Posts Tagged ‘genomics’

Google Mapping the Human Metabolism

 :: Posted by American Biotechnologist on 03-04-2013

Building on earlier pioneering work by researchers at the University of California, San Diego, an international consortium of university researchers has produced the most comprehensive virtual reconstruction of human metabolism to date. Scientists could use the model, known as Recon 2, to identify causes of and new treatments for diseases like cancer, diabetes and even psychiatric and neurodegenerative disorders. Each person’s metabolism, which represents the conversion of food sources into energy and the assembly of molecules, is determined by genetics, environment and nutrition.

The researchers presented Recon 2 in a paper published online March 3 in the journal Nature Biotechnology.

Read more …

Basic Science Alert: Every Cell in Body Does NOT Contain Identical DNA

 :: Posted by American Biotechnologist on 11-19-2012

The prevailing wisdom has been that every cell in the body contains identical DNA. However, a new study of stem cells derived from the skin has found that genetic variations are widespread in the body’s tissues, a finding with profound implications for genetic screening, according to Yale School of Medicine researchers.

Published in the Nov. 18 issue of Nature, the study paves the way for assessing the extent of gene variation, and for better understanding human development and disease.

“We found that humans are made up of a mosaic of cells with different genomes,” said lead author Flora Vaccarino, M.D., the Harris Professor of Child Psychiatry at the Yale Child Study Center. “We saw that 30 percent of skin cells harbor copy number variations (CNV), which are segments of DNA that are deleted or duplicated. Previously it was assumed that these variations only occurred in cases of disease, such as cancer. The mosaic that we’ve seen in the skin could also be found in the blood, in the brain, and in other parts of the human body.”

The longstanding belief has been that our cells have the same DNA sequence and this blueprint governs the body’s functions. The Yale team’s research challenges this dogma. Some scientists have hypothesized that during development, when DNA is copied from mother to daughter cells, there could be deletions, duplications and changes in the sequence of the DNA, and an entire group of genes could be affected. This premise has been incredibly difficult to test, but Vaccarino and colleagues have done so in this new study.

The team used whole genome sequencing to study induced pluripotent stem cells lines (iPS), which are stem cells developed from a mature-differentiated cell. The team grew cells taken from the inner upper arms of two families. The team spent two years characterizing these iPS cell lines and comparing them to the original skin cells.

While observing that the genome of iPS cells closely resembles the genome of skin cells from which they originated, the team could identify several deletions or duplications involving thousands of base pairs of DNA. The team then performed additional experiments to understand the origin of those differences, and showed that at least half of them pre-existed in small fractions of skin cells. These differences were revealed in iPS cells because each iPS line is derived from one, or very few, skin cells. Vaccarino said these iPS lines could act as a magnifying glass to see the mosaic of genomic differences in the body’s cells.

“In the skin, this mosaicism is extensive and at least 30 percent of skin cells harbor different deletion or duplication of DNA, each found in a small percentage of cells,” said Vaccarino. “The observation of somatic mosaicism has far-reaching consequences for genetic analyses, which currently use only blood samples. When we look at the blood DNA, it’s not exactly reflecting the DNA of other tissues such as the brain. There could be mutations that we’re missing.”

“These findings are shaping our future studies, and we’re doing more studies of the developing brains of animals and humans to see if this variation exists there as well,” Vaccarino added.

Thanks to Yale University for this story.

Around the Nucleus

 :: Posted by American Biotechnologist on 07-24-2012

H/T to Kevin Ahern for the find.

Scientists prove why every sperm is sacred

 :: Posted by American Biotechnologist on 07-19-2012

OK. Perhaps not in the way it was presented by Monty Python in The Meaning of Life, but a new study out of Stanford University Medical Center has shown that sperm cells exhibit a significant degree of genetic variation even when produced by an individual male.

According to study co-author Barry Behr:

For the first time, we were able to generate an individual recombination map and mutation rate for each of several sperm from one person. Now we can look at a particular individual, make some calls about what they would likely contribute genetically to an embryo and perhaps even diagnose or detect potential problems.

Click here to read more.

DO YOUR PROTEINS HAVE THEIR OWN SOCIAL NETWORK?

 :: Posted by American Biotechnologist on 07-09-2012

Diseases are the result of underlying system interactions NOT simply physical underpinnings. Watch the following talk from Northeastern University Professor Albert-László Barabási to learn how mapping cellular protein reactions can help us discover how diseases work.