text:
In what sense is the "histone code" a code?
Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell biology (i.e. DNA RNA Protein), I still feel very confused about what exactly constitutes the histone code. Is this term code being used rigorously like it is for the central dogma? That is,  is there an actual code? If so, what is its alphabet (e.g. GTAC for DNA, GUAC for RNA, the amino acids for  proteins)? What kind of words does it encode (e.g. codons for RNA to protein)?
If these things are not known, how do we know it's actually a code then?
Thanks!

Here is a good resource I found on what all the known histone modifications are, their proposed functions, and literature references.

Yes that was helpful. Grazie.

As already mentioned by Stefan, the "histone" code is not really a universal code; it is restricted to eukaryotic systems and even then, not unambiguous. It is, at present related to two kinds of histone modifications and their correlation with the transcriptional activity at that locus:

Methylation
Acetylation

Other modifications such as phosphorylation and ubiquitylation also exist but they are not generally considered in this "code".
Acetylation masks the histone's positive charge and thereby loosens the chromatin (DNA wrapped around the histones), which in turn facilitates transcription. Therefore acetylation is almost always activating in the sense of gene expression.
Methylation, on the other hand has different effects. Methylation on Histone-3 at 4th lysine (H3K4) and H3K36 causes activation whereas H3K9 and H3K27 are repressive. There is also some difference between different extent of methylation i.e monomethylation, dimethylation and trimethylation. The effect of methylation is executed by proteins that have domains such as chromodomain and PHD fingers, that identify these modified histones. Sometimes the histone can carry both kinds of methylation marks H3K4me3 and H3K27me3 and these are called bivalents.
Other histones of the octameric nucleosome can also be modified. However as with other kinds of modifications that I mentioned previously they do not seem to be very common and are therefore not generally considered in this "code".

Is it known that only two kinds of modifications exist or do researchers expect more to be discovered?

@StanShunpike as I mentioned that there are other modifications as well but they are either transient (phosphorylation) or used only under specialized conditions (ubiquitylation). Arginine can also be methylated but it is perhaps not as common as lysine methylations.

The histone code isn't a sequence of letters like you see in DNA and RNA but rather refers to the pattern of post-translational modification of histones. This is then, by definition, an epigenetic control of gene expression.
Histones are basic DNA binding proteins around which DNA is wound to form chromatin. For transcription to occur, transcription factors and RNA polymerase must bind DNA, which generally cannot happen if DNA is wrapped tightly around histones. DNA must therefore be able to come off from and translocate relative to histones in order to expose bare regions. Based on the level of compaction, chromatin can be generally classified as two types:

euchromatin: loosely bound, transcriptionally active
heterochromatin: tightly bound, transcriptionally repressed

The state of chromatin compaction is determined by specific  post-translational modifications to the residues in the histones' amino-terminal tail. This is the histone code. One commonly talked about and perhaps easiest to understand modifications is acetylation of lysine residues: this is generally considered to activate transcription since it neutralizes the positive charge of the amino acid so the negatively charged DNA isn't attracted as tightly. Phosphorylation of serine or threonine can have a similar effect by introducing negative charges. Other modifications include mono-, di- and trimethylation of lysine and arginine, ubiquitinylation and others that I haven't memorised. Each histone monomer can be modified independently and each has several residues that can be modified; this leads to staggeringly large number of ways in which just a single nucleosome can be modified. Importantly, these modifications can recruit proteins including transcription factors, histone modifiers and chromatin remodellers (which can condense or loosen the chromatin). All of these serve to tightly regulate gene expression. This is an active field of research and what all discovered combinations of modifications do is largely unknown, but certain modifications are often characteristic of active and repressed transcription.
There is a standard convention for conveying histone modifications. For example, if lysine 23 of histone H3 was acetylated, you would write H3K23Ac. For trimethylation of arginine 3 on histone H4, you would write H4R3Me3.

It's not a code in the strict sense of the word. With proteins and nucleic acids you have a strictly defined set of letters and strict rules for them to match one another (note that in some cases atypical base pairing occurs in nucleic acids). The "code" part in histone code is meant to convey the notion that modifications in the histone proteins influence the expression of genetic information. The main mechanisms of histone modification are methylation, acetylation, and ubiquitilation. In a very rough analogy, these would be the "letters" of the histone code (NOTE that this is a very imprecise analogy).

So it's not a true code in the math-cs sense, but a code in the loose sense of the word code. As in, it stores information that can be likely accessed, recalled and copied.

Yes, a "code" in a loose sense. Don't forget to up-vote ;)


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What is SDS PAGE gel polymerization time?
I am working on 20% SDS PAGE. I want to know optimum polymerization time for 20% resolving gel and 6% stacking gel. If I increase the time then would it affect the band pattern?

it depends on many factors such as APS concentration, TEMED concentration and ambient temperature

APS and TEMED concentrations matter a lot. Even with that standardized, your polyacrylamide on the shelf is losing reactive groups as we speak. Who know how long it sat in the warehouse? It all adds up to the fact that the minimum required time is practically impossible to predict.
On the other hand, once polymerized, a gel is stable for days without apparent loss of quality. Overnight polymerization will be "optimal" in the sense that the gel won't get any better with longer or shorter polymerization. But so will be a two-days old gel. People used to cast gels every Friday, and leave them in wet paper towels in the cold room for the next week.

There is nothing like a general polymerization time, as this is a chemical reaction which depends on many factors. The most important are:
APS: Concentration and and the age of the chemical are important. APS decomposes over time when it is not stored completely dry (which it is not on most benches) and also with freezing thawing cycles in storage. APS provides the free radicals necessary for the reaction; without it no polymerization will happen. In my experience APS is the most critical part of the reaction, with old solutions making the polymerization really slow. I would make a stock solution, freeze it in aliquots. For making gels I thaw on aliquot and keep it in the fridge afterwards for a week and then discard it.
TEMED: Is the catalyst for the reaction, too much of it will start the reaction very fast.
Temperature: The warmer it is, the faster the polymerization will be. In the cold room you will not get complete reaction, if any.
What you can do is to store the remaining acrylamide in the beaker and wait until it is polymerized. Then your gel should also be ok to use. A longer polymerization time (assuming that your gel was completely polymerized before) will not change the resolving capacity of your gel.

"with old solutions making the polymerization really fast"... I guess you meant fresh solutions. Old solutions are bad.

-1 For having to scrape acrylamide out of the beaker! (I didn't actually down vote)

@canadianer You can do the mixing in a plastic tube if you want and discard it when the polymerization is finished. Makes more trash though.

Others have already explained the effect of different factors on polymerization time. This answer is mostly about:

If I increase the time then would it affect the band pattern?

It may.
Some tips:

Make a little extra mix so that you can leave some in the beaker to know if polymerization has happened.
Always layer the poured resolving gel with water so that the gel doesn't get dried up.
Don't leave the gel for long time after polymerization. Not only it wastes time, it also may cause the gel to dry up and SDS/Urea to precipitate/crystallize.
Wash the gels with the running buffer after removing the comb/before loading the sample. You can use a fine needled (high gauge) to do that.
Pre-run the gel to equilibriate it; this not generally necessary and as Nick Sandor said, would destroy stacking gel. However it is important for big urea gels and somewhat important for continuous SDS-gels if you have left it for a quite some time post polymerization. So it is better to not leave the gel for a long time

In theory, pre-running SDS-PAGE discontinuous gels will destroy the stacking gel, because glycine, which doesn't belong there, will go in. In practice, I see a lot of people recommending it, regardless of theory, and in the absence of any empirical evidence. "To remove unpolymerized acrylamide", some say, to which I reply that it will take just as much as passing bromophenol blue and glycine through the gel.

@NickSandor For usual SDS-PAGE it is not necessary- I agree and thanks for the point; it would change the pH and composition of stacking gel. I edited the answer. But for urea gels (continuous) it is always recommended.

The polymerization time is strongly dependent on APS and TEMED concentrations. I do not think that the increased time for polymerization would somehow influence the division of the proteins in negative way. Actually the time varies from 20 min to 1 h, but I personally leave the gel to polymerize longer. Unpolymerized Acrylamide could build adducts with some proteins which could result in multiple bands. In addition acrymamide itself is toxic, so I always give it additional time to polymerize. Good luck!

source: Stack Exchange

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

sort: votes


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What does the empty space in the bamboo stem do?
Is the empty space inside a bamboo stem a xylem? And why is the space so large?

No, its not xylem. Bamboo is a grass, and the stem (culm) of many grasses are hollow in the middle (see e.g. Grass Structures from Oregon state for some more info).
The exact reason for why Bamboo have hollow stems is most likely due to evolutionary contingencies. However, from a mechanical stability point of view, a hollow stem is much more rigid and stable than a solid (but much thinner) stem composed of the same amount of biomass (Niklas & Spatz, 2012, p. 191ff). So from the perspective of efficiency, the hollow stems of grasses are very useful. The solid node discs found in grass stems (and in other plants with hollow stems) are however really important for increasing overall stability and ability of stems to resist deformations, while only contributing to a very small amount of the total biomass.

Interesting. But why is it hollow?

@ChrisStronks Because that is the growth pattern of the ancestor of grasses along with current grasses. Why do oaks lack a hollow core? Why do you have 2 ears and not 4? Why do octopus have 8 arms and not 10? Most explanations for these kind of evolutionary contingencies do not have a clear explanation, and most possible explanations will be rather speculative and tentative.

I'd also suggest that having a hollow stem allows for height to be obtained much more quickly (and therefore access to sunlight in a forest/jungle). A solid stem at the same rate of biomass addition would be about 1/3rd the height of the hollow stem.

