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Question about proto-oncogenes and oncogenes?
My textbook says:

Growth-promoting genes are called proto-oncogenes. Some can be changed into oncogenes by a point mutation that alters the ability of the proto-oncogene to be switched off. They remain permanently switched on. Oncogenes promote unregulated cell division. Such cell division leads to a tumour.

Does this mean that the change from proto-oncogene to oncogene is not a mutation in the exon, but rather in the intron?
I hope I used these terms correctly. Thank you for any help :)

I think that this is a good example of how a question should be asked. You provided the passage that was causing you some confusion and you posed your question based on how you were thinking through the situation. Good job. :-)

I am going to add to @MattDMo 's answer a bit.
Proto-oncogenes Function, Developmental Program, and Regulation
Proto-oncogenes are normally functioning genes that are more often than not in the pathways that lead to mitosis and cellular replication. They have important roles in the development, growth, and maintenance of the organism. Proto-oncogene is an accurate description of the genes, but I unfortunately think that sometimes people think that the genes themselves are bad and that isn't the case.
Growth and development in multicellular organisms are highly regulated processes with many checks and balances. Certain cells need to grow in certain places at certain times, and then they need to go into and remain in interphase. If they don't, or they do things at the incorrect times, the multicellular organism will not develop properly or will develop conditions such as cancer.
It is often these points of regulation that become dysregulated when a proto-oncogene becomes oncogenic. If there are regions of allostery that are affected by a mutation in the coding sequence (exon) and a control molecule that represses the activity of the enzyme through conformation change can no longer bind, then that enzyme can remain active, always turned on.
You can also have a situation where you have transcriptional regulators of proto-oncogenes that can be effected making the gene product oncogenic. If there is a mutation in an enhancer (intronic) of the gene that affects the binding kinetics of enhancers leading to a great increase in transcription, this concentrational difference can lead to uncontrolled grown and tumor formation.

You could also have a situation like MattDMo talked about where you generate frameshifts and premature stop codons, though I would think this is more relevant in tumor suppressor gene mutations, as these types of mutations tend to kill the protein rather quickly, but it is possible that it can cause a problem.

RAS
There are however other types of mutations that can effect proto-oncogenes, making them oncogenic. One classic example is RAS. RAS is a G-protein that associates with G-Protein Coupled Receptors at the cell surface and transduce signals into the cell leading to the initiation of the cell cycle. In its inactive form, RAS is bound to GDP. When a signaling molecule binds to the plasma membrane receptor it is associated with the RAS molecule, a Guanosine-Exchange Factor removes the bound GDP, and because of concentration, GTP enters the binding pocket and activates RAS, which activates a phosphorylation cascade, leading to transcription of growth factors.
Normally RAS has GTPase activity and will quickly cleave the gamma phosphate of the GTP in its binding pocket, leading to GDP and inactivating itself. However if the mutation were to knock out this GTPase activity from RAS, then it would have no way to cleave the Gamma phosphate, and therefore it would remain activated and continue the signal transduction, even when it should not.
However, the problem does not need to be with RAS to drive RAS to oncogenesis. If RAS GEF becomes hyperactive and starts to exchange GDP for GTP constitutively, whether or not there is a signal, then RAS will constantly be activated, even if it is still able to cleave the Gamma phosphate and inactivate itself. So there can be Cis-acting drivers of oncogenesis and Trans-acting drivers as well.

I am providing you a link to Scitable's page on Proto-oncogenes to Oncogenes to Cancer. It gives the following summary which is a helpful summary:

Point mutations, deletions, or insertions that lead to a hyperactive
  gene product
Point mutations, deletions, or insertions in the promoter region of a proto-oncogene that lead to increased transcription
Gene amplification events leading to extra chromosomal copies of a proto-oncogene
Chromosomal translocation events that relocate a proto-oncogene to a new chromosomal site that leads to higher expression
Chromosomal translocations that lead to a fusion between a proto-oncogene and a second gene, which produces a fusion protein with oncogenic activity

thanks for expanding, I didn't have time to write this much :)

The mutation(s) can be anywhere, but frequently they are in the coding region of the gene - the exons. These oncogenic mutations can result in a reading frame shift, a premature stop codon, or a codon change that results in a different amino acid being incorporated into the protein.


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Effects of HRT on transgender(M to F) physiology and athleticism.
I often heard of athletes in the Olympics who would be accussed of having an advantage because they were intersexed.
Now I know transgenderism and being intersexed are not the same thing, but they can both involve Hormone replacement therapy.
Therefore would a transgender women (ie: a person assigned male at birth, who transitioned to female) have advantage over cisgendered(not transgender or intersexed) women in sporting events due to anatomy or physiology from previously having a male form?
To add detail, I guess it would depend on the state of their transition, so one could use MMA competator Fallon Fox, as an example, or any other transgender women.
My thoughts on the effects of HRT on athleticism for transgender people is that if they were more advantageous, then they should be dominating their respective fields.
As for the biology, I know that bone growth stops at around 20, but how would the HRT affect their muscles, and would muscles even matter without the corresponding frame?
.

The only advantage that I could see is if they stopped taking HRT female hormones and allow their male hormones to build back up in their system, though I think that people probably made the choice to undergo reassignment for reasons other than gaining competitive advantage in sports.

@AMR            I totally sympathize with trans people and their desire or need to transition, but as to your point, why would a build up of male hormones give them an advantage?

Why do athletes inject themselves with testosterone? It is needed to increase muscle mass. Male hormones lead to bigger muscles, so if the person was originally XY, then they will begin to produce more testosterone if they come off of the HRT. If they had reassignment surgery, then it will obviously be less than an XY person with testicles, but there will be a higher level of testosterone and other androgens that will cause the body to begin to masculinize again. I am not going to say that there are women who cannot outperform men, but all things being equal, that may lead to an advantage.

One thing I think I left out, is that I believe that Male to Female transgender individuals also take androgen blockers to bring them down to similar levels as XX females. Females also produce androgens, but in much lower concentrations or they make fewer androgen receptors in their cells than males.

Interesting question, but pragmatically, the answer is irrelevant because despite the current state of your naturally occurring hormones, you cannot compete in any sport while using HRT, even if for legitimate medical reasons, such as having only one testicle. As for how any sporting commission would choose to classify any transgendered person, whether male or female, probably greatly depends on which sporting commission.

@fredsbend.       But fallon fox is on hrt according to this article, http://www.mmaweekly.com/transgender-fighter-fallon-fox-says-she-is-actually-at-a-disadvantage-to-her-opponents.       .        and she is an active combatant.

@RoSiv Interesting. MMA is a relatively new sport and the rules are still quite fluid. I doubt we'd ever see this in baseball or traditional triathlons (i.e. Ironman), for example. This is interesting: "When you test her, she’s gonna come out with low testosterone levels and muscle mass that is remarkably similar to her counterparts." It seems that they would advocate that the MMA allow any opponent against another as long as they hormonally appear similar. That would change male/female divide sports to something else entirely. This is all off-topic though.

We have two groups of people or better to say scientists and specialists that have their own ideas and theories and approvements.

People that are relay on genetic related ideas that mostly consider rule of Y chromosome on men and how some genes' rules will not be diminished only by hormone therapy or non genetically engineering methods.

Case example:

Chloie Jonsson, 34, who transitioned more than eight years ago, is legally recognized as female in the state of California. Despite the medical community's consensus that transgender women do not have a competitive advantage over cisgender (nontrans) women, Jonsson's application to participate in CrossFit's women's division was rejected with a bizarre letter claiming she and her supporters do not understand "the human genome" and "fundamental biology." In response, Jonsson filed suit against the fitness giant.
The letter from CrossFit general counsel Dale Saran reads:
"We have simply ruled that based upon [Chloie] being born as a male, she will need to compete in the Men's Division. The fundamental, ineluctable fact is that a male competitor who has a sex reassignment procedure still has a genetic makeup that confers a physical and physiological advantage over women. ... Our decision has nothing to do with 'ignorance' or being bigots — it has to do with a very real understanding of the human genome, of fundamental biology, that you are either intentionally ignoring or missed in high school."
  Later, Saran disputes the statement made by Jonsson's attorney that "by all accounts, both physically and legally, Chloie Jonsson is a female."
"This is simply wrong as a matter of human biology and if you can't see that, there really isn't much to talk about," writes Saran, citing Encyclopedia Britannica. "Chloie was born, genetically — as a matter of fact — with an X and a Y chromosome and all of the anatomy of the human race. Today, notwithstanding any hormone therapy or surgeries, Chloie still has an X and a Y chromosome."

To add some details to group one's idea, if you think of some genes and their rules in men that makes them more accurate and more muscular than women in the field of physical activities, you'll get to the point of how to control or change behaviour of these genes in the body of a man to make him woman, both muscularly and neurologically which is not possible for now because we need some very detailed and powerful calculations to know the exact equilibrium of a man genome as if he was a woman.
To change the complicated mechanism of Y chromosome on Biochemistry and behaviour of other chromosomes we have so much to learn and we need very fast computers to simulate the behaviour of molecules and new formation of mass body.

And we have other ideas by people who insist on level of hormones that has a great effect on mass of bone and muscles in men and women regardless of how their sex and genome is.

Case example:

Eric Vilain, Director of the Center for Gender-Based Biology and Chief Medical Genetics Department of Pediatrics at UCLA, says of any perceived advantage a transgender woman may have, “Research suggests that androgen deprivation and cross-sex hormone treatment in male-to-female transsexuals reduces muscle mass; accordingly, one year of hormone therapy is an appropriate transitional time before a male-to-female student athlete competes on a women’s team."

A great article and detailed explanation by an example that helps to answer your question is here.

source: Stack Exchange

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

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Animal gene in plants
Usually only microbes, specifically bacteria are used to express genes of other species for various functions. But, it is possible to try and express an animal gene into a plant. Bacteria like Bacillus thuringiensis is used in many plants like cotton, to modify them to BT cotton with insecticidal properties. Can one use an animal gene to get those characteristics in the plant?

What kinds of characteristics you are looking for ? I mean you can express successfully lot of animal proteins, pharmaceuticals and antigens into plant (Julian KC 2003). But I don't think they are any way important to plants.

