genetics - How many nucleotide pairs code one gene?

You seem to have some confusion, so let's clear things up.

A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.
Each gene consists of nucleotides bound together, which are interpreted by the cellular machinery in groups of three, called triplets.
DNA is first transcribed into messenger RNA (mRNA), which is then translated into proteins.
Each triplet codes for one aminoacid not one gene! In fact genes are not "coded" by anything, they are the code!

Now, what I just wrote is extremely simplified, there are other important details that I omitted, but hopefully it cleared your doubt.

To give you some further detail: not every single nucleotide in a gene will code for an aminoacid. There are regulatory elements such as the promoter of the gene, which allows the enzymes that transcribe the DNA to attach to the gene (essentialy it says: "hey, start transcription right here!"). Similarly, enhancers and silencers can tune up or down transcription of the gene.

In eukaryotes there are big stretches of DNA called introns that are not coding for anything but have big importance for regulating transcription. In fact a single mRNA can be used to code more than one protein, using a process called alternative splicing.

There are also regions of DNA that code for RNA sequences not translated into proteins at all, but which have all sorts of regulatory functions in the cell.

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

How essential is vitamin B3 to the diet?

According to one study:

It was calculated that if the excretory percentage of niacin metabolites in the urine were 60%, of the tryptophan ingested, the conversion factor would be a value of 67, meaning that is 67 mg of tryptophan is equal to 1 mg of niacin.

However, the study has a pretty low power with only 10 participants and an indirect measure of niacin.

Is it possible that a person could get all of their niacin from tryptophan? Probably - you just need to eat enough tryptophan, which is also an Essential Amino Acid. The body may preferentially keep Tryptophan (which it does not store) until Niacin runs out (which also cannot be stored).

organic chemistry - What is the effect of flash pasteurisation on Maillard reactions or production of AGEs in milk?

This is only an partial answer, as I do not have the time now to look for other references.

In the chapter about milk, Harold McGee's beautiful book "On Food & Cooking" says (pg. 21 of the 2004 edition, bold is mine):

Flavors from cooking
Low-temperature pasteurization slightly modifies milk flavor by driving off some of the more delicate aromas, but stabilizes it by inactivating enzymes and bacteria, and adds slightly sulfury and green-leaf notes (dimethyl sulfide, hexanal). High-temperature pasteurization or brief cooking - heating milk above 170°F/76°C - generates traces of many flavorful substances, including those characteristic of vanilla, almonds and cultured butter, as well as hydrogen sulfide. Prolonged boiling encourages browning or Maillard reactions between lactose and milk proteins, and generates molecules that combine to give the flavor of butterscotch.

He continues by speaking about the different types of pasteurization, and says (pg.22-23)

The third method of pasteurizing milk is the ultra-high temperature (UHT) method which involves heating milk at 265-300°F/130-150°C either instantaneously or for 1 to 3 seconds, and produces milk that, if packaged under strictly sterile conditions can be stored for months without refrigeration. The longer UHT treatment imparts a cooked flavor and slightly brown color to milk; cream contains less lactose and protein, so its color and flavor are less affected.
Sterilized milk has been heated at 230-250°F/110-121°C for 8 to 30 minutes; it is even darker and stronger in flavor, and keeps indefinitely at room temperature.

So, it appears as if indeed there may be some Maillard reaction going on in UHT, although it is probably minor (otherwise the milk would be much darker in color, as it is the case for sterilized milk).

The book also speaks about homogenization, but it does not mention anything specific about Maillard reaction there (homogenization is not carried on at high temperatures, so it does makes sense not to have it).

To answer your question:

Does this effect the nutritional value of the milk?

Well, according to this presentation (but, be warned, it does not cite any reference!) it seems that it does, although I don't think the Maillard reaction is specially involved.

http://www.slideshare.net/Aslal_saja/effect-of-uht-treatment

Specifically it says that the irreversible changes that occur are:

• Whey protein denaturation (35 to 100% of denaturation of $\beta$-lactoglobulin)


• Slight increase in the size of casein micelles


• Whey protein-casein micelle interaction


• Maillard reactions


• Fat globule composition changes (although no changes in nutritional value of milk fat)


• Vitamin content changes (20-30% loss in vitamin B1 and B12. Markedly reduced content in vitamin C and folic acid if high level of oxygen were present during the treatment, no changes in vitamins A, D, E and beta-carotene).

