molecular biology - Should I design a primer to detect virus based on NCBI genebank?

Any other database better than NCBI ?

A lot of people overlook some sub-databases inside NCBI and search the main nucleotide database only.

If You never tried it, you can blast the HIV sequence which You have found, against other databases. On the ncbi blast webpage, just choose the options other than nucleotide collection (nr/nt). I tend to find new sequences in Expressed sequence tags (EST), Genomic survey sequences (GSS) or Whole genome shotgun contigs (WGS). Some of these databases cover unfinished sequencing project and should be a source of new data.

(I am a plant person, not virus person, so maybe you will find out, that different databases are worth searching for you. Or you will find it a waste of time.)

BTW, now some time had passed since your question. How did you solve Your HIV sequence problem ?

Recombinant protein fraction in E. coli

Miroux and Walker (1996) Over-production of Proteins in Escherichia coli: Mutant Hosts that Allow Synthesis of some Membrane Proteins and Globular Proteins at High Levels. J Mol Biol. 260: 289–298

The authors report on problems of over-expressing membrane proteins in E. coli using a T7 (pET) system. They isolate mutant strains which show improved levels of expression compared to the parent strain, BL21(DE3). In their Table 1 they document levels of expression of 17 proteins including, as a control, GFP. GFP was found as a combination of soluble and inclusion body protein at a level of 37 mg L^-1 in BL21(DE3) and 140 mg L^-1 in one of their mutant strains (C41(DE3)). The highest level of expression that they observed was 300 mg L^-1 for bovine OSCP.

Unfortunately the authors document neither the total protein content, nor the cell density of the cultures that they analysed.

Let's assume that the cultures were 10e9 cells mL^-1 = 10e12 cells L^-1.

According to this source (citing Neidhardt F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. Vol 1. pp. 14, ASM Press 1996), the dry weight of an E. coli cell is 2.8e-13 g

The generally accepted figure for protein as a fraction of dry weight in E. coli = 0.55

I calculate from these numbers a value of 1540 mg protein L^-1. For the three protein expression levels described above this means:

GFP in BL21(DE3) = 2.4%

GFP in C41(DE3) = 9.6%

bovine OSCP in C41(DE3) = 19.4%

I conclude (from these numbers, and from personal experience) that overexpression levels are highly variable, and are going to be strain and protein-dependent. Values in the range of 1-20% total cell protein may be anticipated.

evolution - Why don't all ants have wings?

When is it good to have wings?

When you need to move a great distance in as short a time as possible with minimal risk.

Clearly wings would have enormous benefit at a time when you need to get far away from the nest really quickly, perhaps at a time when you believe the weather would be particularly favourable. This benefit increases exponentially when procreation is involved.

When is it bad to have wings?

Almost any other time.

• When it is raining.

Rain and wings just do not go well together. If you get hit by a raindrop while wearing wings you are basically stuck where the drop lands until it evaporates completely.

• When it is windy.

I rest my case.

• When you are under attack.

Agility, while wearing wings, just cannot be considered one of your evolutionary advantages.

• When you are trying to gather/carry food back to the nest.

Surely an ant trying to carry a piece of a leaf, however small, would consider wings a severe burden.

• When times are hard foodwise

The protein investment in wings would surely be better spent on survival when food is scarce.

• Encounters with birds suck

Wings make you incredibly easy to grab hold of in mid-air, unless of course you can shed your wings when stressed, and many ants can (while obviously butterflies and moths cannot).

Surely my arguments suggest that having no wings would be a serious advantage in almost any situation except on the rare occasion when you need to move a long way really fast. Clearly the ant has an amazing skill to only have wings when they are needed and not at any other time.

Added after a number of comments

You have to remember that much of an ant's work is maintaining the colony as a collective. Preserving its cohesion, feeding the young, caring for eggs. The whole point of having a colony is to have far fewer individuals spread out, in danger, gathering food. This is to reduce the risk of complete colony death, which is essentially the death of the queen and therefore the gene pool of the colony.