One example that I am aware of where an animal transgene was put into a plant was to produce the ZMapp, a chimeric, monoclonal antibody against the Ebola virus.
This is a wikipedia article on ZMapp, that gives you an idea of the process.
Other than this, I am not all that familiar with plant transgenics, other than Round Up resistance genes that were transfected from soil bacteria that developed a resistance to the active chemical in Round Up.
Hopefully other answers can provide you with more details, but these are the two examples that I know off the top of my head.

A few years ago plant scientists introduced a protein (afa3)in tomato from Winter Flounder, a type of fish surviving freezing conditions. The idea was to make a frost resistant tomato but I believe they did not have much success. Anti-GMO activists had a field day however with baseless claims of making tomato's smell like fish and other nonesense.

I was looking at adding a particular gene of the penguin that makes its skin thick to survive the winter, in a cotton plant. Do you think that could work?

I don't know much about pinguin skin but I know it is very very different compared to plant epidermis. It seems rather unlikely but it all depends on the gene

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


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Which algae grow fastest under optimal conditions?
I'm interested in what the fastest growing microalgae are under optimal conditions for photoautotrophic growth (energy from photosynthesis only).  Fastest can be interpreted as either shortest doubling time, or maximum biomass yield per day per unit area.
Many of the algae investigated for biofuels are fast-growing, for example Nannochloropsis and Ankistrodesmus.  There are many publications that give yields in pond culture or in outdoor photobioreactor, for example Nannochloropsis at 20g/m^2/day (dry mass).  However it is not as common to see yields for lab photobioreactor (axenic, possibly with continuous illumination, and all other conditions optimized for fast growth).  I'm mainly interested in what family of algae would be evolved for fast growth, and where they may be found in nature.
EDIT As one of the answers pointed out, algae can grow heterotrophically as well and that may not be a fair comparison.  I changed the question to be about autotrophic growth (from photosynthesis) only.

The answer to your question depends on many variables. To narrow down the list of possible species it might be helpful to list under which conditions you intend to grow this algae and whether you want to give an additional carbon source such as glucose or acetate.
To give you an idea why this is important: the fastest growing alga I have ever worked with is Chlorella sorokiniana with double timings in the range of two hours. However this was in acetate containing medium and it would not have relied a lot on photosynthesis to grow nor would this make a lot of sense in open pond cultivation systems.
In terms of photoautotrophic algae, we have seen the most consistent quick growth (OD) in our system (Algem photobioreactor) for Dunaliella species. But this is based more on experience than rigorously testing a lot of species. In general there also seems to be a correlation between size and growth speed. Some cyanobacteria have a growth rate of around two hours Article

Thanks!  You are quite correct, I should have mentioned that I'm interested in the fastest possible photoautotrophic growth.  There could be extra CO2 but not extra organics in the growth medium (well, maybe vitamins but not organic energy sources).


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Why don't the minus ends of microtubules shrink?
Is this because $\alpha$-tubulin is always in the GTP state? Or is it because $\gamma$-TuRC stabilizes the minus end?

Depolymerization of microtubules does occur at both ends, it is only that the kinetics are different at the plus-end than at the minus-end. Due to dynamic instability, depolymerization occurs about 100 times faster at the GDP end than the GTP end, but both will depolymerize, just at different rates.


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How does increased heat increase the rate of metabolism?
I have heard that taking a hot shower helps

blood circulation
metabolism.

For (2) metabolism, I think that the rate is increased since kinetic energy is given to compound to bond with enzymes to react. Is this the only reason? In addition, why is (1) true?

I don't think a hot shower has any substantial effect on body temperature, since this is carefully regulated by several mechanism to remain around 37$^\circ$C. When you expose the body to heat, you induce a response where the body increases heat loss and possibly reduces internal heat production in order to maintain the core temperature.
It is true that heating the body will increase blood circulation in the skin; this is a way for the body to carry heat from the core to the surface, where it can dissipate (radiate away). As for metabolism, I think the response to heat is less well studied than the response to cold, but presumably metabolic rate (specifically, mitochondrial respiration) will decrease in order to reduce internal heat generation, in order to maintain body temperature. Again, these are homeostatic responses that occur before there is any marked change in body temperature. Here is a review article on these mechanisms.
If you would expose the body to enough heat so that these normal responses cannot compensate, the body temperature will actually rise. Beyond 2-3 degrees (a normal fever), this is very dangerous because it will disturb a number of cellular processes. Cellular metabolism would certainly be affected, but mostly  because some enzymes have narrow temperature ranges where they can function; I don't think the actual heat energy of metabolites is an important factor here, but I don't know of any study on this. A variety of other proteins and cellular structures will be similarly affected. This will eventually affect key functions in the nervous and circulatory systems, which is life threatening. The Wikipedia page on hyperthermia is a good starting point for more information on this.


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Metrics or operations on genome sequences in human genomic research?
Edit distance may be an important metric for measuring the similarity of two genome sequences.  For example, if A = GCAATT and B= CGAATA, then the edit distance of A and B is 3. Such a metric is intuitive and may be useful in comparing the similarity of two sequences.
I wonder is there any more complex or advanced metrics used in human genomic research?

The question of how similar two DNA or protein sequences are, is one of the most important problems in bioinformatics. While there is no definitive answer Bayseian statistics are often used to group sequences. There is a good explanation of the theory on this wikipedia page.
Alternatively one of the most commonly used programs to find similar sequences is BLAST. It is getting a little bit dated but you can find an overview on the statistics used by this program on this page
But there are many other methods out there.


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How does discontinuous distribution provide evidence for evolution?
One of the evidences for evolution is bio-geographical evidence.
In it,'discontinuous distribution' is mostly cited as an evidence.
For example,
Alligators are found only in south-eastern US & eastern  China; elephants are found only in Africa & in & around India; lung fishes are found only in South America, Australia, Africa.
Their distribution is discontinuous due to possible changes like continental drift etcetera.
But, I am not understanding how these discontinuous distributions prove evolution.
Can anyone help me explain how they provide evidence for evolution?

Could you link to a source using the discontinuous distribution as evidence for evolution?

@rg255: After googling it, I got this: https://books.google.co.in/books?id=E_ooNitL-pkC&pg=SA1-PA88&lpg=SA1-PA88&dq=discontinuous+distribution+proof+of+evolution&source=bl&ots=jkto-JYwcb&sig=Xh2RcSy3tVxRecdtNKxC0t6IYvw&hl=en&sa=X&ved=0ahUKEwi3-aO7xYTLAhVGH44KHQdOCMEQ6AEISjAI#v=onepage&q=discontinuous%20distribution%20proof%20of%20evolution&f=false

It doesn't let me view that - do you have another source? ("you have either reached a page that is unavailable or you have reached your viewing limit for this book")

@rg255: Well, you can google out that; you can find many links. Would it work if I take snapshot of my book and upload it here?

I would like to see how people are using it as evidence, so context would be good (perhaps quote the text) - then I can try to explain why they consider it evidence

@rg255: Actually it would be too long if I quote; I'll upload a snapshot.


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How does one find the corresponding SNPs in the pair of chromonosmes in a FASTA file?
You might say I'm an amateur bioinformatician, or trying to become one.  I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format.  I now see a single series of nucleotides, and their complements, for each chromosome.  What I don't see is two corresponding sequences.  SNP data (e.g., SNPedia ) cites (if I understand it correctly) the SNP at the same site on each chromosome in the pair.  I don't know how to determine my variation, since I see only one nucleotide at any given site, not the pair.
Pretty sure I'm missing something fundamental here.  Thanks for any help navigating this jungle!

"Two corresponding sequences": corresponding to what? What SNP data? What SNP should be on both chromosomes? The link you gave seems to be for a SNP that can be either hetero- or homozygous. Why are you assuming it is homozygous in your data? What are your data? Please [edit] your question and clarify, it is very hard to understand what you're asking at the moment.

Sorry if I'm not expressing myself well... I'm kinda new to all this.  I am, in effect, talking about what I should expect to see in the case of a heterozygous SNP.  The question is simply this: If the particular genome I am examining happens to have a heterozygous SNP at some site, let's say (C;T), then how/where would I expect to see this in my data?  A consensus reflects the more prevalent read at that site, but, in this case, I would expect about 50% of the reads to be C, and 50% T... so the consensus isn't useful.  Am I wrong?

If you are looking for simple one off queries it might be better to load the BAM file and a relevant reference genome into a browser like IGV and simply navigate to that specific position.
For some data I had lying around a heterozygous SNP would look like the picture below, there has been an A to G SNP and a C to T:
For longer lists of queries I would take a look at BEDtools: https://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html
If this does not help you, I recommend you ask your question on https://www.biostars.org/ There you will find help from true bioinformaticians.

Right, so I've been looking at the BAM file, but I've yet to find any instance of a site where I see 50/50 reads of two nucleotides (e.g. 50% C and 50% T).  Is this what I should expect to find in the case of a heterozygous SNP genotype?  If so, then should I just ignore the consensus and just look at the BAM file?  I'd just like to validate that I am on the right track here...

I adjusted the answer to include a picture. Hopefully everything is more clear now

I wouldn't necessarily expect regions of heterozygosity to be apparent from a consensus fasta.  I'd eyeball if you know some potential sites, or run your .bam through something that will call SNPs.


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Lac operon: How can lactose enter the cell in the absence of lactose permease?
My textbook states that

lactose permease...transports lactose into the cell

and

When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor protein

My question is, how can lactose enter the cell to bind to the repressor protein to allow beta galactosidase and lactose permease to be synthesised if there is no lactose permease present to transport the lactose into the cell?

Based on the questions you are asking, you have good intuition about the information you are reading. Out of necessity introductory textbooks are cursory and only cover the very basics of only the most important of topics. They basically are teaching you the vocabulary of biology and keeping the detail at arms length. Keep reading and keep looking deeper, you are on the right track.

