text:
Can defibrillation be done with a car battery?
Can successful defibrillation be done with a car battery? Is it POSSIBLE for this to work?
Let's say you are stuck on a very remote place and something happens to someone...
Moreover, can you jump start someone's heart using the battery of a car and the jumper cables, keeping in mind that:

in order to start a stopped heart you need electrical current applied in a short period, like 20 ms, and at a relatively high tension (200v) and small intensity?
car battery provides low tension current (12v) at a relative high intensity (70-80A) and the period cannot be 20 ms, but around 200-300 ms giving the fact that humans are not able to react that fast.

Welcome to BiologySE - you're going to have to give a little more research effort to try and figure out this question. Have you tried google to see what might be known about that? Your question would be better if you could add more to it - especially with some rationale

don't know what else can be added

in order to start a stopped heart you need electrical current. A battery has current. So...

Tension and Intensity can be slightly changed...

your above comments are useful - you should add them to your question... it's always helpful to show some research effort... http://biology.stackexchange.com/help/how-to-ask (also, you might want to clarify that you're interested in defibrillating the heart, which is only part of cardiopulmonary resuscitation)

I believe the type of current is not appropriate... at least when you need synchronized cardioversion. For defibrillation, possibly, but the problem would be to administer in a correct spatial fashion the current, and also delivering it precisely when appropriate.

You need to look up what CPR is - and also see defibrillation.

I did, my question was that if it is possible, not appropriate or 100% doable :)

CPR is not really about restarting the heart. See paragraph 3

defibrillation, good point

In general, no.
Car batteries are designed to provide a large amount of amperage, to turn the starter with a high amount of torque via an electric motor.  Generally this is done at 12 or 24 volts.
The current recommendations for a defibrillator requires 200V, and a very small amount of amperage.  This is one of three settings in a standard defib procedure.  The second setting is 300V, and the final is 360V.  The point of defibrillation is not to provide power to the heart, it is to disrupt the heart's built-in electrical (biological) circuitry, such that the heart can go to rest (not beating).
Many cardiac events involve the heart beating in an uncoordinated manner, such that many or all of the muscle fibers in the heart beat in a manner that doesn't provide the squeezing action on the chambers to push the blood forwards.  Defibrillation seeks to correct such an uncoordinated beating by resetting the heart to rest, after which it will hopefully start beating again in a coordinated manner.
In short, attaching a car battery is more likely to cook the heart (if it even gets that deep) because it is providing too much power, and it is unlikely to disrupt the heart's electrical field because it is too low of a voltage.  With this in mind, one could theoretically attach enough electrical transformation equipment to a car battery to use it as a power source for defibrillation.  But there are other issues with such an idea.
Car batteries are not designed for the usage that would mesh well with a defibrillation machine.  Car batteries are designed to be recharged.  Your car battery basically drains pretty heavily upon starting a car, and then the alternator recharges it by harvesting mechanical power from the engine during your trip.  This heavy drain / heavy charge cycling is hard on batteries, and car batteries have been specifically designed to endure in such a scenario.
A defibrillator machine has a different use scenario.  Basically it sits idle for long periods of time, and when it does require charging, it gets electricity from a wall socket, at higher voltage (and generally lower amperage).  This means it tends to charge more slowly, which in general means longer battery life.  Also the battery is built differently, to hold charge better at the expense of not being recharged as quickly.
In short, a car battery is really the wrong tool for the job.

Welcome to BiologySE... nice answer - we always appreciate some references that other users can go to for more information... if you could add those to your answer it would greatly strengthen it

@VanceLAlbaugh Feel free to edit and improve upon up my statement, and I understand the desire to make things into a "referenced encyclopedia" like format; but, I have have other goals in life.  If anyone wants to check any item above, they can use google.  If something was wrong with my answer, there'd be 20 guys crawling all over it telling me I was wrong anyway.

@EdwinBuck you may have other goals in life, but we expect answers here to be adequately sourced. Please read this meta post for discussion on this topic. Your answer may be flagged and removed if citations are not added.

Great and interesting answer--I was happy to read it despite the negative press covfefe,


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Have people in Africa already started evolving resistance to AIDS?
Are people living in areas where AIDS is rampant (for e.g. Africa), less likely to die from it than they once were because some of the people without genes/mutations that give them resistance already died off?
Is there any data on this?

HIV-resistence is indeed a thing (see Pancino et al., 2010 for example).

You seem to focus on African populations but there are non-african countries that have quite a high HIV prevalence too such as Jamaica, Haiti, Russia or Ukraine. Generally speaking, the highest prevalence are in southern Africa (Swaziland, Bostwana, South Africa, Namibia, Lesotho, etc..) though. Swaziland has the highest world-wide prevalence with an impressive frequency of 26.5% of the 19-42 years old people being infected (wiki)

Your comments on parasite evolution are wrong and your question is therefore opinion-based. Highest resistance will not select for lowest virulence. You might want to read on the subject. Here are two related posts on Biology.SE: Viruses selected by evolution (which is a horrible title btw) and Why do parasites sometimes kill their hosts?.

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What are Some Classical Examples of Local Adaptation?
Question
Can you please give a list of classical (textbook) examples of local adaptations?

How to answer
Examples don't necessarily need to include what evidence supports this specific example of local adaptation. A simple description of the local adaptation (e.g. coat colour changes from black on dark soil to white on light soil) and an brief explanation of the reason (e.g. because being nicely camouflaged prevents from predation from hawks) is enough.
I think a list of 10 or more such examples would be great.
Definition of local adaptation
Note that I define here local adaptation as differentially adapted subpopulation of a single species (with existing gene flow between subpopulations especially for sexually reproducing species).
Justification for the question
I found surprisingly complicated to find such list online. I think it could be a valuable post for many.
Examples
Examples of local adaptation (that you are free to add in your answer with a description) include beach mice camouflage, altitude adaptation in tibetans and peppered-moth camouflage.

Would you consider adaptation to be reversible i.e. just phenotypic adaptation to a condition. IMO, the term -- adaptation, also has multiple interpretations.

Adaptation is a change in a trait as a response to selection. As you ask for local adaptation I assume you want examples where sub-populations have either come under different selection and adapted differently, or cases where sub-populations have come under similar selection but not all have had the necessary genetic variation to evolve, i.e. selection has caused differentiation between sub-populations. Local adaptation can lead to varying degrees of divergence, so some for some examples it may be worth exploring speciation events. Here's some examples:
Galapagos Tortoises
There are two general shapes to the shell of tortoises on the Galapagos Islands. On islands with little low-lying vegetation the tortoises seem to have evolved long necks & limbs and different shell shapes which allow them to reach up more easily.

"The shell distortion and elongation of the limbs and neck in saddlebacks is probably an evolutionary compromise between the need for a small body size in dry conditions and a high vertical reach for dominance displays."

Silent Crickets
Marlene Zuk has some very famous work on crickets that evolved to be silent on a Hawaiian island where parasitic flies were using the call as a targeting method. It's a great example of rapid adaptation occurring under observation in the wild. During the 1990's the population of crickets was in decline as a result of parasitism. At some point a mutation arose where the crickets no longer produced song, and this allele spread rapidly and cricket numbers bounced back strongly.
Other possible examples. Some of these are not "classical examples" but serve as interesting examples nonetheless.

Peppered moth colouration in response to the industrial revolution
Sickle cell anaemia and Malaria
Artificial selection in crops, livestock, and domesticated animals
Darwin's Finches
Antibiotic resistance in diseases; resitance to pesticides and herbicides; resistance to diseases unique to/more prevelant in sub-populations
Seasonal and continuous breeding by species present in both temperate and tropical climates
The Stephens Island Wren adapted to life without predators, and then failed to adapt to life with predators
Barn owl colouration across Europe
Predator-prey co-evolutionary dynamics as demonstrated by Guppies in Trinidad and Tobago
Drosophila melanogaster and adaptation to starch and maltose based foods
Adaptation to different salinity across gradients in marine organisms

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How can alcohol cause blindness?
Strong alcoholic beverages (e.g. moonshine) are reported to have caused blindness amongst some people.
How exactly can alcohol make someone go blind?
Is that because different forms of "rubbing" and homemade alcohol: ethanol, methanol, isopropyl and moonshine cause damage to the optic nerve?

Disclaimer: I am interested in what exactly is the biological process of certain alcohols on the optic nerves and what in particular triggers the blindness.

It'd be better if you cite such a report.

Why do you first talk about homemade alcohol (moonshine) and then about rubbing alcohol? Both have no connection. Can you please clarify this?

Methanol is probably the culprit in those cases. As little as 30mL of pure methanol can kill a person. While it's pretty safe to handle as long as you don't drink it, my lab here in Japan won't let me use it outside a hood designated for toxic substances. The reason it's so toxic is because it gets metabolized to formic acid.

@user137 As long as you do not drink it or pour it in large quantities over your skin (it will be taken up to some amount) you are pretty safe. This is the typical overreaction of safe guard measures.

@Chris They won't even let me put 70% ethanol down the drain, it's an organic solvent and must be disposed as such.

@user137 Formaldehyde is the toxic product. Formic acid is not that toxic.

@WYSIWYG I got the information from Wikipedia, " The conversion to formate via ALDH proceeds completely, with no detectable formaldehyde remaining. Formate is toxic because it inhibits mitochondrial cytochrome c oxidase, causing hypoxia at the cellular level, and metabolic acidosis, among a variety of other metabolic disturbances." This suggests that the formaldehyde doesn't stick around long enough to be an issue, and that formate itself is also toxic. Wikipedia could be wrong though.

