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Category Archives: Genetic Medicine

New Layer of Genetic Information Discovered

Newswise A hidden and never before recognized layer of information in the genetic code has been uncovered by a team of scientists at the University of California, San Francisco (UCSF) thanks to a technique developed at UCSF called ribosome profiling, which enables the measurement of gene activity inside living cells including the speed with which proteins are made.

By measuring the rate of protein production in bacteria, the team discovered that slight genetic alterations could have a dramatic effect. This was true even for seemingly insignificant genetic changes known as silent mutations, which swap out a single DNA letter without changing the ultimate gene product. To their surprise, the scientists found these changes can slow the protein production process to one-tenth of its normal speed or less.

As described today in the journal Nature, the speed change is caused by information contained in what are known as redundant codons small pieces of DNA that form part of the genetic code. They were called redundant because they were previously thought to contain duplicative rather than unique instructions.

This new discovery challenges half a century of fundamental assumptions in biology. It may also help speed up the industrial production of proteins, which is crucial for making biofuels and biological drugs used to treat many common diseases, ranging from diabetes to cancer.

The genetic code has been thought to be redundant, but redundant codons are clearly not identical, said Jonathan Weissman, PhD, a Howard Hughes Medical Institute Investigator in the UCSF School of Medicine Department of Cellular and Molecular Pharmacology.

We didn't understand much about the rules, he added, but the new work suggests nature selects among redundant codons based on genetic speed as well as genetic meaning.

Similarly, a person texting a message to a friend might opt to type, NP instead of No problem. They both mean the same thing, but one is faster to thumb than the other. How Ribosome Profiling Works

The work addresses an observation scientists have long made that the process protein synthesis, so essential to all living organisms on Earth, is not smooth and uniform, but rather proceeds in fits and starts. Some unknown mechanism seemed to control the speed with which proteins are made, but nobody knew what it was. Ribosome structure

The structure of a ribosome

To find out, Weissman and UCSF postdoctoral researcher Gene-Wei Li, PhD, drew upon a broader past effort by Weissman and his colleagues to develop a novel laboratory technique called ribosome profiling, which allows scientists to examine universally which genes are active in a cell and how fast they are being translated into proteins.

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New Layer of Genetic Information Discovered

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New layer of genetic information helps determine how fast proteins are produced

ScienceDaily (Mar. 28, 2012) A hidden and never before recognized layer of information in the genetic code has been uncovered by a team of scientists at the University of California, San Francisco (UCSF) thanks to a technique developed at UCSF called ribosome profiling, which enables the measurement of gene activity inside living cells -- including the speed with which proteins are made.

By measuring the rate of protein production in bacteria, the team discovered that slight genetic alterations could have a dramatic effect. This was true even for seemingly insignificant genetic changes known as "silent mutations," which swap out a single DNA letter without changing the ultimate gene product. To their surprise, the scientists found these changes can slow the protein production process to one-tenth of its normal speed or less.

As described March 28 in the journal Nature, the speed change is caused by information contained in what are known as redundant codons -- small pieces of DNA that form part of the genetic code. They were called "redundant" because they were previously thought to contain duplicative rather than unique instructions.

This new discovery challenges half a century of fundamental assumptions in biology. It may also help speed up the industrial production of proteins, which is crucial for making biofuels and biological drugs used to treat many common diseases, ranging from diabetes to cancer.

"The genetic code has been thought to be redundant, but redundant codons are clearly not identical," said Jonathan Weissman, PhD, a Howard Hughes Medical Institute Investigator in the UCSF School of Medicine Department of Cellular and Molecular Pharmacology.

"We didn't understand much about the rules," he added, but the new work suggests nature selects among redundant codons based on genetic speed as well as genetic meaning.

Similarly, a person texting a message to a friend might opt to type, "NP" instead of "No problem." They both mean the same thing, but one is faster to thumb than the other.

How Ribosome Profiling Works

The work addresses an observation scientists have long made that the process protein synthesis, so essential to all living organisms on Earth, is not smooth and uniform, but rather proceeds in fits and starts. Some unknown mechanism seemed to control the speed with which proteins are made, but nobody knew what it was.