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


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When are a female's eggs created?
Since a human woman is born with a set number of eggs, and meiosis is the process by which sex cells are produced, would meiosis in a woman happen before she is born or soon after she was born?
If meiosis creates sex cells and women are born with a set number of sex cells, when in the development of a woman are her sex cells created?

I can't understand your question.

@WYSIWYG If meiosis creates sex cells and women are born with a set number of sex cells, when in the development of a woman, are her sex cells created?

Oocytes, or immature female eggs, develop in the fetus's ovaries during pregnancy. This graph (U. New South Wales) shows the oocyte population over time in a human female:

Although the x-scale is kind of confusing (months when negative, years when positive), you can see that the fetus has all the oocytes it will ever have at the peak 18-22 weeks after conception. Since age 0 is birth, meiosis in a woman happens long before she is born.

Meiosis starts before birth but finishes after.


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What causes muscles to generate heat on contraction?
I'm curious what the exact cause is of dramatic heat generation that comes along with muscle activity. Can anybody explain this in understandable language?

does "conservation of energy" count as a valid answer?

@JanDvorak Well, I'm looking for an answer that is understandable with a shallow knowledge of biology/bio-chemistry/bio-physics. An answer consisting out of only this phrase, assumes background knowledge of those scientific areas. It's basically like: "Dad, why does the ball fall down when I throw it? Well, E=MC2, son."

How about the wikipedia article on motor proteins?

... or, rather, the article about muscle contraction?

Short answer: energy transport always has heat loss.

First, it might be helpful to talk briefly about what heat is. It is a form of energy - molecular energy. Basically, heat is the amount of jiggliness of the molecules of a substance or object. When we look at a hot object, it doesn't apear to be moving any more than a cold object, but on a scale much smaller than we can see, it's molecules are moving faster than in a colder object. Read this for more information if you want.
There are at least two things going on in muscle contraction (as well as in other metabolic processes) which produce heat. The first is the chemical reaction that powers muscle contraction. You probably don't want to get into great detail, but basically there is a molecule which your cells use to store power, which we abbreviate as ATP. When our muscles use that power, an exothermic chemical reaction occurs that "burns" ATP, breaking it into two pieces (ADP and phosphate). That reaction releases energy. Some of that energy is used in the actual movement of the muscle. But some of it just "jiggles" the nearby molecules. Again that jiggling is the very definition of heat.
The second source of heat is probably much smaller: friction. In short, just about any time anything moves, nearby molecules get jiggled some more. Imagine trying to walk through a room packed full of harps. Everywhere you move, some of those strings get plucked and vibrate. It's a little bit like that. When your muscle fibers tighten and flex, they rub past each other and jiggle each others atoms. All of that jiggliness is heat, and the jiggling continues until it can transfer to some other medium, as when, sweat evaporates from your skin.

Aside of an extremely clear explanation on the source of heat, +1 for explaining what heat is and +1 for explaining what friction is. Not that I totally didn't know that, but the way you explained it makes me realize that the heat we feel with our skin receptors is tiny waves, caused by molecules jiggling at a higher rate. Also I get that if you manually push the molecules to jiggle faster, they start producing waves (heat). And that's all there is to conversion of kinetic energy into thermal energy (friction). Your answer explains heat production, heat transfer and my microwave oven. Thanks!

@Mark. "When your muscle fibers tighten and flex, they rub past each other and jiggle each others atoms." What a fantastic comment. We should have gotten you in my physiology class.

This is oversimplified, but hopefully clear.
When we eat food, metabolic processes break down larger, multi-carbon molecules (like glucose) into smaller molecules. This process is called catabolism, and it releases energy. Here's a simple example of a catabolic reaction:
AB -> A + B + energy

For more on this principle, look at the section on Le Châtelier's Principle on this page from Washington University.
Our body can use the energy released to drive more chemical reactions. Specifically, our cells make a molecule called ATP, which is used all over the cell when energy is needed. However, our cells can't convert 100% of the energy from catabolic processes into chemical energy, some of it is lost as heat (or entropy). When we use ATP, a high energy phosphate group is hydrolyzed (chemically split) from the ATP molecule (ASPU, look at the arrow on the right for energy release):

This releases energy, some of which (during exercise) is used to make muscles contract, but much of it is lost as heat. We heat up when we exercise because the muscles are being used more than at rest, which means more ATP is being used to contract the muscles, which means more heat is being released by the ATP hydrolysis reaction.

Also to be noted that exercise causes increased blood circulation. That also generates heat.

Well explained. Please check if I summarize this correctly: the heat is generated as a side effect of splitting molecules to generate energy needed for muscle contraction.

@WYSIWYG How does blood circulation generate heat? Doesn't it only spread the heat that is generated elsewhere?

I agree with @Alph.Dev - blood circulation in itself generates a negligible amount of energy through friction. Nothing more.

@Alph.Dev Yes you are right that it spreads the heat. Circulation per se can also generate some heat because of movement- it would not be that much. I think that circulation is just correlated with heat and this perhaps has got to do with epinephrine signaling.

@WYSIWYG Yeah, I wouldn't really say high blood circulation causes heat at all. The primary correlation between heat and circulation is really just that the body uses circulation to regulate core temperature. But in fact, when the body has a fever, it increases temperature by decreasing circulation, leaving the extremities cold, and triggering shivers (muscle movement) in order to produce the required heat. You can read more about that here if you want.

Thank you @MarkBailey that point about fever was interesting. I was generally guessing that the hydrodynamics would generate some heat, but it seems that it is insignificant.

@WYSIWYG Well, the friction of blood flow generates some small amount of heat, but assuming blood volume throughput stays the same (which I would expect to correlate approximately to heart rate) I would think that again, decreasing circulation (tightening the blood vessels) would increase friction as the same blood volume is pressing through a smaller, tighter space. Increased heart rate during exercise, on the other hand, would raise temperature a bit. Higher blood flow increases friction a bit, and more significantly - the heart muscle activity generates more heat.

@WYSIWIG Increased blood flow actually helps your body to dissipate heat, this is one of the mechanisms that allows NSAIDs to work as anti-febriles


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Cytochalasin B in cell movement
In an experiment by Pollard, T.D. and R.R. Weihing, amoeba cells injected with  Cytochalasin B were inhibited of movement, while the control group amoeba cells did move. A hypothesis was made that Cytochalasin B blocked polymerization of actin monomers into actin filaments, thus preventing the cell from moving. To validate this hypothesis the experiments were made again with cycloheximide (inhibits new protein synthesis), and dinitrophenol (inhibits new ATP formation), and colchicine (inhibits polymerization of microtubules Here are the results:$\\$
$\begin
Condition:                                  % of cells that didn't move
No drug                                      3
Cycochalasin B                            95
Colchicine                                   4
Cycloheximide                             3
Cycloheximide + Cycochalasin B    94
Dinitrophenol                               5
Dinitrophenol + Cycochalasin B      85$
$\\$
Question: Why were these control important? How did they help validate the hypothesis?
Note: this is for self-study.

The other inhibitors work on other processes, as you already noticed. There is almost no difference between the conditions when they are added and the corresponding condition when they are missing, suggesting those other processes play no role in the observed phenomenon. Eliminating those other processes makes it more believable that actin polymerization is important, rather than being one of multiple factors.
Moreover, often cell will adapt to an inhibitor by increasing or decreasing other kinds of activity. For example, it could be that actin polymerization inhibition prevents amoeba from eating. In this case, because any imaginable motive mechanism requires energy, starving amoeba may become unable to move, even though it was not using actin for movement. In order to refute such scenarios, where actin polymerization is not directly inducing movement, and where cytochalazine does not inhibit movement directly mechanism, supplementary experiments were performed.
DNP induces something similar to starvation, yet, in these experiments, did not abolish movements when given alone. Nor did DNP rescue movement, because the combination (DNP + cytochalazine) is virtually identical to cytochalazine alone. In both circumstances, DNP did nothing, thus showing that ATP depletion is not influencing movement. This is proof that actin polymerization is directly causing amoeba movement, and not an indirect ATP-mediated effect. Similarly, cytochalazin's effect is independent of protein synthesis, once more supporting the hypothesis that actin polymerization is important on its own.

When you work with living cells, there are usually more pathways which can be affected, when you start treating the cell a drug. To make sure, which pathway is specifically inhibited, you need these controls, as an inhibition of any of them could theoretically have the same effect:

Protein synthesis (cycloheximide) as this provides new actin monomers which are important for the enlongation.
ATP synthesis (dinitrophenol) as ATP is necessary for the movement
along actin filaments.
Inhibition of microtubuli (colchicine) inhibits the microtubuli found
in the flagella of amoeba, which also provide a form of movement

The controls show that only the addition of Cytochalasin B to the culture inhibits the movement by inhibiting the enlongation of the actin filaments which proves the hypothesis of the group.

authors: Никита Дорошенко


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Is funnel web spider venom poisonous?
Does the venom of the Sydney funnel web spider have to be injected into the bloodstream to have an effect? If the venom was swallowed (e.g. if a spider was eaten), would it still have an effect? Or wouldn't it be able to pass through the gut lining, or be broken down in the gut?
I understand that the funnel web's venom is different to most spiders', but would this answer apply to spider venom in general?

Interesting question.

@Chris: Very interesting.

For the above reason, I'd also be interested to know if ethanol would degrade spider venom...

