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Cleavage of RNA by restriction enzymes?
Six restriction enzymes discussed in Sequence-specific cleavage of RNA by Type II restriction enzymes (Murray et al.) have the ability to detect and cut RNA strands with that enzyme's recognition sequence.
As you know, restriction enzymes come from a system carried by some bacteria referred to as a restriction-modification system.
With this fact in mind while reading the paper above, I wondered how the bacteria carrying one of these six systems protects it's own RNA from restriction. Do the corresponding methyltranferase in each system methylate DNA as well as RNA? Would this not greatly sacrifice gene expression rates seeing as the methyltranferase surely cannot methylate all the RNA sequences being produced?
Perhaps I misunderstood the paper somehow. Could it be only in some circumstances outside the cell that these restriction enzymes have this unique ability?

When you take a look at Table 2 in the article, the activity to cleave RNA–DNA substrates is quite low. This means you should be careful to think that the enzymes actually cut RNA–DNA substrate in bacteria. The activity could be just artificial and may not happen physiologically.

This paper found that these enzymes recognize RNA:DNA heteroduplexes. Such duplexes are unlikely to be encountered in vivo. They are present when DNA is primed for replication, but these duplexes are relatively short and thus are less likely to randomly contain a recognition sequence. Furthermore, if the recognition sequence is found in the primer, the gDNA will be methylated specifically to protect it from degradation. RNA:DNA duplexes are also found during transcription, but they are also short and the gDNA would be methylated. Additionally, the transcription bubble where the heteroduplex forms is protected by RNA polymerase, which subsequently displaces the transcript from the gDNA as it leaves the elongating complex.
It's also important to note that this paper found that these enzymes don't cleave RNA:DNA as well as they do DNA:DNA duplexes and these results occurred under experimental conditions with relatively high concentrations of enzyme and substrate. The lower catalytic efficiency is likely due to lower binding affinity, which could be caused by:

presence of uracil in RNA (this was explicitly mentioned in the paper)
2'-OH presenting a steric barrier
helix shape (RNA tends to adopt an A-form helix)

Further into the paper they discuss the ability of these enzymes (specifically TaqI and HaeIII I believe) to also cleave RNA alone.

@CDB Duplex RNA? I shall read the paper later and delete my answer if it's incorrect.

Again, I could very easily be wrong, but that is my understanding of the paper. Feel free to correct me.

@CDB Are you referring to the paper by Molloy and Symons that was discussed in the introduction? TaqI and HaeIII were found to cleave the RNA strand in RNA:DNA heteroduplexes. I skimmed the paper and didn't find any mention of cleavage of ssRNA or RNA:RNA homoduplexes.

RNA:DNA heteroduplexes are encountered in vivo fairly regularly during replication. The RNA primer created at the beginning of DNA replication must be removed, and this is done with RNAse H, an enzyme that cleaves the RNA strand of RNA:DNA double helices. Though the abstract seems to indicate that these enzymes are cutting both RNA and DNA strands, so they would not be like RNAse H.

@user137 That's a good point about primers, but they are short and less likely to contain the recognition sequence and, if they did, the DNA strand would be methylated to prevent gDNA digestion.

@canadianer It would appear that you are correct. I must say though, this paper really confused me as to the results of the experiment. However, now I have another question. Perhaps I should post this as a whole new question, but I wonder why these restriction enzymes cannot cleave duplex RNA. I understand why uracil would present a problem, however HaeIII has a recognition sequence of GGCC, so nothing would really change with that... maybe something to do with the different RNA ribose backbone?

@CDB I don't know that they can't cleave dsRNA, it's just that this paper doesn't talk about it. I would expect that the 2'-OH presents a steric barrier since these enzymes evolved to recognize dsDNA. It seems from this paper that RNA:DNA duplexes lower the binding interaction so that, with RNA:RNA duplexes, the interaction may not be strong enough for efficient catalysis.

@CDB The shape of the helix may play a role as well, RNA double helices tend to favor the A form of the helix, while DNA double helices tend to favor the B form. The A form might be just different enough that the binding sites don't like it.

As to why they don't recognize RNA-DNA heteroduplexes (which are present during transcription, for example), I suspect that the methylation which protects bacterial genomic dsDNA (see the DNA modifying enzyme section of this Columbia University lecture for more info) also protects RNA-DNA hybrids, as the genomic DNA would still be methylated.
Note that most of the enzymes featured in the paper are listed by New England Biolabs as methylation sensitive (for example: AvaII, BanI, HinfI, TaqI).
@canadianer and @user137 provide a host of reasons that these restriction enzymes cannot cleave ds/ssRNA in the comments on canadianer's answer (different helix form, different interaction strengths between strands).

RNA-DNA heteroduplexes (which are present during transcription) are transient and are unlikely to be targeted by either RNAse-H or these restriction enzymes.

True, but it also doesn't take very long for a restriction endonuclease to cleave dsDNA

I just modified my comment. If such heteroduplexes really formed then the RNA will be first degraded by RNAse-H which is abundant. That, however does not happen

Yes, that was basically canadianer's answer. I wanted to provide additional insight based on bacterial self-methylation of its restriction enzyme recognition sites

@WYSIWYG Maybe this justification is clearer. Q: Why don't bacterial restriction enzymes degrade RNA? canadianer: That paper talks about RNA-DNA heteroduplexes, which are rare in vivo. me: Also, a RNA-DNA heteroduplex would likely not be recognized for the same reason that bacterial genomic DNA isn't recognized.

I imagine that the RNA:DNA duplex formed during transcription would be protected from  degradation by RNA polymerase. Assuming that the RNA doesn't reanneal to the template strand after it leaves RNAP, the duplex is only ~10 nts.


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Question about contents of small bowel
I know, or at least I think I do, that the contents of the stomach are called chyme and that it is acidic.  What are the contents of the small bowel called and is it acidic?

I think its still called Chyme:

After hours of mechanical and chemical digestion, food has been
  reduced into chyme. As particles of food become small enough, they are
  passed out of the stomach at regular intervals into the small
  intestine, which stimulates the pancreas to release fluid containing a
  high concentration of bicarbonate. This fluid neutralizes the gastric
  juices, which can damage the lining of the intestine, resulting in
  duodenal ulcer. Other secretions from the pancreas, gallbladder,
  liver, and glands in the intestinal wall help in digestion.
When food particles are sufficiently reduced in size and composition,
  they are absorbed by the intestinal wall and transported to the
  bloodstream. Some food material is passed from the small intestine to
  the large intestine. In the large intestine, bacteria break down
  proteins and starches in chyme that were not digested fully in the
  small intestine.

http://en.wikipedia.org/wiki/Chyme

source: Stack Exchange

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

sort: votes


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How does myopia actually work?
This is potentially more or less a question about optics, but I've never been truly satisfied with any explanation that I've been given about Myopia. In fact, I almost can't even believe it. There are a million different versions of this diagram:

I understand that images of things could appear blurry when those things are focused in front of the retina, but then what discriminates between near and far things? Shouldn't everything be blurry? What exactly is different about this image when the thing being viewed is in close proximity to the eye?

The image you gave is not clear because it does not show the fact that the divergence pattern of light from a close object is different from the divergence pattern of light from a distant object.

Light rays from a close object (first image) diverge, and therefore they are in focus for the myopic eye.
Light rays from a distant object (second image) is approximately parallel, and therefore they are not in focus for the myopic eye. The lens corrects for this inability to focus and allows the distant object to become in focus.
Also note that the myopic person is still capable of focusing on close objects despite the lens because the lenses are still capable of dynamic adjustment, but less so than a person with perfect eyesight. You can test this by focusing on a near object, then putting on your glasses. The object should be initially out of focus, and then become in focus as the eye lenses adjust to the distance.
Myopia/presbyopia is fundamentally an issue of the focal range of the eye becoming limited to a specific range. If the ability of the eye lenses to dynamically adjust is further weakened, it may require progressive lenses or bifocals to correct the issue.

This is a great answer! I read originally that it was because of the angle of incidence of the photon and I didn't believe it for the following reason: if a 4m tall statue stands a large distance away from me, it's blurry. If I have a 10cm version of the same statue and I hold it at a distance away from me so it appears the same height as the statue in the distance, it's still sharp. In that scenario, the light from both statues is parallel(or so I thought) but NOW it makes sense, since the incident photons are still going to be at an angle because they're coming from ALL points of the statue.

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Stable and strong promoter?
I need a mammalian promoter that will maintain stable expression through differentiation.
I was originally planning to employ UbC for this specific project, however new information from a different experiment has come to light and now I need a promoter that has both extreme stability and high strength (as you know, UbC is renowned for it's very low expression rates).
Do any of you have suggestions? Perhaps I should look into a hybrid promoter of sorts...
Thank you,
CDB

I know the CMV promoter is pretty strong, not sure about its stability.

How about SV40?

is there any specificity for cell type or do you need a ubiquitous promoter?

@MattDMo In my experience, the SV40 promoter is at least 10 fold weaker than the CMV and only expresses for 4 - 5 days. I haven't seen how long CMV expresses for.

@user137 Yes, I have looked into CMV a little, it has low stability in quite a few cell types though.

@MattDMo I will look into that.

@RoverEye It must be ubiquitous (might I add that this requirement has been quite a pain?)

beta-actin promoter?

While looking into your suggestions I came across two promising candidates. Does anyone have experience with PGK-1 or EF1a? How stable are they and what is their expression rate?

HSV-TK promoter is also quite good. Never used PGK-1 and EF1a

There seems to be quite an amount of resources to help OP.
Addgene has a page on topic with list and description of common promoters usable in variety of organisms: Plasmids 101: The Promoter Region
Experimental biophysics textbook mentions some useful promoters as well, or this review.
Surprisingly, there has been some quantitative analysis of promoter strength: Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter, as well as effort toward stronger synthetic (version of CMV) Synthetic design of strong promoters
My conclusion is that either viral, or CAG (based on chicken actin) promoters might be useful candidates. But one cannot expect ubiquitous and even expression in various tissues/cells types without fine-tuning expression cassette.


