text:
Spread of a benign virus in a population over time
This is a somewhat difficult (for me) population dynamics question and I wonder if someone with experience in this area could suggest a reasonable approach?
My simplifying assumptions: As a gross oversimplification, let p(k) be the world's population at generation k, and assume a smooth exponential curve that models p(k) from $k=0$ at 10,0000 B.C.E to generation $k=600$ in 2000 C.E. A generation is 20 years, and in acc. with this Wiki there are about 4 million individuals at $k=0$ and 6070 million at $k=600.$
(Of course the exponential model is bad, as world population growth appears to have been sluggish before recorded history.)
Now assume a benign virus infects 120 individuals in $k=0.$ It benignly infects all individuals who have at least one infected parent. Perhaps unimportantly, it also continues to infect 30 new individuals per million in each generation (because its found in the soil), but would not infect those already exposed.
Call infected individuals II and non-infected NI. They are indistinguishable without clinical tests--which are not done, since the virus is harmless. Since II individuals are almost certain to mate with NI individuals, in earlier generations, the number of II will grow very quickly. For a time the growth rate of II will exceed that of p(k). At some point it will be unlikely that an II individual will encounter an NI mate, however a few NI persons will still pair with NI mates--for a while.
My question is, after 600 generations, what is a reasonable estimate of the percentage of II in the population? Is is possible that there would be any NI individuals left? Or would we have some sort of dynamic equilibrium between II and NI in which (I think) the former would strongly dominate?
FWIW, the population growth model is $p(k)=4e^{0.012 k}$ with $p(k)$ in millions.

For simplicity, I denote the population of non-infected individuals by $N$ and the infected ones by $I$.
Model without soil infection
As your phenomenology is generation-based, the best approach would be to make an iterative population-based model. Let’s first forget about the new infections by soil. I will first give you the equations and then explain them:
$$
\begin{alignedat}{3}
 N_{k+1} &=       &   &g \frac{N_k}{N_k+I_k}N_k &   =~& g \frac{N_k^2    }{N_k+I_k},\\
 I_{k+1} &= g I_k &~+~&g \frac{I_k}{N_k+I_k}N_k &~=~& g \frac{2N_kI_k+I_k^2}{N_k+I_k}.
\end{alignedat}
$$

$g=\left(\frac{6070}{4}\right)^\frac{1}{600} ≈ 1.012$ is the growth rate per generation.
$\frac{N_k}{N_k+I_k}$ is the likelihood a given non-infected individual to mate with another uninfected one.
Now, we have $N_k$ such individuals and they multiply by $g$ and thus the next generation of non-infecteds is $g \frac{N_k}{N_k+I_k}N_k$.
Infected–infected matings produce infected offspring regularly, accounting for the $gI_k$ term.
$\frac{I_k}{N_k+I_k}$ is the likelihood a given non-infected individual to mate with an infected one.
Now, we have $N_k$ such individuals and they multiply by $g$ and thus the next generation of infecteds gets an additional $g \frac{I_k}{N_k+I_k}N_k$ individuals.
Sanity check:
$$g \frac{N_k^2}{N_k+I_k} + g \frac{2N_kI_k+I_k^2}{N_k+I_k} = g (N_k+I_k)$$

Model with soil infection
Now, let’s add the soil infection to the model.
It simply means that each generation another $\frac{30}{1000000}N =: rN$ individuals get subtracted from $N$ and added to $I$:
$$
\begin{alignedat}{3}
 N_{k+1} &= g \frac{N_k^2    }{N_k+I_k} &~-~& rN_k,\\
 I_{k+1} &= g \frac{2N_kI_k+I_k^2}{N_k+I_k} &~+~& rN_k.
\end{alignedat}
$$
Result
With this it is easy to insert your initial conditions and run a simulation, here in Python:
# Parameters
g = (6070/4)**(1/600)
r = 30/1000000
K = 600

# Initial Conditions
I = 120
N = 4000000-I

# Iterate
for k in range(K):
    N,I = (
            g*N**2/(N+I)-r*N,
            g*(2*N*I+I**2)/(N+I)+r*N
        )
    print(k,N,I)

It shows that there are no non-infected individuals left after 600 generations. In fact, $N$ drops below 1 after generation 17.
On equilibria

Or would we have some sort of dynamic equilibrium between II and NI in which (I think) the former would strongly dominate?

No, there is no mechanism that somehow favours the non-infected population.
But this doesn’t exist:
The infected population gets to grow as fast as the non-infected on its own plus infecting parts of the offspring of the non-infected.
In fact, as described in the other answer, we can look at the evolution of the fraction $n$ of non-infected individuals in the model without soil infection:
$$n_{k+1} ≡ \frac{N_{k+1}}{N_{k+1}+I_{k+1}} = \frac{g \frac{N_k^2}{N_k+I_k}}{g (N_k+I_k)} = \left( \frac{N_k}{N_k+I_k} \right)^2 ≡ n_k^2 $$
The only way that some non-infected individuals survive is if they multiply faster than they are infected, i.e., if:
$$g \frac{N_k}{N_k+I_k} = g n_k > 1.$$
Since $\lim_{k→∞}n_k=0,$ this does not work even with an absurdly high growth rate.

To many, many decimal places, the percentage of II in the population is 100%.
To answer this you need to make some assumptions about mating structure. I assume mating is panmictic here for simplicity. Ditto sex ratio, but I'm assuming equal number M/F (and equal risk of environmental infection). Finally, I’m assuming NI and II are at equal risk of soil-borne infection (and infections to II are simply wasted), rather than the environmental reservoir somehow seeking out a fixed proportion of NIs, which I think is probably what you meant. I’m also applying the soil-acquired infection to generation 0 here (so they have a chance to become infected before they mate). Finally, II and NI are more traditionally called $I$ (for infectious) and $S$ (for susceptible) in this type of model, so I've followed that convention below.
Unless I’m missing something the population size makes no difference: the chance of a child acquiring infection does not depend on the number of children, and the background rate of environmental infection is proportional to population size, so it all cancels out. I'll therefore stick to proportions from here on, which means $I$ and $S$ are proportions below, not absolute numbers.
Each generation, the proportion of matings between two $I$s is $I^2$, between two $S$s is $I^2$, and between an S and an I is $2·S·I$. So the proportion of Is in the next generation is $I^2 + 2·I·S$. Or, more simply, $1-S^2$.
So:

$S(0) = \frac{3,999,850}{4,000,000} = 0.9999625$
$S(1) = S(0)^2$
$S(2) = S(1)^2$, which is ${S(0)^2}^2$

More generally,
$S(n) = {S(0)^2}^n$
So at generation 600:
$S(600) = {S(0)^2}^{600}$
$2^{600}$ is a very large number. So it shouldn’t be too surprising that everyone is infected by this point.
We can mess around (technical term) with the equation:
$S(n) = {S(0)^2}^n$
...to solve for (for example) how many generations it takes for 50% of the population to be infected:
$$\begin{alignat}{1}
0.5 &= {0.9999625^2}^n \\
\log(0.5) &= \log(0.9999625)\times2^n\\
\frac{\log(0.5)}{\log(0.9999625)} &= 2^n\\
\log_2\left(\frac{\log(0.5)}{\log(0.9999625)}\right) &= n
\end{alignat}$$
So 50% of your global population is infected by generation 15, only 300 years into the simulation.

however a few NI persons will still pair with NI mates--for a while

The probability of anyone ($S$, or $I$) mating with an $I$ individual is directly proportional to the $I$ proportion of the population, so the chance of this happening just keeps going down faster and faster.

Both answers here are fine. I am upvoting this and accepting the other (would accept both if I could). A small nitpick is that while you don't mean to say that the number of I gets bigger than the population, you don't explain how growth slows as the number of I gets significant, unless I am missing it.


text:
Could alpha-numeric taxonomy of fungi make things simpler?
Please feel free to construe this question broadly--I don't see why the question would not apply to branches of biology other than mycology.
If the goal of taxonomy is to create classification of fungi that reflect evolutionary relationships, and if this results in a more or less unmanageable proliferation of names, might it not be a good idea to use a numeric or alpha-numeric system instead of a verbal one? One author estimates there may be as many as 5 million species of fungi (and it may take 1000 years to catalog them). If we did manage to note them all would the result really be useable? The ease of storage and retrieval alone would seem to commend a numerical approach.
I assume someone has thought of this before and I guess viral taxonomy does this to some extent. Are there any proposals like this afoot?
Thanks for any insights.

(First of all the term numerical taxonomy has a completely different meaning. Here you are talking about nomenclature.)
(To make it clear: you are talking about species.)
Simpler for whom?
For humans numbers are much less memorizable than pronounceable and often meaningful words. For database management identification numbers are unavoidable - that's true, because numbers require less disk space and lead to smaller indices and faster access, but that doesn't mean that the text field "title" should be abandoned.
In IndexFungorum, for example, they have id's for every name: e.g. www.indexfungorum.org/Names/NamesRecord.asp?RecordID=228098 for Boletus edulis, but they do not expect the user to use 228098 in place of the name, because that would be inconvenient.
On Mycobank different id's are used: www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=356530. I'd agree, that would be good to have the same id everywhere, but database managers nicely trace these numbers for us (see e.g. the "Other fungal links" section).
By the way, nomenclature of Fungi is controlled by the International Code of Nomenclature for algae, fungi, and plants. Nomenclature of viral species is still based on memorizable names.

Actually I think I was talking about numerical taxonomy in the context of fungi but this answer was useful. Thanks.

In 2017 Rambold et al. have proposed to cite a taxon name identifier instead of taxon name author citation: https://doi.org/10.12705/665.12 But I very like the proposition of Dubois (2008) to cite year of taxon publication instead of author: https://doi.org/10.1111/j.1095-8312.2007.00900.x

This is actually already done in some contexts.
For instance: yeast (a fungus) is a pretty extensively studied organism, and this means that there are a vast number of yeast strains which are know/used by biologists.  Many of these strains are referred to simply by an alphanumeric string rather than a "verbal" name.  (some examples in link 1)
This is also the case for bacteria, and maybe most of microbiology.

source: Stack Exchange

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

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

sort: votes


text:
Do I need to use the same WT C57BL individual for back-crossing or can I use a new one for each generation?
I've just received heterozygote C57BL mice from COMP and I need to start back-crossing them. I've read many colony management protocols, but couldn't understand if I need to use the same WT mouse for all ~10 generations of back-crossing or use a new one for each generation.
Thanks!

