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Divalent cation binding to calmodulin
I have carried out a native PAGE with 4 reaction mixtures. To each I had added an equal volume of EDTA (1 µl/1mM) to sequester any divalent ions and an equal volume of calmodulin (5 µl/0.5 mg/ml). I added 2 µl of calcium (2 mM), magnesium (2 mM) and manganese (2 mM) ions respectively to three reaction mixtures and had a control that was made up to an equal volume with Tris-HCl. All reaction mixtures were made up to 10 µl with Tris-HCl. Here I ran into a problem with the waterbaths and the reactions couldn't be incubated at 37 degrees Celsius.
After I added the loading buffer to each, I added the 4 reaction mixtures to the polyacrylamide gel and electrophoresed for 45 minutes at 150 V. After this I placed the gel in Coomassie Blue stain for 20 minutes.
After the destaining process, I reviewed the gel to find that the calmodulin in the 4 lanes had migrated the same distance. I had expected the EDTA control to have migrated the furthest on the gel, with Ca2+ and Mn2+ migrating similar distances due to their similar ionic radii; making it a good substitute for the binding to the calmodulin. I was unsure of how far the Mg2+ would travel as I thought it would have a lower affinity to the calmodulin due to its binding to the N-terminus rather than the C-terminus. However, I was wondering if this was negligible in the absence of Ca2+, although now I can't be sure due to the results of the gel.
I was wondering what errors in the experimental design or process could have resulted in this? And if the experiment was run correctly, what results would be expected?
The first image is the result I was expecting. The second is the results from my gel electrophoresis.

Why add EDTA if you want calmodulin to bind ions? Are you expecting just ion binding to influence migration rate?

Binding of a cation would not change the mobility much so as to be detectable by electrophoresis.

If you want to sequester the bivalent ions, you need ways more EDTA. It complexes an equivalent amount of ions, so 1mM EDTA complexes 1mM of calcium (for example). If you EDTA solution is 1mM, but your ion solution is 2mM, this will never work.

Apologies, edits have been made to include the concentrations. EDTA was added under the instruction of my supervisor, which I did question at the time. I was under the impression that the migration would be detectable through the existing literature.

And with the EDTA being added to each reaction mixture was to sequester any divalent ions from the protein before the target ions (Ca2+, Mg2+ and Mn2+) were added respectively. I thought the ion binding at this step would not be interrupted as the ions are in a two-fold molar excess of the EDTA, and therefore could bind calmodulin and cause its retardation? Which would be picked up on the gels?

What article is that figure from? Also, you should destain your gel.

You cannot see a mobility shift in SDS-PAGE (even in this picture that is claiming so). Shift in native-PAGE is due to conformational changes upon ion-binding. Moreover it is unlikely that an ion remains bound to a protein in denaturing conditions of SDS-PAGE.

The change in gel migration distance is due to the conformational changes due to the binding of the ion, and have nothing (detectable) to do with the ionic radius of the ion.
The left image shows calmodulin with no ligand bound, and the right image shows it with calcium and peptide bound to it.

As you can clearly see, the unbound calmodulin is significantly thinner, and therefore can migrate faster through the gel. The change in charge on the protein due to cation binding in native PAGE may also affect the result.
Since the calmodulin conformational change is enhanced by both a peptide and calcium cations, as well as its phosphorylation state, it would be reasonable to investigate the contributions of these factors to your result. Reading the original paper again to see what you missed the first time may also be helpful.

Yes the left panel is apo-calmodulin, but Ca(II)-calmodulin also resembles structure in the left panel (with minor structural adjustment). The major conformational change on the right panel is a result of peptide binding, which is not part of experiment in the question.

@SYK I am pretty sure that peptide cannot bind without calcium also binding.


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What, if any, diseases do larder beetles carry?
I found one of these beetles on my bed as I was attempting to get in. I'm 80% sure my cat carried it in (I found it in the exact same space he had been sitting ten minutes previously).
My question is what, if any, diseases do these bugs carry? It did not bite me, though it may have bitten my cat. I'm more worried about bacteria etc that it may have carried around my bed/room. Can they transmit salmonella? Should I break out the disinfectant, or is it no big deal?
I have researched them as best I can, and I found someone noting that they can spread bacteria, but found nothing on how severe it is. For example, my cat obviously spreads bacteria, but I let him on my bed without worry. I have never see one of these beetles before.
I have a secondary question, if that's allowed - what are the chances it laid eggs on my bed? It was there for possibly 4-5 hours if my cat indeed carried it in. I have rodents (pets) in my room and am peripherally worried about an infestation happening.
For context, I live in the center of the UK.

Looks like you planned to put up a pic but it is missing

I have never heard of larder beetles carrying any serious diseases and chances are slim that it could have laid any eggs, so you probably have nothing to worry about. If you want you can spray the area down with a cleaner, but as I said earlier, it's probably fine.

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Hydrogen peroxide decomposition and catalase uses
All google searches have simply returned more info on catalase. I'm looking for a catalyst that isn't found inside living organisms which  can break down H2O2. Looking for any resources to look at, or just examples of other catalysts.
Side question since I don't want to clutter with a new thread.
Can catalase be used for anything other than the decomposition of h2o2?

https://en.wikipedia.org/wiki/Hydrogen_peroxide#Decomposition - you're looking for non-biological catalysts so you should ask on Chemistry SE

@Mithoron yea I suppose, I just received this question in bio class so I thought there might be some relevance.

Manganese(IV)oxide can be used as a catalyst to speed up the decomposition of hydrogen peroxide

A reference would be appreciated Hamza.

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What is a new biotechnology issue?
I'm looking for any new biotechnology issue related to Biochemistry, Metabolic processes, molecular Genetics, or other relevant fields. If anyone knows of an issue that has solid resources around I'd love to hear all about it.

You use the term 'biotechnology' in a wrong way. It is a field of science and is somewhat mixture of what you've listed. I don't know what you're looking for, so could you pleas clarify what you mean by biotechnology? I'm voting for close this question as 'unclear what you're asking', that I'm willing to retract.

Edited, hope it makes more sense now.

It makes more sense, yet it is till unclear and / or too broad. There are tons of biotechnology papers, journals, full of research. Interesting to who? For eg. plant biotech. is could be interesting to someone (for eg. you), but I'm totally uninterested in it right now. Interesting at what level? For an average person beer and champagne production can be interesting ( it is a sort of biotechnology)....

Biotechnology is a gigantic field. You should have a look at the wikipedia entry for biotechnology.
Because of the size of the field "biotechnology", because the word biotechnology accept different definitions and because the word interesting is extremely arbitrary it is pretty much impossible to give a good answer to this question.
I am using below wikipedia's definiton of biotechnology that encompass...pretty much everything! The wiki definition include fields such as:

chemical and bioprocess engineering
bioinformatics and biostatistics
biorobotics

From @poka.nando's comment, the UN definition is
Hoping it will help you, below are few random examples of research in biotechnology: "Biotechnology is the use of living systems and organisms to develop or make products, or "any technological application that uses biological systems, living organisms or derivatives thereof, to make or modify products or processes for specific use" (UN Convention on Biological Diversity, Art. 2)" Under this definition fields such as bioinformatics would probably not really fit within the field of biotechnology.
Using wiki's definition of biotechnology below are few examples of s^hitngs you might be looking for.

Improve the statistical tools to detect differential selection pressure in a phylogeny (methods such as PAML)
Improving fungiculture by improving our understanding of the mushroom life cycle variation in response to temperature.
Track down genes of resistance to drought in tomato (GWAS)
Design better artificial hearts or get a better understanding of cell differentiation in order to be able to rebuild lost tissues or even organs (see regenerative medicine).
Improve understanding of the transmission of the African swine fever in order to improve its use as a biological warfare.

I think we have different understanding of biotechnology : "Biotechnology is the use of living systems and organisms to develop or make products, or "any technological application that uses biological systems, living organisms or derivatives thereof, to make or modify products or processes for specific use" (UN Convention on Biological Diversity, Art. 2)" taken from wikipedia, an basically this is what I was taught under biotech.

I am using wikipedia's definition which also include bioinformatics and this kind of tools. Let me update my answer with your comment in mind.

The very page you link list quite different fields and to make it clear:
"In many instances, it is also dependent on knowledge and methods from outside the sphere of biology including:
bioinformatics, a new brand of computer science
bioprocess engineering
biorobotics
chemical engineering

" I think you copied the wrong part...

Oops you're right.... ok. I got lazy to work for a poorly defined question. I vote for closing! Hum... I can't delete my answer as it has been accepted now!


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Applying kiwis on gelatin
Kiwis have the enzyme actinidain. This enzyme will break the peptide bonds from the gelatin. Making gelatin with raw kiwis will not work, because the peptide bonds in the gelatin will be broken down.
But what if you would make plain gelatin, and apply raw kiwis to it? Do the enzymes break down the gelatin when the gelatin already has set?

It's ok, you did the edit, and now everything is fine.:D One more thing can you link a reference that kiwi truly has that enzyme and it does what you say it does. It's not known to me.

Do you mean actual kiwis (a family of birds native to New Zealand), or the fruits that are marketed as Kiwifruit?

@jamesqf just grab the bird and rub it on the gelatin.

@user137: One would first have to kill & dress it before slicing.

According to the (non peer reviewed) scientific experiment found here, simply placing a piece of kiwi onto gelatin that has set will cause the gelatin to be hydrolysed by actinidain.

This experiment aims to show the effects of Proteolytic enzymes on proteins and, subsequently, the effects of extreme temperatures on the proteins themselves. Petri dishes filled with gelatin, a derivative of collagen, were acted upon by kiwifruit samples overnight. Some samples were fresh and used as controls; others had been frozen or boiled for two, four, six, eight or ten minutes. The mass of digested gelatin was taken the next day. The results ultimately reflect the effectiveness of the actinidin, the kiwi’s Proteolytic enzyme, under normal conditions and after exposure to extreme temperatures.


