Information much denser than any modern hard drive and uses orders of magnitude less energy per calculation than a conventional computer ($10^{-22}$ vs $10^{-10} \frac{J}{operation}$) however, so far i/o is slow and calculations are comparatively error prone, limiting the practical use of DNA computing.
Also, a recent article has demonstrated that molecular motors can perform basic addition and solve the NP-complete subset sum problem by exploring nanolithographically fabricated networks. This could also, in principle, be used to construct a turing machine.

Thx, that's about artificial ones. What about Turing machines in nature?

Well, the brain most likely fulfills the criteria for a turing machine on some level. Also, there is this very nice answer to the question "is DNA a turing machine" on quora. That details how protein biosynthesis could be viewed as (almost) a turing machine. Finally, transposons fulfil many of the criteria of a turing machine. However, none of these examples are turing complete, except maybe for the brain but there it is not well understood how.

Thx very interesting.


text:
What prevents the human intestine from 'exploding' as a consequence of bacteria growth?
Usually bacteria grow by dividing and they can do that very fast. So after a couple of hours or days you have many bacteria in your intestines.
And we keep feeding them by eating. In some way you would expect that the growth of bacteria has been so overwhelmed that after a week our intestines would 'explode'.
Of course this doesn't happen, but what factors protects our intestines from bacteria overgrowth?

I have a feeling stomach acid is to play here, but I can't seem to find any sources at the moment

The intestine actually has specialised immune cells just for itself, much like it has a specialised nervous system. I can't provide you with a detailed overview as it's been a while since I've studied intestinal immunology, but one component that I do remember is the secretion of specialised IgA antibodies which to some extent could regulate the baterial load in the intestine (and certainly regulates the types of bacteria "allowed" to grow there).

Bacteria also regulate themselves so as to not overwhelm their surroundings. The gut microbiome is an incredibly complex place, with multi-species biofilms that signal amongst themselves to prevent the outgrowth of any one species. The host's immune system is also involved to a significant degree. Remember, these are not laboratory-grade E. coli growing in Luria broth, and they are not pathogenic. They are symbiotes with the host, and both participate to not overwhelm the other.

If you take a nutrient agar and do a lawn culture, the bacteria won't grow on forever. There's a limit to the max population. This is without considering the host's immune factors which would play a major role in the gut

Bacteria can't create mass, even when they divide. During division, you go from one "big" bacterium to two "little" bacteria, which then have to accumulate nutrients and grow bigger before they can divide again.
When nutrients are plentiful, this can happen rapidly, and you do see exponential growth. But the exponential growth phase is only valid when there is an excess of food in the environment. Bacterial growth curves follow a typical lag/log/stationary/death profile. The log (exponential) phase only applies when nutrients are in excess. Whenever some nutrient becomes limiting (because it's already incorporated into another bacterium, for example) the bacteria switch to stationary phase growth, and reduce replication or stop it completely.
So you would never get an "explosion" of intestinal bacteria - the bacterial mass is strictly limited to the amount of mass (food) input into the system. Once that's all (or mostly) converted, the bacteria will stop growing and start dying.
If you kept accumulating mass in your intestine, you're correct that eventually it would "explode". However, most people regularly (pun intended) eliminate excess intestinal contents. (Which, as bpedit mentions in their answer, contains a high proportion of bacterial cells.) This limits the total mass contained in the intestine, and keeps it from "exploding".

There are very likely other factors at work as well, I'm no expert. But the following always surprised my Biology students.
About 30% of feces is bacteria.
http://bionumbers.hms.harvard.edu/bionumber.aspx?id=108514
Peristalsis continues to move food, food waste and bacteria through your digestive system. So, as new bacteria arise, other bacteria are eliminated.


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Is ATP produced in a different manner during glycolysis from that generated by the Krebs Tricarboxylic Acid Cycle?
The ATP in glycolysis is produced in the cell cytoplasm but that from the Krebs Cycle is produced in the mitochondria. The mitochondrial membrane contains an ATP-synthase protein complex that harnesses a proton flow into the production of ATP from ADP and Pi.
Is the ATP made in the cytoplasm during glycolysis made in a similar or different way?
https://www.youtube.com/watch?v=mfgCcFXUZRk

The ATP in glycolysis is produced directly in certain reactions of the type:

X-PO32– + ADP → Y + ATP

in a process is called substrate-level phosphorylation.
A key preceding reaction in the pathway is the one catalysed by glyceraldehyde 3-phosphate dehydrogenase, in which free orthophosphate is incorporated into a sugar phosphate in a reaction of the type:

Z + PO43– → X-PO32–

(I have used X, Y and Z because other changes occur in the structures.)
This is totally different from the oxidative phosphorylation that occurs in the mitochondrion. In both cases the (free) energy driving the generation of ATP comes from oxidation of sugars involving cofactors such as NAD+ to NADH. In oxidative phosphorylation the reoxidation of NADH in the membrane (ultimately by molecular oxygen) is used to set up a proton gradient, which can then be used to drive the ATP-synthase. In substrate-level phosphorylation the chemistry of the intermediates is manipulated so that particular reactions involve sufficient free energy change to drive the conversion of ADP to ATP directly. (The anaerobic reoxidation of the NADH does not produce ATP in this latter case.)
You should read a text-book of biochemistry for the details, which are too extensive to present here. Berg et al. Section 16.1 covers this well, and is available on-line.

