Category Archives: Transhuman News

Genome Holiday Card

By: AccurateDesign

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Genome Holiday Card - Video

Common Pathway of Carcinogenesis
Common Pathway of Carcinogenesis Carcinogenic agents are heterogeneous, physical chemical and biological. Yet they all share a common mechanism. For the unified theory of carcinogenesis I...

By: Gershom Zajicek M.D,

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Common Pathway of Carcinogenesis - Video

PUBLIC RELEASE DATE:

29-Sep-2014

Contact: David Gilbert degilbert@lbl.gov DOE/Joint Genome Institute @doe_jgi

The U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, has announced that 32 new projects have been selected for the 2015 Community Science Program (CSP). From sampling Antarctic lakes to Caribbean waters, and from plant root micro-ecosystems, to the subsurface underneath the water table in forested watersheds, the CSP 2015 projects portfolio highlights diverse environments where DOE mission-relevant science can be extracted.

"These projects catalyze JGI's strategic shift in emphasis from solving an organism's genome sequence to enabling an understanding of what this information enables organisms to do," said Jim Bristow, DOE JGI Science Deputy who oversees the CSP. "To accomplish this, the projects selected combine DNA sequencing with large-scale experimental and computational capabilities, and in some cases include JGI's new capability to write DNA in addition to reading it. These projects will expand research communities, and help to meet the DOE JGI imperative to translate sequence to function and ultimately into solutions for major energy and environmental problems."

The CSP 2015 projects were selected by an external review panel from 76 full proposals received that resulted from 85 letters of intent submitted. The total allocation for the CSP 2015 portfolio is expected to exceed 60 trillion bases (terabases or Tb)or the equivalent of 20,000 human genomes of plant, fungal and microbial genome sequences. The full list of projects may be found at http://jgi.doe.gov/our-projects/csp-plans/fy-2015-csp-plans/. The DOE JGI Community Science Program also accepts proposals for smaller-scale microbial, resequencing and DNA synthesis projects and reviews them twice a year. The CSP advances projects that harness DOE JGI's capability in massive-scale DNA sequencing, analysis and synthesis in support of the DOE missions in alternative energy, global carbon cycling, and biogeochemistry.

Among the CSP 2015 projects selected is one from Regina Lamendella of Juniata College, who will investigate how microbial communities in Marcellus shale, the country's largest shale gas field, respond to hydraulic fracturing and natural gas extraction. For example, as fracking uses chemicals, researchers are interested in how the microbial communities can break down environmental contaminants, and how they respond to the release of methane during oil extraction operations.

Some 1,500 miles south from those gas extraction sites, Monica Medina-Munoz of Penn State University will study the effect of thermal stress on the Caribbean coral Orbicella faveolata and the metabolic contribution of its coral host Symbiodinium. The calcium carbonate in coral reefs acts as carbon sinks, but reef health depends on microbial communities. If the photosynthetic symbionts are removed from the coral host, for example, the corals can die and calcification rates decrease. Understanding how to maintain stability in the coral-microbiome community can provide information on the coral's contribution to the global ocean carbon cycle.

Longtime DOE JGI collaborator Jill Banfield of the University of California (UC), Berkeley is profiling the diversity of microbial communities found in the subsurface from the Rifle aquifer adjacent to the Colorado River. The subsurface is a massive, yet poorly understood, repository of organic carbon as well as greenhouse gases. Another research question, based on having the microbial populations close to both the water table and the river, is how they impact carbon, nitrogen and sulfur cycles. Her project is part of the first coordinated attempt to quantify the metabolic potential of an entire subsurface ecosystem under the aegis of the Lawrence Berkeley National Laboratory's Subsurface Biogeochemistry Scientific Focus Area.

Banfield also successfully competed for a second CSP project to characterize the tree-root microbial interactions that occur below the soil mantle in the unsaturated zone or vadose zone, which extends into unweathered bedrock. The project's goal is to understand how microbial communities this deep underground influence tree-based carbon fixation in forested watersheds by the Eel River in northwestern California.

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2015 DOE JGI's science portfolio delves deeper into the Earth's data mine

September 29, 2014

Brett Smith for redOrbit.com Your Universe Online

New research from the University of California, Santa Cruz has revealed that two sets of primate genes have been battling it out over the millennia and this conflict has driven the complexity of primate genomes.

Published on Sunday in the journal Nature, the study found that genome jumping retrotransposons are constantly developing new ways to escape repression by another set of genes called repressors.

We have basically the same 20,000 protein-coding genes as a frog, yet our genome is much more complicated, with more layers of gene regulation. This study helps explain how that came about, said study author Sofie Salama, a research associate at the UC Santa Cruz Genomics Institute who led the study.

Retrotransposons are segments of genetic code that can copy themselves and then insert that copy back into the genome. These events can interrupt genes and trigger disease, based on where a new copy slips into the genome. Frequently the effect is negligible, and occasionally the effect is advantageous, potentially enhancing gene expression.

The high chance of negative outcomes means natural selection favors mechanisms that prevent jumping events in the form of repressor genes and proteins.

The repressors named in the new study are part of the biggest category of gene-regulating proteins in mammals, called KRAB zinc finger proteins. The human genome has more than 400 genes for these repressive DNA-binding proteins, and about 170 of them have developed since primates split from other mammals.

