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Genes and Intelligence
Assuming that intelligence has a genetic component,
• do we know which genes contribute to it?
and, if so,
• can we predict intelligence from genomic analysis?

I'm voting to close this question as off-topic because it concerns a construct — Genetic IQ — that has no meaning, certainly no biological meaning.

@David Questions about predicting phenotypes from genotypes are perfectly valid and on-topic questions about biology.

@Eff — Remind me what "phenotype" the poster was asking about.

@David IQ. If you read this question--with respect for the fact that laymen will have trouble formulating their questions in very precise terms--OP is asking whether we can predict a person's IQ from their genotype. This is a problem actual biologists (specifically, geneticists) work on, so clearly it is a problem that is relevant to biologists.

@Eff — This is not a site for laymen, but for "biology researchers, academics, and students". My whole point was that the "phenotype" in the question was something referred to as "Genetic IQ" which is meaningless. Further IQ is not a phenotype and by its nature cannot be measured at birth. Intelligence is different. You appear to think that the question means "Assuming that intelligence has a genetic component, do we know which genes contribute to it, and can we predict intelligence from genomic analysis?", so I have edited it, but it is a duplicate.

Please cite your sources when you say that "IQ is not a phenotype and by its nature cannot be measured at birth". According to most definitions of the word "phenotype", it includes not only "structural" traits observable at birth, but also developmental processes, biochemical and physiological properties, behavior, and the products of behavior.

A few words on genomic prediction
No complex trait is 100% heritable, hence no prediction based entirely on DNA would ever be perfect. With that said, predictive genomics is progressing at a quite amazing rate right now. So while predictions can be nowhere near perfect, it is getting possible to make DNA predictions that correlate substantially with observed values.
The genes that correlate with phenotypic differences are found using genome-wide association studies (GWAS). The total effects are then aggregated up to what is called a polygenic score.
A success story --  Height
Height is highly heritable, meaning that much of the phenotypic variance (although not 100%) is due to genetic differences. Height is also highly polygenic -- it's a trait influenced by many genes, each of small effect.
Many variants that correlate with height have now been found. Polygenic scores of height correlate higher than ~0.60 with observed height. DNA predictions are generally within a few centimeters of true height (Lello, Avery, Tellier, Vazquez, de los Campos, Hsu, 2018). According to an interview with Stephen Hsu, one of the authors of this paper and co-founder of the company Genomic Prediction, they can correctly predict the height ordering of siblings within the same family 80-90% of the time (source). So based purely on DNA, can we say which of two siblings are going to be taller than the other? Not perfectly, but with decent reliably, yes.
This is about as good as predictions of complex traits can be based on current methods. There are a few principal reasons that correlations are not higher (even though it is quite impressive already in its own right). First, as I said, complex traits are not 100% heritable and therefore predictions are not expected to ever be perfect. Second, current GWAS are typically based on SNPs which are common gene variants. Rarer gene variants are expected to contribute to the variance and their effects are still needed to be uncovered. Third, only additive effects are taken into account, not gene-by-gene interactions.
Genetic IQ Prediction?
IQ, like height, is a heritable trait and is highly polygenic.
There are several approaches to finding gene variants correlated with IQ, however they can broadly be categorized into two. The most obvious approach is to simply give people intelligence tests and get their DNA. The problem with this is that it is difficult to get large samples with good intelligence tests. When this approach is used, usually a very short (say, 2 min) intelligence test is used. The second approach is to use a proxy phenotype. With this approach, the variable years of educational attainment has been used to good success, and has been shown to have a high genetic correlation with intelligence ($r_g \approx 0.7$).
Many variants that are associated with intelligence or educational attainment have been found, see e.g. (Lee et al, 2018; Savage et al, 2018). While many variants are known, IQ is not as well understood as height, and current SNP predictors correlate about ~0.3 with observed IQ (See e.g. Allegrini et al, 2018). This correlation is bound to increase in the coming few years.
Further Information
If you want a simple introduction to what can be read from the genome so far, there is a TED talk on this subject, TED2016: How to read a genome and build a human being. Although, major improvements have already been made in the years since 2016. For anyone that is more interested in the mathematical techniques used for prediction and the underlying theory, I recommend this talk by Stephen Hsu if you're further interested in genomic prediction of complex traits. I also recommend reading this review by Robert Plomin and Sophie von Stumm to get an easily understandable overview of the current state of knowledge on the subject.
References
Lello, Avery, Tellier, Vazquez, de los Campus, Hsu (2018). Accurate Genomic Prediction of Human Height. DOI: https://doi.org/10.1534/genetics.118.301267
Marty Nemko (2018). The Future of In-Vitro Fertilization and Gene Editing. Psychology Today Link.
 Lee, ..., Cesarini (2018). Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. DOI: https://doi.org/10.1038/s41588-018-0147-3
Savage, ..., Posthuma (2018). Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence. DOI: https://doi.org/10.1038/s41588-018-0152-6
Allegrini, Selzam, Rimfeld, von Stumm, Pingault, Plomin (2018). Genomic prediction of cognitive traits in childhood and adolescence. DOI: https://doi.org/10.1101/418210
Sabatini (2016). How to read a genome and build a human being. TED2016 Link to Talk.
Hsu (2018). Genomic Prediction of Complex Traits. Youtube Link to Talk.
Plomin, von Stumm (2018). The new genetics of intelligence. DOI: https://doi.org/10.1038/nrg.2017.104

This answer is clearly better than mine! +1

IQ typically has a relatively high heritability (see this post). Please have a look at this post to understand the concept of heritability.
In order to know what loci (QTL as the trait of interest is quantitative) are associated with a specific trait of interest, one must perform a GWAS The studies listed in the first pots linked above do not involve GWAS but only some kind of parent-offspring regression or twin studies to estimate heritability. From these studies, one cannot infer anything about a person's IQ from its genome.
GWAS studies on IQ do exist though (reviewed in Pfiffer 2015). It would be possible from one to make predictions and compute confidence intervals as well of someone's intelligence based on their genome, yes. I doubt anyone ever wrote such algorithm though. Without having such algorithm in front of one's eyes, it is impossible to tell, whether the confidence intervals are going to be very wide or very narrow though.

Why do you say you would need Bayesian statistics to get predictions?

To get a confidence interval at least. Or maybe one could use resampling but then you need to re compute the GWAS plenty of time which should take forever. I did not think this through though but it does not sound like easy statistics to me. The details of how to compute this confidence interval is not really on topic with the question but if you have some thoughts, I'll be happy to hear them for curiosity.

I was mostly just curious. I didn't think that Bayesian GWAS was done that much, because of the slowness in MCMC sampling vs. fast matrix algebra for "frequentist" GWAS. The traditional way will yield intervals as well, but probably too wide.

The Pfiffer paper compares IQ and genetic traits between distinct countries and ethnicities rather than IQ for single people as outlined in question above.

In order to make predictions for a single individual, you need to know the association between loci and the trait of interest through a GWAS. None of the cited paper offer an algorithm to make such prediction from a single person but one who would want to develop such algorithms will need access to this type of GWAS.

No, because the trait you describe does not exist
Your question betrays a common misunderstanding of how genetics and the environment interact in order to produce complex phenotypes. In fact, every biological trait is 100% genetic and 100% environmental. Don't believe me? Try teaching algebra to your cat, or see what height someone is after you've dropped them into the sun.
The only sense in which you have an "IQ you were born with" is the measurable IQ of a newborn child which I'm guessing this comes out as 0. Instead your IQ is a result of continuous interaction between genes and environment. You can say that at the end of process, across the population, 70% (say) of observed variation is explicable by genetic variation but this does not mean that you got 70 points of IQ from your genes and 30 points from the environment. The whole score is attributable to an interaction between the two. There is no "null" environment in which you would observe pure genetics, nor does it follow that increasing the range of environments encountered across your sample will increase the proportion of variation explicable by the environment. A gene that has no effect on IQ in one environment may have a marked effect in a different environment and you'd only discover this by varying the environment so both are encountered.
So, there is no trait "genetic IQ" to predict from someone's DNA, even if we had perfect knowledge of the link between genes and intelligence. Which we don't.

What I meant by "genetic IQ" was "What a person's IQ would be assuming optimal environmental conditions".

@Thomas That's not a meaningful concept.

@Thomas To expand on that: there is no way of knowing what the optimal environmental conditions would be, or that there actually exists a peak environment, and if it exists it will almost certainly be completely different for different backgrounds.

I notice that the question was substantially edited some six months after I posted this answer: the original asked "is it possible to tell a person's genetic IQ (the IQ he/she was born with) just by examining his/her DNA?"

IQ is pretty much like muscle strength, in the sense that you may have the right combination of genes that would give you extra strong muscles but the environmental factors do play an essential role as well.
Nutrition, training etc will have a profound effect on the development of your muscles. You cannot predict the effect a priori.
For IQ, it is the same thing. On one extreme you may have genetically-linked developmental diseases, physically impairing the normal brain functions, i/e/ negatively affects your IQ.
In most of the cases however, the effects of genetics on IQ is shadowed by the actual "brain training" you get during your life, by nutrition, and by other environmental factors.
So, yes, IQ is influenced by the underlying genetics.
Yes, in some extreme cases you can predict a very strong detrimental effect of some genes/mutations on the IQ.
For most of the cases, it's very hard to predict and genetics alone would not be enough to do so.


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Does the brain consume more energy when a person is stressed or anxious
When a person is anxious or stressed or suffering from chronic depression, it is observed that the person is usually tired.
Is there there a connection between fatigue and racing thoughts/obsessions.
Also I want to know what damage can anxiety do to brain and body over time.