@naught101 Ethanol would not degrade this venom. In practice, it actually stabilizes protein by inactivating proteases (enzymes that degrade protein)

I think this question is hard to answer as toxicity will depend to a large extent on the amount of toxin ingested. Even peptide-toxins normally degraded in the gastrointestinal system may eventually become toxic when enough is ingested.

The Sydney Funnel Web Spider's venom is called δ-atracotoxin and it is especially toxic to primates. It is a peptide toxin, which means that it has the potential to be digested in the stomach before having any physiological affect. However, many peptide toxins are not inactivated by swallowing--you don't want to be eating any Botulinum toxin.
Characterization of insecticidal peptides from venom Australian funnel-Web spiders (Vonorax et al. 2006) harvested venom from Hadronyche infensa, the Darling Downs funnel-web spider. This spider is closely related to the Sydney Funnel Web spider and also produces δ-atracotoxin.

An oral ingestion activity test was undertaken using crude H. infensa venom.

The ingestion test was performed with insect larvae, which are susceptible to the venom when injected. (Aside: there's a lot of interesting research on the toxin's effect in insects). They didn't find much:

Oral ingestion activity test of crude H. infensa venom
No effect was observed in this test, even though approximately 4 times the dose required for lethality by injection was orally consumed by the larvae.

I don't think anyone has performed a study of toxin ingestion in primates (if they have, I couldn't find it). The researchers don't speculate as to why the toxin has no effect when ingested. As expected, the toxin had no effect on (non-primate) mice:

Effect of atracotoxin-Hv1 on newborn mice
All mice in both test and control groups survived without apparent toxic effect beyond 24h post injection.

Whether this is applicable to other spider venom depends on the nature of the venom. A non-peptide, low molecular weight venom able to be absorbed by the lining of the esophagus could be very toxic by ingestion.

Further reading:
Scanning Mutagenesis of ω-Atracotoxin-Hv1a Reveals a Spatially Restricted Epitope That Confers Selective Activity against Insect Calcium Channels (Tedford et al. 2004)
Isolation and pharmacological characterisation of δ-atracotoxin-Hv1b, a vertebrate-selective sodium channel toxin (Szeto et al. 2000)
(for more info on peptide toxins): Cyanobacterial Peptide Toxins


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About radiation therapy
With radiation therapy, could some of the radiation used cause new mutations in non-cancerous cells that are near the tumour that is being irradiated? If so could these new mutations lead to new cancerous cell colonies (which might later metastasize)?

Yes, this can happen, although the risk is low. The problem is that some tumors need to be irradiated since the cannot be operated (this is true for some brain tumors). Here the radiation therapy is the therapy of choice. The effect of the therapy is that the tumor cells get a high radiation dose which either kills them or drives them into apoptosis.
The problem the irradiation is that you will always affect healthy cells, of which most will die. This causes some of the negative effects of the radiation therapy, but it is also possible that a healthy cell receives a dose which is "only" damaging and causes a secondary tumor. Here a benefit analysis needs to be done to see if the benefit from the therapy is woth taking the risk of acquiring more damages. See the references for some more background.
References:

Long term side effects of brain tumour radiotherapy
Second Cancers Caused by Cancer Treatment
Therapy-Related Secondary Cancers

I thought the apoptosis mechanisms in a cancerous cell have malfunctioned or are damaged ( that's why a cancer cell can't be shut down by its own 'self-destruct' mechanisms) so if a cancer cell is 'killed' by a high dosage of radiation how does this happen?

DNA double strand breaks, damage to proteins or the cell itself due to the high energy and so on.

How likely is a high dose of radiation going to cause DNA double strand breaks or damage to proteins or damage to the whole cell and so on regarding any type of cells in the high dosage 'path'? This sounds a lot like some sort of disintegration ray gun you here about in science fiction stories. How long has radiation therapy been used? 50 years?

Has anybody lived for 10 years after their last 'set' of radiation doses?

If radiation therapy can lead to new mutations but the risk is low..; how does anyone know if the risk is low as cancerous cells are hard to detect ,probably harder to detect when metastasizing. Even when a new colony of cancerous cells coalesce they.re hard to detect. So how is it determined if the risk is low?

@201044 It is clearly a trade-off between benefit and harm. Often cancers which are irradiated are the ones, that cannot be removed surgically (or completely). Then the tumor is immediately dangerous for the patient. From the dose the patient gets, you can calculate how likely additional damage is. And then you need to make a decision...

What kind of radiation is used in radiation therapy?

Since cancer cells are a lot more unstable than 'regular' cells couldn't a type and duration of radiation be found that would destabilize a cancerous cell and not harm a 'regular' cell?

A recent news item mentioned women who have had more than the usual amount of some type of scan ( Xray or C.T?) are more likely to develop further cancerous growths. Is this true? Using radiation to kill tumors is sort of like using a small amount of fire to 'get rid of' a big fire.

Are there ANY other types of radiation or radiant energy that could kill tumors. Like infrared radiation or microwaves?

@201044 Since the radiation therapy has to do harm in order to damage (to drive it into apoptosis) or kill the cancer cells, it is harmful. And thus it can cause cancer by itself. The question is the benefit of the patient and if it is ok to take this risk. As far as I know no other radiant energy sources are used, as these transport less energy into the tissue.

I don't think any others are used.

It should tell you something that they are not used, right? General rule for cancer therapy is: Everything what helps, does no harm and makes sense is used.

Radiation therapy has been used for 50 years at least; Marie Curie helped to start the practice. I was wondering if ANYBODY  has worked on the idea of using microwaves or infrared radiation or something else in all those 50 years??

In the last 50 years is cancer treatment JUST surgery or chemo therapy or radiation therapy and possible slight variations or combinations of these?

'Everything that helps, does no harm and makes sense is used..' ; yet radiation therapy can do harm and make a person feel sick ,right? Could narrow beans of intense microwave radiation kill tumors without doing much other damage? Microwave radiation wouldn't cause new tumors..

@201044 It is always the decision what is more harmful in the short and in the long term. Yes, radiation can be harmful, but cancers pose a much more immediate danger. I think microwave radiation is absorbed by the upper layers of the skin, so it won'T work in the lower parts.

Well if two narrow beams of microwave radiation that intersected where a tumor was it would be more intense  at the tumor site and have less energy elsewhere so it might not be absorbed by the skin. In a microwave oven the microwaves heat the food from the inside out ,( I don't know if that is because many of the beams of energy intersect at the 'insides' of the food).


text:
Downloading specific yeast genes in an automated manner?
I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, orf19.2119, orf19.4998 and orf19.4056. And I have found the corresponding ortholog genes from Broad Institute website of other 16 species of yeast. So I have all gene names. Now how would I specifically download these genes and from where can I do this, preferably in an automated manner?
Also is there any standard naming convention? Because the ORF names given have other names too like BCR1, EFG1 and NDT80.
The list of gene names I have :
The orthologs of C. Albicans with S. cerevisiae
orf19.2119  YHR124W
orf19.4998  YBR033W YKL034W
orf19.5908  YBR083W
orf19.610   YMR016C YKL043W
orf19.723   NONE
orf19.4056  YMR136W

The orthologs of C. Albicans with S. paradoxus
orf19.2119  spar33-g1.1
orf19.4998  spar197-g23.1   spar324-g3.1
orf19.5908  spar200-g4.1
orf19.610   spar184-g1.1    spar324-g10.1
orf19.723   NONE
orf19.4056  spar165-g2.1

The orthologs of C. Albicans with S. mikatae
orf19.2119  NONE
orf19.4998  smik146-g12.1   smik109-g17.1
orf19.5908  smik83-g2.1
orf19.610   smik571-g2.1    smik109-g10.1
orf19.723   NONE
orf19.4056  smik1535-g1.1

The orthologs of C. Albicans with S. bayanus
orf19.2119  sbayc514-g9.1
orf19.4998  sbayc611-g22.1  sbayc652-g20.1
orf19.5908  sbayc678-g131.1
orf19.610   sbayc638-g23.1  sbayc652-g27.1
orf19.723   NONE
orf19.4056  sbayc657-g41.1

The orthologs of C. Albicans with S. castellii
orf19.2119  Scas697.24
orf19.4998  Scas625.4
orf19.5908  Scas718.27  Scas635.12
orf19.610   Scas106.1   Scas709.52  Scas625.8
orf19.723   NONE
orf19.4056  Scas680.22d

The orthologs of C. Albicans with C. glabrata
orf19.2119  CAGL0L13090g
orf19.4998  CAGL0L01947g
orf19.5908  CAGL0M01716g    CAGL0F04081g
orf19.610   CAGL0M07634g    CAGL0L01771g
orf19.723   NONE
orf19.4056  CAGL0I00902g    CAGL0L06776g

The orthologs of C. Albicans with S. kluyveri
orf19.2119  SAKL0E11330g
orf19.4998  SAKL0A09812g
orf19.5908  SAKL0B06578g
orf19.610   SAKL0D13442g
orf19.723   SAKL0A03476g
orf19.4056  SAKL0E04862g

The orthologs of C. Albicans with K. lactis
orf19.2119  KLLA0F24420g
orf19.4998  KLLA0F25674g
orf19.5908  KLLA0E12507g
orf19.610   KLLA0F04840g
orf19.723   NONE
orf19.4056  KLLA0F17116g

The orthologs of C. Albicans with A. gossypii
orf19.2119  AGR347W
orf19.4998  AFR275W
orf19.5908  AER177W
orf19.610   ABR055C
orf19.723   NONE
orf19.4056  ADR249W