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White blood: cells concentration
Anyone knows of a table with average concentration that can be found in  white blood?
Something like:

Neutrophils - 80%
Mast cells - ?%
Dendritic cells - ?%
B cells - ?%
Helper T cells - ?%
Killer T cells - ?%
Natural killers - ?%
Others - (whatever is left)
(the sum should be 100%, of course :))

Also: are helper T cells and killer T cells visually different? I can only find pictures of T cells, but not of each. I am also unable to find pictures of natural killers. - Thank you!

You mean the concentration of these cells in the blood of "normal" and healthy people?

Wikipedia to the rescue!

@Luigi, I have looked up wikipedia. It does not discriminate lymphocytes nor does its source.

Here are some figures from Cellular and Molecular Immunology, 8th Edition:

Hopefully they're helpful in some way.

Perfect. That's exactly what I needed - btw, do you know if (and why) it is so rare to find photos of helper T cells, killer T cells and B cells? (I can only seem to find pictures of the lymphocyte class ...)

I'm a little confused as to what you mean by photos. Like bright field, scanning electron, transmission electron, etc?

Yes, pictures of Th, Tc and B cells... I can only find picture of generic lymphocytes. (I am not a biologist!) ps: I know Th,Tc,B,etc are all lymphocytes, but I would like to have pictures of each, if those exist. Do you think they do?


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Why are Oxyuranus snake species named Taipan?
It is interesting, why are Oxyuranus species called Taipan. The snakes are Australian but taipan looks like of Chinese origin word (it means big shot - important person).

An answer is found at the Wikipedia page for Taipan:

The common name, taipan, was coined by anthropologist Donald Thomson after the word used by the Wik-Mungkan Aboriginal people of central Cape York Peninsula, Queensland, Australia.

This passage is citing Sutton. 1995. Wik Ngathan Dictionary as support. I cannot evaluate the truth in this statement though.
For another reference see McKnight. 1981. The Wik-mungkan concept Nganwi: a study of mystical power and sickness in an Australian tribe. Bijdragen tot de Taal-, Land- en Volkenkunde 137, which refers to Taipan as the Rainbow serpent (an Aboriginal mythical creature) of the Wik-Mungkan tribe.
Even more folklore is found in McNamee. 2000. The Serpent's Tale: Snakes in Folklore and Literature in "Taipan the snake and the blue-tongued lizard".


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Would somebody born 'reversed' (e.g. heart on their right side, etc.) be completely healthy?
By reversed I mean their body is a complete mirror image of a normal human's.

Yes, such a conditions exists. It is called "situs inversus" (literally "inverted sites"). All major organs are placed on the opposite site, the condition is relatively rare with an incidence rate of 1:10.000. There are some even rarer forms occuring, when the organs are flipped, but the heart is still on the left side (levocardia) as opposed to the case when it is also on the other side (dextrocardia).
While some  of the patients are phenotypically normal (besides having their organs on the "wrong" side), congenital heart disease and ciliary disorders (also known as Kartagener syndrome) can occur. See the linked paper below for an overview.

For more information see here and here and the article:

Situs inversus and ciliary abnormalities: 20 years later, what is the
connection?

They're not always normal and healthy, situs inversus is related to primary ciliary dyskinesia: http://en.wikipedia.org/wiki/Primary_ciliary_dyskinesia

@CactusWoman I have updated the article, thanks for the critics.

And they tend to be sterile.  If the handedness of their MTOC is reversed then the spermatozoa tails cannot beat properly for swimming. Most XY's with situs inversus are identified via fertility clinics.


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rRNA colony PCR amplification not working
We used some universal primers to amplify rDNA in a certain isolated bacterial specie. The problem is that rDNA PCR is not amplifying.
Primers were working well in other strains of same bacterial specie.
Do you know what could be happening? Maybe strain-specific PCR inhibitors? This strain was successfully amplified using ERIC PCR.


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Why are there more stomatal openings on the lower surface of a dicot leaf?
This causes more transpiration to occur from lower leaf surface. What's the exact reason for why are there more stomatal openings on the lower surface of a dicot leaf?

I believe water conservation is the main reason. I'll try to write up a proper answer when I have time

@CactusWoman Could you please post an answer if you have time now? :)

Firstly, it is not necessary that all dicots have stomata on their lower surface of their leaves. The lotus Nelumbo nucifera has its stomata on its upper surface, due to the lower surface of its leaves being in contact with water, and therefore unable to transpire effectively.
The reason that stomata are usually on the lower surface has been analysed in this paper, which rejects the commonly held hypothesis that stomata appear on the lower surface of leaves (hypostomatous) as a response to dryness, by citing that hypostomatous leaves are relatively less common in dry environments.

The paper then analyses the correlation observed between parameters of leaves and their stomatal locations.

By using a number of computational models (which conclude that given the set of assumptions in the paper, leaves should not generally be hypostomatous), the paper addresses the faults of the model and concludes that there is no one single reason why leaves are usually hypostomatous, and then brings up a couple other possibilities that may help in explaining the majority of plants being hypostomatous.


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How many NOD like receptors in Human?
This is pretty specific question maybe. Anybody have an estimate? For Toll Like Receptors there are something like 10...
http://www.jbc.org/content/276/4/2551.long
I'm only finding NOD1 and NOD2 => only 2?

The following wikipedia article has an aggregation of some of the different members of the NOD-like receptor family, and the following journal article goes over the nomenclature for the NLR family, and I believe will assist you.

This review 22 proteins in the NOD like human repetoire. It was published in 2013...
The families are broken down into 9 general groups according to their domain composition in Figure 1 from that review.  Most of them are not named "NOD".


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

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

what do you mean by transform bacteria?

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


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Terminology for inefficacy of selection on recessive alleles
I am wondering is there some proper terminology which is used to say that deleterious recessive alleles might be able to hide, reducing the the efficacy of selection, in diploid organisms/chromosomes.
I was thinking about Y chromosome linked mutation and their inability to hide from purging by selection behind other alleles by being recessive... perhaps something like recessive sheltering? e.g. "In the Y chromosome mutations are more easily purged because recessive sheltering does not occur" ?

I don't think you require a special term. In this context recessive implicitly connotes hidden, as in the genotype is hidden  because the phenotype is masked (a.k.a. known as wild-type).

I think "penetrance" (http://en.wikipedia.org/wiki/Penetrance) might be the term you're seeking

No, penetrance is the fraction of homozygous mutants that display the loss of function phenotype--for recessive alleles.

I think recessive refuge is the term you are looking for (this is the best link I could find, sorry: https://quizlet.com/4176029/bio-experiment-1-and-2-flash-cards/)

Masked allele is a term that is sometimes used for recessive alleles, and it should be suitable to the situation you describe. A common phrasing could be; "The wild type allele is masking the expression of the deleterious allele X.".
For your particular example you could use:

Deleterious mutations on the Y chromosome are more easily purged since they cannot be masked by alleles on a homologous chromosome.

An example can also be found in the abstract to Otto & Goldstein (1992):

With two copies of every gene, a diploid organism is able to mask recessive deleterious mutations. In this paper we present the analysis of a two-locus model designed to determine when the masking of deleterious alleles favors the evolution of a dominant diploid phase in organisms that alternate between haploid and diploid phases ("alternation of generations").


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Dominant and recessive epistasis
Can anyone clarify my confusion about that the epistasis seen in "Labradors , an example of recessive or dominant epistasis? ?
 I am not getting definite results . It's dominant somewhere and recessive in some.:(
May anyone provide me with some definite sources??
Thank you! !:)

unclear what you're asking

@rg255 ,I just want to ask -'is it an example of recessive or dominant epistasis? '   or could you please provide me with some definite sources. ..

what epistasis seen in Labradors? you need to be far more specific (did you miss something??)

I agree that the question is unclear. I personally don't know the example of the labrador and would need a reference (or a description from you) to talk about this specific case study.
The following tables are displaying all possible kind of interactions (in a haploid and in a diploid) of two bi-allelic loci. Hope that helps! source (wiki)
For Haploids (the concept of dominant epistasis does not apply)

For Diploids

it's given in Campbell biology 9th edition. ..  its like... there , in theory its mentioned E/e is epistatic over black or brown colour allele and in diagram it's given acc. To that 'e'... i. e its an example of recessive epistasis. ..   so I am pretty confused that is it an example of recessive or dominant epistasis?     Because our teacher told that its an example of dominant epistasis! !:(         anyways, thanks for the extra info. .. I didn't know this much about epistasis; )

Ok. If my answer answered your question you can check it. If not: knowing that your question will likely soon get closed. If you manage to repeat the text (and figures) of the campbell to clarify the question in time, you may get better answers. The post can also be reopened afterward. Good luck.


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how to find accurately the closest species to my plant species?
I'm working on some bioinformatic analysis of a non-model woody plant within the family with least information. So, I'm looking for a closest species to my plant. Any suggestion would be highly appreciated. Also, It will be great if I have know about the divergence time (? million year) between two species. Is there any documents or website to address this issue? Thanks

Please [edit] your question and explain what data you have. What species is this?  Do you have its entire genome? Specific genes? Are there any sequences for this species or no sequences at all?

If you know the species name, you can search TreeBase to find previously published phylogenetic trees which will point you towards close relatives to your species. Depending on how obscure your taxon is, though, you might not find much.

Maybe you could get some information from the Angiosperm Phylogeny Group:
http://www.mobot.org/MOBOT/research/APweb/
They even have a tree where model organisms are highlighted:
http://www.mobot.org/MOBOT/research/APweb/trees/modeltreemap.html

You can try http://timetree.org/ to get the divergence time if you already have the names of the taxa.


