Category Archives: Genome

Public release date: 9-Jan-2013 [ | E-mail | Share ]

Contact: Laura Crozier crozier@dbi.udel.edu 302-831-3424 University of Delaware

Two prominent microbiologists have launched a new peer-reviewed publication focusing on microbiome research in environmental, agricultural, and biomedical areas. Eric Wommack, from the University of Delaware's College of Earth, Ocean and Environment and Jacques Ravel, from the University of Maryland School of Medicine's Institute for Genome Sciences are the Editors-in-Chief of Microbiome, a BioMed Central (BMC) publication, which launched its first issue this week.

The new publication reflects the growing importance of the need for studying communities of microorganisms microbiomes and their functions in their natural environment whether that environment is the human body, the ocean, or any other habitat.

"Microbiology was once thought of as two exclusive subdisciplines clinical microbiology and environmental microbiology but the substantial technological advances, particularly over the past decade in DNA sequencing and analysis, have given scientists new common and interdisciplinary research interests," explains Ravel, who is studying the effect of the human microbiome on women's health, and is part of the NIH-funded Human Microbiome Project (HMP).

"Microbiome will facilitate the cross-fertilization of ideas, research methods and analyses, and theory between clinical and environmental microbiologists exploring the emergent impacts of microbial communities on the ecosystems they inhabit," says Wommack, a University of Delaware professor who researches the inner workings of microbial communities.

The central purpose of Microbiome is to unite investigators conducting research on microbial communities in environmental, agricultural, and biomedical arenas. Topics broadly addressing the study of microbial communities, such as, meta-genomics surveys, bioinformatics, other '-omics' approaches and surveys, and community/host interaction mathematical modeling will be covered.

The new issue of Microbiome features several innovative research papers from scientists at various institutions worldwide. For example, a team from the University of Guelph in Canada, summarized their novel stool substitute transplant therapy research. The team treated two patients with Clostridium difficile using a bacterial strain cocktail in an attempt to alleviate this difficult infection of the lower GI tract. Other innovative genomic research approaches are also featured in the first issue.

The journal includes a new section, "Microbiome Announcements," that will contain short reports describing microbiome datasets and their associated clinical or environmental data.

Jacques Ravel, is a professor of microbiology and immunology and associate director for genomics at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine. IGS scientists have pioneered studies in microbiome research and are continuing to be at the forefront of the human microbiome project. Eric Wommack, is a professor of environmental microbiology in the Departments of Plant and Soil Sciences, Biological Sciences, and the College of Earth, Ocean, and Environment at the University of Delaware.

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Genome scientists launch Microbiome journal

New sequencing data challenges prior thinking that sponges were the most ancient animals in evolutionary history

By Amy Maxmen and Nature magazine

The ancestors of comb jellies such as Mnemiopsis leidyi may be the earliest creatures in the animal kingdom. Image: William Browne/Univ. of Miami

Animals evolved gradually, from the lowly sponge to the menagerie of tentacled, winged and brainy creatures that inhabit Earth today. This idea makes such intuitive sense that biologists are now stunned by genome-sequencing data suggesting that the sponges were preceded by complex marine predators called comb jellies.

Although they are gelatinous like jellyfish, comb jellies form their own phylum, known as ctenophores. Trees of life typically root the comb jellies' lineage between the group containing jellyfish and sea anemones and the one containing animals with heads and rears which include slugs, flies and humans. Comb jellies paddle through the sea with iridescent cilia and snare prey with sticky tentacles. They are much more complex than sponges they have nerves, muscles, tissue layers and light sensors, all of which the sponges lack.

Its just wild to imagine that comb jellies evolved before sponges, says Billie Swalla, a developmental biologist at the University of Washington in Seattle and a leading member of the team sequencing the genome of the comb jelly Pleurobrachia bachei. But the team is suggesting just that, in results they presented at the annual meeting of the Society for Integrative and Comparative Biology, held on 37 January in San Francisco, California.

Despite comb jellies' complexity, DNA sequences in the Pleurobrachia genome place them at the base of the animal tree of life, announced Swalla's colleague Leonid Moroz, a neurobiologist at the University of Florida in Gainesville. Another team presented results from genome sequencing for the comb jelly Mnemiopsis leidyi, and found that the phylum lands either below, or as close to the base as, sponges on the tree.