Here's everything you need. It's called the lactose paradox:
http://sandwalk.blogspot.it/2008/10/lactose-paradox.html

Introductory textbooks will not get into the details of the lac operon.
Basically, the operon is expressed constitutively at a low level that means that Beta Galactosidase and Lactose Permease are expressed at low levels by the bacterium. This is because it takes a little bit of time to build up the concentration of LacI in the cell before it can start to bind the operator.
The LacI repressor only binds the operator in the absence of Lactose in the cell's environment due to the fact that allolactose allosterically binds the LacI repressor and affects that molecule's ability to bind the operator. So RNA polymerase can bind the promoter of the Lac operon at some low rate and continue to produce the protein.
When the cell no longer has glucose, it generates cyclic AMP, which induces the CAP protein to bind to the CAP site, just upstream of the promoter of the Lac Operon. CAP associates with RNA Polymerase, and this makes the promoter very active. Beta Galactosidase and Lactose Permease levels increase rapidly.
Where you see the full effects of the LacI repressor is when neither Glucose nor Lactose are present in the environment of the cell. At this point the repressor binds to the operator and blocks transcription by DNA Polymerase.
I hope this helps. I have an entire book that covers the Lac Operon, so even though this is a bit expanded of an explanation from a basic textbook, it is still a summary.

Thank you for your informative reply! I'm just still slightly confused; by 'the operon is expressed constitutive lay at a low level' do you mean that even with no lactose present, a repress or protein is not constantly bound and therefore some beta galactosidase and lactose permease are expressed? This seems to contradict with 'when neither Glucose nor Lactose are present in the environment of the cell...the repress or bonds to the operator and blocks transcription by RNA polymerase'. I apologise for misunderstanding and being quite slow with this, and thank you again for your help :)

@21joanna12 it is going to take me a bit of time to update my answers. But very briefly, DNA binding proteins all have a certain on/off rate associated with them. There will be certain instances where the operator is clear and RNA Pol can bind. Also proteins have half-lives and are degraded, so depending on the cytoplasmic concentration, there is a probability that the promoter will be free to be bound by RNA Pol. Cell biology is unfortunately not digital as it is often described in textbooks. I'll try to get to a better answer soon.


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What does 'direction' mean in the statement "mutations are non-directional"?
I was reading the Mutation theory of De Vries; there I encountered this following statements

Mutations are discontinuous, random & non-directional.This is in contrast to Darwinism where variations are continuous & unidirectional.

and

[Hugo deVries] believed that it mutation that causes evolution and not the minor variations (heritable) that Darwin talked about. Mutations are random and directionless while Darwinian variations are small and directional. Evolution for Darwin was gradual while deVries believed mutation caused speciation and hence called it saltation (single step large mutation).

Could anyone please explain what direction means in the two statements above?

Can you please indicate your sources?

(I give an explanation to the statements, please understand that almost all  evolutionary changes are mutational in the basis).
Let's say the greater height is advantageous in one area, while in other area the smaller height is advantageous. In the former area, the direction of phenotypic changes will be to the individual with higher height, while in the latter the direction will be to smallest one. The evolution "seeks" example to follow, so you "can" find which one was an example to move towards to (who is the reference point).
In the case of mutations the is no apparent direction. These chaotic changes can be advantageous, or may be not - one cannot find a particular direction towards some "example" / reference model.

Hi, sir. Does that mean mutation is not influenced by Natural Selection?

Natural Selection is not a physical object, it is artificial term which describes the general biological changes in species. The process of "natural" selection is naturally-"passive" in the terms of causality. Mutations in turn are physical changes that take place in genes, they can be beneficial, detrimental or neutral, they are influenced by multiple factors and the result of all of these influences  over time can give us "Natural Selection" picture.

Thanks; +1 ! But could you tell what continuous means in the quoted line above?

If you will work hard in ten years you will earn 1 billion dollars - it is continuous process, you can explain it in understandable terms. If you win  1 billion in a lottery today - it is discontinuous, abrupt change, which actually have no any other explanation other than chance. Good luck %)

"In the case of mutations there is no apparent direction."
The following paper published on August 25, 2015 claims that there are indeed directed mutations.
Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005477

The evolution "seeks" example to follow, so you "can" find which one was an example to move towards to (who is the reference point). It is often tempting to give a agential view of evolution when explaining to a lay person but one must keep in mind that such agential view will be taken much more literally in their mind than they will in the mind of the one who explains it. I think we should really avoid it. It is actually not so hard to avoid it.

It simply means that mutations happen and do not, in and of themselves drive evolution.
Mutations do not necessarily need to be advantageous or deleterious, they just happen and exist within the population at some low background. However when you combine mutation with environment and Natural Selection, then certain characteristics are favored while others are not. If there is a change in the environment, then what was once advantageous could become neutral or disadvantageous, while mutants that were always in the background end up with a competitive advantage. Also note that mutations need to occur in the germ-line in order to have any effect on the population. Mutations in somatic tissue cannot be passed from one generation to the next.
Evolution by Natural Selection (Darwinism) in contrast moves forward in one direction. Once change is selected for and speciation takes place, there is no turning back. The new species can not revert back to the old one. It moves in one direction, based on the conditions in the environment and individuals in the population capable of adapting to change should it arise. If the mutation has given those individuals a reproductive advantage within that environment, then their progeny will inherit the trait while the progeny of other may be less fit and reproduce less or not at all, and Evolution moves forward.

"It simply means that mutations happen and do not, in and of themselves drive evolution."
The following paper published on August 25, 2015 claims that there are indeed directed mutations.
Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005477

One poorly written paper with no significant data does not overturn a theory. You can always design an experiment to produce the results that you want. And nothing evolved. They didn't have a new species, just bacteria that were able to survive selection. They did not test to see if the bacteria that "reverted" were diploids a functional gene on a F Plasmid. Also the bacteria have a AmpR marker, but they do not once mention that they used antibiotics in their medium. With the small number of "revertants," those could have just as easily have been contaminants.

And nobody said that you cannot have revertants. There are a good number of examples of gene conversion that occurs from yeast through to mammals. Look up Yeast Mating Type Switching.

"One poorly written paper with no significant data does not overturn a theory."
Would you explain in detail why you think the paper was poorly written?
Also would you elaborate on why you think it has no significant data?

If you do not know how to read a research paper critically and determine its significance, then maybe you should stop vandalizing the site with posts that add nothing to the discourse.

That's not an answer to my questions. Do I have to repeat them?

@AMR I think you understood the term directionless as to mean that a given mutation is not necessarily beneficial or deleterious while I think the term 1) can apply to other phenotype than fitness and 2) it probably refers to the average effect of mutations at a given locus than to a given specific mutation.

@AMR Evolution by Natural Selection (Darwinism) Darwinism is so much more than just natural selection. It is a basic misrepresentation of Darwin that all he is panselectionist and understood nothing about evolution but natural selection. This misrepresentation often lead some lay people to believe that there is nothing in evolution but natural selection

You also consider speciation as a necessary consequence of natural selection which is obviously wrong. -1

Directional vs directionless
What is the meaning of directionless in this context
First note that the term directionless is not used (or not often at least) in the scientific literature.
I will explain the term "directionless" by talking about mutations first. Consider a given phenotype, say height. What directionless means in this context is that new mutations aren't more likely to increase than to decrease the phenotype.
Are mutations really directionless
It makes things easier to explain to someone the very basics of evolutionary processes to tell that mutations are directionless. It is however not necessarily true. When mutations are not directionless, we talk about mutation bias (see for example Eyre-Walker 1998, Harr and Schloterrer 2000 or Shah et al. 2010 ).
An obvious trait on which mutations tend to be bias is fitness. A mutation is much more likely to be deleterious than beneficial.
Is selection directional
Yes, if you talk about fitness. Selection select variants yielding that are associated to higher fitness. Note however, that if you look at, say, height, some environments may select for taller individuals, while other environments may select for shorter environments. As such selection is no "directional" on any phenotype.
Mutations and selection
Something is potentially misleading in your quote
It is true that Darwin did not quite grasp the saltatory nature of mutations, however the text puts in opposition the concept of natural selection and the one of mutation which is can be very misleading to a layman. I would need the entire text to really give you a better opinion on. Please always indicate your source!
Mutation and natural selection
In short, mutations (whether biased or not) is the ultimate source of variation on which selection can act. Selection increase the frequency of the variants (called alleles) that are associate to higher fitness. Through selection a few alleles end up to very high frequency up to the point that all individuals carry the same allele. This cause an increase in the mean fitness of the population but also removes variation (as deleterious alleles are washed out). Mutations introduce new variation that selection can select on.


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Osmolarity vs. Tonicity
We're learning about osmoregulation in AP Biology and the terms Tonicity and Osmolarity are really confusing me. I watched this video on Khanacademy to try to understand what the difference is, and from my understanding Tonicity refers to strictly two solutions (ex: you can't take a cup with water and salt in it and claim it's hyper, hypo, or iso- tonic because there's nothing to compare it to), whereas Osmolarity refers to the composition of the single solution itself.
But then my Campbell's biology textbook completely confuses me. It has the following picture and text:

...osmosis, a special case of diffusion, is the movement of water across a selectively permeable membrane. It occurs whenever two solutions separated by the membrane differ in osmotic pressure, or osmolarity (total solute concentration expressed as molarity, that is, moles of solute per liter of solution).....If two solutions separated by a selectively permeable membrane have the same osmolarity, they are said to be isoosmatic. Water molecules continually cross the membrane, but under these conditions they do so at equal rates in both directions....

And then as if to clarify, they claim that tonicity refers to "solutions of known solute concentrations"...but how does this differ from osmolarity?

You're correct that tonicity needs two solutions to define.
Osmolarity (or osmotic concentration) is the measure of solute concentration, defined as the number of osmoles of solute per litre (L) of solution (Osm/L).
Tonicity, on the other hand, refers to the relative concentration of two solutions separated by a semipermeable membrane.
The difference is based what is considered for osmosis and tonicity. In case of osmosis, it is the water (or solvent) which moves across the membrane, while tonicity depends on the solutes which cannot move across the membrane. From Wikipedia:

... osmolarity takes into account the total concentration of penetrating solutes and non-penetrating solutes, whereas tonicity takes into account the total concentration of only non-penetrating solutes.


