text:
How large might a paper wasp nest become?
About two weeks ago I noticed a new wasp nest in my back yard. I generally leave them as long as they aren't interfering with anything, but this nest has suddenly grown quite large and they are swarming when I mow the lawn. From the nest appearance, I was afraid these were bald-faced hornets, but up close they look more like yellowjackets, I'm uncertain of the species. This is as close as I dared to get with the camera.

I am willing to live and let live until October (when the nest is vacated), but I have two concerns that may change my mind:

How large might this nest become?
If I leave them this summer, are they likely to return to the same place next year?

About double to triple that size if there is plenty of food in the area.

I used a magnifying glass and it does look like yellow jackets.  I don't think they are the more laid back species (European) but the OTHER species that is much more aggressive.

For a closer look, try taking a picture at night with the flash. Wasps usually don't fly a lot at night.

Wasp nest growth rate is inversely proportional to the frequency at which you hit it with a rake.

According to multiple reports (here, here and here), a 7m (22ft) paper wasp nest was found in an abandoned home in San Sebastian de La Gomera on the island of Tenerife (~100km off the shore from Morocco)!! The nest was estimated to be home to over 22,000 wasps! The picture is included below:
This nest broke the previous world record, a nest discovered in Waimaukau in New Zealand in April 1963 that was an impressive 3.7metres, or 12ft 2ins long, more than 5ft in diameter and 18ft in circumference!

Other big nests? ...

According to this site a 10 ft x 7ft x 2ft nest buzzing with about 400,000 yellow jackets was found in a camper in SC, U.S.
Here is a video of an apparent giant (6.5ft x 8ft) yellow jacket nest found in Florida, U.S. in 2013. A Picture of the nest is below:

As to your second question: wasps do not return to a nest, they build a new one every year
However, if you leave the nest it will produce new queens, perhaps enlarging the change they will build a new nest in the area.


text:
How long does it take unused antibodies to clear the system?
Say you have the flu and a normal immune system. Now you're all better but your antibody level is still elevated. How long does it take for those antibody levels to go back to a base value?

This is quite broad since there are many different classes and subclasses and each has a different half life which ranges from hours to weeks.

Wouldn't nearly all major classes of antibodies have about the same life expectancy? @canadianer

No. Very generally, you can find numbers like 3 weeks for IgG, 1 week for IgM and IgA, 3 days for IgD and 2 days for IgE. Also, these isotypes differ vastly in serum concentration and are expressed at different times.

@canadianer - your comment basically answers the question. So perhaps it is not so broad? Further, to discard issues with initial Ab concentrations the Q may be focused on half-life and perhaps the Q could go for IgG alone, or another Ab type typical of the Flu to narrow it down further?

@AliceD The question really is about more than antibody half lives and there are many factors that could contribute. Actually, I can imagine some study would have answered it by measuring antibody titre over time, so I have retracted my close vote.

I agree that this question may be broader than a simple half-life question in theory, however, I think that it is still basically a half-life question. For instance, does the presence of the virus (using the flu example) contribute to opsionization and clearance? Possibly, but this would be variable and difficult to generalize about.
The question has been asked in a number of ways (for endogenous / exogenous antibody). For simplicity, Mankarious et al examined transferred antibody in IVIG therapy and found, "For total IgG, the half-life found was 25.8 days; for IgG1 it was 29.7 days; for IgG2 it was 26.9 days; and for IgG3 it was 15.7 days." - an answer in line with that proposed by canadianer, above.

source: Stack Exchange

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

sort: votes


text:
How does botulinum toxin enter the blood stream from the digestive tract?
To my understanding, large polypeptides such as botulinum toxin cannot pass the intestinal lining intact. How, then, can it enter the bloodstream and cause botulism poisoning?

Transcytosis is a process by which large macromolecules are transported across a cell, such as those in the intestinal epithelium. It is used by many toxins and even whole organisms to enter the body. Botulinum toxin also apparently uses this mechanism. I'm not sure how detailed of an answer you want, but the linked to-review is pretty in-depth.

That's interesting +1.

@AliceD "Isn't nature wonderful."

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


text:
Why does mouldy food make you sick?
Bread gets mouldy pretty quickly. My parents (both of whom are nurses) throw out a loaf of bread after a spot of mould is seen (because "if you can see one spot, it means the whole thing is covered in mould spores") because they say you'll get sick if you eat it. The USDA also has a handy chart on it's mould page telling you when you should discard food with mould on it.
Is it the mould itself that makes us sick or is it something that the mould is releasing?
What are the mechanisms that cause us to feel sick after eating mouldy food?
The USDA says that there can also be bacteria along with the mould on the the food - is this what is really making us feel ill?

Depends on the kind of mould. There is a story that an entire French village died because of ergot infested bread. They died of exhaustion.

One of the most common toxins in mouldy food/bread is aflatoxin.
The exposure to high amount of aflatoxin can lead to acute aflatoxicosis with fulminant hepatic failure and even death.
While mild exposure to aflatoxin could be asymptomatic, it is better not to take a chance considering possible complications (citation from the link above):

Aflatoxins produce acute necrosis, cirrhosis, and carcinoma of the
  liver in a number of animal species; no animal species is resistant to
  the acute toxic effects of aflatoxins; hence it is logical to assume
  that humans may be similarly affected. A wide variation in LD50 values
  has been obtained in animal species tested with single doses of
  aflatoxins. For most species, the LD50 value ranges from 0.5 to 10
  mg/kg body weight. Animal species respond differently in their
  susceptibility to the chronic and acute toxicity of aflatoxins. The
  toxicity can be influenced by environmental factors, exposure level,
  and duration of exposure, age, health, and nutritional status of diet.
  Aflatoxin B1 is a very potent carcinogen in many species, including
  nonhuman primates, birds, fish, and rodents. In each species, the
  liver is the primary target organ of acute injury. Metabolism plays a
  major role in determining the toxicity of aflatoxin B1; studies show
  that this aflatoxion requires metabolic activation to exert its
  carcinogenic effect, and these effects can be modified by induction or
  inhibition of the mixed function oxidase system.

Here's a bit of additional information (Although there's an answer from Ilan that satisfied you.)

Is it the mould itself that makes us sick or is it something that the
mould is releasing?
What are the mechanisms that cause us to feel sick after eating mouldy
food?
The USDA says that there can also be bacteria along with the mould on
the the food - is this what is really making us feel ill?

There are two things to consider.

Food infection : bacteria or other microbes that infect the body after consumption
Food intoxication : ingestion of toxins contained within the food (includes modls), including bacterial produced exotoxins

Majority of food poisoning is caused by bacteria, viruses, and parasites rather than toxic substances in the food. e.g. Staphylococcus aureas, salmonella, Bacillus cereus, three common types of bacteria that can lead to food poisoning.
Molds are neither plant or an animal. They are microscopic fungi. Some food molds produce toxins that cause allergic reactions and respiratory problems. And a few molds in the right conditions, around the Mycelleum,  Mycotoxins are produced; poisonous substances that can make you ill. Mycotoxins also tend to affect more biological systems in our body than do pesticides or heavy metals, partly because fungi have the ability to dodge our immune system by rapidly mutating, while at the same time producing chemicals that suppress our immune system. (You will find more information Mycotoxins here.)
Mycotoxins as a group cannot be classified according to their mode of action, toxicology or metabolism. These vary according to the different chemical structures, sensitivity of the species to the toxin and also factors such as sex, age, health and diet. There are a large number of mycotoxins with a great diversity in their mode of action. Additionally, additive and synergistic effects can occur in the presence of two or more mycotoxins. Following there are the most important mycotoxins and their mode of actions, toxicology and metabolism as well as main symptoms and target organs. (This link explains in great detail.)

» Aflatoxins (discussed above by Ilan)
» Trichothecenes
» Ochratoxins
» Fumonisins
» Zearalenone

Ochratoxin A (OTA) is a carcinogenic compound produced by several species of molds, such as Aspergillus and Penicillium, found in a wide range of foods, including cereals, dried fruits, coffee, cocoa products, wine, grape juice, beer, liquorice, blood products, baby foods and spices.

New studies confirm Ochratoxin A inhibits Neurogenesis(the formation of new neurons in the brain). Other than that, its toxicological effects include nephro-
toxicity, nephrocarcinogenicity and immunotoxicity as well.
Aspergillus on Bread - Mold.

The molds that we see on the surface of the food is just a tip of the ice berg. It is an invader, whose roots like threads may have gone deep down entire food (although some says bleu cheese with mold is edible). Growing right along with mold are what are called "gram negative" (e.g. Escherichia coli) and "gram positive" bacteria. Just like mold, they require moisture and organic material to thrive and are often found growing in the same places as mold, and the synergistic action between mold and bacteria further worsen inflammatory health conditions. Oftentimes, those bacterial infections occuring alongside fungal infections make treatment more complicated.

"New studies confirm Ochratoxin A leads to Neurogenesis (inhibits the formation of new neurons in the brain). " - this sentence should be revised as Ochratoxin does not lead to -, but inhibits neurogenesis (the clause and the clarification do not match).

@Ilan, ouch :) thank you I seemed to have made a mistake here. Let me correct it.


text:
Osmotic Pressure and Enzyme Activity
Is it true that in an enzyme-catalyzed reaction, the rate of reaction does not vary with varying osmotic pressure?
Instead of just a true or false answer, why does it, or why does it not vary with osmotic pressure?

This paper is a compelling example of an effect of osmotic pressure on enzyme function. Restriction enzymes are normally very selective in the base sequences of sites at which they cut DNA, but in some conditions they show cutting at off-target sites, called "star activity." "Star activity" increased for some restriction enzymes almost linearly with osmotic pressure generated by a range of non-ionic solutes. Supporting the idea that the higher osmotic pressure was directly responsible, increased hydrostatic pressure reversed the effect of increased osmotic pressure.
Increasing the osmotic pressure is essentially decreasing the chemical activity of the water in the system. So it's not surprising that any enzyme reaction might be affected, particularly if the structures of active sites of enzymes are altered as suggested by the authors of the paper cited above.

