Archive for October 11th, 2011

October 11, 2011

Giant viruses may have evolved from cellular organisms, not the other way around

Viruses are generally supposed to be the minimal forms of life – if they can even be regarded as “alive” at all. The discovery of very large viruses, as large as bacteria, has suggested that some modification of that view may be necessary.

A few months ago, the discovery was announced of a virus with more than 700,000 base pairs in its genome (more than some bacteria) and that is so large it may host other viruses as parasites.

Before that, another virus (mimivirus) had already been found with a million base pairs in its genome and some genes previously found only in full-fledged cells. A year ago an apparent mimivirus relative was found with 700,000 base pairs. This one also attracts molecular parasites. And though it is related to mimivirus, the two have only about a third of their genes in common – meaning that many of the genes of both came from somewhere else.

Now a virus has been discovered whose genome sets a new record size (for a virus) – 1.26 million base pairs. This one, Megavirus chilensis, seems to be a closer mimivirus relative. It has 1120 protein-coding genes, only 250 of which don’t have a mimivirus equivalent. Of the genes that are shared, about half are transcribed to the same proteins. And a comparison between mimivirus and the new one suggests something rather surprising about virus evolution.

Giant viruses may have evolved from cellular organisms, not the other way around

[The] find supports the view that the virus started out with a much larger complement of genes. For example, Mimivirus has a suite of genes that can help repair DNA. Megavirus has those plus one other that is specialized for the repair of DNA damaged by UV light. The additional gene appears to be functional: Megavirus was able to grow following an exposure to UV that was sufficient to disable Mimivirus.

Both viruses share an identical set of genes involved in transcribing their DNA into RNA, and use an identical set of signals to indicate where the transcripts should start and stop. Mimivirus also contains a number of genes used in the translation of RNA into protein. Megavirus has those plus a few more, including additional genes that attach amino acids (components of proteins) onto RNAs for use in translation.

Clearly, the common genes suggest that the viruses share a common ancestor. This leaves two possibilities for the novel ones: either the ancestral virus had a larger collection and its descendants have lost different ones, or each virus picked up different genes from its hosts through a process called horizontal gene transfer. The authors favor the former explanation, because most of the genes specific to one of the two viruses don’t look like any gene present in their hosts (or any other gene we’ve ever seen, for that matter). This implies that horizontal gene transfer doesn’t seem to have done much to shape the viruses’ genomes.

Given two fairly similar yet different viruses, inferences can be made about their evolution. The surprising conclusion is that these viruses had a common ancestor that was a very early eukaryotic cell. So instead of complex units of life having evolved from simpler forms, the exact opposite seems to have occurred in this case.

Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae

Megavirus exhibits three additional aminoacyl-tRNA synthetase genes (IleRS, TrpRS, and AsnRS) adding strong support to the previous suggestion that the Mimivirus/Megavirus lineage evolved from an ancestral cellular genome by reductive evolution. The main differences in gene content between Mimivirus and Megavirus genomes are due to (i) lineages specific gains or losses of genes, (ii) lineage specific gene family expansion or deletion, and (iii) the insertion/migration of mobile elements (intron, intein).

That evokes eerie echoes of other research reported only a few days ago: Last Universal Common Ancestor had a complex cellular structure

Further reading:

Megavirus claims ‘biggest genome’ crown

World’s largest virus proves giants came from cells

Ocean hunt nets world’s biggest virus

Ocean trawl reveals ‘megavirus’

October 11, 2011

Dietary Supplements Linked To Higher Mortality In Older Women

People want simple answers even to difficult questions. Unfortunately, reality does not always oblige. For instance, people want a simple, easy way to be healthier and live longer. It would be so nice if just taking a few pills – or even a lot of pills – every day would be as helpful as adjusting one’s lifestyle and having regular medical checkups.

But it’s just not that simple.

Dietary Supplements Linked To Higher Mortality In Older Women

A report in the October 10 issue of Archives of Internal Medicine, one of the JAMA/Archives journals ‘Less is More’ series reveals that consuming dietary supplements, such as iron and coppers, multivitamins and folic acids seems to be linked to a higher risk of mortality in older women – the exception appears to be calcium supplements.

The conclusion is based on a longitudinal study of 38,772 women that began in 1986. The average age of participants was 61.6 years at the start. Use of dietary supplements was self-reported. Upon follow-ups, 40.2% of participants had died after an average period of 19 years. (That’s the average follow-up time, not the average length of life of those who died after the start.)

Certain Dietary Supplements Associated With Increased Risk of Death in Older Women, Study Suggests

The authors found that use of most supplements was not associated with reduced total mortality in older women, and many supplements appeared associated with increased mortality risk. After adjustment, use of multivitamins, vitamin B6, folic acid, iron, magnesium, zinc and copper, were all associated with increased risk of death in the study population. Conversely, calcium supplements appear to reduce risk of mortality. The association between supplement intake and mortality risk was strongest with iron, and the authors found a dose-response relationship as increased risk of mortality was seen at progressively lower doses as women aged throughout the study.

Findings for both iron and calcium supplements were replicated in separate, short-term analyses with follow-up occurring at four years, six years and 10 years.

“Based on existing evidence, we see little justification for the general and widespread use of dietary supplements,” the authors conclude. “We recommend that they be used with strong medically based cause, such as symptomatic nutrient deficiency disease.”

Note especially that there was a dose-response correlation between use of iron supplements and (higher) mortality risk. In other words, the more iron supplements consumed, the higher the risk.

Further reading:

Vitamin pills do more harm than good

Dietary supplements risky for older women, study finds

Should older women take those vitamins or not?

Vitamin and Mineral Supplement Use in Relation to All-Cause Mortality in the Iowa Women’s Health Study

Dietary Supplements and Mortality Rate in Older Women

October 11, 2011

A subluminous, normal-width lightcurve Type Ia supernova in the middle of nowhere

Astrophysicists have gradually been refining a system of classification for supernovae. The most basic characteristic of interest is whether or not there are spectral lines that indicate the presence of hydrogen. If these lines are absent, the supernova is Type I, which implies the progenitor star was rather old and had used up all of its hydrogen. If there are lines for hydrogen, the supernova is Type II. In this case, the supernova more likely was a very massive star which collapsed because nuclear fusion in its interior was no longer sufficient to support the weight.

Further subdivisions within each type are possible, especially in the Type I case. If there is a certain type of line from ionized silicon, the supernova is Type Ia. If there is no silicon line, but a line from helium, it’s Type Ib. Otherwise, it’s Type Ic. It is hoped that these subdivisions reflect characteristics of the progenitor that culminated in the supernova, but there’s still a lot of uncertainty about the mechanisms involved in various cases.

Type Ia supernovae are of particular interest, since observations of relatively nearby examples show that most events have a predictable intrinsic luminosity. This makes them very useful as “standard candles“. Most models of Type Ia supernova ascribe the event to hydrogen-depleted white dwarf stars that have exceeded the Chandrasekhar limit of about 1.38 solar masses because of accretion of matter from a companion star. It’s not clear how ofter this results from mergers between two white dwarfs, or simply from matter drawn from another star that survives the event, though the latter model has generally been preferred.

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