To find out, Weissman and UCSF postdoctoral researcher Gene-Wei Li, PhD, drew upon a broader past effort by Weissman and his colleagues to develop a novel laboratory technique called "ribosome profiling," which allows scientists to examine universally which genes are active in a cell and how fast they are being translated into proteins.

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New layer of genetic information helps determine how fast proteins are produced

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Genetic Causes Found in 17 Percent of Patients with Dilated Cardiomyopathy Heart Failure

Newswise MAYWOOD, Ill. -- Researchers have identified genetic causes in nearly 1 in 5 patients who suffer a type of heart failure called dilated cardiomyopathy. Carolyn Jones, MD, PhD, of Loyola University Medical Center, is co-author of the study, published in the Journal of Cardiac Failure. First author is Neal Lakdawala, MD, of Brigham and Women's Hospital.

Researchers did genetic testing on 264 patients with dilated cardiomyopathy and found that 17.4 percent had gene mutations associated with the disease. Pediatric patients were more likely to have the mutations than older patients.

The findings will help in the development of new treatments, Jones said. "By understanding the genes involved in dilated cardiomyopathy, we possibly will be able to circumvent the defect."

Also, if a genetic test shows a patient has an inherited form of the disease, it would indicate that other family members also should be tested, Jones said.

Dilated cardiomyopathy is a condition in which the heart becomes weakened, enlarged and unable to pump efficiently. It is the leading reason for heart transplants. In addition to genetic causes, there are environmental causes, including alcohol abuse, atrial fibrillation (irregular heartbeat) and autoimmune diseases such as lupus.

Earlier studies involved genetic testing on carefully selected research subjects. The new study, by contrast, involved genetic testing in real-life clinical practices. Jones was among the physicians in the study who saw patients, obtained their family histories and arranged for their genetic testing, which was done at the Laboratory for Molecular Medicine at the Partners HealthCare Center for Personalized Genetic Medicine in Cambridge, Mass.

The study included an ethnically diverse sample of patients ranging in age from newborn to 71 years. The average age was 26. Children with dilated cardiomyopathy frequently tested positive for mutations, even if they did not have a family history. Conversely, no patient over age 40 had mutations, unless they also had a family history.

Jones is director of Clinical and Cytogenetics and an associate professor in the departments of Pediatrics and Pathology of Loyola University Chicago Stritch School of Medicine.

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Genetic Causes Found in 17 Percent of Patients with Dilated Cardiomyopathy Heart Failure

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Genetic causes found in nearly 1 in 5 patients with dilated cardiomyopathy heart failure

Public release date: 27-Mar-2012 [ | E-mail | Share ]

Contact: Jim Ritter jritter@lumc.edu 708-216-2445 Loyola University Health System

MAYWOOD, Ill. -- Researchers have identified genetic causes in nearly 1 in 5 patients who suffer a type of heart failure called dilated cardiomyopathy.

Carolyn Jones, MD, PhD, of Loyola University Medical Center, is co-author of the study, published in the Journal of Cardiac Failure. First author is Neal Lakdawala, MD, of Brigham and Women's Hospital.

Researchers did genetic testing on 264 patients with dilated cardiomyopathy and found that 17.4 percent had gene mutations associated with the disease. Pediatric patients were more likely to have the mutations than older patients.

The findings will help in the development of new treatments, Jones said. "By understanding the genes involved in dilated cardiomyopathy, we possibly will be able to circumvent the defect."

Also, if a genetic test shows a patient has an inherited form of the disease, it would indicate that other family members also should be tested, Jones said.

Dilated cardiomyopathy is a condition in which the heart becomes weakened, enlarged and unable to pump efficiently. It is the leading reason for heart transplants. In addition to genetic causes, there are environmental causes, including alcohol abuse, atrial fibrillation (irregular heartbeat) and autoimmune diseases such as lupus.

Earlier studies involved genetic testing on carefully selected research subjects. The new study, by contrast, involved genetic testing in real-life clinical practices. Jones was among the physicians in the study who saw patients, obtained their family histories and arranged for their genetic testing, which was done at the Laboratory for Molecular Medicine at the Partners HealthCare Center for Personalized Genetic Medicine in Cambridge, Mass.