I'm totally unqualified for this, but if you used the same mouse to father 10 generations of mice, wouldn't you have mice that are nearly identical to the wt mouse? If the offspring get half of their DNA from the father, the 1st generation is 50% identical to him, 2nd is 75%, 3rd is 87.5% and so on with 10th at about 99.9% identical. So you might spend a lot of effort to get a WT mouse. I might be wrong too, never had to breed mice.

I do not think a single male stud mouse can remain active for 10 generations of mouse to become available for mating, taking the gestation period (~ 19-21 days) and the mating age (~ 6-8 weeks) into account (http://jaxmice.jax.org/support/husbandry/colony-planning.html). By my math for 10 generations that is ([21+56]x10) 770 days.

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


text:
Where I can find information about the study of animal vision?
I read a lot of articles on the internet about how dog see the the world. But I can't find the source of these study. I want to know how did scientist setup the experiment to find out animal vision. I don't know which keyword should I use to search for the information on the internet. Can anybody please send me some research paper about the problem?

A few days back I watched a documentary called Your Inner Fish. In it, there was a small segment about animal vision studies. Basically they had monkeys in a lab, looking at a screen which showed e.g. mostly blue bubbles, but then at some specific spot also red bubbles (sort of like those red-green color blindness tests). Every time the monkey poked the correct spot on the screen, it got a reward. So then they had added a third opsin gene (e.g. humans have three) to this monkey and it could separate colors that other monkeys couldn't.

While their work was in the cat rather than the dog, your starting point should be the work of Hubel and Wiesel.  They are the indisputable pioneers for vision research in general.  They won the Nobel Prize in 1981 for Physiology and Medicine.
See their Wikipedia entries (Hubel and Wiesel), the original 1962 paper, their popular press book, the Nobel Prize speech about their work and Roger Sperry's, and Wurtz's review (cited below).

Hubel, D.H. and Wiesel, T.N. (1962). Receptive fields, binocular interaction and functional architecture in the cat's visual cortex, The Journal of Physiology, 160(1), 106-154.
Wurtz, R.H. (2009). Recounting the impact of Hubel and Wiesel. The Journal of Physiology, 587, 2817-2823. DOI

Color vision was shown to be dichromatic (sensitivity to two color peaks) by Neitz et al. (1989). For a broader review of color vision of mammals, see Jacobs (1993).
Literature Cited
Jacobs, G.H. 1993. The distribution and nature of colour vision among the mammals. Biological Reviews 68: 413-471.
Neitz, J. et al. 1989. Color vision in the dog. Visual Neuroscience 3: 119-125.


text:
Which point mutations in proteins are OK, and which cause significant change?
I heard that some point mutations in proteins are OK, like from alanine to glycine (I'm not sure, it's just an example), some will change the protein significantly. I want to understand deeper but don't know the right keyword. I have tried some but none of them works. Can you give me a good keyword to start searching? Thank you.

Try googling "tolerated amino acid changes."  The connection between amino acids, overall structure and function is complex, and not completely solvable.  People can make guesses based on similarity between different amino acids, and can make better ones by consulting the protein structure, if it's known, but it's not possible to predict with total confidence that an amino acid change will be harmless or not.

As others have said, although certain amino acid substitutions are considered to be conservative, the effect of a particular substitution will very much depend upon the context. Here are some examples:
gly>ala can change stability of glyceraldehyde-3-phosphate dehydrogenase
gly>ala mutations in a fungal glucoamylase increase thermostability
asp>glu in a lysosomal α-glucosidase is responsible for a glycogen storage disease
asn>gln will abolish glycosylation at NXS/T sites which can have effects on stability and secretion
ser>thr at the active site has profound effects upon catalytic activity of an alkaline phosphatase

There are twenty standard amino acids, and some of them are structurally/functionally similar to each other, such as aspartate and glutamate, or asparagine and glutamine, or glycine and alanine. In general, mutations that cause these amino acid switches don't change the function of the protein, but that's just a general rule - it also depends on where these amino acids are in the protein structure. These are called conservative mutations.

I think you are referring to the concept of conserved substitution, which tends not to change the property/function (http://en.wikipedia.org/wiki/Sequence_alignment) of a protein although thats not necessarily true if the mutated AA (point mutation) changes a functional residue in an enzymatic domain such as GAP or kinase domains or even certain residues that are important for PP interactions such as tyrosine Y, which can become phosphorylated and thats important at times for its interaction with other proteins or the activation/inactivation status of a protein such as receptor tyrosine kinases (http://en.wikipedia.org/wiki/Receptor_tyrosine_kinase). But in most cases it depends where the AA is and the role of the AA. For example two AA can have the same charge/polarity but if their sizes are considerably different, then that could interfere with the way protein folds (conformational changes) and end up affecting its function. So AA substitution and its effects is not necessarily straight forward and its very much dependent on other factors!


text:
Do females living on mountains have more RBCs than a normal male
I got this doubt when I was studying about haematocrit value. According to my NCERT textbook males have greater number of RBCs than females. But who will have more RBCs when comparing a normal male and a female who lives at a higher altitude?
*edit
the magnitude of altitude would be less than 8,586 m (28,169 ft) as the woman I know is not exactly at the top summit of Kanchenjunga so what would be the answer then?

Why should it be different there?

@Chris i didn't get you

http://en.wikipedia.org/wiki/High-altitude_adaptation

@Raghavakrishna i have read that article but my doubt is who will have more no. of RBCs now a normal male living at normal sea level or a female living at higher altitude? because normally males have more no or RBCs when compared with females

@agharehanabbas You can not compare this directly since the conditions are completely different. And if men and women are both at high altitude, I would expect men again to have higher counts.

@agharehanabbas May be this could be useful http://www.ncbi.nlm.nih.gov/pubmed/11256567

your edits still do not provide enough clarification and suggest that it is medical advice you seek (it regards someones specific RBC count).

@GriffinEvo what more should i add in my question then

Specific altitudes that you had in mind. The male and female. <8586m is not specific, it is anywhere from 0-8586.

Currently impossible to give a definite answer... It depends what altitude you look at.
Going from @Alan_boyd's answer the normal range is 40-50% for males and 36-44% for females. If the altitude at which a person is acclimatized to correlates well with red blood cell count (RBCC), and this effect is not gender specific (i.e. both sexes are affected similarly), then an average woman from high altitude should have a higher RBCC than an average from low altitude. But whether or not the high altitude female RBCC exceeds that of the male depends on the altitude of the two measured.
This rough graph, assuming RBCC and altitude correlate and that male RBCC is higher than female RBCC, shows the problem. Female (red dashed line) A is from a higher altitude than the selected male (blue dashed line) and has lower RBCC. Female (red dashed line) B is from a higher altitude than the selected male (blue dashed line) and has higher RBCC.

Define altitudes and the question may be answerable.

i have edited my question now what must be the answer

According to the MedlinePlus site these are the normal ranges for haematocrit:
Male: 40.7 - 50.3%
Female: 36.1 - 44.3%
Unfortunately it isn't clear if these ranges are for people living at low altitude, but since most people in the USA do, I think this is a safe inference. So clearly there is already some overlap.
The paper accessible here reports various changes in haematocrit due to moving between different altitudes. Broadly speaking these changes are in the range of 10 - 15 percentage points (e.g. a change from 39% to 49%).
So yes, a female who has moved to a high altitude is likely to experience an erythrocytosis (or polycythaemia) which would mean that her haematocrit would exceed that of many males.


text:
Protein purification methods
Which of the following methods would yield the most purified protein fraction?
A. Salt precipitation
B. Charge separation
C. Affinity purification
The first one is the most commonly used, is it the best ?

The choice of strategy for protein purification of course varies by application.  As @A.Kennart points out, affinity chromatography is the most popular right now.  It can be expensive.  If you have an expression system for a recombinant protein its more common than not to add a poly-Histdine tag on the N or C terminus or some other protein fusion.  So there are cases where you won't be able to use it.
For instance if the protein you are looking for is not coming from a recombinant source / is not sequenced, it can get expensive and time consuming - getting an antibody made requires that you have a somewhat pure prep of the protein in the first place.
The most common reason we still use all these methods are because different levels of purity and different raw materials show up in different contexts.
In the case where the protein has never been isolated before or you have a sample (like a cell sample rich in a particular protein) then salt and sizing columns are very useful.  Salt precipitation is useful when you have a lot of sample and you need to make some rough cuts.  Even if the gene is well characterized, it may depend on expression in its native organ.
I've prepped protein using ammonium sulfate precipitation from homogenized whole tissue for instance.  That's great - the result got rid of well over 90% of the material, but the outcome has hundreds of bands on the gel.  In this case an affinity column was used next; immobilized conconavalin A would bind to the glycosides on the target product.  If I had put the whole tissue homogenate I would have destroyed the affinity column by stuffing it full of meaty gunk.
Charge affinity columns with salt gradients are often still needed after affinity chromatography. Some folks don't need pure protein, but affinity chromatography (esp his tags) will still have many bands left on a protein gel and those contaminants always leave your experiment in question.

thanks :) my first tech job involved collecting adrenal glands at a slaughterhouse.  they did not smell or look good - no way you'd put that on a $300 column!  Salt and centrifuge. was the only way to clean that up.

Well, I see that this is the accepted answer, and I don't disagree with any of it, but it isn't really the answer to the question that was posed. In terms of a purification factor (e.g. increase in specific activity of an enzyme), affinity purification will win out every time.

In my protein purification experience, affinity purification is the most selective purification strategy. This makes sense because affinity tends to be very specific, and only one protein should in theory be preferentially separated by the column. Think how specific the antibody-antigen interaction is compared to the differences in, say, charge between proteins (which could be very slight). When I was purifying proteins I would pretty much always start with affinity purification. If more purity was desired after the affinity purification step, I could perform salt precipitation or charge separation on the affinity-purified sample, which had already been cleared of major contaminants/nuisance proteins by affinity purification.

