Category Archives: Genome

October 27, 2013

redOrbit Staff & Wire Reports Your Universe Online

Scientists working to sequence the genome of the kiwifruit have revealed that the berry has recently undergone a pair of whole-genome duplication events, according to new research published earlier this month in the journal Nature Communications.

Zhangjun Fei, an associate professor at the Boyce Thompson Institute at Cornell University, and his colleagues also discovered that there were many similarities between the kiwis more than 39,000 genes and those of other plant species, including tomatoes and potatoes.

However, they were surprised to learn of the duplication events. When genes are duplicated, they explain, the extra genes can wind up mutating in order to perform new functions previously lacking in the organism. This process, which is known as neofunctionalization, turned out to be beneficial to the kiwi, according to Fei.

The duplication contributed to adding additional members of gene families that are involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism, he said in a statement Friday. Previous research had extensively analyzed the metabolic accumulation of those substances, but this marks the first time that genome sequence data had been available.

Fei was one of several US and Chinese researchers who participated in the project, which used a Chinese variety of kiwifruit known as Hongyang in order to produce the draft sequence. After comparing its genome to those of grape, rice, tomato, and a type of mustard weed called Arabidopsis, they found 8,000 genes that were common among all five species, including some related to fruit growth and ripening, nutrient metabolism, and disease resistance.

One of the most remarkable findings of the study was uncovered when scientists observed a high percentage of similarities within the kiwifruit DNA, the university noted. The data revealed two unusual mishaps that occurred in the process of cell division about 27 and 80 million years ago, when an extensive expansion of genes arose from an entire extra copy of the genome, followed by extensive gene loss.

Fei, who called the kiwi an economically and nutritionally important fruit crop, said that the genome sequence he and his colleagues have created will serve as a valuable resource for kiwifruit research and may facilitate the breeding program for improved fruit quality and disease resistance.

The fruit, which has fuzzy brown skin and green flesh and a taste similar to that of a strawberry, originated from the mountains of southwestern China and did not become known throughout the world until the 20th century. According to the researchers, it is a type of berry that, like grapes, grows on woody vines. The kiwifruit is a member of the order Ericales, a classification it shares with blueberries, tea bushes and Brazil nuts.

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Kiwifruit Became More Nutritious Following Genome Duplication Events

Nisson Versa Passion Genome Campaign - ZayZay.Com
Watch as ZayZay and "Mad Scientist" Steve Urich discover ZayZay #39;s hidden passion as part of the Nissan Versa Passion Genome Campaign. Discover your hidden passion and see how we #39;re all connected...

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Nisson Versa Passion Genome Campaign - ZayZay.Com - Video

Neanderthals and Humans, Rewritten Bacteria Genome, and More!
Join Elise each week to see the all the latest and greatest stories from the lighter side of science, including popular science, space, biology, nature, and ...

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Neanderthals and Humans, Rewritten Bacteria Genome, and More! - Video

MOUNTAIN VIEW, Calif. & HOUSTON--(BUSINESS WIRE)--

The Human Genome Sequencing Center (HGSC) at Baylor College of Medicine and DNAnexus today announced a broad collaboration focused on advancing the state-of-the-art in the large-scale clinical analysis of genomic data. Through this collaboration, the HGSC has adopted the DNAnexus enterprise cloud platform to power its Mercury pipeline, a semi-automated and modular set of tools for the analysis of next-generation sequencing data in both research and clinical contexts. The collaborators also worked with Amazon Web Services (AWS) to process data from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium using the Mercury pipeline, generating 430TB of results and making them available to hundreds of researchers participating in this global project.

The HGSCs Mercury pipeline identifies mutations from genomic data, setting the stage for determining the significance of these mutations as a cause of serious disease and is used as the core variant-calling pipeline for the CHARGE Consortium. The CHARGE Consortium is aimed at better understanding how human genetics contributes to heart disease and aging. The CHARGE Consortium has a longstanding collaboration with the HGSC to fuel disease gene discovery. These discoveries are instrumental in understanding disease and aging in mechanistic detail, enabling the development of new medical interventions and analysis tools.

