neuroscience - Is there a biophysical causation from local field potential (LFP) to spikes?

Many experiments showed that neurons tend to fire at some phase (usually trough) of local field potential (LFP) oscillations, such as theta or gamma rhythm. LFP is supposedly generated by a population of neurons with coherent currents induced by spikes. So there is a causal link from spiking activity to LFPs. Is there also a significant influence on the spikes directly from LFP (not via the hidden spikes that generated the LFP)?

Is it just an epiphenomenon, and or is there a possibility that it is partly a serious mechanism for neural computation?

gel electrophoresis - What would cause bands to appear lower on a nonreduced SDS-PAGE gel?

The major effect of changing the redox environment of a protein is the formation or breakage of disulfide bonds. Under sufficiently reducing conditions no disulfide bridges will be present, while under oxidizing conditions your protein will form disulfide bridges if it has the ability to do so.

Disulfide bridges can significantly change the tertiary structure of a protein and change the behaviour of the protein on a gel that way. Generally, disulfide bridges should make the protein more compact and make it run faster on a gel.

It is therefore plausible that your faster band is the protein with disulfide bridges, which will appear to run like a smaller protein as it is more compact. The slower band then is the protein without disulfide bridges which can adopt a more extended conformation.

I'm assuming you're talking about native gels here, as denaturing gels usually contain DTT or beta-mercaptoethanol in the sample buffer to reduce any disulfide bonds and avoid this effect altogether.

nutrition - What does the term 'bioavailability' mean?

Bioavailability is a concept which applies to nutrients and drugs which pass through first-pass metabolism, i.e. orally (and to some extent nasally) consumed substances. Anything absorbed in the gut first passes through the liver before reaching the rest of the circulation, and both the gut and liver may metabolise it to some extent. The liver in specific has the powerful Cytochrome P450 system, a huge variety of enzymes to break down all sorts of substances, although in some cases it can actually produce more active or even toxic forms instead of breaking them down.

This can lead to drastic reductions in the amount available in the systemic circulation after oral administration. E.g. propanolol (a beta blocker) needs to be given in 100mg doses orally while intravenously (avoiding first-pass metabolism) only 5mg are needed.

physiology - What is the effect of exendin on beta-cells?

I recently tested exendin on INS1e cells in an Edu incorporation assay (similar to BrdU incorporation) to observe if this compound induces proliferation of the cells. Compound incubation was for 24 hours. I saw no incorporation of EdU with this compound over untreated levels. In addition, during the assay I look at overall cell number with a DNA stain, but I did not see any effect on total cell number with exendin (ie, if it were toxic the total cell number should go down which I have observed with other compounds).

nutrition - What are minerals (other than zinc) that the human body cannot store

Essential "minerals", i.e., metal cations are magnesium, zinc, iron, potassium, sodium, manganese, molybdenum, selenium, cobalt, copper and even calcium, as we lose a tiny amount of it through urine and sweat. They are all "stored" in some way, but only temporally, so some amount has to be taken up daily. It would show only weeks later, however, if you have a deficiency.

Wikipedia adds phosphorus and iodine but they are not metals.

human biology - When to measure resting heart rate and blood pressure for following day-to-day trend?

I would be very surprised if the time of day made a difference. I've personally never heard mention of such a phenomenon in discussions with intensive care practitioners (where of course HR and BP are measured constantly). However this is only the case during rest, this paper (on horses) suggests that there is some difference in HR and BP after exercise depending on time of day.

You are right to attempt to control it however, I suppose. It doesn't matter when you take your measurements, as long as you take them at the same time each day.

I would say that one of your first suggestions of taking the measurements almost immediately after waking. Of course you would have to be relaxed as you assembled your equipment then rest for a few minutes in the posture you have chosen (this will matter) before taking the measurements but otherwise I can't see you having too great a problem.

zoology - Do cows produce milk excessively?