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Why do apples taste sweeter at the bottom?
Sometimes when eating an apple, I notice that the bottom (blossom) end of the apple has a lot more sweetness and flavour to it, whereas the top half (stem) is often more watery, crispier and feels less dense than the bottom part.
A quick search on the internet revealed that I'm not the only one asking this question, but answers seemed to be mainly opinions. The largest discussion I stumbled upon can be found here, but comes to no satisfying conclusion.
Apparently, this phenomenon seems to occur in pears (supposedly even mentioned in a japanese saying, but the article does not provide a solution to the question) and pineapples as well.
I am looking for a more scientific explanation, as I believe that the biology of apples might be more complex than to allow a simple "sugar is denser than water and gathers at the bottom"-solution.
Do apples ripen unevenly (the blossom-end growing first, allowing it to ripen for a longer time)?
Might this phenomenon be the result of how apples meant for long-term controlled atmosphere storage are picked slightly less mature?

I was always taught that it's an example of dependent evolution. Fruit with higher concentrations of sugar at the blossom end are easier for bees to get to.

For whether or not your assumption is correct, I have found the following (here), which states that sweetness indeed differs, as well as pH level:

The bottom sections of ‘McIntosh’ apples were sweeter; whereas the bottom sections of ‘Jonagold’ were less crisp and more fruity.
  The bottom sections of both the ‘McIntosh’ and ‘Jonagold’ apples had significantly lower pH than the top.

Fruits consist of two main parts, the pericarp and the seeds. The pericarp can be further divided into the followings: exocarp, mesocarp and endocarp. In the case of apples, the one responsible for composing most part of the fruit flesh is the mesocarp, so I would like to disregard the other two. The mesocarp consists of ground tissue almost exclusively[1] and no vascular system, thus the only way for sugars to travel inside the flesh of fruit is diffusion, which is mostly determined by gravitation, hence the result.

I haven't find any hint in the reference about the rather surprising fact that diffusion of dissolved sugar inside an apple is determined by gravitation.

The reasoning behind this answer seems flawed. Why would a denser solution travel 'inside the flesh of fruit' mainly through gravity?

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Why have a placebo control group when testing a new drug if existing drugs can be used?
It is general practice to compare a new treatment against a sham treatment (placebo), and then use those results to compare efficacy of the new treatment (call it B) to an existing treatment (call it A), at least when existing treatments are available.
However, it seems reasonable and more ethical to use A and B together in a study, rather than giving one group a sham treatment. In other words, instead of a placebo group and a treatment group, why aren't there two treatment groups, one with A and one with B? Statistical noise such as regression to the mean, natural progression of the disease, etc would all show up in both groups, so if B gave better results than A, we should be able to say directly from that result that B works better than A, and we would be doing so in a more direct way than comparing the effect sizes of B vs placebo to the effect sizes of A vs placebo.

While more ethical and reasonable, and often / usually legally required, comparing a drug to another drug can also has one potential draw-back: assume that drug A) improves survival from 1% to 10%, and drug B), which would be tested after A), would improve from 10% to 11%. In this case it might be practically impossible without a large group of patients to statistically show an improvement over A) - as the potentially less sophisticated, drug A) would have already been released

I fail to see the point.

Ben Goldacre talks about this is in his book "Bad Science" for a fair while. He makes the point that good science now-a-days compares against the current market leader, while bad science compares against a placebo. It's relatively easy to do better than placebo. It's also worth noting that just because a drug doesn't do outright better than the market leader doesn't mean it isn't useful. For example, it may be applicable to people with certain allergies or have a less intense dosing regime. It may be able to be used in a combination therapy while the market leader can't.

When you want to check if your light bulb is broken or not, do you flick the light switch and see if the room gets illuminated; or do you measure the difference in light intensity between one room and another? The two tests are completely different. The first tries to confirm that the drug works; the second compares the drug's working to another drug. You're essentially suggesting that a driving exam (testing aptitude) can be done by having students race (testing who's best) and giving a driving license to whoever wins the race (as they are clearly better at driving than the others).

(To finish my thought) Relative results are potentially meaningless. That student who wins the race may be better than the other students, but that doesn't give you an objective confirmation that the student actually meets the required skill level for driving a car in traffic.

@Flater Relatively studies are meaningless with no base idea. Obviously, to get to large scale human studies, you have to prove that the drug is non-harmful (to the extent that harm can be expected for the treatment). When Doctors are comparing medication, they're not concerned about whether the drug has passed FDA approval, they're concerned about who "won the race", as per your example. The driving test is FDA approval, the race is the treatment comparison.

@Don Branson: You would just ask all patients for allergies against anything in A, anything in B, and additional other random allergies that might generally influence results (as some allergies might interfere with how they feel in general, which is something you might be asking about regularly)

@SGR: This may be going out of scope for my on-topic knowledge, but isn't there more than one measure for the effectiveness of a drug? Assuming that drugs are rated by "winning the race", why would we still commonly have many different types of pain killers etc. available, instead of just the "winner"? Aren't there other considerations too, e.g. having lower efficacy but avoiding otherwise undesirable side effects? Who would win in a race between ibuprofen and paracetamol, and why are both still available if one wins over the other?

@Flater Yes, there are, which I highlighted in my first post. I was reducing my argument down to your analogy. To expand on it, a Doctor isn't concerned about whether the light turns on or off, but whether the light bulb they're considering using is brighter, or more energy efficient, or the hue is better for reducing eye strain, etc. They assume the light bulb works and only having a placebo trial just tells them the bulb is functioning.

@SGR: Sure, but comparing drugs is a second step, after you've first tested that the drug works. OP's assertion is that we can skip the first step because the second step invariably proves the first; which may be true in regards to efficacy, but not necessarily to note side effects, especially those that may be opposite. Imagine if drug A makes your skin go lighter, and drug B makes your skin go darker (but they both cure the disease). Without a placebo trial; you'd only see the relative difference, but can't tell which drug is causing the most discoloration.

@SFR: The example of discoloration is a bit simple, given that you can take pictures of the people in advance. But not every side effect is objectively measurable by an outside observer (hence why we do trials in the first place), I picked a simple side effect for the sake of example.

Flater, we're assuming that the standard of care has already been tested against something else, or a placebo. If it has been established that the standard of care works, then your argument falls flat.

You are correct. For serious diseases, it would be unethical to withhold the existing treatment (Treatment A) for a placebo. Treatment A is called "standard of care", and new treatments are compared to this.

I can't ask this as a main question, but I guess in comments it's fine. How frequently is an A vs B as opposed to placebo vs B method used, or can you at least provide an example clinical trial?

@DanielGoldman This review seems to be an extensive discussion and provides examples.

Could you perhaps expand on your answer a bit, and maybe include something from what tsttst said? I could just take your answer and the comments and write my own answer, but I think if you expanded on yours, I could tag yours as accepted.

@canadianer Doesn't seem to provide figures for rates of A vs B vs Placebo vs B, just a comprehensive answer for the question here.

It's worth pointing out that the purpose of the placebo isn't really to test against no treatment, it's to test against the belief of receiving an effective treatment, for both the subject and the researcher.  Loooong answer incoming...
Firstly, it's a lovely issue with medical trials that if you get a statistically valid comparison between a group who don't believe they're taking an effective drug and a control group that know they aren't taking anything, you'll find the placebo group has a better result.  Part of it will be psychosomatic, part of it will be biased reporting of symptoms, part of it might be slight changes to routine during the trial.  The end result, though, is that a placebo treatment does tend to have a slight effect in the direction intended.
IIRC, there were some less ethical studies at one point that demonstrated that if you tell a subject that their placebo drug has negative side effects, they may actually experience those effects even though the drug has no ability to cause them.  Certainly there are studies in of the negative effects during studies not intended to cause them, documenting such things as withdrawal effects from being on a placebo course.  In the case of negative results the term "nocebo" tends to be more appropriate.
Secondly, a placebo is important for the researchers as well.  The core requirement of a double blind test is that neither the subject nor the researcher knows which treatment the subject is on.  You might be able to pull off a single blind test for a comparative test but I would personally say it would be ethically problematic for a researcher to be administering an active treatment without knowing which it was.  You can dodge the problem with a placebo by making the inactive treatment identical in administration to the active one.
If your test isn't double blind, there's a real risk of researchers having expectation bias skewing the data collecting and results.  Unchecked this can result in tests seeming to show a treatment as being far more effective than it actually is, or as having far less serious side effects than it actually causes.
Thirdly, building on those two points and more directly answering the question, you tend to need a placebo group because that can be considered a standard reference.
So, in the first case, even assuming a blind trial, there is going to be some placebo effect going on, but having only two active groups means you can't filter out that effect.  How much of the new treatment's effect was due to placebo?  Would the old treatment's group have gotten better or worse results if they knew they were on a "proven" treatment?  Would the new treatment's group have gotten better or worse results if they didn't think there was a chance of them being on the old treatment?  You can't easily and reliably answer these questions without control groups, or if you can the results still won't be accepted as readily.
In the second case the issue is that of comparability.  Even with decent correction for researcher bias you can't really get rid of the issue that the results are a comparison between two treatments.  To compare to a third you'd have to try and infer it against the existing treatment's results against placebo.  It'd go something like "Treatment A resulted in 10 more successful cases than Treatment B; Treatment B resulted in 20 more successful cases than placebo; Treatment C resulted in 40 more successful cases than placebo, so we thin Treatment C would be more effective than Treatment A when compared with no treatment at all".  How much trust would you place in that sort of reasoning?  And that's assuming you have comparisons against placebo for the other treatments... if every treatment has been measured against one or more other active treatments in studies you'll instead have some horrible network of relative efficacy to work though.  Common reference points are your friend.
That's for the simple case... now imagine the more complex case.  Your two groups are being tracked for a dozen or more data points, the new treatment does better than the old in some but worse in others.  You have lists of side effects from both groups and there's only partial overlap there.  Of course you have no control to help you remove biases and placebo effects.  The resulting paper is going to end up as a straight comparison between the two treatments and a pretty high standard of objectivity and clean structuring is going to be needed to avoid a reviewer concluding that the results are subjective and unreliable.  Trying to go from that paper to compare with other treatments is similarly harder.
It's easier to convince someone that your treatment is safer and more effective if you have clean studies to back it up.  That's not to say comparison trials aren't useful in some cases, particularly where there's a strong ethical reason for not withholding a known treatment, but I personally would prefer to have an experiment against an inactive control group before trying to compare two active processes.
I'm also reasonably sure that tests against placebo are done with the subject's expectations being managed appropriately.  Ethically the subject has to be informed that there is a chance they will be in the control group and a chance the treatment won't have the expected results.  To give informed consent to the trial the subject has to understand that the treatment might not be as good as the older treatments.  Thus while there is the ethical issue of effectively withholding treatment, it's being done with the consent and co-operation of the patient, hopefully with the intention of improving medicine as a whole.  Having a test protocol that doesn't feature informed consent is risking some serious consequences down the line due to the much bigger ethical no-no that is forced human experimentation.
Even finding a universal cancer cure won't save a researcher from a major breach of ethics in the process of finding it.