I have edited my original answer that had the unintended implication that ATP was generated in the G3PDH reaction. I have also tried to illustrate the principle of substrate-level phosphorylation, but have used general reactions to avoid the distraction of the actual chemistry, which can be found elsewhere.


text:
Role of the Hypothalmus in the control of Blood Sugar
In homeostatic regulation of blood glucose, the receptor and effector is the Pancreas, but how does the control centre — the Hypothalamus — connect and link into this process?

Welcome to Biology Stack Exchange. At the moment, this question risks being closed for not showing an attempt at prior research, and possibly for being 'too broad'. https://en.wikipedia.org/wiki/Blood_sugar_regulation describes blood sugar homeostasis in some detail. You could improve this question by pointing out why you think something important is missing in Wikipedia's description of the system, and asking specifically about the missing part.

I've made your title more specific (and hence more useful), although I tend to agree with @bshane. I don't like, but refrained from altering, your references to "receptor" and "effector", as in the field of endocrinology they have different connotations at the molecular level. You might consider a simpler statement like "In homeostatic regulation of blood glucose, the pancreas plays a major part. Is the hypothalmus also involved and, if so, how?" or "…the hypothalmus is also involved, but how does it influence the pancreas" if that is what you mean.

Your question doesn’t make it clear whether you think that the pancreas must be under the control of the hypothalmus, or whether you are asking whether it has an influence on the pancreas in relation to the secretion of insulin and glucagon, which control the concentration of blood glucose.
First, it has been long known that secretion of insulin can be influenced by the concentration of glucose in isolated pancreatic islets in vitro, so it can not be true that the effects must involve the hypothalmus. This is implicit in most book or general information articles you might find on the web, but for an original reference a review by W.J. Malaisse in Diabetologia 9, 167–173 (1973) seems highly cited.
I know almost nothing about physiology, but on searching the web for the role of the hypothalmus in glucose homeostasis, found a most readable prize-winning postgraduate essay on the topic by Syed Hussein of Imperial College London. I trust that it is in order to append an edited extract of this:

How does your brain control sugar?
  …altered delivery of glucose to specific parts of the hypothalamus can change insulin, glucagon and glucose levels [2]. …alterations in hormones and nutrient sensing by the brain in rodents leads to marked changes in glucose control. Evidence suggests that distinct regions of the brain have roles in controlling blood glucose in response to changes in glucose, insulin and fatty acids [ref]. These discrete brain nuclei regulate glucose output from the liver, insulin resistance, counter-regulatory responses to hypoglycaemia, glucose-stimulated insulin and glucagon release from the pancreas.
How does your brain tell the pancreas and liver what to do?
  …blood glucose levels and hormones, such as insulin and glucagon, are influenced by the autonomic nervous system [ref]. This system …consists of two parts: a sympathetic nervous system which deals with ‘fight or flight’ responses such as stress and a parasympathetic nervous system which deals with ‘rest and digest’ and ‘feed and breed’ responses. This system arises in the brainstem of the brain and is under the control of the hypothalamus. Nerves from the autonomic nervous system innervate almost every organ in the body including the cells and blood vessels of the pancreas and liver. The ‘wandering’ vagal nerve, a key component of the parasympathetic nervous system, is shown to play an important role in this. This nerve is necessary for the brain to influence blood glucose. The autonomic nervous system can influence insulin release, glucagon release, liver glucose output and even the size and number of insulin producing cells in the pancreas [ref]. …Exactly how these nerve fibres regulate hormone release is still being slowly unravelled [ref].

The essay cites references which you may wish to follow up for further information.


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How to look for different transcripts for a protein?
I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein.
However, when I look it up online, there is no clear organized data on different documented isoforms (at least not for the one I am looking for...) (For example, entries at NCBI Protein database do not match with those at ENSEMBL).
It would be great if someone can suggest a more systematic way (or previous such studies) to find out the sequences of different isoforms of a protein.
To elaborate, here the link at ENSEMBL database (9 transcripts, of which 5 are protein coding, of which 2 have identical AAs seq) and here's what I found at NCBI Protein search (4 isoform and a 5th one from literature). It is evident that there are discrepancies between the two.