The fact that all of the tagging methods used for purification of proteins expressed from cloned genes (his tags, FLAG tags etc.) are designed to facilitate affinity purification approaches underscores this answer.


text:
Why do humans circulate monosaccharides instead of disaccharides as in plants?
Plants transport food mostly in the form of disaccharides like sucrose but humans transport them in the form of a monosaccharide -  glucose.
What is the reason behind this ?

One of the reasons could be  -

humans and many other animals have active circulatory systems,
  there is little need for targeting sugars for specific parts of the
  body. The entire body would rapidly reach equilibrium with the glucose
  level of the bloodstream, and thus there likely never evolved the need
  to target specific organs to receive sugars via disaccharides

Source : This
Other reason could be that disaccharides are harder to transfer inside the cells than monosaccharides.

plants are earlier than animals in the phylogenetic tree.  animals later evolved the circulation of monosaccharides I would assume, so there could be an advantage to monosaccharide circulation.  I would look at fungi to see what they do there.


text:
Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood?
It's almost half a century since the lac operon was discovered but isn't it weird that the precise role of transacetylase isn't clearly understood ?
Here a wikipedia article with a link to a journal article which proposes a function of this enzyme. This article was written in 2002 but in most of the text books I have referred to ( written well after 2002 ), no function is mentioned.
MY QUESTION : What are the difficulties that are not allowing us to understand the precise role of this enzyme ?

the mechanism of the reaction catalysed by this enzyme is understood. what is not understood is why is this reaction important. perhaps it increases the rate of lactose metabolism in some conditions. knockouts cannot always elucidate roles of genes because there may be only a set of conditions when they play an important role.

Note: This is NOT my field. However, given @biogirl's question, it appears that there aren't many people in this field in the first place. From what I can gather, here are the reasons why I think it has been difficult to study.
I. The lac operon has strong polarity. By this I mean that when the lac operon is induced, lacZ (the first gene in the operon) is translated much more than lacA (the last gene in the operon). Measurements have recorded the molar ratio of $\beta$-galactosidase : thiogalactoside transacetylase (the protein products of lacZ and lacA) upon induction of the operon at 3:1 to 5:1; i.e. when the lac operon is induced 3 to 5 molecules of $\beta$-gal are produced for every one of the transacetylase. If you factor in the relative length of each of these proteins ($\beta$-gal is 1024 a.a.s, transacetylase is 203), it works out that lacZ is being translated at least 10 times faster than lacA when the lac operon is induced. Sidney Altman's lab has attributed this to the fact that there is a cleavage site between lacY and lacA where RNAses can cleave the nascent mRNA transcript, removing lacA from the operon and reducing the production rate of transacetylase. So it appears the cell needs quite a bit less lacA than lacZ---if indeed they need it at all, see point 2---which makes it harder to study.
Sources: Brown JL, Brown DM, Zabin I. (1967). J Biol Chem. 242(18):4254-8.
Li Y, Altman S. (2004). J Mol Biol. 339(1):31-9.
II. lacA seems to provide only a small fitness advantage under somewhat contrived conditions. In A paper from the 70s researchers presented competition experiments between $lacA^{+}$ and $lacA^{-}$ strains in media with $\beta$-galactosides as the only carbon source. For 50 generations there was no competitive advantage of one strain over the other (ratio of $lacA^{+}$ : $lacA^{-}$ stayed at 1). When after 50 generations the researchers added a lot of IPTG, a non-hydrolyzable $\beta$-galactoside, $lacA^{+}$ outcompeted $lacA^{-}$; the absolute fitness of wild-type:mutant could be calculated to be $\approx 1.05$. This means that the wild-type produced 105 cells for every 100 produced by the mutant. I am not a population geneticist, so I don't know if that is a large value or not. For comparison, I used to work in cyanobacterial circadian rhythms, and the absolute fitness advantage for having a circadian clock with the same period as the light-dark cycle in the environment works out to $>1.11$, which is twice as advantageous as the one reported for $lacA^{+}$ over $lacA^-$. In any case, the experimental situation in which $lacA^+$ has a competitive advantage seems rather contrived: growing with $\beta$-galactosides as the sole carbon source with a significant amount of non-hydrolyzable analoges around gumming up the $\beta$-galactoside metabolic machinery.
Source: Andrews KJ, Lin EC. (1976). J Bacteriol. 128(1):510-3.
My read from these observations is that the physiological role of lacA is challenging for a biologist to untangle due to the small size of its effect on bacterial physiology. Fitness advantages of 5% may certainly be useful on evolutionary timescales, but they suggest that the benefit afforded by the enzyme will be very hard to discriminate from noise or other confounding factors in the system. The fact that lacA production is much lower than lacZ in times of lac operon induction also would make it hard to measure.
A postdoc I used to work with advised me, "don't go looking for 2-fold changes in biology," by which he meant don't spend too much time on questions where the size of the effect you are looking at is minor and very difficult to distinguish from noise, bias, measurement error, or other confounding variables. Obviously there are limitations to this advice; a lot can be learned from the the combination of several seemingly minor effects that have big cumulative consequences for an organism. But as a rule of thumb, it's so hard to get strong results when your effect size is so small that going after small effects is justifiable only if you have a good reason to believe there is some profound, fundamental biology behind them. My view is that the consensus of the scientific community up to this point has been that untangling the role of lacA in the lac operon and more broadly in bacterial physiology would involve too much work for too little payoff.

Thank you for your awesome answer ! I would like to point out that 1.1 isn't double of 1.05 so I don't understand how that's twice as advantageous.

Thanks! It's a great question that I'd wondered about, too, so I had fun thinking about it and looking it up. My reasoning for "twice as advantageous" is that the 1 in 1.1 or 1.05 you kind of get for free: the fitness number 1.1 or 1.05 means that 110 or 105 bacteria are produced in the more fit condition vs. 100 in in the less fit condition. So the fitness difference is really  only responsible for an extra 5 or 10 bacteria. So by that measure, a fitness of 1.1 is responsible for twice as many additional bacteria as a fitness of 1.05. Though that might not be the best way to summarize it.

Alright. You have really done a lot of work to find all those references !


text:
Do desulfhydrase-catalysed reactions take place in animal cells?
It isn't a homework question. I'm just stuck with desulfhydrase reactions and am unable to find enough information in the usual places.
Any external source on this topic would be helpful.

A desulfhydrase catalyzes the removal of hydrogen sulfide from a compound. So the answer is yes, but it's not the most-commonly annotated reaction for the enzyme cystathionine gamma-lyase.
I didn't know off-hand. Here's how I answered the question:
I searched Entrez Protein (or NCBI...whatever the thing's called) with the following terms:
(desulfhydrase) AND "Homo sapiens"[porgn:__txid9606]

And got three hits for isoforms of cystathionine gamma-lyase. I clicked on one of them and started reading. Key things I noted:

EC_number="4.4.1.1"
...
Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes
  the committed step of methionine biosynthesis. This pathway is
  unique to microorganisms and plants, rendering the enzyme an
  attractive target for the development of antimicrobials and
  herbicides.

So it's a good question because, if people normally characterize this enzyme in terms of Met biosynthesis, then we don't have a desulfhydrase. But I trusted the thing was annotated properly and that the comment above was just too medicine-oriented (as much biochemical literature is).
So to really understand the enzyme itself I searched MetaCyc for the Enzyme Commission identifier 4.4.1.1.
This let's me easily visualize the catalyzed reaction. And the annotation spells it out clearly:

Enzyme Commission Summary: A multifunctional pyridoxal-phosphate
  protein. The enzyme cleaves a carbon-sulfur bond, releasing L-cysteine
  and an unstable enamine product that tautomerizes to an imine form,
  which undergoes a hydrolytic deamination to form 2-oxobutanoate and
  ammonia. The latter reaction, which can occur spontaneously, can also
  be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate
  deaminase.
Also catalyses elimination reactions of L-homoserine to 2-oxobutanoate and ammonia, of L-cystine, producing thiocysteine,
  pyruvate and ammonia, and of L-cysteine, producing pyruvate,
  hydrogen sulfide and ammonia.

I removed my comment, my mistake on the EC number.

In addition to the reaction described in Ryan's answer, cystathionine beta-synthase (CBS) also catalyses a reaction that yields hydrogen sulfide. These two reactions are thought to be the major sources of hydrogen sulfide in mammals.


text:
Why is coffee a laxative?
How does caffeine (or any additional agents) act as a laxative when ingested? I'm interested in the metabolic/signaling pathway.

https://www.quora.com/What-happens-when-you-water-plants-with-coffee-or-tea


text:
Which is the tissue damaging agent in krokodil (street desomorphine)
I've just read about krokodil and saw some quite hideous pictures about what it does to the human body. I guess just desomorphine alone wouldn't have this effect.
Which ingredient(s) causes the damage to the tissue?

Desomorphine is made from Codeine back in USA in 1932. But Codeine is made from caffeine, paracetamol, or diphenhydramine in Russia. Finally Krokodil as it is called in Russia is made from crude method by mixing codeine-based headache pills with iodine, gasoline, paint thinner or alcohol. I do not know what else they mix as it is done by purely amateurs. So these toxic substances might produce some byproducts which might cause those damages.

Note: Don't click on the links, or even search for information, if you don't have a strong stomach
From what I've read, it's not necessarily 100% known, most likely because it's not easy to study (small, reclusive users who die quickly of a complex concoction) but the line everyone has quoted is:

"They extract [the drug] and even though they believe that most of the oil and gasoline is gone, there is still remnants of it. You can imagine just injecting a little bit of it into your veins can cause a lot of damage… it eats you from the inside out".

That's from Dr. Frank LoVecchio in Phoenix, Arizona, who saw two cases within a week.  It's not hugely scientific, but it's not wrong.  Krokodil is never pure and highly toxic chemicals are thus injected into the veins.  If you want specifics, then gasoline, hydrochloric acid, phosphorous scraped off matchboxes, paint thinner, iodine, and cleaning oils.  Injecting any one of those should be enough to kill a repeated user.  Those substances rupture blood vessels, and the subsequent leakage creates gangrenous wounds like you see in the pictures.


text:
Does the brain and the body use the same energy source (glucose/ATP)?
I've heard that the brain consumes quite a lot of oxygen and energy, compared to the rest of the body. What I'm interested in is if this is the kind of energy and oxygen that the rest of the body competes for?