Also, be aware of the existence of counterintuitive non-transitivity in cases where you are trying to say A>B & B>C => A>C in a statistical context. Look up Nontransitive dice and Simpson's Paradox for examples.

@user6697063 yeah, Simpson's is really vicious if not accounted for.  Non-trans dice is an interesting one, the fallacy is obvious only once you're looking for one. An obvious degenerative for Wiki's example is "1/3 A > B > C; 1/3 B > C > A; 1/3 C > A > B;" to give a 2/3 chance for each of A>B, B>C and C>A

Approval pathways for investigational treatments for a particular indication involve a development program in which multiple studies at different phases are conducted in order to establish statistical evidence of efficacy and safety.  A well-designed program proceeds from animal studies of the mechanism of action and toxicology, to large-scale pivotal (adequate and well-controlled) studies that furnish the bulk of evidence to support regulatory filing and approval; and if approved, are followed by post-marketing studies that continue to collect safety information and how the treatment is utilized in less structured clinical settings and patient populations.
As such, early-phase clinical studies expose a limited number of subjects and may not be controlled (whether with placebo or an active comparator or standard of care).  The study population may not even have the condition being treated.  The goal here is to show the treatment is safe, or safe enough to expose a larger population to it.
Mid-phase studies are intended to begin gathering preliminary evidence of efficacy as well as to explore avenues by which efficacy can be established (e.g., endpoint selection, population selection, dose selection) in order to support the design of a pivotal trial.  These studies have medium-sized sample sizes and should employ a type of treatment control, whether with placebo, placebo on top of standard of care, or with active comparator, depending on numerous factors, such as whether there exists approved therapy for the indication or if it is an orphan indication; if it is ethical to use placebo alone; and so forth.  This is the essence of your question and to address it fully is beyond the scope of this reply.  It is the responsibility of IRBs to ensure that the trial is designed ethically and the rights of participants protected.  However, because in a mid-phase trial the goal is not to formally conclude efficacy but merely establish preliminary evidence of such, less importance is placed on comparing the experimental therapy to existing available treatments.  In these studies, it is generally acceptable to use placebo control (unless doing so is clearly unethical) and implement a protocol-defined rescue therapy option.
For a late-stage or pivotal trial intended to support NDA, there are clear statistical requirements for ensuring that the evidence for a treatment effect is in fact valid and genuine.  If a previously approved therapy is available, such a trial will generally be required to compare the experimental treatment(s) against it, in order to answer the question of whether the experimental therapy offers a superior benefit/risk profile.
The takeaway is that there are many considerations that delineate how trials may be designed:  what is the indication; who will be exposed; are there other available therapies; does the route of administration permit placebo; and so forth.  As a result, scientists and statisticians have developed numerous and often clever approaches to designing controlled clinical trials in such a way that participants are not unduly harmed, even when placebo controls are used.

"such a trial will generally be required to compare the experimental treatment(s) against it" <--- that's an interesting piece of information... who actually has that requirement?  Are we talking legal, FDA approval or medical association setting that requirement?

Drug companies often do exactly what you describe. That's why there are active control drug trials where there is no placebo - one group receives the experimental drug, and the other receives the "standard" treatment.
I worked on the technology side of drug trial administration for a Contract Research Organization (CRO) for awhile, and many of our clients (which included large, recognizable pharmaceutical companies) were doing this.


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How can biologists rule out multiple early organisms that went through conjugation?
The current idea is that all life evolved from a single cell. Analysis indicates the probability of two different origins being very unlikely, given shared DNA. However, why couldn't numerous organisms have evolved and then conjugated, with a few lineages surviving? It would vastly increase the odds of modern organisms sharing the DNA that they do.

Because they would not use the same DNA codons. Codons are extremely conserved across life, with only minor variations, there is no reason this should be the case unless those codons are inherited from a common ancestor. This is contingent on what you mean by organism, prior to the incorporation of ribosomes it would be more possible.
If what you suggest had occurred it would drastically DECREASE the odds modern organism would share the same DNA.

How many different collections of codons would be useful for encoding genetic information in an environment in which life evolved?

Another thought: if different systems of codons existed in different lineages, wouldn't that decrease the probability of conjugation so that if any cells did go through early conjugation, they were likely with similar codon systems?

they would have to have identical codons to fuse, the likelihood of separate lineages ending up with identical codons is close to nil. multiple codon lineages could and likely did existed but only one of the contributed to existing life.

Could you provide some data to that effect? Again, how many different systems of codons function reasonably well in the environment in which abiogenesis likely occurred?

Also, are you talking about the codons or the nucleotides themselves?

codons although it could also apply to nucleotides. Codons are arbitrary so any of them would work, but they would not be compatible, organism with different codons could exchange DNA but they would be complete gobbledygook to each other. https://link.springer.com/article/10.1023/B:BIPH.0000024412.82219.a6

Not all organisms do share the same codon configuration. And "gobbledygook" might not necessarily be detrimental, so it could be added in as a plasmid, and eventually come to serve a function. I'm just not convinced that the codon argument is sufficient, but I do appreciate the answer. Thank you.

could and at all likely are different things, very few things can ruled out entirely.

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Deciduous trees in tropical rainforest
Some books says the dominant plant form in tropical rainforest biome is broad leaved evergreen trees. Other books say it is broad leaved evergreen trees and deciduous trees. What is the most accepted way (or the truth)? Also how do you explain the deciduousness adaptation in tropical rainforest (e.g., when do they shed leaves)?

Please could you provide sources?

For example, Cain, Bowman, Hacker's ecology textbook [2nd edition] (ISBN 978-0-87893-083-8) says the latter (i.e., evergreen and deciduous trees).

Are you sure that both talk specifically about tropical rainforests? There is also temperate rainforest, where deciduous trees are common. However, there is also seasonal (eg monsoon) tropical rainforest, which have many/mostly decidious trees. I cannot say which types are most common overall though (as in area).

Deciduous trees are those which shed their leaves once a year at the time of winter season and later grow new leaves, plants those keep their foliage throughout the year are called evergreens. Deciduous trees usually have broad leaves e.g., ash, beech, birch, maple and oak. There is a confusion exists over the dominance of trees in rain forest, but most of the resources suggests broad leaf evergreen trees as the most dominant. But deciduous trees are equally important because the difference may be negligible.

Deciduous trees shed their leaves usually as an adaptation to a cold or dry season. Evergreen trees do lose leaves, but each tree loses its leaves gradually and not all at once. Most tropical rainforest plants are considered to be evergreens, replacing their leaves gradually throughout the year as the leaves age and fall, whereas species growing in seasonally arid climates may be either evergreen or deciduous.Reference

The dominant plants in the tropical rain forest are broadleaf evergreen trees. Unlike evergreens that grow in colder parts of the United States, those of the tropical rain forest have no protection against cold weather or droughts.Reference

Adaptations of Deciduous trees

Broad green leaves capture sunlight needed to make food through photosynthesis.
They cuts off the supply of water to the leaves and seals off the area between the leaf stem and the tree trunk, as sunlight and water become scarce, the leaves are unable to continue producing chlorophyll and this produce vibrant colors in the leaves.
In winter, they simply loose their leaves and seal up the places where the leaves attach to the branch. Losing their leaves helps trees to conserve water loss through transpiration.
In spring the trees grows back their leaves and start the cycle once more.

In the spring, deciduous trees begin producing thin, broad, light-weight leaves. This type of leaf structure easily captures the sunlight needed for food production (photosynthesis). The broad leaves are great when temperatures are warm and there is plenty of sunlight. However, when temperatures are cold, the broad leaves expose too much surface area to water loss and tissue damage. To help prevent this damage from occurring, deciduous trees make internal and physical adaptations that are triggered by changes in the climate.
Cooler temperatures and limited sunlight are two climatic conditions that tell the tree to begin adapting. In the Fall, when these conditions occur, the tree cuts off the supply of water to the leaves and seals off the area between the leaf stem and the tree trunk. With limited sunlight and water, the leaf is unable to continue producing chlorophyll, the "green" stuff in the leaves, and as the chlorophyll decreases the leaves change color. The beautiful display of brilliant red, yellow, and gold leaves, associated with deciduous forests in the fall, is a result of this process. Most deciduous trees shed their leaves, once the leaves are brown and dry.
Reference

authors: Анастасия Долинская


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If Tumors have lots of mutations in them how is it the immune system can't detect them?
If a cancerous tumor has a lot of mutations in them why can't the immune system detect them? If a person has cancer could this somehow alter the person's immune system so it doesn't function effectively to detect greatly mutated cells? Does the fact that a tumor is 'made' of 'mutated' non-foreign human cells help it to be undetectable?

"Does the fact that a tumor is 'made' of 'mutated' non-foreign human cells help it to be undetectable?" This is pretty much it. The more mutations a cancer has, the more likely your immune system will respond. I saw a talk by Steven Rosenburg about cancer immunotherapy, might be interesting for you.