The study included an ethnically diverse sample of patients ranging in age from newborn to 71 years. The average age was 26. Children with dilated cardiomyopathy frequently tested positive for mutations, even if they did not have a family history. Conversely, no patient over age 40 had mutations, unless they also had a family history.

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Genetic causes found in nearly 1 in 5 patients with dilated cardiomyopathy heart failure

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Partek and Life Technologies Partner to Speed Genetic Analysis Validation

ST. LOUIS & FOSTER CITY, Calif.--(BUSINESS WIRE)--

Partek Incorporated, a global leader in bioinformatics software, and Life Technologies, a maker of systems, consumables, and services that enable researchers to accelerate scientific and medical advancements, announced a partnership to allow users of Partek Flow, Partek Genomics Suite, and Partek Pathway a streamlined selection of Life Technologies TaqMan assays directly from the software user interface.

Parteks suite of software aids scientists in their analysis of their next generation sequencing and microarray data with powerful statistics and visualization tools.Real-time PCR forvalidation and further functional characterizationsis widely used downstream of these genomic experiments.TaqManprobebased chemistry is considered the gold standard for real time PCR. By adding a seamless connection from any of Parteks software lists of genes or regions of interestto the relevant TaqMan assays associated with those genesusers have the convenience of a relevant list of appropriate TaqMan assays, but more importantly they have increased accuracy by avoiding the manual, time consuming research required to choose the correct TaqMan assay. This direct interface is available for any list of genes or regions for any application including RNA-seq, transcriptome, miRNA, SNP genotyping, and copy number analysis. Were pleased to work together with our partner Life Technologies to combine two very widely used features by our common customers, saving them valuable time so they can focus on research instead of technical details, said Tom Downey, President of Partek.

Life Technologies has developed the most comprehensive set of real-time PCR assays available, with over 8 million predesigned assays covering 23 species for gene expression, microRNA, noncoding RNA, protein analysis, mutation detection, copy number variation, and SNP genotyping. The field of genetic analysis and next generation sequencing is moving at a fast pace and we are excited to offer researchers an integrated solution to help them advance their research, said Larry Milocco, Life Technologies.

About Partek

Partek Incorporated develops and globally markets quality software for life sciences research. Their software suitePartek Flow, Partek Genomics Suite, and Partek Pathwayprovides innovative solutions for integrated genomics and is unique in offering comprehensive support for all major next generation sequencing and microarray platforms. Workflows offer streamlined data analysis for: RNA-Seq, ChIP-Seq, DNA-Seq, DNA Methylation, Gene Expression, Alternative Splicing, miRNA Expression, Copy Number, Allele-Specific Copy Number, LOH, Association, Trio Analysis, Tiling, and qPCR. Since 1993, Partek has been turning data into discovery.

About Life Technologies

Life Technologies Corporation(NASDAQ: LIFE - News) is a global biotechnology company dedicated to improving the human condition. Our systems, consumables, and services enable researchers to accelerate scientific and medical advancements that make life even better. Life Technologies customers do their work across the biological spectrum, working to advance the fields of discovery and translational research, molecular medicine, stem cell-based therapies, food safety and animal health, and 21st century forensics. The company manufactures both molecular diagnostic and research use only products. Life Technologies' industry-leading brands are found in nearly every life sciences lab in the world and include innovative instrument systems under the Applied Biosystems and Ion Torrent names, as well as, the broadest range of reagents with its Invitrogen, GIBCO, Ambion, Molecular Probes and TaqManproducts. Life Technologies had sales of $3.7 billion in 2011, employs approximately 10,400 people, has a presence in approximately 160 countries, and possesses one of the largest intellectual property estates in the life sciences industry, with approximately 4,000 patents and exclusive licenses. For more information on how we are making a difference, please visit our website:www.lifetechnologies.com.