In order to achieve initiation of DNA replication in vitro at the E. coli chromosomal origin of replication, Arthur Kornberg's lab had to include polyethylene glycol (PEG) in their reactions.
The proposed mechanism for this enhancement was termed "molecular crowding" which was thought to increase the local concentration of the substrates.
A similar effect has been seen in reactions with T4 DNA ligase. Blunt-ended ligations are more efficient in buffers containing PEG.


text:
How does the MET gene work and what happens when the promoter region gets mutated?
I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET gene. (http://www.snpedia.com/index.php/Rs1858830)
After digging a bit deeper I found that hepatocyte growth factor is a pretty ubiquitous compound in the body and it's necessary for growth/repair of many tissues, namely the liver and digestive tract. I am trying to separate the direct causal effect of the mutation itself from the effects it has on other tissue which may themselves have an effect on ASD risk.
My question comes from a study which measured reduced serum HGF levels in autistic children with this mutation. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694825/)
I am confused about the implied causal effect of the 'CC' variant on HGF levels even though it is merely the ligand for the MET gene? Please help me understand where in the gene signalling process does HGF come in, what does it do, what proteins are transcribed by the MET gene, and how this mutation effects the transcription of these proteins.

HGF is the ligand for Met, which is a membrane receptor involved in multiple transduction pathways. Gene ID 4233 we're looking at a single gene product for MET.
If we're just reading through the wikipedia page for c-Met, when HGF binds to Met, it activates the tyrosine kinase activity of Met. Met recruits Gab1, and this complex mediates interactions with Ras, P13K, ß-catenin.. not just pathways associated w/ Autism, but also associated with invasive growth cancers. An interesting note about the C allele, it's associated with decreased Met transcription. Quoting a recent article,

The present morphological and functional studies have revealed a highly novel mechanism conferred by MET receptor signaling, which we show serves a pleiotrophic role in controlling both neuronal and spine morphology, and the time course of glutamatergic synapse maturation on CA1 hippocampal neurons. Such findings are consistent with the possibility that mistimed maturation of glutamatergic synapses underlie aberrant function of neural circuits that are enriched in MET during development.

Source
So the critical results from the same study showed that when Met got knocked down or deleted, we saw maturation of neural tissue. So now, if i'm thinking about Met and HGF, your article notes that HGF is decreased in autism brains. If we (1) need HGF for Met function, and (2) ASD may be attributed to decreased Met function, and (3) the C allele decreases Met levels, we're basically looking at a system that's modulating for ASD.

Thank you very much for your thorough answer. Could you explain what you mean by "modulating for ASD"? I'm not completely sure what you meant by that, as I see two possibilities:
1.) HGF production is downregulated due to a reduced binding with MET

Basically all I was saying is the system of circumstances was pushing toward a state that would make ASD more likely. For the actual reason HGF level become reduced I'm actually not too informed!

2.)HGF is the limiting reactant in the pathways you mentioned above.
If you would like some context, I am investigating the effect of supplemental HGF in an attempt to normalize dendritic spine outgrowth and recover cognitive function in this particular mutation. I would also like to know what you think of the impact on cell growth/differentiation in  other tissue/is this an issue of merely HGF shortage or are the effects of this mutation mostly downstream of the ligand binding?

I've read through some articles where Stat3 and c-Src play a role downstream of c-Met, where they found Stat3 and c-Src in the promoter of HGF increasing HGF transcription. If it's a decrease in relative c-met levels that's heavily impacting Stat3/Src mediated HGF transcription, it could be that the actual issue is with the levels of c-Met.

One more question: The mutation itself is a change of base from a Guanine to a Cytosine. Do promoter region mutations generally mean RNA polymerase cannot fully attach itself to the promoter region resulting in reduced replication of the associated protein? When you say "decrease in c-met" do you actually mean there is less c-Met protein being produced?

I'm not sure exactly what, but either for transcription factors or for the polymerase at the promoter. Affinity is reduced for the mutated promoter, and so less transcripts are made, and less protein is actually available for the cell.


text:
Saline solution for animals
A popular "well-known fact" is that all creatures on Earth consist mostly of water (i.e. H2O). Indeed, a liquid called "normal saline solution" is just a solution of 0.9% sodium chloride in distilled water. It is generally considered the "safe" liquid to be injected into human body in relatively high volumes without any bad effects.
I know that the same 0.9% solution is also used in vet practice for at least cats and dogs. As far as I understand, that's because blood circulation structure and basic blood regeneration specs are more or less the same for cats and dogs as for humans.
But what about other animals? My wild guess is that same 0.9% solution would be ok for all mammals (probably because their blood tract is similar), but what about others? Birds? Fish? Vertebrae? Invertebrae? Animals? Plants?
If 0.9% solution is not universal, what are the other possible variants? (i.e. could you provide examples of other compositions for some other species?)
If 0.9% is indeed universal, I'd be glad to hear any pointers on why does it happen (i.e. is it related to evolution of life in Earth history, is it related to chemical composition of bodies, related to some specific cells, etc).

Not saying that it is universal, but the reason the that we use 0.9% saline is so that osmosis doesn't cause all of our cells to suddenly try to draw in water to create an equal concentration on both sides of the cell membrane. It all has to do with the "stuff" inside our cells.

Great insight, thanks! Now I just need to dig in through how cell membranes evolved and which creatures started having these "modern" 0.9%-level membranes in their cells...

Try looking into concentration of ocean water. If we have all evolved from the cells that swam the ocean there is a good chance there is something to it. Also look into fresh water fish too. If there is going to be a difference in osmosis with the 0.9% solution it will most likely be in fish.


text:
How is centriole number maintained during meiosis?
I've found a website (Pearson's BioCoach) that claims centrioles duplicate in Prophase II. Is this accurate? Does it depend on the species in question?
Looking at three textbook illustrations of meiosis, none of their illustrations are consistent. All depict the movement and number of centrioles through Telophase I the same way: centrioles replicate in S of Interphase, then do their thing through Meiosis I. We end up at Telophase I with 2 centrosomes, each with 2 centrioles. There is one centrosome at either pole of the cell.
After that, the diagrams are unclear:
One text (general biology) seems to indicate either centrioles or entire centrosomes replicate after Telophase I, because Prophase II is shows both cells with 2 centrosomes, each with 2 centrioles.
Another (basic genetics) illustrates 2 daughter cells of Meiosis I inherit one centrosome each following Telophase I. In Prophase I, the centrioles in this centrosome splits, with one centriole going to either pole. Cytokinesis after Meiosis II results in 4 daughter cells, each with one centriole.
A third (more thorough genetics) stops depicting centrioles after Telophase I, instead showing the spindles growing in an aster formation from an empty space, the space where there were 2 centrioles up until Telophase I.

Interesting question, I'm not sure that the answer is actually  entirely known. Here's some articles that may interest you: one, two

Indeed a nice one. The reality may not be exactly a duplicate, but varies in number - may be in terms of cancer. I am curious as well. You may take a look at this article as well.

It makes sense that it would have to be in Prophase II or in an interphase between the two meioses; the kinetochores need to be captured by the microtubules during Metaphase II. Campbell's Biology has that a stage in Prophase II is formation of Spindle and migration of chromosomes towards the metaphase II plate late in prophase II. If you look at an upper level textbook they will have a phase between telophase I and prophase II called Interkinesis. It is similar to Interphase in Mitosis, but without the duplication of chromosomes. So it is likely in interkinesis that centrioles double.

When a cell enters the cell cycle and passes through S phase, each centriole is duplicated. A "daughter" centriole grows out of the side of each parent ("mother") centriole. Thus centriole replication — like DNA replication (which is occurring at the same time) — is semiconservative.

Centrioles migrate to opposite poles at the end of meiosis and then the centrioles duplicate in the new cell and during the S phase. One centriole grows from the parent centriole. Therefore, like in DNA replication the centriole replication is semi-conservative.

You are correct about the replication being a result of a semiconservative mechanism, however the question is asking about the duplication between Meiosis I and II. There isn't a synthesis phase in this period. Consider adding a reference an incorporating your comment into the answer, as it is likely that most people are not aware that Centriole replication is via a semi conservative  mechanism.

A reference from my book -

Interkinesis or Intrameiotic Interphase
It is metabolic stage between
  telophase of meiosis I and prophase of meiosis II. Chromosome are
  elongated but chromatin reticulum is not formed. Protein and RNA
  synthesis may occur. Centrosome or centriole pairs undergo replication
  in animal cells. However,
  there is no DNA synthesis. It is important for bringing true haploidy
  (haploidy of DNA) in daughter cells.

From this site - https://openoregon.pressbooks.pub/mhccmajorsbio/chapter/meiosis-ii/
(search for centrosomes in that page)

The centrosomes that were duplicated during interkinesis move away
  from each other toward opposite poles, and new spindles are formed.

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


text:
Correct enzyme nomenclature
I notice many wikipedia articles, courses, pathway sites use a different abbreviation for the same enzyme. Eg: Wikipedia lists the abbreviation of phosphoglycerate mutase as PGM, whilst wikipaths lists it as PGAM in the glycolysis pathway. Then there's enzymes like glyceraldehyde 3 phosphate abbreviated either as GAPDH or G3PDH. This has led to many confusions, particularly when the enzyme abbreviation is completely different to the gene abbreviation, eg: protein kinase A (PKA).
For the official names of genes, I'm using genenames.org. I thought it might be common practice to abbreviate an enzyme with its gene abbreviation, but I see this is problematic due to many enzymes being encoded by multiple subunits and genes from different locations.
Is there a site, or a way, to unambiguously know the correct, and most widely recognized, official name/abbreviation for an enzyme, like there is for genes?

