Category Archives: Transhuman News

An enormous tree's enormous genome, genes for strong-swimming sperm and more presented May 7-11 in Cold Spring Harbor, N.Y.

An enormous tree's enormous genome, genes for strong-swimming sperm and more presented May 7-11 in Cold Spring Harbor, N.Y.

By Tina Hesman Saey

Web edition: May 16, 2013

Loblolly pine trees (shown) are used for lumber, paper and many other products. Scientists have compiled the organisms genome, the largest ever attempted.

Credit: National Park Service (NPS); U.S. Department of the Interior

A record-setting genome for a towering giant Deciphering the genome of the loblolly pine is a tall order, as is perhaps fitting for a tree that can grow to be 30 meters in height.

Researchers sequenced the conifers (Pinus taeda) approximately 24 billion bases of DNA, Steven Salzberg of Johns Hopkins University reported May 10. That surpasses the previous record holder, wheat, by more than 7 billion bases. The DNA is distributed over 12 chromosomes, each about two-thirds the size of the entire human genome.

A preliminary analysis suggests the trees may have up to 64,000 protein-coding genes, although Salzberg says the number is probably smaller. Humans have just over 22,000 protein-coding genes.

Next, the researchers will tackle the sugar pine genome. That one is even bigger, with more than 35 billion DNA bases.

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News in Brief: Highlights from the Biology of Genomes meeting

GAITHERSBURG, Md.--(BUSINESS WIRE)--

OpGen, Inc. today announced that new data on the utility and application of its Whole Genome Mapping technology in the public health and health care settings will be highlighted at a company-sponsored symposium and poster presentation during the American Society for Microbiology (ASM) 113th General Meeting. The meeting is being held May 18-21, 2013 at the Colorado Convention Center in Denver. OpGen will be exhibiting at booth #1216 during the conference.

Mike Miller, Ph.D., Associate Director for Laboratory Science (Retired) for the National Center for Emerging and Zoonotic Infectious Diseases, CDC, will present new data on OpGens Whole Genome Mapping technology during a poster presentation on Monday, May 19, 2013. The poster titled Whole Genome Mapping for the Analysis of Bacterial Strains from Foodborne Outbreaks will highlight the application of the technology in the analysis of food-borne pathogens. The poster provides an overview of the utility of Whole Genome Mapping to quickly analyze and map a multi-state outbreak of Salmonella ser. Typhimurium associated with contaminated peanut products.

Additionally, OpGen will host a symposium titled Complete, High Resolution Whole Genome Mapping Applications in Public and Health Care Settings on Sunday, May 19, 2013 at 7 p.m. M.D.T. at the Hyatt Regency in Denver. The symposium will feature presentations by Dr. Miller; Jack A. Gilbert, Ph.D., principal investigator, Hospital Microbiome Project at Argonne National Laboratory; and Bart Weimer, Ph.D., Director, 100K Pathogen Genome Project, Director, BGI@Davis and Director, Genomics Integration Core at West Coast Metabolomics Center at the University of California, Davis.

About OpGen, Inc.

OpGen, Inc. is a leading innovator in rapid, accurate genomic and DNA analysis systems and services. The companys Whole Genome Mapping Technology, GenomeBuilder Software and MapIt Service provide high resolution, whole genome maps for strain typing, sequence assembly and finishing, and comparative genomics in the healthcare, public health, and life sciences markets. OpGens powerful technology dramatically improves the quality of data and time-to results by providing sequence information from single DNA molecules more rapidly and less expensively than previously possible. The company is dedicated to positively influencing individual healthcare outcomes, enhancing public health, and advancing scientific research by delivering precise, actionable information and results. OpGens customers include federal and state public health centers, hospitals, leading genomic research centers, biodefense organizations, academic institutions, clinical research organizations and biotechnology companies. For more information, visit http://www.opgen.com.

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OpGen to Present New Data on the Application of Whole Genome Mapping in Microbial Outbreaks at the American Society ...

Public release date: 17-May-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

May 17, 2013, Shenzhen, China---- Why Tibetan antelope can live at elevations of 4,000-5,000m on the Qinghai-Tibetan Plateau? In a collaborative research published in Nature Communications, investigators from Qinghai University, BGI, and other institutes provide evidence that some genetic factors may be associated with the species' adaption to harsh highland environments. The data in this work will also provide implications for studying specific genetic mechanisms and the biology of other ruminant species.

The Tibetan antelope (Pantholops hodgsonii) is a native of the high mountain steppes and semi-desert areas of the Tibetan plateau. Interestingly, it is the only member of the genus Pantholops. Tibetan antelope is a medium sized antelope with the unique adaptations to against the harsh high-altitude climate. For non-native mammals such as humans, they may experience life-threatening acute mountain sickness when visiting high-altitude regions.

In this study, researchers suggest that Tibetan antelopes must have evolved exceptional mechanisms to adapt to this extremely inhospitable habitat. Using next-gen sequencing technology, they have decoded the genome of Tibetan antelope and studied the underlying genetic mechanism of high-altitude adaptations.

Through the comparison between Tibetan antelope and other plain-dwelling mammals, researchers found the Tibetan antelope had the signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission, indicating that gene categories involved in energy metabolism appear to have an important role for Tibetan antelope via efficiently providing energy in conditions of low partial pressure of oxygen (PO2).

Further research revealed that both the Tibetan antelope and the highland American pika have signals of positive selection for genes involved in DNA repair and the production of ATPase. Considering the exposure to high levels of ultraviolet radiation, positive selective genes related to DNA repair may be vital to protect the Tibetan antelope from it.

Qingle Cai, Project manager from BGI, said, "The completed genome sequence of the Tibetan antelope provides a more complete blueprint for researchers to study the genetic mechanisms of highland adaptation. This work may also open a new way to understand the adaptation of the low partial pressure of oxygen in human activities."

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About BGI

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The genome sequence of Tibetan antelope sheds new light on high-altitude adaptation