The orthologs of C. Albicans with K. waltii
orf19.2119  Kwal33.14699
orf19.4998  Kwal26.8099
orf19.5908  Kwal27.12423
orf19.610   Kwal26.8176
orf19.723   NONE
orf19.4056  Kwal47.17849

The orthologs of C. Albicans with C. tropicalis
orf19.2119  CTRG01097.3
orf19.4998  CTRG03636.3
orf19.5908  CTRG02294.3
orf19.610   NONE
orf19.723   CTRG00608.3
orf19.4056  CTRG04523.3

The orthologs of C. Albicans with L. elongosporus
orf19.2119  LELG01178
orf19.4998  NONE
orf19.5908  LELG02666
orf19.610   LELG05390
orf19.723   LELG03123
orf19.4056  LELG01761

The orthologs of C. Albicans with C. parapsilosis
orf19.2119  CPAG04608
orf19.4998  NONE
orf19.5908  CPAG01691
orf19.610   CPAG00178
orf19.723   CPAG00564
orf19.4056  CPAG05034

The orthologs of C. Albicans with D. hansenii
orf19.2119  DEHA2A07282g
orf19.4998  NONE
orf19.5908  DEHA2G13794g
orf19.610   DEHA2E10978g
orf19.723   DEHA2E05984g
orf19.4056  DEHA2E07172g    DEHA2F25916g

The orthologs of C. Albicans with C. guilliermondii
orf19.2119  PGUG02096.1
orf19.4998  NONE
orf19.5908  PGUG04378.1
orf19.610   PGUG03651.1
orf19.723   PGUG05571.1
orf19.4056  PGUG05533.1

The orthologs of C. Albicans with C. lusitaniae
orf19.2119  CLUG00404
orf19.4998  NONE
orf19.5908  CLUG04694
orf19.610   CLUG02047
orf19.723   CLUG00627
orf19.4056  CLUG05535

You could check out biopython if you are comfortable with Python programming

What OS would you do this on? Do you have access to UNIX tools? Also, please show us the rest of the gene names. What identifiers do you have? The answer will depend on what database the identifiers point to.

@terdon : I have unix tools (debian is the os). OK I will list the genes.

It would be quite easy if you have Refseq/ENSEMBL ids for those genes.

@terdon : I have updated the question.

These sequences do not have any standard i.d. The information in Saccharomyces Genome Database is also obsolete (2005) and does not have these identifiers.
These sequences can be found here (in the same site).
Each species has a short name:

ORGANISM        Short Name
S.cerevesiae    Scer
S. bayanus      Sbay
S. paradoxus    Spar
A. gossypii     Agos

.... and so on.
First letter of genus name in uppercase + first 3 letters of species name in lowercase.
The fasta file (for all ORFs) is:
 www.broadinstitute.org/regev/orthogroups/nt/<Shortname>.fasta
From there you can use grep to retrieve the sequence.
So, if you have saved shortnames and gene names two separate files you can do something like this:
for shortname in `cat shortname.txt`; do wget -O tmp.fa "http://www.broadinstitute.org/regev/orthogroups/nt/"$shortname.fasta; grep -A 1 -f ids.txt tmp.fa >> $shortname"_Select.fa"; done

@dexterdev The searching code can be made better and faster depending on what you really want as output.

Do you know what is the difference between http://www.broadinstitute.org/regev/orthogroups/nt/Scer.fasta and http://www.broadinstitute.org/regev/orthogroups/aa/Scer.fasta

@dexterdev The first is Nucleotide sequence and second is protein sequence. I gave the first link because you said you wanted nucleotide.

Sorry for the dumb question. I did looked at it , but did'nt noticed that. Sorry.

OK, the first step must be to map all these IDs to the same database. Try using http://uniprot.org if you want protein sequences else, look for each of them and find the corresponding Refseq ID. Since you have IDs from multiple databases, you might need to google them individually. If you know the ID type of each identifier you have, you can use a tool like DAVID's gene name converter to automate it.
Once you have a list of IDs from the same database, save them in a file (one ID per line). Then, for UniProt accessions, you can get the FASTA protein sequence by running:
while read name; do wget -O - http://uniprot.org/$name.fasta; done < names.txt

For RefSeq IDs, you can use the batch retrieval tool of Entrez.

Helpful answer. One thing , I am not working on protein sequences, but just nucleotide sequences.

When I googled these ids I couldn't find any match in a database. I checked SGD but their repository (from MIT) is obsolete (2005). Even then the orf fasta file (S.paradoxus) did not have an identifier like spar* or SPAR*. Example; first fasta header: ORFN:24882 YPRWsigma4, Contig c301 66351-67256. These are not even from complete assembly; it says contig.


text:
How does anxiety cause chest pain?
An acute instance of anxiety can cause a sudden sharp chest pain for a very brief period of time.  What is the mechanism behind anxiety leading to chest pain?
Is the pain coming from the heart itself, or surrounding muscles?  What structure is in pain and what is the physiology behind it?

you mean pain similar to a heart attack?

I would also notice that I think that this pain you're talking about is related to the more well-known feeling of heaviness in the chest in the period of depression. Maybe this is the same thing. Or maybe not.. however, I would like to know.


text:
Repair of cloning vector nicks digested with antarctic phosphatase and ligated with T4 enzyme
The vector product obtained by ligation between a vector previously digested with antarctic phosphatase lacks 5' phosphate groups. T4 ligase can ligate it to an insert with complementary sticky ends which provides 2 phosphate groups. But there are still 2 nicks in the vector product! How are these normally repaired ?

The nicks are not repaired during preparation. Instead, the vector (which is circular, despite the nicks) is transformed into the host where it is repaired by endogenous mechanisms, likely through base excision.

Why was this down voted. Am I wrong?

Yes it is possible. However the efficiency reduces. I had seen someone doing it for site-directed mutagenesis. So transforming the plasmid without sealing nicks does produce colonies but they were less than the case when the nicks were sealed. <I don't know the reason for downvote>


text:
Why doesn't Sanger (fluorescent) DNA sequencing double count nucleotides?
My understanding is that PCR is carried out until a fluorescent nucleotide halts replication. The segments of DNA are fed through the capillary tube based on size, sifting through the segments from smallest to largest; subsequently, the sequence is read from one end to the other.
I'm confused as to how we know that each nucleotide in the sequence has been accounted for, or if a nucleotide has been counted twice. If two fragments of the same size, ending with the same ddNTP, pass through the capillary tube at slightly different times, how do we know if that specific nucleotide hasn't been double-counted?

In chain-termination sequencing, a population of molecules is detected as opposed to a single one. The readout looks like this:

[ http://seqcore.brcf.med.umich.edu/doc/dnaseq/trouble/badseq.html ]
The peaks represent intensity of the four different fluorophores at the detector. Every fragment that is terminated at the same spot will have the same fluorophore and the same length. Because capillary gel electrophoresis separates molecules by size, these fragments will pass through at approximately the same time. "Approximately the same time" is why you see broad-ish and overlapping peaks on the readout as opposed to sharp and distinct lines.
Ideally, the readout will appear like the left half of the image, where there's minimal overlap between peaks. However, often you will see overlapping peaks, as in the right half of the image. The link above explains many reasons for why this occurs. Whether or not a peak is correctly assigned is determined by Phred scores, which is a statistical analysis of the shape and resolution of each peak.

I would like to also add that this is precisely why we use a capillary tube. The small surface area  makes it ideal for resolution of small things like nucleotides. That is the whole idea behind chromatography. Trying to separate things that may only be modestly different in size (or charge) to separate. The more resolution something has, the farther each of those peaks will be from each other, and the sharper each peak will be, i.e. a very sharp line instead of a broad peak.

how do we know if a certain nucleotide hasn't been accounted for? (e.g., what if a fragment that terminated at nucleotide #70 was not produced?)

@Alzeon Statistically, that seems unlikely given that there is billions of DNA molecules in a sequencing reaction.


text:
What are the main principles of the Bacteriological Code?
Although the Bacteriological Code is an important guideline for taxonomists and microbiologists, describing the criteria for delineating species and higher taxa of the prokaryotes, I, and plenty of other microbiologists with me, would not be able to describe the main rules by heart. I am also not able to find a clear summary anywhere on the web, and reading and understanding the Code itself is currently taking quite some time.
Furthermore, does the Code say anything about taxa mainly or solely composed of uncultured strains based on 16S sequences, apart from the addition of Candidatus to currently uncultured single species? I am specifically referring to higher taxa, large groups of sequences.


text:
Download FunCat Database for Programmatic Access
I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other information I find interesting in Python or R. There are many websites that have this information, but the most comprehensive appears to be Pedant.
I would like to download a SQL database, a JSON file, or even a text file that contains the information on these sites without having to use a web interface for everything.
The data I need access to is gene code, gene description, DNA sequence, FunCat category, GO category, and maybe others on the Pedant site.  Is there anyway to to programmatically access these fields or download all of them in bulk?
Note: I have been using the python bioservices module, but it only gives access to KEGG, which is missing information on many of the genes in the N. Crassa genome.

Did you try biomart? I don't think it retrieves FunCat information though. But you can get everything else. It has a python API as well as an R interface (in bioconductor). BTW what do you mean by gene code?

By gene code I meant locus number (NCU#####).  I will look into biomart to see if it has the pathway information I need.


text:
Medium for Pseudomonas?
What is a good minimal medium for Pseudomonas bacteria? Do I need different media for different Pseudomonas species?

Pseudomonas bacteria are generally not difficult to grow:

Rugged and opportunistic, Pseudomonas use a wide range of nutritional sources, even very simple nutritional environments without any organic compounds. - Sigma

For specific species, you'll want to use a selection medium. Sigma-Aldrich has a number of  commercial products for selection and I'm sure you can find a recipe that suits your species with a Google search.