It also says that:

Biological value and net protein utilization of UHT milk were lower for stored milk than directly used milk. Lysine loss during UHT is high but not significant to affect milk nutritional values.

---

I don't know whether the fact that you have problems when drinking UHT milk has anything to do with Maillard reaction or any of the other modifications brought by UHT treatment, and I will not venture in there, as I am not an MD and prefer not to give any sort of medical advice.

cardiology - How quickly can the human heart rate rise and fall?

How quickly can the human heart rate rise and lower?

For example lets say a human heart rate is rested and is at 60BPM and that person is suddenly scared to trigger their fight or flight reaction. Lets say their heart rate rises to double (120BPM).

From the above example their rate has gone from 1000ms between beats to 500ms between beats. Can the human heart instantly in one heart beat go from the 1000ms to 500ms between beats or does it need to ramp up? If yes how quickly can the heart rate ramp up?

I understand that each human heart is different, and that the speed increase and decrease will be different from person to person. What I'm looking for is a value that I can safely say the human heart won't exceed.

Similarly the same question goes to your heart going lower.

genetics - Knockdown of long noncoding RNA (lncRNA) - how is it done?

Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the RNase H enzyme, which degrades RNA-DNA duplexes. It degrades the lncRNA.

UPDATE: For reference, I learned about this from a seminar, and it is not very well documented, but after some literature search I found this paper to quote:

Although we (Fig. 3A) and others (42, 49) have used siRNA to knock down NEAT1 lncRNA and although the knockdown of strictly nuclear RNAs has been well described (53, 54), we remained concerned that because NEAT1 is mostly a nuclear RNA (55), it may not be very efficiently targeted by the RNAi machinery. Nuclear RNAs, however, are proficiently targeted using complementary antisense (AS) oligodeoxynucleotides that recruit nuclear RNase H activity to degrade the RNA (56). Hence, we also employed complementary AS oligodeoxynucleotides to knock down NEAT1 lncRNA in HIV-1 NL4-3-infected Jurkat cells (Fig. 4C, left). The AS approach reduced NEAT1 (Fig. 4C, left) and increased HIV-1 p24 production (Fig. 4C, right), providing results consistent with those from siRNA-mediated knockdown of NEAT1 (Fig. 4A and B).

neuroscience - What happens during a Raynauds episode?

Raynaud's phenomenon can be a serious health issue, as the blood flow to the extremities, mainly the fingers is compromised, causing fingers to blanche, and then turn blue. Severe Raynaud's can cause gangrene in illnesses like progressive/ diffuse scleroderma.

I am not asking about connective tissue disease per se, but what occurs during an actual Raynaud event (for a better way of putting it), not what precipitates the condition to occur within a particular person and not another.

what are the underlying biological processes that cause the blood flow to be compromised like this?

zoology - Is there such thing as "meters per calorie" for living organisms?

Halsey & White (2012) Comparative energetics of mammalian locomotion: Humans are not different. Journal of Human Evolution 63:718–722

This paper presents a comparison of the metabolic cost of walking and running in humans, Australopithecus and other mammals. They use a parameter NCOT (net cost of transport), whose units are ml O₂ consumed m^-1. The inverse of this parameter would be related to your metres per calorie.

The authors quote an NCOT of 12.77 ml O₂ m^-1 for a walking human. Using a value of 4 kcal g^-1 for glucose, I calculate that this NCOT is equivalent to 14.6 m kcal^-1.

Here I found an energy consumption value of 5.8 kcal min^-1 (for a 73 kg man) walking at 6.4 km h^-1, which translates to 18.5 m kcal^-1.

Incidentally, according to the authors of the paper:

The predicted net cost of transport (NCOT, ml O₂ m⁻¹) of mammals is related to mass (M, kg) according to 0.54M^0.70.

human biology - Does the brain and the body use the same energy source (glucose/ATP)?

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.