The tiredness associated with depression/stress is not due to the 'brain power' increasing but due to a change in what parts of the brain are active and/or disrupted sleep. Anxiety can cause issues to the brain and body over time.
Brain power is relatively constant
For the average adult in resting state the brain consumes about 20% of the body's energy. It has been shown that the brain requires about as much energy at night when you are asleep as during the day. The increase of energy for 'hard thinking' is about 8% which is very little compared to the baseline usage (leg muscles can have a 300-400% increase when walking compared to sitting).
See this paper for more analysis.
Tiredness and Mental Health
Depression affects neurotransmitters associated with alertness and reward systems thus making you feel less awake, less motivated, and more tired even if you might have sufficient sleep. However depression and anxiety often also lead to disrupted sleep (trouble falling asleep, nightmares/poor quality sleep, waking up too early etc). This would lead to a feeling of constant fatigue. Unfortunately, the feeling of fatigue can also worsen feelings of depression and anxiety though it is often not the root cause of depression.
Effects of Anxiety Over Time
Repeated activation of the stress response (a cascade of stress hormones colloquially known as the 'fight-or-flight' response) takes a toll on the body. Research suggests that chronic stress contributes to high blood pressure, cardiovascular disease, and causes brain changes (including differences in the volume of gray matter versus white matter, as well as the size and connectivity of the amygdala paper) that may contribute to anxiety, depression, and addiction. Preliminary research also suggests that chronic stress may also contribute to obesity, both through direct mechanisms (causing people to eat more) or indirectly (decreasing sleep and exercise). Chronic stress keeps levels of cortisol in the body high.
Source
Another important factor is the effect of stress on the cortisol levels.
Stress leads to an increased release of the steroid hormon cortisol, which can lead to reduced bone formation, favoring long-term development of osteoporosis (progressive bone disease) source.
It transports potassium out of cells in exchange for an equal number of sodium ions. This can trigger the hyperkalemia of metabolic shock from surgery. Cortisol also reduces calcium absorption in the intestine source. Cortisol down-regulates the synthesis of collagen source.
Sustained stress can lead to high levels of circulating cortisol (regarded as one of the more important of the several "stress hormones"). Such levels may result in an allostatic load,which can lead to various physical modifications in the body's regulatory networks source.

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Why magnesium ion is needed for activity of G-proteins?
I was studying about G-protein coupled signaling sysytem, somewhere they have mentioned about need of Mg$^{2+}$ for acticty of G-protein and related it to increase of cyclic AMP production. On further reading I came to know that the said ion is related to GTPase activity of G-protein, but how does it relate to incresed cyclic AMP production?

Welcome to SE Biology. Please take the Tour and read about asking questions here. You will find that you are expected to do some research before posting. Search for “role of magnesium ions in enzyme reactions” to find the answer to this basic biochemistry question. (And please pay attention to capitalisation.)

You will find the basic answer in my response to a question on the role of magnesium in ATP reactions. The situation for GTP is the same. It has nothing specific to do with G proteins.

Ion can change secondary structure of an enzyme. Magnesium ion is coordinated within certain domains (for example, EF-hand motif) and makes them more ordered. Usually it happens via hydrophilic shell of residues embedded into a hydrophobic one (https://www.pnas.org/content/87/15/5648).
You can reverse it by adding a chelator (EDTA, for example) and protein is more disordered which can affect it's activity.

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Why do bacteria adapt quickly to antibiotics but not to much more common threats?
People cook food all the time, why don't common bacteria adapt to extreme heat? It's winter in either hemisphere every year, why don't common bacteria adapt to extreme cold? People use soap or spray cleaners, why don't bacteria adapt to those chemicals?
Why is it specifically only antibiotics that bacteria adapt to so quickly?

Can you provide a source for this claim? Because we have bacteria living at extreme temperatures and even in the detergents of NASA clean rooms. I don't see the point of your question.

Usually you don't cite common knowledge. By this point it's common knowledge that
A: different bacteria have grown a resistance to antibiotics in a matter of years, unless every news outlet and every university in the world is somehow lying for no reason,
B: The first known life was as such for hundreds of millions of years and therefore couldn't have possessed other adaptions except over only a much longer time.
Ergo it is a very basic, common-sense deduction that adaptions to antibiotics happened much faster than adaptions to extreme temperatures and extreme pH imbalances.

You claim, that bacteria don't adapt to extreme high or low temperatures or detergents - but they do.

Yet another shameless strawman, now you're reported for trolling. Nowhere did I say they don't, I only said it has taken longer based on very basic common sense knowledge. I'm guessing you believe the Earth is flat too?

"why don't common bacteria adapt to extreme heat/cold?", "why don't bacteria adapt to those chemicals?" - sorry, I was taking your questions literally..

Unfortunately you never read the title at all, literally or figuratively, nor the last sentence.

ok, let's try again: resistance to heat and detergents is a problem in food processing (https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2672.2011.04943.x, https://www.liebertpub.com/doi/abs/10.1089/10766290260469679) - I didn't know if anyone has ever looked into the rate of adaptation in isolation as compared to antibiotic resistance. That's why I was asking, if you came across a claim/study/number that quantifies the term "quickly". Many people here ask questions about something they have read elsewhere and it can be helpful to know the source.

Antibiotics usually target a single protein (most commonly components of the ribosome machinery). If you have a large population of bacteria, there are bound to be cells with mutations in the gene encoding for the target of the antibiotic that render the antibiotic ineffective. Microbes also have drug efflux systems that can help with resistance to antibiotics. Temperature on the other hand has broad lethal effects from disrupting the cell membrane to damaging DNA and affecting the reaction rates of vital enzymes so that it's impossible to adapt in such a short time by gaining a few mutations.


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Will humans ever evolve to cope with the rising temperature of our planet?
I am a complete layman of this field(Biology).I went through an article about global temperature rise and i wanted to ask this question.

Federal science agencies announced Wednesday that 2016 was the warmest year on record, beating the previous record of global temperature set in 2015, which had beat the previous record set in 2014.

(As seen in the graph temperature is rising rapidly and will increase even more in the near future.)
Can we evolve to cope with high temperature?Will we evolve?Is mutation the only answer?
(Frankly not looking for an answer saying by natural selection,the last thing i want to hear)

The graph actually shows that the temperature has risen although over the last few years it is constant. What it does not, and cannot, show is the direction it will take in the future and, if there is a change, how rapidly it will occur.  There may be other reasons for thinking it will change, but as a layman you should learn that it is unscientific to attribute these to the graph you present. This should be evident from the fact that previous downward trends did not continue.

No, for two reasons.  First, the time scale of human evolution (10K-100K years) is much longer than the time scale of the athropogenic temperature increase (100-1000 years).  Second, if the rise continues, humans will become extinct, along with most multicellular life.

A change in temperature of 1 degree, or even 4 degrees, is less than the variation in temperature that is seen between different areas that are inhabited by humans and less than the variation which is seen annually in those areas. Accordingly it seems that humans are already adapted to these differences in temperature and that our response to the temperature changes are more likely to involve habituation and cultural changes in behaviour and technology use than evolutionary change.

The difficulties for human are not so much a direct effect of the few degrees difference but the effect that temperature will have on ecosystems in general and on our agriculture and its repercussion to us.


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Why are there 2 copies of RNA in the HIV virion?
There are two copies of the RNA in the HIV virion. These are retroviruses. So, they can make cDNA from even just one copy using reverse transcriptase.
What is the use of the other? Are both integrated into host chromosomes?
My guesses are:

To ensure increased chance of getting integrated. But, if one gets in, the other also should be able to.
To increase the amount of protein translated (if both get integrated).
Two for two sets of chromosomes. (Seems juvenile but still a possibility. although, I do not think there are specific sites of preference for the viral DNA. Are there?)

You've probably worked it out by now, but I've added an answer to your cardiology question on Physics SE.

You are not totally correct because these two strands don't have to be the same, they can be genotypically different, which occurs when a cell is infected by two distinct HIV strains. Also HIV uses reverse transcriptase which can "jump" from one strand to the other so sometimes pieces get repeated, skipped etc. So you will get a recombinant --> more genetic diversity(see this article) I won't go into to much detail but if you want to know more I would highly recommend to read the article I linked after genetic diversity. So to summarize:

genetic diversity, because of switching between the two strands (this makes it so hard to cure AIDS e.g.)
If one RNA strand gets damaged it can use parts of the other RNA strand as template, so to synthesize DNA
apparently the dimeric form of RNA in HIV is essential for successive replication of the virus

Source: previous mentioned article(HIV-1 RNA dimerization: It takes two to tango.)

This indeed is the best article on the matter and is worth the time to read.

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Do DNA viruses have their own DNA dependant DNA polymerase?
There's an exception to the general observation that eukaryotic DNA viruses need to enter the nucleus in order to replicate. Poxviruses do not require to do so because they can make protein from mRNA transcribed by their ery own DNA-dependant-RNA-polymerase.
But that still leaves the question of how they make new DNA (for daughter virions). Do they also have their own DNA-dependant-DNA-polymerase?
So here are my questions:

Do pox viruses also have their own DNA-dependant-DNA-polymerase? If so, are they unique in this respect?
Why do other DNA viruses generally need to enter the host nucleus? Is it for making the mRNAs needed for protein synthesis using the host DNA-dependant-RNA-polymerase or for replication using the host DNA-dependant-DNA-polymerase? Or for both?
Do DNA viruses other than pox viruses need to become integrated into the genome to be able to replicate, and do so along with the cellular genome? Are there instances where the host DNA-dependant-DNA-polymerase is expressed at times other than the cell's S-phase?
Or are there viruses that replicate inside the cell's nucleus without being integrated into the genome?

Note: My question excludes Hep B (hepadna virus).

Please avoid asking multiple questions in a single post.

Probably I won't be able to answer all of your questions satisfactorily, but let's begin one by one.

Does the pox virus also have its own DNA-dependant-DNA-polymerase?