Methanol is rapidly absorbed not only after oral ingestion but by inhalation or after cutaneous exposure and becomes oxidised in the liver to formaldehyde and to formic acid, metabolites which are more toxic than methanol itself and which inhibit mitochondrial ATP production.
Histopathologically, circumscribed myelin damage behind the lamina cribrosa of the optic nerve has been reported. The electrophysiological changes following acute methanol ingestion suggest that methanol affects photoreceptors, Muller cells, and the retrolaminar portion of the optic nerve.

Source : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1771266/
Several years ago there were numerous cases of blindness and death due to Methanol in Estonia.
If you ask : What exactly happened?
Waste from wood (sawdust, shavings), and other cellulose-containing materials (paper, rags, etc.) can be processed by applying excessive heat and acids, resulting in degraded cellulose into sugar (glucose). Sugar obtained is fermented to get ethanol. However as a side-effect, some methanol is produced as well. This compound is not safe to drink. Basically, someone sold it (illegally) as an ethanol drink (I am not sure if they stole it and tried to monetize it this way.).
There was a (stupid) joke that somewhat popularized knowing about this problem:

(roughly translates to) "Guys, let's drink faster, it is getting dark."

Other impurities in the alcohol could have similar effect, but I can confirm at least the methanol part.

You can perhaps add that the toxicity is because of formaldehyde which is formed by oxidation of methanol in the body.


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Biological meaning of Lotka-Volterra Jacobian matrices
In a book about community ecology, I learned about Lotka-Volterra models and dynamic food web models (I am not an ecologist in the first place).
In one of the chapters, a Jacobian matrix of partial derivatives of the Lotka-Volterra model at equilibrium densities is given:
\begin{bmatrix}-&-&0&0\\+&0&-&0\\0&+&0&-\\0&0&+&0\end{bmatrix}
where + and – represent positive or negative values.
This matrix is later interpreted in terms of direction of trophic links in a food web, but the reasoning allowing to jump form one to the other is not detailed.
So what is the biological meaning of these values?

The Jacobian tells how the system changes along different state variables (which can be, for instance, the concentrations of the predator and the prey).
The Jacobian matrix by itself doesn't give you a lot of intuitive information. However, the eigenvalues of the Jacobian matrix at the equilibrium point tell you the nature of the steady state. For example if all the eigenvalues are negative then the system is stable at that point and the equilibrium point is called a stable node. If some of them are positive and some are negative then the system is metastable at that point and the point is called a saddle point. If all eigenvalues are positive then the point is unstable. If the eigenvalues have an imaginary part then the system exhibits oscillations. All these properties are local i.e. they just tell you the behaviour of the system near the equilibrium point.
I hope I am clear. This is not in a strict sense, a biological question. If you want to know more then read a book on nonlinear dynamics. Non-linear dynamics and Chaos by Steven Strogatz is a good place to start.

EDIT
When the system is locally linear (linearized at a given point) then the system dynamics at that point can be described as
$$\frac{dx}{dt}=J.x$$
Where $x$ is the state vector (a vector of the variables in the system) and $J$ is the Jacobian matrix. In this situation, the signs will denote the effect of a variable on the other variable. However, I am not sure (I feel it is highly unlikely) if this can be used to make any inferences about the food web.

Then I really don't understand how negative and positive values are expressed in terms of link directions in the food web, at least according to this book...

@KermittDuss I made some additions. Please check the answer.

Loop Analysis is an approach for taking a signed digraph to qualitatively understand dynamics of a community/food web. See this website, the book chapter on Loop Analysis behind a paywall, or a very succinct description (ssec 2.2).

The matrix above depicts the signs of the partial change of a function with respect to each species. Because there are 4 rows and columns, this means there are 4 species. Each row represents a partial change in each of the 4 differential equations representing the rates of change for each species with respect to each species, which is each column. To rewrite the Jacobian for species 1–4 ($N_1, N_2, N_3, N_4)$:
$$\mathbf{J} = \left[\begin{smallmatrix}
\frac{\partial F_1}{\partial N_1} & \frac{\partial F_1}{\partial N_2} & \frac{\partial F_1}{\partial N_3} &\frac{\partial F_1}{\partial N_4} \\
\frac{\partial F_2}{\partial N_1} & \frac{\partial F_2}{\partial N_2} & \frac{\partial F_2}{\partial N_3} &\frac{\partial F_2}{\partial N_4} \\
\frac{\partial F_3}{\partial N_1} & \frac{\partial F_3}{\partial N_2} & \frac{\partial F_3}{\partial N_3} &\frac{\partial F_3}{\partial N_4} \\
\frac{\partial F_4}{\partial N_1} & \frac{\partial F_4}{\partial N_2} & \frac{\partial F_4}{\partial N_3} &\frac{\partial F_4}{\partial N_4} \\
\end{smallmatrix}\right]
$$
The signs above correspond the effect of species on each other's rates of change. For a first example, the first row and column is effect of species 1 on its own rate of change. It's negative, meaning that it's rate of change decreases with increasing density (crowding). A second example is the first row and second column—species 2 has a negative effect on the growth of species 1. In a food web context, this means that species 2 consumes species 1. A third example is the first row and third column—there is no effect of species 3 on species 1. Lastly, the second row and first column has a positive sign, meaning that species 1 has a positive effect on the growth rate of species two. In a food web context, that means that species 2 consumes species 1.
Notice that in food webs, for each positive effect, there is a corresponding negative effect and vice versa (i.e., species grow from eating another species, and species shrink from being eaten).
In sum, (1) species 1 is the only species who is affecting by crowding, (2) species 1 is consumed by species 2, (3) species 2 is consumed by species 3, (4) species 3 is consumed by species 4, and (5) no other species interact.


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Please identify bird call / animal call
What species is making this sound?
You can hear it from the opening samples of this song: Earthgarden by Nada (2003).
I wish to study the frequency distribution of the bird call.

just to know the species of bird in the sample. thanks

Sounds like a Curlew (Numenius arquata).

http://www.british-birdsongs.uk/curlew/
https://www.youtube.com/watch?v=q7V25M0szqU

Awesome knowledge there. it may not be the precise same bird but it is very close and it may be, unless someone has a better idea, we can say it's as good as same bird.


text:
3 flaws of genes from the perspective of a programmer

Having a double helix structure seems like a waste of space. In programming you would have a single array and just before mitosis you would double the single helix.
Having an exact copy of a cromatid. As long as a cromatit exists, there is always a possibility of errors, for example if something attacks the chromosome. So why isn't the cromatid just before mitosis, just like in 1? Then you are 100% certain, you have an exact copy. Again, a waste of space, but additionally vulnerability now.
Having 2 nucleobase (adenine, thymine, guanine, cytosine) seems like it makes more room for errors. Why aren't there just two of them? They are complementary anyways, so adenine for example can only be on the opposite side of thymine. Is it so that splitting is easier? In programming, if you only have to deal with a boolean value, you would always take it over having to deal with 4 values.

So, what does nature do different than a computer and why does it behave so differently?

Simple answer, nature doesn't think. all 3 flaws you mention are OK for natural selection as compared to some other ancient alternative, so nature preferred them.

Re #3. If you had only two, how would your alphabet code for the 20-odd amino acids?

Re #1: Would your alternative structure have similar chemical stability? Also, without redundancy, if there were any externally induced damages how would you rectify the damage?

Why? It's because it evolved that way. Period. Please refrain from asking broad open ended questions. Nobody ever claimed that this is the most perfect mechanism. However, it works quite well and it has not been selected out. Plus the double helix also allows for repairing errors. Please refine your question (keep it precise and fact based, and avoid asking multiple questions in a single post) or else it would be put on hold.

Moreover diploidy has its advantages for certain strategies. However, many organisms are haploid and they also survive well.

@curious_cat Yes, I address external damage in 3, where I find it bad that the 2nd chromatid is exposed to potential damage, which is, why I would only create it right before mitosis.

@kim366 I didn't get that bit. What if your single chromosome got damaged? How would you repair that?

@WYSIWYG Sorry, I don't know about any other amino acids. What I learned at school is, that the DNA consists of nucleobases, which form some kind of binary code. But the same could be achieved with just two of them and reading the DNA would be easier.

@curious_cat Well when one chromosome gets damaged, what happens in the real world right now? When a single chromatid gets damaged, how does the system know which of the 2 is correct? It seems like there would be a discrepancy, so which one is the right one?

@kim366 Please read about genetic code. It is not binary. It is 4 letter based and each word is 3 letters long. That way you can ensure that all amino acids are represented and you have synonymous codons too (which are sometimes helpful). If you want to achieve the same with a binary code, then your word length should be at least 5. Also read about DNA repair mechanisms. To fully answer your questions (as you explain in the comments) one might have to write a book. Therefore the question is broad. Please read these topics and ask a precise question.

@kim366 Without the redundancy of a 2nd strand you wouldn't even realize that there was a mistake, right? Error detection vs Error Correction.

@WYSIWYG Thanks! Either I understood it wrong or we are learning BS at school...

Either I understood it wrong or we are learning BS at school  -- or both.

Conversely, if errors never happen then neither does evolution.

Somewhat related with answers discussing the problems with computer/DNA analogies: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO? and Can DNA & RNA be considered as nature's programming language?

Wow, this question is quite controvertial... 5 upvotes and 5 downvotes...

You are missing the point that DNA is a better information storage system than the currently used computer equivalents on many levels: DNA stores Information more dense, more energy efficiently, and over much longer timescales. Only the I/O speed is slower. This means that DNA would be an ideal long-term data storage system even for conventional computers.