No, not that I have ever seen. Classically, the Enzyme Commission (E.C.) identifiers are the only way to be certain that two (or more) abbreviations or acronyms are all referring to the same enzyme activity. Sometimes, when the situation becomes very complicated interested parties will co-author a proposed new naming convention within their subfield. Some journals may require specific abbreviations, but otherwise authors are free to use whatever nomenclature they like.


text:
Do domesticated animals necessarily live longer than wild animals? counterexample wanted!
Generally domesticated animals do not need to worry about their food and other predators, and they have a lower probability of getting sick.
However, it seems there is no sharp difference between the life expectancy of wild pigs and domesticated pigs. Both can survive more than ten years if they are not killed.
Is it normal for domesticated animals to have a longer life span? Is it necessarily so?
Is there an example of a wild animal that statistically lives longer than its domesticated counterpart?

generally we haven't been selecting for long life, given the amount of inbreeding many species go through and possible trade-offs (milk production in cattle for example, might be stressful for the animal) it is likely that many domesticated species live shorter than their natural counterparts. I think this question may be a) near impossible to answer (its not likely that a properly designed experiment has been conducted) and b) too broad, there's a lot of domesticated species

For a properly designed experiment you would need both sets of animals being kept in the same conditions (food space, climate, stressors, medicines), and these are likely to be further from what one group is adapted to than the other, and given the complexity, requirement of large sample sizes, cost of the experiment & how little there is to be gained from doing such an experiment, it is unlikely to have been done.

I think this will either encourage opinion based answers, or bring to light a paper that looked into this in great detail. Either way, my money is on a pug surviving longer in a Parisian apartment rather than the Chinese wilderness!

Yeah this question will potentially draw many isolated answers. For example, indoor-cats are indeed known to grow older than cats that spend a lot of time outdoors (e.g. feral cats) because the latter contract more disease and get killed by cars, or get baited by nasty folks etc.

guys, can we just make this question simple?  e.g.  wild birds vs. pet birds ?  I just need a counterexample which statistically speaking lives longer than its domesticated counterpart .

@questionhang - that's exactly what we are trying to analyze for you. It is up to you to make this question answerable. If you think you know exactly what you want, why isn't it in the question? The concluding question is simply too broad. I vote to close until edited.

@aliceD  OK, I have revised the question.

I think the heart of the matter is in the "not killed". A domestic animal which slows down due to age often will be cared for by its humans. The same animal in the wild is almost certainly food for another animal.

@jamesqf  On the other hand, there are domesticated animals which do not like their man-made environments and crowded people who stares at them.

@questionhang Consider we raise pigs to eat them, longevity is not a priority, in fact breeding them to get larger faster probably would shorten their normal lifespans. Consider comparing species bred for a purpose other than consumption.


text:
Is it possible to merge the genomes of photosynthesizing and electron-transporting bacteria to make an electric cell?
I had an idea of making electric current from bacteria. There are some bacteria that can photosynthesize, and some others are capable of transmitting electrons through each other. Is it possible that through genetic engineering, we could insert the genome that allows bacteria to perform photosynthesis, with other capable of transmitting electricity, and therefor making a bacterial culture, big enough to make a free energy source?

"through genetic engineering" I think this is the kicker. I think you've just described how it would be possible, however actually making it with the current technology would be impossible. Using bacteria to make crude oil is the current best shot at making renewable energy from the sun with biotech as far as I'm aware.

What you're describing is a phototrophic biofilm microbial fuel cell! They're pretty neat.
Essentially the sun powers the bacteria and the bacteria in the anaerobic side passes electrons through the graphite electrode to use oxygen at the cathode. There's another explanation here. You could also "unfold" cyanobacteria and layer them and you'd probably get an efficiency increase but the system would be pretty fragile. Compared to other MFCs, though, everything is fragile. Dirt even works(not very well, but it's dirt).

You do not need to merge anything. Photosynthesis already includes the electron transport across the inner membrane of the chloroplast (in case of plants) or across the bacterial membrane (in case of bacteria), creating voltage difference between inner and outer side. The only problem, this voltage is relatively difficult to take away.


text:
What is the fluid clearance rate inside the retina?
I'm attempting to model the chemical concentration between several compartments of the eye, including the retina. Does anyone have any idea what the rate of fluid removal is in the retina, or could direct me to a study of this?
EDIT: It appears that Müller cells play a crucial role in this, dehydrating the retinal tissue. I am attempting to find the rate at which they achieve this. (see link)
http://retinatoday.com/2008/11/1108_07.php/

For the best of my knowledge the structure that dehydrate the retina is Retinal Pigment Epithelium, not Muller cells.

look at the answer, do you need subsequent clarification?

As I mentioned in a comment, the RPE (retinal pigment epithelium) is in charge of absorbing the "water" from the retina and beneath it.

Water is eliminated from subretinal space by active transport by the
  RPE. The transportation rate was estimated to range from 1.4 to 11 µl
  x cm-2 x h-1.

Oh you are fantastic! Thank you very much. This is exactly what I need.

@Freeman You are always welcome %)


text:
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:
What flowering green plant is this?
I got this green plant as a gift many years ago, but I have never seen it flower before. It has a strong, pleasant scent and cool flowers so I'd really would like to know what it is.

The plants sometimes are native to a certain region. Care enough to share yours?

@bonCodigo Sure! I'm in Sweden but I'm quite certain that these are not native here :)

It is member of family Amaryllidaceae (of monocot)

also called spider lily. some other related plants also called spider lily. https://en.wikipedia.org/wiki/Spider_lily

It looks like a "Spider lily" from the Hymenocallis genus.
Here is a picture of Hymenocallis caribaea from wikipedia for comparison:

There are however ~65 species in the genus (according to wikipedia), and I cannot say exactly what species you have.


text:
Why are plants referred to by their Latin species names, and not by their popular names?
Often the names of herbal ingredients in certain cosmetics products are given by their scientific names like Anthemis nobilis instead of chamomile or Lavandula angustifolia instead of lavender.
Is there any reason why this practice is followed? Wouldn't those who have allergies to certain plant materials be better off reading "coriander leaf extract" instead of scratching their heads over what "Coriandrum sativum leaf extract" is? Why put something more complex when something simpler would be more beneficial to the consumer?

Maybe because it sounds fancy. I do know that there are labeling regulations that companies have to abide by for cosmetics via a google search. http://www.fda.gov/Cosmetics/Labeling/Regulations/ucm2005194.htm

The use of a genus-species notation gives more exact information. For example there are multiple species of chamomile: There is Roman chamomile (Chamaemelum nobile), German chamomile (Matricaria recutita, or Chamomilla recutita) and Dyer's chamomile (Anthemis tinctora). The first two species are appraised for their medicinal properties and help to calm upset tummies and to aid sleep, among other things. The latter species, however, does not have these properties and is used for dyeing. This illustrates the fact why 'chamomile' alone is insufficient.
Popularly, classifications of living organisms arise according to need and are often superficial. Anglo-Saxon terms such as 'worm' have been used to refer to any creeping thing including snakes, earthworms and intestinal parasites. The term 'fish' is used in shellfish, crayfish, and starfish. However, there are more anatomical differences between a shellfish and a starfish than there are between a bony fish and man.
In science it has been the convention to use the genus-species notation since Carl Linnaeus introduced it in the 1700's. This formal classification serves as a basis for a relatively uniform and internationally understood nomenclature. A uniform classification system simplifies cross-referencing and retrieval of information. The Linnaean taxonomical system aids in this purpose and is widely used. The genus-species system can be extended by including subspecies and varieties. Many (plant) species don't even have an (English) trivial name. Taking your lavender example: there are some 39 Lavendula species known and obviously, many of them don't have a trivial name. Here one has to fall back to the Latin names to be sure what it is.

If chamomile is sold as an herbal supplement I think it's safe to assume they're not packaging the variety meant for dyeing. It really seems like a marketing ploy to me.

@canadianer I strongly disagree. It's note safe to assume anything; the labels should be clear and unambiguous.

Why assume it will be called chamomile and not Roman chamomile, German chamomile and Dyer's Chamomile? Your first paragraph seems to counter itself by providing unique common names that could be used then saying you must use only the base term for some reason.  I actually think it is--as you later suggest--scientific convention over user interface, scientists don't typically consider usability very important.

@Ajasja There's a big difference between what should be done and what is done.

@BillK - good point - I added a few sentences on lavender that illustrate why relying on trivial names is not always reliable

@canadianer US law requires cosmetic labels adhere to given lists of ingredient names.

The Latin names are known in all countries. The "popular" names are only popular in one or maybe two languages/countries. So, learning the Latin names, enables you to communicate international more easily.

It generally won't be more helpful.  Not only will the names be different in different countries, there may be different types of the same species with different properties, or even different species with the same common name.  If you have an allergy to something like coriander, being able to read the label and see what contains actual coriander and what contains curry leaf is essential.
Lavender is a great example.  Any gardener could tell you that English lavender (angustifolia) is a very different plant from French lavender (dentata), even though they're the same family.  I've no idea what the essential oils will smell like, but I'm pretty sure they won't be identical.  And more importantly, if you're talking allergies then I'm pretty sure they won't have the same chemical composition.
Even worse, consider bergamot.  Bergamot oil should come from the skin of the bergamot orange, but there's also a species of flower (monarda) which is commonly called bergamot because its scent is similar to bergamot orange.  If your contents just said "bergamot", which one? And even worse, there are two types of monarda which are completely different plants.