You have to look at each ant colony as a single individual when you look at them on an evolutionary scale. In this way the life or death of one, or even 1,000 ants is not important, it is the survival of the colony. From this perspective, wings are dangerous for all my reasons above. The only time they are of value is during diaspora and that is the only time ants have them, which I think is incredibly clever.

Evolving a detachable appendage to an ant is like humans evolving detachable breasts at menopause. An astonishing achievement even humans have failed to achieve.

human biology - Do hormone drugs affect whether a person feels sexual attraction to males or females?

I know that ingesting testosterone and other hormonal drugs may stimulate libido and increase sexual desire.

But I wonder, if a man ingests female hormones such as estrogen, will he experience sexual desire towards other men or not?

Similarly, the other way around, whether a female ingesting male sexual hormones will experience desire towards other women?

The question is motivated by the interest to know whether transgender people, particularly, the MtF transsexuals engaged in prostitution experience genuine attraction to males.

digestive system - Long term liquid food diet by blending/grinding all quality foods one would normaly eat, not any weight loss or prepared drinks

I want to know what are the effects of not using your teeth to grind foods but preparing it before eating with blending and grinding them into a liquid.

Here I am not talking about any weight loss or fitness industry prepared drinks. I mean the ordinary raw and cooked foods like meat, vegetables, cereals, and fruits that one would normally eat in classic meals.

Would this decrease of work done by teeth and digestion system have positive or negative health effects?

human biology - Where does all the food go?

Whatever the diet, the food intake contains macronutrients: carbohydrate, fat and protein. When they are metabolised all of these molecules will end up, for the most part, as carbon dioxide, water, and ammonia, unless they are incorporated into components of the body.

These waste products are, of course, lost via breathing, and via the urine. That's where the "missing mass" goes.

A related question is here.

microbiology - How was the diversity between ethanol fermentation and lactic acid fermentation evolved?

First, it is not clear from the physiology or biochemical information alone to determine what evolved from what. The intermediate pyruvate is always there, so lactose dehydrogenase (LDH) and pyruvate decarboxylase (PDC) could have each evolved anytime, and there are good reasons for both:

1. LDH: the reaction pyruvate + NADH/H+ = lactate + NAD+ + 25 kJ/mol is highly exergonic, i.e. produces heat


2. PDC: the reaction pyruvate = acetaldehyde + CO2 (and with ALD present) acetaldehyde + NADH/H+ = ethanol + NAD+ where ethanol is poisonous to other species

Add to it that there are organisms like Sch. pombe that have both enzymes, so can do both reactions, your questions should be rather:

How has the enzyme LDH evolved?

The enzyme is similar to malate dehydrogenase, both form a family. They belong to a group of enzymes that all have a NAD(P) binding domain, so it's not too far-fetched to state that LDH and MDH evolved from another enzyme with NAD(P) binding domain.

http://www.ebi.ac.uk/interpro/IEntry?ac=IPR016040

How has the enzyme PDC evolved?

Protein sequences of pyruvate decarboxylase (PDC) derived from cloned
yeast (Saccharomyces cerevisiae) and bacterial (Zymomonas mobilis)
genes were compared with each other and with sequence databases.
Extensive sequence similarities were found between them and with two
others: cytochrome-linked pyruvate oxidase from Escherichia coli and
acetolactate synthase (ilvI in E. coli; ILV2 gene in S. cerevisiae).
All catalyse decarboxylation of pyruvate using thiamine pyrophosphate
(TPP) as cofactor. General overall similarity suggests common ancestry
for these enzymes.

cited from abstract of

Green, Jeremy. "Pyruvate decarboxylase is like acetolactate synthase (< i> ILV2) and not like the pyruvate dehydrogenase E1 subunit." FEBS letters 246.1 (1989): 1-5. http://www.ncbi.nlm.nih.gov/pubmed/2651151?dopt=Abstract