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Category Archives: Genetic Medicine

Hearing and touch have common genetic basis: Gene mutation leads to impairment of two senses

ScienceDaily (May 1, 2012) Vision and hearing are so crucial to our daily lives that any impairments usually become obvious to an affected person. Although a number of known genetic mutations can lead to hereditary defects in these senses, little is known about our sense of touch, where defects might be so subtle that they go unnoticed.

People with good hearing also have a keen sense of touch; people with impaired hearing generally have an impaired sense of touch. Extensive data supporting this hypothesis was presented by Dr. Henning Frenzel and Professor Gary R. Lewin of the Max Delbrck Center for Molecular Medicine (MDC) Berlin-Buch, Germany. The two researchers showed that both senses -- hearing and touch -- have a common genetic basis. In patients with Usher syndrome, a hereditary form of deafness accompanied by impaired vision, the researchers discovered a gene mutation that is also causative for the patients' impaired touch sensitivity.

The examination was preceded by various studies, including studies with healthy identical and non-identical human twins. In total, the researchers assessed sensory function in 518 volunteers.

In all vertebrates, and consequently also in humans, hearing and touch represent two distinct sensory systems that both rely on the transformation of mechanical force into electrical signals. When we hear, sound waves trigger vibrations that stimulate the hair-like nerve endings in the cochlea in the inner ear. These then transform the mechanical stimuli into electrical signals, which are transmitted to the brain via the auditory nerve. When we touch something a similar process takes place: The mechanical stimulus -- sliding the fingers over a rough or smooth surface, the perception of vibrations -- is taken up via sensors in the skin, converted into an electrical stimulus and transmitted to the brain.

Twin study with 100 pairs of twins

In recent years about 70 genes have been identified in humans, mutations in which trigger hearing loss or deafness. "Surprisingly, no genes have been found that negatively influence the sense of touch," Professor Lewin said. To see whether the sense of touch also has a hereditary component, the researchers first studied 100 pairs of twins -- 66 pairs of monozygotic twins and 34 dizygotic pairs of twins. Monozygotic twins are genetically completely identical; dizygotic twins are genetically identical to 50 percent. The tests showed that the touch sensitivity of the subjects was determined to more than 50 percent by genes. Furthermore, hearing and touch tests showed that there is a correlation between the sense of hearing and touch.

The researchers therefore suspected that genes that influence the sense of hearing may also have an influence on the sense of touch. In a next step, they recruited test subjects at a school in Berlin for students with hearing impairments. There they assessed the touch sensitivity in a cohort of 39 young people who suffered from severe congenital hearing impairment. The researchers compared these findings with the data from their twin study and discovered that not all of the young people with hearing loss had impaired tactile acuity. "Strikingly, however, many of these young people did indeed have poor tactile acuity," Professor Lewin explained.

The researchers decided it would take too much time to analyze which of the approximately 70 genes that adversely affect the sense of hearing may also negatively affect the sense of touch. Therefore, the researchers focused specifically on patients with the Usher syndrome, a hereditary form of hearing impairment, in which the patients progressively become blind. Usher syndrome patients have varying degrees of hearing impairment, and the disease is genetically very well studied. There are nine known Usher genes carrying mutations which cause the disease.

The researchers examined one cohort of patients in a special consultation at the Charit -- Universittsmedizin Berlin for Usher patients from all over Germany. A second cohort was recruited at the university hospital La Fe in Valencia, Spain. The studies revealed that not all patients with Usher-syndrome have poor tactile acuity and touch sensitivity. The researchers showed that only patients with Usher syndrome who have a mutation in the gene USH2A have poor touch sensitivity. This mutation is also responsible for the impaired hearing of 19 patients. The 29 Usher-syndrome patients in whom the mutation could not be detected had a normal sense of touch. The researchers thus demonstrated that there is a common genetic basis for the sense of hearing and touch. They suspect that even more genes will be discovered in the future that influence both mechanosensory traits.

Women hear better than men and have a finer sense of touch

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The genetic links between different diseases

Diseases that strike different parts of the bodyand that don't seem to resemble each other at allmay actually have a lot in common.