Are you looking for isoforms or just differential transcripts? Isoforms can be produced from completely separate genes that have undergone duplication at some stage. 2. We need to know what gene you are interested in and in what tissue. Don't be coy. If you find differences between ENSEMBL (no E) and NCBI there must be a reason — both are reputable sources, but may be providing different info. I don't see going to the UCSC browser resolves that. Tell us how the info on the two sites differs and give a link.

I think David's first question bears repeating - are you looking for varying transcripts from the same gene, or related proteins with high sequence homology from different genes?

Hi!

I am looking for varying transcripts from the same gene.
I have also added the links to my search from both the databases. Hope you can see the discrepancy I am facing.
Please let me know if I have missed/misread something here.
Thank you!

I've revised my response to your question, but I think you will find that there is no easy "answer" to it. If you are involved in practical research that depends on your analysis of this question, you are going to have to do some serious reading before investing time and money.

As will be clear from the question and various replies, there are several different repositories for data emerging from the various nucleic acid sequencing projects. The two main gene oriented ones — NCBI and ENSEMBL — are funded by the US government and European goverments, respectively, and share primary sequence data. However they differ in their interpretative focus and the secondary data (often from elsewhere) that they present in combination with the nucleic acid sequences. There are other valuable webs services that are more limited in scope — the UCSC browser (mentioned by Maximillian Press) providing graphical views of several reference genomes. The main protein-oriented repository is UniProt, as @Michael_A mentioned.
The poster is interested in the transcripts for a particular gene (Transmembrane protease serine 3), and the NCBI and ENSEMBL facilities he consulted were, in my opinion, the most appropriate. As he found different transcripts presented by the two facilities, he might follow the suggestion of consulting UniProt, but it transpires that the set of isoforms it presents differ again. (The UCSC browser displays the ENSEMBL set which originate from the GENCODE project.) This is summarized in the table below — three common isoforms, but ones absent from other data repositories.

NCBI
ENSEMBL
UniProt
Size (aa)

NM_024022.4, NP_076927.1 (iso 1)
TMPRSS3-203
P57727 (-1)
454 aa

NM_032404.3, NP_115780.1 (iso 2)
—
P57727-2
327 aa

NM_032405.2, NP_115781.1 (iso 3)
TMPRSS3-201
P57727-3
344 aa

NM_001256317.3, NP_001243246 (iso 4)
TMPRSS3-208
P57727-5
453 aa

—
TMPRSS3-202
—
451 aa

—
—
P57727-4
293 aa

AAT66641.1 (iso 5)
—
P57727-6
538 aa

[NM_024022.3 (= NM_024022.4)]
[TMPRSS3-209 (= 208)]
—
[duplicate]

Why could cause this conflict, and what can one do to resolve it? Transcript data may be obtained for individual genes in specific studies, or in large projects like ENCODE. Whereas I imagine the commonalities probably arise from the larger projects, it seems likely that the smaller ones are represented in the individual unique cases. The reason that this might be so is that the pattern of differential splicing often differs between tissues and at different developmental stages, so that such transcripts might be missed in whole body studies or in studies in which a tissue was not included. In this case uneven coverage of tissues involved in hearing could possibly be the problem. Mistakes can also arise: this is presumably the reason for the two identical transcripts being listed. And it is difficult for NCBI to co-ordinate different submissions — hence the strange situation of the missing transcript map for ‘isoform 5’.
So there can be no general answer as to which data repository is the “best” or the one to “believe”. One has to find where the evidence is for a particular transcript, i.e. identify the original papers, read them, and make one’s own decisions as a scientist.

This is almost a complete revision of my previous answer. Apologies, but I think it provides a more balanced view of how things are. However, anyone who voted for the previous one but doesn't like this one should retract their vote.

I would suggest using the UCSC genome browser for the organism in question (assuming that they have your organism loaded), and use either the GUI or otherwise to pull out the transcripts you are interested in after searching the gene. For example, here is a view of transcripts for the CFTR gene in humans.
You can click on the transcripts in the cartoon, leading you to a page such as this that has a lot of information.

As you are interested in protein coding transcripts it would be worth using a protein database. You can search for curated protein isoforms in Uniprot by limiting your search to "UniProtKB" + the species. Searching for "TMPRSS3" shows 6 protein isoforms. The cross-references section of the page provides links to the RNA transcripts for each isoform in a various DBs. A quick scan confirms that there are direct links to transcripts for 4 of the isoforms; if you check a little closer it should also provide a direct link to the other 2.

