Category Archives: Genome

Research team will look at medical and social consequences

Computational Biologist Steven Brenner will be part of an ambitious effort toassess whether large-scale gene sequencing aimed at detecting disorders and conditions can and should become a routine part of newborn testing.

Brenner, a professor in the Department of Plant & Microbial Biology at UC Berkeley, is part of a UC San Francisco team granted $6 million by the National Institutes of Health to identify the accuracy and feasibility of providing genetic sequencing as part of, or instead of, the current newborn screening that relies on biochemical changes in the blood. It also will assess what additional information would be useful to have at birth and the ethics and public interest in having such tests performed.

"Genome sequencing has the potential to reduce costs and improve theeffectiveness of newborn screening," Brenner said, allowing early intervention for infants and fundamental changes in the tehcnology for screening newborns.

The project has three broad goals:

The cost of genome sequencing has plummeted but the ethical and moral questions surrounding genetic testing loom large.

The first genome sequenced, about a decade ago, cost nearly $3 billion.Today scientists can sequence all of anindividual's genes for a few hundred dollars. The Brenner Lab, experts at computational biology, are at the forefront of this new area of science.

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Should genome sequencing for newborns be routine?

Sep. 9, 2013 A wide range of biologically inspired materials may now be possible by combining protein studies, materials science and RNA sequencing, according to an international team of researchers.

"Biological methods of synthesizing materials are not new," said Melik C. Demirel, professor of engineering science and mechanics, Penn State. "What is new is the application of these principles to produce unique materials."

The researchers looked at proteins because they are the building blocks of biological materials and also often control sequencing, growth and self-assembly. RNA produced from the DNA in the cells is the template for biological proteins. Materials science practices allow researchers to characterize all aspects of how a material functions. Combining these three approaches allows rapid characterization of natural materials and the translation of their molecular designs into useable, unique materials.

"One problem with finding suitable biomimetic materials is that most of the genomes of model organisms have not yet been sequenced," said Demirel who is also a member of the Materials Research Institute and Huck Institutes of Life Sciences, Penn State. "Also, the proteins that characterize these materials are notoriously difficult to solubilize and characterize."

The team, lead by Ali Miserez, assistant professor, School of Materials Science and Engineering, Nanyang Technological University, Singapore, looked at mollusk-derived tissues that had a wide range of high-performance properties including self-healing elastomeric membranes and protein-based polymers. They combined a variety of approaches including protein sequencing, amino acid composition and a complete RNA reference database for mass spectrometry analysis. They present their results in a recent issue of Nature Biotechnology.

The researchers looked at three model systems. The protein containing egg case membranes of a tropical marine snail are intriguing because they have unusual shock-absorbing qualities and elasticity. Investigation using the variety of methods showed this material has a coiled structure with crosslinking that absorbs energy. This information can be applied to biomimetic engineering of robust yet permeable coiled, protein-based membranes with precisely tailored mechanical properties.

The array of techniques applied toanalysis of a mussel foot showed that a species-to-species variation exists in mussel, including unusual variation in the protein. These variations suggest that protein engineering could produce a range of self-healing properties.

The final model used jumbo squid sucker ring teeth (SRT), grappling-hook-like structures used for predatory attacks. Analysis of the squid teeth showed nanotubular structure and strong polymers. While there was some similarity to silk and oyster shell matrix proteins, the protein was novel and the researchers named it Suckerin-39. Further analysis showed that Suckerin-39's structure allowed it to be reprocessed into a variety of shapes.

"While some biological materials have interesting properties, they cannot be reshaped or remolded because they do not soften upon heating," said Demirel. "The SRT is an elastomer, which is moldable, it is a thermoplastic and can be reshaped."

The materials properties of SRT do not change after heating and reshaping.

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Genome of elastomeric materials creates novel materials

Genome Liberty - Which medications do not work with your DNA
Dr. Barken is introducing Genome Liberty start up company which is founded on the principle that the DNA is a gateway to personalized, more accurate medicine...

By: DrBarken

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Genome Liberty - Which medications do not work with your DNA - Video

By studying the interactions between our bodies and our microbes, a startup hopes to find new ways of treating disease.

The trillions of microbes that live in our bodies play an important role in our health and disease, but researchers have found that understanding this diverse and complex stew of bugs is daunting.

One company, Second Genome, has turned to DNA analysis and biochemical studies of mixtures of microbes and human cells in culture to better explain things. The company ultimately wants to identify therapeutics that restore balance to an off-kilter community by changing its composition or its effects on the human body.

The diversity of the human collection of microbial residentsknown as the microbiomebecame more clear last year when the Human Microbiome Project described the diversity and abundance of microbes living in and on the human body (see Researchers Catalog Your Microbial Zoo). For every one human cell in the body, there are an estimated 10 microbial cells. Changes in this microbial zoo have been correlated with many health problems: from gastrointestinal disease to diabetes, obesity, and inflammation.

The microbes that live with us have a lot of impact on our health, positive as well as negative, says Gary Andersen, a microbiologist at Lawrence Berkeley National Laboratory and a cofounder of Second Genome. But its been hard figuring out within an individual person what is a positive microbiome or community of organisms, he says. Thats because from person to person, the structure of the communities varies greatly, he says.

One reason it has been difficult to profile an individuals microbiome is that most of these organisms cant grow in pure cultures of a single species. So Second Genome uses DNA sequencing along with another DNA analysis technology developed by Andersen to identify community members and to look at gene activity in both the bugs and the human body. We are really focused on the interaction between the microbiome and the host, says Second Genome CEO Peter DiLaura. The community of bacteria in our guts interacts with receptors and other targets in our body, he says: When we think about therapeutics, its about impacting the interaction that is beneficial for disease.