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Games with non-uniform interaction rates
Background:
Many models in evolutionary game theory assume uniform interaction rates. For instance, consider the $2\times 2$ game:
\begin{array}{l c c}
    & A & B \\
    A & a & b \\
    B & c & d
\end{array}
The fitness of the strategy $A$ is $xa + yb$, where $x$ and $y$ are the frequencies of the strategies $A$ and $B$, respectively.
Taylor and Nowak "Evolutionary game dynamics with non-uniform interaction rates" (link to the paper) rewrite the fitness function to allow for non-uniform interaction. In particular, the fitness of the strategy $A$ and $B$ become:
\begin{equation}
f_{A} = \frac{ar_{1}x + br_{2}y}{r_{1}x + r_{2}y}; \quad f_{B} = \frac{cr_{2}x + dr_{3}y}{r_{2}x + r_{3}y}
\end{equation}
According to this model, ``[a]nalogous to a chemical reaction, an $A$ player interacts with another $A$ player with reaction rate $r_{1}$, an $A$ player and a $B$ player interact with reaction rate $r_{2}$, and a $B$ player interacts with another $B$ player with reaction rate $r_{3}$." (p.244).
Question: What would be an intuitive interpretation of $f_A$ and $f_B$ (as defined by Taylor and Nowak)?

Further comments: When $r_1 = r_2$ and $r_2 = r_3$, we have the situation with uniform interaction. But I am not sure how to interpret the above fitness function for when $r_1 \neq r_2$ (and $r_2 \neq r_3$). I thought of interpreting $r_1$ and $r_2$ as the conditional probabilities $P(A\mid A)$  and $P(A\mid B)$. However, if I'm right about this, $f_A$ would have to be  $r_1 a + r_2 b$ instead. For this reason, I am under the impression that the $r$s should not be conditional probabilities. But if the $r$s are not conditional probabilities, what are they exactly?

To make sure I understand your interpretation, does it involves that 1) $r_1+r_2=1$, 2) if $r_1=r_2$, then individuals interact randomly without preference, 3) If $r_1>r_2$, then individuals interact preferentially when individuals playing the same strategy and 4) if $r_1<r_2$, then individuals interact preferentially with individuals playing a different strategy? If the above is true I would expect the mean fitness in the population to be $\frac{1}{2 (x+y)(r_1x+r_2y)}$ while the equation suggests that the mean fitness is $r_1x+r_2y$.

@Remi.b 1). Yes, if my interpretation is correct. 2). Yes. 3 and 4) Here is a quote from the paper "If r1 > r2 and r3 > r2, then players prefer to interact with their own kind. If, however, r1 < r2 and r3 < r2, then mixed interactions (between A and B) are more likely."

@Remi.b Note that I added a formula for $f_B$ to make my question more clear.


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Blood draw from the elderly or those with tiny veins
A lot of people have very small veins making it next to impossible to draw blood.
Would a nitroglycerin tablet (or some other vasodilator) before drawing blood help to enlarge veins?

When we need to collect blood from patients we typically draw blood from peripheral veins that are superficial. These are the veins that you can see in some individuals hands and forearms. There are superficial leg veins that are visible. Drugs like nitroglycerin or other vasodilators do not have significant effects on the superficial veins that you'd be trying to withdrawal blood from in the extremities (i.e. arms and legs).
If you wanted to really engorge someone's veins, you'd likely have to load them up with intravenous fluids. However, this would not be safe in patients needing routine blood draws; especially elderly people who might become fluid-overloaded to the point at which the develop congestive heart failure. Younger patients might temporarily have minimal increases in their circulating blood volume, but their kidneys would very quickly eliminate the excess fluid as urine.

I think the use of drugs for simple things like a blood draw should be a last resort. Having a cup of tea or two can work wonders at raising your blood volume and making the blood draw easier.
A nitroglycerin tablet would risk systemic side effects in many patients, so a topical ointment could be used to minimize these effects. Nitroglycerin has been applied topically over the venipuncture site to cause a transient vasodilation, and potentially make the blood draw easier. There are varying reports on its efficacy - Hecker et al. (1983) found nitroglycerin ointment helped venipuncture, Griffith et al. (1994) found it made no difference in vein size.

the Hecker et al. study is a small, poorly conducted study - you can't even tell if they used the proper statistical analysis. I wouldn't get very excited over it - I would bet someone could not reproduce this experiment. The size of the veins doesn't even appear to be changed with the nitroglycerin in almost all of the patients, and it appears that 2 or 3 patients were particularly difficult sticks (and just happened to be in the placebo group). We don't routinely use this clinically in the ED or anywhere else in the hospital/clinics - I doubt nitroglycerin ointment actually helps.


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What is the role of glycine in the running buffer for SDS-polyacrylamide gel electrophoresis
We used pH6.8 in stacking and pH8.8 in resolving gel. In the class, the professor explained that the glycine change is like:
glycine+ <-------> +glycine- <------> glycine-

it is said that most of the form will be +glycine- and glycine-. Why? And why does it change the charge when it runs from the stacking gel to resolving gel? What is the role of glycine in the running buffer for SDS-polyacrylamide gel electrophoresis?

In your original query I believe that you are confusing/conflating the electrophoresis with the transfer to a membrane. The electrophoresis is abbreviated SDS-PAGE. After the electrophoresis is complete you have several choices, including: fixation of the proteins in the gel followed by staining to visualize the protein bands; autoradiography if any of the proteins are radiolabelled; or transfer to a membrane if you have an antibody that recognizes the protein of interest. I have edited the post to correct this. I believe you are asking about the composition of he Tris-glycine buffer.

Gly is an amino acid its charge depends on the pH. It is probably ladder component, but I am not an expert of this. http://gmwgroup.harvard.edu/pubs/pdf/951.pdf

The pH of stacking and resolving gel are set in such a way that one is above and one is below the pI of gly (5.97).Therefore, Gly has two different charges in stacking and resolving gel. That is in stacking gel gly has no charge (which will allow the protein to stack according to size in this part of the gel rather than separating because of presence of gly in between the protein molecules, constraint in separation of proteins) but in resolving gel charge is negative since the pH is higher (constraint in movement of proteins no longer present so separation of protein based on size possible).
Hope this was helpful..

Could you add a reference or link to allow for background reading?

since the stacking gel have a ph of 6.8 the glycine will attain a neutral charge(by the isoelectric point and ph relation)thus the chloride ions travel faster followed by the sample and then at the last glycine ions,thereby stacking the sample in between both.when it reaches the resolving gel the ph increases which gives glycine a negative charge.so they travel faster along with the chloride ions leaving back the sample to get seperated without any hinderence

Welcome to Bio. Could you add sources to your answer?


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Why are kidney discard rates so high?
A recent report from UNOS states:

The kidney discard rate has returned to pre-KAS levels, dropping from 20.2 percent in the first six months to 18.4 percent in months 7-10.

To me, this seems quite high considering the number of people waiting for a kidney. Why is this rate not lower?

If you click through the link on the page you linked to is a presentation, https://www.transplantpro.org/wp-content/uploads/sites/3/KAS_analysis_6month.pdf Towards the end is a slide that shows reasons for discarding. The majority were biopsy findings (probably some infection or precancerous lesion) no donor found in time (Not all organs are a match of the people on the transplant lists)

Not a transplant surgeon, but... we're not going to rush to put a mediocre kidney in someone when that kidney may not do well in the long term. There's always a chance of developing renal failure again - and, if you've already exposed the patient to those foreign antigens on the donor kidney, then they are even more highly sensitized to any future transplant kidneys.


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How important is non-binding site of protein?
Just a curious question:

What will happen if i remove most protein sequence that encoded for non-binding site of Restriction Enzyme to make a new enzyme, can the new restriction enzyme still work?

No. The rest of the protein contains catalytic and structural domains that are essential for its proper function. Some domains may be redundant, but you can't willy-nilly chop everthing off and still expect one part to work.

As it seems with about everything in protein science, the answer is it depends on the protein.  Many proteins will lose activity if they are truncated; however, I've worked with GPCR's that were truncated down to the extracellular portion only and they showed consistent kinetic results.  Antibodies have been cut into pretty tiny chunks (scFv's) to create some drugs like Pexelizumab. Some proteins can be hacked down quite a bit, some can't be at all.

The active site usually consists of amino acids from multiple different regions of the enzyme. So if you remove or replace parts of the protein chain then the structure (folding) of the enzyme will be most probably different and the active site will cease to exist. On the other hand in lucky cases replacing a few amino acids can increase the catalytic activity.


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How much genomic variation one usually find within a given bacterial species?
If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to find the same position in a different member of the same species?

If you are using the reference sequence from a database, then it is not necessarily the case that you will have a base for base replica for a randomly selected cell. If you were to select two clonal cells from a colony of bacteria, all those cells would have arisen from a single progenitor, so there would be a high degree of homology between the two cells, but they would likely not be exactly the same for every base in the entire genome.

Be careful! As bacterial genomes are circular and we have to write down their nucleotide sequence as linear, the "break point" of the circle does not necessarily have to be in the exact same point for two genomes in the database (as it is kind of based on the assembly where a break would be, unless you manage to end up with a fully circular genome and can decide). Therefor, while the sequence in question might not have changed, the nucleotide in question could still be in a different "position". And otherwise: that depends. Some genomes are more stable than others. Some genes are, too.

There are bacteria with linear chromosome. https://microbewiki.kenyon.edu/index.php/Chromosomes_in_Bacteria:_Are_they_all_single_and_circular%3F#Summary_of_Currently_Known_Bacterial_Chromosome_Organizations

Yes, but are those the species you are working with?

Genetic variation within bacterial species can be much higher than one might expect.
First, this can be a difficult question to answer quantitatively because even just testing whether two strains are part of the same bacterial species is difficult: the "gold standard" method is actually experimental and involves whole-genome DNA-DNA hybridization (with a cutoff of 70% relatedness). Modern sequencing approaches have shown this usually corresponds to around 95% average nucleotide identity (ANI) (see here).
However, an ANI of 95% does not actually mean that the genomes are 95% identical: it means that of the shared sequences, one expects 95% of the nucleotides to be the same. The percent of the sequences that are actually shared in the first place can be much, much lower. For example, this paper compared 61 sequenced strains of E. coli. Out of the ~15K genes observed in at least one genome sequence, only 6% of genes were observed in all strains. Variably-present genes made up around 80% of a typical E. coli genome. This is a high level of variability, but not outrageous: an analysis of only nine P. putida genomes, for example, showed a core of at most 33% (ref).
So, if a gene is indeed indeed present in two strains of the same bacterial species, then it is likely to be highly conserved. But there is also little guarantee of finding the exact same set of genes in two strains of the same species. This means you cannot naively take chromosomal coordinates from one strain and apply it to another: you need to actually figure out which sequences correspond to one another in your genomes.