I think people more or less expect to do BLAST searches, and also to check the literature when it's available, when they really hope to find all potential splice forms that are currently known.  Deciding when a transcript is genuine mRNA rather than partially spliced RNA from the nucleus can be tricky, and may depend on the specifics of how the RNA was isolated (e.g. polysomes vs. whole tissue homogenate; though the difference, while real, seems to be less than expected).  Also, there's a philosophical problem: some of the transcripts from your first link barely overlap with one another, and I don't think it's uncommon to look at a stretch of genome with exons ABCDE where AC, DE, and BCDE are all possible splice products - are they "the same" gene?


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Have humans finished evolving?
I thought that massive changes among organisms are over long periods of time. This is caused by, to my knowledge:

Evolutionary pressure
Natural/artificial selection
Mutations
Genetic drift

Will mutations be the only factor in human change? Will humans change at all over a long time?

Issue in your introduction

I thought that massive changes among organisms are over long periods of time.

Actually, some evolutionary events can happen on a very short time scale. A single mutation can have a massive impact on the phenotype of an individual (see for example Doebley 2004). If this new phenotype has much higher fitness, then the mutation might spread over the whole population in a matter of weeks (typically if the population is not too large, without barriers to gene flow and more importantly if the generation time is short).

This is caused by, to my knowledge:

Evolutionary pressure

Natural/artificial selection

Non-detrimental mutations

The term evolutionary pressure typically encompass natural and artificial selection, mutations (regardless of their mutational effect, that is regardless of whether they are beneficial or detrimental) and other processes that you don't mention (such as genetic drift for example; you have now edited your post to include drift).
Answer to your questions

Will mutations be the only factor in human change?

By "human change", I will assume you mean "human evolution". The answer is: no, mutations are not the only process that leads to human evolution. All standard evolutionary processes are at play in humans as they are in other species. You might want to have a look at the posts Human Evolution in Modern Times and How is evolution possible in contemporary humans?.

Will humans change at all over a long time?

Yes, humans are currently (and will continue to do so in the future) evolving. Again, you might want to have a look at the linked posts.
Want to know more?
Your questions are quite introductory and show a number of misunderstanding you have about evolution. I would recommend having a quick look at Understanding Evolution by UC Berkeley which is a very introductory course to evolutionary biology that is fast and easy to follow.

Great references and thanks for the correction

@Adamawesome4 My pleasure! I added a small comment on the very first sentence too.

I disagree that humans will continue to change over time - evolve, yes, of course! But as the population grows and travel increases, there is no Galapagos-style isolation; the human genome is "averaging out" and similar traits may eventually dominate the species. Additionally "survival of the fittest" has been heavily reduced due to modern medicine - how can traits be filtered out?

@Zxyrra You can't say humans won't change over time but they will evolve as evolution is defined as being a change over time. Potential absence of complete reproductive barrier does not change anything to the fact that all standard evolutionary pressures exist. Medicine does reduce selection pressure for sure but selection pressures still exist. Plenty of examples exist, just have a look at the linked posts. You should have a look at an intro course to evolutionary biology and to the posts I link in my answer.

In sexed organisms, evolution is largely due to errors during chromosome duplication, cutting/copying/pasting/swapping/shortening/duplicating full genes sections. It is a way more efficient and fast way to evolve, since mixing sentences have more chances to make sense than mixing letters.
Many fast local evolutions can be seen: for instance, Sickle-cell_disease is favored a lot in some part of Africa because it happens to protect against malaria. At the scale of a few centuries, human height is growing, women pelvis is shrinking, etc.  At the scale of a few millenniums, some human can digest milk while the others can't. The population at altitude got different adaptation to multiply the amount of red blood cells. etc.

You first paragraph is very misleading (or even wrong). You should come up with a citation to support that rate of evolution (are you referring to phenotypic evolution I would assume but that was left unclear in your answer) is mainly caused by recombination. In any way, linkage disequilibrium gets away pretty quickly and therefore this first paragraph makes little sense. For your second paragraph, you could just link to other posts (see my answer) which offer much more thorough explanations of the examples you mention.

This answer is flat-out wrong. Chromosome duplication usually causes severe health problems. Random mutation edits to human cells usually either breaks the cells, causes malfunctions, or produces oncogenes that either cause cancer or predispose the cell's lineage to become cancerous in the future. There's a ton of research out there and many lists of indels, point mutations, genetic fusions, translocations, and duplications (copy number mutations) associated with cancer.

The genes associated with people who have more surviving and reproducing children will be more prevalent in the future. If you live in a multicultural society where different ethnic groups have different amounts of children you can get a perception of how the humans in your country will evolve over time. Also if you live in a country where there is a huge influx of people who are genetically different from the people who already live there, that will have a serious impact on the short-term change. But basically, if you want to get a hunch of where humans are evolving where you live, you can have a look at the people producing offspring and try to find out if they are different somehow in their genetic composition compared to the population at large. If stupid people are having more children, people will be dumber, if taller people are having more children, people will be taller etc.