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What recovers normal polarisation after hyperpolarisation?
I have been taught that a $\ce{Na+/~K+}$  pump helps to recover normal polarisation after-hyperpolarisation in neurones. I could not find out how it does that, since I've also been taught that such a pump moves $\ce{3Na+}$  out of the cell and $\ce{2K+}$  into the cell. That implies that the potential can only get more negative. How does this work?
My hypothesis was that the potential 'leaks' out and recovers the 70 mV that way. I couldn't verify that, however.

Can't give a full comment at the moment, but... Na+ and K+ have different electrochemical equilibriums, and in addition to the Sodium-Potassium Pump there are many porins that act as passive diffusion routes to re-establish the cell's preferred equilibrium.

Na/K ATPase will pump as long as it is energetically favourable. At about -70mV ATPase work is balanced by leackage

Remember that the action potential gets more positive in the first place, so increasing positivity is achievable. Net Na+ movement into the cell makes the potential more positive. This occurs as the Na+ gate (right on the image below) are open. The key message is that the membrane can move charge to cause an increase in either positive and negative potential.

Imagine one side becomes more negative. The Na+ diffusion will correct this to reach an equilibrium around 3 to 4 milliseconds (ms) after the stimulus to reach the resting potential
 (as alluded to my @MCM in the comments).
There are some great animations demonstrating this principle on the University of Bristol's website. They clearly show how positive charge can be conferred over the membrane.
A (now deleted) comment linked to the below image that shows the potential and when the gates are opened and closed. I would still go to the bristol website too to see it in action, but this figure is a quick go to once you get your head around the timing of ion flux.

As with most biology, it is a little more complicated than that overly simple model. There are entire books on how neurones control their charges.

Note: The key terminology is somewhat muddled and there doesn't seem to be a standard term. I have seen this "recovery" phase called undershoot, overshoot (and overshoot rather unhelpfully also refers to another part of the action potential), the refractory period, and discussed as part of hyperpolarization. The go to term is afterpolarisation if you want to research this more thoroughly.


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What is the location of the Hypoglossal nerve?
I kind of know where the hypoglossal nerve is located when I look at the diagram, but I'd like to know how far is the nerve from the skin and where is the closest area to the skin before and right after it's branching?
Is there any video or schema showing the location of the Hypoglossal nerve relative to skin and not the skeleton?
From this pic. I can't really tell the closest location of being able to detect the nerve near the skin.

I found a video of a surgery on youtube where the surgeon locates both the facial nerve and the hypoglossal nerve. It is a surgery so I "warn" you before clicking the link. https://www.youtube.com/watch?v=_5brqIa_KLk

The following image of a cadaver shows the hypoglossal highlighted:

 Source: StudyBlue
You can see the flap of skin/muscle that has been removed to get an understanding of the thickness of tissues separating the nerve from outside the body.
Additionally, here is an image showing a person receiving an operation. You can see the relative depth of the nerve fairly well:

 Source: Cambridge University Press

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


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Why are there ghost images of objects just out of focus
I have observed an interesting phenomena with my vision lately. I just think I have never reflected over this before but it might always have been this way.
I am nearsighted and have no problem with double vision as long as an object is in focus, either with or without glasses.
However when I take my glasses off and look at, e.g. my phone screen, and push it slowly just out of focus, there is a phase where multiple distorted weak ghost images appear before everything just becomes a more Gaussian like blur. It is especially clear with bright lines on a dark surface.
I do not believe that there is anything else wrong with my eyes, since as soon as an object is in a range where I can focus on it, all ghosting disappears.
I am interested in knowing if anyone else observes this.
But more interesting is what are the possible optical properties of the eye that contributes to this, or is it a property of how our brain processes the input from the eyes.

Could you generalize this question? Personal questions are discouraged here as this site is meant to answer questions of value to the community. If you can show this phenomenon is not only applicable to you, it is of interest here. Note I am happy to look into this :) In addition, personal medical questions are discouraged as we strongly urge folks to seek professional help. Until edited, therefore, I vote toclose this question. A +1 for the exciting topic though. If you reply to this post, ping me by using @AliceD, please.

I think it is a general question about the phenomenon. I just had to describe what I have observed. I am not looking for a diagnosis, I want to know the reason for what I have observed

@AliceD I agree with the OP that this is not a personal medical question but rather one asking about how the eye itself works.

@terdon agreed, but its too specific slash anecdotal to my taste

@AliceD All interesting questions and later scientific progress starts with one persons observation. This is not the same as Anecdotal evidence, since I do not claim that caise A leads to effect B. I an just asking for the reason why an observation is as it is.

@AxelOmega - yes of course, the question is whether that sort of question fits this site . I started a discussion on meta actually


text:
Is there an absolute minimum intensity level to the stimuli we can perceive?
By stimuli that we can perceive, I mean what our five senses can perceive.
Is there an absolute minimum for humans, or can we "train" ourselves to perceive stimuli at lower intensity?
And if there is an absolute minimum intensity, do we know what its value is?

Why the downvote? Downvoting without commenting is useless.

downvoting without comment is the best.

i think absolute lower limit is defined by chemical bonds energy and activation energy of enzymes. For eye, for example, lowest energy of photons that produce visual response is somewhere around 750nm

@aandreev - The title mentions 'perception' and Matt asks about training as well. Chemical bonds are far away from perception, and cannot be changed with training. This question is about the perceptual level I guess.

You should specify what kind of perception you are interested in. Though the voltage threshold for action potential may be more or less same for all neurons, the different neuromodulators and other modulatory neurons (interneurons) would affect different neural paths differently.

@AliceD I think any discussion about votes should go on meta. Also, perception has very defined (in some known cases) chemical&physical basis. Leaving it out and talking only about what people measure/observe is tangential to the question IMHO. Physics of transduction is the ultimate barrier for perception.

@aandreev - we might continue this on chat, but just shortly - eventually the way to measure perception thresholds is by asking subjects if they perceive a certain threshold stimulus yes/no. Going to the test tube isn't perception and more importantly, the ultimate bottleneck determining the threshold isn't the question I think?

@AliceD chat is fine. My line of thought is following: between cognitive perception (or any other observable manifestation of excitation by stimulus) there are several layers of amplification and inhibition. Each of which might be optimized (in principle). The only true limit to my taste is around energy of chemical interactions. Or maybe I am off the course of OP's thoughts

@aandreev,  I would consider answering the question then, it sounds plausible. Bio.SE Often answers questions, but often lacks multiple answers. Mine hasn't been accepted.

There are limits to what a sensory system can detect, which is called the detection threshold. To determine the detection threshold psychophysical methods can be used. A straightforward way to determine the detection threshold is with a yes/no task, where the subject receives stimuli with various intensities. An arbitrary point, mostly the 50% correct-rate, is then defined as the detection threshold. At this point, the subject correctly detects the stimulus 50% of the times. The response curve in a psychophysical task typically takes the shape of a cumulative function such as the one shown in Fig. 1.
Hence, the detection threshold is an arbitrary point, because people are not machines and show variability in their decisions. The detection limit of, e.g., electronic devices is much more precisely defined. The exact values of the detection limits depend on the exact stimulus (visual, tactile etc.) and depend highly on the exact stimulus. For example, in the visual domain the detection limit of light depends on the color, the location in the retina tested, dark adaptation etc etc, and in the tactile domain static pressure stimuli have a different threshold than vibratory, different body parts have different thresholds etc. etc.

Fig. 1. Psychometric curve showing 50% threshold of a visual stimulus. source: Webvision
Training to lower the detection threshold (i.e. improve detection limits) is indeed possible (Sterr et al., 1998).
Reference
Sterr et al., J Neurosci (1998), 18: 4417-23


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How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation?
In this link, it states:

It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).

I do not understand how polyadenylation protects the intracellular RNA from ribonuclease. I always thought that polyadenylation was a way to mark RNA for degradation, not protect it from degradation. Perhaps it is speaking of protection from exoribonuclease only and not endoribonuclease?
Can someone explain this?

Actually, whether polyadenylation protects an mRNA or makes it susceptible to degradation depends on the organism. From Dreyfus and Régnier 2002:

In eukaryotes, poly(A) tails usually act as stabilizers of intact mRNAs, whereas in E. coli they serve to accelerate the destruction of fragments.

This is due to different protection mechanisms in prokaryotes and eukaryotes:

The Poly(A) Binding Protein (PABP) inhibits deadenylation in mammalian cell-free assays. Although poly(A) binding proteins exist in E. coli as well and although they can protect poly(A) tails against PNPase in vitro (Feng et al., 2001), they may be unable to exert a significant protection in vivo because poly(A) tails never grow long enough to enable them to bind.

Important to note is that bacterial mRNA degradation usually starts internally, in contrast to eukaryotic mRNA degradation which happens (exonucleotically?):

As noted above, another distinctive feature of bacteria is the fact that polyadenylation usually affects the degradation of fragments only, because the initial attack on most intact mRNAs is endonucleolytic.

All of these quotes come from the review I referenced at the top of my answer, I recommend reading it as it's very comprehensive (and interesting).

According to my book Molecular Biology Principles of Genome Function by Craig et al, eukaryotic RNA degradation does not have an initiation, as in bacteria where pyrophoasphate hydrolase hydrolyses the 5'-triphosphate to 5'-monophosphate, and is therefore the initiatior.
In eukaryotes the polyA-tail is shortened by a deadenylase enzyme complex which contains a 3'to 5' exonuclease called CCR4. But deadenylation of polyA-tail doesn't necessesarily need to lead to degradation since it is reversible by post-translational readenylation.
Poly A tail protects the mRNA by not letting the nucleases reach the mRNA itself. As long as poly A tail is degraded, its just fine, since it can readenylate back again. The figure below shows the degradation of mRNA in eukaryotes, which can be either in 5' to 3' direction or 3' to 5' direction.

What you are thinking of is ubiquitination of proteins, which is a post-translational process which can mark the proteins for degradation.