Related reading:
Medium for the Selective Isolation of Members of the Genus Pseudomonas from Natural Habitats (Grant and Holt, 1977)
Evaluation of various selective media for the detection of Pseudomonas species in pasteurized milk (Van Tassell et al., 2012)


text:
Color perception vs shade perception demo
I can't seem to find one of the best demos I've seen of color vs brightness perception.
It consisted of a rotating animation of earth made of red of bright red points on a dark green background. As the animation plays, the red points slowly get darker while the green background gets brighter. At some point they are of the same brightness (but different colors), which is where something very cool happens; your brain no longer perceives the red points as a 3D object, and they just look like a jumble of points bouncing around the screen. When the red points are darker than the background, the 3D object appears again.
Does anyone know what is this animation called, or where to find it? It's hard to find on google without knowing what to call it.


text:
How does the body "know" how to metabolize foreign substances
As a freshman biochemistry major, I find myself befuddled by our body's ability to perform complex chemical reactions to break down foreign substances. I can see how we would evolve explicit pathways to deal with substances we would find often in our environment of evolutionary adaptedness, but we also process things we would never have encountered before. How does the human (or any organism's) body do that without explicit programming?

Can you comment a little further? Do you mean in the context of immunology, i.e. processing foreign pathogens? Or do you mean processing small molecules, i.e. drugs?

@jwillis0720, I think he means processing small molecules such as drugs that the body might metabolise in the liver.

@jwillis0720 The term for such substances is Xenobiotics.

you are right. had to refresh my memory :)

One strategy for xenobiotic metabolism seems to be making a lot of similar enzymes with different substrate specifities. Lets take the cytochrome p450s as an example. These are a class of enzymes with 57 genes identified for humans, and I don't know how many alternative splicing products are made from those genes. As a class, they are responsible for about 75% of drug metabolism and are predominantly found in the liver. They work by using a heme group with a carbon monoxide to add oxygens to xenobiotics. Here is a diagram of the mechanism:

It's been too long since my drug metabolism class to go into more detail on these enzymes, but there are other classes of enzyme that fit this multiple enzyme strategy such as the 2 monoamine oxidases, 5 flavin containing mono-oxygenases, and 4 epoxide hydrolases. So the body doesn't really know how to break down xenobiotics, but has a wide array of enzymes with broad and overlapping substrate specificities that work on whatever they happen to bind to, whether it's an endogenous hormone or pharmaceutical compound or toxin.


text:
Need help in codon optimization
I want to chemically synthesize a GFP gene for expressing in rice.I am using the IDT Codon Optimization program and found that not all the codons are 100% optimized. Some of them are the 2nd or 3rd in frequency of usage. Also, the stop codon in the gene optimized is the least used in rice. I don't think all the codons can be the ones that are the most used in rice as there is need of translational pauses to get optimal protein expression. But how do I decide which codons are to be used in what positions to get maximum efficiency. Do I just use the automatic codon optimized gene given by IDT or further optimize it manually?
So should the stop codon used be the one which is the most frequently used in rice for proper mRNA termination?
Please help me as I am new to this and want tips and suggestions for getting optimized codons in this gene.

Generally the codon optimization is the most frequent tRNA found in your species of interest. However, your codon must not result in something that disrupts standard molecular biology practices. For instance, if your codon places a restriction site in a unique cloning vector, then the algorithm will just look for the next best codon which does not cause unwanted addition or elimination of a cloning site. Places like IDT will also weigh the cost of the codon vs. the ease of manufacturing in their algorithm (see here.)
What you describe as translational pausing that is 'needed' by the organism to optimize proper gene expression is a consequence and not a necessity of infrequent codons (to my full understanding). See here. That means you don't want to add this translational pausing in optimized gene expression. It is a simply an evolutionary byproduct.
Edit -
To answer your question more bluntly, I can tell you with some experience to trust the codon optimization algorithms from biotech companies like IDT. I find they work very well. Rice is a common enough organism :)

The optimization done by service providers like IDT should be fine because they weigh in multiple factors like avoiding mRNA secondary structures and specified restriction endonucleases. Even I was considering manual editing but then some research on the internet revealed that codon usage is not the only factor involved :)

This is not an answer to the question.

@WYSIWYG Why not? It seems to be poorly supported, but it does seem to answer the question.


text:
Are we more/less resistant to infectious diseases during an allergic reaction?
To my understanding, an allergic response is a non-adaptive response of the immune system to some molecule. The molecule in question is therefore "thought by the immune system" to be infectious although it is not. An allergic response is triggered by immunoglobulin of type E ($IG_E$) and causes an immune reaction.
I'd expect immune responses to not be instataneous, that is I would expect that it takes some time in order for the immune system to achieve some reaction peak. In consequences, I have been wondering whether someone that is under an allergic reaction is more resistant to early development of infectious disease because the immune system is already "switched on" prior to the infection. On the other hand, I would have thought that the body resistance to anything is lowered during an allergic reaction 1) because the allergy diminishes "general health" and 2) because allergic response may kill body cells.
Are we more/less resistant to infectious diseases during an allergic reaction?

An allergic reaction is caused by by IgE antibodies - which are part of the adaptive immune system. When you are allergic, the reaction happens very fast after the exposure to the antigen.

There are a number of issues with your question, and the short answer is no.
Immunity to pathogens is conferred by antibodies, but not usually of the IgE group. Pathogens usually stimulate IgM -> IgG; IgAs are present in mucosal surfaces.
There are multiple kinds of "allergic responses", and each carries its own risks.

Type I reactions (ie, immediate hypersensitivity reactions) involve immunoglobulin E (IgE)–mediated release of histamine and other mediators from mast cells and basophils.
Type II reactions (ie, cytotoxic hypersensitivity reactions) involve immunoglobulin G or immunoglobulin M antibodies bound to cell surface antigens, with subsequent complement fixation.
Type III reactions (ie, immune-complex reactions) involve circulating antigen-antibody immune complexes that deposit in postcapillary venules, with subsequent complement fixation.
Type IV reactions (ie, delayed hypersensitivity reactions, cell-mediated immunity) are mediated by T cells rather than by antibodies.

Limiting ourselves to allergic responses mediated by IgE, we have anaphylaxis, allergic asthma, urticaria, angioedema, allergic rhinitis, some types of drug reactions, and atopic dermatitis. These reactions can result in something as mild as urticaria or as life-threatening as anaphylaxis. None of these conditions carries an increased or decreased general immunological response to pathogens.
If allergy affected immunocompetency, one would expect to see, for example, an increased incidence of fungal infections in allergic individuals, but this is not the case. Allergy does not result in an immunocompromised condition, nor does it result in a primed response (an idea popular in the 90's). They are mediated by different pathways.
Effector mechanisms in allergic reactions
The production of IgE
Allergy, Parasites, and the Hygiene Hypothesis
Immunocompetence and allergy

I also had this doubt once; is it not possible that there is a general hyperactivity irrespective of the antigen involved (Something like excess interleukin signaling. I don't know if there is a condition like that).

@WYSIWYG - There are 37? ILs now which do different things. If you're referring to autoimmune disorders, then yes, it's a "hyperimmune" IL- mediated response of a certain kind (or, better, kinds). That's a huge can of worms (or maybe chicken-and-eggs). Some kinds of autoimmune disorders carry an increased risk of infections, but this is usually due to tissue damage, not decreased responsiveness to pathogens. Maybe I'm not understanding the deeper issues here (more likely they're too complex for me). But I don't see much in the literature about protective effects with autoimmune disease.

Isn't allergic rhinitis compromising the mucociliary escalator?

@abukaj - allergic rhinitis affects the nasopharynx, not the trachea, so, no.

@anongoodnurse I am sorry but I see no connection with trachea... One of causes of common cold is a malfunction of the escalator in nasopharynx due to a sudden change of temperature. Why then rhinitis has no similar effect? Or am I extrapolating meaning of the mucociliary escalator?

@abukaj - There are no cilia in the URT until the tracheal level. If you believe there is an "elevator" in the nasopharynx, I'd love to know why. I think you may be extrapolating the "mucociliary elevator"'s functions to where they do not exist. The cilia in the trachea down are vital to protection against pathogens.

@anongoodnurse I have read somewhere (googling for connection between weather and common cold), but as I googled to check whether I am extrapolating I have found: http://carrsconsulting.com/thepig/disorders/defence/mucociliaryescalator.htm  (From the nose to the end of the bronchi (inside the lung), the surface is lined with a series of barrier cells. [...] These barrier or epithelial cells also have small “hairs” or cilia on them) and https://www.colorado.edu/Outreach/BSI/k12activities/interactive/actidhpamucociliary.html (The mucociliary escalator covers most of [...] nose.)

@abukaj - The very first sentence in your first link explains that cilia start at the tracheal level. I am happy to discuss/teach people who are sincere in their desire to learn and who are open to learning. Misrepresentation of the contents on one's own links means you either do not understand or you just want to prove a point. I will consider this discussion now closed.

Let us continue this discussion in chat.

This is a very good question which is an active research topic!
I can just say that we do not know the correct answer to it but we have some evidences that some allergies are connected with autoimmune diseases.
You called this

1) the allergy diminishes "general health" and 2) because allergic response may kill body cells.

I would say that there can be a mechanism between allergies and autoimmune diseases.