The way this type of repressor works, part of it binds to a specific DNA sequence and part of it binds other proteins to recruit a whole complex of proteins that creates a repressive landscape in the genome, Salama said. This affects other nearby genes, so now you have a potential new layer of regulation available for further evolution.

Previous research on KRAB zinc finger proteins found they repress jumping genes in mouse embryonic stem cells. In the new study, scientists placed primate retrotransposons in mouse embryonic stem cells that had a single human chromosome. The primate jumping genes suddenly sprang to life in the mouse cells. The study team developed a test to see which individual KRAB proteins could turn off a primate jumping gene in the mouse cell system.

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Evolutionary Arms Race Within The Human Genome

15 hours ago Professor Vanessa Hayes in the field. Credit: Chris Bennett photography

What can DNA from the skeleton of a man who lived 2,330 years ago in the southernmost tip of Africa tell us about ourselves as humans? A great deal when his DNA profile is one of the 'earliest diverged' oldest in genetic terms found to-date in a region where modern humans are believed to have originated roughly 200,000 years ago.

The man's maternal DNA, or 'mitochondrial DNA', was sequenced to provide clues to early modern human prehistory and evolution. Mitochondrial DNA provided the first evidence that we all come from Africa, and helps us map a figurative genetic tree, all branches deriving from a common 'Mitochondrial Eve'.

When archaeologist Professor Andrew Smith from the University of Cape Town discovered the skeleton at St. Helena Bay in 2010, very close to the site where 117,000 year old human footprints had been found dubbed "Eve's footprints" he contacted Professor Vanessa Hayes, a world-renowned expert in African genomes.

At the time, Hayes was Professor of Genomic Medicine at the J. Craig Venter Institute in San Diego, California. She now heads the Laboratory for Human Comparative and Prostate Cancer Genomics at Sydney's Garvan Institute of Medical Research.

The complete 1.5 metre tall skeleton was examined by Professor Alan Morris, from the University of Cape Town. A biological anthropologist, Morris showed that the man was a 'marine forager'. A bony growth in his ear canal, known as 'surfer's ear', suggested that he spent some time diving for food in the cold coastal waters, while shells carbon-dated to the same period, and found near his grave, confirmed his seafood diet. Osteoarthritis and tooth wear placed him in his fifties.

Due to the acidity of the soil within the region, acquiring DNA from skeletons has proven problematic. The Hayes team therefore worked with the world's leading laboratory in ancient DNA research, namely that of paleogeneticist Professor Svante Pbo at the Max Planck Institute for Evolutionary Anthropolgy in Leipzig, Germany, who successfully sequenced a Neanderthal.

The team generated a complete mitochondrial genome, using DNA extracted from a tooth and a rib. The findings provided genomic evidence that this man, from a lineage now presumed extinct, as well as other indigenous coastal dwellers like him, were the most closely related to 'Mitochondrial Eve'.

The study underlines the significance of southern African archaeological remains in defining human origins, and is published in the journal Genome Biology and Evolution, now online.

"We were thrilled that archaeologist Andrew Smith understood the importance of not touching the skeleton when he found it, and so did not contaminate its DNA with modern human DNA," said Professor Hayes.

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Ancient human genome from southern Africa throws light on our origins

17 hours ago Brachypodium distachyon is being studied by bioenergy researchers as a model system for grasses that could serve as sustainable plant biomass sources for biofuels. Credit: Sarah Gregg via Flickr, CC BY-NC-SA 2.0

Researchers used deep sequencing to look at whole-genome sequence variation in seven lines of the model grass Brachypodium distachyon and found previously unannotated genes. They also looked at genome-wide gene expression under drought-stress conditions.

Hundreds of genes not present in the reference genome and many unannotated genes were identified through this process, leading to the development of a public database for visualizing and investigating sequence variants in these lines.

Changes in the global climate, and closer to home, the ongoing drought in California, emphasize the importance of developing crops for fuel and food security that can tolerate low-water conditions. The grass Brachypodium distachyon, Brachy for short, is a model for candidate biomass feedstock crops, particularly those that can be grown on marginal lands. To assist in studying candidate biomass crops, a reference Brachy genome was sequenced and published by the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, in collaboration with U.S. Department of Agriculture researchers through the Community Science Program.

A single plant reference genome, however, cannot reflect all of the potential gene variants in a species, and Brachy is found in many climate zones, which would suggest that there are several adaptations for each habitat. In a study reported in the August issue of The Plant Journal, a team including DOE JGI researchers conducted deep sequencing ("the equivalent of 900-fold sequence depth of the 272 Megabase B. distachyon genome," according to the researchers) on several Brachy lines.

To understand the roles of the genome-wide sequence variants they found, the team conducted a series of experiments in which they simulated drought-stress conditions on several Brachy plants. They then looked at the transcripts from the plants to identify genes involved in the plant's response to drought stress. The team found nearly 900 genes "that responded significantly" to water stress.

"Our validated datasets demonstrate the existence of extensive natural variation in B. distachyon," the team concluded, "[and] demonstrates the utility of our resequencing data as a foundation for studies of natural diversity in B. distachyon."

Explore further: A decade of improvements on the reference green alga genome

More information: Gordon SP et al. "Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines." Plant J. 2014 Aug;79(3):361-74. DOI: 10.1111/tpj.12569.

The high-quality genome sequence of the tiny single-celled alga Chlamydomonas reinhardtii has proved useful for researchers studying photosynthesis and cell motility.

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Unannotated genes identified through sequencing multiple lines of brachypodium distachyon