This is a good question and I have upvoted already, but you could consider adding some more information from your own background research (e.g. on minimum and typical numbers of mutations occurring in cancers) to make it more helpful to future readers.

Have you done any research at all into how the immune system works?

This is a good question and it gets to the most basic foundations of immunology. Your immune system is made to be flexible - able to adapt to almost any challenge. However, with so much flexibility comes the potential to generate immune cells that react against the 'self'. So, at the other extreme, the immune system needs to be limited.
In order to meet these two (potentially conflicting) goals, immune (at least lymphocytes) cells have a two-step development pathway. In the first step, the body randomizes its immune receptor specificity. In the second step, it ensures that these receptors are not auto-reactive.
Doing so means that immune cells are aware of their environment at the time that they are 'born.' Take a look at this review from the Fuentes-Panana lab to read about how tumors actively cultivate the immune system of their host in order to maintain a more favorable environment.

Great question and in part, you are correct. However, you must also remember that this greatly depends on what genes have undergone mutation.
In the case of cancer, it's usually either a gene that regulates cell proliferation rates, induces programmed cell death or helps to repair damaged DNA. When one (or all) of these genes is mutated, the cell constantly proliferates and/or does not die when it is "programmed" to do so or cannot repair mutations to it's DNA, thus creating a cancerous tumor.
Now, on to the immune system. The reason a persons immune system does not target and kill it's own cells is because of a certain set of genes that is specific to each and every person called Major Histocompatibility Complex (MHC). These genes encode specific cell surface molecules that the immune system cannot produce antibodies to bind to because they are "locked", if you will (see, the immune has a sort of built-in list of genes that code for antibodies that bind to different sequences of molecules (that's how you develop immunity and fight pathogens), the genes that code for the specific molecules that your cells have on their surface are just not on that list.) In order for a person's immune system to recognize cancerous cells as a pathogen and destroy them, the cancer cell's MHC genes would also need to be mutated drastically.
For instance, breast cancer is usually caused by a mutation in the BRCA1 or BRCA2 genes. These genes assist in DNA repair. Even if this mutation happens, these cells still have the same MHC as the rest of the cells in your body because BRCA1 and BRCA2 don't really have much to do with MHC. Because of this, the immune system does not recognize the cancerous cells as a threat and is unable to destroy or even detect them.
I hope this answers your question.
CDB

This is very wrong. T-cells recognize MHC + peptide combinations. Immunogenic mutations in non-MHC genes can drive an anti-tumor response.

Did I fail to convey this? Perhaps my wording was confusing. I meant that most main CANCER causing genes do not cause a major change in the surface molecules of the cell. However you are correct, some genes that are not considered MHC linked genes can affect this, but most are not cancer causing.

It reads as if you completely misunderstand how the MHC-T-cell interaction works. MHC class I molecules on the cell-surface are loaded with the peptide fragments from intracellular proteins degraded by the proteasome. In infection, this can be proteins from viruses or microbes that are recognized as foreign. In cancer, this can be mutations that generate a peptide with novel structure. Many mutations, especially deletions, but also many oncogenic point mutations do not necessarily generate novel immunogenic peptides.

I apologize for not explaining this concept very well. It would seem, if you were that confused, I have failed completely at explaining it. I have done my best to explain and it is understandable to me, so I do not know how to clarify. Please, if you can explain more efficiently, feel free to edit my answer.

If a cell's apoptosis mechanism is not functioning would this disrupt or cause to malfunction the MHC in the cell?

Yes, quite a bit actually. Since this is a comment and I have limited characters, I would point you to this link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489746/                             From the first paragraph after the abstract; "Moreover, many tumors downregulate the expression of MHC molecules..." read on. I would also suggest the paragraph labeled " Why Does Antitumor T-cell Responses Often Prove Defective?" located further into the article. Basically, it's a more complex version of my answer above.

A 'regular' human cell has a lot of inherent 'strategies' for 'avoiding' immune system 'attacks' unless of course there is an auto-immune disease 'situation' involved.  So if such a 'regular cell' becomes cancerous with a lot of mutations , does it  and it's daughter cells retain all the immune avoidance abilities it had before it became cancerous? Do the 'acquired mutations it has in fact  not interfere with the immune avoidance 'abilities' it has?

Do 'regular' non-cancerous cells have many traits or strategies within their genes or epigenetics or whatever ,that allows them to be unharmed by the immune system? ( assuming no auto-immune problems. )

Since a malignant tumour cell used to be 'normal' or still functioning with its mutations ; as a 'former' normal cell it would have a lot of 'in-built' strategies to avoid attack from the immune system . Then when it changes into malignancy it would still have these immune avoidance strategies to use to be 'hard to detect'. If some of these natural immune avoidance abilities that must be in all normal cells were targeted or 'temporarily shut off' by a designer virus or some special chemicals then the tumour might be made apparent and attacked by the immune system.

Answering your two questions together, all cells enjoy many mechanisms that try to prevent the mutated ones from surviving. During the cell cycle of somatic and germinative cells, for example, there are three moments of verification in which the cell will undergo a kind of internal "check up". During the interphase, this process takes place between phases G1 and S and also at the end of phase G2. In the division, as soon as the interphase ends, there is also one more verification. If during one of these three steps any mutation is recognized, the cell will undergo apoptosis (regardless of whether the identified mutation(s) were in fact to induce a neoplasm in the tissue or not.
Now, if even with these three checks any or some mutations go unnoticed, the cell in question will go through cell division and the mutation(s) will be inherited by the new lineage that will follow; but this does not indicate that the cell will be cancerous, because for a cancer to develop it is necessary for specific mutations to occur in specific genes.
This was just some information I wanted to give you, now answering your question more directly: cancers as a whole enjoy very cunning mechanisms that aim both to make tumor cells indistinguishable from normal cells for the immune system as well as they try to make it very difficult for the many proteins of the Complementary System, which is a vital part of the recognition of abnormalities of the Immune System, to get closer. There are many mechanisms that tumor cells enjoy, but one that stands out is what is called the Malburg Effect. This effect, described by the German physician Otto Walburg, in the 20th century, in a simplified way, consists in the fact that cancer cells consume a much higher amount of glucose than healthy cells and still convert a good portion of this glucose into lactose. This considerable production of lactose makes the environment around the tumor or neoplastic tissue more acidic than usual, acidic enough to compromise the activity of the many proteins that play a role in recognizing abnormalities in the immune system. This is one of the many mechanisms that many cancers use, which, directly or indirectly, makes it difficult for the immune system to recognize it.
The Warburg Effect: How Does it Benefit Cancer Cells?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783224
Another interesting point is that of the five existing therapies to treat cancers currently (chemotherapy, immunotherapy, target therapy, hormone therapy and surgery), immunotherapy consists precisely in "training" the immune system to know how to differentiate a cancer cell from a healthy cell . In a very simplified way, what they do is surgically remove a slide of your tumor or neoplastic tissue, identify the proteins present in the cell membranes of the cells that make up the collected material (among other molecules) and differentiate what is there only in the tumor. From the moment the tumor's own molecules are identified, a kind of vaccine is made, in order to introduce a cocktail with these tumor-specific molecules into the patient's body so that the immune system can then chase the tumor cells, knowing how to differentiate of healthy cells.
Cancer Treatment Vaccines - Immunotherapy - National Cancer Institute
https://www.cancer.gov/about-cancer/treatment/types/immunotherapy/cancer-treatment-vaccines
There is also an explanatory video, if I'm not mistaken from Nature, very good to introduce the idea in a very general way of how immunotherapy and cancer vaccines work: https://youtu.be/jDdL2bMQXfE


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What specific mutations can cause an apoptosis mechanism to malfunction?
What specific mutations can cause the apoptosis mechanisms in a cell to malfunction? Are any such mutations 'reversible' , somehow or are they generally permanent? what kind of mutations can happen without disrupting the apoptosis mechanisms?

About which apoptosis pathway are you thinking, the intrinsic or the extrinsic? There are numerous proteins involved in controlling, promoting and preventing apoptosis, so this question is pretty broad at the moment.

I'm asking about any such pathways. I'm not asking about all the numerous intervening mechanisms which would be too broad. Is there a specific single mutation that can cause the apoptosis mechanisms to malfunction. Forgeting about any of the other contributing factors. What is one such mutation ( if a single mutation can do this)?

Wouldnt the mutations be in whatever genes code for whatever proteins responsible for apoptosis are?

That's interesting where such mutations would be; but I'm asking for the designation of one such mutation.

Read the full text of Hallmarks of Cancer: The Next Generation down in the section titled "Resisting Cell Death." I'd read the full article, however.

@ Kendal ;Looks fascinating..

There are lots and lots of specific single mutations that cause problems with apoptosis.
Some of the most common are in P53, PTEN, MYC, APC, and KRAS. If you want a specific amino acid change, KRAS G12D is particularly potent. It works by disabling a regulatory domain and causing KRAS to be constitutively active.
These aren't "reversible" in a strict sense (except, I guess, for the struck-by-lightning-while-holding-a-winning-lottery-ticket level improbability of a second replication error in the same place back to the original base) but in many cases the cells will upregulate compensatory pathways or activate senescence pathways instead, rather than instantaneously becoming full-blown malignant.
As for mutations that don't cause disruptions to apoptosis,there are almost an infinite number, in that silent mutations or mutations to genes that aren't involved in apoptosis would count.
If you mean what kind of non-silent mutations can happen to genes that are important to apoptosis without causing problems, there are still a lot: swapping similar amino acids in non-active parts of proteins are unlikely to have huge effects.

If a cell develops KRAS G12D , a potent mutation why is this cell itself hard 'to detect' by the immune system? A lot of these mutations that harm or shut-off the apoptosis mechanisms in various cells are not 'seen' by the immune system; are these mutation changes 'masked' by some biological processes?

Tumor immunosurveillance is a whole new topic worth its own question, but there are two basic reasons: (1) Mutated KRAS is not immunologically very different from wild-type KRAS-- it just doesn't change the overall surface shape of the protein that much, and (2) even when the immune system does recognize mutated cell products, the tumor cells react by upregulating anti-inflammatory pathways, such as recruiting regulatory T cells.