For example, does running divert resources from the brain to the
muscles, leading to decreased cognitive performance?
Does digesting food divert resources from the brain to the gut?

Does the heart rate or blood pressure have anything to do with how much resources, like oxygen and energy are available to neurons?
Thank you for your input!

Running involves quite a bit of brain resources.  Coordination, balance, obstacle avoidance, etc..  So the total energy requirement for running would have to include the need of the muscles and the brain or running wouldn't occur.

While in general the answer is "yes", the brain does use the same type of resources as other parts of the body, you cannot from that alone derive conclusions about the brain competing with other organs. Also, I think that cognitive performance is not a function of availability of resources. In fact, the moment that the brain lacks crucial resources like oxygen, it simply shuts down. But you don't faint when you start running (if you do, go see a doctor). "Power-saving mode" for the brain is not "reduce IQ by 20 points", but "just make sure the body is breathing and shut down everything else".
Also, I do not think that digesting food requires any comparable amount of energy that it would require the brain to give up on some of the oxygen it needs.


text:
Which X-Y chromosomes have the developmental genes for mammals?
I know that for a given mammal, half the chromosomes come from father and half from mother. This is typically denoted as x-y. I've recently read about "toolkit" genes that control how a cell develops into an embryo into an organism. I'm interested which set of chromosomes(x,y or both) contains these toolkit genes for development of an organism from a fertilized cell?
In other words, does an X chromosome know how to build a female and Y chromosome how to build a male, or is it some "overriding" of developmental instructions that Takes place when Y is present?

Can you clarify what "toolkit" genes you are referring to? Do you have a link/citation for the source you read about them from? I'm guessing you are not referring to the toolkit genes listed here, so a bit more clarity might be helpful.

That sounds like the toolkit genes I'm referring to

First, while half the chromosomes come from each of the two parents, these two sets of chromosomes are not termed X and Y (they would usually be called maternal and paternal).  The terms X and Y refer to potential members of just one pair of the 23 pairs (in humans) of chromosomes, and X chromosomes can come from either the mother or the father.  The presence or absence of a Y chromosome determines sex in mammals.
The Y chromosome contains one gene, SRY, which determines sex, and almost no nother genes.  SRY simply switches on the "make a male" program in the cells.
Essentially all other genes, including any toolbox genes, come from both parents, one copy from each.  (An exception, in males, are those genes on the X chromosome, which in males are present in only one copy and which came from the mother.  Another exception is mitochondrial genes.)

In addition to @mgkrebbs response, I'd add that many genes are controlled by epigenetic mechanisms which may mask one of the parental copies by methylation.  This can be a specific effect where, the active gene is specifically from either the father or the mother. Mosaicism, where one copy of gene is randomly inactivated in any given cell, is also possible.  The classic example of this is X chromosome mosaicism, where the entire X chromosome in each cell of a female is silenced. (At least in the case of humans and animals like humans)

There's also this really cool example of a gene for a voltage-gated potassium channel, in which the paternal copy is methylated by a paternally-expressed ncRNA from the same locus (that site is methylated maternally).  If this is disrupted, it results in developmental defects. <Shameless plug for an unanswered question of mine that has the relevant links.>

There are surveys of such genes from mouse studies, my favorite is MEST. I took a shot at that one @dd3 :)


text:
Which shades/hues of color are easiest to distinguish for humans?
I'm trying to represent data graphically and am using a variation of hue/lightness to distinguish one data point from the next. I would like to use a color that would allow me to convey most information visually.
What I'm interested in is which color I should use. I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?
Has there been any studies to distinguish the number of shades that a typical westerner can distinguish? I'm looking for information like : ### shades of green, ### shades of red, ### shades of cyan, etc.
Thank you for your input!

don't forget the XKCD Color survey - see the color cube map http://blog.xkcd.com/2010/05/03/color-survey-results/

I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?

I'd say it's plausible, depending on your definition of "Green." While your eyes do, indeed, have RGB receptors (cones) and Rods for grayscale - they don't perceive the Visible Spectrum equally. Here are a few graphs I found from Photo.net regarding the human eye and the sensitivity of the Cones (first and second) and Rods (third):

What you should be noticing above is not necessarily the Y axis, but the X axis - which represents the Wavelength, and amount of Wavelength our eyes are sensitive to each color. While our eyes perceives the most Red wavelengths and the least Blue wavelengths, Green comes in just under Red's range for Wavelength coverage. However...

When combined with our Rod sensitivity, though, Green wavelengths produce nearly double the sensitivity the Red Wavelengths - and nearly quadruple the Blue wavelengths. What that means is that in low-light situations when the Cones are unable to produce a precise color image, your Rods will be able to pick out Green things (with a slightly loose definition of 'Green') more than other colors - which is perhaps the reason why night-vision goggles often use Green since they increase the Intensity of the light, which presumably stimulates the Rods more (although not knowing precisely how the image is produced - if the green coloring is enhancing that particular bit of the spectrum of falsely colored - take this with a grain of salt).
Does that explicitly prove you can see more Green shades than others? No. Your brain does a lot of processing - the entire color Yellow is a construction of your brain, and Tetrachromats (people with 4 types of Cones) are real.
However, like I said above, I'd say it's plausible.

Thank you for a very in-depth answer! I'll stick with green then.

Light is either monochromatic, or a combination of different wavelength in different proportions.
In the eye, there're 4 types of sensor cells: one is greyscale-only, another 3 is for color vision. See the graph here with the spectral sensitivity of the 3 color vision cells.
So, for any giver hue, you have very wide possibility of the light spectrum that makes you see that hue.
When you see the yellow color from the sodium-vapor lamp you see almost monochromatic yellow light. When you see the photo of the lamp on your PC display, there’s no yellow light at all. Instead, you see some combination of red and green light produced by PC display which doesn’t have yellow subpixels, only red green and blue.
That's why there's no simple answer to your question. The answer depends not just on hue (which only exists inside our brain), but also on the spectrum of the light you see (which also exists in the real world).
P.S. Even if you'll specify "color on a PC display", the question is still vague: there're different types of displays with different spectral characteristics.

Thank you for a clarification. I should say that I'm working with a backlight-based LCD display of an iPhone.

LCD display of an iPhone
For portable devices there's another important factor - ambient lightning. For example, under direct sunlight human eye can barely distinguish black from white (unlike AMOLED displays for example)


text:
Are there differing organelle to cytoplasm ratio in animal cells?
Could anyone provide me with examples of cells with high organelle to cytoplasm ratios (heavily packed), and examples of cells with low organelle to cytoplasm ratios (sparsely packed)?

If you want to sketch the cells, it might be easier to compare plant cells. Usually plant cells have a large vesicle contains fluid in the middle of the cell. However, root cells don't have this type of vesicles. It's the easiest to draw according to my knowledge.

This depends a bit on how you define the ratio. What precisely do you mean by "organelle" and "cytoplasm"? If you consider the entire cell volume as cytoplasm, then fat cells (adipocytes) would have an extremely low ratio, as nearly all of the cell volume is just fat. But if you consider cytoplasm to be just the water-soluble part, then it's very different. Also, a lot of cell structures are hard to classify as "organelles", for example glycogen and microtubules. Perhaps just the water content of a cell would be a good measure? That would include all macromolecules as "organelle" mass.

@Roland yeah i would exclude macro molecules, I'm talking about stuff like mitchondria...

Yes.
The structure of a cell is highly related to its function. For example, a plasma B cell (a type of immune cell) contains lots of ER and Golgi because its job is to secrete antibodies, which are proteins, in your body. It has to create a lot of proteins, so a plasma B cell has a lot of organelles that help create, assemble and secrete proteins.
There are so many examples you can use.

can you give a low ratio example as well? I am computer scientist modelling cell internals so it's not really in my wheel house

@RRs_Ghost examples of animal cytoplasm ratio: see the difference between monocytes and other lymphocytes. Monocytes have larger "white" area under microscope, which is the cytoplasm area(so it has a more condensed nucleus and organelle complex. However it's not the case for other lymphocytes.


text:
What does it mean for a chemical pathway to be conserved?
In many papers the MAPK pathway, (along with many others) is referred to as being conserved:
Example: "The mitogen-activated protein kinase (MAPK) cascades are ubiquitous in eukaryotic signal transduction, and these pathways are conserved in cells from yeast to mammals"
example 2 "The Hippo signaling pathway appears to be highly conserved."
What does it mean for a pathway to be conserved?

A conserved pathway is a pathway that exists in a variety of species, by virtue of that pathway being conserved throughout the evolution of those species. A pathway must by neccessity have appeared for the first time in one particular species. If that species gives rise to new species, but the pathway in question is identical or very similar in all the new species, it is sensible to say that pathway has been evolutionary conserved. This may imply that the pathway in its conserved form is important for the fitness of those species.
For some examples, here is a page on evolutionary conserved pathways in Drosophila: http://www.sdbonline.org/sites/fly/aimain/aadevinx.htm

Thanks, so it's conserved as in kept back, in the same way one would conserve a limited energy supply.

@RRs_Ghost I would rather say conserved as in unmodified (over long periods of time and across species).

More in the way that the pathway is found in a wide variety of species.

Good answer. You might add that there isn't really one MAP cascasde in mammals, although textbooks often speak of it as such --- there are several isoforms of each protein in the cascade, and probably many alternate signaling pathways connecting to different things. Which makes the idea of evolutionary conservation a bit more complicated ...