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Does a mutation in the sense strand of a particular gene affect the polypeptide formed?

Recently, I came across this picture which represents the DNA sense strand of a gene.
The ‘Altered’ picture shows a (frameshift) mutation in the nucleotide sequence in which a T base is deleted.
The sense strand is not transcribed — the anti-sense strand is transcribed. So why is there a change in the amino acids of the translation product when a mutation occurs in the sense strand, if the sense strand does not produce amino acids? Does a mutation in the sense strand change the nucleotide sequence of the transcribed sense strand?

I have edited your question so that it uses only unambiguous strand designations as discussed in my answer to your recent related question.

We’re doing it for the children!
The basic misconception in this question is that the important effects of mutations are seen in the cell that undergoes mutation. This is not the case. So focusing on the whether the strand that receives a mutation is the non-transcribed, sense, strand or the transcribed (anti-sense) strand is of little relevance.

What is important is whether or not the mutation is passed on to the progeny.

Don’t we have a life too?
Why isn’t it important? Consider a mutation occurring in a single E. coli cell in a population of millions of E. coli, or a single muscle cell in a human muscle. Even if there is a mutation in the strand that is transcribed into mRNA and translated into protein, the change in that one cell will not have a significant effect on the overall population.
The birds and the bees
The way in which a mutation — on sense or anti-sense strand — can affect a population of bacterial cells or whole tissue in an organism is:

(For bacteria or in tumour cells) if the mutation is passed on to some of progeny, which then have a selective advantage so that they can outgrow the wild-type population
(For normal tissues in animals) if the mutation is passed on to the progeny through the germ line so that it is present in all (e.g. muscle) cells

Still harking on about sex (Yawn)
The key point is easier to explain with bacteria. Consider a simplistic situation in which a mutation occurs on one strand (and is not corrected by the DNA-repair mechanisms). Before the cells divide into two daughter cells the double-stranded DNA replicates — each strand is the template for a complementary strand in a daughter double-stranded DNA. One cell will have the daughter dsDNA (double-stranded DNA) copied from the unmutated strand and the other will have the daughter dsDNA copied from the mutated strand.

In the case of the dsDNA copied from the mutated strand, both
  strands will clearly carry the mutation, so it is irrelevant whether
  the mutated strand in the parent was sense or anti-sense.

If the mutation is advantageous these cells will grow and divide and out-compete the other bacteria in the population.
A similar explanation holds for tumour cells in a differentiated animal tissue.
In the case of germ-line cells in animal tissues the situation is slightly different — the mutation either will be present or absent in both strands of the dsDNA in the fertilized egg, and so will affect all of the cells in the tissues of the progeny in which it is expressed.

Thank a lot. The mutation doesn't always occur in the original DNA strands, right? Can there be mistakes in the replicating strand? For example, if there is an A nucleotide on one original DNA strand, can the replicating strand accidentally bring a C? Not sure if the term replicating strand is correct.

I'm not quite sure what you mean. Both strands are replicated in ds genomes. There are several different types of mutation with different mechanisms and consequences. I suggest you look at the Nature Scitable article which covers them quite well.

Does a mutation in the coding strand change the base sequence of the template strand?

The DNA molecule is composed of two paired, complementary strands of DNA which--by definition--must be paired and complementary. A deletion of a base on one strand would be replicated such that the new DNA molecule would be deficient at that position on both strands. Here's a nice summary that also includes animations.
And, if you are instead asking whether there are ever exceptions to this very basic rule of molecular biology, then yes, so-called "bulged bases" have been reported (e.g.here) but they are still considered anomalous.

Sorry, but what does deficient mean in a biological sense?

@ChristopherU'Ren — It has no special biological meaning. DavidR clearly meant "deficient in a base" in the sense of lacking or missing a base — the base that was deleted in the first strand.


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What happens to the precursor protein's signal sequence after it is cleaved?
Where does this signal sequence "go" after it has been cleaved by signal peptidase and what is its next function?

Doesn't that entirely depend on the protein? This is too broad.

I think specification of the question (example protein perhaps) may indeed help.

For example, a transmembrane protein in the ER with a N-terminal signal sequence. Are there molecules or proteins that transport the signal to other precursor proteins or does it remain in the membrane of the ER?