Ditto on the "multiple species with the same common name". I was really worried the other day when I was reading about the risks of consuming the plant "fireweed", until I realized that my "fireweed" was a completely different plant from the "fireweed" the author was talking about: https://en.wikipedia.org/wiki/Fireweed_(disambiguation)


text:
Can someone identify this stinging plant?
I have no idea where this plant came from, or what it is. What I do know is its leaves are covered in little hairs, there's little thorns growing all over it, and just by rubbing its leaf it burns you and leaves a red mark as well as blisters. It stung my mother and I would like to know what it is so I can find a remedy.

larger image:
http://i1094.photobucket.com/albums/i449/cupcaketurtle1/20150714_225505_zpskr24gklq.jpg

It would help if you could add in what country you mother was stung by this plant.

The littles hairs are called trichomes :) I had bad experience when visiting a tropical bushy area. If you don't mind, could you please share where (roughly the region and city) your mother came into to contact with this plant?

Looks like a member of Urticaceae.

I think it is a common stinging nettle, Urtica dioica. It is a native to Europe, Asia, northern Africa, and western North America and is the best-known member of the nettle genus Urtica. As commented by others, your geographical location would be helpful to obtain a more accurate identification.
Like other stinging nettles, it is unpleasant to the touch, but harmless. Just be patient. The redness and burning/itching will disappear. If the pain gets serious or other complaints arise, go to your GP.

Stinging nettle. Source: Health Direct.

It's a nettle (genus Urtica).
The one on your photo really looks like the one I'm used to see in France:
Urtica dioica.
I read in herbal lore books that the sting of the nettle could be appeased by rubbing it with Plantago leafs. But that might just be placebo effect.
See also this section of the wikipedia page.

Common folklore where I live is to sooth the irritation by rubbing the affected area with the leaves of Dock (Rumex obtusifolius) - which often grow near nettles. As a child I recall it being effective (though some of that was probably psychological reassurance).


text:
Does 405 nm light set off phosphorescence in the eye?
While playing with a blue/violet laser (5 mW, 405 nm) tonight, I noticed that on dark, non-fluorescing surfaces, the beam reflection was trailed by what looked like a dimmer reflection of the beam. The effect was most easily observed when I moved the laser in a circular motion. The apparent 2nd reflection was not produced by a side lobe of the laser diode, as it always trailed the main reflection, regardless of clockwise or counterclockwise rotation. Also when I stop moving the beam, the second 'reflection' quickly merged with the main beam reflection.
I doubt it is caused by phosphorescence of the material (cloth) I was lasering, as it also showed up when I pointed the laser at the floor, other sorts of cloth and painted walls.
So, do rods, cones, visual purple or other eye components phosphoresce when hit with deep blue light?

Instead of phosphorescence, a more parsimonious explanation is the perception of afterimages. Afterimages regularly appear after viewing a bright stimulus. They occur in the same location in the visual field as the original stimulus, but lack clarity. Afterimages depend on the intensity and contrast of the original stimulus (i.e., they are more pronounced with bright stimuli in a dark environment), the time of fixation (i.e., longer fixation generate more persistent afterimages), and retinal adaptation (i.e., dark environments enhance afterimages).
After images are almost always the complementary color (negative afterimage) to the original stimulus, but can very briefly be the same color (positive afterimage) when viewing an exceptionally bright stimulus. A stimulus consistently produces the same afterimage, which varies in size based on the distance between the person and the background. After images are often revived by blinking.
Afterimages are thought to derive mainly from photobleaching of the retina, although cerebral processes may contribute too.
Phosphorescence in the retina has to be induced by injecting phosphorescent markers (Wanek et al., 2013). As far as I know, the retina is not autophosphorescent.
References
- Gersztenkorn & Lee, Survey Ophthalmol, (2015): 1-35
- Wanek et al., Curr Eye Res (2012); 37(2): 132–137

The main reflection of the laser off a dark surface doesn't appear all that bright. Your ref doesn't say whether after image intensity is wavelength dependent, but red and green lasers at the same rate of laser movement, both produce continuous light trails; persistence of vision. There's some funny kinetics going on with blue to generate a distinct trailing spot.

Blue cone pigment is coded by a gene less closely related to red and green pigments. Could be different adaptation kinetics.

So not phosphorescence, which is what I asked. Blue cone is far less sensitive than red or green: http://www.physicsclassroom.com/class/light/Lesson-2/Visible-Light-and-the-Eye-s-Response (It'd be nice to see units on that Y axis). But that doesn't explain why I see a trailing dot rather than a trailing streak as with other colors. Watching that dot merge with the main beam reflection after I stop moving the beam is truly an odd sight. Guess I'll go with funny kinetics for now.

@WayfaringStranger - generally the laser beam is only visible when there are scattering particles. Only the point of impact is seen on the ground, a beamer screen etc. But no, pretty definitely not phosphorescence. Thanks for accepting!

AliceD: Yes, this is all about the behavior of spots at the point of beam impact, and slightly trailing it depending how fast I move the beam, not smoke or dust in the air.

Did you try recording this on camera and stop the video at one point?
if the trailing dot is visible there, it must be some light, emitted by the material. if not, its an effect, caused by your eye.


text:
Species Identification: Spider
I usually would search for myself, but I need to be super sure about the identification because I need to know if I need to get an exterminator in here or not. (I think it might be a giant house spider, but don't let me influence your analysis.)
So I live in the northern part of Ireland (About 40 minutes from Derry Northern Ireland over in County Donegal) and I went to my bathroom to a VERY fun surprise this morning. It was this wonderful spider in my bathroom. For reference, the lip of the glasses it is depicted in are 8 - 8.5 cm in diameter.
The missing leg was not my fault either, I was very gentle with the spider and released it outside post photo-shoot. (Warning: these are macro shots of the said spider)

More high resolution photos available on my Flickr (SolarLunix).

"I live in the northern part of Ireland and I went to my bathroom" - assuming the bathroom is within walking distance of the house, its the northern region of Ireland ;P

An image from the top in good light would help, maybe a wolf spider

@rg255 That was the best I could do given the circumstances and the need to get it outside before my hubby woke up and freaked out.

The images in the question are of a giant house spider, as hypothesized in the question. (Eratigena duellica/atrica/saeva). These (along with the hobo spider, Eratigena agrestis) do not have any banding or annulations in their legs (dark/light stripes/rings).
The spider in the other answer of Tegenaria domestica do (always) exhibit leg banding. So, it is not the spider in question.
Both Eratigena and Tegenaria are in the funnel weaver family.

Looks like a house spider (Tegenaria domestica)

I just love these to-the-point answers +1

This is close, but not quite correct


text:
Identification of black growth on onion skin
I have encountered this black-colored growth on onion skins a lot. It seems to develop over the course of weeks and I have rarely, if ever, encountered the material on fresh ones. If I peel the onion and it streaks the onion flesh, it appears, dark blue-ish. It looks like a fungus, perhaps a bacterium, but I am unsure. It is often found 'hiding' under the outer layer of skin on the deeper skin layers. In the photo the outer layer of skin was peeled off. It never seems to invade the edible parts below, though.
The pictures below are standard white onions from the local supermarket in Canberra, Australia (Canberra [Australia's capitol yes!] lies between Sydney and Melbourne). I must admit, I don't know if they are imported. The pictures below were taken mid-winter. Temperatures in our kitchen plummet during the day because of bad insulation. In the evenings and weekends it's room temp with heating. The onions are stored in the dark, in a kitchen cabinet. Humidity is low and mostly the days are dry and sunny. However, we cook in the kitchen so at times there is plenty of moist.
Also, I wonder, would it be harmful? No self-help medical issues here, I always wash and fry/cook my stuff and no issues whatsoever, just curious.

I understand there is little to go with. However, a general genus or group of fungi would already be cool. I googled and sought for images to no avail.

I think it is Aspergillus niger:

On the second place I'd suggest  Black Mold disease caused by Alternaria species.

Are they bad for your health? Something rings a bell that A. Niger has some bio-active compounds.

@AliceD They will not improve your health definitely. A. niger could produce ochratoxin A (OTA) and fumonisin B2 (FB2) as well as other potentially toxic substances.

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


text:
At what levels of muscle energy intake does catabolism start?
From my own reading, there are three ways used by the body to produce energy:

Alactic anaerobic (direct degradation of ATP and creatine phosphate for regeneration of ATP)
Lactic anaerobic (breakdown of muscle glycogen with lactic acid production)
Aerobic (breakdown of carbohydrates and fats primarily and secondarily of proteins)

My questions are:
1) Knowing that the anaerobic mechanisms (alactic and lactic) are triggered when the effort is intense and / or greater than body oxygenation capacity, it seems logical, at rest, the body uses mainly aerobic way for producing energy. Am I right?
2) If 1) is true, what are the conditions (trigger elements, trigger events) which lead to muscle catabolism (so protein degradation) in order to produce energy? ? Is it well the last resort used by the body to produce energy that is to say after degradation of total carbohydrates and lipids?

(1) is basically correct.  I don't see how (2) is related to (1) ? Also, there is no single answer to whether protein is the "last resort used by the body to produce energy", because different tissues of the body have widely different fuel preferences, and also it depends on the extent of fasting, level of exercise, amount of muscle and fat stores, and a bunch of other things. Can you be more specific?

Precisely, in a bodybuilding context, I would like to know the conditions which lead to muscle catabolism (so protein degradation) in order to produce energy?

Okay, can you please edit your question then so that it is specific to muscle catabolism during exercise.

@backlash that's an entirely different question.