The average domesticated dairy cow produces far more milk than would be required to feed their calf. All cows, wild and domesticated, will only lactate in the period between their calf's birth and weaning. Milk is calf-food, and when there's no calf, there's no evolutionary advantage in producing milk.

On dairy farms, cows are milked twice daily, from spring (when they give birth) until late autumn. This mechanical milking 'fools' the cow into continuing to lactate. When a cow has stopped lactating, they will only start again after giving birth. This means that you can't just start milking a cow and expect to get milk.

Generally farmers milk their cows from spring (birth) until late autumn. The reason for stopping in autumn is simply because the grass grows much slower in winter, so there isn't enough food to support lactating cows. However, it is entirely possible to milk longer than a year; I know of farmers who milk their cows continuously for two years. These farmers will have to purchase a lot of supplimental food (like hay or silage) during winter. The advantage of milking for longer than one season is that the cows do not have to give birth every spring, but instead only every second spring.

I believe (but can't guarantee) that in winter, most milk purchased in a shop comes from the opposite hemisphere. I do know that here in New Zealand, we export a lot of milk to northern-hemisphere countries.

If you were to suddenly stop milking a cow, they might get sick but generally they will survive. It's still something to avoid!

I do not have an 'official' source for these facts. However, I grew up on a dairy farm, so this was my life.

dna - What is the contribution of viruses to the evolution of mankind?

Human endogenous retroviruses (HERVs) have been an interesting (and expanding) topic of research in evolutionary biology and medicine. A retrovirus has an RNA genome in the virus particle, and integrates with the host cell's DNA upon infection to hijack the transcription/translation machinery and produce copies of itself. For this reason, it is not possible to "cure" a cell of a retroviral infection; instead all of the infected cells must be destroyed or commit suicide through apoptosis, also known as programmed cell death. Common examples of retroviruses include HIV (causative agent of AIDS), HTLV (human T-cell leukemia virus), and the Hepatitis B virus.

Viral infections are most common in somatic cells, where any change in the DNA sequence is not passed along to the next generation. However, any retroviral infection in germ cells (eggs, sperm, and the progenitor cells that make them) could be passed on to the next generation, and over time spread throughout a population. Some HERV fragments are apparently completely inactive (at least as far as we are able to tell currently), and are a possible source for some of the so-called "junk" or non-coding non-regulatory DNA that makes up a significant part of our genome - one estimate claims that 8% of our genetic material is of retroviral origin. Other HERVs have been implicated in various pathological conditions, including multiple sclerosis.

I'm not sure that any human genes have been found that were picked up by a virus, stayed with it for a time (and potentially mutated), then was reinserted back into the human genome, if that's what you're asking. There are certainly many cases of genes and gene fragments (coding regions, promotors, enhancers, etc.) being moved around as a result of viral integration/splicing. http://en.wikipedia.org/wiki/Endogenous_retrovirus#Genome_Evolution is a large, rather well-written section with numerous links to the primary literature showing how our genome has been altered over the years by HERVs.

Defining paper(s) in epigenetics - Biology

I understand that Robin Holliday was the first to discuss the possible role of DNA methylation
in the control of Gene expression. In his paper "The inheritance of epigenetic defects"
he presents what is one of the first modern formulations of what we now regard as epigenetics. The term "epigenetics" itself was coined by Conrad Waddington although this predated our modern understanding of heredity.

Holliday, R., The inheritance of epigenetic defects, 1987, Science, 238, 4824

gel electrophoresis - Alternatives to ethidium bromide for staining small nucleic acids?

While ethidium bromide works well for staining larger single-stranded RNA or double-stranded DNA molecules, it doesn't stain smaller nucleic acids very well. I observed that at around 20 bases and below single-stranded nucleic acids are difficult to see with EtBr-staining unless the nucleic acids are highly concentrated.

What are good alternatives for observing small nucleic acids in polyacrylamide gels? The main consideration would be ease-of-use, and it should be possible without any unusual equipment.