IgE Mediated allergy to wheat in a child with celiac disease. There has been later found other cases on this but not published in PubMed.
The link between coeliac disease and IgE-mediated allergy is not very clear.
Pharmacological intervention with Montelukast (a leukotriene-antagonist) can possibly in all sorts of ways. However, research is going on about this because the mechanism is unknown.

I picked celiac disease here because it is been connected to many other autoimmune diseases and is the most undiagnosed disease.
I consider Montelukast because its mechanism in IgE and because of its latest research findings with childhood asthma (about 2001), see this search in PubMed, and in successful treatment of opportunistic diseases in HIV/AIDS, see this publication.


text:
How much difference in genome is enough to prevent interbreeding?
I am not a biologist. I am a software developer interested in genetic algorithms therefore i am probably talking to biologists who also have a knowledge of genetic algorithms. I need to "breed" different solutions to a problem while allowing the number of genes in my solution to vary because i don't know in advance how many genes i need. This is why i need to be able to cross solutions with N genes with solutions with M genes and this is a serious problem. If N and M are very different the problem would be even more serious. I want to know what happens in the biological world. I am trying to understand how much difference in genome is "enough" to prevent interbreeding between different organisms. Would it be possible to say that if less than (approximately) X% of the genes of two organisms are different then they can probably mate and have offspring?
Thank you
Wentu

It is not just genomic differences that prevent interbreeding. The synteny also matters.

Welcome to Biology SE! I think this question holds potential, but probably it needs some narrowing down or splitting up in multiple questions: e.g. (1)  On the other hand, members from different species have genomes different enough to make interbreeding impossible. Is it possible to explore what happens in-between these two cases? and   (2) what happens during evolution? is it just geographical separation that allows genomes two diverge up until the point when two species exist instead of one? are quite different questions.

A first idea would be that inbreeding is only deleterious because of the possibility of creating homozygous recessive genotypes which then cause lethal phenotypes. If there were no deleterious recessive alleles in either parent, it could perfectly be the case that interbreeding would still be possible.

MarchHo, i personally can't have offspring if i mate with a chimp female but i can have it if a mate with a human female. The genes of these two organisms differ for something like 1-2%, right? But i don't know my genome differs from the average woman genome. I suppose that 1% difference is already too much but... how much is too much?

@JohannesWentu It isn't as simple as genomic %-difference. If there is a mismatch in crucial systems, this can be enought for incompatibility, even if the genome difference is miniscule. You also need to consider other barriers for reproduction, such as behavioural and mechanical barriers.


text:
When did our ancestors switch to a menstrual cycle instead of the estrous cycle?
The Wikipedia page on the Estrous cycle says:

Humans have menstrual cycles instead of estrous cycles. They shed their endometrium instead of reabsorbing it. Unlike animals with estrous cycles, human females are sexually receptive throughout their cycles.

The page on the menstrual cycles says:

The cycle occurs only in fertile female humans and other female primates

Do we know how many million years ago that switch happened and our female ancestors got sexually receptive throughout their cycles?

See also How is menstruation not suicide in the wild?. Although it doesn't speak to your question of when, I discussed the theorized adaptive benefits of the cycle in an answer there.

Emera et al. argue that menstruation is not directly adaptive but a side effect of adaptations pertaining to the maternal-fetal conflict.

Menstruation occurs only in most of the primates, and a handful of other mammals. It is tempting to speculate that place the switch to menstrual cycles evolved right after the split between non-menstruating primates (tarsiers and their relatives) and menstruating relatives (almost all others), which is about 63 million years ago.
There are other menstruating animals, so I am not sure if nature reinvented menstruation whenever social conditions required unproductive sex, or menses are in fact a more archaic trait.
I doubt we have material evidence about all these speculations.

Any sources to add?


text:
What's the smallest size a human eye can see?
During a biology experiment at school, where we would look at waterweeds under a microscope, my teacher said something about that it's impossible for the human eye to see the cells without a magnifying glass of some sort. So, I saw that as a challenge, and decided to check if I could see the cells. And after holding the leaves really close to my face, I was indeed able to see tiny rectangles.
Since I was curious about it now, I decided to look some more things up. First, I tried to find out the actual size of waterweed cells. Based on this 640x enlarged image, which features cells of 5mm wide and 10 - 15mm long in the picture (which corresponds with of roughly 8µm wide and 15µm long).
I left this in the back of my head for a long time then, but I just looked at my cotton sleeve, and noticed tiny fibers. Not the ones that are woven together, but ones that are standing out from it. So, after looking it up, it turns out that cotton fibers are 10 µm wide.
So, I wondered, what is the smallest size a human eye can actually see? According to a whole bunch of sources all across the internet, it's either 200-400µm, 100µm, or 58-75µm. I also hear 'the width of a human hair' very often, but those can range from 17 to 181µm.

Many plant cells are visible, onion cells being a good example. As to seeing, that depends on your definition of seeing.

Well I mean something like being able to distinguish a shape of a certain size (so in this case a plant cell or a cotton fiber).

Very nice question!
First of all, the 'smallest size' that a human eye can perceive is called visual acuity, and can be expressed in various ways. It cannot simply be expressed by means of size measures, as objects with a fixed size are perceived as smaller when viewed from a distance (perspective). A familiar example is the train track:

Hence, visual acuity has to be measured as a function of viewing distance, i.e,  in degrees of visual view. Measured in degrees, the visual acuity of the average normally sighted person is 1/60 degree, or 1 minute of arc (1 MAR) (Webvision, chapter "Visual Acuity", by Kalloniatis & Luu).
Using the basic structure of the eye and some trigonometry one can deduce the smallest visible size :

The trigonometric formula becomes: $2d \times tan(\frac{\alpha}{2})$ with d being the viewing distance and alpha ($\alpha$) the visual acuity expressed in radians ($\pi \times \frac{degrees}{180}$) (NDT resource center).
Assuming the closest distance an adult can focus (~100 mm) and an average maximal acuity of 1 MAR, the smallest visible size boils down to 29 microns.
A young child can focus at distances down to ~50 mm, and can have a visual acuity of 0.4 MAR, which yields 6 microns.
Note that 1 MAR encompasses 288 microns on the retina, and some 180 photoreceptors. The optical limitations of the eye (such as diffraction by the lens and light scatter by the neural cells in the retina) limits the resolution of the human eye below the theoretical 'pixel limit' of the eye.
So to sum up, depending on one's age, one should be able to see targets in the order of 6 - 29 microns. The lower bounds of this range are indeed in the range of the waterweed cells and cloth fibers you describe.
PS - the values described are representative under ideal conditions, i.e., under situations of abundant lighting and high contrast.

Really well worked out answer. Thanks! The conditions were indeed ideal as you described, there was quite a lot of light, and as you can see in the picture, waterweed cells do indeed have quite a lot of contrast with the cell walls. Great answer!

This might be true under some assumptions ("ideal conditions") but in general the problem is more complex. Visual acuity is about resolving details (eg. ability to recognize a character) and not about seeing or not seeing things. We can for example see stars, even though they are hundreds times "too small" (viewing angle much smaller than 1 min of arc). So, the stars are more ideal than an ideal? Exactly, because they are extremely bright = high contrast. Tiny bright particles over black background would be more visible under microscope, too (with adequate lighting).

Absolutely, this answer is under ideal conditions as specified in the answer. It's all about contrast. Without contrast, no vision.

Excellent work Mr. AliceD


text:
How do catalase and other antioxidants neutralize free radicals?
In learning about how cofactors are essential to proper enzyme function, my textbook mentioned catalase and its relation to the human body. According to my textbook, catalase is similar to hemoglobin in that it has 4 hemes which cradle an Fe (iron) atom; the iron atom is used to neutralize free radicals when it "pulls on the substrate's electrons, which brings on the transition state" after catalase is holding a substrate in its active site. I already know that free radicals have one or more unpaired electrons which make them dangerous as they "seek out" an electron to complete its pair on any molecule, atom, or ion it can find, perhaps causing significant tissue damage in the process. I also know that the transition state is a key point in a reaction in which the activation energy required has been met and the reaction will continue spontaneously until it ends.
My question is, what exactly is happening here that helps to neutralize a free radical, and what is the part after the transition state doing?
If I had to guess, based on that cofactors generally can be affected during a reaction, perhaps Iron somehow binds with the free radical and share its electrons, effectively neutralizing the unpaired electron as well as using up the Iron atom? I imagine the "pulling" in the book could fit a description of a weak chemical bond/attraction, but I'm still unsure.

Catalase (hydrogen peroxide oxidoreductase) does not actually quench free radicals. It catalyzes the conversion of hydrogen peroxide to water; the former is a source of a free radical, not a free radical in itself.
This is the proposed mechanism of action of catalase: First one of the oxygens is deprotonated by at the active site of the enzyme. Then the Iron atom that is bound to heme forms a co-ordination complex with the deprotonated oxygen and pulls it away from the other oxygen. As a result the O-O bond breaks.
Free radical quenchers/antioxidants react with the free radicals and form non-toxic products.


text:
How does salinity affect the bonds of an enzyme?
According to my textbook, "Too much or too little salt can interfere with the hydrogen bonds that hold an enzyme in its three-dimensional shape". I know that NaCl is held together by an ionic bond, meaning that one atom is strongly positive (in this case sodium) and one atom is strongly negative (in this case chlorine). I would guess the polarity of salt has something to do with its effect on hydrogen bonds, which consist of a hydrogen atom which bonds weakly to a strongly electronegative atom, resulting in a similar behavior to its ionization in glass of water, since water molecules are also polar and form hydrogen bonds with one another.
My question is, how exactly does salinity affect the bonds of an enzyme?