Scientists have identified the genetic basis for many separate diseases. Now, some researchers are looking at how the genes interact with each other. They are finding that a genetic abnormality behind one illness may also cause other, seemingly unrelated disorders. Sometimes diseases are tangentially linked, having just one gene in common. But the greater the number of shared genetic underpinnings a group of diseases has, the greater the likelihood a patient with one of the illnesses will contract another.

Researchers have found evidence, for example, that there is a close genetic relationship between Crohn's disease, a gastrointestinal condition, and Type 2 diabetes, despite the fact the two conditions affect the body in very distinct ways. Other illnesses with apparently close genetic links are rheumatoid arthritis and Type 1 diabetes, the form of the disease that usually starts in childhood, said Dr. Joseph Loscalzo, chairman of the department of medicine at Brigham and Women's Hospital in Boston.

This network approach, known among scientists as systems biology, could change the way medical specialists view and treat disease, according to some researchers. Rather than only looking to repair the parts of the body that are directly affected by illness, "we should be looking at what the wiring diagram [inside of cells] looks like," said Dr. Albert-Lszl Barabsi, a physicist at Northeastern University's Center for Complex Network Research in Boston.

The information could help better predict a person's risk of developing diseases, researchers say. It also could aid drug development. By figuring out which proteins are most critical to the normal functioning of the body, pharmaceutical companies could target those key proteins to treat disease. In some cases, drug companies may want to avoid interfering with key proteins to avoid too many unintended side effects, says Marc Vidal, director of the Center for Cancer Systems Biology at Dana-Farber Cancer Institute in Boston.

Since all the DNA in the human body was first sequenced in 2000, some 4,000 diseases with a known genetic basis have been identified, according to the National Institutes of Health. But only about 250 of those diseases have treatments, leaving many genetic puzzles left to untangle.

Scientists have long known that proteins and other molecules in the body don't act alone. In order for the body to operate efficiently, biological substances must bind to or pass chemical messages to each other to start and stop working. The system is complex: Each gene is thought to produce, on average, five separate substances, mostly proteins, and these products interact with each other. When a protein, or group of proteins, malfunctions, it appears to give rise to a variety of distinct illnesses.

Barabsi and his colleagues set out to see which diseases shared genetic underpinnings. They used information from a vast database at Johns Hopkins University in Baltimore that pulled together research from around the world on diseases and genes they were linked to. The scientists then mapped out a network indicating which diseases were seemingly connected to each other through common genes.

Of the 1,284 diseases mapped, nearly 900 had genetic links to at least one other disease. And 516 of these formed a so-called disease cluster, in which illnesses, mainly cancers, were linked to each other through multiple genetic connections.

Click here to read more from The Wall Street Journal.

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Improved Adult-Derived Human Stem Cells Have Fewer Genetic Changes Than Expected

--Study lends support to safe use for therapy

Newswise A team of researchers from Johns Hopkins University and the National Human Genome Research Institute has evaluated the whole genomic sequence of stem cells derived from human bone marrow cellsso-called induced pluripotent stem (iPS) cellsand found that relatively few genetic changes occur during stem cell conversion by an improved method. The findings, reported in the March issue of Cell Stem Cell, the official journal of the International Society for Stem Cell Research (ISSCR), will be presented at the annual ISSCR meeting in June.

Our results show that human iPS cells accrue genetic changes at about the same rate as any replicating cells, which we dont feel is a cause for concern, says Linzhao Cheng, Ph.D., a professor of medicine and oncology, and a member of the Johns Hopkins Institute for Cell Engineering.

Each time a cell divides, it has the chance to make errors and incorporate new genetic changes in its DNA, Cheng explains. Some genetic changes can be harmless, but others can lead to changes in cell behavior that may lead to disease and, in the worst case, to cancer.

In the new study, the researchers showed that iPS cells derived from adult bone marrow cells contain random genetic changes that do not specifically predispose the cells to form cancer.

Little research was done previously to determine the number of DNA changes in stem cells, but because whole genome sequencing is getting faster and cheaper, we can now more easily assess the genetic stability of these cells derived by various methods and from different tissues, Cheng says. Last year, a study published in Nature suggested higher than expected cancer gene mutation rates in iPS cells created from skin samples, which, according to Cheng, raised great concerns to many in the field pertaining to usefulness and safety of the cells. This study analyzed both viral and the improved, nonviral methods to turn on stem cell genes making the iPS cells

To more thoroughly evaluate the number of genetic changes in iPS cells created by the improved, non-viral method, Chengs team first converted human blood-forming cells or their support cells, so-called marrow stromal cells (MSCs) in adult bone marrow into iPS cells by turning on specific genes and giving them special nutrients. The researchers isolated DNA from--and sequenced--the genome of each type of iPS cells, in comparison with the original cells from which the iPS cells were derived.