If all your samples are, say, E,coli K12 MG1655, there will be very little difference between the published sequence and what you have.  If you have another strain of E.coli, you can't count on there being no indels at all between the two strains.

The locations of a gene on a bacterial chromosome is determined arbitrarily, so you would not expect coding sequences to necessarily have the same numerical values. Remember that the bacteria's transcription machinery will use promoters in the genetic sequence to determine where to start transcription, so the actual start location doesn't really matter -- it's pretty easy for random mutations to add or delete a few base pairs between several genes!
Instead, you would search for the genetic sequence of the gene you were interested in on the genome of a closely related species. Since many genomes are annotated by identifying genes from closely related species, it is possible that two closely related genomes start at exactly the same place, but you should definitely not assume that this will always be the case.

not true...genes in bacteria experience some degree of positional conservation


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How is curcumin effective in fighting cancer?
Can you explain the mechanisms of how curcumin affects cancer cells and how effective it is?
More reading:
http://www.ncbi.nlm.nih.gov/pubmed/25667441
http://link.springer.com/article/10.1208/s12248-009-9128-x

Can you please add some references to this research?

http://www.ncbi.nlm.nih.gov/pubmed/25667441

Since I cannot post more links with my reputation I will post them here  http://www.cancerletters.info/article/S0304-3835(07)00105-X/abstract
http://europepmc.org/abstract/med/1578097
http://www.tandfonline.com/doi/pdf/10.4161/cbt.7.9.6659
http://europepmc.org/abstract/med/16521985

Inflammation is a promoting factor in tumor progression.Curcumin has been proven to be a potent anti-inflammatory agent.
A warning:
There has been considerable amount of bogus research in "miracle natural" compounds, including curcumin. I vouch personally for the study (PMID: 19793800) where curcumin has been studied in inflammation/tumor progression mouse model.

I did not check curcumin in depth, but I think its mechanism is similar to resveratrol's. Both activate SIRT1, which suppress tumors.

Activation of SIRT1 by curcumin blocks the neurotoxicity of amyloid-β25-35 in rat cortical neurons.
SIRT1, Is It a Tumor Promoter or Tumor Suppressor?

I threw a reference in the OPs comments. May also inhibit SP-1, STAT3 and NF-kß pathways.


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What is the advantage of indirect ELISA over direct one?
I guess the answer is about indirect one giving less error due to selectivity but how exactly does that happen?

It's often not necessarily an advantages vs disadvantages question, but one determined by available reagents and what question is being asked.
For example, if you are developing a test for the antibody response to an antigen following immunization, you likely use a protocol like this:

coat plates with antigen of interest (assume block / wash as appropriate going forward)
add diluted serum from test animals / subjects
add a labelled secondary antibody specific for this animal/subject

a labelled secondary antibody must be used because the animal's own antibody is not (of course) labelled.

if you are making your own labelled antibody in the lab and you have done this before you might do both a direct and indirect ELISA to verify that you have labeled the antibody and to determine the quality of the labeling. Assume you made a biotinylated mouse antibody.
do one direct ELISA (to quantitate label):
1. coat with target antigen
2. add dilution series of your antibody-biotin
3. add Streptavadin-Alkaline phosphatase to detect
a second indirect ELISA(to quantitate antibody):
1. coat with target antigen
2. add dilution series of your antibody-biotin
3. add biotinylated anti-mouse antibody
4. add Streptavadin-Alkaline phosphatase to detect
Now you know how much antibody (from the indirect ELISA) will give you how much signal (from the direct ELISA) against known amounts of your coating antigen.
One time you might actually have the option to do a direct or indirect assay is when you have all the reagents you need, but you need to amplify your signal sufficiently to detect low amounts. In that case a direct ELISA only has one antibody's worth of label, while coming in with a secondary (e.g. anti-heavy chain) can result in many antibodies worth of label per target.
Thermo has a nice page on this.

You are correct, the selectivity advantage of an indirect or sandwich ELISA comes from the fact that two antibodies are employed - one to capture the analyte, the other to detect it.
Here is the classic illustration of how this type of ELISA works. First ([1]), the capture antibody is coated onto the plate and bound via one of a number of different types of chemistry. The plate is then washed (this occurs between all steps). [2], the analyte is added, sometimes in a homogenous solution (i.e., pure recombinant protein), other times in a matrix like serum, cell lysate, etc. The plate-bound antibody has a certain specificity for the analyte — let's say it binds the wrong epitope one time in 1000. [3] The detection antibody is added, and let's say it has the same specificity of 1/1000. Finally, [4] the secondary antibody (with the enzyme linked to it) is added, and [5] the enzyme's substrate is added, producing the color or light output.

From Wikimedia
If we were to use a direct ELISA, the error rate would be 1/1000. However, by combining two antibodies, our error rate is now 1000 times lower — 1 in 1 million. Since both antibodies are required to bind properly in order to get a signal, this makes the results much more reliable.

One thing is not being clear to me... if the primary antibody does a mistake (i.e. sit on wrong antigen), still the secondary antibody should detect that wrongly-seated primary antibody (thereafter showing colour). Which is same as using a single, label-containing primary antibody. So I can't visualize how it increase specificity. Rather the secondary antibody could induce a second level of mistake if it does not detect a antigen-bound-primary-antibody. What point I'm missing?

@AlwaysConfused - You are correct, if a primary antibody that is not highly specific to the antigen is used, you can get a false positive signal. This is often referred to as "background." In order to reduce the possibility of this happening, there are two things you should do: one is to use as specific a primary as you can, and the other is to wash the ELISA plate between incubations. I generally use 1X PBS with 0.05% Tween-20 as a wash buffer, although there are many other recipes. Three washes after the primary and 3-5 after the secondary will reduce non-specific binding significantly.

Thanks, I wanted to mean this situation seems  to me different from multiplication rule of probability... if the primary antibody do 1 mistake (non-binding for say(i'm avoiding background you said)) in 1000, yet the secondary antibody won't be able to mask it, moreover if the secondary antibody do another mistake (say 1 in 1000) (and say non-binding) to recognise the primary antibody; the resultant error should be greater than 1/1000. I can't right now express it mathematically. But it seems to me, the situation is different from a setup for multiplication rule.

As well, did you obtained the mathematical fact (decrease of error) using any source or reference? or did you derived intuitively?

I agree with the other answers and the biggest difference is indeed the specificity. An indirect ELISA is indeed more specific, but also for a reason which isn't described here yet: Using indirect ELISA means your plate is coated with the primary antibody. Since this primary AB is attached to the well surface with its heavy chain, the 2 light chains (= the parts which bind antigens, in this case the secondary ABs ) are available to bind the secondary AB. This means that each 1 of the primary ABs has the potential to bind 2 secondary ABs, thus increasing the specific signal considerably.

Can you please add a reference for the picture?

the image comes from Thermofisher : https://www.thermofisher.com/be/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-elisa.html (other ELISA assays are explained here clearly, with also some explanatory video's)

It would be great if you could add this information to your answer, so it will be there for others.

Stack sites use comments for improvement of answers; and comments are prone to deletion/clean-up. This is why including the informations in proper place inside the answer is necessary.


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How do mutations actually occur?
DNA replication seems so mechanical- the DNA polymerase just running along the template strand. I just don't understand how mutations can arise. When it comes to substitutions, I get that a wrong nucleotide may just bind and it won't be as strong a binding as with the complementary base, but I suppose it can happen. However when it comes to mutations such as insertions or deletions, I dont understand how the DNA polymerase could just skip a section of the DNA or add in extra bases. Chromosome translocation also seems like a mystery to me- almost as if the cell believes it should undergo meiosis but with the wrong chromosomes paired up and it only occurs with one pair...
I realise that this is quite a broad question, but any information on the mechanism of how mutations occur would be much appreciated :)

There are various mechanisms. If you just want to know the ways by which mutations occur then this question is not broad. However, if you want each of the mechanisms explained to the molecular level then the question is definitely broad. I suggest that you focus your question on replication errors and remove other stuff. Add more background for this specific area if possible.

I think the DNA polymerase itself is not completely perfect as you'd presume in theory,  it does make mistakes which result in mutation.

Mutation of DNA can be caused by an exogenous or endogenous source. Many external factors like irradiation or chemicals induce mutations. Some endogenous mutations arise from oxidative stress, insufficient DNA repair or spontaneous mutations on the molecular level.
There are many mechanisms for DNA repair like base excision repair, nucleotide excision repair, homologous end-joining or nonhomologous end-joining (Löffler, Biochemistry and Pathobiochemistry).
But it is more difficult for the cell to repair the mutation if it is present in both DNA strands.
According to your second question:

DNA polymerase could just skip a section of the DNA or add in extra bases

DNA polymerase cannot reconstruct what was the original strand or the orientation of the strand. To prevent cell death, some DNA repair mechanisms include alteration in the genome. The DNA polymerase can reads through and the mutation will be replicated when the cell divides. Consequently, the key question is how the effects of the mutation influence the ability of the cell to survive.

It will be nice if you add few references.


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How are neural networks encoded in the DNA?
The central nervous systems as well as the brain->muscles and sensory cells->brain nervous pathways, need to be precisely wired for life to be possible. Moreover they are wired almost exactly the same way for the individuals of a same species (animal, man, insects, etc.).
This information, must therefore be somehow encoded in the DNA.
I have never heard of any study or theory on how this would be possible - only about how proteins are encoded, and I couldn't find any bit of information on this topic (I am not a biologist though).
I would like to have a broad idea of what is currently know about the construction of such networks, i.e. not detailed explanation but rather takeaways facts and references.

How is information about neural connections encoded in the DNA?

e.g. are there any genes linked with neurons (e.g. coding for neurotransmitters)? Do the DNA code for precise neural connections? Can development of specific parts of the brain be linked to specific parts of the DNA? How does a neuron knows from the DNA to which neurotransmitter be sensitive?

How are connections between specific neurons established?

e.g. how an axon does know where to establish deliver a potential? How can the end of an axon move to the correct place?

A small note on semantics: Science doesn't know anything. Humans know stuff; science is nothing but human knowledge.