Great answer - would there be a bioinformatic way to query for degree of conservation of  pathway or how do people come up with the definition?


text:
Iron deficiency anemia symptoms explanation
In my classes and on the internet, brittle nails and dry hair (or hair loss) are described as symptoms of iron deficiency anemia, but none explains the cause of such symptoms.
Does anyone have any clues or explanation of such symptoms?

http://en.wikipedia.org/wiki/Iron_deficiency_anemia#Signs_and_symptoms

Can you provide the link to the sources that say so?  Because frankly I havent heard of these as anemia symptoms

It would likely depend on the type of anaemia - deficiencies in iron, B12 & folate, anaemia of chronic disease, haemolytic anaemia etc.  I haven't heard of this as a symptom of anaemia myself, however it is possible that it could be as a side effect of the problem that is causing anaemia (anaemia never being a spontaneous disease, always having an underlying cause).

Another clarification I would like to make. Anemia is a condition which is defined by reduced RBC count. Anemia is one of the things that Iron deficiency causes. Other effects of iron deficiency can be syndromic or even correlated (without dependence) with anemia but cannot be called as symptoms of anemia.
And as @RoryM mentioned there can be other reasons for anemia.

The molecular basis of copper-transport diseases in Trends in Molecular Medicine, Volume 7, Issue 2, 1 February 2001, Pages 64–69, has a link to a 1973 paper by JM Gillespie entitled "Keratin Structure and Changes with Copper Deficiency," stating

Menkes patients are often diagnosed from their unusual hair structure – termed pili torti – also known as kinky or steely hair, caused by reduced keratin cross-linking, a process that is catalyzed by an uncharacterized copper oxidase.

I haven't been able to find anything further, but since iron and copper levels can both be affected in anemia, this may be the link you're looking for. There may also be other enzymes involved that use iron-mediated catalysis. Since there are so many different kinds of keratins (the major protein that makes up hair and nails, among diverse other functions in the body), there may easily be multiple cross-linking and assembly pathways.
Other websites I found have also claimed that anemia-associated pathologies with hair and/or nails may be related to reduced oxygenation as a result of low iron levels, but they don't give any citations, and given the nature of the sites (nail care, fashion, etc.) it may just be an educated guess.

"but since iron and copper levels can both be affected by anemia" ..... It is the other way round. Iron deficiency causes anemia not vice versa. A small addition to your answer (some guesswork): proline and lysine hydoxylase require iron cofactor and this enzyme helps in forming mature collagen. Nonetheless the symptoms mentioned in the question are unlikely to be first signs of iron deficiency

sorry, I could have worded it better, I was in a hurry :) Yes, anemia (in general) is defined as a deficiency in something, and in common usage the word anemia alone is typically taken to mean iron anemia or iron deficiency. What I meant is that copper levels can also be affected by iron anemia.

But do you think collagen synthesis can be affected ??

@WYSIWYG I'm not sure what collagen has to do with it - fingernails and hair are make up primarily of keratins...

it has got nothing to do with fingernails but the thought just popped in my head that iron deficiency may affect ECM. NOnetheless, all this fingernail and hair symptoms seem dubious to me.. I cant find any reliable source which claims so

I did some searches on the relationship between iron deficiency anemia (IDA) and hair loss. Surprising, there are lots of debates about this and I don't think anyone has a solid reason.
If iron deficiency is related to hair loss then taking iron supplement may potentially reverse the effect. However, this article pointed out that:
....there is insufficient evidence to recommend giving iron supplementation therapy to patients with hair loss and iron deficiency....
My understanding is, human body actually contains very little amount of iron. And most of the iron are involved in cellular respiration and oxygen exchange. Free floating iron is very toxic and bad for the body. Therefore most of the iron storage are in Hemoglobin (2/3), followed by ferritin+hemosiderin (about 1/3), some are utilized by the mitochondria (those awesome cytochromes and electron transport chains), lastly the transport vessel trans-ferritin.
I think Hair loss and brittle nail are just indirectly caused by IDA. Because most of the time IDA is cause by malnutrition. And usually the food sources that are contained the most iron are meat, poultry and egg. These food are also rich in protein. I think lack of meat protein-rich diet is the main reason of hair loss and brittle nail, and such diet leads to IDA. (Strict vegans, be careful about your food choices!)

There are several non-animal sources of iron- spinach, beans etc.

@WYSIWYG You are right. But as I said above, I think hair loss and brittle nails are not directly caused by IDA. It's caused by malnutrition.

Roger that.. :) [somehow the name tagging is not working]


text:
How does population stability evolve?
The number of individuals constituting a population is called population size.  Over time population size does not remain constant, it fluctuates to different extent over generations because of several internal and external factors.  Populations with violent fluctuation in population size are called unstable and are more prone to extinction as they hit lower population sizes frequently.  And once a population in extinct, it is gone for ever.  Thus it would be interesting to investigate how population stability evolves.

Could the word 'evolve' be confusing the issue here?

Maybe changing it to develop would be a good idea?

I guess you meant the population size stability.
It is considered that the biosystems will increase their capacity of adaptation when evolving in very fluctuating environments. I believe the population stability is embedded in the adaptability of individuals.
There is a measurement about it, evolvability, when the environment changes, the faster the population adapted to the new environment, the higher evolvability it has. This means that if the population has higher evolvability then the population may be more stable to environmental variation.
Even so, there might be plenty of underlying mechanisms to enable a certain population stability. I recently read a paper about two mechanism: phenotypic switching and sensing machinery, which are common in bacteria and fungi. Please refer to Edo Kussell and Stanislas Leibler's science paper (2005).
As the organism increase its complexity, biosystems invented many more tools to make the individual survival from disasters. Such as human's intelligence. Well it would be an endless issue.

You should consider linking to papers that you mention in answers to help save time for readers :)


text:
Could someone recommend an introductory book on epidemiology?
I'm hoping to learn the basics of epidemiological methods, terminology, etc. I come from a background in statistical economics, and I'm moving into the economics of public health. I don't know if epidemiology uses separate statistical methods, but I presume it does. I know discussion questions aren't recommended, but please list any reasons you have (personal experience, ease of introduction, etc.) for texts you would recommend.

There are two books I'd highly recommend for someone starting to dabble in Epidemiology. The first is Kenneth Rothman's Epidemiology: An Introduction, which I'm affectionately going to refer to as "Baby Rothman" from hereon out for reasons that will become obvious.
Baby Rothman is an excellent "getting your feet wet" book. It's simplistic, and clearly designed for someone with no background in Epidemiology, so it starts from things that, if you have a statistical background, you might find a bit dull. But it accomplishes two key tasks:

A basic treatment of the subject from a pre-eminent methodologist and advocate for the field that doesn't make some of the sloppy slight-of-hand mistakes many introductory books do.
An introduction to the "vocabulary" of Epidemiology as a field - what we call things, how we thing about effect estimates, etc.

The second book I would buy would be Modern Epidemiology: 3rd Edition by Rothman, Greenland and Lash. This is the definitive reference book for most epidemiological methods  currently used in the field. As I said on a related CrossValidated question, ME3 is the only epidemiology book that has always come with me, regardless of what project I'm doing, and which I have routinely found invaluable.
The other benefit of the book is that it's "platform agnostic". It's not going to try to teach you a statistics package - its going to teach you the science and philosophy of Epidemiology, the actual doing of the science, rather than the toolkit. Without that kind of methodological rigor, you can be a wizard at your language of choice and still do bad science.
If I were only going to buy one book, it would be ME3.

Excellent answer. The other post you linked is also extremely helpful. I actually had Rothman's beginner introduction in the stack of books I borrowed from my uni's library already, and upon first read I quite like it. Thank you!

Here is an online book of epidemiology for the uninitiated. I used it to get a basic understanding of epidemiology.
http://www.bmj.com/about-bmj/resources-readers/publications/epidemiology-uninitiated

I don't suppose that book is available as a PDF too, correct?

@pythonscript no, but it should be simple to cut and paste into a libre office doc and export to pdf. Or if you need it in epub not sure how to do that.

I found Clinical Epidemiology by Robert and Suzanne Fletcher extremely useful  to gain some quick insight in to the broad area of epidemiology during my first year of post-doc. It covers a wide-range of topic in clinical research and epidemiology in an accessible format with several examples and extensive illustrations.

That may be a bit advanced for me, since I do not come from a pharmacy or medical background, but I'll take a look at it for good measure once I gain a stronger understand of the field.


text:
Does apheresis damage any components of blood? If not, why not?
Blood donation involving apheresis is becoming increasingly common. It looks like the process involves centrifuging blood at very high speeds* before removing the desired fraction and returning the rest to the donor. Is there good reason to believe that the centrifuging process is harmless to all the various cells, proteins, lipids, and other substances in whole blood? Or is it possible that some blood constituents are damaged or altered?
* I don't know if the speeds are particularly high compared to other biomedical processes, but they're drastically outside the conditions in which biological products evolved to function, hence my question.

As someone who handles blood regulary in the lab, I can tell you that cells (and other components of the blood) withstand this conditions without any problems. You can afterwards still grow single cell populations in cell culture.

The centrifugal speed is around 300-500g : this wont disrupt any cells.

@WYSIWYG Is that specific to blood donation? I wasn't able to find that information, but when I looked up other blood fractionation procedures (typically for lab use) they had values around 1500g. Or would that even make a difference?

Thank you both for the comments. I'm obviously not a biologist, so it was counterintuitive to me that forces of that kind would be unproblematic to cells. Is the same thing true for things other than cells, like albumin, liproproteins, etc?

Chris or WYSIWYG One of you should attempt an answer.

@octern: even that shouldn't affect the erythrocytes.. I don't work on blood so I don't know much but most animal cell types can tolerate upto 1000g. But we generally use 300g for spinning down cells.


text:
How did the activities of protocells become inheritable?
I have learned that first a protocell came to exist and its characteristics came to be passed on by genetic material. So how come genes for all the activities come to incorporate into genetic material? Did genetic material come first and random sequences made random proteins that were used to make cells ?

another side of the argument, which Richard Dawkins made is that replicators are necessary for selection.  Sure other metabolizing and energy utilizing systems might have shown up, but those which replicate are the only ones you will see over time.

I dont want to debate what came first. I want to know how RNA or DNA or whatever genetic material came first began to be " genetic material " . How did it "know" that this particular polypeptide ( for example ) will be coded by this particular sequence ?