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What is the difference between a mechanistic and a statistical predictive model?
The simplest description of the difference between these two approaches that I have found are on this site who summarise the difference as:
Mechanistic model: a hypothesized relationship between the variables in the data set where the nature of the relationship is specified in terms of the biological processes that are thought to have given rise to the data. The parameters in the mechanistic model all have biological definitions and so they can be measured independently of the data set referenced above.
Phenomenological/Statistical model: a hypothesized relationship between the variables in the data set, where the relationship seeks only to best describe the data.
Could someone exemplify this difference with a short example. I have used and understand the principals of a statistical model (multiple regression etc) but haven't come across any simplistic examples of a mechanistic model and I don't understand what the difference would be in practice.
Edit: I am leaving the question open for a week to see if anyone wants to create a very small 'MWE' of the two types to illustrate what the difference would look like in practice, if not I will accept Memmings answer

If you are interested in mechanistic models a great resource comes from books on statistical thermodynamics and in general anything coming out of physically motivated biological research. A good reference is "Physical Biology of the Cell" which is supposed to be a physics driven equivalent to the Alberts et al "Molecular Biology of the Cell" book.

The question is interesting (+1) and on-topic here. However, I think that you might want to consider asking such question on Philosophy.SE.

Mechanistic model answers the how question. These models are usually biophysically detailed, and designed to be causal. Say you discovered a linear relation between blood pressure drug and heart rate. This would be a statistical model. It doesn't tell you how the two are related biophysically. One could build a detailed model that describes intermediate processes from the drug entering the system, to binding to receptors, and modulating levels of hormones, and acting as a signal to the heart rate modulation system. This model would have more parameters, and if it predicts the phenomena and generalizes well, then it might be a good approximation of the system. Moreover, it generates hypotheses and is more interpretable.
That being said, I do not think the two concepts are mutually exclusive. Some mechanistic/biophysical models can also be statistical at the same time. It's a matter of having enough data and constraints to be able to fit the model or not.

Thank you for your answer. So for the mechanistic model lets say that the processes you mentioned are the only ones (enter the system, bind to receptor, modulate levels of hormones, signal to the heart rate modulation system). So for the first stage the mechanistic model would take into account amount of drug and work out absorption relating to the concentration gradient? While a statistical approach would look at marginal increases in drug absorption given a set increase in drug administered?

@PaulBarr I think you are missing the point. If you had the appropriate data, you can always use statistics to answer the how question. Mechanistic models sometimes don't have that luxury, and are pieced together from partial knowledge from here and there. Statistical modeling exploits the observed variables, in my example, those would be only the drug administration and the heart rate.

I understand that you can use statistics to answer how something works. Specifically I don't understand the difference in how the model would actually look in practice, when it has been coded in R etc. As a side question are you saying mechanistic models work best when there is partial knowledge, it appears intuitive to me that the opposite would be true. Thanks for your help

@PaulBarr Usually, you can simulate the mechanistic model, but often difficult to fit its parameters from data. To build the mechanistic model, it is often necessary to make assumptions about the dynamics and parameters which are not strongly supported by data.

Thank you, this is really helpful. Could you add to your answer a very short MWE of what two models may look like in practice at the actual code level?

@PaulBarr I can't write MWE for those, since mechanistic models are usually complex...also I don't have the time. Sorry.

No worries, I'm not looking for an actual realistic model I just would like to see the difference illustrated if possible. I will leave the question open for a week and if no-one is keen Ill accept your answer. Thanks again


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Why Insect bites are itchy rather than pain?
i don't understand if some thing bites or hurt we feel pain, but its differ for insect bites, why so?

maybe because those bites cause allergic reaction

Has a wasp ever stung you? It is quite painful

You're more likely to have an allergic reaction if you're stung by an insect. The reaction can be classed as:
Minor localised reaction – this is normal and doesn't require allergy testing, although the affected area will often be painful for
  a few days
large localised reaction (LLR) – this can cause other symptoms, such as swelling, itching and a rash
systemic reaction (SR) – this often requires immediate medical attention because it can cause a potentially life-threatening allergic
  reaction (anaphylaxis)

Taken from : http://www.nhs.uk/Conditions/Bites-insect/Pages/Symptoms.aspx
You can read up on this here:
http://en.wikipedia.org/wiki/Inflammation
http://primer.crohn.ie/the-inflammatory-response
For a more detailed look, I would suggest papers like this:
Loza, Matthew J., et al. "Assembly of inflammation-related genes for pathway-focused genetic analysis." PLoS One 2.10 (2007): e1035.
or a good immunology textbook.


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Feeling of spicy
I have done a survey on my friend
When everytime they eat something spicy, They will eat ice or drink icy water. First, Mostly they feel nothing but a cool sensation. However when they finished, they feel spicy again.
Sometimes, they will drink warm mill or hot coco. Now everybody feel extremely spicy at first and less spicy afterwards
My question is:
1) Why don't I feel spicy when drinking icy water or eat ice?
2) Why do I feel spicy after the action at 1) ?
3) Why do I feel extremely spicy when drinking warm milk or hot coco but less spicy afterwards?

What kind of spice? Chili-based flavours?

Yes, mostly chili and curry

The spicy feeling essentially is the feeling of heat and pain. It is caused by the molecule Capsaicin (https://en.wikipedia.org/wiki/Capsaicin) binding to the ion channel TRPV1 (https://en.wikipedia.org/wiki/TRPV1), activating it.
You can temporarily get rid of the pain by cooling (as you would with any other injury) - hence the effect of ice.
Unfortunately, this does not get rid of the cause of the pain, i.e. the molecule bound to the ion channel. Capsaicin is not very water soluble, but only fat soluble. This is why drinking milk helps: it contains microdroplets of fat, which can solvate the Capsaicin, which then can get washed away from the "pain receptor".

What is cooling doing exactly to the perception here? Any references that would support your claim?

You can't really say pain.. These channels are sensitive to heat and are involved in temperature perception (also nociception). When capsaicin opens these channels you get the feeling of heat.

@WYSIWYG "nociception" is the encoding and processing of harmful stimuli in the nervous system, which, at a certain threshold, is interpreted as pain.

@MattDMo but TRPVs are also involved in normal temperature sensing and do not necessarily activate pain pathways.


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Why doesn't mitochondrial DNA accumulate damage over successive generations?
From what I recall, mitochondrial DNA is very susceptible to damage from oxidative stress because it is a site where free radicals are generated and their DNA isn't packed into chromatin like nucleic DNA is. How then is it possible that mitochondria can stay in-tact when it is repeatedly passed on to offspring?
I would have thought that an accumulation of errors would cause them to malfunction over time.

If it was the case that we were inheriting damaged mtDNA, we would be inheriting ageing from our parents which in itself is not advantageous in terms of evolution.Considering that the germline mitochondria is purely maternal, nature has evolved a way to switch off the mitochondria of oocytes, and keep it in a simple state, mainly to serve as a template. This template is essentially error free, as the levels of ROS generated, is very low.

Mutations in DNA (mitochondrial or nuclear) in most cells in the body can be harmful to the health of the individual, but will have no influence on the next generation. The genes which we pass onto the next generation are separated off during early development into special ‘germ line’ cells which form sperm and eggs. Great care is taken to minimise the risk of mutation to these genes – genes in germline cells act as a blue print for the next generation. This is essentially why aging is not heritable, and it is a system that works pretty well.
Research has uncovered a rather elegant solution to this problem – those mitochondria that will be passed to the next generation are maintained in an inactive state.Mitochondria are only inherited through the maternal line – every mitochondria in your body came from your mother, and this is true for most animal species. The mitochondria in sperm are generally discarded at some point prior to fertilisation.
Membrane electrical potential, a measure of the activity of the electron transport chain, was reduced in oocytes compared to both sperm and the surrounding tissue. Further, ROS production was 50- and 100-fold lower in the eggs of fruit flies and zebrafish respectively. Finally, they confirmed that oocyte mitochodria in both species exhibit a simpler structure, indicative of reduced activity. So, it seems that in both fish and flies, the mitochondria in egg cells represent little more than a blueprint, ready to be passed on to the next generation error-free. By deactivating ovarian mitochondria, the fidelity of information is ensured across generations, and aging is not heritable.

Taken from: http://blogs.ucl.ac.uk/gee-research/2013/11/11/damage-and-fidelity-the-role-of-the-female-germline-in-mtdna-inheritance/
You can read the article here: de Paula, Wilson BM, et al. "Female and male gamete mitochondria are distinct and complementary in transcription, structure, and genome function." Genome biology and evolution 5.10 (2013): 1969-1977.


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How does cancer of the larynx (laryngeal cancer) affect the respiratory system?
The larynx is part of the respiratory system and is responsible for producing sound (our voices). My question is how cancer in the larynx (voice box) affect the respiratory system overall? I appreciate any answer, but if it's not too inconvenient, please don't use too complex terminology (I'm in grade 10 Canada).
Thanks

Welcome to Bio@SE. What kind of googling have you done on topic? More precisely, what kind of information you want to get on that topic? Please, be advised that this site has policy on what questions are appropriate. Currently your question is too broad + you didn't provide any background or effort of your own.

According to this website:
http://www.spirometry.guru/fvc.html
it causes difficulty with inhalation but exhalation is normal...

"Typically the expiratory part of the F/V-loop is normal: the
  obstruction is pushed outwards by the force of the expiration."
  "During inspiration the obstruction is sucked into the trachea with
  partial obstruction and flattening of the inspiratory part of the
  flow-volume loop."

the exact symptoms of a laryngeal tumor depends on where it is located on the larynx... above the vocal cords, on the vocal cords, or below the vocal cords...
but more generally:
anatomy:
mouth/nose-->pharynx-->larynx-->trachea-->bronchi-->lungs
a tracheostomy may be necessary... basically the surgeon makes a connection between the skin outside the throat and the trachea... this bypasses the larynx (as well as pharynx and nose/mouth)...