Related post: http://biology.stackexchange.com/questions/31459/how-is-instinct-carried-from-one-generation-to-another

This question is broad. The genetic basis of instincts itself is a broad question and is something that is still not elucidated. I would, therefore suggest that you focus your question on a specific instinct or a neural pathway. You should also read about Hox genes and their effect on early embryonic patterning. It would be difficult to explain the level of complexity you are asking without you knowing about the early events in development. In short, as the question is written, one can write an entire book which would still not answer the question fully.

Hi WYSIWYG, I don't have the relevant background to ask specific questions about specific neural pathway as you suggested. However, I believe it is an interesting question and any piece of information is welcome. I am not looking for a book long answer neither precise description of all the mechanisms involved, but rather to have of a rough idea of what is going on and how much is known about this.

@Nicolas The edit is good, but I'm still unsure about what you want to know in a clear succinct answer. Re your bullet points 1.Networks are above a cellular level, the underlying genetics work at a protein level. To describe a genetic instruction for networks would take a monumental effort by an answerer. 2. This is more answerable, but still would take a lot of effort to answer and only for half the question. Consider rethinking this question and resubmitting it as a new question by itself.

HI Good Gravy. I understand the concern. However, it s a bit of limbo: the question is about the encoding of neural connection in the dna, which you say can't be answered. About the second point, I see it linked to the first: how is the information in the dna exploited to build the connection. I refocused the question on point to point connections.

HHMI Biointeractive has a whole series of resources on Developmental Biology.  This subtopic deals specifically with Neuroscience and neuronal development. There are some case studies, but there are also some basic information resources as well.

Here's at least one paper describing some of what is known about development of neural network in Caenorhabditis elegans
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001044
It mentions at least one relevant gene
" There is evidence showing that several guidance molecules like Netrin and Nerfin-1 are expressed in the early stages of development. Netrin is a protein involved in axonal guidance in vertebrates as well as in invertebrates [21], [22], [23] and is specifically known to influence early path-finding events [23], [24], [25]. Nerfin-1 belonging to a highly conserved family of Zn-finger proteins, is found transiently expressed in neuron precursors and plays a role in early path finding. Studies involving pioneering neurons in the central nervous system of Drosophila melanogaster have shown that Nerfin-1, whose expression is spatially and temporally regulated [25], is essential in early axonal guidance. "
You can also have a lot at the Wikipedia article called  "Development_of_the_nervous_system_in_humans"
One interesting fact is that C. elegans has 20 000 genes, 302 neurons and about 5000 chemical synapses, 2000 neuromuscular junctions and some 500 gap junctions. In humans there are an estimated 20 000-25 000 genes in humans, about 85 billion neurons and 100 trillion synapses.
This excerpt from http://www.tandfonline.com/doi/full/10.3109/0954898X.2011.638968 explains this seeming paradox though
"studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. ‘Small-world’ topology and highly connected regions (hubs) are prevalent across the evolutionary scale, ensuring efficient processing and resilience to internal (e.g. lesions) and external (e.g. environment) changes. Furthermore, in most species, even the establishment of hubs, long-range connections linking distant components, and a modular organization, relies on similar mechanisms."

Thanks for your answer. I understand that neuron migration is an important part of the process, that long distance connections are established early on, and that neural hubs also develop early on. Is it known if the the migration mechanisms using identical signal for each neurons or if they widely differ from neuron to neuron? I unfortunately can't access the second article which is not open access. Would you recommend any paper specifically about the encoding in the DNA?

I don't have a very detailed overview of all migrations mechanisms, but I think there's a handful basically. Here's one paper you might find interesting http://www.med.nyu.edu/dasenlab/assets/publications/Neuron_Review_2013.pdf

Not sure if it's allowed to write here, but I usually use sci-hub.io if there's a paywall article I can't access.


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Why does a cell produce a lot of p53 protein only to later degrade it?
It is known that the half life of p53 is short and so does that play a role in the amount of energy the cell would need to expend to degrade all the p53? By that does the fact that the half life of p53 is so short does that just allow for the cell to not have to expend very much energy to degrade the p53 so in a way the cell doesn't "mind" having to degrade the p53 since it wouldn't take a lot of effort?

Transcription, splicing, translation, and protein degradation all require significant amounts of energy for the cell.

This answer is not reserved for the example you cite but for all proteins/RNAs which have high turnover. So your question generalizes to
What is the advantage of having high turnover? or in other words, What is the advantage of regulation via degradation?

Fast responsiveness. If your protein/RNA has a low turnover then it would take a lot of time for it to clear up from the cytoplasm even after the activating signal is gone. Enhancing the degradation will make the response fast. Cell cycle proteins such as p53 have to clear up as soon as the cell progresses to the next phase.
In certain cases an additional degradation control makes the regulation more efficient. If the "regulated" gene happens to be in turn an activator of many downstream genes, then efficient control actually helps in saving the cellular resources. I can't cite any literature for it but I have observed this in one of my unpublished research work using mathematical models.


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How to find name of the gene
Considering the kegg page, this page contains the description of the gene Edwardsiella tarda EIB202: ETAE_0074 . Now this gene has a name given in the page as : wabG.
Now considering another gene 1 and gene 2 , what is the name of these genes? How to I find the name of these gene and from which website?

The gene (gene-2) name is VC4260B_02250. Many microbial genes are named like that (like MTB with RVxxx). You can try downloading the genome annotation file for this species. It may have alternative names and ENSEMBL/Refseq ids.

then what is wabG

That is from a different species altogether.

i understand, but wont names be present?? like wabG??


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Can RNases/DNases survive in strong acid/base solutions of around 10M?
This might be a very stupid question, but I am worried about RNase/DNase contamination of my samples. Since I use 37% HCl and 10M NaOH to pH almost all my buffers, this is a potential source.
I have read however, that both NaOH and HCl should hydrolyze the peptide bonds in amino acids at high concentrations. For HCl, however, I have read that a heating step is required to facilitate the protein hydrolysis, so am a bit confused. Perhaps someone with a better background in chemistry could help?
Thanks a lot!

I could just guess it could be safe, because I have not seen the data suggesting it is OK. NaOH or KOH is used to wash glass ware because it has excellent cleaning effect. You could wash away even if you have some RNase in NaHO. But you might miss something making more trouble than that. How about the electrode of pH meter. So, it is good idea to make efforts to remove RNase activities after making buffer. If you really want to RNase free reagents, check if any companies are selling Nuclease free products.

RNAse-A is a very stable protein and tolerant to alkaline conditions. It  is used in alkaline lysis and remains unaffected by moderately high pH (0.2N NaOH- Solution II). It even survives GTC and GnCl treatment (refolds when the denaturant is removed). I think 10M NaOH is a very high concentration and the acid/alkali stocks are certainly not a source of RNAse contamination. Pipette tips are one place to look for contamination.

You are safe here.
RNase is much more stable than DNase (of any flavor). Extreme pH would destroy even RNase, especially considering time (it has to sit in the bottle with all that acid/base..)
Also, consider this: it is highly unlikely that high-tonnage chemicals like HCL or NaOH could be contaminated with organic enzymes.
If you have a problem with RNase/DNase contamination I would look elsewhere for the source of it.

Treatment with NaOH is one of the methods used to prepare equipment that needs to be RNAse free. DEPC is preferred in my experience, but NaOH certainly works as well. Highly concentrated NaOH like in your case will certainly destroy any RNAses present.
I'd assume the same for concentrated HCl. RNAse is very stable for a protein, but concentrated HCl is not something I'd expect it to survive.

RNAse-A at least survives 0.1N NaOH (in solution-I of alkaline lysis 1:1 with solution-II containing 0.2N NaOH)

@WYSIWYG Interesting. There are quite a few protocols I've seen that use relatively low NaOH concentrations over night to remove RNases, though the one I used myself used 2M NaOH and worked for me.


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relationship between cytokines
This is for a mathematical research. I am building a model to identify severe dengue patients through the interaction of cytokines S1P,IL1b,TNFa,PAF and IL10.
For this I would like to know if there are any relationships among these cytokines. That is for example: when PAF increase S1P should decrease. or when IL10 increase Il1b too should increase likewise.
There are seperate articles on the individual effect of these cytokines but I couldn't find any that exhibit any kind of relationship among these cytokines.

Probably you used bad keywords. It is called cytokine (or interleukin) network what you are looking for. There are several articles in the topic.
For example:

Cytokine patterns during dengue shock syndrome
Multiplex cytokine profile from dengue patients: MIP-1beta and IFN-gamma as predictive factors for severity

You can find here more:
https://scholar.google.com/scholar?q=cytokine+networking+in+dengue

Thanks for the links. But all they  say it that for example IL1b was depressed and returned to normal or IL1r was significantly elevated in DHF patients. They have findings like that. But what I want is to know if there is any relationship or association between the cytokines. Like when  cytokine A increases since it has some kind of ineraction with cytokine B, then the cytokine B too should increase. These kind of relationships do they exist?

@sam_rox I don't know. I'll check it in the afternoon.

@sam_rox Sorry, I forgot this question. I think I have found what you need, check this article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527385/


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How to perform a DNA structural alignment in pymol
How can I "fit" two DNA structures having different nucleotide sequences in PyMol?
I would like to use the structure of a DNA-binding protein in PDB (1h9t), which is bound to DNA in the PDB file, and fit a longer DNA built in silico with a 3D dart (haddock.science.uu.nl/dna/dna.php).

Welcome to Bio. Perhaps a link would be helpful, or some background info about your experiment.

Hi @Claudio and welcome to Bio.SE! I've hopefully shown you how to align DNA quickly in PyMol, but I'm not sure if you even need to for Haddock docking.

Aligning in PyMol
PDB ID 1h9t contains a structure of both a DNA and a protein. It starts as one object.
Before we perform an alignment, we need to separate your DNA from the protein.

Show sequence (click the S at the bottom right).

Highlight all the "residues" from the chains X and Y (these chains contain each strand of your DNA) in the sequence bar at the top.

Use the GUI to extract selection to new object (it's a faff doing this by terminal I find).

Rename new object (automatically named obj01 probably) to DNA1, or whatever you prefer.

Load your new, unaligned piece of DNA (I used fetch 1BNA).

Pymol uses the CEalign algorithm to align structures in 3D space. You can call it using the following command:
cealign DNA1, 1BNA, object=aln

Output:

Another 3D alignment software I really like is the Dali server.
Haddock
Haddock doesn't care if two molecules are aligned pre-analysis assuming you are submitting each DNA separately alongside a protein for binding analysis. This is because it tries a huge variety of orientations. Here is a list of things that you do need to do to your pdb before submitting to HADDOCK

And don't forget (like I did) to colour properly and raytrace (ray) the figures before putting them anywhere important!