The reason I mentioned the 'replicator' is that it posits that while the primordial chemical soup probably contained many millions of kinds of molecules, the nucleotide bases which were capable of reproducing themselves would win out very quickly.  it sounds a little circular, but that is how it 'knew' if you make 100s of billions of millions of RNA molecules, only those who replicate will quickly be the only ones you see.  we don't know much more detail than that.  the people looking at RNAworld research are trying to get a handle on that.

Well.. This is a tough question (Something that has bugged me for years and still doing so). I don't fully agree that replicative potential came first. This is just my opinion based on some reasoning and I dont really have any reference.
If you compare a nucleotide and a protein, the likelihood of formation of protein is much higher because:-

Amino acids are simpler molecules and simplest of them did appear in the famous Urey-Miller experiment. Nucleotides on the other hand are much more complex
Peptide/amide bond formation is a well known phenomenon even in non-biological chemistries whereas Phosporic esters cant be called common compounds.

In my opinion function evolved first and then its codification. Initially the cell division must have been just like a huge drop dividing into two. I would like to differ from mgkrebbs on this. Lipids are simple molecules and they can spontaneously form compartments such as miscelles based on simple principles of thermodynamics. If miscelles get huge they can divide.
I still cannot understand whether it is chemical reproduction that came fist or sustained multispecies chemical reactions. I tend to believe the second with relatively more confidence.
The popular RNA world hypothesis is justified by certain observations and fits nicely in the Darwinian scheme of biology that we are so used to believe in all the time. But it doesn't answer the previously mentioned thermodynamic perspective. Also I fail to understand why an ancient RNA would code a protein. What advantage would it have to code a protein in the first place. So to conclude I don't have a doubt that proteins came first. The initial soup and the basic functionalities were provided by them. Then nucleotides evolved parallely and they became catalysts of protein synthesis. So the reactants came before the catalysts and the better catalyst got selected.
I again iterate that this is just my opinion which you may consider pondering over along with the answers that others have provided.

The sequence is believed to be opposite of that implied by the phrasing of the question: the inheritance of structures supporting inheritance came before protocells.  The important point is that you need a system of reproduction before building more complicated structures (such as a cell).  Without replication (reproduction), a cell would be little more than a soap bubble, and would disappear without a trace before long.
The initial (or very early) form of replication is thought to be based on a simple form of RNA. The reason for this is that (1) RNA does encode genetic information in a way that is replicatable, and (2) RNA can take on shapes and chemical structures that act as an enzyme (called a ribozyme) that catalyze chemical reactions.  The hypothesis is that an RNA molecule formed that catalyzed assembly of copies of RNA chains, including itself.
After such replication was established, probably some kind of enclosure like the cell membrane evolved to contain the chemicals, making the reactions more efficient.  After (or maybe before) this, RNA catalyzing assembly of simple protein-like molecules whose sequence was encoded by RNA sequences evolved, leading to protein-based cellular machinery.  This mechanism is still evident in life today in that protein assembly uses a ribozyme-based molecule assembly (the ribosome) to translate messenger-RNA into proteins.

The general theory is RNA came first, then DNA. Both are able to replicate with simple changes in temperature (see polymerase chain reaction). So if we imagine a world with nucleotides making RNA, the idea is the survival of the fittest RNA. RNA for example that also had enzymatic activity was "fitter" than RNA that did not. Then go further down the line where RNA that made a certain protein was more "fitter" as thus it's concentration increased. Keep going down the line as this continues, whatever was favourable in the surrounding environment increased until we have what we have today.
Of course this is widely disputed.

AndroidPenguin and mgkrebbs both gave excellent answers to this. There are currently several ideas about the first life on Earth. Data for these methods are pretty useless because we can argue for what is the most probable and what can be modeled in the lab, but we can't (as yet) look for any fossil remains of molecules to see what really happened.
One of the most satisfying hypotheses is that protocells and self-replicating molecules (like RNA) probably came about independently, but in the same location. If the self-replicating molecule found a way to hide out in the protocell, this might be the beginning of something like what we call life.
A good talk on this topic is Martin Hanczyc's TED talk.


text:
What happens between making a DNA library and screening by nucleic acid hybridization?
I understand how a plasmid library is made and how each clone is put on the nitrocellulose membrane and nucleic acid hybridization is done. What I don't understand is how each clone is "identified" and separately put on the membrane?

The library is 'created' during a ligation reaction: plasmid vector + insert (e.g. cDNA). That DNA is used to transform E. coli, and, after plating out the transformation mixture, single bacterial colonies are obtained. Each colony contains, to a first approximation, a single plasmid species (i.e with a single insert). So each colony represents a clone, in the terms that you use.
I don't know if anyone really does things like this any more, but originally each plate would be transferred to nitrocellulose, for probing, and to a fresh plate for archiving. This way, any colony identified as positive after nucleic acid hybridisation could be picked from the archive plate for further characterisation.
This screening can be done on large format Petri dishes to reduce the number of plates needed. I know of one lab which in the 1980s used to screen λ libraries after plating out for plaques on cafeteria trays. That was the heroic era of molecular biology.


text:
Can we attack viruses by attaching proteins and such to their shells?
Haven't looked into this to very long, but an initial search didn't return anything.
HIV uses certain co-receptors to enter our cells. Could we flood the blood stream with specially designed proteins that mimic cell receptors, either locking the virus out of vulnerable cells, or even causing the virus to release its genetic material (pre-mature ejc. for viruses... :|), so it can't accidentally get away and infect a cell anyway? It seems like an obvious idea, so the fact that it may not already be happening must mean there are a host of challenges to it? Basically we design a protein that acts like a strait jacket, with tags that allow our body to recognize it as a 'friendly' body. T-cells use the same receptor though, so are there ways to identify a T-cell compared to a HIV virion?
Obviously this wouldn't prevent some viruses managing to infect actual cells, but over time, if we can attack enough, say 2/3 of the virions, for each generation, we could seriously harm the population, and maybe keep it in check?

Sorta near the mark, but this is a case of virus-on-virus crime: http://discovermagazine.com/2009/jan/033                                             It still shows a viable concept for attacking viruses though...

Maybe antibodies. If you could grow large amounts of neutralizing humanized antibodies in cell culture and inject them IV it might help reduce active virus loads. Antibodies would probably have better stability and higher affinity than receptor mimics, and the technology behind them is well developed. And as far as HIV treatment is concerned, small molecule antiretroviral drugs are already pretty good as long as you take them early on in the infection and take them regularly. These can keep viral loads so low that passing the infection to others is very difficult.

Here review  and here are reviews such approaches.  The complex peptide Trimeris/Enfurvitide and small molecule Maraviroc are FDA-approved inhibitors of HIV entry into cells.

This is the whole end goal for vaccines

Yes, that should be possible. And it is one of the ways antibodies work. It is already used as a treatment against rabies. There you get a dose of immunoglobulins directed against the rabies virus together with the vaccine. The immunoglobulins neutralize the virus.
The same is possible when you vaccinate against the surface proteins which a virus uses to dock to a cell. With the resulting antibodies this docking is at least hindered if not completely prevented. And there are interesting results from the Ebola research which used a small molecule inhibitor to identify the protein which is important for cell binding of the virus. It is called NPC1, when the receptor on the virus surface is blocked, no docking can take place. This will be one of the approaches to make a therapeutic. See here for more details.
And it is of course possible to design more of the molecules - the problem is to find substances which do not interfere with body functions or which stimulate other pathways.

Ah...so this HAS already been considered and is actively being researched. I had already run into the idea of the issue with anti-viral medications interfering with our normal bodily functions, oddly enough in an article about Ebola, as you were mentioning. I am very interested in Micro-biology, just haven't taken the time to sit down and learn in depth about it, so I wasn't aware this was how anti-bodies worked. But I was just wondering, with the developments in recomb. genetics, if anyone was researching synthetic drugs. Thanks for your answer.

This approach actually works on almost anything, given enough proteins and nanoscale "griefing".
There was an experiment a few years back where scientists wrapped normal cell membranes around polyurethane beads. The surface looks like a normal cell, allowing it to soak up toxins and trap viruses.
Then there's the offensive approach where proteins are used to block structures on a virus, preventing it from recognizing and entering host cells. Alternately you could include immune-reactive structures on those proteins, painting them for clean-up.
This approach also works on bacteria. Block membrane channels used to get rid of waste, or outright cover the bacteria in sticky garbage "griefing" gunk preventing them from eating. Build exceptionally heavy proteins that bind to bacterial flagella and stop them from moving.
Scale it up to worm parasites. Build proteins that stick to their mouths and refuse to leave. While you're at it, build another set that sticks to the opposite end of the worms' digestive tracts, preventing them from eating or removing waste. It's a major headache and a pain in the behind - at the same time.


text:
What is the expected effect of pH on the activity of a fungal pectinase?
I am working on an enzyme assay for a fungal pectinase.I assayed the enzyme in different buffers from pH 1-12.5 However,the enzyme has good activities starting from pH1-10.5.
Is it possible to have enzyme activity over such a broad range of pH?

Can you tell us which pectinase you are using? Besides that, is the activity the same over this pH range or does it vary? Can you show a curve of the activity plotted against the pH?

Could you also give more details of methodology and controls - pectin can be hydrolysed non-enzymatically at low and high pH.

I actually doubt that the pectinase has such a broad pH range in which it works optimally. Searching the web I found two figures which support my doubts:

The first is from an article ("Immobilization of pectinase by adsorption on an alginate-coated chitin support") which compares the activity of native and immobilized pectinase under different conditions. The second is from the datasheet of a company which sells the enzyme. Both show an activity over 50% roughly between pH 3.5 and 5.5 but not at higher or lower pH values.

I extracted the enzyme from 48 hours actinomycete culture ( submerged fermentation) the methodology I used is miller DNSA method


text:
Why is it that bacteria and fungi cannot develop resistance against essential oils?
I wonder why bacteria and fungi cannot develop resistance and mutate agains essential oils?
For example, some fungi get killed by oregano oil.
Being not a biologist, I hope my question is not so stupid..
Thank you!

Can you cite a specific example? For any given fruit or plant, I'm sure there is at least one fungus or bacterium that can colonize it successfully.