Yes. See this article from Wikipedia:

The replication of poxvirus is unusual for a virus with double-stranded DNA genome (dsDNA) because it occurs in the cytoplasm, although this is typical of other large DNA viruses. Poxvirus encodes its own machinery for genome transcription, a DNA dependent RNA polymerase, which makes replication in the cytoplasm possible. Most dsDNA viruses require the host cell's DNA-dependent RNA polymerase to perform transcription. These host DNA are found in the nucleus, and therefore most dsDNA viruses carry out a part of their infection cycle within the host cell's nucleus.

If yes, is it unique in having so?

Actually no. Hepatitis B virus also has its own DNA polymerase. And there's also the classic example of retroviruses: they have an RNA-dependent-DNA-polymerase (but yes, you can't consider it since it isn't a DNA-dependent-DNA-polymerase). See this wikipedia article:

Some viruses also encode special DNA polymerases, such as Hepatitis B virus DNA polymerase. These may selectively replicate viral DNA through a variety of mechanisms. Retroviruses encode an unusual DNA polymerase called reverse transcriptase, which is an RNA-dependent DNA polymerase (RdDp). It polymerizes DNA from a template of RNA.

Another example, as mentioned by @David in comments, is the Herpes simmplex virus (HSV) which contains a bunch of its own enzymes for DNA replication on its own. See this article:

Herpes simplex virus (HSV) encodes seven proteins necessary for viral DNA synthesis—UL9 (origin-binding protein), ICP8 (single-strand DNA [ssDNA]-binding protein), UL30/UL42 (polymerase), and UL5/UL8/UL52 (helicase/primase).

The rule that they need to get into the host nucleus - is it for making protein using the host DNA-dependant-RNA-polymerase or for replication using the host DNA-dependant-DNA-polymerase? Or for both?

Umm, both. Viruses (generally; there might be exceptions) need to reach to the nucleus of host to replicate as well as transcribe their DNA. See this article (emphasis mine):

Most DNA viruses replicate in the cell nucleus, which is where cellular replication and transcription proteins are localized. After infection, the nucleocapsid of DNA viruses is therefore usually delivered to the nucleus where uncoating occurs. An exception is poxviruses, which replicate in the cytoplasm of infected cells.
The first stage in the viral replication cycle is expression of the viral early genes. Transcription of these genes occurs using cellular RNA polymerase II and cellular transcription factors. These proteins bind to the viral DNA in regions called early promoters/enhancers, and promote synthesis of the early pre-mRNAs.
Once the viral early genes have been expressed, and the cells have been induced to enter S phase, viral DNA is replicated. This occurs in the nucleus of infected cells, and gives rise to new viral genomes. Many hundreds or thousands of new viral genomes can be produced in the nucleus of a lytically infected cell.

Are there instances where the host DNA-dependant-DNA-polymerase is expressed at times other than the cell's S-phase?

I think it has already been answered in your 2nd question. No, and the exception is the poxvirus itself. Again see the same article (emphasis mine):

Most DNA viruses replicate in the cell nucleus, which is where cellular replication and transcription proteins are localized. An exception is poxviruses, which replicate in the cytoplasm of infected cells.

Are there viruses that replicate inside the cell's nucleus without being integrated into the genome?

Wait! There's a difference between being inside the host cell's nucleus and being integrated into the host genome. Integration of the viral genome into the host genome requires a special enzyme called integrase and, you know, DNA viruses don't have integrase because they don't need it. So your question can be changed a bit to Are there viruses which replicate inside the cell's nucleus by getting integrated into the genome? Now, I could find only one such example i.e. Ectocarpus siliculosus Virus (EsV).

Ectocarpus siliculosus virus-1 (EsV-1) is a lysogenic dsDNA virus belonging to the super family of nucleocytoplasmic large DNA viruses (NCLDV) that infect Ectocarpus siliculosus, a marine filamentous brown alga...the EsV-1 and FirrV-1 genomes encode a large putative integrase/recombinase for which no counterpart exists in current protein databases. Only the Tyr-recombinase domain at the carboxy terminus of this enzyme is similar to phage integrases. Therefore, this enzyme might be involved in the integration and/or recombination of the integrated viral fragments.

References:

Pox virus

Hepatitis B virus DNA polymerase

Herpes simplex virus

Herpes Simplex Viruses: Mechanisms of DNA Replication

Wikigenes: UL9, ICP8, UL30, UL42, UL5, UL8, UL52

Reverse transcriptase

Viral Life Cycles in Cells

Integrase

Ectocarpus siliculosus Virus-I

You may wish to add Herpes viruses to your answer. There is a good open-access review considering all the viral-coded proteins involved in DNA replication at http://cshperspectives.cshlp.org/content/4/9/a013011.full. There is also an extensive review of polymerases and viral replication at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711277/

@david surely I can add many more examples (obviously we don't even know all yet) but thr pirpose was just to tell OP why the answer is yes or no, so just 1 or 2 examples should be appropriate. Anyways, I'll add them too, thanks :)

Hepatitis B virus is a bad example, it is very close to retroviruses in its replication strategy (except that reverse transcription occurs before the virion egresses), its so-called DNA polymerase is essentially a reverse transcriptase.

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Do two hormones have the same effect on a cell if the second messenger is the same?
There are so many hormones/cytokines/neurotransmitters and receptors, all of which act through about 4-5 second-messenger systems. So if one particular cell has receptors for say, two different hormones which act via the same second messenger, is there any way that the cell can distinguish the two stimuli? I’m guessing there must be some distinguish between the two, otherwise, wouldn’t the effect of both the hormones be the same?
For example, in a hepatocyte, beta-adrenergic receptors and glucagon receptors both act via Gs-coupled receptors, downstream of which, cAMP is increased. Since the cAMP is the same, the changes it would make are also the same. So does it to the hepatocyte, make no difference if the first messenger was epinephrine or glucagon?
I’m assuming the receptors would make a difference, but aren’t the coupled G-proteins (Gs) also the same? Is there a difference of amplitude?
Note: I understand that it is not necessary for the hormones to produce an exclusively different effect. I also understand that systemic effects can be different because of differential distribution of receptors. My question pertains to the effects on a single cell.

Technically, yes. But signalling molecules/receptors often elicit multiple responses.

Thanks @wysiwig could you pls give an example?

Here is some further discussion on the question https://www.reddit.com/r/Biochemistry/comments/5pig7x/do_two_hormones_have_the_same_effect_on_a_cell_if/

Sorry. I just forgot. I'm a bit occupied right now. Will get back. Ping me if I forget again.

@WYSIWYG the reditt thread I started is good.. but could you give a referenced answer? Thanks :)

Perhaps an interesting read with an example is the following: https://www.ncbi.nlm.nih.gov/pubmed/24365330
Two ligands (LH and hCG) binding the exact same receptor, yet differing in their actions. Part of the difference is mediated via the second messenger they share (cAMP).

I have edited the post. Please note the term is "second messenger", not "secondary messenger". These have different linguistic implications. Suffice it to say that a second messenger is not secondary, it is integral to the response which consists of 1-2-3 (or more).

Secondary signaling molecules like cAMP, Calcium, and Ras-Raf are common in many pathways and I think its a way of integrating different signals.We cannot say that at a moment only one pathway operates in a cell or a single pathway will be enough for a process to happen.I think common second messengers is a resource and time-saving method adapted by our system to coordinate different response efficiently.https://www.nature.com/scitable/topicpage/cell-signaling-14047077
Then how a cell can identify which pathway and process should go on? I think that each time this second messenger will make a small change in choosing down stream effectors.Like Calcium binds to calmodulin which in turn choose next binding partner.Maybe the number of second messengers like concentration and affinity decide which downstream effector will be appropriate for the required stimuli.You can see in this link about how different secondary messengers make different results https://www.ncbi.nlm.nih.gov/books/NBK9870/
About GPCR, more than 800 GPCR are there and you can see from this link http://jcs.biologists.org/content/116/24/4867
So, Do two hormones have the same effect on a cell if the second messenger is the same?
I think yes, see this table (https://www.ncbi.nlm.nih.gov/books/NBK21705/)

Here, from the table, you can see adrenaline and glucagon are having the same effect in the liver cell and both have cAMP as a second messenger.But in cardiac muscle and intestine, adrenaline is having a different function. So I think it depends on the cell also.

So is your answer to the poster’s question Yes or No? And why exactly?

I think yes, for details you can see my edited answer.Thank you


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Red neurons - Acute neuronal injury

“Red neurons” are evident by about 12 to 24 hours after an irreversible hypoxic/ ischemic insult. The morphologic features consist of shrinkage of the cell body, pyknosis of the nucleus, disappearance of the nucleolus, and loss of Nissl substance, with intense eosinophilia of the cytoplasm.  -Robbins textbook of pathology

Taken from Robbins pathologic basis of disease, 9e, pg.no1265, fig: 28-13B

Why in case of neurons there is shrinkage instead of swelling as in other cells?

There is not some simple dichotomy of "neurons shrink and other cells swell" in response to hypoxia/ischemia.
Neuronal death can be necrotic or apoptotic or both, and at different stages different morphology is observed: generally swelling earlier, shrinkage later, though both are observed together early as well. Eosinophilia/"red neurons" tends to occur later as mentioned in this passage (after 6 hours, consistent with 12-24 hours) so that's probably why the author is referring mostly to shrinkage. Cells can also have swelling of some organelles, like mitochondria, despite shrinking overall.
Without further context of the passage you provided it's hard to say much more.

Garcia, J. H., Yoshida, Y., Chen, H., Li, Y., Zhang, Z. G., Lian, J. I. N. Y. I. N. G., ... & Chopp, M. (1993). Progression from ischemic injury to infarct following middle cerebral artery occlusion in the rat. The American journal of pathology, 142(2), 623.
Jenkins, L. W., Povlishock, J. T., Lewelt, W., Miller, J. D., & Becker, D. P. (1981). The role of postischemic recirculation in the development of ischemic neuronal injury following complete cerebral ischemia. Acta neuropathologica, 55(3), 205-220.
Portera‐Cailliau, C., Price, D. L., & Martin, L. J. (1997). Excitotoxic neuronal death in the immature brain is an apoptosis‐necrosis morphological continuum. Journal of Comparative Neurology, 378(1), 10-87.