Safe Harbor Statement

Certain statements contained in this press release are "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995, and Life Technologies intend that such forward-looking statements be subject to the safe harbor created thereby. Forward-looking statements may be identified by words such as "expects," "anticipates," "intends," "plans," "believes," "seeks," "estimates," "will," or words of similar meaning and include, but are not limited to, statements about the expected future business and financial performance of the company. Such forward-looking statements include, but are not limited to, statements relating to financial projections, including revenue and pro forma EPS projections; success of acquired businesses, including cost and revenue synergies; development and increased flow of new products; leveraging technology and personnel; advanced opportunities and efficiencies; opportunities for growth; expectations of prospective new standards, new delivery platforms, and new selling specialization and effectiveness; and corporate strategy and performance. A number of the matters discussed in this press release and presentation that are not historical or current facts deal with potential future circumstances and developments, including future research and development plans. The discussion of such matters is qualified by the inherent risks and uncertainties surrounding future expectations generally and other factors that could cause actual results to differ materiallyfrom future results expressed or implied by such forward-looking statements. Such risks and uncertainties include, but are not limited to: volatility of the financial markets; and the risks that are described from time to time in Life Technologies' reports filed with the SEC. This press release and presentation speaks only as of its date, and the company disclaims any duty to update the information herein.

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Partek and Life Technologies Partner to Speed Genetic Analysis Validation

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Genetic study unravels ancient links between African and European populations

Public release date: 26-Mar-2012 [ | E-mail | Share ]

Contact: Peggy Calicchia calicchi@cshl.edu 516-422-4012 Cold Spring Harbor Laboratory

March 27, 2012 Large numbers of people moved between Africa and Europe during recent and well-documented time periods such as the Roman Empire, the Arab conquest, and the slave trade, and genetic evidence of these migrations lives on in Europeans today. But were there more ancient migrations? In a study published online today in Genome Research, researchers present the first genetic evidence for prehistoric gene flow between Africa and Europe, dating back as far as 11,000 years ago.

To trace the evolution and ancestry of humans, scientists study the DNA sequence of the mitochondria, a specialized cellular structure that produces energy for the cell and carries genetic information that is separate from the rest of the genome that resides in the nucleus. While the nuclear genome is a mix of genetic information from both mother and father, the mitochondrial DNA (mtDNA) is passed directly from mother to child without any contribution of DNA from the father. But not everyone's mtDNA is exactly alike: over long periods of time, small changes in the mtDNA sequence have arisen in different populations. Geneticists can use these changes as markers that indicate the movements and migrations of humans in the past, and classify them into specific "haplogroups."

In this study, an international team of researchers performed the largest analysis of complete mtDNA genomes belonging to haplogroup L (a lineage of sub-Saharan Africa origin) in Europe to date, aiming to untangle the history of genetic links between the two contents. By comparing the sequences of mtDNA genomes from various regions of Europe with mitochondrial genomes from around the world, they made a very surprising observation regarding when sub-Saharan lineages appeared in Europe.

"It was very surprising to find that more than 35 percent of the sub-Saharan lineages in Europe arrived during a period that ranged from more than 11,000 years ago to the Roman Empire times," said Dr. Antonio Salas of the University of Santiago de Compostela and senior author of the study. The other 65% of European haplogroup L lineages arrived in more recent times.

The authors explain that these contacts likely connected sub-Saharan Africa to Europe not only via North Africa, but also directly by coastal routes. Salas said that it still remains unknown why there was genetic flow between the Africa and Europe in prehistoric times, but one possible scenario is that some bidirectional flow was promoted when the last glaciation pushed some Europeans southward, until the glacier receded and populations returned north.

In addition to tracing the genetic links of Africa and Europe back to prehistoric times, Salas expects that their work will also help those individuals who want to learn more about their own ancestry. "There is a growing interest in direct-to-consumer genetic testing, including those aimed to serve a public interested in reconstructing their ancestry," Salas said. "Studies like the one presented here will help to unravel inferences made in these studies."

Scientists from the University of Santiago de Compostela (Galicia, Spain), the University of Perugia (Perugia, Italy), the University of Pavia (Pavia, Italy), the Sorenson Molecular Genealogy Foundation (Salt Lake City, UT), the University of Oxford (Oxford, UK), and the National Institute of Toxicology and Forensic Science (Sevilla, Spain) contributed to this study.

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Genetic study unravels ancient links between African and European populations

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