The management and analysis of genomes at the scale needed to appropriately power clinical studies requires computational infrastructure that exceeds the capacity of most institutional resources, said Jeffrey Reid, Ph.D., Assistant Professor, Department of Molecular and Human Genetics, Baylor College of Medicine. Working with DNAnexus and Amazon Web Services, we were able to rapidly deploy a cloud-based solution that allows us to scale up our support to researchers at the HGSC, and make our Mercury pipeline analysis data accessible to the CHARGE Consortium, enabling what will be the largest genomic analysis project to have ever taken place in the cloud.

The CHARGE project involves more than 300 researchers across five institutions around the world analyzing the genome sequence data of over 14,000 individuals (3,751 whole genomes and 10,771 exomes), requiring approximately 2.4 million core-hours of computational time and some 860 TB of storage. At the projects peak, HGSC used the DNAnexus platform to spin up more than 20,000 cores on-demand in order to run the CHARGE data through the Mercury analysis pipeline. During this period, HGSC was running the largest genomics analysis cluster in the world, hosted by AWS.

Many large-scale population studies to date have been limited in scope by a lack of the necessary compute power; this is a real hindrance in realizing the full promise of genomic medicine, said Richard Daly, CEO of DNAnexus. The DNAnexus platform offers research and clinical enterprises the requisite computational resources that allow them to focus on the data and provide the ability to share and collaborate in a secure compliant environment. Through this collaboration with the HGSC and Amazon Web Services, 300 scientists can now perform downstream analyses on these invaluable health and aging data at a scale not previously possible.

DNAnexus provides an enterprise-focused API-based platform-as-a-service that enables clinical and research enterprises to efficiently move their analysis pipelines into the cloud, using their own algorithms alongside industry-recognized tools and reference resources to create customized workflows in a secure, cost-effective and compliant environment. With DNAnexus, labs of any size can build and run their data analysis applications and workflows from anywhere in the world, and work securely with research and clinical collaborators.

For more information please visit: https://dnanexus.com/usecases-charge.

About the Human Genome Sequencing Center at Baylor College of Medicine, (HGSC)

As one of three U.S. Centers that contributed to the Human Genome Project, the HGSC played a pivotal role in the emergence of genomics as a core discipline in modern biomedical and translational research, and has been at the forefront of technical innovation and testing of next-generation sequencing technologies. The HGSC is also a leader in developing large-scale sequencing and analysis solutions, and has emerged as a world leader in the analysis of personal genomes and the introduction of genomics into medicine. For more information please visit:https://www.hgsc.bcm.edu.

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DNAnexus and the Human Genome Sequencing Center at Baylor College of Medicine Announce Ultra Large-Scale Collaboration ...

The Wellcome Trust is piling almost 10 million additional funding into transformational upgrades to its Genome Campus conference facilities in the Cambridge UK medical technology cluster.

The Conference Centre will look to host an increased programme of events that attract wider audiences including school children as part of the Campuss public engagement strategy.

Planning consent has just been granted for the 9.7 million project, known as the Kitchen Garden Enclosure; the design is reminiscent of the famous glass ceiling in the British Museum and will include a new exhibition centre, modern meeting rooms and a bar.

Groundbreaking for this major new project will begin in January and is due to be completed by December 2014. All facilities at the Conference Centre are due to be opened by January 2015.

In total the Conference Centre will have undergone a 19 million renovation to modernise and improve all available facilities. This project is set to improve the international reputation of the Wellcome Trust Conference Centre, and celebrates the communication, collaboration, achievement and creativity of the overall Genome Campus, according to Linda Prior, sales and marketing manager at the Conference Centre

She said: Not only will this place us at the forefront of the scientific conferences sector, but also the development will better integrate us into the wider vision of the Genome Campus.

This new building work will see the current cloisters and grassed areas opened up and enclosed under a spectacular glass roof to create a multi-use space for both day and evening activities.

The roof, which is the central feature of the build, is designed to create a light and elegant space through the transparent and translucent areas of glass panelling above.

By opening up the area surrounding the auditorium, the Conference Centre will create space sufficient to support exhibitions both fixed and temporary, poster sessions, catering and a relaxation area for delegates and speakers.

David Davison, director of the Wellcome Trust Genome Campus, said: We welcome the development of the Kitchen Garden Enclosure on campus, which will complement perfectly the public engagement activities of both the Wellcome Trust Sanger Institute and EMBL-EBI.