Weve always thought that predatorprey interactions and sensory adaptations evolved long after the origin of sponges, Swalla says. Now we need to imagine early life as a sponge, ctenophore and everything in between. Because millions of species have gone extinct since animals appeared some 542 million years ago, Swalla says, the ancestor of all animals might look different from modern comb jellies and sponges.

Gene families, cell-signaling networks and patterns of gene expression in comb jellies support ancient origins as well. For example, Moroz and his team found that comb jellies grow their nerves with unique sets of genes. These are aliens, Moroz jokes. He suggests that comb jellies might be descendants of Ediacaran organisms, mysterious organisms that appear in the fossil record before animals. Indeed, in 2011, paleontologists claimed that one of these 580-million-year-old fossils resembled comb jellies.

Andy Baxevanis, a comparative biologist at the US National Human Genome Research Institute in Bethesda, Maryland, and a leader on the Mnemiopsis genome project, says that comb jellies are the only animals that lack certain genes crucial to producing microRNA short RNA chains that help to regulate gene expression. Moreover, he points out, sponges and comb jellies lack other gene families that all other animals possess.

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Genome Reveals Comb Jellies' Ancient Origin

Hacking the Human Genome Using Clojure and Similarity Search - Arnoldo Jose Muller-Molina
The Genome inside each cell works like a massively parallel computer. Some proteins called Transcription Factors (TF) attach into specific regions called "promoters". This attachment starts a complex process that can have different outcomes. One of the possible outcomes is the creation of another TF that will in turn attach to some promoter(s) creating a cascade of events. TFs are like functions that have side effects, call other TFs and also can call themselves recursively. In this talk, I will describe a machine learning technique that attempts to reverse engineer the Genome. To achieve this tricky task, you need versatile tools. First of all, Clojure plays an instrumental role in the development of visualizations and data processing pipelines. Clojure makes it really easy to filter, visualize, and synthesize many gigabytes of data. In addition, similarity search is used extensively to find patterns in a huge set of possibilities. I hope to convince you here that similarity search is the next "NoSQL" and that Clojure is an ideal tool for data science projects.

By: ClojureTV

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Hacking the Human Genome Using Clojure and Similarity Search - Arnoldo Jose Muller-Molina - Video

Genome MIDI Sequencer / Animoog iPad problem
I set everything up according to all the manuals an online tutorial videos available. However, when I drew the notes into the Genome pattern the sound was 100% different from the sound that was coming from Animoog when I played directly on its keyboard (the sound is a continuous bass, and when triggered by Genome it sounded like a bass drum - short spiky sound). Plus, out of many notes that were present in the pattern only the first one was triggered, the rest were silent. After trying to find what the problem was I found out that the sound was played as it supposed to only when I would turn on the key hold button in Animoog. I am completely clueless on what it is caused by.

By: Ivan Kuptsov

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Genome MIDI Sequencer / Animoog iPad problem - Video

SCIENCEEE! - Episode 1 - Bacon: The Genome
On this brand new show David, Brett, and Andy attempt to boost your IQ with some bacon talk with Kyle Schachtschneider about his previous research project about bacon (a link to his intense but awesome research project). He mapped out porcine genome, and plans to continue to rock the world with his SCIENCEEE!! Stay tuned for future episodes of this show where we poke and prod at the world of science in order to grow, learn, and get smarts.

By: GeekifyEntertainment

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SCIENCEEE! - Episode 1 - Bacon: The Genome - Video

MENLO PARK, Calif., Jan. 8, 2013 (GLOBE NEWSWIRE) -- Pacific Biosciences of California, Inc. (PACB) provider of the PacBio(R)RS High Resolution Genetic Analyzer, and the University of California, Davis (UC Davis) today announced a partnership for the 100K Pathogen Genome Project. As part of the project, Pacific Biosciences' Single Molecule, Real-Time (SMRT(R)) technology will be used to sequence the genomes from at least 1,000 foodborne pathogen samples to completion, and to elucidate their epigenomes. These bacteria represent major illness-causing pathogens, including Salmonella, Campylobacter, E. coli, Vibrio, and Listeria.

