Friday, January 16, 2009

Research Link: RNA Viruses Invade Host DNA (Viral vs. RNA Conflict)

"RNA viruses were believed not to integrate into the host's genome under any circumstances (check out HIV, Shingles, EB). We found that illegitimate recombination between an exogenous nonretroviral RNA virus, lymphocytic choriomeningitis virus, and the endogenous intracisternal A-type particle (IAP) retrotransposon occurred and led to reverse transcription of exogenous viral RNA (enemy at the gates). The resulting complementary DNA was integrated into the host's genome with an IAP element. Thus, RNA viruses should be closely scrutinized for any capacity to interact with endogenous retroviral elements before their approval for therapeutic use in humans."

Research Link: Worm Research (Elegans, No?) - RNA, Odor Pathways, and Reproduction

"This implicates the real importance of RNA in controlling when proteins are made, and shows that the environment can actually change what RNA does."

Saturday, January 10, 2009

Self-Replicating RNA Born at Scripps & Bloggers' Respond

It was a big week for evolutionary/systems biologists and proponents/critics of RNA World Theory (vast oversimplification). Let's take a grade-school simple look at emerging RNA research.

The Big Bang: Gerald Joyce and Tracey Lincoln of Scripps Institute in La Jolla, CA, created short, simple RNA molecules (RC3) that could replicate themselves indefinitely.

Results of the research were published in Science's online journal January 8th.

Genoanthropology implications abound. As of yet, the adame RNA molecules (Adam/Eve; male-female RNA tribal orientations) created are can't acquire/process energy (metabolism). They also can't respond to their environments. Yet.

The seemingly crazy "we are soft spacesuits for our RNA" hypothesis is suddenly front and center, at least providing some decent weekend mental floss.

If the earliest self-replicating RNA couldn't acquire/process energy independently, this may have created the collaborative impetus for partnerships/coalitions between mitochondria, bacteria, and other sugar-processing compounds and organisms.

Mobility and the capability to respond to their environments (as well as a need to defend RNA individuals and colonies from attacking marauders such as viruses and other pathogens) could provide impetus for 'coding' lifesuits utilizing DNA. Thus an RNA - LUCA - DNA progression begins to look more theoretically interesting and potentially testable at some point in the near future.

All of this would be interesting enough if only a single type of self-replicating RNA were created, but Joyce and Lincoln created 12 'disciples' of self-replicating RNA.

In addition, some of the molecules were better able to compete for resources (corresponding genoanth tenet = tribal/cultural orientation of RNA involving competition and collaboration with each other and against external forms such as bacteria and viruses for resources).

Very exciting times, even for a hobby scientific theorist.

Further food for thought: (pictures!)

Saturday Bonus: Recent antibacterial/RNA research from Germany

Tuesday, December 30, 2008

LUCA Research Gets Interesting - From an RNA Advocate's Perspective...

Great blog post at SciencePal:

"The group's findings are an important step towards reconciling conflicting ideas about LUCA. In particular, they are much more compatible with the theory of an early RNA world, where early life on Earth was composed of ribonucleic acid (RNA), rather than deoxyribonucleic acid (DNA)."

"It is only in a subsequent step that LUCA's descendants discovered the more thermostable DNA molecule, which they independently acquired (presumably from viruses), and used to replace the old and fragile RNA vehicle. This invention allowed them to move away from the small cool microclimate, evolved and diversify into a variety of sophisticated organisms that could tolerate heat," adds Dr. Lartillot.

The study was authored by Bastien Boussau (CNRS, Université Lyon), Samuel Blanquart (LIRMM, CNRS: France), Anamaria Necsulea (CNRS, Université Lyon), Nicolas Lartillot (Université Montreal), and Manolo Gouy (CNRS, Université Lyon).

Funding was provided through grants from Action Concerteé Incitative IMPBIO-MODELPHYLO and ANR PlasmoExplore.

Interesting RNA Research re: 1918 Influenza Epidemic

Saturday, December 27, 2008

Research Update: Sexually Antagonistic Zygotic Drive

Genoanth principle: Battle of the Sexes...male/female 'tribes' of RNA. Offpsring/fetus as 'peace treaty' in 'arms race.'

PLoS Genet. 2008 Dec;4(12):e1000313. Epub 2008 Dec 19.Links

Sexually antagonistic "zygotic drive" of the sex chromosomes.

Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.

Genomic conflict is perplexing because it causes the fitness of a species to decline rather than improve. Many diverse forms of genomic conflict have been identified, but this extant tally may be incomplete. Here, we show that the unusual characteristics of the sex chromosomes can, in principle, lead to a previously unappreciated form of sexual genomic conflict.

The phenomenon occurs because there is selection in the heterogametic sex for sex-linked mutations that harm the sex of offspring that does not carry them, whenever there is competition among siblings. This harmful phenotype can be expressed as an antagonistic green-beard effect that is mediated by epigenetic parental effects, parental investment, and/or interactions among siblings.

We call this form of genomic conflict sexually antagonistic "zygotic drive", because it is functionally equivalent to meiotic drive, except that it operates during the zygotic and postzygotic stages of the life cycle rather than the meiotic and gametic stages. A combination of mathematical modeling and a survey of empirical studies is used to show that sexually antagonistic zygotic drive is feasible, likely to be widespread in nature, and that it can promote a genetic "arms race" between the homo- and heteromorphic sex chromosomes.

This new category of genomic conflict has the potential to strongly influence other fundamental evolutionary processes, such as speciation and the degeneration of the Y and W sex chromosomes. It also fosters a new genetic hypothesis for the evolution of enigmatic fitness-reducing traits like the high frequency of spontaneous abortion, sterility, and homosexuality observed in humans.
Blogger's Note: Wow.

PMID: 19096519 [PubMed - in process]

PMCID: PMC2596966

Research Update: Osteoporosis, Bone Regeneration, Antlers - Red Deer and Man

Identifying novel genes involved in both deer physiological and human pathological osteoporosis.

Mol Genet Genomics. 2008 Dec 24. [Epub ahead of print]

Department of Genetics, Eötvös Loránd University, Pázmány Péter s. 1/c, 1117, Budapest, Hungary.

Osteoporosis attacks 10% of the population worldwide. Humans or even the model animals of the disease cannot recover from porous bone. Regeneration in skeletal elements is the unique feature of our newly investigated osteoporosis model, the red deer (Cervus elaphus) stag. Cyclic physiological osteoporosis is a consequence of the annual antler cycle. This phenomenon raises the possibility to identify genes involved in the regulation of bone mineral density on the basis of comparative genomics between deer and human. We compare gene expression activity of osteoporotic and regenerating rib bone samples versus autumn dwell control in red deer by microarray hybridization. Identified genes were tested on human femoral bone tissue from non-osteoporotic controls and patients affected with age-related osteoporosis. Expression data were evaluated by Principal Components Analysis and Canonical Variates Analysis. Separation of patients into a normal and an affected group based on ten formerly known osteoporosis reference genes was significantly improved by expanding the data with newly identified genes. These genes include IGSF4, FABP3, FABP4, FKBP2, TIMP2, TMSB4X, TRIB, and members of the Wnt signaling. This study supports that extensive comparative genomic analyses, here deer and human, provide a novel approach to identify new targets for human diagnostics and therapy.