Not much infiltration of phagocytes is seen in above figure. Shouldn't apoptotic cell need more phagocytes in close vicinity to immediately clear of the bits of cytoplasm which are shed off?

@JM97 Sorry I'm not sure what the answer to that question is for sure from the perspective of histopathology, just conceptually though I don't see any reason that absence of phagocytes demonstrates lack of apoptosis. Certainly microglia would be present to clean up at some point of healing but apoptosis itself can be initiated intrinsically.

There has to be something special as coagulative necrosis, a usual feature of ishcemia is not seen in CNS as given in chapter 2 of Robbins.

Search for Exicitotoxic programed cell death. Acute Neuronal injury occur by this pathway. This is like Necroptosis. Cell shrinkage is seen due to Glutamate.  I have added some screenshots of my search,, rest you can search yourself.

Read more at
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398818/

@JM97, please do reply if this was helpful.

thanks for your efforts. I will certainly read excitotoxic cell death now. again thanks.


text:
Renorenal Reflex
According to this:

The kidney contains afferent sensory nerve fibers that are located primarily in the renal pelvic wall where they sense stretch.

I think the stretch is due to urine. If I am correct then, I am unable to understand the following:

Stretch activation of these afferent sensory nerve fibers elicits an inhibitory renorenal reflex response wherein the contralateral kidney exhibits a compensatory natriuresis and diuresis due to diminished efferent renal sympathetic nerve activity.
  There is a negative feedback loop in which efferent renal sympathetic nerve activity facilitates increases in afferent renal nerve activity that in turn inhibit efferent renal sympathetic nerve activity so as to avoid excess renal sodium retention.

If I am correct , then how is renorenal reflex a negative feedback loop? Doesn't decreased efferent sympathetic activity increasing diuresis thus causing further increase in pressure in renal pelvis( contra lateral)?
Also how is sympathetic activity increasing renal pelvic pressure in the first place?
If I am wrong then, what is causing increase in renal pelvic pressure?

Support for my claim:
Hydronephrosis, a blockage of the outflow of urine or reverse flow of urine already in the bladder (called reflux) can cause the renal pelvis to become enlarged.
So, I think I am right in saying that urine increases pressure in renal pelvis, thus activating stretch receptors.

Unfortunately, I am still confused, please give a hint.

How is renorenal reflex a negative feedback loop?

You are confusing two different negative feedback loops.

1) There is a negative feedback loop in which efferent renal sympathetic nerve activity facilitates increases in afferent renal nerve activity that in turn inhibit efferent renal sympathetic nerve activity so as to avoid excess renal sodium retention.

This occurs on ipsilateral kidney only and is not renorenal reflex.

2) Stretch activation of these afferent sensory nerve fibers elicits an inhibitory renorenal reflex response wherein the contralateral kidney exhibits a compensatory natriuresis and diuresis due to diminished efferent renal sympathetic nerve activity. The renorenal reflex coordinates the excretory function of the two kidneys so as to facilitate homeostatic regulation of sodium and water balance.

This is renorenal reflex, while it is negative feedback again, since reduced urine passage in one kidney paves way for other to increase urine passage/output.

Doesn't decreased efferent sympathetic activity increasing diuresis thus causing further increase in pressure in renal pelvis( contra lateral)?

Contra lateral kidney is not having same renal obstruction as in ipsilateral(unless otherwise stated). So, diuresis leads to increased loss of loads of electrolytes and water, thus, reducing hypertension.

Also how is sympathetic activity increasing renal pelvic pressure in the first place?
  If I am wrong then, what is causing increase in renal pelvic pressure?

Sympathetic activity is not increasing renal pelvic pressure here. Increased renal pelvic pressure was caused by obstruction to urine flow, eg. ureteral caliculi. Due to this obstruction urine could not pass from pelvis to bladder which increase pelvic pressure.
Contrarily, increased sympathetic activity in ipsilateral kidney tends to reduce pelvic pressure by reducing GFR. In contralateral kidney, decreased sympathetic activity will cause increased diuresis and reduced tension on diseased kidney for urine output.
Note: Increased GFR here, as a result of decreased symp supply, does not cause increased renal pelvic pressure since urinary passage is clear and not obstructed.

No, I don't no how is sympathetic activity increasing pressure in renal pelvis, asaik sympathetic activity will reduce gfr so reduced pressure in the renal pelvis.

Refer to edited answer.


text:
Why some cells don't produce purines?
It is said that erythrocytes, polymorphonuclear leukocytes and brain cannot produce purines. And the reason given as per this site is:

Human brain tissue has a low level of PRPP glutamyl amidotransferase (reaction Image, Figure 33–2) and hence depends in part on exogenous purines. Erythrocytes and polymorphonuclear leukocytes cannot synthesize 5-phosphoribosylamine (structure III, Figure 33–2) and therefore utilize exogenous purines to form nucleotides.

My question is why do these cells don't produce the required enzymes for the synthesis of purines? What could be the functional significance for such absence?
My attempt : At first I thought that Erythrocytes as such don't have nucleus so they don't need purine synthesis for cell division , but I don't understand why then they need purines from external source( as said in the above site). Also brain cells are neurons and neuroglia, of which former doesn't divide( except in some areas of brain) but they too need purines.
 The later divide but they don't produce required enzyme. Why?
So my questions are:

Why do cells which don't replicate need purines?( May be for formation of Coenzymes , correct me if Iam wrong)
Why do the cells which divide too don't produce required proteins(enzymes)?

Should I make it in two parts?

I can't answer it, but it seems a reasonable question to me. It has received a close vote as too broad. But perhaps you should remove questions 3 and 4 as understanding why the nucleated cells here differ from other cells in purine metabolism will probably suggest answers to those questions.

@David I have edited the question, have a look at it.

Question seems valid enough to me. And interesting.

I agree.  A stellar question.  Erythrocytes start with nuclei and jettison them before leaving the marrow so that is not it.  There are active synthetic systems making the stuff nearby and so it would be no big deal for these cells to do it too.  The synthetic path must be off for a reason.

I am going to throw this idea out there. I was unable to find it stated anywhere so far.
There are several very ancient parasites that make their homes inside erythrocytes and neutrophils. Plasmodium is one, the causative agent of malaria. Trypanosoma is another. These things are ancient degenerate eukaryotes and their lifestyle as intracellular parasites is probably ancient too.
These things cannot make purines either but they need them and they need a lot of them, because they are reproducing fast. If the host cell does not have the machinery to make purines, that machinery cannot be hijacked by the parasite to really crank out the purines.  The best they can do is hijack the salvage pathways these cells have.
From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC259377/

The apparent competition between parasites and host cells for available purines suggests that depletion of extracellular purines should be considered as an approach to treating extracellular trypanosome infections.

From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405406/

Plasmodium species parasites, like many other protozoan parasites, are purine auxotrophs, unable to perform de novo purine biosynthesis. They rely on the host to provide purines

That does not explain brain cells  - unless lack of purine synthesis is a defense of brain cells against Toxoplasma, yet another eukaryotic parasite.
Nothing would please me more than for someone to poke holes in this theory. A prediction from this theory: erythryocytes in all animals should lack purine synthesis - including birds, who suffer from a form of malaria and whose erythrocytes do have nuclei.

Quite interesting theory.

What about hepatocytes? They too get infected by plasmodium, but are the major sites of purine synthesis.

@JM97: I suspect the circulating cells & esp erythrocytes are more dispensible (like pawns in chess) so adaptations there are less detrimental to the organism.  Hemoglobinopathies (sickle cell, thalassemia) are thought to have evolved as defenses against plasmodium infection and their actions are also specific to the erythrocyte.

Then why Polymorphonuclear leucocytes too don't produce purines?

@JM97 Same argument as RBC.  PMNs are shortest-lived wbc and dispensable: shock troops.  They engulf parasites and then die, taking parasite with them.  Some parasites (Leishmania, trypanosomes) can survive and reproduce in  PMNs.  Lack of endogenous purine synthesis machinery makes life harder for these parasites.  Be aware: I am making this up as I go.


text:
What does "each pathway define an independent genotype" mean?
In a section of this paper.

However, if the question of independency is posed in the
  form: “Does each pathway shown define an independent
  genotype?,” then each of these three pathways is indeed
  independent. This is the way that MPS defines the independence
  of pathways.

What does “Does each pathway shown define an independent
genotype?,” mean?

Pathways cannot define a genotype. They are product of the genotype and they define the phenotype.

This is somewhat outside my field, but basically it seems they're defining the independence of the three hypothetical metabolic pathways in two different ways:

Mathematically the pathways are not independent since P₃ is a combination of P₁ and P₂.
Biologically the pathways are independent since each requires a different combination of enzymes and therefore genes (the genotype). This is the method used in MPS.

Does that answer your question?

I don't know, the answer you gave seems satisfiable so i would go with it...


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What is meant by clonal isolates?
With respect to this website:
http://horfdb.dfci.harvard.edu/
what does the term clonal isolates mean?

Often genes or other DNA fragments are inserted into an expression vector and used to transform bacteria or other cells. When a mixture of vectors is used containing various DNA fragments (e.g. a chopped-up genome), then individual (bacterial) colonies need to be isolated to make sure they carry only one insert. This can be done, e.g., by plating the transformed cell culture such that individual colonies are obtained. Theoretically, one colony represents the offspring of one cell, hence the colony as a whole has one DNA insert and is a clonal isolate.

what do you mean by transform bacteria?

@user3237995 http://en.wikipedia.org/wiki/Transformation_%28genetics%29


text:
Use cases of RNA secondary structure prediction
I'm an undergraduate currently writing a thesis on RNA secondary structure prediction, specifically building upon analysis done by the RNAStructure and Unafold software packages by modifying certain algorithms here and there. I'm actually not a biologist, however. I've taken all of my classes in physics and computer science, and I sort of stumbled into my current research, and since it seemed to be a good fit for my skill set I stuck with it. However this leaves me curious of a motivation for my current work. Why is RNA secondary structure prediction important and what are some of its applications?