After cleavage, the signal sequence is generally thought to be degraded by intramembrane proteases (since it is embedded in the endoplasmic reticulum membrane). For at least some proteins, the signal sequence is further processed and released into the cytoplasm or ER lumen.
Martoglio B. 2003. Intramembrane proteolysis and post-targeting functions of signal peptides. Biochem Soc Trans 31:1243-1247

When translocation continues, the signal sequence’s c-region appears in the ER lumen and becomes accessible to signal peptidase, which cleaves the signal sequence from the pre-protein. The latter is further translocated into the ER lumen, while the liberated signal peptide is usually not detected in assay systems, implying rapid degradation. In a cell-free in vitro system with ER membranes from canine pancreas, we reported several years ago that after cleavage by signal peptidase, the liberated signal peptide is transiently embedded in the lipid bilayer and undergoes further processing to be released from the membrane.

The activity of released signal sequences is not entirely known and only partially characterized for some proteins. The following review discusses some functions of signal peptides after cleavage:
Martoglio B, Dobberstein B. 1998. Signal sequences: more than just greasy peptides. Trends Cell Bio 8(10):410-415
The signal peptide of bovine preprolactin and HIV gp160 can bind calmodulin.

…the signal sequence of bovine preprolactin, which consists of 30 amino acid residues, is cleaved by signal peptidase and then further processed by an unknown signal peptide peptidase (SPPase; Fig. 4) … This signal peptide fragment resides initially in the membrane and, after a chase period, is released into the cytosol. Once in the cytosol, the signal peptide fragment binds to calmodulin in a Ca2+-dependent manner. A signal peptide fragment derived from HIV-1 gp160 also binds to calmodulin when it is released into the cytosol … With their n-regions having the potential to form a basic amphiphilic α-helix and their hydrophobic C-terminal region, they are similar to other calmodulin-binding domains. Calmodulin is a small, acidic protein involved in the regulation of many cellular processes controlled by Ca2+-dependent signalling pathways. It is possible that binding of signal peptide fragments to calmodulin influences Ca2+/calmodulin-dependent cellular signal-transduction pathways. Further studies are required to elucidate the physiological consequences of interactions between signal peptide fragments and calmodulin.

The signal peptides of MHC class I proteins are presented to NK cells by MHC-I (with HLA-E alpha chain). This allows monitoring of MHC-I expression, which is often disrupted in virally infected or cancerous cells.

Peptides presented by classical MHC class I molecules represent the broad spectrum of peptides generated by the proteasome. In contrast to this general use of peptides, only a very specific signal peptide fragment is presented by so-called nonclassical MHC class I molecules (HLA-E in human). These molecules monitor the presence of classical MHC class I molecules by presenting a signal peptide fragment derived from HLA-A, -B or -C to natural killer (NK) cells (Fig. 5b). NK cells destroy cells unable to activate inhibitory receptors specific for MHC class I molecules.

This book section discusses the function of signal peptides in some viruses:
Kapp K, Schrempf S, Lemberg MK, Dobberstein B. 2009. Post-targeting functions of signal peptides. In: Protein Transport into the Endoplasmic Reticulum, Zimmermann R.


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What is the proper naming of Aminoacyl-tRNAs?
I want to refer to an aminoacyl-tRNA with the anticodon 3'-UAC-5' that is charged with methionine. What is the proper name for this molecule?

I don't work with tRNA, but the convention I was taught for such a tRNA was $Met-tRNA^{Met}$. I don't know of any standard nomenclature incorporating the anticodon, which is not to say that there isn't any.

@canadianer —There is, but it is only adequate to a point, and the particular example raises one type of complication. I'll post in detail tomorrow if no one else has.

@David, I would be very much interested in your explanation.

OK. A bit obsessive, but many years ago I was responsible for a chapter on protein synthesis in a text book. The lack of a standard nomenclature (unless I have missed something) reflects both the smaller number of people working on RNA, rather than DNA, today, and the large number of tRNA genes in eukaryotes.

Minimal Answer
If all you want to do is exactly what you have specified, on the basis of a 2013 paper on the human tRNAs identified in the 1000 genes project, the format would seem to be:

Met-tRNAMet(CAU)
or
methionyl-tRNAMet(CAU)

Notice that the anticodon is written in the 5ʹ→3ʹ direction, as in the paper, and that Met is capitalized, as recommended in this IUPAC publication of 1970 (sic).
I do have reservations about this as I have been unable to find tRNA nomenclature recommendations (not even in RNA journals), and the paper concerns genes (although a different nomenclature is used there — transfer RNA-Met (CAT) 1-1 etc.). Furthermore, my recommendation to use CAU, rather than CAT (used in the quoted paper) is only based on my experience of scientists who work on tRNA, rather than their genes would use (although it can be justified in a broader context: see below).
A variation on this is to be found in a 2017 paper:
$\mathrm{Met\text{-}tRNA^{Met}{}_{CAU}}$
So I suspect there is no ‘official’ nomenclature.
Problems in giving a more comprehensive answer
The answer above is adequate in certain circumstances, e.g. in differentiating in a paper or a lecture between two species (e.g. with different anticodons, although this does not occur with methionine). The problems occur when you wish to distinguish one tRNA from all other tRNAs present in a cell or encoded in a genome. I list some potential ambiguities:

Initiating v. elongating Met-tRNAs (in the case cited)
Anticodons containing modified bases
Distinct tRNAs with the same amino acid specificity and the same anticodon
Cytoplasmic v. mitochondrial tRNAs in eukaryotes
tRNAs from different species

Possible solutions
Different Met-tRNAs
This is often most important as both initiating and elongating Met-tRNAs have the same anticodon but are structurally and functionally distinct. Differentiation is generally done by way of a subscript: originally ‘f’ or ‘m’, respectively, but for eukaryotes now generally ‘i’ or no subscript:
$\mathrm{Met\text{-}tRNA^{met}_f} \quad or \quad \mathrm{Met\text{-}tRNA^{met}_m}$
$\mathrm{Met\text{-}tRNA^{met}_i} \quad or \quad \mathrm{Met\text{-}tRNA^{met}}$
Anticodons containing modified bases
It was observed early on that the anticodons of tRNA contained modified bases — e.g. inosine, which had particular patterns of ‘wobble’ codon recognition (see my answer to another SE question). Therefore, in many cases it would be important to specifiy these — which is why I recommend using U, rather than T, e.g.

Tyr-tRNATyr(GΨA)

tRNAs with same anticodon
Gene duplication often results in tRNAs with the same specificity and the same anticodon. In some cases the sequences are identical, so there is no way of distinguishing them, but in other cases mutations will occur that do not change the function. To distinguish such species with a single base (here at position 40) the 1000 genomes paper uses the following style:

(G40) tRNAArg(GCA)
or
(C40) tRNAArg(GCA)

At the genetic level arbitrary numbering is used for human tRNAs, e.g.

transfer RNA-Met (CAT) 1-1
transfer RNA-Met (CAT) 1-2

whereas in Drosophila a variant of this style is used, e.g.

transfer RNA:Methionine-CAT 1-1
transfer RNA:Methionine-CAT 1-2

Cytoplasmic v. mitochondrial tRNAs
It is important to remember that the mitochondria of eukaryotes contain their own set of tRNAs, and to distinguish these if necessary by a preceeding ‘mitochondrial’. In Drosophila the symbol would be ‘mt:tRNA:Met-CAT’, and the name ‘mitochondrial transfer RNA:Methionine-CAT’.
Species
Obviously, one can specify the species by a preceeding adjective. I mention this to point out that set of tRNAs is different for different species.

Good answer. I typeset your Word equations with LaTeX and changed methionine-tRNA to methionyl-tRNA based on the recommendations of the 1970 IUPAC publication.

@canadianer — Thanks. One becomes so concerned with the difficult things that one doesn't notice mistakes in the simple ones.

@David, This is great. I do not work with RNA except when I teach my biology students about transcription and translation. I want them to have a consistent naming system when I tell them about different tRNA molecules with their respective amino acid attached.

I think for the initiator, it is at least quite common to say tRNA(superscript)fMet in bacteria, rolling the indication into the AA part. It seems to be the same situation for tRNA^(iMet) in eukaryotes, at least within the nomenclature of GtRNAdb.

@MingyeWang — Thank you for this. The genomic tRNA database you mention did not exist when I wrote my original answer, but it is easy to see why they adopted this style: database storage of text with both subscript and superscript at the same level is more difficult (for users as well as programers) than a single superscript. For academic publications and textbooks I personally would advocate the more traditional form as it does not indicate that the methionine is actually formylated (which it may not be in some bacteria), and iMet is chemical nonsense. But there is no standard.


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What structures (i.e. organs) are suspended by tensile forces?
In several areas of biomechanical literature I have read, the concept of "tensegrity" has arisen. Definitions are as follows:

“The integrity of a stable structure balanced by continuous structural
  members (cables) in tension and discontinuous structural members
  (struts) in compression.” (Zhang, 1)

and then

“A tensegrity structure is recognized by its distinct set of
  compression elements (struts) that appear to float within a network of
  tensioned cables.” (Scarr)

I am highly skeptical about its applicability. Some authors (e.g. Evan Osar) suggest that tensegrity can be applied to the spine. However, the spine fundamentally does not fit the definitions provided above because its non-tensile components are connected / touching. Tensegrity involves floating
My Question:
Are there any areas of the body that would potentially qualify under this definition of tensegrity?
One example I can think of is the suspension of organs in the body, but I am unsure about this.

Sources:
Osar, Evan. Corrective Exercise Solutions to Common Shoulder and Hip Dysfunction. BookBaby, 2012.
Scarr, Graham. Biotensegrity: The Structural Basis of Life. Handspring Publishing, United Kingdom, 2014.
Zhang, Jing Yao, and Makoto Ohsaki. Tensegrity structures: form, stability, and symmetry. Vol. 6. Springer, 2015.