So tumor cells can use regulatory Tcells? It sounds like a tumor cell can hijack various parts of the immune system. Maybe since tumor cells are 'non-foreign' 'formerly regular' cells they have access to and can use any part of the immune system.

That's part of it. They also downregulate their MHC complexes and secrete their own inhibitory cytokines. It's a big and complicated problem that's had a lot of research done on it. Here's a review: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857231/

Even though it's a complicated problem is there a way to stop or supress a tumors ability to use parts of the immune system , like T cells.

Yes, it's just not a magic bullet. There's been lots of research on this-- try reading the review I linked above. Also, try looking into the concept of "immune checkpoint inhibitors" that shut down genes like CTLA4 and PD1. Those are showing some promise in certain settings.

Can a virus shutdown genes the tumor might 'use' to 'hide' itself? ( seeing as a non-lethal virus might suppress certain 'abilities of the immune system..)


text:
The properties of benign tumours
Do benign tumours have no functioning apoptosis mechanisms ? If so what stops benign tumours from excessive growth? Also can a benign tumour have a functioning apoptosis mechanism?

To rephrase ; 'Does a benign tumour have no working apoptosis mechanism?' If they have no self-destruct mechanisms what stops them from excessive growth?

If a benign tumours genome is analyzed would this give clues as to how it has no functioning apoptosis mechanisms yet it doesn't grow or metastasize ?

Benign tumors can absolutely have mechanisms available to them to commit to and carry out apoptosis.  An example of this would be benign prostatic hyperplasia, in which the balance of apoptotic and proliferating cells is offset, but apoptosis is still occurring, simply at a lower comparative rate than the proliferation.
Benign tumors can therefore be caused either by excessive proliferation or inadequate cell death; evidently, a complete failure of programmed cell death in many tissues would result in a tumor, benign or no.

Source:

Kyprianou N, Tu H, Jacobs SC. Apoptotic versus proliferative activities in human benign prostatic hyperplasia.  Hum Pathol. 1996 Jul. 27(7): 668-75.


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Can ' functional' stress 'forced upon' a cell actually cause cell mutations when they divide and reproduce?
If a group of cells are forced to go beyond their regular biological parameters that they should be under given ' healthy' functioning and while existing in these stressed states some of the cells divide and multiply would the added stressful states make them mutate?

On a tangent, lots of stressors abrogate division completely in healthy cells. One of the first things cells do in response to heat stress, for example, is stop pushing toward replication and begin transcribing heat shock factors. Compression can lead to cell cycle arrest, and establishment of many cells in a given area leads to contact inhibition of cell division.

Can prolonged exposure to various environmental toxins,even if in low doses, cause 'functional' stress on certain cells subject to the exposure and eventually abrogate cell division or accelerate it or cause it to operate unpredictably?

TL;DR Yes! I would take a look at how normal, healthy cells progress into neoplasia and eventually cancer. Up to a certain point cells will undergo apoptosis, in effect dying before becoming "too abnormal," but one of the hallmarks of cancer is that the cell may somehow evade death (in addition to abnormal proliferation, etc.). Certainly, stressors which cause damage to the DNA (but not so much that the cells dies) are, at least over time, are going to begin to cause abnormalities in the tissues they affect.

Asbestos exposure comes to me as a good example: http://www.atsdr.cdc.gov/csem/csem.asp?csem=29&po=10

If some type of 'functional stress' causes a cell or a group of cells to mutate and gain more and more mutations does this eventually cause the cell's apoptosis mechanisms to 'malfunction? Do some of these mutations 'interfere' with the functioning of the apoptosis 'mechanisms'?

Since it is a 'normal' cell ('before' 'functional stress' and any mutating ) that is gaining mutations does it have 'natural' abilities to avoid immune system attacks?  And if so these abilities that are within it and its 'progeny' when mutated help them to avoid immune system detection ; is this true?


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Why proteins are not visible on my membrane after ponceau staining?
I have a problem in western blot that I can't resolve by myself.
When I am use to add 100 microgram of proteins for each sample but after running and transfer its impossible to me to see bands of protein.
What can be the reason of that?
Thank you for your help

What kind of protein are you using: Whole cell extracts or purified samples? What are your running and transfer conditions? Have you tried to stain the gel with coomassie blue to make sure you have sample on the gel? How do you measure your proteins? What are the buffers in which you measure?

so I need to quantify globin which is protein of 16 kda. I extracted my proteins from MEL cells after treatment by using buffer lysis and protein inhibitors. I do the running at 80volt in running buffer ( tris,glycine) and then I do a wet transfer for an hour with transfer buffer ( tris, glycine, methanol).  I didn't think to stain the gel but it's actually a good idea that will proof if my problem in the running or transfer step... To measure my protein I am doing Bradford method when my Lysats are in 200 micro liter buffer lysis .

Did this blot ever work before? What is in your lysis buffer, by some chance SDS or something like DTT?

I was first using a tris-triton buffer lysis then I use a buffer lysis that contain tris, triton, NaCl,EDTA and . I try to to use in an other blot and same result: I can see proteins band in the upper side only...

What do you mean by seeing proteins only in the upper side?

I see bands after ponceau staining only on the top of the membrane

What percentage has your gel?

It's a 15% gel .

Did you boil or denature your samples before loading them?

Yes i boiled my samples for 5 minutes after adding sample buffer

From what you say, I can only give a few advices:

For the quantification, make sure your sample does not contain any substances which disturb the assay. The Bradford assay is for example sensitive against SDS or DTT. See here for more details. This prevents you from loading a sample without enough protein.
Make sure that you really have protein on your gel. Run a gel as normal and then stain it with Coomassie Blue (it cannot be used for western afterwards).
Don't loose your sample - this happens easier than most people think.
Make sure your transfer works. This can either be done by using pre-stained ladders (which are helpful anyway) or by doing Ponceau Red staining. This can be washed off with water and doesn't disturb downstream applications.
Depending on the type of membrane you are using, they might need pre-treatment. PVDF membranes are extremely hydrophobic and need to be activated in methanol.

Thank you I will check for the buffer lysis . How can I be sure that I will not just loose  the proteins?

Hi Chris, i have joined to the question a picture of my membrane after ponceau if you can take a look.

I will have a closer look later. Can you tell me the size of the marker (bottom 4 or 5 bands are enough).

It's a 10-250kd marker of 10 band

I don't see any bands here, but only a smear. I would first suspect degradation of your sample. It would be really important to simply run a gel and stain it to see how this looks like and to find out the problematic step here. It's probably already the gel...

I also thought that the problem was in the samples but don't know where is my problem... To prepare my sample I first wash my cells with pbs .After removing the superior liquid I am adding buffer lysis and then do a freezing/ de freezing of my samples in liquid nitrogen and then centrifugation at 14,000rpm for 20 mn....

Do you use protease inhibitors in your lysis buffer? If not, this might be the reason the sample is degraded. As I wrote, I would run a gel, stain it, and see how it looks like.

Yes I am adding pmvf and a cocktail of protease inhibitors ...

Thank you very Much Chris I plan to stain the gel with coomasie blue today !

After I had check so many possibilities I finally resolve the problem. It turns out that ph of the tris 1,5M for gel preparation was too many basic...which explain a smear of the proteins into the gel

authors: طالب طيب شيبه


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Are there any disadvantages to HRP conjugated PRIMARY antibodies
I need to detect a FLAG tagged protein on a western blot and have to order an antibody. I'm not expecting to see a massive amount of my protein. To keep analysis time to a minimum  I am considering a HRP-conjugated anti-FLAG. Are there any disadvantages to it (e.g. sensitivity)? First hand experiences/problems?

Welcome to BioSE. It would be better if you make your question more precise? Disadvantage compared to what? Have you tried an experiment yet?

Compared to the classic incubation with primary anti FLAG or HA and subsequent detection with a secondary antibody coupled to HRP (e.g. anti goat/rat/mouse)

The obvious problem is signal amplification as pointed out in the answer. I don't have a first hand experience but I think that chemiluminescence based substrates would be better for a one-step WB.

You can compare directly coupled antibodies to the classical indirect primary-secondary systems:
Directly coupled antibodies
Advantages:

quicker workflow as only one antibody is used
eliminates the chance of a cross-reacting secondary antibody (possibly less background)
possibility to use differently labelled antibodies on the same blot

Disadvantages:

lower sensitivity because the signal is not amplified
only few labels are available
directly labelled primary antibodies tend to be expensive and you need relatively high amounts of them
the labelling can damage or reduce the immunoreactivity of the
antibody

Indirect Primary-Secondary Antibody systems
Advantages:

the secondary antibody amplifies the signal (which is especially
interesting for weakly expressed proteins)
differently labelled secondary antibodies can be used on the same
primary
primary antibodies from different species can be used simultaneously
one secondary antibody can be used with different primary antibodies
(for example for the protein of interest and the loading control)
the labelling reaction does not affect the primary antibody

Disadvantages:

cross-reactivity of the secondary antibody can lead to non-specific
bands
the method takes longer, as more steps in the process are necessary

For me the most important point is the higher sensitivity of the indirect method, for comparision see these images (from Life technologies):

Thank you for confirming my suspicions! Primary-Secondary it will be then.


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Is there a consensus on the CaMV 35S minimal promoter sequence?
We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely low. I heard this could be overcome by fusing it to a minimal 35S promoter fragment but I can't seem to find a clear sequence for this minimal promoter.The best I could find was on the cambia website where they say it is -90 http://www.cambia.org/daisy/promoters/242/g1/250/264.html
1) Does anybody have experience with increasing the expression of enhancer elements like this?
2) And what sequence did you use for this?