RNA-protein interactions?

Our lab has a very particular goal of increasing the amount of double strandedness in RNA so we can intercalate stuff in it more efficiently. Being able to calculate amount of double strandedness under physiological conditions would be nice.

This question is actually a little broad. There are several interactions that RNA has because of its structure. This is because unlike genomic DNA, RNA is single stranded and can thus form different kinds of secondary structures. Common structural motifs include hairpins, pseudoknots, triplex and quadruplex. One can write a huge review on this.

Anyone who's taken introductory biochem has been beaten to death with this phrase: structure is important for function. Usually they're talking about proteins but it really applies to everything.

@WYSIWYG I don't think broadness is a problem here. A detailed review of structural elements is not required for an answer, just an explanation why RNA secondary structure is important to know (and to some degree why RNA is important).

I tend to agree that it is too broad as defined by the rules of this site but it seems like somewhat of a technicality. I'd hate for it to be closed since it is quite interesting so I've edited it slightly to hopefully keep it open.

Short answer
I can think of at least a dozen applications for which it would be useful to know the secondary structure of a given sequence of RNA off of the top of my head. In no particular order:

Simulation/visualization of RNA
Riboswitches
MicroRNA
RNA interference (RNAi)
RNA-RNA interactions
RNA-DNA interactions
RNA-protein interactions
Ribosomal protein expression
Ribozymes
Forced evolution of RNA aptamers
Synthetic tRNAs with four and five base-pair codons
Termination of transcription (the process that makes mRNA from DNA)

Basically anything to do with RNA, which is one of the fundamental building blocks of all living creatures.
More in-depth
Simulation/visualization of RNA
Secondary structure (2°) forms the second (yep) level in the standard 4 level hierarchy of macromolecular structure, and consists of short-range interactions between and among residues. In RNA, 2° is usually thought of as being loosely identical with base-pairing interactions. In order to do a proper simulation/visualization you'll probably also need at least the 3° information, but 2° is important too.
Riboswitches
As an mRNA gets translated by a ribosome, in many cases it can form into a complex 3D structure that will affect the translation process. For example, some of the mRNAs that encode proteins related to the metabolism of metal ions have a riboswitch that will themselves bind to metal ions and inhibit/upregulate expression of the related protein. For various reasons it's usually extremely difficult to get the full 3D structure of a riboswitch, so getting to know the 2° remains an important source of information about them.

Huh, where did you get the idea that it is impossible to get the full 3D structure of a riboswitch? There are structures published for most of the known classes of riboswitches.

@MadScientist citation, please? (good sir, etc)

http://www.rcsb.org/pdb/101/motm.do?momID=130

Another thing, you mention only mRNA translation. Riboswitches can act at transcription or translation, transcriptional riboswitches typically terminate the transcription early to regulate, translational riboswitches typically sequester the Shine-Dalgarno sequence to regulate expression.

Knowing the secondary structure of nucleic acids is very useful in many cases when working with them. The simplest case, and probably the most often used case is when you order or synthesize a small RNA or DNA and actually don't want this to have any stable secondary structure. There are many methods where you use a small nucleic acid that can bind to a complementary part of another nucleic acid (hybridization).
For example in PCR, which is used to amplify small amounts of DNA, you use small DNAs called primers that bind to specific parts of a larger DNA template. If those primers can form stable secondary structures by themselves, those structures would have to be broken up before the primer can bind to the template. Such competing structures can drastically reduce the efficiency of such experiments and are something that people try to avoid, e.g. by predicting secondary structures before choosing primers.
There are also methods that use short nucleic acids with attached labels such as fluorophores. Those labeled probes bind to specific target sequences, and you can then e.g. determine with a microscope where those probes are bound. In all such techniques you don't really want secondary structures in your probes as they interfere with the binding to the actual target.
When RNA is introduced first, it is often said to be single-stranded and secondary structure is not even mentioned. But even when acting as messenger RNA, secondary structure of RNA does play a role. One mechanism for transcription termination works by forming a stem-loop within a certain range of stability, and predicting those is necessary to predict the site where transcription is terminated.
There are also many types of regulatory RNAs, this is a very active and hot topic at the moment. The most well known are probably RNA interference (siRNA and miRNA), but there are also many ribozymes and especially in bacteria also riboswitches. I won't try to list the different types of regulatory RNAs here, there is a large number of different classes that are known, and new ones are still discovered. To understand those it is often necessary to know the secondary or tertiary structure of the RNAs.
You can often at least create some hypotheses on how an RNA could work by looking at the secondary structure. In riboswitches for example you typically have an on- and an off-conformation, and those can often be explained by secondary structures.
While the secondary structure is often not enough to understand how a specific RNA works, you still start by predicting it in most cases. In many cases you would additionally use experimental data to verify the prediction (e.g. SHAPE or inline probing).
Determining the actual three-dimensional structure of RNA is pretty hard. How hard depends heavily on the exact RNA, but it can easily take years to do this. If you're lucky you can crystallize it easily, but RNAs with flexible parts tend to not crystallize well. In that case you can do NMR to determine the structure, but that has a rather severe size-limitation and can easily take years for larger RNAs.
In case of NMR, knowing the secondary structure is very useful in pretty much every case. You need to assign your signals to specific bases, and this is much easier if you know the secondary structure. You can also use NMR to support or disprove specific secondary structure predictions.
More reliable secondary structure prediction would be pretty nice, the current methods still fail often enough. Though there is probably a limit on how good you can get such methods for RNAs with extensive tertiary structure.


text:
How does chromosome number get halved in meiosis I?
In meiosis 1, it is said that chromosome numbers become halved in the two daughter cells. For example, in a 2n human cell there are 46 chromosomes. During meiosis 1, the cell will undergo interphase and probably the S-phase, where chromosome number becomes duplicated. Now the cell is 4n (i.e. 92 chromosomes). During anaphase 1, 46 chromosome out of 92 would go towards one pole and 46 would go opposite. Thus the resulting two cells will have 46 chromosomes in each. So why should we say that, in meiosis 1, the chromosome number is reduced? I say that S phase shouldn't occur in meiosis 1 but rather it should occur in meiosis 2. Is my reasoning incorrect?

If you consider sister chromatids to each be a chromosome, meiosis I, rather than halving the chromosome count, separates the homologous chromosomes, which result from sexual reproduction, from one another. Meiosis II then separates the sister chromatids from one another resulting in the final halving of chromosomes.
On the other hand, many if not most biologists don't consider the sister chromatids to be individual chromosomes until they are segregated during meiosis II. In this sense, meiosis I does reduce the chromosome count to half.


text:
Is a mycelium sewage pipe possible?
Over the past few years I've seen mycelium used as a supplement for various building materials. I was wondering if mycelium could be successfully used as construction material for a sewage pipe.
Furthermore, would this sewage pipe be able to provide any filtering of waste, given the mycelium?
Sources:

mycelium packaging
mycelium plastics
mycelium bricks

Providing some reference to instances in which mycelium have been used for building materials previously would strengthen this question. Further, perhaps a quick comment about why you want to know this information -- this would help guide those providing answers to stay relevant for you.

@theforestecologist agreed — please offer examples of mycelium incorporation into construction!

I'm assuming here and here are examples of what the OP is referring to? I'd seen both of these stories about 7 or 8 months ago I think.


text:
Spectroscopy on plant leafs
I'm trying to do spectroscopy readings on plants where I shoot electromagnetic waves and look at their signature/profile.
I want to be able to do this at a distance, in the field and on live plants so that I can modify my rig later to automatically do this on multiple plants daily.
I have no background in spectroscopy, but I heard that waves directed  through leaves can then be received on the other end using something like waveguide spectroscopy. I do not know the frequency range I should be looking at and was wondering how can I identify the range of interest for my plants.
Let's say I want to approximate the chlorophyll content in leaves and see if the leaf is healthy or not and look at its change daily. Some references to learn about this would be very helpful. Thanks!


text:
Which part of the genome are the developmental sequences of embryogenesis located?
Which part or parts of the genome are the sequences located. Are they spread across the chromosomes? If so, how are they accessed sequentially with precision during embryogenesis?

This is a very general question. The "developmental sequences" are just genes like any other. Like all genes, they are semi-randomly distributed through the genome. While there are gene-rich and gene-poor areas in the genome, with some exceptions—notably the homeobox genes—genes are not grouped by function.
As to how they are accessed sequentially, that is a huge question but it is not specific to embryogenesis. Genes will always need to be turned on/off at specific times and in response to specific stimuli. This is particularly obvious during development but is not exclusive to it.
The basic way this happens is through feedback and control loops. Gene A activates the transcription of gene B which activates gene C which then deactivates A. If you manage to turn on A, the rest will follow. One of the ways this can happen in developing embryos is through maternal mRNA. These are mRNA molecules that are present in the fertilized egg and which begin to be translated. This gives us a starting point to activate gene A, which then turns on B etc.
This answer is a huge simplification, but a full answer could take up a couple (or 40) of PhD projects.

Terdon is right on the money when it comes to how is the coordination done, and I know of at least one student working on this for her thesis. However, to answer your other question directly, there was a great review in 2010, which was taught in my genetics class that year.
It is important to note that we still don't know all the genes that are involved with meaningful certainty.  Further, it would be exceedingly difficult to fund and conduct Hong et al's work in the US.
If you read the article you will notice that several genes that are involved are genes that are active through out life at various levels.  Figure 4 gives a good example of how spread out the information.
Notice that the three categories of genes they used were even quite different: Stem Cell Specific Genes, Muscle, fat and connective tissue genes, Significantly Enriched GO term
So when you think about how diverse the genes are, it would be even odder for them to be clustered together.  Again, they are probably not truly random, but they don't seem to have a pattern.
To quote their take home:
Furthermore, by comparing with published data, we identified three groups of maternal genes with distinct regulation profiles during wk 4–9 of development, which provided a molecular basis for the anatomically distinct developmental events that occur between early embryogenesis and subsequent organogenesis and histogenesis.

