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. rice@lifesci.ucsb.edu

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.

Thursday, December 11, 2008

Unusual Suspects: Guided Imagery Fertility Treatments and the Red Queen Theory


The success of using meditation, visualization and journaling techniques to heal and cultivate fertility has been strongly documented by Alice Domar in Healing Mind, Healthy Woman and by Niravi Payne in The Language of Fertility. Fifty percent of women who have participated in Domar's groups, in which meditation, relaxation, and journaling techniques are employed, were able to conceive and give birth. In contrast, only 20% of women who solely used traditional "infertility treatments" were able to conceive. Niravi Payne's work focuses on illuminating and healing family secrets and beliefs surrounding fertility. Her program also reports increased pregnancy and birth rates for her clients.

Looking forward to Ignite Boulder 2 where I'll speak with the author.

Friday, December 5, 2008


Tuesday, December 2, 2008

Research Link: Minds+Machines - Why We are Soft Spacesuits for Our RNA

Blogger's Note: If this update were a song, it would be "Life is a Highway"...

Memories may be stored on your DNA

REMEMBER your first kiss? Experiments in mice suggest that patterns of chemical "caps" on our DNA may be responsible for preserving such memories.

To remember a particular event, a specific sequence of neurons must fire at just the right time. For this to happen, neurons must be connected in a certain way by chemical junctions called synapses. But how they last over decades, given that proteins in the brain, including those that form synapses, are destroyed and replaced constantly, is a mystery.

Now Courtney Miller and David Sweatt of the University of Alabama in Birmingham say that long-term memories may be preserved by a process called DNA methylation - the addition of chemical caps called methyl groups onto our DNA.

Many genes are already coated with methyl groups. When a cell divides, this "cellular memory" is passed on and tells the new cell what type it is (coding for type) - a kidney cell, for example. Miller and Sweatt argue that in neurons, methyl groups also help to control the exact pattern of protein (RNA directing traffic lights on genetic highway - DNA are the cars) expression needed to maintain the synapses that make up memories.

They started by looking at short-term memories. When caged mice are given a small electric shock, they normally freeze in fear when returned to the cage. However, then injecting them with a drug to inhibit methylation seemed to erase any memory of the shock. The researchers also showed that in untreated mice, gene methylation changed rapidly in the hippocampus region of the brain for an hour following the shock. But a day later, it had returned to normal, suggesting that methylation was involved in creating short-term memories in the hippocampus (Neuron, DOI: 10.1016/j.neuron.2007.02.022).

To see whether methylation plays a part in the formation of long-term memories, Miller and Sweatt repeated the experiment, this time looking at the uppermost layers of the brain, called the cortex.

They found that a day after the shock, methyl groups were being removed from a gene called calcineurin and added to another gene. Because the exact pattern of methylation eventually stabilised and then stayed constant for seven days, when the experiment ended, the researchers say the methyl changes may be anchoring the memory of the shock into long-term memory, not just controlling a process involved in memory formation.

"We think we're seeing short-term memories forming in the hippocampus and slowly turning into long-term memories in the cortex," says Miller, who presented the results last week at the Society for Neuroscience meeting in Washington DC.

"The cool idea here is that the brain could be borrowing a form of cellular memory from developmental biology to use for what we think of as memory," says Marcelo Wood, who researches long-term memory at the University of California, Irvine.

From issue 2684 of New Scientist magazine, page 12. Subscribe and get 4 free issues.

Research Link: RNA "A Molecular Multi-Tasker"


From Genome Technology, 12.2.08:

A review by Australian researchers discusses the challenges in differentiating protein-coding and noncoding RNA. They go through a variety of strategies such as comparing open reading frame length or conservation, as well as structural and experimental approaches. They also wonder if this is a false dichotomy. "Looking ahead, we must also be prepared to cast off our historical biases toward what appears now to be an increasingly false dichotomy, and instead embrace the likelihood that RNA is a molecular multi-tasker," they write.

Research Update: Gender, mRNA, and Aging Gray Matter

Gender and the Aging Brain

By Richard Shank

From "Aging in Action (Mather Lifeways)"

Researchers at the University of California at Irvine report that the brains of men and women age differently. Their postmortem study indicates that, not only do the genes of men’s brains change earlier than in women’s brains, but the types of changes that occur also differ between the sexes.

The research involved collecting brains from people who had died between the ages of 20 and 99. The researchers isolated mRNA (messenger RNA) which carries instructions for building the proteins that helps the brain communicate with the rest of the body. (Active genes produce higher levels of mRNA). They discovered that disease-susceptible parts of the brain have the least amount of change in gene activity with age. The area of the brain responsible for perception (postcentral gyrus) changes the most.

Men showed more changes in metabolic activity while women showed greater change in genes that establish neural connections and control information exchange. This implies that the energy levels in the brain are more likely to decline in men, and that lifestyle and medical interventions should be targeted toward enhancing metabolic function in the brain of men.

Source: Cotman, C. Berchtold, N. October 2008. Proceedings of the National Academy of Sciences

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