Apparently some other plant vectors define it as -46 to +9 relative to the start codon. Even more confused now:
https://books.google.co.uk/books?id=oATyCAAAQBAJ&pg=PA220&lpg=PA220&dq=%22minimal+35s%22&source=bl&ots=WMuuFK7ZSk&sig=exscxB6RpFKTGmSQ3XtR8gNBeP8&hl=nl&sa=X&ei=iXRoVf6mNYiu7gbl0oOABA&ved=0CCAQ6AEwADgK#v=onepage&q=%22minimal%2035s%22&f=false

In case anybody ever has the same question: I found the answer in this paper by Ow et al. 1987 (fig1)
http://www.pnas.org/content/84/14/4870.full.pdf
Just to clarify, I did not want to boost expression of the enhancer element in my algae, it needed boosting in tobacco protoplasts/leaves.


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Stem cells and if they can correct a lack of apoptosis
If a cell ,call it C1 has no functioning apoptosis mechanism could a stem cell somehow be 'induced' to be like C1 , at least have the same genome as C1. Then use this stem cell 'duplicate' to 'restart' the apoptosis mechanisms in C1 or even replace C1? ( forgive any broadness or vagueness, I'm trying to be specific)

If I understand what you're asking (which I'm not sure I do...), no, it's not possible. Cells don't transfer their genomes between each other, so any defects or advantages in one cell won't transfer to a neighboring cell. The only way genes are transferred is down a lineage, with the genome of a parent cell being replicated and passed on to daughter cells.

But can a stem cell be made to 'copy' the genome of a cell with no apoptosis mechanism. Or at least be almost identical to the damaged cell?

Once you copy the genome of a cell into another cell (something that has to happen in the lab, a cell just can't "pick up" a neighboring cell's genes), it becomes a clone of that cell, and loses whatever properties it had before. So, if you have a cancer cell with no functioning apoptosis mechanisms, and copy its genome into a stem cell, the stem cell becomes a cancer cell, and no longer has the properties of "stem-ness".

I think you might have a fundamental misunderstanding of what stem cells are, and what they can do. Given the proper chemical pushes, a stem cell can differentiate into nearly any cell type in the body. However, its DNA remains the same - it's just gene expression that changes. Like I said earlier, genomic changes (mutations) cannot be transfered from one cell to the one next to it.

Can a stem cell's gene expression be made to be like some damaged cell's gene expression that has no apoptosis mechanism.

No, unless you make the exact same genetic changes in the stem cell as occurred in the damaged cell. Once you do that, it's no longer a stem cell. In fact, there's no point in starting with a stem cell, because you're not taking advantage of any of its unique properties.

Maybe you should step back and explain the bigger picture - what exactly are you trying to do? I think you're focusing too narrowly on one particular thing which doesn't do what you think it does.

I'm trying to research or figure out if there are useful ways to reactivate an apoptosis mechanism in a damaged cell. If a cell's gene expression has been damaged or distorted by many aquired mutations and it's apoptosis processes aren't functioning maybe if the cell's gene expression can be somehow 'reset' to when it didn't have mutations it's apoptosis mechanism would 'work' again.

That would be nice, but unfortunately it's impossible, at least with today's knowledge and methods. It takes a lot of mutations to completely knock out all mechanisms of apoptosis, and along with that a ton of other mutations occur, as well. The genome of a cancer cell is pretty screwed up. There's just no way to repair it, you've just got to kill the cell and start over. Incidentally, this is one reason why cells have so many different ways to commit suicide - as they start accumulating all these mutations, if they can detect them, they take themselves out of circulation.

And these aren't just nice little point mutations, either - entire chromosomes get duplicated, chopped up, rearranged, amplified, etc. There's no template present to "start from scratch."

If it takes a lot of mutations to shut down all mechanisms of apoptosis does that mean apoptosis 'shut-down' doesn't occur that much? If a cancerous cell is extremely 'screwed up' why can't the immune system detect it? Do cancer cells emit some chemicals that can mask it?

The answer is no.  There is no method currently known whereby we could get a stem cell to transfer its genome to a cancerous cell and thus get its apoptosis mechanism functioning again.  It's just not that easy to get a genome transfered - destroying the defective copy of the genome which is stored in the nucleus and getting a new copy of the entire genome into the same.
Remember that to transfer almost anything (except small non-polar molecules) in and out of the cell, you need highly specialized transporters (ie., ion channels, Na+/glucose pumps).  This is particularly true of large molecules like glucose and sucrose (plants). But even those molecules are extremely small compared to an entire chromosome, for which there is nothing even close to a transporter.  It would therefore be impossible to get the chromosome into the cell.
But even if you could, you have yet another hurdle: you have to get the new chromosomes into the nucleus... and that only after having destroyed the original genome in Cell 1, without making the environment in the nucleus toxic for the new genome (ie., CAD activity...)  This represents innumerable challenges, including the fact that you're going to need to alter the nuclear membrane to allow the entry of a massive macromolecule, without impeding the function of the cell...  The problems, unfortunately, go on and on.
TL;DR:  Nice idea, and would be really cool if it worked, but it has way, way, way too may complexities and insurmountable hurdles to be even remotely workable.

Sources:

Lemoine R. 2000. Sucrose transporters in plants: update on function and structure. Biomembranes 1465 (1–2): 246-262.


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Regarding benzoic acid and its effects
One of the users on the chemistry s.e. mentioned that when benzoic acid forms in the body in response to other chemicals it might have a mutating effect on one's DNA. Is this true?

Can you please provide a link to that statement? Just so I can see it in a broader meaning and not just what another user mentioned. Thanks!

I  wrote in the question 'Regarding common preservatives and their effects' as user 128932 ; I commented after the question about benzoic acid..

Is that a link?

Can benzoic acid form in the body?

Is this a health risk?


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What is the effect of persistent hypothermia on cardiac performance?
I define persistent hypothermia in this thread about the mechanisms of persistent hypothermia.
The Graph of Katzung et al. in Pharmacology about Heart Failure:

I am thinking which parts here are critical on temperature.
Temperature has a direct effect of reaction rates of chemical reactions here, for instance NE, AII and probably chemical reactions in endothelin such as ET.
Therefore, I am thinking that the relationship between temperature and cardiac performance cannot be linear at all.
Some have said me that low temperature can decrease metabolism and oxygen consumption.
However, I started to think differently when time goes enough far that is when heart cannot anymore supply enough blood with oxygen. Thus, hypoxia can occur and asymptomatic exodus may occur.
Physiological case
Based on physiology, I can propose that the cardiac output curve shifts to the left (CO1 $\to$ CO2), due to less oxygen being supplied to the heart, similarly EDV1 (end-diastolic volume) shifts $\to$ EDV2 and SV1 (stroke volume) $\to$ SV2.
However, the venous return (VR) curve can shift much more, since I propose that the effect of temperature on smooth musculature is relatively bigger than on heart because of proportional size of tissue.
So the VR1 shifts to VR2, so EDV2 $\to$ EDV3 and SV2 $\to$ SV3.
Consequently, SV3 > SV1, while EDV3 < EDV1.
See my draft figure about this:

where EDV (End Diastolic Volume) in the x-axis and SV (Stroke Volume) in the y-axis.
In a healthy person, who have no hypertrophy of ventricles and elastic myocardium, the heart can tolerate this. So such a condition of cardiac failure as in the figure 13-3 is possible.
However, if flexibility of the myocardium, for instance, is not possible, such a pathway may not be possible.
The autonomic nervous system may enter the picture and increase vagus nerve stimulation (PS more).
However, not sure about the exact pathway.
What is the effect of temperature on cardiac performance?
How can temperature decrease cardiac performance?

Many processes are affected by temperature including metabolism and growth rates. Reaction rates increase with temperature but not in case of catalysed reactions where the catalyst can operate at only an optimum temperature. See this related post.

Why is the venous return increasing as temperature decreases? Please label the X and Y axis more clearly

Winter swimming and infarcts
The publication Long-term risks of cardiac and cerebral vascular diseases increased following winter swimming in the cold seawater which came out just some weeks ago shows a link between long-term winter swimming and CVD.
I think this is the best evidence so far about the possible link.
WYSIWYG's comment has some good general idea:

Many processes are affected by temperature including metabolism and
  growth rates. Reaction rates increase with temperature but not in case
  of catalysed reactions where the catalyst can operate at only an
  optimum temperature.

Some related topics

temperature effect on the rate of protein degradation

So further studies

protein degradation in the heart in persistent hypothermia
...

Effect of persistent hypothermia on processes of cAF
[1]
Let's have cAF (chronic atrial fibrillation) here as an target.
Electrophysiological study shows that cAF-related remodeling is typically divided into three categories: 1) electrical, 2) contractile and 3) structural.
They cause respectively

1) shortening of both the action potential (AP) duration and effective refractory period (ERP)
2) possibly a result of impaired Ca2+ intracellular handling
3) changes of cellular level (hypertrophy, glycogen accumulation and modified mitochondrial morphology) and tissue fibrosis

cAF's processes in persistent hypothermia
I cannot say now more anything about persistent hypothermia and cAF by confidence.
Those mechanisms of Koivumäki et al are cellular processes, while the representation of the heart requires integrative analysis in the cellular, tissue and organ levels.
In cellular level

Only some catalyzed reactions can work in persistent hypothermia. TODO consider which enzymes of the heart and body work in low temperature in short-term and long-term cases. Depletion cases too.
Effect of persistent hypothermia on the outflux of Calcium (probably, slows down).

In tissue level

I can say without rigor that electrical coordination is uncoordinated in tissue fibrosis.

In organ level

I say say without rigor that the mean electrical axis should be determined and fixed in the study.
Effect of Arterial hypertension must be fixed. Sokolew-Lyon index can a starting point for the indicator but better indicator is required with higher specificity.

Persistent hypothermia from the extreme side (Sauna)

[2] Regular Sauna is with better hemodynamic function; however, the association of sauna bathing with cardiovascular and all-cause mortality is not known.

so possible effect of persistent hypothermia can be

lower hemodynamic function if no compensation mechanism
better hemodynamic function if some compensation mechanism (genetics; unknown)

Some research topics

Effect of Persistent Hypothermia on the Arterial Hypertension. This may be associated with coagulopathy, especially in the lower limb.
Effect of Persistent Hypothermia on Atherosclerosis. It would be very nice to see long-term study about the effect of regular 4-7 winter swimming on the cardiovascular risk score, SCORE and others.