In programming, if you need to ensure your data has integrity, a single array won't do.
We have cyclic dependency checks in programing to determine if the data is corrupt.  We have hamming codes to permit detecting a fixing one bit corruption.  If we want to really fix multi-bit corruption, we need at least one copy of the data.  Lossless compression routines can make the storage of that copy smaller, but it doesn't remove the concept that the data is copied.
DNA provides a copy built-in, albeit a mirrored copy.  The structure of the molecule is such that the data is on the inside of a positionally stable backbone of sugars.  Since atoms and molecules are not likely to have the same sizes when attached to this sugar, a mirrored copy has the advantage of keeping the DNA molecule relatively stable in width along it's entire length.
This relative stability is also seen in the proteins that bind to and maintain the DNA.  Basically they don't require shapes that match a would-be rugged terrain of jagged connecting bits, only the ones that need to verify against the information require regions that match the "informational terrain" they are seeking.
It is really all chemistry at the lower levels, just at a very large scale.  Unfortunately (or fortunately) atoms don't come in standard sizes, with uniform properties much like bits in a computer do.  As such, the modeling of information crosses over from Biology to Computer Science well, but the implementation of it doesn't.
To get an appreciation of the differences between modeling and information in computation, look at the various lego / tinker toy / water computing modules.  You can build a computer out of anything; however, if you needed to integrate a lego logic module into a modern computer, it would be "less than elegant"

This addresses #1 but not #2 or #3. Though, the answers are all available in the question's comments.

The section including the statement "The structure of the module is such" indirectly hints why you don't have only two bases.  Two bases would require the same height relative to the DNA sugar backbone, or they would have to be "super bases" that spanned across to both sides of the backbone.  With the relative heights being the same, strands would (more easily) slip across each other, leading to new complexities. With "super bases" crossing both strands, the covalent bonds would make the two strands one, so there would be no duplicate.

Your individual questions here are reasonable enough - although you could do a bit better at knowing some more details of the systems you are dismissing as 'flawed'. However, I think the bigger problem is your overall approach, which seems to be to make analogies between human-made computers and biological systems and then critiquing the 'missing' parts from biological systems.
Analogies like this are necessarily limited. Take the idea of DNA as 'like' a hard-drive of a computer. The nucleotides = bits, genes = contiguous segments of memory, promoters = pointers, etc. Where does this model go wrong?
Well, hard-drives are not (currently!) self-assembling structures that read themselves by coding for more, smaller fragments of hardware that additionally compress or expand parts of the structure of the hard-drive according to which part needs to be read. Moreover they don't do this while floating in liquid and self-repairing from chemical and radiation damage.
There is an excellent book called "Cats' Paws and Catapults: Mechanical Worlds of Nature and People" by Steven Vogel that covers this kind of flawed analogical reasoning between biological and human-made systems. It's not that such analogies are useless, but it is very important to recognise the limitations and fully understand why certain design choices are made by biological systems due to the particular environmental and evolutionary constraints that they work under.


text:
What kind of detergent should I use in cell culture laboratory for cleaning purposes?
I work on establish a cell culture laboratory in the company where I work. All equipment are new and I want to clean lab before I start to work with cells. Is there any special detergent for cleaning cell culture lab?

No, standard soaps used for washing lab equipment are enough. Our stuff simply goes through the dishwasher and is autoclaved afterwards.

Are you cleaning the equipment, surfaces such as benches or floors, or supplies like glassware?

I can't tell if you're asking about glassware or work surfaces (hoods, benches etc), but...
We use regular old dawn dish soap in my lab because what's more important than the soap you use to wash you're glassware is the water you use to rinse it.  We teach our undergrads the 3-rinse-rule.  After soaping, every item gets 3 rinses with normal tapwater (or until no more suds forms- whichever comes last) followed by 3 rinses with deionized water.  We have DI water on tap which makes things easier.  I remember rinsing some glassware with acetone or other solvents in organic chem lab, but you shouldn't need to do anything like that for TC.
The same principle holds true for work surfaces.  After cleaning, decontaminate with 70% ethanol, 10% bleach, envirocide or any other BSL2 recommended cleaner.

I agree with Mike, but would like to add that if you are trying to do protein expression for purification, some detergents contain polyethylene glycol (PEG), which will readily bind to many proteins, causing shifts in protein size/weight and potentially effect activity or toxicity. In particular, I have heard that Liquinox can have PEG (depending on the batch?). To avoid this, we'd use DetoJet for low-density cultures and add tergazyme for fermentation-density cultures.

Could you add sources?


text:
What kind of kale is this?
I'm from Pennsylvania and I used to get this kale all the time at the grocery store, but I moved to the West Coast recently and can't find it anywhere! It looks exactly like this photo:

Image source: http://www.specialtyproduce.com/produce/Kale_Purple_764.php.
I've seen this referred to as purple kale, salad savoy, and flowering kale, but I don't think any of those are 100% accurate. The purple kale I've found here is tougher and more bitter, with spikier leaves and a more reddish color, and it doesn't come as a bunch like this but as individual stems. Does anyone know exactly what this variety is called?

It's just a variant of kale, part of the genus Brassica. I think you'd call this particular variant redbor or purple, bluntly, but you could go further because kale is often classified by the type of leaf. So in your picture, curly 'redbor' or 'purple' kale.
This is your specific name: Brassica oleracea Acephala Group.
(just sort of look at wikipedia)


text:
Which animal that lives in the forest makes this noise?
Which animal makes this noise? Link to audio file
The file was recorded next to a forest in Germany.

You might get lucky, but noise to animal mapping is rare indeed.  Your recording is only picking up the higher frequencies this animal made, and I know a few human animals that can make a variety of non-human animal noises :)  Good luck with it!

It is a bird sound and most probaby a young bird of prey. It might be a young buzzard. Or, if it's in the eveving or night it might be the sound of a young owl.


text:
When is Pheophytin used in electron transfer to the q cycle in plants?
If I understand it correctly:
(short version)
The Q cycle starts with PQH2 it removes the 2H(+) and gives one electron to Plastocyanin and the other to a stored Plastoquinone to charge it to Plastoquinone (-). This process is repeated and adds the electron to the stored Plastoquinone(-) to create a Plastoquinone (-2). This then gets 2H(+) to form PQH2. And the cycle begins anew.
But in a lot of pictures is shown that the excited P680 gives the electron to Pheophytin and that gives it to the Q cycle.
Please let me know when and where the Pheophytin interacts to give the electron.

Not sure if there is a definite answer. However, from structural studies, its proposed that essentially the Chlorophyll a and pheophytin(Pheo) are positioned ~10A away, and the transfer of a radical electron from the P680 center to Pheophytin does occur. The exact mechanism is possibly mediated by a tyrosine

Durant J.R et al (1995). Proceedings of the National Academy of Sciences of the United States of America, 92, 4798–4802
Oleg Victorovich (2006). Retrived:5/25/16. Site: http://samlib.ru/o/oleg_w_m/cdocumentsandsettingsolegmoidokumentythefunctionandthestructureofporphyrinmoleculesrtf.shtml

3.Zouni A et al (2001). Nature, 409, 739-743


text:
Is there a difference in how Gas is produced which determines if it becomes a burp or flatulence?
I know that some gases are heavier than air and in the case of a gas leak it's best to escape to higher ground, while some gases are lighter than air such as Helium. However unlike Helium I haven't seen a burp burst into flames while I have had the unfortunate pleasure of being present at a party where flatulence was lit on fire.
So I am wondering if there is a difference in how the gas is produced which determines if it's becomes a burp or flatulence.

The gas expelled as a burp originates from the stomach. It is either gas swallowed together with food or gas that was dissolved in the drink. One prominent example for the latter is sparkling water where $\ce{CO2}$ is dissolved in the water at high concentration as carbonic acid ($\ce{H2CO3}$). Because of the acidic environment in the stomach the equilibrium between carbonic acid and $\ce{CO2}$ gas is shifted. Consequently $\ce{CO2}$ accumulates and needs to be expelled as a burp.
The gas expelled as a fart is mainly produced by microorganisms in the intestine and usually contains a lot of methane which makes it flammable.


text:
How to find PDB id of an amino acid sequence
Suppose I have an amino acid sequence whose PDB id  is unknown. Is there in online server that can find the PDB id of the corresponding amino acid sequence?  is there any site that will find the pdb of a protein closest to the query protein?

One way of doing this is to run a protein BLAST search at NCBI in which you specify the Protein Data Bank as your database, as in the example shown below:

The results will be all for proteins in the PDB.

You can also search for amino acid sequences directly at the PDB repository.


text:
Darwin's first sketch of a phylogenetic tree
Coming from Darwin's notebook this first sketch of a phylogenetic tree became one of the most emblematic image from Darwin's work.

I have a hard time to read what is written on it.
What is written on this page?

Where did you obtain the image from - is it a reproduction? The source of the reproduction may hold clues perhaps. +1

Related: A "new view of the tree of life" was just published in nature microbiology.

This is from Darwin's Notebook B: Transmutation of species from 1837–1838. From what I understand, the tree is a hypothetical depiction of descent used to discuss differences and relatedness between forms/species. This is the text that accompanies and follows the sketch (notebook pages 36-44):

I think
 (sketch)
Case must be that one generation then should be as many living as now. To do this & to have many species in same genus (as is) requires extinction.
  Thus between A & B immense gap of relation. C & B the finest gradation, B & D rather greater distinction. Thus genera would be formed. — bearing relation
(page 37)
to ancient types. — with several extinct forms
  for if each species an ancient (1) is capable of making 13 recent forms, twelve of the contemporarys must have left no offspring at all, so as to keep number of species constant. —
  With respect to extinction we can easy see that variety of ostrich, Petise may not be well adapted, and thus perish out, or on other hand like Orpheus being favourable
(page 38)
many might be produced. — This requires principle that the permanent varieties produced by inter confined breeding & changing circumstances are continued & produced according to the adaptation of such circumstances, & therefore that death of species is a consequence (contrary to what would appear from America)
(page 39)
of non-adaptation of circumstances. —
  Vide two, pages back.
  Diagram
  The largeness of present genera renders it probable that the many contemporary, would have left scarcely any types of their existence in the present world. — or we may suppose only each species in each generation only breeds; like individuals in a country not rapidly increasing. —
(page 40)
If we thus go very far back to look to the source of the Mammalian type of organization; it is extremely improbable that any of his relatives shall likewise the successors of his relations shall now exist — In same manner, if we take a man from any large family of 12 brothers & sisters in a state which does not increase
(page 41)
it will be chances against any one of them having progeny living ten thousand years hence; because at present day many are relatives, so that by tracing back the descen fathers would be reduced to small percentage. — & in therefore the chances are excessively great against any two of the 12. having progeny after that distant period. —
(page 42)
Hence if this is true, that the greater the groups the greater the gaps (or solutions of continuous structure) between them. — for instance, there would be great gap between birds and mammalia, Still greater between
(page 43)
Vertebrate and Articulata, still greater between animals & Plants.
  But yet, besides affinities from three elements, from the infinite variations, & all coming from one stock & obeying one law, they may approach, — some birds may approach animals, & some of the vertebrates invertebrates —
  Such a few on each side will yet present some anomaly & the g bearing
(page 44)
stamp of some great main type, & the gradation will be sudden.
  Heaven know whether this agrees with Nature: Cuidado.

