Tag Archives: model organism

Vast Gene-Expression Map Yields Neurological and Environmental Stress Insights

Berkeley Lab scientists lead broadest survey yet of RNA activity in any animal

A consortium led by scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has conducted the largest survey yet of how information encoded in an animal genome is processed in different organs, stages of development, and environmental conditions. Their findings paint a new picture of how genes function in the nervous system and in response to environmental stress. (more…)

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Method makes it easier to separate useful stem cells from ‘problem’ ones for therapies

UCLA study IDs small molecule that destroys potentially dangerous cells

Pluripotent stem cells can turn, or differentiate, into any cell type in the body, such as nerve, muscle or bone, but inevitably some of these stem cells fail to differentiate and end up mixed in with their newly differentiated daughter cells.  

Because these remaining pluripotent stem cells can subsequently develop into unintended cell types — bone cells among blood, for instance — or form tumors known as teratomas, identifying and separating them from their differentiated progeny is of utmost importance in keeping stem cell–based therapeutics safe.  (more…)

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Genomic Detectives Crack the Case of the Missing Heritability

Despite years of research, the genetic factors behind many human diseases and characteristics remain unknown. The inability to find the complete genetic causes of family traits such as height or the risk of type 2 diabetes has been called the “missing heritability” problem.

A new study by Princeton University researchers, however, suggests that missing heritability may not be missing after all — at least not in yeast cells, which the researchers used as a model for studying the problem. Published in the journal Nature, the results suggest that heritability in humans may be hidden due only to the limitations of modern research tools, but could be discovered if scientists know where (and how) to look. (more…)

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Yale Team Finds Order Amidst the Chaos Within the Human Genome; Mom and Dad’s Contributions Counted and Fossil DNA Not Dead After All

The Encyclopedia of DNA Elements (ENCODE) project is the effort of hundreds of scientists to describe the workings of the human genome. Their research, outlined in 30 papers published in multiple journals Sept. 5, has confirmed our genome is far more complex than originally thought.  Regions that contain instructions for making proteins, which carry out life’s functions, account for only about 1 percent of our genome. ENCODE has shed light on the other 99%. Almost 80 percent of the genome is biochemically active, much of it involved in some sort of regulation of genes. Vast regions of our DNA once considered “junk” contain some 400,000 regulators called enhancers, which play a key role activating or silencing genes despite residing far away from the gene itself. Yale University researchers played a key role ENCODE, helping to author 9 of the 30 papers published in four journals on Sept. 5. Some of their work is described below.

The massive Encyclopedia of DNA Elements (ENCODE) unveiled Sept. 5 reveals a human genome vastly more rich and complex than envisioned even a decade ago. In a key supporting paper published in the journal Nature, the lab of Yale’s Mark Gerstein, the Albert L. Williams Professor of Biomedical Informatics, has found order amidst the seeming chaos of trillions of potential molecular interactions. (more…)

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Berkeley Lab Researchers Create First of Its Kind Gene Map of Sulfate-reducing Bacterium: Work Holds Implications for Future Bioremediation Efforts

Critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment have been revealed in a study by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). The researchers have provided the first ever map of the genes that determine how these bacteria interact with their surrounding environment.

“Knowing how bacteria respond to environmental changes is crucial to our understanding of how their physiology tracks with consequences that are both good, such as bioremediation, and bad, such as biofouling,” says Aindrila Mukhopadhyay, a chemist with Berkeley Lab’s Physical Biosciences Division, who led this research. “We have reported the first systematic mapping of the genes in a sulfate-reducing bacterium – Desulfovibrio vulgaris – that regulate the mechanisms by which the bacteria perceive and respond to environmental signals.” (more…)

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Sea Squirt Cells Shed Light on Cancer Development

*Specialized structures used by cancer cells to invade tissues could also help them escape protection mechanisms aimed at eliminating them, a UA-led research team has discovered.*

Delicate, threadlike protrusions used by cancer cells when they invade other tissues in the body could also help them escape control mechanisms supposed to eliminate them, a research group led by led by Bradley Davidson in the University of Arizona’s department of molecular and cellular biology reports in Nature Cell Biology.

Studying embryos of the sea squirt Ciona intestinalis, the researchers discovered that even non-invasive cells make the delicate, highly transient structures known as invadopodia. The group found that future heart cells in the Ciona embryo use invadopodia to pick up chemical signals from their surroundings. These so-called growth factors provide the cells with clues as to where they are in the developing embryo and what type of cell they are supposed to turn into. (more…)

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