More important, our genome-wide and detailed developmental profiling
  of the patterns of gene expression has revealed that genes involved in
  the same biological processes are often regulated coordinately. This
  finding has led us to hypothesize that patterns of gene expression, if
  known in sufficient detail as in the present study, might be used to
  predict a role for the gene in a developmental process.

Hong Yi, Lu Xue, and Ming-Xiong Guo, et al. FASEB J. 2010 September; 24(9): 3341–3350.
doi:  10.1096/fj.10-158782 PMCID: PMC2923361


text:
Does a certain tumor type being invasive mean that it is highly metastatic?
Does a certain tumor type being invasive mean that it is highly metastatic?

Oncologists examine the margins of a biopsy for morphology and invasiveness. A tumor that is becoming invasive has a high potential to become metastatic, based on numerous factors. I would be hard pressed to tell you that a tumor is highly metastatic without testing, though. I am not an oncologist, either.

They are different things, metastasis is not the same as invasion.
Highly invasive cancer means that the tumor spreads beyond the layer of tissue in which it developed and is growing into surrounding, healthy tissues.
Highly metastatic tumors cause secondary malignant growths at a distance from a primary site of cancer.
In order for tumors to become metastatic, they must move and grow beyond their initial location and reach the circulatory system in order to travel to another location. During this phase, depending on the tumor, the malignant growth will acquire the ability to escape (tumors cannot do this at first, because it requires genetic mutations in genes responsible for cell adhesion). There are many other known factors which co-occur in cancer development - it is a rich field of research.
Here is an informative website for you to browse about the medical side of it: http://edcan.org.au/edcan-learning-resources/supporting-resources/biology-of-cancer/defining-cancer/invasion-metastasis


text:
What does curated gene mean?
I see in databases "curated" or "not curated" for genes. What does that mean?

https://www.google.fr/#q=curated+genes

Welcome to Biology Stack Exchange. Could you provide an example of a database where genes are classified this way?

Thanks! For instance: http://www.wormbase.org/species/c_elegans/gene/WBGene00009562#0-9g-3
I also saw some genes that mentions as "not curated"

"Curated" is mostly synonymous with "manually curated", which means that these genes have been experimentally validated. Most non-curated genes are just predicted by a software.

In Bioinformatics, the term "curated" indicates that the information has been validated either experimentally or using predictions from a software. Often the manually and experimentally curated sections are more dependable than the ones by software. When a gene is curated, it means certain desired information about the gene such as its location on the chromosome, its function, the proteins it encodes for are known.

Welcome to BiologySE... thanks for your contribution, but can you please add some links/citations that back up your claims? We always appreciate references on the site and it will increase your reputation much more than comments/answers without any citations/references.


text:
What is mRNA expression level?
I cannot find a clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference.

you can see this post

The RNA expression level is an estimate of the amount or proportion a given gene's RNA found in a sample of cells (such as a tissue sample) or even a single cell.
Expression is used because the RNA sequence is translated from DNA to RNA according to the signals within the cells.
There are various means of estimating this.  They often involve a sequence specific probe - a short length of DNA usually - which will bind specifically to the RNA in question.  The exclusiveness of the probe sequence, which is usually 20-45 bases long, to the RNA in question can vary and so this is a bit of an art sometimes.
Examples are qPCR (quantitative PCR), expression microarrays.  Both of these technologies have  many flavors and variants.
Another category of expression estimation include RNASeq - which will sequence all the RNA polymers in a sample and estimate all the sequences at one time.  The result is similar to a microarray, but RNASeq does not necessarily require the use of specific probes to an RNA to measure it, though it can.
These estimates are usually relative - except for careful qPCR perhaps.  The numbers are not usually interpreted as "X copies of the RNA" in the sample.


text:
Why do bulls have a hump?
Camels have a hump as an adaptation to the heat. They store fat so that it minimizes the insulating effect the fat would have if distributed over the rest of their bodies.
Why do buffaloes/ oxen/ bulls have a hump then? The climates they are found in, I assume, are not as hot as that of the camels.

Bison humps are made of muscles, huge muscles. According to this and this pages bisons use their heads for snowplowing. This hump provides head support. It seems that also other animals have structures like that: giraffes, rhinoceroses, elasmotheriums,... this list can go on since this structure should be homologous of other animals'. From this page rhino humps made from muscles, nuchal ligament, fat, and dermis. And from the page, probably fat quantity depends on the nutritional state of animal.
I searched nuchal ligament, the remarkable structure of hump according to rhino page. This is a ligament spans from upperback vertebra to neck vertebra and to skull. Can be found on humans too. Also muscles of hump should be homologous to humans' notice that vertebras have spines not just for supporting ligaments they also for muscles. Human skeletons just don't have vertebra with long big muscle connection points and huge neck/back muscles connecting huge bones, this is why we don't have a hump or an obvious large hump. And I think even camels do have slighly bigger muscular humps but theirs are covered with big fat hump.
Bison skeleton and elongated spines supports huge muscles and ligaments.

Horse's nuchal ligament

Human nuchal ligament

Human nuchal ligament drawn with red lines and muscles (bison hump also consist of muscles).

Giraffes' this is an energy saving feature. Giraffes don't need to use muscles to hold their neck. They just use when flexing their necks down, when drinking water etc.

According to Wikipedia, for an alternative hypothesis Ouranosaurus have a hump. (Other hypothesis is display sail or termoregulation sail of course. Also spinosaurus have this kind of alternative hypotesis but this hypothesis not accepted much as sail. and spinosaurus' spine different from bisons. Bison spines concentrating at shoulder but spinosaurs' not at the shoulder. You can find spinosaurus info from this page.)

Thanks! But how does the hump help the bull?

bull hump provides all same of other animals'. and at the same time they are fighting for females. www.zoochat.com/community/media/the-skeleton-after-a-successful-bull.189073/full?d=1339424780 see from the picture if bull pushed their head to his opponent neck needs supported to pull head up. spines also connecting point of shoulder blade muscles. so maybe hump also gives extra strength on forelimbs too. i think ox humps are similar purpose but today ox hump provides pulling cart without slipping yoke from neck. i read, probably hump growth of bulls related to testosterone. @polisetty

but in some cases some cattles have fat hump at their backs this is from  selective breed or something like that. if last link doesnt work www.zoochat.com/community/media/the-skeleton-after-a-successful-bull.189073/

seems my answer/comments are needs to be improved a little. but because i think my answer and comments too much detailed for a desired answer anyways. so i can leave it unedited for not to spend extra time. if you confused ill leave a brief correction: correcting first comment: bull humps are for fighting for females and also provides support just like as in other animals. second comment: indian bulls etc.

http://9gag.com/gag/aAwKGgo i guess this is can be explained with hump. hes not got an very obvious hump but hes have one.


text:
Do tRNAs that recognize multiple codons have any preference for one over another?
What are the effects of the different binding strength/affinity between the synonymous codons corresponding to a single tRNA ?

Your question could do with clarification. You ask a specific question in your title, but you need to spell out what you mean by "preference" in the body of the question. Asking if literature exists, is not a scientific question of any sort, and appears to be concerned with something different, more in the realm of chemistry. Nor do you give us any indication of what you have found out for yourself on this topic. See  the help on "how do I ask a good question". Nevertheless, I have given you an answer.

I have now edited your question to a form that is more acceptable to SE Biology.

There is an extensive literature on synonymous codons and their usage in different organisms. I shall assume that the question concerns relationship between strength of codon–anticodon interaction and the efficiency (speed in this case) of translation.

It is not disputed (I am aware of few experiments on this) that the strength of codon–anticodon interaction depends on the number of hydrogen bonds made.
It was predicted that for optimal rate of translation one needs a balance between association and dissociation of the codon–anticodon pair. Hence weak interactions (all AU) — which would disfavour association — or strong interactions (all GC)  — which would disfavour dissociation — would not allow a rate of protein synthesis as fast as that for intermediate interactions (mixed AU,GC).
This appeared to be borne out
in the codon usage patterns of rapidly growing organisms such as Escherichia coli, something subsequently confirmed by more extensive studies. To be precise, the more highly expressed proteins (e.g. ribosomal proteins) were encoded by mRNAs containing the intermediate  codon–anticodon interactions predicted to allow rapid translation. In contrast, poorly expressed proteins (e.g. repressors) were encoded my mRNAs predicted to produce slower translation.
One should be aware, however, that there are other factors that influence the codon usage in different organisms, and that these can overide the effect of codon–anticodon interaction strength.


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Does Pasteur's experiment contradict an origin of life?
To my understanding, Pasteur’s experiment demonstrates that life is only made from life. If this is true, then how could origin of life (aka. abiogenesis) ever have happened?
It seems to me that Pasteur’s experiment and the theory according to which there is abiogenesis contradict each other. Do they?

If I may, your goal should not be to try to convince your friend but to understand whether the meaning of Pasteur's experiments on evolutionary biology.

@Remi.b Well yes, that is what I thought. It's not my primary goal to convince my friend, but to understand where I misinterpreted it

Please describe briefly Pasteur's (note the apostrophe) experiment. Without it your question is meaningless and you cannot start thinking logically about what his experiment demonstrated (I presume that the cause of food spoiling by bacterial growth is not due to "spontaneous generation"). You can only argue about science with someone if you understand and define what you are talking about.

@AyyLmao I've edited you post to try to highlight your interest and not the argumentation you're having with your friend. Feel free to roll back if you don't like the edit.