The text together with actual pictures of the notebook pages can be seen at http://darwin-online.org.uk. Pages ~38-41 are often seen as key ideas for Darwin's formulation of natural selection. Also note that the presence/absence of a horizontal line at the tips are apparently used to denote extant vs extinct groups (see notes in link above).


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How do organoarsenics improve digestion efficiency in poultry?
It struck me as very surprising that these organoarsenic compound with structure looking not very compatible with living system is widely used as food additive to increase weight gain and improve food efficiency in poultry. I wonder what is the mechanism of action that causes the effects in these animals?
For instance, here is the structure of one particular additive - Roxarsone:

We used to treat a lot of poultry workers around here - before the plants closed down - for coccidial diarrhea. My guess (and why this is not posted as an answer) is that it's added for its anticoccidial actions. Coccidiosis - an intestinal parasite which decreases the effectiveness of ingested nutrients - is the most costly disease threat to poultry production.  Keep the poultry intestinal tract healthier => poultry do better. If it's more than this, I'm intrigued.


text:
Can a single strand of mRNA form different polypeptide chains?
My book has a statement:
A single strand of mRNA is capable of forming a number of different polypeptide chains.
In my opinion this statement is wrong because a single strand of mRNA will have same sequence of codons. So, every time it gets translated, it produces same polypeptide chain. But, according to my book this statement is correct.
Am I wrong or is my book wrong?

Is your book talking about eukaryotic or prokaryotic mRNAs? You (and anyone answering) need to know as the rules are completely different in the two cases.

And you should also provide the name and edition of your book. We may then be able to check if your are misquoting it or quoting it out of context. (We have ways of finding these things...)

Could you please add some more context to the quote from the book (i.e. what is the topic of the paragraph/chapter, what is the title of the book etc.)

I believe, your book refers to  polycistronic mRNA. This is mRNA where multiple genes are encoded together in one mRNA and are often (but not necessarily) translated one after another. This is mainly found in prokaryotes where the proteins encoded on the same mRNA often form a metabolic pathway together.

I would change 'mainly' to 'only' unless you or anyone else can give a eukaryotic example. The mRNAs that use IRESs only have a single one as far as I'm aware. Polio, for example makes a single polyprotein which is proteolytically cleaved.

@David: There are a few rare cases of polycistronic mRNA in insects.

@David IRESs can lead to production of multiple polypeptides. The mRNA is essentially polycistronic in this case. Example http://www.ncbi.nlm.nih.gov/pubmed/19285701. The proteolytic cleavage is a different mechanism.

Thanks for the links. This stuff has clearly passed me by. It would be interesting to know the mechanism in the case of the insect short peptides — whether it's leaky scanning or what.

You can come at mRNA from two directions. Remember that human genes are largely monocistronic, in other words they often code for a single protein. If we look at prokaryotes, however, polycistronic genes such as those in operons are very much possible. From a single lac mRNA you can get multiple proteins.
For humans with monocistronic genes, you can code for multiple isoforms, however. A good example is protein kinase C: You have PKC-α, PKC-δ, and so forth. So how can this be? In part, you can look at splicing. What gets initially transcribed from your human gene is a pre-mRNA, in that the entire gene contains introns and exons. The spliceosome knows where to cut out introns, and you technically get a mature mRNA that is made of only exons and codes for protein.
In special cases, however, RNA-binding proteins and—at times in concert with, at times to the detriment of—the spliceosome machinery alternatively splice some other combination of introns and exons (sometimes, introns are kept!). And so from the PKC gene, you still get PKC, but a different isoform of it. The different proteins that different types of cells or tissues express that can interact with the splicing machinery are capable of taking the same genetic information, the same pre-mRNA, and make different polypeptides out of it.

Alternatively spliced transcripts are technically different mRNAs.

@WYSIWYG yes, but the OP's book doesn't specify whether this is mature or pre-mRNA.

I don't see how you can assume the book refers to eukaryotic mRNAs. Especially if the book is old, it could quite well refer to bacterial polycistronic mRNAs, which could well be the answer. But without qualification the question cannot be answered, and this point should be emphasized to naive users (and responders). Certainly differential splicing is completely irrelevant and quite misleading, as WYSIWYG might have said if he were as blunt as I am.

I agree that Splicing is off topic and should be removed from the answer.

@terdon the quoted statement in the question clearly states mRNA not pre-mRNA.

@Thawn yes, but it could be misquoted since there is no context and it doesn't seem very trustworthy as a quote to begin with since it claims that mRNA can "form" proteins. I just figure it might refer to polycistronic prokaryote mRNAs or unspliced eukaryotic transcripts. For all I know, the book's authors might even have been thinking of post-translational modifications. Without more context, it's hard to know.

@terdon I just asked the OP to add more context to the quote. Hopefully he complies and we can find out :)

As much as I love Biology SE, I will need down-votes to defend their votes here because I see nothing wrong with this answer. The assumption is that we have mRNA, and unless explicitly noted I've assumed any mRNA to be included, including pre-mRNA.

@CMosychuk I read the question twice and while I understand the criticism, I believe the book is talking about splicing variants as well. It is just badly worded. In any case, I vote to keep this answer here so that both scenarios (1 mRNA -> multiple proteins and mRNA -> multiple proteins) are covered.

@CMosychuk There is nothing wrong with this answer as long as you clarify the premise, which you did. Someone downvoted my answer too, which is certainly not "not-useful" or "poorly researched". Nevermind.

Apart from the polycistronic case there is another possibility of one mRNA yielding multiple proteins. By one mRNA, I mean that the RNA is not in any way altered because of RNA editing or other mechanisms.
Translation can be initiated at alternative sites leading to production of different protein products (Touriol et al., 2003). VEGF is one of the genes that exhibits this phenomenon. However, the precise factors that regulate the choice of the translation start site are not very well known. The basic mechanism, however, seems to be masking of the alternative start sites by different factors such as secondary structures and/or trans regulatory factors.
Similarly a stop codon can be skipped. This is frequently seen in the case of the UAG (Amber) stop codon. This phenomenon is called amber suppression (see this post). Again, the factors that regulate this phenomenon are not well known.
Having said all this, I am 100% sure that your textbook refers to polycistronic mRNAs only.


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What are the theoretical and actual (measured) minimum water potentials in plants?
I'm a plant physiology researcher, but water potentials are not really my thing, so I don't have a great grasp on the literature. I'm dealing with water potential data right now though, and it seems questionable to me. Some of the measured water potential (solute + metric potentials, after lysing cells to break turgor) are as low as -48 bars (most in -10 to -35 range).
That would, if my math is correct, translate to a solute concentration in the 2000 mOsmol range, which seems extremely high to me. Consequently, I'm trying to determine if there is an analytic issue with the data collection. I've run through the equipment chain, checked calibrations, and everything seems ok. I've also been combing plant physiology lit. for comparable data, and I find some in that range, but I can't find any theoretical work that would help set a 'ceiling' for what constitutes a reasonable solute + metric potential.
So, my questions are these:

What is the theoretical maximum capacity for dissolved ion concentration in water, and what pressure potential would that represent, compared to pure water.
Is anyone aware of plant physiology research that has attempted to establish a minimum in vivo water potential in plants (either total potential, or S+M if it's broken out)?

Sodium Chloride (which I am here assuming to be the major salt in your solution) has a solubility of 6 Moles/L this corresponds to 12000 mOsmol, so the 2000 mOsmol you are measuring is not entirely implausible. However normally plant cells should have an osmolarity on the order of 300-400 mOsmol. In order to judge if your value was calculated correctly, it would be necessary for you to tell us exactly how you calculated and how you measured.
I am not aware of such literature but I am not a plant physiologist myself.

Thanks. Measurements were taken two ways: tissue was measured in the field, with a 'pressure bomb' (https://en.wikipedia.org/wiki/Pressure_bomb) and additional measurement was done with both needle and woody tissue using chamber psychrometers  (a small sealed chamber that holds tissue and contains an electrode, the resistance of which changes depending on humidity, which changes based on the tissue's hydraulic status). The pressure bomb is pretty much foolproof, but the psychometry work depends on calibration, which i've checked, repeatedly, using lab standards.

Also, I'll add that your linked source for osmolarity isn't necessarily troubling for my result--osmolarity increases vertically with plant height (to pull water against gravity) so the lowest osmolarities would be seen in root tissue (tubers) and it would increase as you rise through stem, branches, and leaves. Hard to say though, since tubers aren't 'regular' roots, and plants deliberately manipulate solute concentration in 'storage' tissue, like tubers. I've done a similar teaching lab, and the variance between potato varieties is pretty huge.