Here are my thoughts on this, taking your example, oregano oil.
The active anti-microbial ingredient in this essential oil is carvacrol. The WP article states that it probably acts by disruption of the membrane.
 There appear to be no examples of carvacrol resistance, as suggested by your question. In mammals the compound is detoxified in the liver via esterification to increase solubilty, thus promoting excretion.
Assuming that we can create a situation with a strong selective pressure for the development of resistance in a microbe, what would that resistance look like? If the carvacrol does indeed disrupt the membrane, then it is probably useless to develop intracellular degradation - what is needed is the secretion of an enzyme that is able to inactivate the compound, analogous to the β-lactamases that inactivate antibiotics like penicillin (which also has an extracellular mode of activity).
Furthermore, unlike β-lactams, carvacrol is insoluble in water. This suggests to me that most of the time, in the natural environment, free-living bacteria will not experience significant levels of the compound.
In summary - it may be difficult to evolve a system for the degradation of a lipophilic compound, and because it is lipophilic it may be that it is rarely a problem for bacteria unless they are being subjected to laboratory tests for antimicrobial activity.


text:
mRNA synthesis for in vivo injection
I found a commercial reagent called in vivo-jetPEI® from Polyplus-Transfection that is able to delivery mRNA in vivo. I'm planning to do an experiment with it, but I'm worry about how to synthesise mRNA and purify them clean enough to inject to living body.
I also found a recommended Kit called HiScribe T7 High Yield RNA Synthesis Kit that can help me to synthesise mRNA but I'm not sure if I can use the final product for an in vivo injection. Anyone have any experience with it?

For in-vivo injection do you mean to inject into the bloodstream? Or micro injection into cells?

@alec_djinn Hi! I mean 'inject to the bloodstream' of living organism. Like living human, living rat for therapies.

Have you ethical clearance to inject mRNA into humans? I would very much doubt it if you are unsure how to prepare the mRNA.

@David Hi David! thank you very much for your reply and concerns. I'm not testing on human yet, I just planning to make an experiment on mice. Everyone have their first time, this is the first time I make an experiment on mRNA so there are some problems I need to elucidate before doing it.

My preferred method is to use the Ambion T7 Megascript kit, but I haven't made a full comparison to other kits. They should all be more or less the same. But the transcription itself may not be enough.
Be sure that the mRNA contains a 5' cap. This is needed to bind the translation machinery and produce protein. You can include this in one of 2 ways, a cap analog, or capping enzymes. The cap analog is easier, because you just put the analog in the transcription mix. But this reduces yield, because you typically need to replace 80% of the GTP with your analog. You also won't get 100% capping, the best case scenario would give you 80% capping, but typical results are often much lower than that. If you use an older cap analog, half of the caps will be inserted the wrong way, but ARCA will prevent that. The Capping Enzymes are usually more efficient, but not cheap, and adds an extra reaction and purification step to your protocol.
A good mRNA also needs a 3' PolyA Tail. This can be added enzymatically, or it can be built into the DNA template. The enzymatic method isn't hard, it just uses E. Coli PolyA Polymerase and ATP, and can often be added to a mRNA reaction without additional purification in between. But the tail length would be a little random. Building the tail into the DNA offers more control over length, and eliminates an additional reaction step. But ordering a DNA with 100 to 200 consecutive A's is a little difficult, because quality control is hard with consecutive bases.
Finally, the RNA needs to purified. The method alec_djinn describes isn't bad, but I prefer to use Phenol:Chloroform extraction and isopropanol precipitation. It's rigorous, but it takes more time and uses potentially dangerous chloroform. You can find details on the internet, or just ask me for instructions.
I've made lots of RNA this way, and injected that RNA into a lot of mice. But I'm skeptical of JET-PEI, or any PEI product, for in vivo use. Protecting mRNA in vivo is very hard, and the simple ionic interactions between PEI and mRNA fall apart in the bloodstream. PEI is probably better than nothing, but take a look at the data on that page. The RNA all goes to the lungs. This behavior is typical of a cationic particle that aggregates in the blood, and these aggregates get trapped in the narrow capillaries of the lungs. If this was normal PEI, that mouse would die. Also, they're using 50 µg doses of mRNA. I was doing my work with 1 µg doses, but I was using a different type of transfection reagent and hydrodynamic injection. I also don't see any numbers reported on their bioluminescent imaging data. It's pretty easy to make that data look better than it is by adjusting the scale.

Extremely enthusiastic answer! I don't know why you don't have any name, i really really thankful to your answer. Actually, I found this publication by Huang et al., 2015 using in-vivo-JetPEI and modified mRNA to delivery to the cardiac organ. They also use Ambion T7 Megascript kit as your recommended so it's a good point to start with. Outside of that article, i can't find any other publication about inject mRNA to the bloodstream for delivery to all organs. Could you please tell me which type of reagent are you using to delivery?

@joe I prefer a certain level of anonymity, which is why I can't tell you much about the transfection reagent we used. Our lab invented it, and we were the only ones to ever use it. The paper you mention injects the RNA PEI mix right into the heart tissue, which avoids the requirement for circulatory stability. Injecting any particles into the blood stream typically leads to accumulation in the liver, spleen, kidneys, or lungs, but mostly the liver. Unfortunately, this accumulation is usually through a destructive pathway that degrades the RNA before it can make protein.

I hope your lab will commercialize it as soon as possible so anyone can use it. That's so bad if I cannot delivery mRNA to all organs. Anyway thank you very very much!  I will find more information or/and contact them to elucidate this issue before I buy this reagent.

You should purify your RNA after transcription from any buffer/enzyme contaminants. There are several kits available in the market for that. One is GeneJET DNA & RNA Cleanup and Concentration that uses standard silica-beds packed columns to absorb nucleic acids. You can then elute them in pure water and you should be ready to go. Once the RNA is purified you will use the vivo-jetPEI for the delivery.

Thank you very very much! I just take a look at it and planning to purchase it. I hope it will work well, many thanks to you!


text:
Why are trichromat cone cells unable to sense ultraviolet and infrared radiation?
I understand that cone cells vary in the color they sense, is this because of wavelength, frequency, something else, or a combination of the previous? I also understand that tetrachromats can see an extended spectrum of color because they have four as opposed to three (for trichromats) color channels, hence, I believe, an extended variation of cone cells.

The range of color perception in humans is primarily limited by the sensitivity of cone cells (specifically, the opsin proteins in cone cells) to various frequencies of light.  This sensitivity drops off at 700 nm on one side and 380 nm on the other, which is where infrared and ultraviolet begin, respectively.
Even with hypothetical infrared or ultraviolet cones, we wouldn't necessarily be able to perceive color much further beyond our current range anyway.  The various parts of the eye (cornea, lens, and the liquid inside) block both ultraviolet (starting around 400 nm) and infrared (starting maybe at 1400 nm) beyond certain wavelenghts.
http://en.wikipedia.org/wiki/Color_vision
Tetrachromaticity, at least in humans, does NOT confer an extended spectrum of color perception.  Tetrachromaticity results from a mutation on one of the light sensing proteins, changing its peak sensitivity by a few nanometers. So a tetrachromat can't see beyond the normal color spectrum, but they can probably distinguish shades of green and blue more precisely than trichromats. This has been an area of active scientific research recently; I think most scientists didn't think they existed.  Now studies suggest they're 2-50% of the population.  Humans with 5+ cone types are also hypothesized, and with the ubiquity of genome sequencing I imagine we'll be learning a lot more about that soon.
Other species have more diverse color perception, with ultraviolet being especially common in insects and birds. The mantis shrimp has an astounding 16 different kinds of photo receptors, plus a few specialized eyes for detecting polarized light. For a loving account of mantis shrimp, I recommend this comic. http://theoatmeal.com/comics/mantis_shrimp

Wikipedia says "the rods and cones located at the back of the human eye cannot detect the short ultraviolet wavelengths" but you say otherwise, could you possibly give evidence for your claim? Edit: Also mutation could also change the trough, right?

I also understand that ultraviolet radiation is absorbed by varios tissues of the eye (which is what causes photokeratitis, is this the same for infrared?

Sorry, I meant that as a hypotical, i.e. if we DID have extra chromophores, they still might not work.  I did see one reference that infrared doesn't actually start getting absorbed until 1400 nm by the eye though, so we might be able to extend a fair distance in that direction, but not infinitely.

I indeed read somewhere (and have never been able to find the source) that it would only take a single base pair mutation for us to see much further into ultraviolet. But that it wouldn't matter because our lens starts absorbing it very close to our existing limit. There is apparently no true infrared vision, possibly because the photons are too low energy. Animals that "see" infrared do it through other types of organs.  So I wouldn't bet on a mutation on that end.

You mean that if we had extra chromophores, humans still might not be able to see them or that the chromophores just wouldn't work?

I still need to know, do cones act on frequency, wavelength or both?

Scientists have genetically engineered mice (normally dichromats) to give them their missing red chromophore (I think).  The mice used them just fine. So the point is just that, at some point, the physiology of the lens and cornea would be the limiting factor. As for frequency vs. wavelength, I suggest you go look up wavelength on wikipedia.


text:
functional hypocholesterolemia due to very high HDL or low LDL?
Nutritional and medical recommendations about cholesterol seem to focus exclusively on hypercholesterolemia, and as such, they provide only a maximum desirable level for LDL and a minimum for HDL. I've found a little bit of information about hypocholesterolemia caused by inadequate cholesterol in the body (due to overuse of statins, malnutrition, or other disorders), but not about cholesterol deficits due to lipoprotein levels.
It seems like it should be theoretically possible to have so much HDL or so little LDL activity that organs don't maintain enough cholesterol to function properly, even if cholesterol synthesis is adequate. Obviously this might or might not ever occur in reality. Is there any research that has found an upper bound on desirable HDL in humans, or a lower bound on desirable LDL or LDL:HDL ratio?