I can't find a good reference for this, but I know the DNA double helix is only stable in the presence of cations such as Na+, K+, or Mg2+. The cations help neutralize the negative charges on the phosphate backbone and prevent repulsion. This allows the bases to form hydrogen bonds and hold the structure together. Without the cations the hydrogen bonds wouldn't have enough strength. Something similar may happen in proteins, where ions help to neutralize charges or bridge certain amino acids together and allow the hydrogen bond to form.

@user137 In the presence of water (which is the usual state in living cells) there are no ions bound to DNA.

@Chris But there has to be some interaction, when using RNA I have to use a 150mM NaCl buffer to get Poly A and Poly U to bind well.

@user137 I am not saying that there is no interaction (which is of course present), but not in the form of "bound" positive ions to the DNA backbone.

Sodium Chloride is not "polar". It is an ionic compound and dissociates into the respective ions in water (because of the latter's high dielectric constant).
Hydrogen bonds are similar to of dipole-dipole interactions (van der Waals) but much stronger and are therefore classified as a separate type of bond. However excess salt can lead to ion-dipole interactions (which are stronger than H-bond) that may prevent the formation of the hydrogen bond.
Ions such as Cl - can act as chaotropes (cause disorder)[ref]. K+ is also chaotropic while Na+ is kosmotropic (reduces disorder). However both Na+ and Cl - affect the entropy of water very slightly. So the effect of NaCl should be mostly due to ion-dipole interactions.


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I brought a hibernating yellow jacket queen into my house accidentally. What will happen?
There was apparently a hibernating yellow jacket queen in my stack of firewood outside.  An hour or so after bringing in the firewood, we saw the queen fly off into the house, where we can't find her.
What will happen?  Will she lay her eggs and start a nest somewhere in our house?  Will she just find somewhere and go back to sleep?

I'd just sell the house and move as quickly as you can... ;)

lol, that doesn't seem like too bad of an idea at the moment :-)

She will likely die somewhere unseen in the house, probably by a window. She won't dive bomb anyone, though, if that's what you're worried about. We used to find a dead queen every year in our old house. Never understood why.

Well; if mostly your house is sanitized; poor queen will die somewhere in the house. Queens are not "designed" to attack; so I wouldn't have worried about it if I were you........Only, I couldn't get my eyes closed at night :D.

Yellow jacket is a very general term, that covers a wide variety of species with different biologies. Can you be more specific?


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What's the meaning of 'plasma' in 'plasma membrane'?
I wonder why is it called plasma membrane - what's the biological meaning of the word 'plasma'?

Plasma comes from the greek word which means something created or forged

I thought it was a no-brainer, apparently it's more of a historical journey into the origins of Botany. But I have a hypothesis: During the debate of whether the cell or the fluid within it was the origin of life, that fluid was called 'protoplasm' - first formed, i.e. it's the origin of life. The plasma membrane, then, is simply that which surrounds the 'plasma' - the protoplasm.

If you wanted the etymology of the word, would better have gone to english.stackexchange.com. Also, note that in etymology, there is a large disparity between what hypothesis sounds logical to a layperson and what hypothesis is true.


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If ants have an antibiotic gland, how can they spread hospital infections?
Wikipedia describes how antibiotics are produced in ants:

"Metapleural glands ... are responsible for the production of an
  antibiotic fluid that then collects in a reservoir ... also referred
  to as the bulla ... From the bulla, ants can groom the secretion onto
  the surface of their exoskeleton. This helps to prevent the growth of
  bacteria and fungal spores on the ants and inside their nest."

So how are ants often cited as an important problem in hospitals, spreading infections from garbage and through the patients? Shouldn't their natural antibiotics prevent that?

Who says that ants are spreading infection from garbage to patients? Do you have a reference for that?

No, that's just a truism that I heard sometimes.

Truisms are not a very good source of information on this site.

A quick google at "ants hospital infection" shows a lot of scientific papers...

@anongoodnurse A truism is something that is so obviously true that you don't need to justify it. I suspect Rodrigo meant to use some other word.

Let me rephrase your question: if a penicillin pill is rubbed on a MRSA-infested surface, will the pill be safe? Supposing that it is true that ants carry infections and secrete significant amounts of antibiotics (both big ifs), there is no such thing as an universal antibiotic.

Human beings also have many glands which secrete antibiotic fluid, including our tear ducts. Yet humans are certainly an important source of infectious bacteria.

I agree with @tel

I have worked in hospitals (US) most of my life, treating both community-acquired, and more pertinently to this question, nosocomial (hospital acquired) infections, and have read many articles on the subject.
I have never, ever seen ants mentioned anywhere.
People, flies, cockroaches and rats, yes.
Ants, no.
However, ants are vectors in a few foreign studies. The key word in these studies is potential.
As you stated,

From the bulla, ants can groom the secretion onto the surface of their exoskeleton. This helps to prevent the growth of bacteria and fungal spores on the ants and inside their nest.

No antibiotic covers all organisms. Also, the secretions are to protect the ants against infection, not against the carrier state.
Pathogenic bacteria is cultured from ants themselves. The ant can be thought of as similar to a human: humans make antibodies to pathogens but are vectors of many diseases. Ants protect themselves via secretions, but are hosts to potential pathogens.
Part I: Review of Scientific Data Regarding Transmission of Infectious Agents in Healthcare Settings
Hospital hygiene and infection control
Ants associated with pathogenic microorganisms in brazilian
hospitals: attention to a silent vector
Ants in a hospital environment and their potential as mechanical bacterial vectors
Insect/Bacteria Association
and Nosocomial Infection

I agree with that - I have been a lot to hospitals lately and not noticed any ants.

Ants can and do carry loads that are several times their own weight. I grew up in an area with a lot of ants, and a common scene was a long trail of ants acting as a food supply line. Once a morsel is located, they create a long feremone trail to that morsel. A large clump of ants is always working to break the food into smaller pieces, and several ants are usually on their way back to the colony carrying large crumbs. Often these crumbs are the first thing you notice, rather than the actual ants, because they are often so much larger than the ants themselves.
In a hospital, most of the food that ants would scavenge would have fallen from the plate of a human being. Many of those human beings would be carriers of disease. I would expect that the trail that these ants walk is littered with plenty of crumbs-of-crumbs that fall off of their load along the way. If these were large enough for us to see, they would get the attention of the ants and they would carry them back to their colony. But a particle of the microscopic crumb dust they do leave behind might carry several specimens of the germ that sickened some messy patient, even if the ant that dropped it was relatively sterile.

Other than the fact that ants carry bacteria on their food particles, there could also be alternative reasons that they can spread infections.
Just like antibiotics derived from bacteria and fungi have caused resistant pathogen strains to evolve (MRSA for example), it could also be the case that the bacteria naturally living around the ants have evolved some degree of resistance to the antibiotics, perhaps by effluxing sufficient amounts of them by overexpressing pump proteins to the levels that the antibiotics are only mildly bacteriostatic instead of bacteriocidal. These bacteria can then fall off the ants while in the hospital and lead to disease.
It is reasonable to assume that this could evolve, since the ants frequently communicate socially with one another, and any resistant bacteria or fungi can then quickly colonise a previously empty niche, thus creating significant evolutionary pressure for this.


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Why don't we see turbulence in the aorta even in normal situations?
I read about the Windkessel effect. Then I read about pulse pressure waves getting reflected from the periphery. If the pulse pressure wave is reflected during diastole and at the same time blood is being pumped forward by the aorta due to the Windkessel effect, then we have two opposite forces acting which should create turbulence even in a normal aorta. Why doesn't this happen?

Why don't we see turbulance in Aorta even in normal situations?

There are different parts of aorta where turbulence is possible and where not.
It is often said that in normal situations, we cannot see turbulence in aorta because aorta is very stiff and its surface is very smooth.
However, this is a simplification and involves an average person (middle aged) which has stiff aortic arch too.
Note that the elasticity of arcus aortae is responsible for 50% of the volume to the peripheral circulation, thus creating a nearly continuous peripheral blood flow as anongoodnurse says, see this publication.
However, not all of this blood travel to the backward direction.
It would be interesting to see how much blood is travelling backward.
This would help to understand what is the likely hood for turbulences.
Those models linked by Anongoodnurse's answer are a few models used to locate places of possible turbulences discretely but they do not seem to consider the amount of blood capable of creating turbulences, just discrete models:

Stalder et al. I do not like the first publication because it is using Reynold's number that is designed originally for laminar flow. Problem with viscosity etc. There are better ways to the same thing and consider explicitly the creation of turbulence. It does much simplifications there. Fitting the equation to the physiological ranges of some set of data is bad procedure.
Fukuda et al. I like the second publication. High velocity and turbulence and nonlinear streamlines in the ascending aorta in normal situation. In other words, high magnitude of the strain rate tensor along aortic curvatures. So we need nonlinear distribution of at least 4D (later 6D) to quantify the amount and degree of nonlinear processes in turbulences.
Lantz et al. Third publication. Linear model for nonlinear situation. I am not convinced by their Mesh selection. Only in Mechanics' journal. Very far from Medical publication or from Mathematical. Not rigorous.

In summary, there are many models and publications to answer the question where are the turbulences. However, they try to answer nonlinear problem by linear models.
I have not seen any models where they do this rigorously.
I think we should narrow this problem even more, like Fukuda et al has done.
They manage to provide some good pieces of information by just considering an intervention with least turbulence in the aorta.
Generally speaking, we can see some turbulence in arcus aortae in the diastole when blood bounces back from the aortic valve.
The walls of arcus aortae can store about 50% of left ventricular volume.
However, I do not know how much of this blood is travelling backward and reflecting back from the atrial valve and causing possibility for turbulences.