1) Yes, most cells in the body derive energy from oxidative metabolism, unless oxygen is not available for some reason. There are some exceptions, for example red blood cells lack mitochondria and so have no respiration, and various types of rapidly proliferating cells such as activated immune cells have high glycolysis and lactate production (for reasons that are still not well understood).
2) The main fuel of exercising muscle is glycogen, which can account for 60-80% of energy requirements (article). Triacyglycerols (fat) stored in muscle tissue may account for most of the remainder (artice). Normally, muscle protein is not a major energy source during exercise. Some muscle protein breakdown has been observed after 2-3 hours of intense exercise (think marathon runners), when glycogen stores are depleted. See this review article.
If glycogen is not synthesized and stored normally while resting, then muscle may be more likely to catabolize protein during intense exercise. This can happen to some extent in diabetes, see for example this paper. There are also severe genetic disorders that disrupt glycogen synthesis, but those are very rare. I would guess fasting also makes it difficult to replenish muscle glycogen stores (and muscle triglycerides as well), so strenuous exercise combined with fasting might result in muscle protein breakdown, but I don't know of a study on this.

Prolonged fasting/starvation promotes muscle protein catabolism.
During starvation blood glucose must be maintained in order to provide fuel for red blood cells and brain in particular. Amino acids from muscle breakdown are used as gluconeogenic precursors by the liver and kidney. However fat is also mobilised and fatty acids are converted to ketones by the liver. Most organs/tissues can use ketones, including the brain (but not red blood cells or the liver). This use of the fat store reduces the body's demand for glucose and slows the process of muscle breakdown, allowing survival for weeks rather than days.


text:
Is NADPH unstable in UV light?
I am working on an enzyme activity assay using NADPH as a cofactor. The MSDS for NADPH Tetrasodium Salt, tells to store it in a place away from heat and light. Does this include UV light or just visible light? I was told that a pure NADPH stock solution (with pH 7 phosphate buffer as solvent) could be re-used after absorbing UV light at 340 nm, but based on my understanding of the MSDS it seems that shouldn't be the case. So my question is: could I reuse a sample of pure NADPH stock solution that was exposed to UV for my enzyme activity assay?

In my experience, reuse of NADPH stock solutions maintained at pH 7.0 or above is perfectly acceptable. Taking an absorbance spectrum every half-hour or so will probably show that definitively.  However, NADPH is VERY unstable in acid, leading to a 'bleaching' of the absorbance at 340nm.  Try measuring a rate at pH  6 or below, 340nm,  with 100 micromolar NADPH and no enzyme or cosubstrate. There will be a very significant decrease in absorbance with time (ie a 'blank' rate) which will make estimation of enzymic reactions at low pH virtually impossible.


text:
Why is dopamine or a dopamine-receptor agonist not pumped into the brain of Parkinson patients?
I am aware that dopamine cannot cross the blood-brain barrier, but can't it be pumped inside the cerebrospinal fluid via some permanent tube implant? Wouldn't Parkinson patients chose that over succumbing to the disease? Why hasn't it even been ever tried?

Levo-Dopa is used as a first-line treatment of Parkinson's disease. Unlike dopamine, L-Dopa is able to cross the blood-brain barrier. There it is converted into dopamine. To prevent premature breakdown in the gastro-intestinal and circulatory system after oral intake, carbidopa can be co-administered. Also MAO-B inhibitors and COMT inhibitors can be applied to prevent breakdown of L-Dopa in the brain. Oral medication is preferable over invasive intracranial infusion of medication.

Conversion of L-Dopa into dopamine. Source: ADHD treatments.
Dopamine agonists are also in use. Unlike L-Dopa, dopamine agonists are not converted into dopamine. Instead, they mimic dopamine effects in your brain. They aren't as effective as L-Dopa, but they last longer and may be used alongside L-Dopa to smooth the sometimes off-and-on effect.
Parkinson's disease is not fatal, but it can reduce longevity. The disease progresses more quickly in older patients, and may lead to severe incapacity within 10 - 20 years. Older patients also tend to have muscle freezing and greater declines in mental function and daily functioning than younger people. L-Dopa treatment in the long run causes adverse effects, such as dyskinesias, toxicity, or loss of efficacy (Marsden, 1994).
Reference
- Marsden, Clin Neuropharmacol (1994); 17: S2:S32-44

so why do patients die in the end instead of living on "dopamine replacement" ?

@shortage_radeon - L-Dopa is a treatment, not a cure. Parkinson's is a progressive, degenerative and incurable disease, but not fatal. I amended the answer in response to your comment

Quoting a faculty member at Moffitt Cancer Center: sometimes the goal now is to get patients dying with their particular disease, and not simply because of it using the treatments and therapies at medicine's disposal. Cures are remarkably elusive for complex diseases, where effective management strategies exist.

@AliceD I don't think this answers OP's question, which is why dopamine or an agonist cannot be pumped into the brain and thereby cure Parkinsons, or why that has never been tried. I do not know that answer, but I want to know it too. What's interesting is that it has been tried in 2 monkeys

@AliceD ...(you have to scroll through that to find the part on monkeys)  at least once, and for one of them it rescued the motor deficit from an MPTP induced lesion for 9 days before problems with the method caused the pump to stop working. I was somehow both surprised and not surprised that this would work. I'd love to know whether anything more was ever followed up with this sort of approach.

@Chelonian - my answer is that we don't have to with L-Dopa as a treatment. L-Dopa can be taken orally and is converted to dopamine in the brain. Why pump it in? Maybe I'm thinking too practical?

@AliceD I see; yes, if the OP doesn't realize that the DAergic cells eventually all die and L-DOPA no longer helps, that's a good point. But since they do, it is an interesting question to wonder whether some kind of chronically implanted canula could deliver DA to the right targets, thereby keeping people asymptomatic for life (given that it seemed to help that monkey, at least at first), and, if so, why it hasn't been tried in people (or has it?) or at least pursued further in primates? I'm curious.

The blood-brain barrier isn't a bag that surrounds the brain that you could puncture and then inject dopamine. It is a thin layer of cells around every blood vessel and capillary in the brain that mediate transfer of substances between the blood and the brain cells. As such, it is incredibly complex and branched (as complex and branched as the myriad blood vessels in the brain).
In theory, you could inject dopamine directly into the cells of the brain, inside the barrier. But, the dopamine wouldn't diffuse far, and so wouldn't affect anything except for a very small area (millimeters?) around the injection point. So, to get an even distribution of dopamine, you'd need to inject at thousands (millions? more?) of points throughout the brain, and do it repeatedly.
And even with that, there's no guarantee that directly applying dopamine to the brain cells would actually help. In fact, bathing nerve cells in a neurotransmitter seems like a great way to mess up their signal transmission system.

FDA recently approved the duodenal levodopa infusion pump.  Idea is to wear the pump 18 hours a day, removing it at night.  This allows for a small dose of levodopa to be injected through the day.
I can not yet add comments, only new post.
@shortage_radeon The leading causes of death, among patients with Parkinson's, were pneumonia and bronchitis. Swallowing becomes more difficult with time, leading to aspirated liquids into the  lungs.  While a feeding tube can assist, the most effective is working with a Speech Therapist on keeping those muscles active.
Thankfully exercise and diet have huge benefits for those of us with Parkinson's.


text:
Determining the appropriate bioconjugate
I'm thinking of crosslinking two proteins. The crystallographic nature of the interaction and the binding motif for each molecule is know. The paper says the intermolecular contacts (over 50; van der Waals radius 5 angstrom) are made between the motifs in these two proteins. I also know that one of the motifs on one protein has a sulfhyryl (Methionine) and for the other motif on the other molecule I (think) can use a primary amide reactive moieties. Now this is where my question is.
Would I be correct in thinking that the best cross linker to use is a heterobifunctional cross linker, with a spacer of 10 (or 5?) angstrom in order to pick this interaction up specifically and stabilise it?
I desperately need a guidance on this. I have used the life technologies crosslinker selection tool and the crosslinking technologies hand book but I can't quite figure out based on the information I have, what cross linker length I need to use. I'm not worried about the cleavability, solubility and membrane permeability parameters.
UPDATE:
I know that the binding motif on the first protein it has Tyrosine, Proline and Methionine.
Looking at the groove contacts, the second protein is interacting with this motif, using Tyrosine and Glutamine BUT the second protein also has Tryptophan, Lysine, Glutamic acid and Methionine.
UPDATE 2:
I found specially close Glutamic acid (E) and leucine (L) on my first protein, specially close to Lysine (L) on my second protein although its not in the consensus sequence for the second protein. They are less than 10 angstrom apart. is that any better? So presumably I can use the homobifunctional linker?
Many thanks in advance

Is there a cysteine available, or just methionine? Methionine won't be very useful. What about lysines?

Are site specific mutations a possibility?

Also, does the linkage need to be at the binding site? Because bioconjugate chemistry usually won't get that kind of specificity if your reactive amino acid appears elsewhere on the protein.

I can't do point mutations but I was thinking of doing linkage at the binding site since that's one of the closest contact points that is known and hence using a 10 angstrom linker would reduce non specific linkages. I'm completely new to cross linking hence any guidance would be appreciated. Currently I am planning and amide amide homobifunctional linker at 10 angstrom. Since I calculated the molecular distance from the binding residues on two proteins. I used the X-ray data and SPDBV for calculations. Is that advisable?

Your first protein is what bothers me. Tyrosine, methionine, and proline are hard to work with. On your second protein, you have a lysine, which would be useful. If there was good amine on the first protein, you could use an NHS ester homobifunctional linker. The glutamate could be modified with EDC to make it react with amines. If there are other lysines on your proteins, they will also be modified, they may not crosslink to another protein, but they will pick up your conjugation reagent.

Met does not contain a sulfhydryl, Cys does.

I have made an update. many thanks for everyones help so far :)

Could you elaborate what the aim of the study would be?

Linking the glutamate to the lysine might be possible by EDC coupling. It would react with the glutmate to make an active ester, which could react with the amine on the lysine. It might be too reactive to safely use in cells though, and would also react with water, limiting it's usefulness. But if the two proteins are already bound when you add the crosslinker, it increases the odds of a successful linkage and EDC that reacts with the incorrect residues might hydrolyze away.