Cheng says they then counted the number of small DNA differences in each cell line compared to the original bone marrow cells. A range of 1,000 to 1,800 changes in the nucleic acid letters A, C, T and G occurred across each genome, but only a few changes were found in actual genes--DNA sequences that act as blueprints for our bodys proteins. Such genes make up two percent of the genome.

The blood-derived iPS cells contained six and the MSC-derived iPS cells contained 12 DNA letter changes in genes, which led the researchers to conclude that DNA changes in iPS cells are far more likely to occur in the spaces between genes, not in the genes themselves.

Next, the investigators examined the severity of the DNA changes--how likely each one would disrupt the function of each gene. They found that about half of the DNA changes were silent, meaning these altered blueprints wouldnt change the nucleic acid building code for its corresponding protein or change its function.

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Nano nod for lab-on-a-chip

The Domino technology uses a plastic chip that can perform 20 genetic tests from a single drop of blood.

You wouldn't know it from appearances, but a metal cube the size of a toaster, created at the University of Alberta, is capable of performing the same genetic tests as most fully equipped modern laboratoriesand in a fraction of the time.

At its core is a small plastic chip developed with nanotechnology that holds the key to determining whether a patient is resistant to cancer drugs or has viruses like malaria. The chip can also pinpoint infectious diseases in a herd of cattle.

Talk about thinking outside the box.

Dubbed the Domino, the technologydeveloped by a U of A research teamhas the potential to revolutionize point-of-care medicine. The innovation has also earned Aquila Diagnostic Systems, the Edmonton-based nano startup that licensed the technology, a shot at $175,000 as a finalist for the TEC NanoVenturePrize award.

Were basically replacing millions of dollars of equipment that would be in a conventional, consolidated lab with something that costs pennies to produce and is field portable so you can take it where needed. Thats where this technology shines, said Jason Acker, an associate professor of laboratory medicine and pathology at the U of A and chief technology officer with Aquila.

The Domino employs polymerase chain reaction technology used to amplify and detect targeted sequences of DNA, but in a miniaturized form that fits on a plastic chip the size of two postage stamps. The chip contains 20 gel postseach the size of a pinheadcapable of identifying sequences of DNA with a single drop of blood.

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Thats the real value propositionbeing able to do multiple tests at the same time, Acker said, adding that the Domino has been used in several recently published studies, showing similar accuracy to centralized labs.

The Domino effect: Personalized medicine

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Pathway Genomics Adds Prominent Bioinformatics Experts to Scientific Advisory Board

SAN DIEGO--(BUSINESS WIRE)--

Pathway Genomics Corporation, a genetic testing laboratory specializing in nutrition and exercise response, inherited disease, prescription drug response and health condition risks, has established a world-leading scientific advisory board. Among the board members are James Fowler, Ph.D., professor of medical genetics at UCSD School of Medicine, Christoph Lange, Ph.D., associate professor of biostatistics at Harvard University School of Public Health, and Nicholas Schork, Ph.D., director of bioinformatics and biostatistics at the Scripps Translational Science Institute.

Additionally, the companys internal computational and bioinformatics team is led by Lixin Zhou, Ph.D., former senior scientist at Illumina and former collaborative bioinformatics investigator at The Institute for Genomic Research, an organization of The J. Craig Venter Institute.

Working with innovators in specific and technical fields helps Pathway bring highly accurate, useful and actionable information to physicians and their patients, said Michael Nova, M.D., Pathway Genomics chief medical officer. Were committed to seeking out this actionable genetic information through computational biology methods, and cloud-based bioinformatics.

An acclaimed behavioral geneticist, James Fowler, Ph.D., is currently a professor of medical genetics at UCSD School of Medicine, and is world-renowned for his breakthrough discoveries in genetics and social networking, behavioral economics, cooperation, and political behavior.