[P]ulse pressure wave getting reflected from periphery.

Pulse pressure is systolic minus diastolic pressure.
Pulse wave is those small waves inside respiratory waves:

where vasomotor waves are controlling the big picture.

If the pulse pressure wave is reflected during diastole and at the same time blood is being pumped forward by aorta - -.

Wrong! Blood is pumped by heart. Aorta is just a vessel for transportation.
Generally speaking, Some blood is reflected back from arcus aortae which bounches back from the aortic valve.

[Because] windkessel effect then we have two opposite forces acting which should
  create turbulance even in normal aorta. Why doesn't this happen?

You confuse here different terms and processes.
Generally speaking.
Arcus aortae stretches during systole.
It is coils back in diastole (left atrium relaxing), blood crashing off aortic valve, possibly creating a heart sound and increasing diastolic pressure. Like anongoodnurse says, in this phase, you can see some turbulence in the aorta but little, since the wall of the aorta is very smooth and only small portion of blood is travelling backward from the walls of aorta:

where see the aorta coils part.

I wish I could agree with you here, but I don't. Furthermore, your notes aren't reflecting what you're claiming (mostly they involve the causes of the heart sounds and where they occur in the cycle seen on an EKG. The fourth Heart Sound is pathological and is caused by increased resistance to filling of the left or right ventricle because of a reduction in ventricular wall compliance, and is called the atrial gallop.

Finally, the elasticity of the aorta has a lot to do with the propulsion of blood. See Elastic properties and Windkessel function of the human aorta: "the elastic forces of the aortic wall forward this 50% of the volume to the peripheral circulation, thus creating a nearly continuous peripheral blood flow."

@masi I'm talking about normal individuals who do not have pathological fourth heart sound. I was referring to concept "pulse wave velocity". Now as heart pushes blood in systole, the aorta stretches, and in diastole and aorta recoils, at the same time there is the reflected pulse wave that is coming in opposite direction to that of blood propulsion due to recoil of aorta.

@anongoodnurse How much of this 50% of LV is travelling backward? I have an intuition that not all of it is travelling backward so only a portion is possibly causing a turbulence.

@gautampw Yes, you are right. The heart sound IV is not relevant here. I consider here a situation when some blood bounces off the atrial valve only so possibly creating some heart sound.

As the author states, blood flow is to the periphery, so that is clearly the major direction of the blood. I have little disagreement with your modified answer (except for some nit-picking, like your use of "atrial valve" (do you mean the aortic valve?) which makes for some lack of clarity. Your modified answer basically states what I stated in my original answer: There is some turbulence in the normal aorta.

@anongoodnurse thank you for correction! Please, say specifically where your disagreements. Yes, some turbulence. Yes, to periphery but for creation of turbulence it does not matter how pressure difference is created. Reflections matter here.

There is turbulence in the normal aorta, which is thought to be one mechanism of endothelial injury leading to atherosclerosis and thrombus formation.
Blood Flow in the Healthy Aorta: Turbulent or not?
Flow velocity and turbulence in the transverse aorta of a proximally directed aortic cannula: hydrodynamic study in a transparent model
WALL SHEAR STRESS IN A SUBJECT SPECIFIC HUMAN
AORTA - INFLUENCE OF FLUID-STRUCTURE INTERACTION

I do not like the first publication because it is using Reynold's number that is desigined originally for laminar flow. Problem with viscosity etc. There are better ways to the same thing and consider explicitly the creation of turbulence. It does much simplifications there. Fitting the equation to the physiological ranges of some set of data is bad procedure.

I like the second publication. High velocity and turbulence and nonlinear streamlines in the ascending aorta in normal situation. In other words, high magnitude of the strain rate tensor along aortic curvatures. So we need nonlinear distribution of at least 4D (later 6D) to quantify the amount and degree of nonlinear processes in turbulences.

Third publication. Linear model for nonlinear situation. I am not convinced by their Mesh selection. Only in Mechanics' journal. Very far from Medical publication or from Mathematical. Not rigorous.

@Masi - I agree with your critiques of the papers for the most part. These are three models used to study aortic turbulence. I could have included MRI studies as well, but the catheter studies are most plentiful, and they seem to agree with each other. Most of the most recent studies on turbulence in the aorta involve heart valve studies. But I think it's important to note that there is turbulence in the aorta.

Yes, there is turbulence! Please, include better studies and MRI so I can review them. I am very interested in turbulence in many environments. The catheter study is mosthe beneficial in this research. MRI can describe some fluid dynamics.


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The origin of molecular machines
DNA holds genetic information and holds the key to the evolution of living organisms. Transcription and translation mechanisms enable living cells to process information encoded in DNA. To that end, transcription and translation are fundamental mechanisms needed to enable the evolution of organisms. Molecular machines (enzymes) carry out these mechanisms by reading the information in DNA and using it to construct proteins.
Did the first living cell contain the machinery needed for translation and transcription? or  Did they evolve over time?
EDIT: Edited the question to narrow the scope.

Thank you for your feedback. Please let me know if the question needs further editing.

I was wondering a similar question but I see you have posted it!

The main hypothesis is that all starts from RNA. "The RNA world". There was no DNA and no proteins. Both function was performed by RNA. Now there are no living organism that carrying information in RNA (only viruses...), but there is "enzymes" from RNA - ribozymes.
The evolution to DNA was later, according to this hypothesis.
There is really good article in wiki.
http://en.wikipedia.org/wiki/RNA_world_hypothesis
or if you want something more look here
http://www.ncbi.nlm.nih.gov/books/NBK26876/
Summary

From our knowledge of present-day organisms and the molecules they contain, it seems likely that the development of the directly autocatalytic mechanisms fundamental to living systems began with the evolution of families of molecules that could catalyze their own replication. With time, a family of cooperating RNA catalysts probably developed the ability to direct synthesis of polypeptides. DNA is likely to have been a late addition: as the accumulation of additional protein catalysts allowed more efficient and complex cells to evolve, the DNA double helix replaced RNA as a more stable molecule for storing the increased amounts of genetic information required by such cells.

It's important to note that the RNA world is a hypothesis, not a theory. Nobody knows how life arose.


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About the apoptosis mechanisms in a cell
The apoptosis mechanisms in a cell are like a type of 'self-destruction mechanism': is this correct?
As with any type of complex system with various necessary functions, if it has a set of self-destruction mechanisms for 'shutting down' the whole system, it would require some sort of 'internal programming' that can somehow 'target' each of the system's necessary functions and 'disrupt' each of them simultaneously or in some 'order'.
In other words a self-destruction system in order to be effective would have to be able to 'target' each necessary function in the system. And if a biological system has a mutation or a set of mutations that 'distort' some parts of the system then the self-destruct mechanisms might not be able to 'target' all of the functions.
So maybe the cellular mutation 'automatically' makes it hard or impossible for the self-destruct mechanisms to work. Is this possible??

Did you happen to look at any of the questions/answers tagged apoptosis? Why were they unhelpful?

I wrote some of those questions.

@201044 Your question was hard to understand. I took the liberty to edit it. Let me know if it is fine.

I am not sure if I understand your question right. Are you asking how and what kind of mutation is disabling apoptosis? What do you mean by "it would require some sort of 'internal programming' that can somehow 'target' each of the system's necessary functions and 'disrupt' each of them simultaneously or in some 'order'."?

Not at all. In order to self destruct, you don't need to disable all necessary functions, you just need to disable one. That's why the functions are called "essential". To take a very simple example, in every movie you've seen where the self destruct has been activated, that self destruct mechanism was almost certainly a bomb that blew the ship/installation/planet or whatever up. The self destruct did not go around disabling individual processes, it just activated a bomb and destroyed everything.
Apoptosis is quite similar. While there are many essential processes in a cell whose failure can activate apoptosis, the mechanism of apoptosis itself usually involves the straightforward destruction (lysis) of the cell. Simply put, the cell digests itself, breaking down its various constituent parts and, finally, destroying the cell membrane and breaking up the cell itself. For a summary see this Wikipedia page or here.
Briefly, when apoptosis is triggered, the caspase cascade is initialized which results in the breakdown of various proteins in the cell and, finally, in cell lysis. It really is analogous to setting of the bomb that destroys the facility of the bad guys.

That's a great point about only having to destroy one essential function. So is it true first comes at least one essential function failure then the apoptosis mechanism is triggered? Could some functional mutation that creates some different 'demands' on the cell make it so even if one or two essential functions are on the brink of failing the mutation masks this or makes these functions not as essential or somehow distorts necessary cellular system information so the apoptosis is not triggered?

If a cell or group of cell is reproducing and dividing a lot more than 'they' usually would if 'their' 'situation' was 'healthier' (because of cellular damage caused by an 'unstable' digestive system for example); if they are dividing and reproducing a lot and random mutations can cause cancer is it more likely the cells will develop some mutations if they are reproducing and dividing a lot 'more than normal'. And as such some of these mutations might shut down some important cell functions thus disrupting any apoptosis mechanism?

If a 'group' of cells divide and reproduce a lot more than usual would this increase the likelihood of mutations that could disrupt maybe some important cellular functions?

The apoptosis mechanism involves the failure of just one essential process , straightforward lysis; this seems simple yet how come in a cancerous cell such a 'shutting down doesn't work or can't be 'activated'. Do cancerous cells have all the essential functions that are normally found in the ' normal' versions of the cell ,yet they are still 'functioning adequately' in this cancerous 'version'?