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Human population growth - where can I find the data?
Out of curiosity, I'd like play around with data of human global demography.
Where can I find data that describe the "per region (per continent for example) population size" versus time since the "Out-of-Africa Event" or earlier?
Here is for example the kind of graph I'd like to reproduce but if possible in a region per region basis.

I don't think that data is available.. For recent data you can look at census of different regions

National censuses are collected, published and disseminated primarily by each country's census or national statistical office (NSO) or its equivalent. Census data are published in each country's vernacular, and as appropriate, many offer English as well as other language versions.
Statistical offices of international agencies (e.g. United Nations, statistical organizations for member states like the ASEAN, Eurostat, and OECD), also publish statistical data including population figures. The most consistent data in terms of format and frequency, whether online or in print are usually generated from them.

The US Library of congress provides some interesting links here:
http://www.loc.gov/rr/business/census/intlcensus.html
Also Cornell provides a few resources also:
https://www.ciser.cornell.edu/ASPs/datasource.asp
If you still need some information, your best bet is to then contact social scientists and ask for their opinion.


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Does embryonic development mimic (partly at least) the evolution of organisms on earth?
What do we know about the forces/mechanisms which lead to this seemingly "fast forward" evolution stages of the embryo? What are the theories dealing with this idea?

You might want to read up upon the recapitulation theory, and reword your question, to be more specific.

Can you provide some kind of evidence for your claim? In the meantime, I'm voting to close.

@canadianer he is talking about the recapitulation theory by Haeckel. Ontogeny recapitulates phylogeny The developmental history of the organism recapitulates the developmental history of the species.

I vote too close because the question asks to review a theory, which is too broad to my opinion.

seems like OP received an answer from @RoverEye already

@RoverEye Thanks. That's what I was looking for.

Voted to reopen, but still feel that the OP should give more background, e.g. by pointing to cases where recapitulation/fast-forward seems to be a good explanation. Why do you think that "embryonic development [should] mimic [...] the evolution of organisms"? What made you ask this particular question?

@RoverEye Yes I saw your first comment. I'm not familiar with the theory but Wikipedia describes it as a "largely discredited hypothesis". If that's true, it is not evidence for the claim that embryonic development mimics evolution.

@canadianer Indeed it has. This paper gives the latest (I think) view on whats going on. Irie, Naoki, and Shigeru Kuratani. "Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis." Nature communications 2 (2011): 248.

@fileunderwater Essentially the hinted wikipedia article says it all: the vague impression is/was there and I was happy to learn how this idea developed and influenced other areas and got debunked... or not.

@pointernil I'm familiar with the theory, and my comment was meant to make the question more complete and self-contained. At the moment, the question is probably very unclear for readers that are unaware of the ontogeny-recapitulates-phylogeny theory.

You only need to read Stephen Jay Gould's entire book on this topic, I believe it is called "Ontogeny and Phylogeny." He argues persuasively that there is no support for Haeckel's ancient theory.


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Drosophila biarmipes gene annotation, transposable element?
When doing an annotation of a contig31 of Drosophila biarmipes genome, the gene predictions(in orange, red, green, tan, blue, brown, and gray) picked up numerous possible genes in the area circled in blue below:

So according to the GEP(genomic education partnership) guide I was reading, I was to then BLASTP the amino acid sequence from these predicted genes to a non-redundant protein database. Using NCBI BLAST I did just that, and observed alot of results of significance (E value < 1 X 10^-5).
Many of the BLASTP results were somthing like:

Reading up on gag proteins I found they were related to transposable element activity, specifically reverse transcriptase activity. So then should I conclude that these regoins are showing a gene because they are a Transposable element, or the remenats of one?
I also found:

And reading on Wolbachia I found that there is Horizontal gene transfer with its genome and Drosophila in general, according to wikipedia:
http://en.wikipedia.org/wiki/Wolbachia#Horizontal_gene_transfer_and_genomics
So then, can I conclude the area circled in blue is a result of Transposable element, and not an actual gene belonging to D. biarmipes?

Do a nucleotide BLAST first. This seems to be just a partial match. You cannot conclude that this is a transposable element. Also see if RNAseq data is available.

@WYSIWYG        THe RNA seq data is in the first picture, under the blue circle, there are black peaks that correlate with RNA seq data, the first is labeled "RNA-Seq alignment summary for mixed embryos". As for the nucleotide BLAST, i did a tBLASTn, since I only had an amino acid file to work with. The results were still a same link to the pol gag protein. The title of the highest significance match was: "Drosophila ananassae retrotransposon putative gag-pol protein gene" .


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A doctor might give bicarbonate (HCO₃¯) to a patient who is breathing very rapidly. What is the doctor assuming about the patient’s blood chemistry?
The answer is:
The doctor is assuming that the rapid breathing is the body’s response to low blood pH.
(Source: Campbell Biology)
But this answer doesn't make sense. Why would the doctor give the patient even more CO2 if the patient is already suffering from an excess of CO2 that is causing the low body pH?

Bicarbonate is not carbon dioxide. In acidic conditions, bicarbonate will be protonated to form carbonic acid which in turn decomposes into carbon dioxide and water. The net result is the removal of a proton and formation of carbon dioxide.

Bicarbonate is not carbon dioxide. In acidic conditions, bicarbonate will be protonated to form carbonic acid which in turn decomposes into carbon dioxide and water. The overall result is the removal of a proton (ie increase in pH) and formation of carbon dioxide (which accounts for the rapid breathing). The idea behind giving bicarbonate is that it will replenish the buffer.

if a person is both (1) hyperventilating and (2) has a low blood pH then this is a case of metabolic acidosis... in metabolic acidosis the patient compensates by breathing heavy... why? because hydrogen ions are captured by bicarbonate (the conjugate base of carbonic acid) which is then exhaled as carbon dioxide...
metabolic acidosis is not caused by excess carbon dioxide... this is the case of respiratory acidosis... but under respiratory acidosis the breathing is supressed, however tachypnea with frequent shallow breaths could lead to poor removal of carbon dioxide...
here are some causes of metabolic acidosis:
http://en.wikipedia.org/wiki/Metabolic_acidosis#Causes


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Multiplex PCR, shorter amplicon inhibiting longer amplicon?
I want to run multiplex PCRs for my genotyping, with a primer pair targeting my construct and a primer pair targeting some housekeeping gene (sort of a built-in control).
I designed the control amplicon to be very short (I tested 3 primer pairs with ~120, 85, and ~50bp amplicons respectively). The main rationale behind this being that usually my amplicons are ~200-400bp, and I want something clearly distinguishable, but shorter rather than longer (I want to keep my options open for longer target amplicons).
In any case, regardless which control primer pair I use, whenever I try to multiplex I only end up seeing the shorter amplicon. See the gel picture below for an example (lanes: 1-ladder, 2,3-target+control, 4,5-control, 5,6- target).

I see that lanes 2,3 have a very faint additional smear compared to 4,5, but I want a band for my target amplicon. Also, my shorter bands are quite blurred.
Also, just for reference, my amplicons do not overlap at all.
So, I guess my questions are:

Why is the longer band disappearing?
Why is the shorter band so blurred?
What can I do to prevent this form happening?

How far are the construct and the housekeeping gene from each other? If they are close there might be transcription interference occuring.

As long as the amplicons do not overlap, I don't see how there could be any direct interference. In any case, they do not overlap and are on different chromosomes.

Overlap is not necessary for transcription interference to occur, but since your genes are on different chromosomes it should not be the case. Did this setup worked before or this is the first use of these set of primers?

What are the $T_m$ of these primer pairs? If one primer pair is significantly more stable at a given temperature, it could explain your results.

58-60°C for all primers. All 3 PCRs are run under the same conditions - would you say that there is no polymerase left to be recruited by the less stable primers?

50bp amplicon is not a good idea.. They will look like primer dimers.

True, I guess that can become problematic if I ever end up using dimerizing primers. Still, the same problem happens with 120 and 85bp.in fact,the figure you see here is 85bp

It turns out that the $T_m$ was in fact the issue, or rather, that the computation algorithm overestimated the $T_m$ of the primer pair for the longer amplicon (or underestimated that of the shorter one). At any rate, it seems that at 60°C the shorter amplicon primers hijack the polymerization mechanism.
Setting the annealing phase temperature to 55°C solved my issue, and now I consistently get better results:


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Basic Modelling in Quantitative Genetics
I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a very simple model. I welcome any explanation of some other classic model of the evolution of quantitative traits.
Scenario
Consider a haploid population of constant size $N$. The fitness of the individuals is determined exclusively by a single quantitative trait $z$. $l$ loci codes for this trait. The genetic value at each locus adds up to give the quantitative trait $z$. The mutation rate at each locus is $\mu$. A mutation changes the genetic value at any given locus by $+ \Delta z$ with probability $\frac{1}{2}$ and by $- \Delta z$ with probability $\frac{1}{2}$. If you prefer to consider the effects of a mutation to be drawn from a normal distribution with mean $=0$ and variance $= \sigma^2$, please feel free to do so. The fitness $w(z)$ of an individual is given as a gaussian function of its quantitative trait $z$
$$w(z)=\exp\bigl(-Vz^2\bigr),$$
where $V$ is the strength of selection. The optimal phenotype is $0$, that is $w(0)=1$. The larger is $V$, the more severe it is to be at a given distance to the optimal phenotype. If you want to assume that the fitness $w(z)$ is some other function of the trait $z$, such as the even more simple $w(z)=z$, please feel free to do so. For simplicity, we assume no environmental variance on the quantitative trait.
Questions
What is the equilibrium mean fitness $\bar w$ of the population?
What is the equilibrium genetic variance (=phenotypic variance) for fitness $w$ and for phenotype $z$?

What have you gotten, so far? This reads like a homework question.