Christoph Lange, Ph.D., is an assistant professor of medicine at Harvard Medical School and an associate professor of biostatistics at Harvard School of Public Health. Langes current research interests fall into the broad areas of statistical genetics and generalized linear models.

Nicholas J. Schork, Ph.D., is a professor at The Scripps Research Institute in the department of molecular and experimental medicine and director of bioinformatics and biostatistics at the Scripps Translational Science Institute. Schorks research focuses are in quantitative human genetics and integrated approaches to complex biological and medical problems. He has published over 350 scientific articles and book chapters analyzing complex, multifactorial traits and diseases.

Pathways scientific advisory board consists of 10 leaders in various fields including behavioral genetics, bioinformatics, biostatistics, endocrinology, human epigenetics, metabolism, nutrigenomics, nutrition, obesity and exercise genetics, oncology, and weight management. To view the companys full scientific advisory board, visit http://www.pathway.com/sab.

About Pathway Genomics

Pathway Genomics owns and operates an on-site genetic testing laboratory that is accredited by the College of American Pathologists (CAP), accredited in accordance with the U.S. Health and Human Services Clinical Laboratory Improvement Amendments (CLIA) of 1988, and licensed by the state of California. Using only a saliva sample, the company incorporates customized and scientifically validated technologies to generate personalized reports, which address a variety of medical issues, including an individuals carrier status for recessive genetic conditions, food metabolism and exercise response, prescription drug response, and propensity to develop certain diseases such as heart disease, type 2 diabetes and cancer. For more information about Pathway Genomics, visit http://www.pathway.com.

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Genetic variants, tobacco exposure and lung cancer risk

Public release date: 25-Apr-2012 [ | E-mail | Share ]

Contact: Zachary Rathner Zachary.Rathner@oup.com 301-841-1286 Journal of the National Cancer Institute

There is an association between the rs1051730-rs16969968 genotype and objective measures of tobacco exposure, which indicates that lung cancer risk is largely, if not entirely, mediated by level of tobacco exposure, according to a study published April 25 in the Journal of the National Cancer Institute.

The rs1051730-rs16969968 genotype is known to be associated with heaviness of smoking, lung cancer risk, and other smoking-related outcomes. Prior studies have generally depended on self-reported smoking behavior, which may have underestimated associations and masked the contribution of heaviness of smoking to the associations of these polymorphisms with lung cancer and other health outcomes.

In order to determine the association between the rs1051730-rs16969968 genotype and self-reported cigarette consumption and plasma or serum cotinine levels, Marcus R. Munaf, Ph.D., of the School of Experimental Psychology at the University of Bristol and colleagues, examined data from six independent studies that looked at self-reported daily cigarette consumption and plasma or serum cotinine levels among cigarette smokers and conducted a meta-analysis of pooled per-allele effects. In addition, the researchers looked at the link between the genotypes and lung cancer risk using published data on the association between cotinine levels and lung cancer risk.

The researchers found that the rs1051730-rs16969968 genotype is strongly associated with tobacco exposure measured through cotinine levels, and that the association is strong even after adjustment for self-reported cigarette consumption. "These data therefore support the conclusion that association of rs1051730-rs16969968 genotype with lung cancer risk is mediated largely, if not wholly, via tobacco exposure," the researchers write.

The researchers point out certain limitations of the study, however, namely that the data were drawn from disparate studies from various populations. The data also relies on current smoking measures, rather than lifetime exposure, which is more strongly associated with lung cancer risk.

However, they have confidence in their results, which show that phenotype precision is important to uphold in GWAS studies, rather than ever-larger sample sizes, they say. "The use of objective measures of smoking behavior in genome-wide studies may reveal novel variants associated with these outcomes, which would be undetectable using conventional self-report measures."

In an accompanying editorial, Margaret R. Spitz, M.D., MPH, of the Department of Molecular and Cellular Biology at the Dan L. Duncan Cancer Center at Baylor College of Medicine, writes that these findings "confirm that cigarettes per day is an imprecise measure of nicotine consumption, and favor the interpretation that the association between these variants and lung cancer is mediated by smoking. But the degree to which the association is mediated by smoking is yet to be determined." They add that more studies, including mouse and cellular models, along with emerging metabolic markers, "may help tease apart the direct and indirect associations of these variants with lung cancer risk."

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