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£19m Genome Campus overhaul targets global business

Next spring, students at local high schools will dive into the study of the marine bacterium Kytococcus sedentarius, thanks to a $1.1 million National Science Foundation grant to UB.

Stephen Koury and his colleagues in the School of Medicine and Biomedical Sciences, received the grant to educate regional high school teachers and recruit high school students to pursue careers in STEM (science, technology, engineering and mathematics) fields. The new program focuses on bioinformatics, an interdisciplinary field that uses software tools to store, retrieve, organize and analyze biologic information. Bioinformatics is a field of rapid growth that provides tools for better health care through improvement in prevention, detection, diagnosis and treatment of diseases.

Koury, research assistant professor in the Department of Biotechnical and Clinical Laboratory Sciences, notes that new jobs on the Buffalo Niagara Medical Campus likely will require training in biotechnology and bioinformatics; the new program will provide a pipeline for educator and student recruitment, training and mentorship in STEM fields at the high school level.

For us to be successful, we need to create the environment where children not only want to get involved, but want to stay in Buffalo, says Norma Nowak, professor of biochemistry, director of science and technology at UBs New York State Center of Excellence in Bioinformatics and Life Sciences, and associate professor of oncology at Roswell Park Cancer Institute. This needs to be the spark that lights the fire.

Over the next three years, the grant will allow 450 high school students and 90 teachers to conduct and present scientific research in bioinformatics. The program will involve educators and students from 13 counties, including Niagara, Erie, Chautauqua, Cattaraugus, Wyoming, Genesee, Orleans, Monroe, Livingston, Allegany, Ontario, Wayne and Steuben.

The educational program will begin with a two-week workshop at UB, where high school teachers will receive training in microbial genome annotation. The teachers then will pass on their new skills to selected students in their schools, with support from UB faculty and staff.

During the first semester, students will be introduced to basic aspects of genetics and genomics. They also will receive career mentoring through a partnership with the New York State Area Health Education Center System (AHEC), a unit of UBs Department of Family Medicine that addresses health care workforce needs.

The second semester will focus on conducting Web-based research in microbial annotation through a program called IMG-ACT, a bioinformatics tool kit available through the U.S. Department of Energys Joint Genome Institute. The program will end with a capstone symposium at which students will present the results of their research to university faculty, researchers and employers in the biosciences fields.

For many local students, this will be their first real-world taste of scientific experimentation. And since its an unscripted project, students will learn to rely on themselves, rather than the specific direction of instructors.

We cant say for sure what they should find, says Koury. They will actually be doing a research project, and by the time they are done, they will probably be the expert on the particular gene sequence they have studied. It will give them that joy of discovery.

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Genome project fosters bioinformatics education in high schools

SANTA CLARA, Calif.--(BUSINESS WIRE)--

Affymetrix, Inc. (AFFX) announces the launch of Axiom Strawberry Genotyping Array (also called International Strawberry 90K SNP array or IStraw90), the only solution that successfully enables high-resolution genotyping and fully automated data analysis of the octoploid strawberry genome. This 90,000 SNP array will enable complex trait research and set the stage for multi-trait, marker-assisted breeding of the cultivated garden strawberry (Fragaria ananassa).

The cultivated garden strawberry is an allo-octoploid with a chromosome number of 2n=8x=56. While there are other genotyping technologies available to scan genomes of agricultural species at high resolution, most have been designed for diploids. With Affymetrix advanced bioinformatics and innovative design strategy, Axiom Genotyping Solution provides genome-wide genotyping and accurately calls the genotypes of both diploid and polyploid species. This technology has already been successfully applied to complex genomes such as maize, rose, wheat, trout, and salmon.

Axiom Strawberry Genotyping Array was designed through a public-private partnership between Affymetrix and theInternational RosBREED SNP Consortium (IRSC), an arm of the "RosBREED" project dedicated to the genetic improvement of rosaceous crops. The RosBREED team including Genotyping Team Leader Nahla Bassil (USDA-ARS, Corvallis), Demonstration Breeder Tom Davis (University of New Hampshire geneticist), and Pedigree-Based Analysis Team Leader Eric van de Weg (Wageningen University & Research Center) partnered with the Affymetrix array design and bioinformatics teams to devise SNP selection and data analysis strategies. RosBREED announced the availability of the array through its September 2013 newsletter. Preliminary results from the array were presented at the 2013 annual conference of the American Society for Horticultural Science.