I would have love receiving this kind of homework. It is not a homework question. Because I was trained in Europe, the last homework I had to do was probably during the first year of my bachelor degree or even in High school. For the moment, I pretty much developed the basis of a model (presented in the post) to think the evolution of quantitative trait but this is it, I fail to bring it any further to answer my question(s).

@dd3 This is a little complicated than a usual homework.

Trait z is represented by k genes: z1....zk (I am using k instead of l because the former is visually differentiable from 1 ).
For simplicity let's assume that there is only one mutable site in a gene. So a mutation can impart a change of $\pm \Delta z$. Starting from initial state of z at zero, the system will proceed to equilibrium where the rate of forward mutation would be same as that of backward mutation; since the rates are same the deterministic steady state of z should be zero.
A mutation event can also be considered a binomially distributed RV. After n events, the mean number of forward mutations would be 0.5×n.   Mean fitness = mean forward mutation — mean backward mutations = 0
You can also model the mutation events as a simple random walk. The mean of that is 0 and the variance is n. But what about large n; I am not sure. You should read about random walks or ask in CrossValidated. With $t\to \infty$, you would get a lot of variants but variants would be filtered out by selection (as the optimum is at 0). I think selection can be incorporated in the random walk with death rate being proportional to the distance from 0. But again I do not have much experience with such hybrid models.
I tried a simulation with n=10000000 (using Monte Carlo); different colours denote different runs (or in another words different loci). Y-axis denotes the value of z.

This is interesting, I didn't think about modelling this with a diffusion process. A diffusion equation contains 2 terms, "diffusion" (equivalent of genetic drift) and "drift" (equivalent of selection). An issue with this methodology though is that we can only track the mean trait and the variance in mean trait (the RV mean trait is normally distribution if the process is a random walk) of the population and not the variance in the trait within a population. +1


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What are those visual and auditory reflex controlled by the midbrain?
The midbrain is a centre for certain visual and auditory reflexes. But what are those reflexes exactly? My study book says that these reflexes are, e.g., responsible for moving the eyes to view something as the head turns. But I don't quite get it. What is the difference between those reflexes controlled by the midbrain and those mediated by the spinal cord?

You probably reading about Vestibulo–ocular reflex. This is one that allows your eyes to follow object of interest even though your head rotates.  I see difference as that spinal cord controls motor neurons of limbs, not controlling muscles of the eye.

Where are you after exactly? Are you after the different types of auditory/visual reflexes mediated by the midbrain? Are you after startle responses? Or after eye movements? I think you need to add a little bit more detail, as I don't quite get "it" is quite vague. Also, the concluding sentence does not really match your question title. Are you interested in the difference between spinal-chord-mediated reflexes in particular? That is again quite broad, as the spinal chord covers the entire body including many receptors (pain, heat...)


text:
What causes muscle spasms?
What causes muscle spasms with muscles that are not in the heart  ? Could it be some sort of stimulus overload that causes a massive contraction?

According to wikipedia and MedlinePlus muscle cramps can be caused by muscle overuse or injury or dehydration and lack of minerals (eg. potassium or calcium). In this wikipedia page you can read about the mechanism of muscle contraction. I'd emphasize and quote the most important parts here:

ATP binds to myosin, allowing it to release actin and be in the weak binding state (a lack of ATP makes this step impossible, resulting in the rigor state characteristic of rigor mortis). The myosin then hydrolyzes the ATP and uses the energy to move into the "cocked back" conformation. In general, evidence (predicted and in vivo) indicates that each skeletal muscle myosin head moves 10–12 nm each power stroke, however there is also evidence (in vitro) of variations (smaller and larger) that appear specific to the myosin isoform.
  Steps 9 and 10 repeat as long as ATP is available and calcium is freely bound within the thin filaments.

As you can see ATP is essential in the release of myosin from actin. In case of muscle overuse and dehydration ATP is depleted from the muscle cells and may cause the muscle to cramp.
Also according to this site it is said that repetitive firing of motor units with high frequency is associated with muscle cramps, although tehe origin of this is yet not clear. It can be either from the central nervous system or the peripherial.

Can the repetitive firing of any group of muscle tissues be 'dampened' by the local addition of certain biochemicals like endorphins ( if that's an appropriate molecule for 'dampening' ). Or maybe having certain receptors related to 'firing cells' blocked somehow.

To be honest, I do not know by heart, but I think you should post this as new question, to attract other people, and hopefully get an answer.

There was a story recently in the CTV news from Toronto ,Canada ; about a woman in great pain who had an electronic device implanted on her spine. This device sent signals to her brain area 'responsible' for the pain signals. Now she feels no pain. They said it was an underused technology. Maybe a similar device could send signals to the brain areas to do with the heart. Maybe if a chaotic spasm in the heart muscle was imminent signals 'could' be sent to the heart system through this 'device' to 'overwhelm' any chaotic signals and 'normalize' the heart rhythm.


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What does a read simulator do?
There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software

Welcome at Biology SE! Your question is interesting althoughI fear it is more related to informatics than biology. The actual algorithms and the internal workings of a software is off topic here.

I'm voting to close this question as off-topic because algorithms and internal software mechanism are not related to biology.

@poka.nandor it is not in a true sense about a general algorithm; it is a algorithm that simulates a biological experiment and so it should be on-topic. Likewise, mathematical models for biological experiments are also on-topic and we do have many questions on that subject. However, I think that the OP could have put in some more effort.

@WYSIWYG perhaps you're right, I agree with you that bioinformatics and mathematical biology should be on topic. I think it depends on how deep the OP is interested in the software. As a programmer I may have jumped to the point to assume that the OP is interested in exact algorithm implementation instead of general features. In the first case I think it's off topic, the latter case could pass as on topic. Until further clarification I'll uphold my close vote, but as always I'm willing to retract....

In general, a read simulator does the following:

Selects regions from a reference sequence with some sort of predefined or user-specified size distribution.
Converts the sequence from those regions into single or paired end reads with quality scores. The quality scores and read lengths are typically user defined.
Introduces errors into the aforementioned sequences, typically with more at the 3' end, which matches what comes from a sequencer.

A simulator may also try to reproduce the uneven coverage that you'd see in real data. In any case, most simulators will place the original coordinates of the simulated reads in the read names so that the quality of the resulting alignments of the reads can be assessed.


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Why do slime molds pulsate when growing into their fruiting body?
An example can be seen in this Youtube video, where the slime mold pulsates as it engulfs a rock in order to form its fruiting body.
Why does this pulsing happen?

Adding to @CDB's answer:

...Saigusa speculates that it instead depends on an internal mechanism
  of some kind, perhaps involving the perpetually pulsating gelatinous
  contents of its one cell, known as cytoplasm. The slime mold's
  membrane rhythmically constricts and relaxes, keeping the cytoplasm
  within flowing. When the amoeba's membrane encounters food, it
  pulsates more quickly and expands, allowing more cytoplasm to flow
  into that region; when it stumbles onto something aversive—such as
  bright light—its palpitations slow down and cytoplasm moves elsewhere.
  Somehow, the slime mold may be keeping track of its own rhythmic
  pulsing, creating a kind of simple clock that would allow it to
  anticipate future events.

from: http://www.scientificamerican.com/article/brainless-slime-molds/
In the paper itself he says:

The model is based on physiological observations. We assume that
  multiple chemical oscillators of a series of periods underlie the
  multirhythmicity of locomotion, as multiple rhythms were observed in
  cellular activities in a Physarum plasmodium. This means that there
  are continuous frequencies of oscillation....
...Oscillators with the same biochemical identity can interact over a
  distance by chemical diffusion and active advection of protoplasmic
  streaming. These direct interactions will tend to synchronize phase,
  but it may not be enough to make a strong synchrony. In fact,
  macroscopic cellular behaviors often show fluctuating oscillatory
  variations rather than clear oscillations with a large amplitude, and
  the fluctuating oscillatory variations of different chemical
  identities display frequent switching between in-phase and
  out-of-phase relationships, although each biochemical component still
  shows the slightly oscillatory behavior. This consideration implies
  that the noise ξ should be small so that desynchronization effects are
  relatively weak.

From: Saigusa, Tetsu, et al. "Amoebae anticipate periodic events." Physical Review Letters 100.1 (2008): 018101.

Very interesting find! +1 and bravo

What you have observed is called shuttle streaming. This is how Physarum polycephalum (I assume this is the species of slime mold in the video) and many other slime molds move.
I found this here;

The movement of P. polycephalum is termed shuttle streaming. Shuttle streaming is characterized by the rhythmic back-and-forth flow of the protoplasm; the time interval is approximately two minutes. The forces of the streaming vary for each type of microplasmodium.
The force in amoeboid microplasmodia is generated by contraction and relaxation of a membranous layer probably consisting of actin (type of filament associated with contraction). The filament layer creates a pressure gradient, over which the protoplasm flows within limits of the cell periphery.
The force behind streaming in the dumbbell-shaped microplasmodia is generated by volume changes in both the periphery of the cell and in the invagination system of the cell membrane.

+1 for identifying the name of the behaviour. But why does this happen (as in, what benefit does the fungus gain from having its protoplasm flow back and forth, instead of directly oozing along?)

@MarchHo Its not a fungus.

@MarchHo This behavior is very similar to our own circulatory system. Even when this organism is not in the act of moving, this shuttle streaming is still going on, only now it is acting more like cytoplasmic streaming, which is what most cells use to move nutrition around the cell. I.e. the main reason for this behavior is to transport nutrition, waste material, etc. wherever it needs to be.

@RoverEye Thanks for clearing that up, you got here a little sooner than I did.

@RoverEye Thanks for the correction, corrected the tag.


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

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

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

Is that a link?

Can benzoic acid form in the body?

Is this a health risk?


text:
Proteins that give color (without fluorescence)
Are there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells?
Searching for reporter, something like GFP, but that we could see it without UV (not fluorescence).
Like chromoprotein - but it is problematic in mammalian cells because most chromoproteins need a prosthetic group.