Sources

In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation. Koivumäki et al. Computational Biology.
Association Between Sauna Bathing and Fatal Cardiovascular and All-Cause Mortality Events, here

Please, see the reference of the publication for more better view.

Both pictures you posted show that increased peripheral vascular resistance decrease cardiac output. If you are talking about someone outdoors not properly dressed in a Scandinavian winter, then their cutaneous vasculature would constrict and Also their extremities would get less blood flow. That would increase peripheral vascular resistance and thus decrease cardiac output. These articles were the first to pop up for me (http://circres.ahajournals.org/content/7/3/366 & http://www.ncbi.nlm.nih.gov/pubmed/10215232) and it seems to say that the primary cause of increased vascular resistance is actually caused by decreased cardiac output as well as local control.
This may seem contradictory to therapeutic use of hypothermia, where it is used to decrease metabolic needs (I don't know what is the mechanism for this) to help compensate for hypoxia (in cardiac tissue and the brain?). Cooling the heart would decrease it's metabolic needs (less perfusion, increased metabolic demands resulting from sympathetic input to heart. I guess the same thing probably happens when doctors prescribe a beta-blocker or non-dihydropyridine calcium channel blocker (CCB), the vascular resistance probably increases (except for the CCB diltiazem which dilates blood vessels in addition to it's effects on the heart). But the main thing is the sympathetic output to the heart, which is blocked by these drugs, and cold; this is more important than the increased peripheral vascular resistance. But remember that afterload is not identical to peripheral vascular resistance!!! The decreased cardiac output would probably decrease blood pressure and afterload, I'm guessing.
As for the slowing of reactions related to vasoconstriction (transmission of nervous signal from hypothalamus via pre ganglionic sympathetic fiber, then synapse in sympathetic chain, then transmission via post ganglionic nerve; release of NE, Epi, AT-II; rate of diffusion to receptor; effect of cold on membrane fluidity; effect on the alpha adrenergic receptor; rate of second messenger signalling cascade; effect of cAMP formation by G stimulator protein or breakdown by phosphodiesterase; effect of Ca++ release; effect on PLC mediated IP3/DAG release; effect on NO release and receptor stimulation of guanylate cyclase;  and the various other factors regulating endothelial function and smooth muscle contraction), I don't know. I also assume that an increase in viscosity (a factor included in the calculation of vascular resistance) could be another factor leading to increased vascular resistance, but even if this happens, this is less important than the decrease of the hearts metabolic rate.
Personally I'm not acquainted with the literature on therapeutic use of hypothermia, aside from the ethical debates about using Nazi hypothermia research. I'm just going at it with the same physiology knowledge you have, and relaying your confusion back at you. I'm just as lazy as you and I don't feel like spending hours delving into review articles on hypothermia research, but I agree that it is an interesting question, and it is also relevant to other very important topics in medicine (ie. use of beta blockers, non-dihydropyridine CCBs other than diltiazem).

I am not speaking about someone not dressing adequately for the winter. Persistent. The temperature remains anytime at 36 C.

Okay, then ignore the stuff on viscosity of blood affecting vascular resistance. And ignore, as you already should have, all my info don't knows on factors affecting endothelial function and smooth muscle contraction. Also a shivering reaction would increase the bodies overall metabolic rate, which would likely increase demand for oxygen, but  who cares, probably none of this matters, since we are only focused on the heart. If the heart is cooled, as in cardiothoracic surgery, it's metabolic rate decreases. There are alternative uses for decreasing cerebral metabolic rate.

Btw I suck at the metric system, is 36 degrees normal or low? Really I don't know the definition of "persistent hypothermia".

36.0 C is very slow. Normal is 36.5–37.5 C.

Okay, so my main point is that most of the damage doesn't come from the dilation of the heart and it's reduced contractility (as far as I know), but the increased metabolic demand placed on the heart: the after load and the increased sympathetic output affecting the heart. I think a heart affected by a negative isotope/chronotrope (drugs previously mentioned) or hypothermia is not pumping enough so I think afterload would fall despite increased vascular resistance. Plus it's insensitive to NE/epi. Problem solved. I am not a cardiologist, so I could be wrong.

Okay, now that I read your other question on this forum, I get that I'm not answering your question. Persistent hypothermia is some odd condition that affects "normal" people, not iatrogenic or a polar bear swim. I've never heard of it, so i can't answer.

Please, search for it as described by the condition. It is covered in some places but with emphasis that we do not understand the mechanisms. This thread is the first place in any literature which tries to understand its mechanisms and try to explain it. Some interesting cases, I have found, where asymptomatic exodus, and where even supporting the temperature by external devices cannot keep the temperature in the normal range. There is very likely change in the set point of body temperature, probably pathology related to hypothalamus.

@Masi What is asymptomatic exodus?


text:
Parallel Autonomic regulation of Cough and Runny Nose
I describe here the serous inflammation of runny nose.
Cough is mediated by Cough center.
I think Runny nose is also controlled by the autonomic nervous system and probably by some reflex.
Assume you have mild runny nose under Montelukast medication.
You have irritated cough (coughing so much you cannot sleep).
You stop the cough by codeine before sleeping.
You sleep at 30 degree angle.
Sometimes, you also feel that the runny nose stops i.e. complete relieve of runny nose in both nostrils and whole nose for about 30 seconds to a minute - perfectly clear nose and no serous inflammation - no symptoms of imflammation in the nose.
Then, it (serous inflammation) starts again - not like mucose running back - but the feeling of uneasiness in the whole nose starts again - then mucose can also continue to migrate from one nostril to another.
What is causing this kind of behaviour i.e complete relieve of of runny nose for about 30 seconds?
What is causing the stopping of serous inflammation in the nose?
I think the Runny nose can also be controlled by medulla oblongata because Codeine is blocking the cough center there.
I tried to achieve this behaviour by stimulating by lymphatic system in regulating breathing by abdominal muscles - lymphatic drainage massage - breathing inside with abdomen (not with thorax) and deeply exhale with abdomen).
At that time, I did not hear any creaky sounds in my throat.
After trying to stop the serous inflammation again, I heard them without managing to stop serous inflammation in both nostrils at the same time.
How is the control of Cough and Runny nose regulated by the autonomic nervous system?
Probably, some parallelism there.
Processes going on regulating Cough and Runny nose

reflex from medulla oblongata
sympaticus and parasympaticus (not sure about these)
possible parallelism of irritated cough and runny nose control

From my experience (and what my kids doctors told me) most of the coughing connected with a cold (especially the sort which occurs at night when you lay down) comes from the mucus which is coming from the sinuses and is moving around due to the changed body position and thus causing problems.

@Chris That is different story. Moving mucose in the nose between nostrils and completely relieve of runny nose (you do not feel anymore the serous inflammation process at all).

To add to your idea of a link between cough and runny nose: Codein binds to opioidreceptors. A runny nose is known to be one of the early symptoms of opioid withdrawal.

Skymninge mentioned opioidreceptors and the withdrawal symptom of opiods as a runny nose: codein binds to opioidreceptors.
I think now that the cough can trigger runny nose.
I breathed with empty nose some 15 minutes.
Then, I had a deep dry cough and right after it a stuffy nose.
I really felt this time the negative gradient at the level of kidneys and also posteriorly.
I do not know how this kind of pain was felt, I think, near or on the kidneys.
I do not understand the effects of deep dry coughs.
They seem to be linked to several processes and locations in the body.
After this deep dry cough, I did some abdominal breathes and this way massaging the lymphatic circulation systemically, the stuffy nose disappeared.
My thorax is opposite of astonic person (say if you remember the name in Propedeutics).
This can be a restricting factor in the circulation of the lymph.
My conjecture is that the people with big chests (opposite of astonic) need to concentrate more on abdominal breathing such that to keep out of stuffy noses.
Restricted lymphatic circulation causes less wastes returned to the blood circulation.
Thus, accumulation of bacteria in the larynges which increases the risk of a dry cough.
Good lymphatic circulation ensures that bacteria is not congested in the larynx.
So cough seems to be a mechanism to start a runny nose.
This all is finely regulated.
There are several receptors in the body.
The deep cough however seems to be linked to a reflex which causes a runny nose.
Some studies about opiates and respiratory activity

The effects of opiates on the respiratory activity of thoracic motoneurones in the anaesthetized and decerebrate rabbit.


text:
The evolution equations under different year classes of a age-structured model?
This sounds a bit complicated but I want to grab more feelings on age-structured problems. Less than 2 days to the exam so I appreciate any help.
So suppose we only get 3 year classes in a school at first. No one can repeat. If you are kicked out of school you must restart from year class $1$. No transfer-in students. Exactly $N$ freshman each year. The portion of being promoted from year class $i − 1$ to year class $i$ is given by $s_i$ (which we can again assume it's constant). Then suddenly at one year $Y$, the school changes its scheme. Only at that year the school take in $N$ year $0$ and year $1$ students respectively. Since year $Y + 1$, the school only take in $N$ year $0$ students each year.
What I want to know the most is how we should decide (1) the steady state no. of the students in year classes $1$ to $3$ before year $Y$, (2) the steady state no. of the students in year classes $0$ to $3$ since year $Y$, and (3) the school years needed to achieve the steady state since year $Y$.

I tried putting forward the Leslie matrix of the old scheme: $$\begin{bmatrix} 1 & 0 & 0 \\ s_1 & 0 & 0 \\ 0 & s_2 & 0 \end{bmatrix}$$ and found the eigenvalues would be $1$ and $0$ (with multiplicity of $2$). $\lambda = 1$ gives $$u_{1, n} + u_{2, n} + u_{3, n} = u_{1, n}(1 + s_1 + s_1 s_2).$$ Am I on the right track? Should I just plug in $u_{1, n} = N$ and then claim the steady state no. to be $N(1 + s_1 + s_1 s_2)$? Or do I need to sort of prove that?