Thanks for the clarifications. If you can exclude any other sources of water potential (capillary forces, air pressure, etc.) I guess the 2000 mOsmol are correct. However I must caution you again that I am a biophysicist, not an expert in plant physiology.


text:
Indoor plants acidic soil
I have a ponytail tree plant. The new growth look anemic, pale and thin. And several leave have browned from the midway to the ends of the leaves. The stem is woody and firm. Though it is in a solid pot, the soil tests dry, and there seems to be reasonable space for root growth. I have just moved it so it can get eastern morning sun for several hours. I have tested the pH of the soil and it tested to be a pH of 4.0. Can someone help me diagnose and treat my plant.
Thank you.

could you add a picture?

That's a super low pH, and I kinda doubt it's real. If you used a cheap home test, it's more likely analytic error (not necessarily your fault, it's just a hard thing to measure) than a real result. 4.0 pH is lower than most plants can tolerate--it's in the range of vinegar. Most plants (I have no experience with this species) prefer a slightly acidic soil, ~6.8pH. So, if your pH is really 4.0, then that's almost certainly a problem. It messes up the cation-exchange capacity of the soil, so even if you fertilize, the plant can't access the nutrients.
You can easily amend with some lime--if you don't want to dig it up, you can just scratch it into the top of the soil, and water through it. It will leech down through the pot. Hope that helps.

I used a Dr Meter soil survey instrument

Although pH 4 is low, it's not impossible. Natural sandy soils in my country can have a pH even below 4 (with aluminium toxicity as result). I agree that liming could work here though.


text:
Techniques for detecting phosphorylation sites in proteins?
I would like to know how phosphorylated sites in proteins are detected in practice. I read some papers where the authors were talking about mass spectrometry techniques.
But my question is that why can't X-ray crystallography or NMR techniques capture phosphorylated sites?
(Note : My background is electronics engineering, so I am not an expert in this area.)

In principle X-ray crystallography or NMR could detect phosphorylation sites but they are much more complex and expensive techniques than mass spec. So for simply figuring out phosphorylation patterns in a protein is much easier using mass spec.
Detailed reasons:
For X-ray you need to crystallize the protein which is often very difficult/impossible and requires quite a lot of sample material. Afterwards you need a good X-ray source (ideally a synchrotron beamline) and record the scattering pattern over an extended range of angles (at least 180 degrees) before your crystal evaporates in the intense X-ray beam. Last but not least, you need additional chemical tricks, elaborate mathematical models and a large amount of computing power to compensate for the fact that in X-Ray crystallography you lose the phase information (because there are no suitable lenses for X-rays).
For NMR, you need large, very strong superconducting magnets, sophisticated radio transmitters and receivers, complicated math and computing power. However even if you have all that, you are still limited to very small proteins because otherwise the NMR spectrum is simply too complicated to be solved.
In contrast, for mass spec, you need a (highly sophisticated) spray gun, a moderate magnetic field and an electron multiplying detector. This is still a very sophisticated machine but much simpler compared to the above. In addition, data analysis is simpler than in the above cases.
Basically if you don't need to know the structural changes induced by phosphorylation (for which you would need to compare the structures of two crystals), you would stick to mass spec.

X-ray crystallography has been used to detect phosphorylated sites.
The RCSB protein database currently contains 856 structures that have both a resolution below 3 angstroms and the keyword "phosphorylated" in their listing.
It also appears to be possible to use NMR to study phosphorylated proteins.
The situations where NMR/x-ray crystallography or mass spectrometry are used differ. These differences may explain why a paper discussing the detection of phosphorylation using mass spectrometry would make no mention of NMR or x-ray crystallography.
NMR/x-ray crystallography provide structural data and almost always utilise known protein sequences.
Mass spectrometry has two major strengths for phosphorylation site detection and these highlight the reasons for using it. The first strength is the ability to gain information about many phosphorylation events, including unknown ones, from a single liquid chromatography MS/MS run. The second strength is the potential to quantify multiple phosphorylation sites from a minimum of 3 runs of a single sample.


text:
Mutating a protein without mutating the gene?
Is it possible to mutate a region of a protein (says about 300 amino acids long) without actually mutating the gene?
One possible way that I can think of is to use RNAi and specifically block that region of the mRNA which codes for the 300 amino acids in the protein?
But then wouldn't it cause a problem in the translation of the remaining region of the protein?
Are there any methods out there to mutate a region of a protein without mutating the DNA?

"One possible way that I can think of is to use RNAi and specifically block that region of the mRna which codes for the 300 amino acids in the protein?".... Not possible. RNAi doesn't work that way.

Maybe there is a chemical to make error during translation by ribosoms.

I assume that you mean changing the amino acid sequence in a single protein in an organism to one that no longer reflects the sequence predicted from the DNA sequence.  In that case, I would suggest using ADAR (Double-stranded RNA-specific adenosine deaminase) or similar enzymes.  ADAR deaminates adenosine to inosine, which is read by the ribosome as a guanine.  I know that it's activity is regulated, but I'm not sure how you could redirect it (perhaps with an antisense RNA that yields a double-stranded binding stretch in the target RNA.

To a certain extent, maybe. However RNAi would not work as you describe because it causes the whold mRNA to be degraded not just a portion of it.
If the gene in question is spliced, you could probably influence the splicing pattern by triggering certain signalling pathways. But this is limited to producing different splicing variants of your gene and is likely equally or more difficult than mutating the actual gene.
Another alternative would be to produce mutated mRNA and inject/transform/transfec that into the cell in question but again this is likely as difficult or more difficult than mutating the gene.


text:
Effect of interruption of photoperiod in a short day plant
When a short day plant is exposed to its critical period of darkness it flowers. But when it is exposed to a small period of red light which exceeds the critical period it doesn't flower.
But when it is exposed to small and equal amounts of red light and far red light it flowers even though it exceeds the critical period of light.
How is this possible?

can you add the source of this info? more importantly, is it homework?

I read it in a magazine

which plant species?

It is not mentioned in it...


text:
Effective Mycoplasma Elimination from Primary Human Cultures
Obviously the best way to avoid mycoplasma contamination is to avoid it in the first place.  In our case, however, it is not possible to avoid.  We are culturing viruses and tissues out of human nasal swabs, washes, and biopsies.
As you can imagine, anytime you are pulling something out of someone's nose, it is quite often full of mycoplasma.  I've reviewed current examples of mycoplasma elimination, but found the section in Current Protocols in Molecular Biology to be the most helpful.
Indeed, we found that checking with a PCR based kit for common lab mycoplasma contaminants often missed detection of mycoplasma, because it did not include "clinically relevant" strains. Kits which did include these species clearly detected mycoplasma, in addition to Hoechst stain confirming their presence.
Now the question is there a good way to remove them?  We've tried serial dilutions, elimination kits (also MycoZap), titrated doxycycline and enrofloxacin doses, and even mouse passage.
Of these mouse passage was probably the most effective, but not desirable because it might induce additional confounding factors.  The kits had fair results, but 5 passages post treatment mycoplasma were again detectable via Hoechst stain (PCR detection persisted through out).
The dox and enrofloxacin may have produced better results at higher concentrations, but cell toxicity became a serious issue.  I was wondering if anyone had examples of combination methods for cleaning primary cells and/or virus stocks (been grown on more standard immortalized cell lines) for a more complete treatment method.
Just as note on our hands, we regularly check our cell lines, and are in fact maintaining a mycoplasma free tissue culture system.  Further, as proof of concept, we were able to clean a culture that was known to be infected with M. hominis with kits.
It doesn't seem worth the effort, but is there any evidence to suggest typing down to the species would be worth it in the eradication effort?  Each donor could conceivably be providing a different contaminate.

did you try using a combination of dox/enrofloxacin? Also, did you try using an iron-free medium during enrofloxacin treatment? enrofloxacin kills by chelating iron, so the less iron in the medium the better (however the cytotoxicity may also increase)

As far as I know Doxicyclin is a bacteriostatic antibiotic not a bactericide which in your case could be the reason why some mycoplasma survived and started to grow again at the end of treatment. As a potential solution, you could try (combinations) of other bactericide antibiotics that are effective against mycoplasma.

@Thawn Dox/Enrofloxacin were used sequentially (in both orders), but we found the direct combination too toxic.  EMEM was tried, which has minimal iron.

@Thawn I believe combinations of antibiotics are used in the commercial kits.

I guess then I am out of ideas, sorry

@Thawn No worries, that's why I posted here. I'm still considering multiple antibiotics where the concentrations aren't proprietary (ie mixing ourselves)

I use plasmocin. I haven't had any mycoplasma contamination, but we use it preventatively so when we make the complete media, it has the plasmocin in it. You have to keep in mind though to make fresh media every 2 weeks or so. The prophylactic, catalog ant-mpp, will cost you around 135.00. For active contamination, the treatment kit ant-mpt is 205.00 (prices through Fisher).

@CMosychuk You don't by any chance know what antibiotics are in Plasmocin do you?  Also, prophylactic treatments are meaningless for us because we will be spiking in/starting from known contaminated samples ("wild" from donors).

@AtlLED It's a proprietary mixture, from their webpage "The first component acts on the protein synthesis machinery while the second acts on the DNA replication." So very vague.

I don't want to defer you but this is also a good paper, and the same authors did another study elsewhere where they used plasmocin very successfully.

@CMosychuk I agree it's a good paper, that's why I linked to the same paper in my question [but in Wiley instead of Springer] :)

@CMosychuk Just to fill you in, gave Plasmocin a shot, at recommended and higher doses, and did not find it better than other kits/antibiotic treatments.  Mouse passage remains the best so far, but still doesn't allow for complete removal (and adds all kinds of other confounding variables).


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Rifle Bullets and Lead Exposure
Does anyone know if simply touching bullets could give you lead poisoning?