IStraw90 gives us the capability to create high-resolution genetic maps of the strawberry genome and work towards enabling marker-assisted breeding for strawberry breeders worldwide, stated Nahla Bassil. The International RosBREED SNP consortium has been working towards enabling discovery and validation of valuable trait loci. IStraw90 will facilitate many of RosBREEDs goals and expedite marker-assisted breeding in strawberry.

The successful design and analysis of the data from the allo-octoploid strawberry genome was possible only because of the expertise, commitment, and collaborative efforts of the Axiom myDesign custom array, bioinformatics, and product support teams within Affymetrix, stated Eric van de Weg. It is awesome to have the tools to construct such high marker-density maps generated in such a short time. We expect this array to be a valuable resource for genome-wide analysis and marker-assisted breeding in many American, European and other breeding programs.

Genotyping the octoploid strawberry genome demonstrates the power and precision of the Axiom Genotyping platform to type genetic variants within complex genomes, said Andy Last, Executive Vice President of the Genetic Analysis Business Unit at Affymetrix. The array design process and updates to the automated analysis software used with Axiom Strawberry Genotyping Array are significant milestones for our platform because they enable the worldwide plant and animal genotyping community to leverage the Axiom myDesign customization process and analysis software to genotype even more species of interest.

Axiom Strawberry Genotyping Array will complement the catalog of Axiom Agrigenomics Genotyping Arrays that are available for multiple species, including bovine, chicken, and buffalo. These products have been used for genome-wide association studies, quantitative trait locus mapping, genome mapping, and breeding activities that make use of marker-assisted selection and genomic selection. As scientists make progress in decoding genomes of various plants, animals, and fish using next-generation sequencing platforms, they can advance their research and commercial objectives by translating those discoveries to routine applications on the Axiom Genotyping platform.

To learn more about Axiom Genotyping Solutions, please visit http://www.affymetrix.com/axiom for applications in human diseases research and http://www.affymetrix.com/agrigenotyping for applications in agrigenomics.

PLEASE NOTE: Affymetrix, the Affymetrix logo, Axiom, and all other trademarks are the property of Affymetrix, Inc. All other trademarks are the property of their respective owners.

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Affymetrix Axiom® Strawberry Genotyping Array Delivers Automated Analysis for High-Resolution Genome Scanning of ...

Oct. 22, 2013 Mantle cell lymphoma is a very aggressive and difficult to treat cancer originated in blood cells and lymph nodes. To identify the molecular alterations responsible for this tumor, and facilitate the development of new treatments, a team of scientists led by Dr. Xose S. Puente and Dr. Carlos Lpez-Otn, at University of Oviedo, and Dr. Slvia Be and Dr. Elias Campo, at IDIBAPS, Hospital Clnic, University of Barcelona, have sequenced the genomes of over 30 of lymphomas. The result of this work, published today in the prestigious U.S. journal Proceedings of the National Academy of Sciences (PNAS), presents the first comprehensive genomic analysis of this disease. "The study provides insight into causes and evolution of this complex neoplasm and has identified targets for new treatments," says Dr. Silvia Be, first author of the study.

The authors analyzed the genome of tumor cells at the onset of the disease and within several years after treatment, when the relapses occur. Thus, it has been possible to evaluate the genomic modifications associated with disease progression. These analyses have discovered the implication of several genes in the progression of these lymphomas and some mechanisms generating resistance to chemotherapy. They also defined a group of patients with very rapid progression of the disease with mutations in NOTCH1 and NOTCH2 genes. These mutations could become therapeutic targets because there are already drugs blocking the activity of these genes which may be useful in complicated cases of mantle cell lymphoma. Researchers also identified a group of patients with a small number of mutations in the tumor whose disease progression was very slow. Thus, knowledge around the genome of these lymphomas might guide the selection of appropriate treatments for each patient.