If my thought process is correct, the Leslie matrix of the new scheme becomes $$\begin{bmatrix} 1 & 0 & 0 & 0 \\ s_0 & 0 & 0 & 0 \\ 0 & s_1 & 0 & 0 \\ 0 & 0 & s_2 & 0 \end{bmatrix}$$ Right? Then its eigenvalues are again $1$ and $0$ (multiplicity $3$), and then $\lambda = 1$ gives (let me denote the intake proportion $s_{-1} = 1$) $$u_{0, n} + u_{1, n} + u_{2, n} + u_{3, n} = u_{1, n}(1 + s_0 + s_0 s_1 + s_0 s_1 s_2) = u_{1, n}\left(\sum_{i=-1}^{2} \prod_{j = -1}^i s_j\right).$$ Did I make any mistakes so far?

I can sort of write out the year class size since year $Y$ explicitly. It should take 3 school years to achieve the steady state again right? Any less tedious and/or more persuasive ways to show the same result?

Thanks in advance.

Welcome. I have the feeling you might get a better response on crohttps://stats.stackexchange.com - we don't usually have many people answering technical stats questions like this (same goes for your other question as well).

I see. I'm actually asking if anyone can verify the general procedure I put forward instead of needing to evaluate the population with specific values.

Your results are correct if $s_i$ is the actual proportion of students which are actually promoted (and if recruitment is actually of $N(1-s_})$ so that year 1 has $N$ students including $Ns_1$ who weren't promoted). Else, if $s_i$ is a probability that applies individually, the results are different.

How is this? I added that those who are not promoted are kicked out of school. So every student is not (directly) repeated. They can of course be kicked out and come back again from year 1.

OK, hadn't seen this kicked out bit, so ignore brackets.

Still, it remains that if it is an individual probability, say rolling a dice for each of the $N$ students, you have a nonzero probability to end up e.g. with 0 students promoted (probability $(1-s_i)^N$ or all of them promoted (probability $s_i^N$).

How about if I modify $s_i$ to be the overall portion promoted from year $i-1$ to year $i$?

Yes, then your reasoning sounds fine.

Good luck with your exam!


text:
Spectroscopic methods for quantifying peptides/proteins with or without Tryptophan or Tyrosine content
I have several peptides (20-50 amino acids long)  which I want to quantify the solubility/concentration in a solvent at certain temperature and pH.
These peptides may or may not contain Tryptophan or Tyrosine (aromatic residues) in them.
What's the preferred quantification method for it?
I came to UV-Vis method (e.g. NanoDrop) and Fluorescence method (e.g. Qubit).
Do those methods strictly require the presence of Tryptophan or Tyrosine?

I can’t write a full answer right now, but absorbance at 280 nm requires aromatic amino acids (tryptophan, tyrosine, phenylalanine) and/or cystine. If these residues are not present, you could potentially label your peptides with some fluorophore. Alternatively, the peptide bond itself absorbs at 214 nm. You can also look into assays like BCA.

@canadianer does fluoresence method also require aromatic residues?

If you’re just looking at intrinsic fluorescence of the peptide, then yes. If you are able to specifically label the peptide with some fluorophore, then no.

I suspect, but don’t know for sure, that the Qubit assay you linked to won’t work well for unstructured peptides. Thermo also sells a Qubit BR assay that apparently reacts with amino groups and therefore should work with peptides. You should ask them directly to be sure.

The A280 value is mainly due to Trp content but if the sequence is known, you can calculate the extinction coefficient very accurately. In addition, you can fully recover the sample after an A280 measurement, whereas fluorescent/colorimeteric methods require some sample loss. I give the key refs below, but this old answer (mine) may be of interest?

Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences

Calculation of protein extinction coefficients from amino acid sequence data

I think it would not be a problem if you use NanoDrop for your measurements. But there are better options if using UV-Vis is not a strict rule. Alternatively, Qubit itself doesn't have any issues since their reagents do not get interfered by aromatics.
As I understood from your description, you preferred using UV-Vis method, which uses wavelengths around 100-400 nm (UV-A 315-400 nm, UV-B 280-315 nm, UVC 100-280 nm). ThermoFischer provides two options for UV-band measurement using NanoDrop (Table 1 of NanoDrop Protein Quantification page), A280 and A205.
The usual A280 method is what you are concerned about, since its absorbance behaviour is strictly linked to tryptophan, tyrosine, and some disulfide bonds. This limits A280 only to protein samples with those residues. To avoid this issue, Anthis and Clore has developed a method of using 205 nm UV-band instead of 280 nm with promising results. You can choose the 205 nm-band method in the NanoDrop settings.
However, if I am not limited to measuring in UV-band, I would personally use Pierce 660 nm colorimetry method to measure my samples. This paper by Antharavally et. al. describes its flexibility on several substances (detergents, buffers, etc.) and its concentration which might suit your treatments. It is also available in NanoDrop settings, even with much greater sensitivity than both UV-Vis methods.
Speaking of Qubit, their BR (Broad-Range) Protein Assays are based on reagents reacting to N-terminals of proteins, not aromatic residues. There should not be a problem for any protein strands.

thanks so much. How reliable is Anthis and Clore method? Also for peptide that contain aromatic can be used?
With their tool https://spin.niddk.nih.gov/clore/ does that mean we can just skip performing measurement with Nandrop/Qubit?

Also, I only have Qubit 3.0 and Flex,  AFAIK I can't use BR. But can I use standard Protein Assays? Does it have any aromatic residue restriction?s

I need to clarify that Anthis and Clore's method of using 205 nm band is also available in the NanoDrop options.
ThermoFischer Protein Assays are quite robust on general protein strands. I don't remember their fluorophores are inhibited by aromatic residues....


text:
The location of pulmonary valve in comparison with the aortic valve

According to most transverse diagrams of heart, the pulmonary valve, in comparison to the aortic valve, angles  towards the left side a little bit. Take, for instance, the pulmonary valve is more close to the left coronary artery than the right one. But the frontal sections, on the contrary, show that the pulmonary valve, in comparison to the aortic valve, angles toward right.
What's wrong?

They both look angled to the left to me. On the left image, left is to the left (you're looking from the top down, as if you came up behind someone and looked through their skull into the torso). On the right image, left is to the right; you're looking straight ahead at someone's chest from the front.

@BryanKrause Forget the angles, for the moment, let's talk about their location. I've edited the image.

I think you're reading too much into the picture. They're basically right on top of each other, and they are crossing along the length. In one you're emphasizing the bottom leaflets of the valves, in the other the top. I don't think there's a meaningful anatomical distinction between the two. That said, I'm a bit more familiar with porcine cardiac anatomy which is more different than these pictures. Maybe someone will have an answer I just don't see why this is important to you.

@BryanKrause One of those vague 'why' questions! I just wonder whether it is actually possible to see the aortic valve in a longitudinal section of the heart or the frontal diagrams are just trying to emphasis on showing that, on its presence.

Well it's certainly visible in some longitudinal section. The help suggests "You should only ask practical, answerable questions based on actual problems that you face." - it's hard to get good answers if you can't explain the purpose of a question.

@BryanKrause Quite agree. Though it is rather personal, let me ask, if you were to choose a frontal diagram for an atricle, what diagram would you choose, the right image, or a version in which the aortic valve is completely hidden?

The image to choose would entirely depend on the goals I had in displaying the image. I'd never put a figure in an article/paper without a purpose.

@BryanKrause It is going to be a typical illustration of the heart chambers with 15-18 year old audience


text:
Is it possible to see some renal pyramids in a transverse section those which cannot possibly be viewed in one longitudinal section at the same time?
This is just a random image I found on Google.

It is showing that, in cross-section, several renal pyramids can be viewed. Is it so?
According to the following longitudinal section of the kidney, I think it is not possible to see more than two or three pyramids in a cross-section. Can anyone throw some light on this?

EDIT:
Apparently there are more pyramids in a kidney than what we see in a longitudinal section of this organ (?). Is it possible to see some pyramids in a transverse section those which cannot possibly be viewed in one longitudinal section at the same time?

Why don't you think it would be possible? Can you cite a source or show another figure?

Consider that both of these are two-dimensional images. Not sure how you think the bottom two-dimensional image rules out structure in the other dimension.

The figure seems about right
In these conference notes the figure posted from Diagnostic Ultrasound (CM Rumack), labelled as a cross section, seems to match your illustration fairly well; I think I count six pyramids.
It makes sense because pyramids are, well, pyramids, so if they are round and evenly spaced, a kidney should have room for about that many when imaged at the level of the ureter.  Unfortunately, I didn't find a good 3D model searching, and while I feel like it should be possible to infer the 3D locations of the pyramids from an image of the vasculature, I am not sure how to do so.
(I should note that the Visible Human Project data can now be downloaded without a license.  The files are large and they now require a helper application for FTP such as Cyberduck.  I should return to this if I can pull something useful out of them)

You see, I am not sure whether the pyramids that are visible in a longitudinal section, are the only pyramids of the kidney or there are more.

This paper about goat kidneys mentions that humans have seven to eighteen pyramids per kidney.  Given the variation of kidneys and figures I'm not sure if you want to chase that figure to its origin.  Logically though, pyramids are all over the kidney, including on the sides, so a longitudinal section can miss them.  Textbook figures like yours, with every renal papilla in the plane of section, are improbable - sometimes you would see just a piece of a pyramid.  The image I want ... is in "SGI RAW format".

That's just it. You've answered my question. So both longitudinal and transverse sections can miss some pyramids.

What if there are just these seven pyramids (textbook figure) that are present in the kidney in all sides of the kidney, but continuous?

They're pyramids.  They come to a point called the renal papilla because it looks like a papilla, though the milk it yields wouldn't go well with morning coffee.  They are approximately round.  This image of unknown provenance illustrates it.  But on any kidney image/model, note that the calyx is shallow - not a groove going all the way around the kidney.