@David yes, I think in the popular culture "Pasteur's experiment" came to refer to the fermentation experiment that offered an evidence against the prevailing idea of spontaneous generation (see description here on wikipedia)

@Remi.b — I would advise the use of plain English in editing unclear questions such as this. Abiogenesis is not a word I had encountered previously, which suggests to me that 90% of the readers of this page will be in a similar position.

@David Good point. Re-edited

Related: Why did abiogenesis only happen once?, Do we see protocells forming in nature today? and Is it possible there were multiple origins of life?

Pasteur's experiment does not demonstrate that life is only made from life (even if he might have thought it did).  It simply demonstrates that life does not arise under the conditions of his experiment, during the short time available.  You might also note that if he'd had some thermophiles https://en.wikipedia.org/wiki/Thermophile in the flasks, he might well have gotten different results :-)

Pasteur’s experiments demonstrated that the appearance of living matter in spoiled food (soured wine and the like) was not due to so-called spontaneous generation of living organisms, but due to the multiplication of pre-existing but invisible micro-organisms, which could be eliminated by sterilization of the food containers — hence the term pasteurization used (in Britain, at least) for the sterilization of milk.
No more, no less. His experiments say nothing about, and were not concerned with, the origin of life on earth. They related solely to the vitalist misinterpretation of everyday observations in 19th century France. As far as I am aware, Pasteur never concerned himself with Darwin’s theory of evolution. French and British science (and Pasteur and Darwin) had different philosophies and emphases at that time, and contacts were limited.
One may ask what is the difference between abiogenesis and spontaneous generation. The former envisages a slow series of chemical processes leading over millions of years to the first self-replicating molecules and subsequently to simple single-celled organisms — an idea that only really gained traction after the Miller-Urey experiment. The latter involves fully developed organisms appearing out of nothing in a couple of days — a sort of arbitrary non-Christian version of creationism.
The scientists who developed the the idea of an origin of life from inorganic matter were well aware of the significance of the work of Pasteur. They were also aware of the subsequent progress of chemistry and biochemistry. It is worth mentioning that Pasteur was so concerned with repelling the vitalist viewpoint (a sort of irrational superstition akin to belief in magic) that when Büchner demonstrated glucose metabolism in yeast extracts containing no living cells he wrongly rejected this. (The word enzyme means in yeast.)
You can read about Pasteur and Spontaneous Generation here, and Büchner and the Liebig–Pasteur dispute here. There is also a long Wikipedia entry on Pasteur — the French version is even more extensive. You can read about his supposed religious views here if you are interested, but you should remember that the views of a scientist, however famous, are only of scientific value if they are supported by his experiments.

Consider the context. In Antiquity and the Middle Ages from Aristotle on, people thought that many living things (from microbes to mice) would arise through spontaneous generation. Seemed sensible enough; if you don't pay close attention to animals getting somewhere, and you have no knowledge of anything microscopic, it can easily look like animals just come out of the environment. After the Enlightenment scientists got better understandings of reproduction on the one hand, and made many experiments showing that under certain conditions (like keeping meat sealed so flies couldn't get to it for example), life didn't, in fact, spontaneously generate in the way it was previously thought it did. At this point the idea that all living things come from the reproduction of other living things of the same species became increasingly accepted.
Pasteur's experiment was more or less the death knell of the spontaneous generation hypothesis; some previous experiments had shown microbes growing after a flask was supposedly sterilized, or kept the flask sterile by keeping air out (which opened one to the argument that spontaneous generation required air). His showed microbes not growing in a flask where air could flow but dust did not settle because of its shape, and immediately growing when the flask was tipped and dust fell in.
Pasteur's experiment didn't so much "prove that life only comes from life", as disprove a specific other hypothesis that existed at the time. And in that sense it is still consensus biology: No biologist today thinks that snakes, mice, microbes, or even viruses can arise directly through abiotic processes. If you replace "life" with "modern life", the principle is true as far as we know.
Now biology has advanced a lot, and there is a different context, with people asking different questions and advancing different hypotheses to answer them. The question of the origin of life is one such question, that has nothing to do with what Pasteur was trying to prove. And that's where the "modern life" caveat becomes relevant; while all modern living things are too complex and specific to arise directly via abiotic processes, it doesn't follow that the same is true of the first living things. We know that living things used to be different from how they are now; and in fact when looking into the past via the fossil record and genetic evidence we find clear patterns of gradual development of the modern biosphere's diversity and complexity from simpler and more generic ancestors. While it is harder to find evidence for the evolution of early cells, because the genetic evidence is muddled by the time scales involved and the fossil evidence near-nonexistent for obvious reasons, it is sensible to figure that similar patterns would occur there, and that the earliest cells were as different and simpler than a modern cell as a Precambrian worm is from us.
Here is a video of Nick Lane talking about a promising hypothesis on the origin of life. It sort of illustrates how different, and simpler, those primordial living things could have been compared to current organisms.
https://www.youtube.com/watch?v=gb7pZyks_HE&t=1151s

Pasteur proved that modern lifeforms can't form from non-living things.  That doesn't prove that there is some hard and bright line that prevents a micell containing enzymatic RNA from changing a bit into something we would recognize as "life".
Does your friend know about Friedrich Wöhler?  Who synthesized urea in a test tube, proving that the chemistry of life is not fundamentally different to the rest of chemistry?


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Forming a cladogram from a table of information

Can someone please give me some tips or help me build a cladogram from the following table of information? The outgroup is Lancelets and the first derived character is vertebrae, followed by Lampreys and jaws I believe.  It’s not until after jaws I have trouble figuring out where to link up the organisms and traits. I’m assuming you cannot repeat or remove traits. When I look online the simpler examples do not help me much for this branching issue...I hope that made sense. It’s probably simpler then I think but I’m having a mental block with it. Any help would be great, thanks

Hi and welcome to this site. There are dozens of "How to draw a cladogram" instructions on the internet. Could be please edit your question and add, how you would follow those instructions with your example, and at what step exactly you are struggling? This community expects you to show you own efforts, otherwise your question might be closed as homework(like) question.

I have looked online at written explanations and videos. I get the concept but for some reason I can only get so far with it until it just doesn’t make sense where to place the organisms in relation to the derived and shared characteristics. Most online examples seem to be a bit simpler with less variables.

@Maria When the data  size increases, one usually uses a computer program to build the tree, because it gets impossible to manually explore all the tree topologies and see which one is most parsimonious.

I think the clue is at each step to look for the trait that is shared by most of the remaining taxa.
In your example: 9 out of 10 taxa are vertebrae. So you are correct to pick this trait first and outgroup Lancelets.
Looking at the remaining 9 taxa:
8 have jaws, and a different set of 8 swim bladders or lungs
At this point you can pick one of those traits, as far as I know.
You chose jaws and outgrouped Lampreys.
In the remaining 8 taxa, the characteristic that is shared by most of them (7), is having swim bladders or lungs. Thus, you can outgroup Sharks here.
In that way, you can go on for the remaining traits and taxa.

Please leave a a comment  on how to improve the answer if you think it deserves a down vote.


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Cellular respiration in carnivorous animals
What is the equation for cellular respiration in carnivores as they don’t consume carbohydrates to break down into glucose in the following manner:
Glucose + oxygen -> water + CO2 +energy.
Do they (mammalian carnivores) primarily use ketones to produce energy without using glucose?
Does this mean that glucose is not the only energy source for humans/other animals?
Am I wrong in thinking that every source (protein, fats or carbohydrates) need to be convert into glucose for energy.

Welcome to SE Biology. I have edited your question, primarily to replace the term diet/sports  term "carbs" by the biochemical "carbohydrates". In addition I have tidied up a bit. I would express the opinion that your question is very naive for this site. Although you have received a useful answer, you really need to read a textbook on biochemistry to appreciate this and the topic in general.

Your guess is correct: glucose is not the sole source of energy in the cell!
While cellular respiration is the classic mechanism for energy production (in the form of ATP) in the cell, there's another process that's equally important and a little less well-known: beta oxidation. Beta oxidation is how fats and other lipids in the cell can be broken down to produce energy. In this process, the last two carbons in the long chain are sliced off and transferred to Acetyl-CoA, which can then be used in the citric acid cycle to produce ATP.
Here's the equation describing it:
$$C_{n}acyl-CoA+FAD+NAD^{+}+H_{2}O+CoA -> C_{n-2}acyl-CoA+FADH_{2}+NADH+H^++acetylCoA$$
And here's a good diagram from the Wikipedia page that summarizes it:

Courtesy of Cruithne9 on Wikipedia [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)]
This process is why fats actually have a higher energy density than sugars: 9 Cal/g, as opposed to sugar's 4. It's also why organisms tend to use fats as energy storage - while sugar and cellular respiration is great for immediate energy, fats are stable and energy dense so it's an evolutionarily favored idea to use them for long-term storage.
You're also quite correct that animals don't tend to have a lot of free sugars and carbohydrates, unlike plants. Instead, we've converted those carbs into the fat molecules via the reverse process, fatty acid synthesis. So, carnivores largely get their energy from beta oxidation and the metabolism of fats, rather than glucose.

Ah thanks for the equation. Wondered how the energy was produced ! Cheers


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Why is it thought that protein folding is determined solely by amino acid sequence?
It seems that it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids, but why do people believe that? Is it simply that no example of a protein with two different functional foldings (possibly with different functions) is known, or is there some theoretical reason that it would be impossible for such a protein to exist?

Comments are not for extended discussion; this conversation has been moved to chat.

See chat for a discussion of whether the premise of the question is valid.. that said, I think an answer can still be given (and it's okay if that answer challenges the premise), unless the community decides to vote to close.

As my comment on the question was removed I have edited the question instead to remove unnecessary and incorrect reference to principles of molecular biology, and to formulate the title in a manner that allows response by those who do not share the assumptions of the poster.