Simply touching bullets couldn't give you lead poisoning, since nowadays bullets are usually coated in a protective copper shell.
What makes bullets dangerous isn't the actual bullet but the way lead is expelled from it upon shooting.

When a bullet is fired, it gets so hot that that lead actually vaporizes.
  ~Sarah Zhang
  http://www.motherjones.com/blue-marble/2013/01/lead-shooting-ranges-osha

Thus, just touching the outside of a bullet wouldn't be damaging. The only real ways to get lead poisoning would be by inhaling lead in the air - but even that would have to be in large amounts - or by touching lead directly and then putting your finger(s) in your mouth and ingesting it.
See this link for more information.


text:
How do we find antibiotics?
So the last class of antibiotics were made in 1984 (I think), which makes it appear as though they are hard to find(/design maybe). How is it then they were discovered? Was it by chance? I know some where accidents, but how are the majority found, testing lots of chemicals on your target?
I imagine now we would have the capability to quickly identify structures and molecules unique to pathogens and be able to model them on a computer, and generate suitable proteins or other compounds that can interfere with their bonding/properties to damage the pathogen?
For something like a 70s ribosome in a pathogen, what is the process of being able to understand its structure, its shape, etc? How much effort does it take to model onto a computer? Or instead a single protein (as a 70s ribosome will be more complex), how long does it take to model a new protein?
Thanks for any help :)

You have lots of questions.  Which is the exact one you want answered?

Was it by chance?

Yes, sometimes, Penicillin was discovered by chance (and good observation), see http://www.nobelprize.org/nobel_prizes/medicine/laureates/1945/fleming-bio.html.

I know some where accidents, but how are the majority found, testing lots of chemicals on your target?

Other important classes, like tetracyclines, were discovered by screening of soil samples for antibacterial activity (The history of the tetracyclines
). At that time it was not known what is the target of tetracycline, it was only observed that it was able to inhibit bacterial growth.
A synthetic antibiotic, nalidixic acid, was discovered as an impurity in the synthesis of another pharmaceutical agent and later became the template for other important antibiotics like ciprofloxacin. (Origins of the Quinolone Class of Antibacterials)

I imagine now we would have the capability to quickly identify structures and molecules unique to pathogens and be able to model them on a computer, and generate suitable proteins or other compounds that can interfere with their bonding/properties to damage the pathogen?

In theory, yes, but from computer simulation to a drug there is a long, bumpy road. Most bacteria have a cell wall (with either one or two membranes, see here for a detailed discussion), so drugs need to penetrate this barrier before reaching their target. Even if they do so, they must also preferably inhibit bacterial enzymes but leave human enzymes active. This is especially complicated for targets, like DNA replication, protein synthesis, etc. which evolved early in evolution and are common to bacteria and humans. Some antibacterial drugs target tiny differences between humans bacteria, for some like Gentamicin it works well, for others like Chloramphenicol the side effects are dose-limiting. Here is a good blog entry on this topic: Antibiotics not as easy as theysay, look at the blog for other excellent comments on drug discovery and antibiotics).
For something like a 70s ribosome in a pathogen, what is the process of being able to understand its structure, its shape, etc? How much effort does it take to model onto a computer? Or instead a single protein (as a 70s ribosome will be more complex), how long does it take to model a new protein?
To quote Wikipedia:

"Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. [..] The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins."

To get a computer model of the structure for a single protein where a similar protein is known, it takes a few hours. But to validate this model, i.e. showing that the hypothetical structures matches the real structure, it takes months of human work. You can imagine how much work it is for 31 proteins. In addition tiny deviations in the model, may cause your predictions to give false positive or negative hits (i.e. your computer model predicts that inactive compounds bind to the target or real inhibitors don't do anything to the target).
The traditional approach, finding compounds which kill bacteria or inhibit their growth, is much more promising since one might discover novel targets in bacteria and microorganisms came up with dozens of ways of killing their competition. One new approach is to cultivate bacteria which cannot be cultivated with traditional methods and screen them for antibacterial compounds, e.g. as described in this summary of this research article
Some more good reads on this topic:

The role of serendipity in drug discovery
A Brief History of the Antibiotic Era: Lessons Learned and Challenges for the Future

I don't think that computer modeling will be the way new antibiotics in the near future are discovered. Besides all the issues with modeling itself as mentioned above, it's also really easy to find something that kills bacteria (semi-relevant XKCD: https://xkcd.com/1217/), but you really need something that's also mostly harmless to human cells. So you'd need to model not only the ribosome (and who says that's the only / best target) but also the whole of the human proteome to see if a compound doesn't to anything bad there.
For the near future I don't think we have anything better than just screening: throwing everything we have at bacteria and human cells, and seeing which compounds specifically kill bacteria. An example of a big project in this field: http://www.nature.com/nature/journal/v533/n7602_supp/full/533S65a.html
To make your hit-rate a bit bigger you can always make a big selection of "antibiotic-like" molecules and test those: http://www.nature.com/nature/journal/v533/n7603/full/nature17967.html


text:
What would happen if nerves didn't have refractory period?
What would happen if nerves didn't have refractory period? And, what part of his nervous system or neurons are not needed?

Who is "his"? Are you talking about a human neurologic system in general?

Yes it is a scenario case.

Is this a homework question? If so, you may want to check this out on the help page... http://biology.stackexchange.com/help/homework

Are you asking about the theoretical implication in terms of the function of neural system? Clearly this is not a biophysically plausible scenario since it will allow infinite number of action potentials in a finite time.

Refractory period returns the repolarization period to the nerve's resting potential . it's the time taken for recovery of a neuron to generate another impulse being excited by another stimulus . so if nerve doesn't have refractory period they wouldn't be able to return to its resting potential & generate new impulse . moreover the repolarization potential further exceeds its value and cause hyperpolarization , so its badly necessary to restore to resting potential by expelling na+ and taking k+ in . unless it would be impossible to restore the resting potential & be ready to get excited to transmit another impulse via the electrochemical pathway . one more benefit of refractory period is that it causes unidirectional impulse conduction.
I didn't get the 2nd part of your question. What are you trying to mean , make it more clear.

Nice answer, but since you are a new user, you should give some source/reference for the answer.


text:
Term of the type xxx-troph for a compound not used by an organism

A prototroph for compound X can make it
A bradytroph grows faster if X is scavenged
An auxotroph needs to scavenge X
A hyperauxotroph lacks both the biosynthetic pathway and the transporters for X

However, I cannot find the term for when the metabolism is rerouted to not need that compound. A term exists and it isn't with an obvious prefix like para, exo, ecto, juxta or similar, but that is as much as I recall: I cannot recall it or where I read it. Has anyone ever encountered said term?

Perhaps you're looking for the word mixotroph?

A mixotroph is an organism that can use a mix of different sources of energy and carbon.

In other words, as stated by Schoonhoven (2010):

The capability of one organism to be autotrophic and heterotrophic at the
same time.

I was thinking in terms of artificially "biotin-independent" bacteria, where the requirement for biotin is circumvented. However, a different group made it first and they simply used the word independent.
Using a different example, E. coli is ascorbic acid-independent (GSH acts as vitamin C), it is auxotrophic for B12 (combalamin), but it is prototrophic for methionine (as it has both routes).


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Links between Genetics and Personality Types
This topic was visited briefly in the thread, Genetic Effects on Personality, but I was surprised not to find more on it. (Is there a taboo I don't know about? What's the ethical stance on this nowadays?)
(An answer in that thread mentions serotonin receptor genetics specifically as having strong links to personality, but provides no explicit references.)
The question: What links have been measured between genotypes and personality outcomes within personality frameworks/models like the Big Five?
Related:
 - An Overview of Personality Models?
 - Genetics and Intraversion/Extraversion

Welcome to Biology.SE. This question is too broad. Also, the statistic you are interested in is called heritability. You should read Why is a heritability coefficient not an index of “how genetic” something is? to understand what it means.

One can find estimates of heritability on H2DB data base.


text:
What are sex linked traits?
Which of the two definitions of sex-linked trait is correct?

Traits controlled by genes present on the non-homologous region of sex chromosomes are called sex-linked traits.
Bodily traits controlled by genes present on the non-homologous regions of sex chromosomes are called sex-linked traits. Here by bodily traits I mean traits that are not involved with sex of an organism.

I read the first definition in the book Competition Science Visionand also from Instant notes genetics (page 163).
The following is an excerpt from the latter

Sex linkage is not displayed by genes which map to a small segment of X chromosome, the pseudoautosomal region, the part of X chromosome that pairs with Y chromosome in meiosis.

The second definition is made up but sounds potentially intuitive to me.

What do you mean by "traits that are not involved with sex"? Do you mean traits that are unrelated to (primary or secondary) sexual organs?

Yes that is what I meant

I edited your post. Feel free to roll-back. If you agree that the format is much more pleasant to read than before then you can inspire yourself for future posts and try to always use a pleasant format for the readers.

The first definition is correct.
A sex-linked trait is a trait affected by a locus on a sex chromosome.
If you google sex-linked trait, you will find this same definition (not the exact same words) over and over again.
The definition of sex-linked trait is NOT restricted to traits that are not unrelated to primary or secondary sexual organs. Any phenotypic trait can be sex-linked as long as the causal locus is on a sexual chromosome.

"a locus that is present in individuals of only one sex..."  isn't that wrong? Genes on the X are sex linked and therefore present in both sexes

Yes, you are right that was wrong! I edited it. Thanks.

@Remi.b What are X-Y linked traits then? Are they what the book says, traits controlled by genes present on homologous regions of sex chromosomes?

yes, traits causes by genes present on NON-homologous (you said the opposite in your comment) sequence on the X or Y chromosome. In case you did not know the non-homologuous sequence of X or Y chromosome.