Do you really mean suspended in air? Because there aren't structures suspended into the air-filled spaces in the body.


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What is the counter-reponse to a sound stimulus?
I am slightly confused on finding out what is the counter-response because of a stimulus.
For example, if we hear a sound, I believe the sound waves are the stimuli? So is the counter-response the vibration of our eardrum or the sensation of hearing the sound?

A tittle should be intelligible on its own. "In this case" is obviously not. Next time put in the effort to make it so.

Is this question one based on clarification of terminology, or rather one on the physiology of hearing? Either way, the question is unclear and needs clarification. E.g., what else than sound waves would be the stimulus for audition? Photons? EM waves? And what is a counter-response? This terminology is akin to Newtonian physics. What is your question?

All stimuli do not generate reactions. It is the CNS that decides if a reaction has to be generated on receiving the information about a stimulus.

External stimuli are capable of producing systemic responses throughout the body, as in the fight-or-flight response. In order for a stimulus to be detected with high probability, its level must exceed the absolute threshold; if a signal does reach threshold, the information is transmitted to the central nervous system (CNS), where it is integrated and a decision on how to react is made. Although stimuli commonly cause the body to respond, it is the CNS that finally determines whether a signal causes a reaction or not.

From Wikipedia
The changes that occur inside ear,vibration of tympanum, movement of ear ossicles and all are responses to the stimulus (the mentioned two are mechanical responses) to transmit the information about the stimulus(sound) to the brain.
If the brain finds out that the sound is actually a noise then it would instruct the body (limbs for example) to move away from the source of the sound. This is then called the reaction.
If the sound is not that loud, i.e. not potentially damaging to the ears then the CNS does not instruct to retreat.


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Do ribosomes read mRNA?
So I understand that tRNA bonds to a codon (with an anticodon) in the translation process. I read in my biology textbook that the ribosomes "read" the mRNA strand.
Why do the ribosomes need to read the mRNA strand? Are the ribosomes able to intepret the message and bring the correct anticodon to it? Or is the main function of the ribosomes just to join amino acids to make polypeptides? I'm just confused why the ribosomes read the mRNA strand when it seems like there is no need to.

Welcome to SE Biology. As your question appears to be just a misunderstanding of rather loose language I am giving a brief response in a comment and pointing you to an online source where you can find more detail. Yes, it is the anticodon of the tRNA that decodes the codons in the mRNA, so strictly speaking it is the tRNA that reads the mRNA (no need for the word "strand"). However the ribosome is required for this complex process, and it is where the tRNA, mRNA and other components bind, so the author is expressing this idea loosely

Since ribosomes act as a catalyst I would assume the reaction could happen without them but is would be many orders of magnitude slower, and likely to produce erroneous results of fail halfway. Its not a bad question but it could be worded clearer. "can it occur without ribosomes" would be a good foundation question.

@John — Protein synthesis is not a single reaction. Whereas peptide bond formation could occur at a slow rate without ribosomes, the other requirement to hydrogen bond to the mRNA at the same time makes that kinetically very difficult, and then you have to start at a particular place on the mRNA and continue. Yes it must have evolved from a simpler system, but no, it's very different from a simple catalyst. And don't encourage people to ask "could" questions — they generally yield subjective answers — we need "can" questions that are answerable.

@David Hence my statement that the question could be reworded as can the reaction occur without ribosomes. Which should be established before the above questions. Also I never implied ribosomes were not important, just that exploring how the system could function without them would be a better way to answer the OP's unfocused questions. For instance one thing we know for instance is that many mismatches in mRNA codon binding is because the RNA molecules are not rigid and can distort to form a wider range of binding, one function of ribosomes may be to limit such distortion.

@John — OK. But I think the poster can answer his question by reading a better account of ribosomal protein synthesis. I neglected to mention that your question is answered in a way by non-ribosomal synthesis of cyclic peptides by certain bacteria. Any new question would need checking that it hadn't been covered previously.

The first two sentences of the Wikipedia Ribosome article say:

The ribosome... serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules.

Slightly later, in the Overview section it says:

Ribosomes can bind to a messenger RNA chain and use its sequence for determining the correct sequence of amino acids for generating a given protein. Amino acids are selected, collected, and carried to the ribosome by transfer RNA (tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA chain. It is during this binding that the correct translation of nucleic acid sequence to amino acid sequence occurs.

And it then tells us "The attached amino acids are then linked together by another part of the ribosome."
So, the function of the ribosome is to make sure each codon of the mRNA is matched up with the correct tRNA, and then to catalyze the linkage of the associated amino acid to the growing chain of the protein being built.