This question is, in my opinion, based on an incorrect premise but nevertheless throws up a number of points about protein folding and protein structure that can be addressed, albeit briefly.
The False Premise

“it is a generally accepted idea that protein folding is completely determined
  by the sequence of amino acids”

(My emphasis.)
No…
What is thought to determine protein folding?
The basic principle thought to be the main determinant in protein folding is thermodynamic. If possible†:

“A protein will fold so that the whole system of which it is a component is
  in the state with the lowest Gibbs Free Energy”

Thus, the protein itself is a major contributor — but not the sole contributor.
There is no argument that amino acid sequence (and composition) will be an important determinant of the contribution of the protein to the thermodynamically most favourable state, as the chemistry of the amino acid residues determine how it can interact chemically with its environment (albeit with weak interactions) and how it may interact with itself to produce a conformation which may have an appropriate effect on the entropy of the whole system.
So this is viewpoint is based primarily on chemical thermodynamic assumptions, rather than special ideas of molecular biology. An elementary exposition of this idea can be found in Berg et al. Section 1.3.4.
How can the environment affect protein folding?
One major influence is whether the protein is in an aqueous (hydrophilic) environment, like the cell cytoplasm, or a non-aqueous (hydrophobic) environment, like the cell membrane. In the former environment a protein will fold so as to expose its hydrophilic residues to the environment, in the latter its hydrophobic residues (discussed, in this paper, for example). Or it may be unable to fold at all in the wrong environment.
Another influence on the folding of a polypeptide chain may be the presence of another polypeptide chain with which it can interact, as in the case of the alpha and beta subunits of haemoglobin (see the classic paper by Perutz (1970))
Small molecules can influence the structure of a protein such as in the case of 2,3-diphosphoglycerate (2,3-BPG) on haemoglobin mentioned below.
When a protein is synthesized in an environment unconducive to correct folding it may require a chaperone protein to transport it to an appropriate environment.
And if the final structure of a protein requires covalent linkages, e.g.  between the SH groups of cysteine residues, an enzyme is need to oxidize them.
What evidence do we have for this?
We have evidence that some proteins that have been unfolded by putting them in environment that is thermodynamically unfavourable to their native (end enzymatically active) structure can refold when the environment is slowly returned to one that is favourable. This is the famous Anfinsen experiment with ribonuclease (described in this book section). Important as this experiment was in supporting the thermodynamic idea and showing that the contribution of the protein was inherent in its own composition,  it does not prove that this is what happens in vivo, nor that the structure formed is the one with the lowest thermodynamic free energy.
The importance of individual amino acids in the sequence is attested by examples such as the mutation of a single amino acid in beta-globin in sickle-cell anaemia (glutamic acid to valine). Under certain circumstances this allows the haemoglobin molecules to polymerize into long fibres because of the interaction of the hydrophobic valine residues with residues in  another subunit rather than with water.
Different states of folding are possible in a single protein
This addresses the section of the question regarding a possible:

…example of a protein with two different functional foldings

There are many so-called allosteric proteins that are regulated by interaction with small molecules (their environment) which cause a shift from one conformation to another. The example par excellence is haemoglobin, which is in an equilibrium between two states that are influence by the binding of oxygen, hydrogen ions (i.e. the acidity of the blood) and 2,3-BPG.
Another type of example is the shift that can occur between the secondary structures producing amyloid proteins.
†Can we be sure that a protein always adopts the structure of the lowest energy?
No.
The manner in which a random coil is a highly complex field, but, in brief, one can imagine that the path to the structure of lowest energy is blocked in some way (an energy barrier that would have to be overcome, perhaps) so that the structure adopted is, instead, the lowest attainable in practice.

[A rugged energy landscape with hills, traps and energy barriers and some narrow throughway paths to native — from Dill & Chan, 1997]

IMO this answer is self-contradictory. The highlighted statement 'A protein will fold ...' is in fact the Anfinsin position. To quote from his Nobel lecture: "...the  three-dimensional  structure  of  a  native protein in  its  normal  physiological  milieu  (solvent,  pH,  ionic  strength ..)  is  the  one  in  which  the  Gibbs  free  energy  of  the whole  system is lowest;  that  is,  that  the  native  conformation  is  determined  by  the  totality  of interatomic interactions  and  hence  by  the  amino  acid  sequence,  in  a given environment" and is  not a 'false premise'

@user1136 — I am answering the poster's question and his assumption, not discussing Anfinen's Nobel lecture. As for your thoughts on VSGs, I suggest that you incorporate them into an answer of your own. As a comment on my answer they seem to have no place.

@user1136 the answer does not contradict itself, and you even pointed out why. It is a false premise to assume that the conformation is totally determined by the sequence. It is true that the conformation is determined by the sequence AND the environment (at least for an instant; disordered regions don't adopt a stable conformation), assuming that 'environment' also accounts for post-translational modifications.


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Are tumor-associated antigens unique to cancerous cells?
Are tumor-associated antigens found only on the membrane of cancerous cells or just over-expressed on the membrane of carcinogenic cells?
In other words, are these antigens also found on healthy cells?

Welcome to Biology.SE! We encourage you to do some research on your own and ask questions  informed by what you have already learned. In particular, your question assumes that all cancer antigens are the same, which reading the brief wikipedia article on tumor antigens reveals to not be true.  ——— Please also take the time to go through the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

@tyersome I already know that cancer antigens aren't all the same but I want to know if these antigens can be found also on healthy cells or at least in some rare cases?

I'll answer a slightly different interpretation of the question, which is whether the proteins (epitopes, actually) that are presented by cancer cells are neoantigens (varieties of proteins that only occur in the cancer cell due to mutations) vs 'wild type' antigens that can be found in other non-cancerous cells, but are over-expressed (or improperly expressed) in the cancer cell.
For melanoma, some of the potentially most useful immune-system targets are 'normal' proteins that are over expressed in cancer cells and rarely expressed in non-cancer cells.  These include cancer testis antigens, which are proteins normally mainly expressed in germ line cells, but are accidentally expressed on cancer cells and lead to these cells being targeted by t-cells.  See (for instance) the paper Cancer testis antigen and immunotherapy, ImmunoTargets and therapy (2013), pp. 11-19.  For non-small cell lung cancer, Analysis of GAGE, NY-ESO-1 and SP17 cancer/testis antigen expression in early stage non-small cell lung carcinoma.

your answer is amazingly clear and useful

Carcinogenic tumor associated antigens correspond to any peptide chain (antigen) which triggers an immune response from the host. This means that they can be found anywhere inside, at the membrane, and outside of the cell: inside the cell (intracellular), at the cellular membrane and exposed to the extracellular environment, or even secreted.
Depending on the oncogene, they can be also eventually be over-expressed (anywhere there are supposed to be, including the membrane of cells).

It would be worth to mention that there is a major difference between antigens recognized by antibodies and peptide antigens presented by MHC-I, since especially in the tumor context small mutations make the latter ones more likely to be significantly different from endogenous non-immunogenic peptides/antigens

Good point Nicolai, thank you for your feedback, I'm going to edit my answer to include these points too.

Your answer would also be improved by recognizing that antigens are not necessarily proteins/peptides — for example, they will often be carbohydrates.


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Bicarbonate concentration in saliva

From the picture it can be seen that Bicarbonate is secreted into lumen of duct of salivary glands by exchanging Cl- ions.
So if flow rate of saliva is increased then its obvious that less Cl- is taken in the cells and less bicarbonate is secreted out.

At high flow rates, there is less time for reabsorption and secretion, and therefore the saliva is most like the initial secretion by the acinar cells. Thus, with the increase in flow rate the concentration of ions changes2

But it is also said that when flow rate increases the bicarbonate concentration also increases and when flow rate decreases bicarbonate concentration also decreases.
Doesn't this contradict the former fact?

The introduction to this paper clearly states that bicarbonate concentration increases with flow rate.

When did I denied that? My question is if bicarbonate is exchanged with Cl- as in the figure then higher flow rate should decrease the bicarbonate concentration as per diagram, but its quite opposite. Why so?

Also if flow rate is slow then bicarbonate concentration n must be higher , since more time for its secretion , bur the final result is opposite again.

I don't understand why you assert that high flow rate would have that effect. In fact since it is clearly an incorrect inference I think that you need to explain your logic. 'I think this thing but it is wrong, why is it wrong?' Isn't a very good question.

Let me explain, primary saliva formed isotonic to plasma, then in the duct much of Cl- is taken in and HCO3- excreted out, so this implies that as long as the saliva is in ducts, its concentration of HCO3- should increase and Cl- decrease. if I am correct till here then slow flow rate means higher HCO3-, but the textbook says quite opposite.

If flow rate is high then less time for Cl- to be taken up and HCO3- secreted so in effect the HCO3- will be less compared to normal flow rate, but the text says quite opposite again.

But all of this assumes that the rate of bicarbonate movement is constant.

Isn't it depended on Cl-? If yes then why there is not a concomitant change in Cl-?

According to this:

Yet another significant finding was the discovery of HCO3− absorbing mechanisms like NHE3 and NBC3 (NBCn1-A) at the luminal membrane of the ducts, which suggested the ducts absorb and scavenge HCO3− in the resting state.

So, initially saliva is isotonic to plasma, it is both reabsorbed and secreted, if its flow is slow, more of bicarbonate is reabsorbed, if the flow is high less bicarbonate is reabsorbed. Therefore when flow rate increases bicarbonate concentration increases.

Source of image:

At low salivary flow rates, HCO3- is reabsorbed by the striated duct cells and so very little reaches the mouth. At high flow rates, the striated ducts can't keep up and so HCO3- reaches the mouth at high concentration (<25mM)).
This makes perfect sense, from a physiological point of view. HCO3- is valuable to the body and not something to throw into the gut for no reason. The main purpose of unstimulated saliva is to keep the mouth lubricated, help you to talk and so on. Unless you are feeding the plaque bacteria, there is no great amount of acid to neutralise and therefore no need for a high HCO3- saliva. When you feed yourelf, and also your plaque bacteria, you stimulate salivary flow and produce a high HCO3- saliva, with a high buffering capacity, just when you need it.(Source)