Sex linked traits are those controlled by genes on the sex chromosomes, regardless of whether or not they are related to reproduction. This can be the major (e.g. X or Z) or minor (e.g. Y or W) sex chromosomes.

"Sex linkage applies to genes that are located on the sex chromosomes. These genes are considered sex-linked because their expression and inheritance patterns differ between males and females." - link

Note. Most traits are polygenic thus some of the causal genes may be sex linked, and others on the autosomes. Phenotypic traits can therefore have varying degrees of sex linkage.


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Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?
Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?

Yes, there are certain amino acid sequences that tend to form alpha-helices, and others that prefer to form beta-sheets. There is no perfect correspondence between sequence and structure, but there is a statistical relation where presence of certain amino acids in particular sequences makes one conformation or the other more likely. For example, alanine, glutamate, leucine and methionine tends to be present in alpha helices.
This topic has been studied for 50 years or so, and there are many methods available for predicting structural features from an amino acid sequence. See this list of available software, and this article about protein structure prediction in general.
See this table from another answer on this site which shows which individual amino acid prefers which secondary structure (higher value shows higher preference):


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distribution of some injected materials/medicines through blood vessels
Fastest distribution of some injected materials/medicines & with no risk of any kind can be achieved by injecting it into - artery or vein?

it depends on where you are injecting it or what is the target organ, etc. In general terms, it'll be artery because arterial blood flows with more pressure and venous blood has to be pumped before being circulated in the body.

It depends on what your target tissue is, as @another 'Homo sapien' stated.
If you want to get something to the hand, for instance, injecting it into the brachial artery will get it there "faster" than injecting it into the cephalic vein.
However,

Fastest distribution of some injected materials/medicines & with no risk of any kind

does not exist. There are risks with any invasive proceedure, and invading arteries is riskier than invading veins. Unless the risk outweighs the benefit, substances which cannot be administered orally are given intravenously. Arterial lines are usually used for purposes other than injecting substances.
Arterial Line Placement


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What are silent carrier traits?
I couldn't find a definition but I have come to know the following from google search:

People who are carriers of a thalassemia gene show no thalassemia symptoms and might not know they're carriers.

So is thalassemia a "silent carrier trait"?

How many times do I have to tell you that you should not ask a question about the definition of a term that is not really a standard term? There are no "definitions" for terms like these; they are just contextual and anyone who understands English language would figure out what these terms mean. You did the same in your other question on "Why is tRNA called an adaptor molecule".

Thalassemia is a recessive trait. That means individuals with only one copy of the allele (Heterozygotes) have the "normal" phenotype (they don't have Thalassemia).
If an individual is homozygous for the recessive allele they will have Thalassemia.
Heterozygotes are often referred to as carriers as they can transmit the allele to their offspring, but do not themselves express the trait.
"Silent carrier trait" is quite unusual terminology, just call it a recessive trait.


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How does mutualism arise?
How can a mutualism between two species arise? I have thinking about this for a while and I have come up with the following points
1.If mutualism gives one specie a competitive edge over its competitors then it could arise. Suppose you are being really pounded by your competitors and there is now way you can survive except if you give in to mutualism, even if it means "selling your soul".
2.The benefits received from the partner species outweighs the costs involved in helping it out.
I cannot think of any more examples. Please suggest a few; also point out if there are flaws in my reasoning.

What does "selling your soul" imply?

I am afraid this question is too broad and I am voting to close. Evolution of inter-specific mutualism is a large subject. Here is not a complete answer but just a few comments on your two conditions

1.If mutualism gives one specie a competitive edge over its competitors then it could arise.

This is mainly wrong. Mutualism is likely to increase if mutualistic behaviour offer increases the fitness of the individual performing it, you would expect mutualistic behaviour to increase. You would not really expect the same by comparing species ability to survive in relation to their level of mutualism.

2.The benefits received from the partner species outweighs the costs involved in helping it out.

Again, you are talking about the benefit for a species. You should boil down your arguments to the individuals. It is true that mutualism can evolve only if the individual performing the mutualistic behaviour enjoy a higher fitness benefit than fitness cost (if any).


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Is evolution a predictive theory?
My feeling is that almost any observation can be explained by current evolutionary theory. Is there any example of someone developing a rigorous framework or mathematical model of how evolution works?

I edited your question to remove the "primarily opinion based" part. Feel free to roll back if you don't like the edit.

While I agree the OP might be opinion-based (see its activity on the site so far), with the edit the question is not anymore. I agree it is impossible to draw a full picture of mathematical models used in evolutionary biology (would be too broad), it is still possible to answer to the question whether or not such mathematical modelling exist in biology. I think this question should remain open especially that it may help future users.

I have removed "useless as" from the title. If you want to know whether the theory of evolution has or does not have predictive power, the shortened title does this perfectly well. Including "useless as" is an unsubtle and unscientific way of indicating that you are expressing an opinion rather than asking a question.

It's still useless

Evolutionary biology is a highly quantitative science and offers a fair amount of predictive power. However, at the same time, there are plenty of things that we are completely unable to predict.
What are we good at predicting?
There are plenty of things and it is impossible to list them all. Here are a few examples of things we can predict.

Number of pairwise differences (or other measures of molecular differentiation) do we expect between two lineages that recently split in a given number of years.
Number of pairwise differences between individuals coming from the same population.
Number of mutations of given fitness effects (whether beneficial or deleterious) do we expect to accumulate over a given period of time in a population. We can predict the age of a lineage.
Predictions about the evolution of multicellularity, sociality, etc. in lineages that are limit-cases (relating again to our ability at a short time only).
Speed of evolutionary change as measured in Haldanes or in Darwins (these are units) (from knowledge about the genetic variance).
Predictions about the heterozygosity of a population and the loss of heterozygosity through time.
predictions about the gene flow, migration rate or strength of selection.
Predictions of the consequences on fitness that a change in population size may cause.

Generally speaking, we have good predictive abilities at short time scale OR for neutral sequences OR for conserved sequences (strong purifying selection).
In short, we can predict a lot of things but by far not everything yet.
Main complications in doing predictions in evolutionary biology
I would suggest decomposing the reasons why predictions can be hard into the following categories. However, I might well forget something and one could argue that my semantic is less helpful some other semantic.

Environment

One issue related to making predictions at long time scale is that the environment changes through time in a way that we are not able to predict accurately enough yet.

Noise (incl. genetic drift)

I am not here talking about measurement error or sampling error (these are statistical concepts you may want to check if you don't know them), I am talking about the stochastic process that is inherent to biological systems such as the randomness of mutation processes and genetic drift.

Genotype-phenotype map

We have too little understanding of molecular genetics in order to be able to predict how different specific mutations would affect the phenotype. As a consequence, today we still have very little predictive power about the evolution of a phenotypic trait that is currently totally inexistent.

Complex systems

For example: demography affects evolution which affects the social environments, which affects demography which affects the pattern of species competitions which affects the evolution of another species which affects its demography which affects the evolution of a third species which affects the demography of our first species, etc... These kind of complex systems are often mathematically not tractable.

Parameters

We often don't know the exact parameters of the lineage we are interested in. There is a lot of measures to take to be able to make predictions and we often don't have the money (or the time) to make all these measurements (assuming we are able to accurately measure them). For this reason, we are often relatively good to make predictions for a few model organisms but pretty bad for the vast majority of species.

Applications of evolutionary biology
There are not a lot of applications of evolutionary biology for the moment but still, there are some proving its predictive power. These applications include

medicine and epidemiology (incl. evolution of resistance)
artificial selection and other techniques mainly to improve crops (e.g. nuts)
Various search algorithms such as the genetic algorithm

Note, my answer was partially recycled from this other answer of mine
Answering directly in your text

It seems like almost any observation can be explained by current evolutionary theory

This is wrong. You should learn more about evolutionary biology (starting with Understanding Evolution by UC Berkeley for example) and you will understand why it is wrong. I can't make a whole introduction to evolutionary biology in a single post.

Is there any example of someone developing a rigorous framework or model of how evolution works?

Yes, there are thousands of such models depending on the exact evolutionary process of interest. Just to give you a feeling of it, you could have a look at any book recommended on the post Book recommendation on population/evolutionary genetics?. If your knowledge in math is a little weak, then you might want to have a look at the introductory book A Biologist's guide to mathematical modelling in evolution and ecology (Otto and Day). While this book is quite introductory, I would still recommend starting with an even more introductory course as suggested above.
Standard mathematics methods used in evolutionary biology include branching processes, birth-death processes and other Markov Models, mathematical statistics and probability theory, diffusion equations, approximation theory, ...
On a side note, you would note that the development of statistics is very much related to evolutionary biology. This is true historically but is still true for the development of modern statistics. Just to cite one person, Ronald Fisher was an evolutionary geneticist (one of the fathers of the modern evolutionary synthesis) and he invented some of the most used statistical tests (t-test, anova-F-test, Fisher's tests).

So in other words the useful evolutionary biology ("complex systems") doesn't exist

Can you reformulate your question in the comment, I don't understand it. What do you call "the useful evolutionary biology"?

If your comment asked "is there any usefulness to evolutionary biology", I redirect you to the application section in my answer. Yes, to medicine, to designing better crops (resistant to drought or to the warming climate), to predict the yield that can be achieve by fly farming and to know what population size should be used for fly farming, etc...

That's agronomy and really has nothing to do with this

You seem to be primarily opinion based. Predicting change in a quantitative trait of interest to agronomist definitely has to do with evolutionary biology. The food industry is an important private sector that hire plenty of evolutionary biologists.

No they dont. It's an almost entirely ivory tower field

You know nothing about this field you are describing (as it is made obvious from your other activity on this site). You are opinion based without having ever opened a book of evolutionary biology (as it is made obvious from your other activity on this site). I will stop answering to your comments from now on as I have better to do with my time. If you are genuinely trying to understand evolutionary processes on a successive post, I'll be happy to help you with that.