@user137 That answers the question! Please consider writing this as an answer so that I can accept it :) it would be great if you could include any references to the EDC variations containing a spacer, if you think that is advisable to use for proteins that are roughly 10 angstrom apart. Also from what I read, EDC works in PBS albeit at lower efficiency right? Also would you happen to know any protocols (incubation times, conc, neutralisation, etc)? as you say the best strategy is to add it to my cells that have already made the P-P connection.

If protein 1 contains a glutamate near the binding site with protein 2 and is close enough to the lysine on protein 2, it may be possible to link the glutamate to the lysine through EDC coupling.

EDC is 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide, which reacts with carboxyl groups to form an "active ester". This ester is highly reactive with primary amines, but can also react with water or hydroxyl ions. The general reactions are outlined below:

The active ester is compound 2, which you probably want to react with the lysine on protein 2 to produce the amide in compound 3, with the isourea 4 as a byproduct. This shows that other products are possible, depending on what hits the active ester first. This reaction is most effective at pH of 4 - 5, and produces a 0 length linkage, so if you have to reach 10 angstroms across, this might not work.
EDC coupling is often followed by NHS ester formation, which is more stable than the EDC active ester, but is usually done when you intend on storing the active ester as a dry product for some time.

There are general guidelines for cross-linking protein-protein interactions, but specific parameters (i.e. cross-linker sub-types,  spacer length, linker concentration, reaction pH and temperature) are often determined experimentally. Common protein cross-linkers target reactive functional groups that are more likely found on the surface of the protein than in its "active site" or "interface" that is often buried.
Given your relatively hydrophobic, non-reactive binging motif (Tyr/Pro/Met), if you do not need a large amount of cross-linked protein sample, then you could label it with photoactivatable amino acid such as L-photo-Met. Since Met is not often found on the surface, internal cross-linking would stabilize your protein and its binding partner.
If you need a large amount of cross-linked protein (e.g. in mg) for further structural studies, labeling can be costly. You could possibly cross-link the protein (complex) crystal itself (since there were crystals as you mentioned), often just by glutaraldehyde. If the complex is there in the crystal, it would now be as solid as rock.

Glutaraldehyde would probably knock out any activity though, so the best method depends on what the proteins will be used for. I glanced through that photolabeling paper, did they say how protein yield was affected by the substitution? I've seen non-natural amino acids added through mutant tRNAs and aaRSs, but yields are typically lower.

Thank you for the response. I can't use Gluteraldehyde as I need the cells alive. Yes I have given the different parameters a though since I need the cross-linking under very specific conditions. Labelling would be costly and is not guaranteed to get integrated into my protein of interest on the cell but that is an interesting option! many thanks :)


text:
Do herbaceous plants have woody parts?
Do herbaceous plants, especially perennial plants have woody parts, like woody stem?

I'm voting to close this question as off-topic because pasting the Q in google gives wiki as first hit - answer is in second line of wiki article.

By definition, no. An herbaceous plant is defined as a plant that has no woody parts. Herbaceous perennials die down to the roots at the end of the year and then sprout up again at the start of the next growing season, but they do not have woody parts. A plant that is small and herblike but has woody parts may be called a subshrub.

a subshrub :) that's cool

'"Subshrub" is often used interchangeably with "bush".' TIL bush isn't a synonym for shrub!

This isn't entirely true since the OP is asking for woody parts (not only above-ground parts), and perennial herbaceous plants can have "woody" roots (depending on how you define woody). See e.g. herbchronology for age determination of perennial herbs.


text:
Is the discovery of dominant and recessive genes the only reason Mendel matters?
We've known that offspring inherit various traits from their parents since (at least) Aristotle. In The Elements of Plant Hybridization, Gregor Mendel treats that fact as common knowledge. Clearly, we don't credit Mendel with discovering it. Accordingly, it seems to me that Mendel's only notable discovery was the discovery of the existence of dominant and recessive genes. However, that discovery doesn't seem to justify the title 'founder of modern genetics', which Wikipedia, and other sources, use to refer to him.
Why is Mendel the big deal that he is?

I think he did more than discover dominant/recessive, he discovered ratios of traits in offspring, like the 3/4 dominant 1/4 recessive phenotype, and that organisms could carry a gene for a trait without showing it, then pass that trait to it's offspring. The whole thing suggested that there were rules governing inheritance which could be deciphered and used to breed plants/animals more effectively. Darwin suggested that traits were selected for by environmental pressures, but Mendel showed how traits were passed down.

Aristotelian pre-science wasn't concerned with experimentation at all - it was just people throwing hypotheses around, basically. Contrast with Mendel, who developed a strong theoretical framework, coupled with precise experiments, tons of data and actually increased understanding of the subject matter. In other words, his was the first book on the subject that actually presented not just ideas, but also hard data anyone could verify for themselves. Not to mention that he also did deliberate genetical engineering on a level never done before.

http://mac122.icu.ac.jp/gen-ed/mendel-gifs/18-mendel-cartoon.JPG

@Luaan there's also the suggestion that he may have "doctored" some of his data...

Independent assortment. Mendel showed that his genetic markers for different traits, or phenotypes are transmitted randomly to the F1 generation. This was before the concept of linkage was discovered, so fortunately he selected unlinked genes.
Segregation of alleles. The dominant and recessive alleles segregate away from each other when the germ cells are created, therefore each parent has two copies of every Gene.
Distinguishing phenotype from genotype in a predictable and testable framework.
The test cross. It was only careful record keeping and back crosses that revealed the recessive copies of mutant alleles in heterozygotes.

One description of his contributions is available on Wikipedia.  Other sites include MendelWeb, Learn Genetics,

great answer +1. A reference would be nice to allow people to look up background info to your answer.


text:
If the average resting potential of a neuron is -70 mV, why is there such a high ratio of potassium ions inside relative to out?
My bio teacher was discussing the ratios of different ions inside versus outside the cell.
$$\text{OUT:IN}$$
$$\text{K}^+ (1:20)$$
$$\text{Cl}^- (11.5:1)$$
$$\text{Ca}^{2+} (10000:1)$$
$$\text{Na}^+ (10:1)$$
Can someone provide specific details as to the relative quantities of these different ions relative to each other? In other words, given these ion ratios, provide me with how much of each type of ion there are and show why this adds to to -70 mV. I just want to make sure I have a realistic picture of the concentrations.
I think I am mixing up concentration with the ratio between inside and out. Although for every potassium ion outside there are 20 inside, the charge from the total number of potassium ions must be less than that of chloride or it would not be negative inside, right?

you need to add up all kinds of ions (K and Na mainly)

Representative ion concentrations are shown in Fig. 1:

The membrane is mainly permeable to K+. Because the Na+,K+-ATPase pumps K+ inside of the cell, it tends to diffuse outward again, thereby taking positive charge outside the cell and making it negative inside (extracellular space is pretty much devoid of charge due to its vastness). Because the membrane is mainly permeable to K+, the membrane potential can be estimated using the Nernst equation by taking into account only [K+]:

This delivers about -90 mV, using the values in Fig. 1, which is quite close to the cell membrane resting potential.
However, other ions have some limited permeability too and especially Cl- also has quite a large leak current. To add the permeability p of the various ions (for K+ p=1, for Na+ p=0.04 and Cl- p=0.45) into the equation and take multiple ions into account, the Goldman equation is needed:

This equation yields closer estimates of the membrane potential than the Nernst equation taking only K+ into consideration. However, other factors such as buffer effects (Cl- is often buffered) as well as active transport mechanisms may alter the outcome of the Goldman equation slightly.

Awesome! I couldn't figure out how that equation worked. Thanks as usual AliceD :D


text:
Why does organ transplant work although it seems organ's motor neuron isn't connected to recipient's CNS
Although it seems impossible with current technology to connect organ's capillaries to the recipient's capillaries and its motor neuron to the CNS, transplanted organ works for years. But why?

could you specify which organ you are talking about?

How about kidney?

Capillaries only transport blood for short distances, and within an organ. The blood supply to/from a major organ is generally carried over a few major blood vessels (usually one artery, one vein). Splicing such larger blood vessels are what surgeons earn their pay to do.
In terms of nerves, most transplanted organs function fairly well without being connected to the CNS.

With respect to OP comment asking about kidney and this fine simple answer, with a kidney you just have a renal artery, a renal vein, and a ureter that need to be connected. Internal vessels and tubules of kidney handled the rest. There are nerves innervating the kidney, but last I knew their function was still "an area of active research interest."

Thanks for your answer, which surprised me a lot. After changing key words on google search, I found several new results. One of them was about heart transplant, and it also works totally fine, except for the fact that the transplanted heart beats faster, responds more slowly to exercise and doesn't increase its rate as quickly as before. I'm expecting to see further development in organ transplant technology, so that transplanted organ will work even better.


text:
Requirements for soil sample transportation over long distance
I need to collected soil sample from agricultural area far away from my lab. It would required about a week for the sample to arrive to lab. I need the soil sample for genomic DNA isolation (metagenomics) as well for isolation of certain species and culture them.
Therefore, the cells in the soil sample needs to be viable. What are the possible ways to long distance transportation of soils sample with intact viable cells?

I would say it depends on the cells you are looking for. Are you the first one in your lab doing this stuff or are there protocols available?

Yes, i am the first doing in my lab. I am targeting ammonia oxidizing bacteria and archaea.

Do what you have to do (extraction, culturing) on site?

I'm no expert, but it would seem to me that as long as the soil's approximate humidity level and temperature are maintained, you should be able to transport it for a week just fine. Think about it - the organisms in the soil are adapted to outdoor life, which (depending on their native climate) probably means varying amounts of water in the soil from time to time, and most likely temperature variations as well. It's not like you're trying to transport a viable human organ or something...