This work was carried out with funding from the Association for International Cancer Research (United Kingdom), the Lymphoma Research Foundation (USA) and the Instituto de Salud Carlos III (Spain), and illustrates how new genome sequencing technologies are revolutionizing the study of different types of cancer. During the last three years the Spanish Consortium for the Study of the Genome of the Chronic Lymphatic Leukemia, where the researchers of the present study already collaborate, has sequenced the genome of hundreds of patients with the more common leukemia in our society, identifying new mechanisms of tumor progression and new therapeutic targets. These studies should allow the application of genomic studies in clinical practice to improve the diagnosis and treatment of cancer patients.

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The above story is based on materials provided by Universidad de Barcelona.

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Genome of aggressive lymphoma sequenced

Cosmic Log

Alan Boyle, Science Editor NBC News

Oct. 21, 2013 at 10:16 PM ET

Kolb et al. / PLOS ONE

A world map charts the classification of herpes simplex virus type-1 genomes into different genetic groups, or clades. Patterns of land migration are shown by yellow lines, and potential air/sea migration by a pink line.

To confirm the theory that humans spread out from Africa tens of thousands of years ago, all you have to do is follow the cold sores. Or, to be more precise, follow the mutation patterns encoded in the genome of the virus that causes those cold sores.

That's what researchers at the University of Wisconsin at Madison did: In the journal PLOS ONE, they describe how they sequenced the genomes of 31 samples of herpes simplex virus type-1 to reconstruct how it hitchhiked on humans as they dispersed around the world.

The results match the pattern proposed by the "Out of Africa" theory, which has become the most widely accepted scenario for ancient human migration. The analysis showed that African strains of the virus contained the most genetic diversity suggesting that they had the oldest roots.

The viral strains sort exactly as you would predict based on sequencing of human genomes. We found that all of the African isolates cluster together, all the virus from the Far East, Korea, Japan, China clustered together, all the viruses in Europe and America, with one exception, clustered together, senior author Curtis Brandt, a professor of medical microbiology and opthalmology, said in a UW-Madison news release.

What we found follows exactly what the anthropologists have told us, and the molecular geneticists who have analyzed the human genome have told us, about where humans originated and how they spread across the planet, he said.

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Herpes virus genome traces the ancient path of human migration

Provided

The recent decoding of the kiwifruit genome has discovered that the fruit has many genetic similarities to other plant species, including potatoes and tomatoes, among other surprises.

A new study that decoded the DNA sequence of the kiwifruit has concluded that the fruit has many genetic similarities between its 39,040 genes and other plant species, including potatoes and tomatoes. The study also has unveiled two major evolutionary events that occurred millions of years ago in the kiwifruit genome.

The kiwifruit is an economically and nutritionally important fruit crop. It has long been called the king of fruits because of its remarkably high vitamin C content and balanced nutritional composition of minerals, dietary fiber and other health-benefits, says Zhangjun Fei, a scientist from the Boyce Thompson Institute at Cornell who contributed heavily to study, which was conducted by a team of plant scientists from the United States and China and published Oct. 18 in Nature Communications.

The genome sequence will serve as a valuable resource for kiwifruit research and may facilitate the breeding program for improved fruit quality and disease resistance, Fei says.

Kiwifruit originated from the mountains and ranges of southwestern China and was not really known to the world until the early 20th century, when farmers in New Zealand discovered the fruit and began breeding it as a commercial crop. It is a form of berry that grows on woody vines, much like grapes, and belongs to the order of Ericales, where blueberries, tea bushes and Brazil nuts are also classified.

One of the most remarkable findings of the study was uncovered when scientists observed a high percentage of similarities within the kiwifruit DNA. The data revealed two unusual mishaps that occurred in the process of cell division about 27 and 80 million years ago, when an extensive expansion of genes arose from an entire extra copy of the genome, followed by extensive gene loss.

Fei explains, The kiwifruit genome has undergone two recent whole-genome duplication events.

When genes are duplicated, the extra genes can mutate to perform entirely new functions that were not previously present in the organism. This process, called neofunctionalization, can occur with no adverse effects in plants and, in the case of kiwifruit, was quite beneficial.

The duplication contributed to adding additional members of gene families that are involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism, says Fei.

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Surprises discovered in decoded kiwifruit genome