If you say so..

Reading your question again, I realize that I mainly answered to the question is the title but I haven't been very specific to the content of the post. I therefore added a section in my answer hoping that will help you. Good luck!


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How to isolate two plasmids from E. Coli strand?
I have an E. coli cell line I use to express a protein using a two plasmid system. One confers AmpR and one KanR.
For mutagenesis I would like to separate the plasmids to increase efficiency of the mutagenic PCR reaction. I was able to cure the cells of the KanR plasmid because it is low copy whereas the AmpR is high copy so I could easily grow the cells in ampicillin only and I ended up with only the AmpR plasmid. However I was unable to do the same to isolate the KanR plasmid.
My next idea was to run the plasmids through a gel and do an extraction. Since I didn't do a digest it was very hard to differentiate the bands and I ended up getting a negligible yield. I believe the plasmids were simply smeared through the gel due to tertiary structures.
My final hope is to perform a digest on the plasmids using a restriction enzyme that cuts each plasmid once. My concern is that I will not be able to get the stoichiometry correct due to the plasmids both being simulatenously present in vastly different concentrations.
Does anyone have any tips on how else I could isolate the plasmids? Or maybe does anyone have experience running a digest on plasmids with unknown concentrations? I really need help doing this. The mutagenesis project has been going on for months and this isn't even a molecular biology lab... so it's detracting time from main research goals!

Couldn't you digest with a restriction enzyme that cuts the Amp plasmid one (or preferably many) time(s) but does not cut the Kan plasmid? Then you could gel purify and transform the result, and presumably it would be nearly all Kan

@Luigi I guess my question would still be how would stoichiometry work? If I have anywhere from 10-50x more of one plasmid than another, would that be a major issue? I suppose I could do a serial dilution...

I don't really why stoichiometry matters here..? You have an excess of the Amp plasmid, but if you cut it all, you'll be left with only Kan. Unless I misunderstand your question

@Luigi I just mean when setting up a digestion or any reaction you prepare the reactants in certain concentrations. For example for digestions they say one 'unit' of enzyme per microgram of DNA.

In my experience as long as you're within an order of magnitude with restriction enzymes you're probably okay. Since Amp is in excess, you could probably operate using the overall DNA concentration and be just fine. It'd be harder to figure out how much to use to digest the Kan, but I'm not really sure why you want to in the first place

The gel solution is a good idea, to avoid smearing try heating up the miniprep for 30 min at 70 degrees centigrade before running it on a gel.

A retransformation should get you a pure plasmid. Transform the plasmid mix into empty E.coli (don't use too much DNA), plate on Kan / Amp depending on what you need. The probability that one cell took up both plasmids is extremely low, and you could check with colony PCR just to be sure.
Otherwise: ask around, there must be (old) stocks of the single plasmids around, or glycerol stocks of E.coli containing only one of the plasmids.
Third option: take a look at your mutagenesis method. For your needs there might be techniques around that'll work on a mixture of plasmids. If you just need one variant or a single site saturation library you could use Quikchange for example. I don't see a reason why this wouldn't work on a mix of plasmids.


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Current state of Gene Therapy
I am interested in learning about attempts to treat adult individuals suffering from a genetic disease in which the underlying changes in the DNA of the gene are understood.
(i) Are there approaches that use drugs or do they use DNA corresponding to the normal DNA?
(ii) Are there attempts to reverse the condition or only ammeliorate it?
(iii) How near is such gene therapy to clinical use and for which diseases?

OK, wow, that's a lot of questions. Theoretically, if you can edit each and every somatic (body) cell in the body, you can cure the person. That's a tad bit difficult, to be honest. However, if the patient were a foetus, then we wouldn't need to make those many edits. However, if the gonadal (sex) cells of the body are edited, the future offspring of the patient would not have the condition. You're going to have to be a bit more specific with this 'condition'.

What you're interested in is a form of Gene Therapy. This is extremely difficult. There are many strategies currently being researched, and the best strategy to use probably depends on the specific genetic condition. In your question, you mention gene editing, which uses CRISPR/Cas9, Zinc Finger Nucleases, or TALEN endonucleases to cut DNA at a specific site, then relies on the cell's DNA repair mechanism to fix the cut, hopefully with a correct of the gene provided alongside the nuclease enzyme. This is very inefficient in cell culture, but at least in cell culture you can find a good cell

and grow as many copies as you need. In a living organism, it becomes much harder. Most of the gene editing nucleases are delivered as a molecule of DNA or mRNA that can then make the enzyme once it gets into a cell. However, delivery of DNA to cells in vivo is an incredible challenge. Modified viruses are more effective than nonviral systems, but have limited carrying capacity and possible immunological effects. Nonviral systems are in still in their infancy after over 20 years of effort. A nonviral gene delivery system must protect DNA from destruction by nucleases, get the DNA into the

right cell type, and then get that DNA into the nucleus. Once in the nucleus, the DNA can make the protein, in our case a gene editing nuclease. Now the nuclease must find and cut the bad gene in the right way, if using CRISPR, that requires a small guide RNA to target the enzyme to the right place. Depending on how this RNA is delivered, not all cells that get a copy of the CRISPR gene will get the RNA, so these cells will not have their DNA cut. Using ZFN or TALENS avoids the guide RNA requirement, but often have a worse accuracy rate and can cut the DNA at incorrect positions.

But the biggest barrier to efficient gene editing is probably homology directed repair. When DNA is cut, your cells have 2 ways to fix it, they can just stick the ends together and fill in the gaps. This usually introduces errors and can often simply destroy a gene, and is usually not desired in gene editing, but it's much more efficient. Homology Directed Repair will take a matching copy of the damaged DNA, usually the corresponding gene on the sister chromatid, and use it to copy the sequence into the damaged DNA. This is what allows gene editing to work, but you have to deliver your good

DNA alongside the CRISPER gene and the guide RNA. The target cells have to get all three components in the right proportions, and they have to choose the good DNA to repair the damaged genomic DNA. Furthermore, you can't simply select correct cells in an in vivo situation, because killing off 90% or more of the cells will kill the patient, so your delivery efficiencies and repair efficiencies must be much much higher than we've achieved in gene delivery so far.

@user137 You couldv'e just put this as an answer, I believe you're right!

@user137 yeah man that's too many comments. Putting an answer instead will increase the chances that someone will read all of it ;)

@user137 Please do not use the comments to write an answer. Put these comments together, add a few references and you have an answer.

I've edited the title of the question to include the term, Gene Therapy, which is what your question is about. I have also clarified it. The 43 year-old man may be perhaps someone you know, but isn't relevant here.

The scope of this question is too wide to be answered on Biology SE. However I will give you very brief answers to your questions (as I have rephrased them) and point you towards some sources of basic information on the Internet. After reading these you may wish to return with more specific questions. I have also briefly summarized some of the problems which it is useful to be aware of before reading details of specific approaches to gene therapy,.
Answers

(i) Some approaches involve attempts to replace a defective gene with
a functional gene or add the latter to the patient’s DNA. Others
involve drugs, often nucleic acid in nature.
(ii) Current efforts often have the more modest aim of ameliorating the disease, although there are also efforts to reverse the condition.
(iii) Gene therapy is not yet in general clinical use, although for some diseases (e.g. Severe Combined Immune Deficiency and Chronic Granulomatus Disorder) there have been reports of success in limited clinical trials.

General Reading
I am not an expert in this area, but by Googling for ‘Gene Therapy’ I came up with the following pages that you may find helpful.

Your Genome
University of Utah: Approaches to Gene Therapy
American Society of Cell and Gene
Therapy

You may also be interested to read about the currently controversial drug, Eteplirsen.
Problems in Gene Therapy
Rather than giving you details of technical approaches to gene therapy, for which you may not have the necessary scientific background, I draw your attention to some of the key problems and questions that have to be addressed in this area.

Does one need to counteract the harmful effect of a mutant gene product (e.g. sickle cell haemoglobin), or is it sufficient to produce a ‘good’ gene product to remedy a deficit?
Is it possible to target new cells or does one have to deal with existing mature cells?
(Some cells like blood and immune cells are constantly renewing themselves, whereas others like muscle turn over much more slowly. The latter are more difficult to deal with.)
How can the DNA (or drug) be deliverdd to the cell, and only to the appropriate cell. (A variety of delivery techniques have been employed in different circumstances.)
How can the therapeutic DNA be incorporated into the appropriate position in the genome, and how can one ensure that it is expressed, and that no other genes are affected. (Early attempts at gene therapy using in which DNA was inserted at the wrong position resulted in cancers. However technology here is moving rapidly.)

"Early attempts at gene therapy using in which DNA was inserted at the wrong position resulted in cancers."  - what are some examples of this?

@mingyeow The most well-known is the attempt to cure SCID in 2002. See Gene Therapy (2003) 10, 4–4. doi:10.1038/sj.gt.3301946.

thank you! this indirectly answers one of my main questions in gene therapy: how is it possible to control the side effects of gene mutation? what  would be your recommended reading for understanding how we are controlling how cells whose genes have been changed are inserted into the target organism's body?

@mingyeow This isn't really my field, but from general reading I am aware that there is a lot of interest in using CRISPR technology because of its precision. A recent commentary I found surfing might be a good starting point:

I understand that crispr offers precision in gene editing, but does that also apply to the way cells reproduce those edited genes?

@mingyeow — The original question was very broad and it was therefore useful to give an answer that was  very general, even though this wasn’t my area. That’s why the question is closed. However as you have more specific concerns, I would suggest that you formulate them carefully into a question of your own and post it here. That way it is more likely to come to the attention of someone who might be able to answer it. (And the answers will be indexed to the benefit of others, which is the way that SE works.)