The 100K Genome Project was founded by the U.S. Food & Drug Administration, Agilent Technologies, and the laboratory of Dr. Bart Weimer at UC Davis to create a consortium of partners from around the world that will sequence 100,000 foodborne pathogens using next-generation sequencing. This initiative addresses a significant shortage of bacterial pathogen information for use in designing molecular diagnostics, creates a resource to expand our understanding of infection mechanisms, and constructs a public repository for new insights into bacterial evolution by using large-scale genomics.

Pacific Biosciences' SMRT sequencing technology generates sequence reads an order of magnitude longer than other leading DNA sequencing technologies, thereby facilitating efficient de novo microbial genome assemblies. Long reads are critical for resolving genetic complexity in the assembly and finishing of genomes. The use of SMRT sequencing for the automated finishing of microbial genomes has been demonstrated in multiple recent publications, including for the genetic analysis of the Haitian cholera and German E. coli outbreaks.

The kinetic information acquired during SMRT sequencing can be used to elucidate the epigenome of bacteria. Epigenetic DNA base modifications, such as methylation, play an important role in the phenotypic variation, adaptability and pathogenicity of many bacteria, but they have been difficult to study due to the lack of a sequencing method to detect them. As part of the 100K Genome Project, the epigenomes of the pathogenic strains subjected to SMRT sequencing will be characterized, adding an important dataset to public database repositories.

"SMRT sequencing has been shown to be a powerful technology for the comprehensive determination of microbial genomes and epigenomes," said Dr. Jonas Korlach, Chief Scientific Officer of Pacific Biosciences. "Through the combination of long reads, high consensus accuracy, and the lack of sequencing bias to GC content or sequence contexts, SMRT sequencing harbors the necessary requirements to construct finished genomes in an unbiased, hypothesis-free manner. The ability to detect methylation as part of the sequencing process is unique to SMRT sequencing, and will provide an invaluable resource to illuminate the epigenetic components controlling bacterial pathogenicity."

"We are very pleased to utilize SMRT sequencing as part of the 100K Genome Project," said Bart Weimer, Professor and Director of the 100K Genome Project, "SMRT technology will enable production of complete genomes that will contribute great value toward databases for biological insight, new biomarker discovery, and reference genomes for food pathogen detection. A project of this scale is needed since microbial genome variations, including structural variations, the acquisition and loss of mobile elements, and phages or plasmids, are very difficult or impossible to detect without a de novo sequencing and genome assembly approach, yet they have a significant impact on food safety."

The partnership will entail the sequencing of at least 1,000 samples by the 100K consortium member labs with access to the PacBio RS instrumentation, including pipeline constructions for high-throughput pathogen sequencing, de novo genome assemblies, epigenome determination, and data curation and deposition. Pacific Biosciences will provide technical guidance and training to support these activities, and interface closely with the involved laboratories to assist in the efficient construction of these pipelines.

For more information, please visit http://100kgenome.vetmed.ucdavis.edu/index.cfm and http://www.pacb.com.

About Pacific Biosciences

Pacific Biosciences of California, Inc. (PACB) offers the PacBio(R)RS High Resolution Genetic Analyzer to help scientists solve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT(R)) technology, the company's products enable: targeted sequencing to more comprehensively characterize genetic variations; de novo genome assembly to more fully identify, annotate and decipher genomic structures; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. By providing access to information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems.

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100K Pathogen Genome Project Selects PacBio SMRT(R) DNA Sequencing to Generate High-Quality, Finished Genomes

How to Add Multiple Tracks on the UCSC Genome Browser
How to Add Multiple Tracks on the UCSC Genome Browser

By: David G

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How to Add Multiple Tracks on the UCSC Genome Browser - Video

How to Add a Custom Track onto the UCSC Genome Browser
How to Add a Custom Track onto the UCSC Genome Browser

By: David G

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How to Add a Custom Track onto the UCSC Genome Browser - Video

How to Add Minimal and Maximal breakpoints on the UCSC Genome Browser
How to Add Minimal and Maximal breakpoints on the UCSC Genome Browser

By: David G

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How to Add Minimal and Maximal breakpoints on the UCSC Genome Browser - Video

Human Genome Project
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Human Genome Project - Video