You've read the wikipedia page I assume? It has some examples.

Yes. I searching for something that may be used like GFP (reporter), but that we could see it without fluorescence and it's not chromoprotein - because like I mention it not perfect in mammalian cells, as far as I know.

The problem with these chromoproteins is that the color comes from a prosthetic group that is added to the protein later. If the cells can't produce the prosthetic group, or can't attach it to the protein, it won't be colored. I know you're not looking for fluorescent proteins, but I have seen E. coli express Red Fluorescent Protein and make reddish colonies, clearly visible on an agar gel. I can't say if mammalian cells would also make visibly red colonies.

I think it would help to add a cell type (e.g., red blood cells have red hemoglobin) or tissue (e.g. pigment epithelium in the retina is colored). As of now this question is quite brood as there are many colored proteins.

@AliceD Something universal - I wrote, like GFP.

with universal you mean occurring in any cell?

"E. coli express Red Fluorescent Protein and make reddish colonies" Because they absorb almost all light from daylight (~white) spectrum

@aandreev Yes, the colonies that had the RFP gene were reddish under visible light, the colonies without the gene were normal E coli color. Made it easy to pick the transformed colonies off the plate. When using GFP, we had to put the plate on a UV light to see the green.

@VGranin I think we should clarify what you want to do with this reporter. Do you want to see color with the naked eye? Are you looking under a microscope? Is this some sort of absorbance assay?

Check out Steve Boxer's papers on engineering single chain myoglobin in prokaryotes. As I recall it describes blood red colonies.

@user137,  with naked eye without UV and without microscope. If it's possible ..

@VGranin Many RFPs have their absorption maxima at around 500nm (green light) and therefore they can fluoresce even under white light. Since red scatters less it is easier to observe too. But the colouration is not very deep. So you can observe reddish colonies.

Have a look at this paper. They have isolated a chromoprotein similar to GFP, and like the latter it does not have any prosthetic group.
This protein — asFP595 (because it was isolated from the anemone  Anemonia sulcata.), is purple coloured under white light and also exhibits a little fluorescent emission in the red region  (λmax = 595 nm).
Also have a look at these two papers:

GFP-like chromoproteins as a source of far-red fluorescent proteins
Major colour patterns of reef-building corals are due to a family of GFP-like proteins

You are looking for light-emitting proteins. They gather energy from either absorption of photon (fluorescence) or via random thermal fluctuations. Problem is that fluorescence might be considered forced emission, whereas what you looking for is results of spontaneous transitions. That means that number of photons per second you can expect from latter proteins is $10^4$ times less (I don't have reference for that statement). You need very sensitive detectors and microscopy (sub- or just cellular) is almost impossible at that rate.
You should look into phosphorescence. Also, such thing as GFP-aeqorin might be of interest. That is a calcium-sensistive construct, might give you starting point in searching for reviews.
Another keyword is bioluminescence. See here for more: http://www.olympusconfocal.com/applications/fluorescentproteins.html

The question clearly specifies "that could be seen without fluorescence"

phosphorescence is relaxation pathway from states with much longer life-time (ms versus ns for fluorescence). Fluorescence persists after "exciting source has been removed" too, relaxation is just much faster

@nico Can you elaborate? My guess is that OP wants to see proteins without any harsh excitation light/in complete darkness, and I support OP in that endeavour

@aandreev the OP says "something like GFP, but that we could see it without UV (not fluorescence)." so giving him information about GFP-related proteins does not really seem a good answer to me... My guess is he's after something like Bacteriorhodopsin which is purple (albeit I'm not sure it's a good idea to use it as a reporter...)

@nico are you talking about GFP-aeqorin? it does not require any excitation, you can observe emitted light in complete darkness. Aeqorin is bioluminesce in presence of high Ca concentration, GFP is just a relay here. http://www.pnas.org/content/97/13/7260.fullhttp://www.pnas.org/content/97/13/7260.full

I was more referring to the link... The way I understand the question he is talking about a chromophore you can see with white light, not in the dark, maybe the OP should clarify...

@nico, right, in white light. I wrote like chromoproteins, and we can see them in white light. I added this point to the question. Thank you.

GFP-like non-fluorescent chromoproteins are colored and non-fluorescent.
A handful of them - Rtms 5, HcRed, cgCP, gtCP and zFP538 - have reviewed pages on Uniprot.
This paper from Nature describes the use of Rtms 5 to make hair dye: https://www.nature.com/articles/s41598-019-50283-0

Whilst true, it's not clear that this answers the question as written, which asks about non-fluorescent proteins found in human cells. Please take our [tour] and refer to the [help] for guidance as to our ways.

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


text:
Multistability in the lactose ultization network
Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram".
Specifically, I'm confused about the use of theta and what it means. I have tried reproducing the figure using MATLAB and the parameters in the paper to see whether I can understand it better, but nothing quite works out.
To be clear, the paper obtains a steady state result for a series of ODEs:
$$
    y = \frac{\alpha  (1+(βy)^2)}{ρ+(βy)^2}
$$
Then rearranges as a cubic:
$$
    y^3 −αy^2 + \frac{ρ}{ β^2} y − \frac{α }{ β^2 } = 0
$$
Apparently, a general cubic with two identical roots has the
form:
$$
    (y-a)(y-a)(y-aθ) = y^3 - (2 + θ)ay^2 + (1+2θ)a^2 y - θa^3
$$
The paper then equates coefficients:
\begin{align}
    ρ &= (1 + 2θ)(1 + 2/θ)\\
    aβ &= \frac{(2 + θ)^{3/2}}{θ^{1/2}}\tag{did you mean?}
\end{align}
And claims that these are the parametric equations that describe the graph in question. When plotting these equations, I get nothing like the graph. I can't really see where it comes from.
The graph in question and some equations are reproduced here on the last page:
http:// web.mit.edu/biophysics/sbio/PDFs/L7_notes.pdf

I don't have access to nature so I have no idea what the figure looks like. You need to post the figure.

The equation in the OP has been updated to $(y-a)^2(y-a\theta)$ which yields the correct expansion. Therefore, by equating the coefficients, we obtain
\begin{align}
\alpha &= (2+\theta)a\tag{1}\\
\rho/\beta^2 &= a^2(1+2\theta)\tag{2}\\
\alpha/\beta^2 &= a^3\theta\tag{3}
\end{align}
Using equations (1) to (3), we get the desired $\rho$ and $\alpha\beta$. Now the authors plotted $\frac{\alpha\beta}{\rho}$ and $\frac{1}{\rho}$.
By plotting $\frac{\alpha\beta}{\rho}$ and $\frac{1}{\rho}$, we can re-create the plot in Mathematica with
ParametricPlot[{1/((1 + 2 x) (1 + 2/x)), (2 + x)^(3/2)/(
  Sqrt[x] (1 + 2 x) (1 + 2/x))}, {x, 0.01, 50 \[Pi]},
 PlotRange -> {{0, .15}, {0, 0.6}}, AspectRatio -> 3/4]

If you dont have Mathematica, here is some Python code that will plot it as well.
import numpy as np
import matplotlib.pyplot as plt

fig = plt.figure()
t = np.linspace(0.01, 25*np.pi, 5000)
x = 1/((1+2*t)*(1+2/t))
y = (2+t)**1.5/(np.sqrt(t)*(1+2*t)*(1+2/t))
plt.plot(x,y)

plt.show()

Here is the Python plot which has smoother lines compared to Mathematica's plot.

Thanks! I thought something was up... Assuming their maths had been correct and the equations for rho and alpha-beta were correct, how would you go about using them? I'm a little confused about the theta?

The plot on the last page of http://web.mit.edu/biophysics/sbio/PDFs/L7_notes.pdf

Sorry could you please add a link to the wolfram alpha graph?

@user2290362 I plotted it in Python since Wolfram will only plot it if you have the full version of Mathematica.


text:
Lentivector biosafety
Lentivectors are widely used in molecular biology, most commonly to transduce in a stable way a desired gene. These vector system takes advantage from the ability of viruses to introduce their own genome in the host cell. Thus the lentivectors are transfected to a producer cell line (typically HEK) and there viruses are produced with the desired insert. Eventually this viruses will be harvested and the desired cell lines transduced.
For bio-safety reasons, this system is engineered in a way that that the risk posed by the "virus system" is reduced. Thus the viruses produced by this system are incapable of replication, meaning with this that, as far as I understood, the viruses that are formed are then unable to form more in the second host as the genes in charge are not recruited. Yet, apparently the plasmids used can recombine and pose a possibility to create a replicating capable virus. Yet as far as I found in the literature this has never been detected and stands as a theoretical possibility.
My first question, in actual numbers, what is the probability that such event would take place (the number of recombinations in the specific locations). In the case that this would happen, the lentivector system would be potentially dangerous, as this system is based in HIV most of the times. Additionally, this vectors use not the endogenous HIV envelope protein but rather VSV/G from vesicular stomatitis virus, in order to increase the tropism and stability.
Additionally, even though HIV derived, most of the HIV genes are taken away from the lentivectors, yet in my opinion the most important ones are there. Second question, taking into consideration all of this, this theoretical "created" virus would be able to eventually cause AIDS or other whatever adverse effect? it is noteworthy that now is able to infect almost all human cells due to the VSV protein, then is it correct to think that the disease would be much worse, and much more contagious than the original HIV? note that even the stability is increased.
Yet, I can additionally think that this recombinant new virus may be indeed destroyed by the immune system, despite the increased tropism, due to the fact that vesicular stomatitis virus does not cause pathologies in humans, and possibly this protein works as an antigen and can induce an enough immune response.
Last, would theoretical recombinant virus be detected by a standard HIV test?
To simplify things, I am referring to third generation lentivectors

I'm not sure what you mean by "the plasmids used can recombine", there is no plasmid containing the viral genome, only the envelope and a few receptor proteins. The rest of the viral genome is not even present, it has been replaced with the gene of interest that you added. Therefore it would be nigh impossible to create an active virus using only three or four genes even if we where trying. Perhaps I misunderstood your above statement, correct me if I did.