We did a soil sampling expedition around farms in the UK a few years ago.  We took with us some insulated plastic picnic drinks cool boxes, and a lot of pre-frozen camping freezer blocks.  We bagged up the soil samples, and put the bags in the drinks coolers with the frozen blocks.  This worked fine for our 48 hour trips.  If you were going for longer, you could try to arrange access to a rotation of frozen freezer blocks, or buy bags of supermarket ice along the way to top up the drinks coolers.  The idea for us was not to freeze the samples, but just to keep them cold enough that the organismal diversity was not changed too much during the transportation.


text:
What is the meaning and significance of extreme pathways
Can someone please explain me what extreme pathways are? I found this definition in this article:

Extreme pathways are a unique and minimal set of vectors that
  completely characterize the steady-state capabilities of genome-scale
  metabolic networks.

Now, frankly speaking, I did not understand the head or tail of this definition? What is steady state? What does it mean by steady state capabilities? Can someone please explain me in a simpler way?
PS: I am a computer Science student

For any dynamic system defined by different components, the steady state is the state of the system in which the components remain constant over time. If you consider the example of growth (by cell division) the point at which the total number of cells remain constant would be the steady state. This is a point at which birth rate = death rate. Similarly for a multi-component system such as a gene and its activator, the steady state would be the point where the mRNAs and the proteins of the gene and its activator are constant. If only few components are constant then the system is said to be in a quasi-steady state.
A point to be noted that in chemical (or biochemical) systems steady state, as a term, is different from equilibrium (in physics these terms are used interchangeably). Equilibrium is a condition when, for a single reversible reaction, the forward rate = backward rate.
In mathematical terms steady state is a point where the rate of change of components = 0. In an ordinary differential equations based model:
$$\frac{d\bar{X}}{dt}=0 \\$$
where $\bar{X}$ is a vector in which each element is a component of the system. In case of the transcription example, $X(1),X(2)..$ would be mRNA, protein, activator mRNA and so on. In other words $\dfrac{dX(i)}{dt}=0$ for all $i$.
Steady state capabilities should mean the properties of the system at its steady state.
The kind of study described in the question is called metabolic flux balance analysis in which different metabolic reactions are described in the form of linear equations represented by $Sv=0$ where $v$ is the vector of all fluxes (metabolic reaction rates) $S$ is the stoichiometry matrix (which has the stoichiometry of all components in different metabolic reactions). The RHS is zero because we are evaluating the system at its steady state i.e. we are interested in finding out the condition in which the net metabolic reaction flux is 0. In other words all metabolic reactions, balance each other.
You need to read more about this. There are a lot of books on this topic. You can start with this review.
In flux balance analysis, the linear equations are overdetermined i.e. there are many solutions. People generally use linear programming (simplex algorithm) to find optimal solutions. In the space of the optimal solutions, the vertices represent extreme reactions. The entire optimal solution space can be described as a linear combination of these extreme reactions.

Schematic representation of a convex cone characterized by five
  extreme pathways. Extreme Pathways 1–5 (EP1, EP2, EP3, EP4, and EP5)
  circumscribe the solution space for the three fluxes indicated (vA,
  vB, vC). EP4 lies in the plane formed by fluxes vA and vB.
  Consequently, flux vC does not participate in that extreme pathway.
  EP3, EP4, and EP5 are all close and represent different uses of a
  network to achieve a similar overall result. All points within the
  convex cone can be described as a non-negative linear combination of
  the extreme pathways [1].

What is RHS? The RHS is zero

@aaaaaa in S.v=0 the zero represents no net flux.


text:
How are the vitreous humour and aqueous humour of the eye, connected?
My question is regarding the biological nature of the separation between the vitreous humour and aqueous humour of the human (or mammal) eye. What connects the two in terms of the passive transport of proteins between the two? Is there a single membrane?
If so what is the name of this membrane and is it the only thing separating the aqueous from the vitreous? What is the anatomical difference between the aqueous and the vitreous?
Apologies, I am far from a biologist.
Specifically what sort of transport is arrow 9 in the figure below representing? And is backward transport (from the aqueous to the vitreous) possible?
Any links to papers detailing this mechanism would be highly appreciated, I can only find references to experimental readings of concentrations, but nothing about the transport process itself.

I do apologise for that. However to me I don't really see the difference, the main body of my question asked about the transport of molecules, I merely drew more attention to that part of my question. I would say previously it was vaguely phrased, as, which I previously mentioned, this is not my field, I was attempting to make up for that, I'm sorry to have offended however.

Retracted comment - sorry! +1 had to make a slight edit before I could upvote again. Feel free to roll back :)

You have changed the question, so my answer looks unrelated. I'd suggest roll question back and ask others in separate question.

@Ilan, will do. Here is a link:
http://biology.stackexchange.com/questions/36140/how-do-drugs-or-other-molecules-move-between-the-vitreous-humour-and-aqueous-h

@Ilan Well the question might have sounded different but the OP asks if there is any connection in the sense of exchange of matter between the two "humours". This doesn't require a different question. OP just clarified their actual intention. You can edit your answer to add if there is any material exchange between them or not. Your answer is still fine.

@Freeman Keep the actual title of the question.. Add details in the body so that Ilan's answer remains pertinent.

@WYSIWYG I've added a little detail regarding the membrane. I believe IIans answer is still very useful. I would however like to know more regarding the actual process.

@Freeman edit the question.. This doesn't need a new question

@WYSIWYG Apologies for the confusion here.

@WYSIWYG I added the clarification to the answer, but I should mention that a question is too broad to answer in a format it is asked.

@Ilan You can tell that to the OP in the comments.

Don't be confused by the word "humour": the vitreous body is presented in birth and has very low "exchange" rate of its components, while aqueous is in constant turnover.
Secondly, the vitreous is an organ-like structure and is separated from other eye structures by its membrane, while aqueous is fluid produced by ciliary body processes into the posterior chamber and moves  anteriorly throughout the pupil. Aqueous can move posteriorly in a case of trauma, operations and other non-physiologic states.
ADD (after attachment of the image)
I'd correct some things in the scheme - call Vitreous as Vitreous, not Vitreous humour, change arrow pointing at the ciliary body as on the following image, depict the vitreous body membrane as I did.

In addition learn two terms: Cloquet canal and Berger's space.
Number 9 shows a vitreo-aqueous route which will follow blood, drugs injected to the vitreous (not an only route), etc.

Thank you for your answer, so are you saying that as soon as a component has managed to pass through the vitreous membrane it is quickly removed by the aqueous? Would you mind looking at this diagram in my edit? I don't understand arrow 9, what sort of transport does this represent?

This is very helpful. Thank you very much for adding details.

Since 2015, have you been able to answer your question "Specifically what sort of transport is arrow 9 in the figure below representing?"

@PeterBernhard 9 had to show drainage pass to the anterior chamber angler (number-arrow 4)


text:
Does tremor frequency generally increase as Parkinson's disease progresses?
I've been trying to research this question, but most if not all the on-line journals require costly subscription, and the studies that are posted look at tremor frequency with regards to other factors.
My question has to do with the tremor frequency, starting at early onset to later stages of Parkinson's disease - over the course of the disease, and without drug treatment (such as L-dopa), does the tremor frequency generally increase?

are you looking for frequency of tremor episodes (once a day, once an hour etc) or frequency of tremor as oscillatory motion (1Hz, 0.3Hz etc)?

Sorry I wasn't clear. I'm interested in the frequency of the neuromuscular oscillations.

The question is still unclear, there are multiple parameters related to tremor. Please, look at this article and decide if you need subsequent changes in the question http://www.mdpi.com/1660-4601/8/5/1478/htm

Mean frequency  (Cf) most likely expresses what I'm looking for.

Frequency of tremor typically remains constant for the person. Levadopa (sinemet) does not change the frequency.
Typically the tremor frequency will be in the range from 3Hz to 7Hz.  There is a common phrase when dealing with PWP (Person With Parkinson's Disease). If you have seen one PWP, you have seen one PWP.
Currently I am part of a study by the Micheal J Fox Foundation using Pebble Watches and Smart phones to monitor PD.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1014720/
Hughes AJ, Daniel SE, Kilford L, Lees AJ (1992) Accuracy of clinical diagnosis of Parkinson’s disease: a clinico-pathological study of 100 cases. J Neurol Neurosurg Psychiatry 55: 181-184.
https://blog.getpebble.com/2014/08/25/mjff-intel-parkinsons/


text:
How do sex biased genes evolve?
I am wondering how do genes become sex-biased? that is, how does a gene evolve expression which is regulated in a sex-specific manner (assuming no effect from sex-limited Y/W chromosomes).
I understand that gene duplication can lead to two sex-limited genes, the derived being expressed in one sex and the ancestral being expressed in the other.
Can the sex determining cascade cause sex-biased expression of a single locus? My thinking is that upstream differences between males and females might bring about regulatory opportunity to loci under sexually antagonistic selection over expression level. For example, if males favour upregulation in a locus, males who evolve some kind of transcription factor affecting that locus which responds to male-specific isoforms of DSX (in Drosophila), which could then cause the antagonistically selected locus to be more highly expressed in males without producing a negatively selected correlated response in females.
Is this correct? Are there other ways?
(Note: I'm looking for a clear explanation of the mechanics behind sex biased gene expression. Drosophila examples would be of particular worth)


text:
Synthetic carbon fixation pathways
Have there been carbon fixation pathways of, in particular, oxygen-producing bacteria, that have been replicated in the lab or at least the enzymes for the pathways have been successfully produced in the lab?

It is not just the enzymes. It is also the way they are arranged in the cell that dictates processes like photosynthesis.