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Natural Killer Cell and Cancer
NK cells are very effective in destroying circulating cancer cells before their extravasation into the organ, However they have only a minimal inhibiting effect on already established micrometastases.
Anyone knows why ?
Regards.

So we know that NK cells work by receiving activating signals through receptors, and then degranulate such that cytotoxic molecules enter the target cell, and induce apoptosis. NKG2D is such a receptor, and cells that are becoming transformatively stressed by mutations and the like upregulate expression of NKG2D ligands on their surface for elimination. This is one example, and NK cells have different subsets of activating receptors, such as NCRs. NKp30 and NKp44 are examples of NCRs and activate NK cells through detection of heparan sulfate compounds on the surface of tumor cells. The question, then, is what happens to cancer cells that can: (1) downregulate NK cell receptor ligands on their surface, or (2) abrogate NK cell receptor function in their vicinity?
In an earlier study, it was shown that mesenchymal stem cells broadly inhibit NK cell activity through activity of prostaglandin E2 and indoleamine-2,3-dioxygenase, which downregulates each of the three aforementioned NK cell surface receptors. A later study using melanoma cocultured with NK cells again came to the conclusion that the same cancer cell secretions would inhibit NK cell activation in their vicinity.
By the same token, if we consider a cancerous cell that upregulates MIC expression, NKG2D receptors will recognize this and activate the NK cells. A cancerous cell with a truncated MIC that lacks an extracellular domain will fail to activate surrounding NK cells through that pathway. Keep in mind: many mutations go into making a cell cancerous, and many more go into giving it enough fitness to avoid getting killed from the start. These are just examples of critical pathways that result in immunoevasion.
As for why are small masses more immunoevasive than single cells? This goes into a sort of power in numbers logic. A single tumor cell doesn't produce as much inhibitor compounds as a mass of tumor cells. This is an interesting concept because in the hunt for pro-angiogenic compounds, a problem for a while was you would remove a large mass, and a smaller unknown mass would quickly begin to grow. They found that although large masses secreted more pro-angiogenic compound, the tumor cells also secreted so much inhibiting compounds that smaller tumors in the vicinity were effectively inhibited. Once the large mass was removed, this inhibition got lifted.


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Resources for similarity between embryos
Is there a scientific paper/reputable image resource out there which I can use that the embryos of different organisms (vertebrata) are similar in their early developmental stages(without falling into the ontogeny recapitulates phylogeny trap) ?
All I am able to find are the haeckel drawings or somethings that suspiciously look like haeckel drawings and after that debacle, I do not want to be using that.


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What is the sequence of pPROLar.A plasmid?
I've been looking for the sequence of pPROLar.A122 plasmid but I haven't found it. Where could I find the sequence?
The first link (addgene) on googling reports a plasmid which is reported to have the pPROLar.A backbone. However, this is a modified version with Ampicillin and LuxR. I'm trying to reconstruct it from it and another plasmid.
The plasmid map looks like this:

Thanks!

This is not. pPROLar.A122 plasmid looks like this: http://apps2.bvl.bund.de/vectorwww/image.do?id=427 and this is a modified version with Ampicillin and LuxR. But I'm trying to reconstruct it from it and another plasmid.

The problem is the reliability of reconstructed sequences. If a problem arrives with the cloning maybe was because of that. I've already searched the whole Google, that's the reason because I asked here.

I am afraid the sequence is not available anywhere. You should write to Clontech to ask for it. If you do get a reply then please post it here. It will be useful for others.

The pPROLar.A112 sequence is:

CCATGGGTGA ACAGAAACTG ATCAGCGAAG AGGATCTGGG TGGAGATGAC GATGACAAGG
  TGGTCGACAA GCTTGGATCC CTGCAGGCCT CAGGGCCCGA TCGATGCGGC CGCTTAATTA
  ATTAATCTAG AGGCATCAAA TAAAACGAAA GGCTCAGTCG AAAGACTGGG CCTTTCGTTT
  TATCTGTTGT TTGTCGGTGA ACGCTCTCCT GAGTAGGACA AATCCGCCGC CCTAGACCTA
  GGGGATATAT TCCGCTTCCT CGCTCACTGA CTCGCTACGC TCGGTCGTTC GACTGCGGCG
  AGCGGAAATG GCTTACGAAC GGGGCGGAGA TTTCCTGGAA GATGCCAGGA AGATACTTAA
  CAGGGAAGTG AGAGGGCCGC GGCAAAGCCG TTTTTCCATA GGCTCCGCCC CCCTGACAAG
  CATCACGAAA TCTGACGCTC AAATCAGTGG TGGCGAAACC CGACAGGACT ATAAAGATAC
  CAGGCGTTTC CCCCTGGCGG CTCCCTCGTG CGCTCTCCTG TTCCTGCCTT TCGGTTTACC
  GGTGTCATTC CGCTGTTATG GCCGCGTTTG TCTCATTCCA CGCCTGACAC TCAGTTCCGG
  GTAGGCAGTT CGCTCCAAGC TGGACTGTAT GCACGAACCC CCCGTTCAGT CCGACCGCTG
  CGCCTTATCC GGTAACTATC GTCTTGAGTC CAACCCGGAA AGACATGCAA AAGCACCACT
  GGCAGCAGCC ACTGGTAATT GATTTAGAGG AGTTAGTCTT GAAGTCATGC GCCGGTTAAG
  GCTAAACTGA AAGGACAAGT TTTGGTGACT GCGCTCCTCC AAGCCAGTTA CCTCGGTTCA
  AAGAGTTGGT AGCTCAGAGA ACCTTCGAAA AACCGCCCTG CAAGGCGGTT TTTTCGTTTT
  CAGAGCAAGA GATTACGCGC AGACCAAAAC GATCTCAAGA AGATCATCTT ATTAATCAGA
  TAAAATATTA CTAGATTTCA GTGCAATTTA TCTCTTCAAA TGTAGCACCT GAAGTCAGCC
  CCATACGATA TAAGTTGTTA CTAGTGCTTG GATTCTCACC AATAAAAAAC GCCCGGCGGC
  AACCGAGCGT TCTGAACAAA TCCAGATGGA GTTCTGAGGT CATTACTGGA TCTATCAACA
  GGAGTCCAAG CGAGCTCTCG AACCCCAGAG TCCCGCTCAG AAGAACTCGT CAAGAAGGCG
  ATAGAAGGCG ATGCGCTGCG AATCGGGAGC GGCGATACCG TAAAGCACGA GGAAGCGGTC
  AGCCCATTCG CCGCCAAGCT CTTCAGCAAT ATCACGGGTA GCCAACGCTA TGTCCTGATA
  GCGGTCCGCC ACACCCAGCC GGCCACAGTC GATGAATCCA GAAAAGCGGC CATTTTCCAC
  CATGATATTC GGCAAGCAGG CATCGCCATG GGTCACGACG AGATCCTCGC CGTCGGGCAT
  GCGCGCCTTG AGCCTGGCGA ACAGTTCGGC TGGCGCGAGC CCCTGATGCT CTTCGTCCAG
  ATCATCCTGA TCGACAAGAC CGGCTTCCAT CCGAGTACGT GCTCGCTCGA TGCGATGTTT
  CGCTTGGTGG TCGAATGGGC AGGTAGCCGG ATCAAGCGTA TGCAGCCGCC GCATTGCATC
  AGCCATGATG GATACTTTCT CGGCAGGAGC AAGGTGAGAT GACAGGAGAT CCTGCCCCGG
  CACTTCGCCC AATAGCAGCC AGTCCCTTCC CGCTTCAGTG ACAACGTCGA GCACAGCTGC
  GCAAGGAACG CCCGTCGTGG CCAGCCACGA TAGCCGCGCT GCCTCGTCCT GCAGTTCATT
  CAGGGCACCG GACAGGTCGG TCTTGACAAA AAGAACCGGG CGCCCCTGCG CTGACAGCCG
  GAACACGGCG GCATCAGAGC AGCCGATTGT CTGTTGTGCC CAGTCATAGC CGAATAGCCT
  CTCCACCCAA GCGGCCGGAG AACCTGCGTG CAATCCATCT TGTTCAATCA TGCGAAACGA
  TCCTCATCCT GTCTCTTGAT CAGATCTTGA TCCCCTGCGC CATCAGATCC TTGGCGGCAA
  GAAAGCCATC CAGTTTACTT TGCAGGGCTT CCCAACCTTA CCAGAGGGCG CCCCAGCTGG
  CAATTCCGAC GTCTGTGTGG AATTGTGAGC GGATAACAAT TTCACACAGG GCCCTCGGAC
  ACCGAGGAGA ATGTCAAGAG GCGAACACAC AACGTCTTGG AGCGCCAGAG GAGGAACGAG
  CTAAAACGGA GCTTTTTTGC CCTGCGTGAC CAGATCCCGG AGTTGGAAAA CAATGAAAAG
  GCCCCCAAGG TAGTTATCCT TAAAAAAGCC ACAGCATACA TCCTGTCCGT CCAAGCAGAG
  GAGCAAAAGC TCATTTCTGA AGAGGACTTG TTGCGGAAAC GACGAGAACA GTTGAAACAC
  AAACTTGAAC AGCTACGGAA CTCTTGTGCG TAAGGAAAAG TAAGGAAAAC GATTCCTTCT
  AACAGAAATG TCCTGAGCAA TCACCTATGA ACTGTCGACT CGAGCATAGC ATTTTTATCC
  ATAAGATTAG CGGATCTAAC CTTTACAATT GTGAGCGCTC ACAATTATGA TAGATTCAAT
  TGTGAGCGGA TAACAATTTC ACACAGAATT CATTAAAGAG GAGAAAGGTA C

It was sent to me directly from Takara Bio.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Are there electron or proton receptors in our nose?
We can easily smell chlorine gas and its irritating odour, but we cannot smell oxygen gas. Do few protons and electrons make such difference to our olfactory receptors?