Upper bound of HDL doesn't really exist. The greeks are known for their incredibly high levels of HDL and the so called mediterranean diet/genetics combination that causes this is only beneficial to health (supposedly - although never been proven that incredibly high HDL levels are beneficial, they're just not harmful).
As for too low LDL levels/cholesterol levels - that's interesting. Unfortunately it isn't possible because any mutations that caused this would be fatal, cholesterol makes up an essential part of cell membranes etc. That's why our body makes our own. A mutation preventing this would not even manifest.


text:
Do blood glucose "spikes" contribute to insulin resistance, or is prolonged elevation required?
There's increasing public discussion about the health risks of chronic insulin resistance* (IR). In many cases there's a focus on high glycemic index foods that "spike" your blood sugar, which implies that a rapid increase in blood glucose is by itself sufficient to contribute to IR.
On the other hand, I've heard the claim that if a person is 1) moderately active, 2) not in caloric surplus, and 3) not already insulin resistant, then they will will quickly clear excess blood glucose by replenishing glycogen or through general energy expenditure. This is claimed to have no effect on IR, even though the individual was temporarily exposed to elevated glucose / insulin.
This leads me to two questions:
1) Is it true that high blood glucose is normalized substantially more rapidly in people who have depleted their glycogen, or who have higher energy needs?
2) Does repeated exposure to high levels of blood glucose contribute to IR by itself, or are high and prolonged levels of blood glucose required?
This has public health implications -- If the "spikes" theory is inaccurate, then glycemic index may not be very important to sufficiently active people**, and low glycemic index meals may not be as helpful as expected for people at risk of developing IR if total glucose exposure is high.

*"chronic insulin resistance" would exclude gestational diabetes and the reversible insulin resistance seen on ketogenic diets.
**For this discussion, let's ignore effects of blood sugar swings on hunger, mood, behavior, etc, since my interest is in the specific physiological triggers for IR.

The topic is immensely interesting, but this question is too complex for me to answer. A very nice, concise and informative review is freely accessed here: http://www.ncbi.nlm.nih.gov/pubmed/12081851

Great Question.
The biggest problem is persistent insulin signaling from prolonged excessive high blood glucose over time. The reason being that it is this kind of signaling that results in insulin insensitivity due to down-regulation of the insulin receptors.
Any bolus of carbohydrates > ~ 25grams in a sitting is going to bump up blood sugar at a fast enough rate to warrant the release of insulin to help lower blood sugar levels.  This can be mitigated by an excessive amount of fat along with the carbohydrates, thus slowing down the spike.

Your question: 1) Is it true that high blood glucose is normalized substantially more rapidly in people who have depleted their glycogen, or who have higher energy needs?

So this is a little confounded by several variables.  The thought process is that people that have less glycogen or higher energy needs, don't have insulin insensitivity; thus the same amount of insulin would do a better job of shuttling glucose into cells.  We know that consistent exercise increases insulin sensitivity, as does lack of persistent insulin signaling (such as comes from being in a glycogen depleted state).  So the answer to your question is generally YES for these reasons.

2) Does repeated exposure to high levels of blood glucose contribute to IR by itself, or are high and prolonged levels of blood glucose required?

What we know from epi studies suggests that it isn't insulin spikes.  It is prolonged insulin signaling that causes insulin insensitivity through down-regulation of insulin receptors.
If you are fuel deprived, or only getting what you need from your food, insulin spikes are normal and transient and don't cause this IR.
Persistent insulin signaling causes many many side effects. Insulin is mitogenic,  has downstream pro-inflammatory cascades, and the insulin insensitivity that results is a major player in non-alchololic fatty liver disease.
Some references for these thoughts and further reading:

This one gives evidence of reduced IR activity, not
downreglation
Insulin signaling and NAFLD
Exercise and Insulin Sensitivity

John, I bet this is a great answer, but a reference or two to allow for further research and background reading is preferable. Ping me once done and I'm happy to upvote

@AliceD Thanks for the suggestion.  I'm new here.

No worries +1 :) Referencing is a great habit.


text:
Why do oranges in the US have a small separate part?
Why do oranges in the US have a small separate detachable part at the tip which is separate from the other pods? It looks like a tiny orange itself and has a long fiber attached to it.

This is specific to navel oranges, which have a conjoined twin fruit.
This blog gives an account of this.


text:
What is optical density in Lowry's protein estimation method?
I have a few questions:

What is an OD value?
Why do we use blank solution in Lowry's protein estimation method?
If The OD of a protein is 0.01, what does it mean?

Thanks in advance.

The OD measurement is the output of what the photometer measures. It is actually the amount of light which is scattered or absorbed by your sample - scientifically called extinction.
A blank is used to be able to substract the influence of reagents, light that is scattered on the surfaces of the cuvette (which is probably also not completely clean) and so on. Every of this influences reduces the amount of light which should reach the detector on the other side of the probe and give you false extinction readings. If you are using a colored detection sample (which colors deeper or looses color during the reaction) this is more obvious. The solution already has an extinction on its own which is not of interest. So you make a blank (which basically substracts all these influences from you sample reading) to correct for this. How this is done depends on the photometer. Some make a correction reading at the beginning, while others use a second cuvette (a blank cuvette) which is permanently measured.
It means that the protein gives you this extinction. Without a calibration curve (made from serial dilutions with known protein concentrations) it is impossible to make any further comment on this number.

Thanks a lot for quick response.but can you elaborate ans no. 2 please.

@N00B Sure, I expanded my answer.

You can think of the blank as a way of calibrating the instrument. The blank defines the amount of light that will hit the photodetector when there is none of the species of interest in the cuvette. By setting this as the zero you have prepared the instrument for measuring the samples of interest.


text:
How did scientists discover HIV?
Imagining that we're now in 1983 (when HIV was discovered), there were no modern machines at that time to sequence massive genome extracted from blood. There was a strange disease and no one know what caused it, it's a virus or a bacteria or something else... So how did scientists find out HIV at that time?
-- Update: I just think that they extracted RNA from blood of those patients who have the same symptoms and using electrophoresis to find out if there was a large ARN fragment exists to indicate that they was infected by a virus, is that true?

See And the Band Played On for a docu-drama retelling of the story, where epidemiology plays an important role. Well worth the watch.

Not to minimize Iayork's fine answer, but the same way they discovered polio was a virus, smallpox was a virus, chickenpox was a virus, Infectious Mononucleosis was a virus, Influenza was a virus, etc., etc.

HIV was identified as an infectious disease through classical epidemiology, and the virus was identified through classical virology.
I won't get into the epidemiology, but briefly it went pretty much as you'd expect -- a cluster of symptoms were identified, patient characteristics were analyzed, the contagious nature of the symptoms were recognized, all through standard approaches of patient tracking and so on.
As for the virus identification, that was long before modern molecular techniques were available.  It was even before PCR was commercially available!  So the techniques that were used were those of classical microbiology.
It seemed most likely that the agent was a virus rather than a bacterium (though every possible angle was covered), and just about every virologist tried looking for their favorite agent, but retroviruses also seemed like logical candidates and several groups tried isolating infectious agents from the blood of AIDS patients.
The two groups who were most successful were those of Luc Montagnier and Robert Gallo.  There turned out to be a lot of politics and personalities involved and I won't get into that.  Here are some comments from Montagnier summarizing the story:

There were only a few patients with this disease in France, but Gallo's idea that a retrovirus was the cause had already crossed the Atlantic. His idea was disseminated by a small group of clinicians and immunologists led by Jacques Leibowitch and Willy Rozenbaum. At the end of 1982, Françoise Brun-Vezinet, a former student of mine and a member of this group, proposed that we collaborate to discover if a retrovirus was the cause of this disease, now called AIDS.
We were ready to start because my laboratory was equipped to hunt for lymphotropic retroviruses in human T cell cultures.  ... On 3 January 1983, Françoise Brun-Vezinet obtained a lymph node biopsy from one of Rozenbaum's patients, ... I minced the lymph node, dissociated the fragments into single cells, and cultured the T lymphocytes with interleukin-2 and antiserum to human interferon. Fifteen days later, Françoise Sinoussi (by then Barré-Sinoussi) found the first traces of RT in the supernatant of the lymphocyte culture, indicating the presence of a retrovirus.  ... A few months later, I received a blood sample from a young hemophiliac (LOI) with full-blown AIDS, and blood and lymph node samples from a young gay man (LAI) with advanced Kaposi's sarcoma. The LAI virus could be isolated from the patient's blood cells and grew very quickly in the patient's cultured T lymphocytes, killing them as well as killing T lymphocytes from blood donors.
New evidence that this strange retrovirus was the cause of AIDS came from our team in the fall of 1983 and the winter of 1984 (7). We observed a high frequency of antibodies against the virus in lymphadenopathy patients, and noted the favored tropism of this virus for CD4+ T lymphocytes. Our results were still controversial, however, and we had difficulty in obtaining the funding needed to better characterize the virus and to develop a blood test. The tide only turned in France when Robert Gallo and his group in the United States made a similar discovery. In the spring of 1984, Gallo published more convincing evidence that HIV causes AIDS ...

--A History of HIV Discovery
Gallo's approach was similar -- focused on isolating replicating virus, more than performing the molecular biology that's become standard in the meantime.

Dr. Gallo would want his name listed first, in your list.

Man, the politicking was so unpleasant and tedious. I really don't want to relive that.

There is a brief, relatively dispassionate, and from my memory reasonably balanced summary of the politicking in HIV, HPV Researchers Honored, But One Scientist Is Left Out, if people don't know what we're talking about

@iayork gah it's behind a paywall for me sadly.

@DRF The fine print for "Science AAAS" says research is free one year after publication if you register.  The paper was published in 2008.  I have not tried but you should be able to read it if you are willing to register

@TonyDallimore Yeah I was hoping so, unfortunately I'm guessing they count this as an op-ed or whatever so it's not accessible even after registration. Still thank you for the link. I think I probably have the hard copy some place.

Just to remind people that science is hard (and all about making mistakes), it could be worth giving examples of one or two of the incorrect claims about the aetiological basis of AIDS (at the time and by reputable scientists, I mean, not modern denialist stuff). For example, there was a paper in the Lancet in 1983 suggesting it could have been caused by African swine fever virus (http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2883%2991345-4/abstract), which is... pretty different, to a virologist (to put it mildly).

...although this may not be the best example; the Teas theory got a pretty cool reception at the time, as far as I can tell (this was all rather before my time).