@WYSIWYG I understand that..


text:
Why doesn't Manipulated Virus for Cancer Cure Work
I'm not a biologist but I have an idea for a cure for cancer and it is very simple and probably has flaws (if it worked it probrably wouldn't be a cure for all) or is not possible but ... I'm still going to ask why because I want to learn why it doesn't work and I want to learn more in general, so you can use all the biology terms you like. The idea is essentially to use a virus and manipulate/change it (this would be mechanized if it were to be mass produced and the type of virus is unknown to me because you want one that is fast growing and goes across only specific parts of the body depending on the cancer). This virus would not have any bad parts (parts that make you sick) to it because when the virus "injects" it's DNA or manipulates the existing for copying it would instead manipulate the DNA in the cell it is going into to have growth limits and other cancer genes that are set to being back to normal and then copy itself. Eventually it would be fought off by the immune system and most of the virus would be gone (along with the cancer) because this virus would last for a long period of time (week(s)).
I appreciate anyone who answers this question because I'm sure it sounds stupid from your perspective but this is the place to learn.
Thanks,
Jackson
Note: This is not an idea I'm trying to make, obviously, I just couldn't get it off my mind and wanted to see what is wrong and if it is fixable.

It's called an oncolytic virus. Hint: in the future, avoid rambling and run-on sentences and parenthetical comments, and re-read your question before submitting it so it is coherent and understandable.

Okay, but my idea is different because mine doesn't kill the cancer cell because I don't know how it would tell the difference; mine just manipulates the DNA.

This is a very broad question. You've basically described viral gene therapy which is a great idea but has many complications that are yet to be solved.

What are some of the complications?

I'd first suggest reading up on what cancer actually is - a collection of thousands (or more) mutations in a cell that leads to uncontrolled cell growth. Each tumor has different mutations, and would require multitudes of individually-engineered viruses to "fix" all of them, which in many cases literally can't be done anyway, as the genome is so unstable.

@JacksonH google "viral gene therapy complications" and learn for yourself!

It is impossible that all cancer cells are infected by viruses treated. Then uninfected cancer cells grow and take over.

This is not an idea I'm trying to make, obviously, I just couldn't get it off my mind and wanted to see what is wrong and if it is fixable.

Since everybody else is giving you a bad attitude in the comments...
While it might work for some cancers, it is completely impractical for the majority of cancers.
SOME cancers do occur because of a specific mutation or specific set of mutations. Some genes predispose people to greater risk for certain cancers. These have a much greater chance of being treatable via viral therapy, but there are still barriers:

The length of coding material (DNA or RNA) a retrovirus can hold and propagate is limited. The mutated gene or stretch of DNA may be much larger than the length a retrovirus could potentially replace.
The retroviral material is not guaranteed to "rewrite" or "overwrite" any bad DNA. Retroviral DNA is inserted fairly randomly into the host genome with little regard for where since it is generally an entire gene meant to be read in its entirety to eventually produce proteins. You'd expect BOTH gene versions to exist simultaneously. This wouldn't end in a cure, but some middleground between cured and affected.
There are tissues where cancers develop that wouldn't be infected. Any sort of brain tumor would remain completely untouched by retroviral therapy, for example.
Targeting specific cancerous tissues while leaving surrounding or other tissues alone is a big problem, even for non-retroviral therapies. Replacing bad genes in a cancerous cell is good, but replacing good genes in a healthy cell could lead to that cell's death or -- ironically -- possibly turn it into a cancerous cell as well.

The majority of cancers are not specific mutations and do not have known genes that predispose their bearers. The majority are an accumulation of mutations across sections of the genome. As MattDMo said in the comments (paraphrased): For these cancers, viral therapy is nearly impossible. Every mutated gene would required its own retrovirus. At that point, the time and financial investments start to rise exponentially.
While I'm not one to say it's impossible (I'm not involved in the research, so if anybody who is can correct me on anything in this post, I'd appreciate it) -- it is certainly very improbable with current knowledge and methods. Every bullet point above (which isn't an exhaustive list) represents a mountain to climb on hands and knees before an "inject-and-forget" end product could be developed.
Kudos for the critical thinking and forming a working theory from the knowledge you had, but unfortunately it does break down with some more specialized information.

I would up vote your answer but I don't have enough reputation.

Retroviral or lentiviral insertion doesn't have to be random - you could load your viral particles with the components of the CRISPR system, assuming the fix you want to make is small. You could also try this method.


text:
How to create a 3D density map of a system of varying number of particles?
I have a time-dependent system of varying number of particles (~100k particles). In fact, each particle represents an interaction in a 3D space with a particular strength. Thus, each particle has (X,Y,Z;w) which is the coordinate plus a weight factor between 0 and 1, showing the strength of interaction in that coordinate. Here http://pho.to/9Ztti I have uploaded 10 real-time snapshots of the system, with particles are represented as reddish small dots; the redder the dot, the stronger the interaction is.
The question is: how one can produce a 3D (spatial) density map of these particles, preferably in Matlab or Origin Pro 9 or ImageJ? Is there a way to, say, take the average of these images based on the red-color intensity in ImageJ?
Since I have the numerical data for particles (X,Y,Z;w) I can analyze those data in other software as well. So, you are welcome to suggest any other analytical approach/software
Any ideas/comments are welcome!

well, have you tried anything so far?

yep; ImajeJ and Origin Pro; both not successful.

R packages misc3d and rgl. The function image3d in misc3d does what you need and is very parametrizable via rgl (change the transparency, the view angle, axes, etc...). I used it with fairly big arrays (~10000000 data points/plots) and it produced great 3D density plots.
Both R (e.g. package biOps) and Matlab (image processing toolbox) have very powerful tools for image analysis if you need to get for example RBG levels in your plots but as far as I understood, you have the 3D arrays containing the interaction values, right?
Matlab proposes similar tools if you prefer Matlab (don't remember the exact functions) over R and both will require a fair amount of RAM as the data must be loaded in the environment.
As your system is time dependent you can also create movies fairly easily if you wish so (e.g. rgl's movie3d function).
Here a quick example of a 3D density plot:

Yep; you're right. I have the arrays of $x$ , $y$ , and $z$, and $w$ for the interactions locations and strength.

Ok, then it is quite straightforward to make such plots using those functions.

Well, I installed R , misc3d and rgl packages. But, to use image3d, one needs a "3 dimensional data array". My collection of $(X,Y,Z)$s makes a 2D array.  Should I convert it to 3D??? and how??

@deeep how is a collection of (X,Y,Z) 2D?

Well, here is the collection of my $(X,Y,Z)$s:
$$x_{1@t1} \quad y_{1@t1} \quad z_{1@t1}$$
$$x_{2@t1} \quad y_{2@t1} \quad z_{2@t1}$$
$$...$$
$$x_{N@t1} \quad y_{N@t1} \quad z_{N@t1}$$
$$--------------$$
$$x_{1@t2} \quad y_{1@t2} \quad z_{1@t2}$$
$$x_{2@t2} \quad y_{2@t2} \quad z_{2@t2}$$
$$...$$
$$x_{M@t2} \quad y_{M@t2} \quad z_{M@t2}$$
$$--------------$$
$$.$$
$$.$$
Where $t1$ refers to time 1, $t2$ time 2, etc. Also $N$ is the number of particles (=interactions) at time 1, $M$ number of particles at time 2, and so on.
To me this is a 2D array, like in Matlab.

@deeep I see. To convert that to a 3D matrix you can use your X,Y,Z coordinates to map the w into a 3D matrix. For example a 3D matrix M@t1 (casted using array() and of the size of your entire space) will contain the value $M(X_1,Y_1,Z_1)=w_1$, $M(X_2,Y_2,Z_2)=w_2$ ... $M(X_N,Y_N,Z_N)=w_N$ and I guess 0 for all values not mapped by any particles. I guess the assignment M(C)=w would work with C being your coordinate matrix @t1. Once this done, you can call the function image3d(M,x,y,z) with x,y,z being the vectors $x={x_1,...,x_N}$ and so on. You will need to create $t$ 3D matrices.

@deeep if you need more help we might chat instead of using the comment section. See https://chat.stackoverflow.com/. You will need 20 reputation points though. Also you might want to shoot me an email with say the data @ t1 so I can make a R script that would do that and so you have an actual example using your data.

Thank you! Like you said chat is not an option for me at this point. I dont have enough reputation. I'll send you the data.

@deeep ok see me my profile.

Cagliari2005, I was able to create a 2D array (=matrix) $N$ x $3$ of N tuples (x,y,z) with the following piece of code (I'm pretty sure there must be a much neater and cleverer way to do so, but I am not familiar enough w/ R). Yet, was not able to convert it to a 3D array using weight factors $w$ .
`df <- read.table("xyzw.dat")
x <- array(df$V1)
y <- array(df$V2)
z <- array(df$V3)
w <- array(df$V4)
ar2d <- array(0,dim=c(N,3))
for (i in 1:N)
{
ar2d[i,1] <- x[i]
ar2d[i,2] <- y[i]
ar2d[i,3] <- z[i]
}`
I sent you an email yesterday w/ the data @ times 1 to 10.

deleted my previous comment as I thought I found a direct solution but no. You will need to estimate a weighted kernel. I am not certain as how to exactly incorporate the  weight. pythonist answer is more complete than mine.

So, suppose that they are all equally weighted, i.e. there is no weight function. Then how should I make a 3D array from $(X,Y,Z)$s?

One approach: fit a kernel density estimator to the observed coordinates $\{ (X_i,Y_i,Z_i) \}$ and color by density: https://stackoverflow.com/questions/25286811/how-to-plot-a-3d-density-map-in-python-with-matplotlib/25354417#25354417
Incorporating the weights $w$ of each observation is a bit trickier, but there's code to do this: https://stackoverflow.com/questions/27623919/weighted-gaussian-kernel-density-estimation-in-python/27623920#27623920 , which you can swap in instead of stats.gaussian_kde.

Trying to analyze that much data in ImageJ seems likely to end in frustration. Matlab is probably a more productive angle. Personally, I would use Python. Specifically, the numpy module. Try looking into the histogramdd function in numpy. It might be able to accomplish what you're after.