I would say it's more likely for a lentiviral vector to be used on a patient who has an active HIV infection. This could also hypothetically allow the recombinant gene to be incorporated into a functional virus. This probably hasn't happened yet because the number of people receiving lentiviral vectors so far is really low (maybe zero? I haven't heard of lentiviral clinical trials, but I haven't looked either)

CDB> the envelope (VSVg), plus gag gene (polyprotein), the pol gene (integrase, reverse transcriptase, RNAse H ,HIV protease), rev gene (viral mRNA export from nucleus) found in the lentivectors transfected can recombine multiple times in order to produce a "proviral" DNA piece capable to code all this genes in the posterior generations.

Luigi> thanks for your answer
user137> I dont get you point. to begin with, how do you want to stably transduce the already existing HIV viruses with this system? besides even if so, you would get a transgenic HIV, but its beyond reason to think that you would target every HIV particle in the body as such, so these would continue perpetuating the infection + disease. Besides, what gene do you want to transduce to the virus in order to kill it? and yes I think there are such studies, but double check.

@Katz I'm saying that you could accidentally use a lentiviral vector in an AIDS patient, or that someone who receives the lentiviral vector could later get HIV. If both viruses happened to hit the same cell, the recombinant DNA delivered by the lentivirus might be transcribed into a viral RNA, packaged into a capsid and sent out into the body to infect new cells or maybe other people. While this new virus would probably be replication deficient, it could cause trouble. This and other reasons are why I don't like viral gene therapy.

as long as it is not replication capable I would not bother for the replication incompetent virus generation, they cannot produce any disease and the only risk they pose is insertional mutagenesis, which I do not think its too bad in terms of statistics (correct me otherwise), the only issue I think is that in case the lentivector produced viruses have an oncogene as an insert then yes this poses a higher risk. Regarding to viral pathogeneicity, the real issue is that even the replication incompetent virus can become replicative due to genetic rearrangements

I want to know the actual risk of this to happen, if happened, the actual chances to generate disease, and also if this theoretical virus would be detectable> if we are totally blind to verify any accidental event that might happen when handling lentivectors or not

How many recombinations are required to achieve an active virus?
The FDA has recognised the likelihood that lentivectors can be converted into actively replicating lentivirus if they undergo recombination with wild type HIV in a HIV positive patient. In this case, two recombination events are required to transfer the lentivector sequence into the HIV sequence (the mechanism of transfer is identical to the case of first-generation lentivectors).
This article from VCU describes another mechanism through which this can occur in first generation lentivector systems, which consists of two recombination events between the lentivector and the helper plasmid. Note that the 3 genes gag, pol and env are present on the same plasmid, and that plasmid is flanked by LTRs. Second generation lentivectors, such as the pLKO system, do not suffer from this problem and require wild type HIV to produce actively replicating lentivirus.

To reduce the likelihood of this happening, second and third-generation lentivector systems split the genes into multiple plasmids, which then requires more recombination events to produce replication competent viruses. Additionally, the polyA tail of the 3' LTR is replaced to reduce likelihood of recombination events occurring.

According to Addgene's article on lentivector biosafety, the gene of interest's transfer plasmid (both 2nd and 3rd generations) has a deletion in the 3' LTR region which prevents it from becoming replicatively active. Therefore, the only likelihood for the recombination to occur is for the cell line expressing the virus to undergo replication with an active, wild-type HIV strain. An example is this pLKO transfer plasmid, which contains a truncated 3' LTR, preventing the sequence from replicating outside of E. coli, which replicates it not using the LTR but instead using the plasmid origin of replication.
Are the active viruses produced by recombinations more dangerous in the wild than wild type HIV?
This is difficult to answer, since recombination only allows an active virus to form, but it does not guarantee that the virus will be dangerous. Dangerous viruses are theoretically possible, but require far more recombinations than the minimal 2 for replication competency in 2nd generation lentivector systems.
For example, lentivector systems generally do not encode for the viral proteins vpr, vif, nef and vpu. These proteins are necessary for increasing the infectivity of HIV in different types of tissues (but not cultured cells such as HEK293). The lack of these proteins in a hypothetical replication competent lentivector would significantly hamper its spread in the wild. Incorporation of these proteins is plausible but extremely unlikely, since more crossover recombination events will be required.
To use your example, the env protein coding for the VSV protein coat resides in the envelope plasmid. Since the replication competent lentivector formed by 2 recombination events will be a pseudotype containing only the HIV env proteins, it will need to further acquire the VSV gene to replace its env proteins, since these genes are not present on the same regions. There is no homology between the two DNA strands, which would significantly hamper the likelihood of the VSV gene somehow being incorporated into active HIV.
The addition of various chimeric proteins and LTR regions in 3rd generation lentivectors only complicates the matter.
Overall, I was unable to find any sources comparing the infectivity of these theoretical transgenic HIV versus the wild type. However, even though it is theoretically possible that a transgenic replication competent lentivector can have better tropism than HIV by acquiring the VSV gene, the likelihood of that occurring is far lower than that of it being produced in the first place.
Can a lentivector be detected by a HIV test?
Regarding the final question of whether a lentivector can be detected by a standard HIV test, the answer is that the detection is possible if the person who was infected with lentivectors, has obtained an immune response to the lentivector gag proteins, and the lentivector loads are high enough.
HIV tests are specific to different parts of the virus, but most of them target the viral protein p24, which is a component of the gag polyprotein.
PCR based HIV tests also exist, but these tests would depend on the specific primers produced and whether the RT-PCR would produce an amplicon given the specific sequence of the plasmids.
Since gag genes are encoded for in most lentivector systems, it is therefore very likely that anyone infected with a lentivector would therefore express antibodies towards p24, and therefore result in a positive for the ELISA as well as the Western blot tests assuming that the p24 and antibody quantities are high enough to reach the cutoff point.
I was unable to find publicly available cutoff levels for the ELISA and Western blot levels, but if (hypothetically speaking) a person was injected with a load of lentivectors, they would likely test positive for HIV. However, since the lentivector is not actively reproducing, it would quickly be cleared out by the immune system.

from your answer, is it correct to think that there MUST be wild type HIV1 present? because if it so, then of course I can guess its no good at all, but if you already have HIV maybe it is not that "important"? I was asking for the possibility of forming replication competent viruses in the conditions in which lentivectors are produced> transfect 293T cells with the plasmids, which I guess do not contain HIV sequences.

additionally there is a third question in the text, which was not somehow highlighted, but related to the infectability and disease outcome that this theoretical virus might have

Updated to clarify some issues, most notably the erroneous description of the vector in the VCU article @Katz

thereby, cannot non-homologous recombination occur between the transfected packaging/envelope/construct plasmids in order to create a replication competent virus without any HIV sequence present? I would say yes.
incidence?
and, the immune response for the VSV/G enveloped recombinant virus? can VSV/G protein act as an antigen? would it be enough to prevent pathology?

@Katz There doesn't seem to be any wild type 3' LTR present in any of the 2nd or 3rd generation plasmids according to the plasmid maps, so even non-homologous recombination will not result in viruses being produced. In healthy individuals, there is no reason why the VSV protein will not be targeted, since they are clearly non-self viral proteins.

sorry to reopen this but, could you specify what functions does the HIV 3 LTR have and what possible effects could this deletions found in the lentivectors have in a mechanistical way on the virus life cycle? i reopen this because I found that LTRs function as regulatory sequences, specifically 3LTR in polyadenilation, but the genes in the lentivector systems ARE indeed expressed, and the insert gene that ussually goes between the LTR is SUPPOSED to be working, thats the whole point,  so I really wonder how fatal this really is.

@Katz The genes in the lentivector are not expressed by the LTR promoter, but by the gene's own promoter. The truncated LTR prevents the transcription of the entire sequence including the LTRs.

I made some research and found that the mechanism of action of the truncated 3LTR is that it produces what is called in the literature "self inactivation". Yet after reading the papers still I do not get the mechanism implied to work, I think I am potentially missing some important part on LTR biology and the role it plays.

@Katz http://www.pnas.org/content/83/10/3194.full.pdf seems to describe the mechanism quite clearly.

ok, the trick was on the RT mechanism which works in a jumping way

yet, as the retroviral LTRs are both identical I could bring the argument of recombination and say that the 3LTR could recombine with a correct one. Additionally I can guess that the homologies this time might actually serve..


text:
Do restriction enzymes on read 3' to 5'?
Every chart of palindromic restriction enzymes I've seen lists their restriction sites from 5' to 3', something like this:
EcoR1 cuts GAATTC between the G and A:
          5' NNNGAATTCNNN 3' --> 5' NNNG____ AATTCNNN 3'
          3' NNNCTTAAGNNN 5' --> 3' NNNCTTAA____ GNNN 5'
Will restriction enzymes match and cut a site if it's running antiparallel? For example, will EcoR1 cut this sequence?
5' NNNCTTAAGNNN 3'
3' NNNGAATTCNNN 5'

Whatever sequence (plus direction) is target, so enzyme will cut. In your example "correct" and "antiparallel" sequences are two different sites.
Actually, your example of 5'-CTTAAG-3' is cut by AflII enzyme.

Additionally, the definition of "palindrome" means that it does not matter which direction the read is in, as either direction is identical.

Another way to think about it is to look at the 3-D structure of GAATTC, I believe there is also a 3-D structure of the Eco RI enzyme. The sequence CTTAAG cannot be superimposed on top of GAATTC--well, when you superimpose them they don't align significantly. Likewise ds GAATTC fits perfectly into the enzyme active site while ds CTTAAG will fit, but poorly.

@mdperry that is what behind (in some part) specificity :)