Chloride (Cl2) carries 34 protons and electrons.
A common example of a relatively heavy odorless gas is CO2, carrying 22 protons and electrons.
All noble gases are odorless. The heaviest, naturally occurring noble gas is Radon, which has a proton count of 86. Ununoctium, an exotic artificial element with atomic number 118, is a noble gas too. However, with a half life of approximately 0.9 ms it's difficult to sniff out whether it's really oderless.
Sulfur hexafluoride is odorless too, with a proton count of 72.
Hence, the atomic number per se is not the determining factor reason for generating the sensation of odor.
What determines whether a compound generates the sensation of odor I am unsure of, but the above compounds mentioned are all chemically inert. Note that Ununoctium decays rapidly, it doesn't react with anything. I have not been able to verify whether inertness always means odorless, but with the above examples I am inclined to believe it holds true. However, the reverse is definitely not true, as carbon monoxide is odorless, but reactive.

Your point is well noted @AliceD .. i am curious about how is the nose able to discriminate these gases... i mean there will be a well marked difference between odorless gases and gases with odor which the nose recognises. Thanks!

Actually this idea that chemically inert substances should not produce odour may seem correct but is not in a strict sense correct. Odour perception as you know happens when the odorant molecule binds to and activates a receptor. Xenon is known to bind to NMDA receptors and cause anaesthesia. It is not strictly an odorant but inert gases my point is that inert gases can initiate/block neural response.

I think we have evolved to develop perception of odours that are indicate  harmful or beneficial substances (wrt CO, I think it is one of the case of why a trait has not evolved). This is my guess that the ubiquitousness of oxygen made its perception unnecessary. Bacteria can, however, sense oxygen and swim towards it (aerotaxis).


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Inheritance patterns in individuals with triploidy
If you search on the genetics of Down's Syndrome, you'll find plenty of results explaining the genetic mechanisms which can result in triploidy. However, I can't find any information on the inheritance combinations of triploidy - i.e. what are the possible genetic outcomes in the event that an individual with triploidy should reproduce.
It might seem unlikely, which is presumably why it's glossed over. However, I'm just curious about it from an academic standpoint.
So: how does one calculate the inheritance probabilities for a trait associated with triploidy, and what are the outcomes?

Triploids are characteristically sterile, but people with Down's Syndrome aren't triploid(they're anueploid technically). There's only one chromosome duplicated, and it's the smallest one. Women with Down's can have kids just fine, but men tend to be sterile(according to WebMD at least).
See here for a full coverage of triploid genetics and why triploids are nearly always sterile. In short: gametes formed during meiosis pair off but there's always one copy of each chromosome that chooses a daughter cell at random. If one daughter cell gets none of the extra copies, you have a haploid gamete and a diploid zygote and everything goes according to plan. If one daughter cell gets all of the copies you have a diploid gamete and you'll have a triploid zygote and everything will be fine-ish, but you'll have another triploid generation.
Statistically this happens for 2(1 for females with asymmetric gametes, but let's fudge it a little) of the possible sorting patterns, of which there are 2^n where n is the number of chromosomes. For a triploid human male(bear with me) mating with a diploid female(the best possible combination mathematically) instead of the more typical 200 million viable sperm he would produce about 50 viable sperm(About 2 in 8 million sperm have a chance.). If you account for 23-triploidy that number goes up to about 100, but that's still worse than a millionth of the fertility.
Other combinations are vastly worse. A human female only has about 2 million eggs lifetime total, so even in the best of circumstances a triploid female has maybe a fifty fifty shot at having a single viable egg in her entire life. The calculation for the probability of a two triploid humans(or any n=23 organism) breeding successfully is left as an exercise for the reader but it's very low indeed.
If you were working in some other organism with maybe n=2 chromosomes the numbers would be more forgiving and it might be worth thinking about making Punnet squares. They'd work much like Punnet squares for diploid creatures, but the sides would be a little longer to accommodate the larger number of gamete genotypes, and you'd have to adjust the probability of some of the squares to account for aneuploidy-related fatalities and other weirdness. For instance, with two triploid parents the probability of getting a successful triploid zygote from any random pair of zygotes is something like 1/2^n instead of the 4/2^2n or whatever it is for diploid or quadruploid offspring. This is counterbalanced by aneuploid gametes perhaps dying(or even being slightly less fit).
If n=1 the math is more tractable, however(surprisingly, this exists. haplodiploidy complicates triploidy considerations so I'm pretending it doesn't exist). Examples like AAaxAa give strange results(only 1/12 are recessively phenotyped) but AaaxAa produces 1/4 recessive phenotypes and 3/4 dominant ones, just like AaxAa.
In sum, I see why triploids are just declared infertile and not dealt with in the fullest, most complex sense.


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Function and expression of pseudogenes
Can pseudogenes be transcribed into mRNA and translated into functional proteins, or should they be regarded as functionless mutated genes?

By definition, a pseudogene has lost its ability to be transcribed or generate functional protein. If you reinstate that ability, it will no longer be a pseudogene.

Attention: Wikipedia is wrong about its definition of pseudogenes. Please see my answer below for a) one of many example of the official organization that defines "pseudo-gene" gene-type for individual genes (NCBI), which lists functions for specific individual pseudogenes b) One of many research articles studying transcribed pseudogenes (here: those which are even translated). wikipedia cites outdated paper from 80ies

A subset of pseudogenes can have a function - even if not translated: For one possibility see the official record for PTENP1, which acts as a tumor suppressor by providing a decoy for PTEN targeting miRNAs
A subset of pseudogenes can be translated. There is a selection for preserving the length of the reading frame, which suggests (but does not formally show) the presence of a translation-dependent function of (at least a subset of) those pseudogenes. - See Xu et Zhang 2016: Are human translated Pseudogenes Functional? (paywall)
As indicated by the above, it seems likely that quite some pseudogenes have a function, which just has not been discovered yet - and that the mode of action can differ between different pseudogenes.

This is very interesting. I have added a conventional answer so that yours can be seen in context. Note that I state what the term was coined to describe, which is not changed by the fact that some pseudogenes have acquired functions distinct from encoding proteins.

The term ‘pseudogene’ was originally coined to described genomic sequences related to protein-coding genes, but which contained:

“defects… which would completely prevent the production of functional protein.”

(Quoted from review by Jeffreys and Harris, 1984.)
There are two distinct types of pseudogene:
Duplicative Pseudogenes
As their name implies, these are produced by gene duplications. As illustrated in the globin gene families, some of such duplications produce new functional genes, whereas others acquire inactivating mutations. For example a pseudogene with a premature stop codon might be transcribed and translated, but the protein would be truncated and probably degraded.
It should be noted that single mutations can, in the course of time revert, and there are examples of multi-gene families in which genes are active in some species and inactive in others. I have referred to the ABO gene family in this respect in an answer to another SE question.
Processed Pseudogenes
These arise from reverse transcription of mRNAs into DNA which is inserted into the genome, presumably by enzymes encoded by transposable elements. This may occur in any cell, but when this occurs in non-somatic cells do they become established. Hence such pseudogenes tend to be for general genes such as non-muscle actins. They are recognizable by their lack of introns, polyA sequences, and lack of promoters. Unless, by chance, they should come under the influence of a promoter they will not be transcribed and, hence, not translated.


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Why do you need primers in PCR?
I have read that DNA polymerase requires a primer to bind to the DNA, but I am confused as to why this is the case. When DNA undergoes replication in the cell, there are no primers in the nucleus. Why are they needed in PCR?
Many thanks :)

Who said that there are no primers in the nucleus? Read about Primase. I advise that you pick up a good book on basic molecular biology and read the chapter on replication. Genes by Lewin is a decent book.

@WYSIWYG Thank you for your reply. I see now that there is RNA primase in the nucleus- this makes more sense! However i'm now confused as to why an RNA strand is synthesised? I understand that RNA polymerase works on only one strand and DNA polymerase works on two, however does it not make a difference to the finished product that the ends of the DNA strands are actually RNA?

There is a question about this here. DNA polymerase cannot synthesize without primers but RNA polymerase can. Primase is a kind of RNA polymerase.

Actually, when DNA replicate in cell, there is primer exists. DNA polymerase only can add deoxyribonucleotide (dNTP) to the 3’end of a growing DNA chain, instead of creating a new strand. Here is the picture for DNA replication in legging strand, but is same principal use in leading strand. Primer is synthesized by primase in replication.

It is also worth to mention that, looking at the last step, there is a primer there and must be removed, and DNA maybe shorter in each DNA replication time, and that is why DNA telomere mechanism is proposed. That may be a key point for aging.
So, in PCR, it also needs primers, for DNA polymerase only can only can add dNTP to the 3’end of a growing DNA chain.


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How are cardiac cells stimulated by an action potential?
Why, and how, does the action potential of one cell in the heart stimulate an action potential in the next cell? I'm interested in an answer with citation.

If you go to probably any physiology textbook and look at the chapter on cardiac action potentials, you'll find a number of diagrams of the different ion permeabilities and channels in the heart (e.g. fast sodium channels, calcium channels, etc) that lead to the depolarization of the cardiac myocyte. As you alluded to in your question, there is one cell, or group of cells, that is part of the sinoatrial node (or SA node) that is referred to as the "Pacemaker of the Heart". It is these cells in the SA node that have the leakiest ion channels and thus most frequent spontaneous depolarizations that set the rate of contraction for the heart.
For the cells in the atrium, the depolarization of the sinoatrial node spreads almost instantaneously across the atria because of gap junctions (see that link for more info...Michela et al. Role of connexin 43 in cardiovascular diseases. European Journal of Pharmacology, 2015) between the cardiac myocytes. Gap junctions are small communicating junctions that link all the cells of the atrium and "electrically-couple" the cells to contract in synchrony. There are typically no gap junctions between the atria and the ventricles, which is why the atria contracts before the ventricles. However, there is the bundle of His that slows the electrical conduction just enough before it rapidly spreads through the purkinje fibers and then to the remaining ventricular myocytes through gap junctions in those cells as well.
**For more information on gap junctions go to any basic cell biology text or Wiki. The picture below is a simplified diagram of gap junctions. For this question all you really need to appreciate is that the electrical depolarization (i.e. the positive charge) spreads quickly across cells connected by gap junctions because they are 'sharing' a common cytoplasm due to these channels. When ions flux during depolarization that current flows through the gap junctions and nearly instantaneously depolarizes the next cell... and so on, and so forth.