After DNA analysis, the company studies the interplay between microbe communities and human cells grown in culture. The next step would be to study the interactions in lab animal models of diseases. The hope is to develop a detailed understanding of how the microbiome affects human physiology, down to the molecular level.

The company is investigating the microbiomes effect on inflammatory and metabolic disorders, including type 2 diabetes. We have focused on places where there is reasonable evidence that the microbiome is playing a causal role, says DiLaura.

In June, pharmaceutical and consumer-product company Johnson & Johnson invested an undisclosed amount in Second Genome. In return, Second Genome will search for potential drug targets to treat ulcerative colitis. Robert Urban, the director of J&Js Boston Innovation Center, says his company is committed to the microbiome idea. Last week, Vedanta Biosciences, a microbiome startup also looking to microbial functions for drug discovery, announced a partnership with J&J.

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Startup Second Genome examines the body’s microbes to find ways to treat diseases

Taxonomic coverage

We collected new genome-wide sequence data from four bat species, selected from the two suborders and encompassing the paraphyly of echolocating bat lineages (see ref. 13). From the suborder Yinpterochiroptera we studied the non-echolocating Old World fruit bat Eidolon helvum (family Pteropodidae) and two laryngeal echolocating species, Megaderma lyra (Megadermatidae) and Rhinolophus ferrumequinum (Rhinolophidae). From the suborder Yangochiroptera we studied the laryngeal echolocating species Pteronotus parnellii (Mormoopidae) that has independently evolved constant frequency echolocation.

From Ensembl (http://www.ensembl.org/), we also obtained sequence data from two additional batsthe laryngeal echolocating species Myotis lucifugus (Yangochiroptera; Broad Institute) and the non-echolocating Old World fruit bat Pteropus vampyrus (Yinpterochiroptera; Baylor College of Medicine Human Genome Sequencing Center)as well as the echolocating bottlenose dolphin Tursiops truncatus. Genomic sequences from 15 additional mammal species were downloaded from Ensembl giving a total of 22 mammals (listed in Supplementary Table 1).

To investigate the prevalence of convergent evolution at a genome-wide level associated with the independent evolution of echolocation in bats and cetaceans, we used a method that builds on maximum-likelihood phylogenetic reconstruction. This method compares, for a given sequence alignment of orthologous coding sequences (CDS), the goodness-of-fit of the accepted phylogenetic tree with that of an alternative convergent hypothesis (in this case, in which echolocating taxa were forced into a spurious monophyletic clade). From our data set, we identified and tested three hypotheses: (1) H0, the commonly accepted species phylogeny (for example, refs 13, 23, 24, 25) in which cetaceans (represented in our data set by the common bottlenose dolphin Tursiops truncatus) are nested within the even-toed ungulates in the order Cetartiodactyla, and the order Chiroptera is split into the suborders Yangochiroptera and Yinpterochiroptera, with paraphyly of bat laryngeal echolocation13; (2) H1, or batbat echolocation convergence (monophyly of all echolocating bats in the data set); and (3) H2, or batdolphin convergence (monophyly of all echolocating mammals in the data set). All three phylogenetic hypotheses are shown in Fig. 1. The scale bar (in amino acid substitutions) is provided for approximate reference only, as branch lengths were optimized at runtime.

Because the H2 (batdolphin) hypothesis is necessarily a radical rearrangement of the commonly accepted species topology, and the concept of an exact branching order or the true topology does not apply in this case, we proposed a number of separate but related versions of this hypothesis, all of which were evaluated equally in the analysis. In each case the rest of the mammalian species phylogeny was fixed, as in the H1 hypothesis. In the first case we constrained all five echolocating taxa to a single ancestral node (hard polytomy); second we enumerated the seven bifurcating trees that are possible where the position of T. truncatus is free to vary, but the suborders of echolocating batsYangochiroptera (P. parnellii and M. lucifugus) and Yinpterochiroptera (R. ferrumequinum and M. lyra)were preserved. A final topology was specified as a soft polytomy, with the resolution of the clade of echolocators being resolved by RAxML at runtime, with the rest of the phylogeny remaining constrained. A majority clade-consensus (MCC) summary phylogeny was constructed from these 2,326 inferred soft-polytomy H2 trees using TreeAnnotator v1.7.4 (in the BEAST v1.7.4 distribution31). This phylogeny recovered the Yangochiroptera and Yinpterochiroptera clades of echolocating bats with good (>50%) node support. When we compared the goodness-of-fit of all phylogenies (as opposed to pairwise comparison relative to the species phylogeny Ho) we found the species phylogeny was preferred at 1,170 loci (55%), with the batbat phylogeny H1 preferred next most often (548 loci; 26%). The soft-polytomy version of H2 (resolved by RAxML) was the preferred phylogeny among 50% of the remaining loci, with remaining support equally split between the other H2 versions. We therefore adopted the soft polytomy, RAxML resolved version of H2 as our main batdolphin hypothesis.

Novel sequence data from the four bat species listed above were generated by BGI on an Illumina Genome Analyzer platform (Illumina), based on genomic libraries of 500-bp insert sizes. Using this method we obtained approximately 3341Gb of short read sequence data per species.

The CLC de novo algorithm (CLC bio) was used for assembling raw reads into contigs using different k-mer size values ranging from 32 to 50. The assembled contigs from the CLC output were then processed using the module Prepare of the SOAP package to do scaffold assembly using the scaff command of SOAPdenovo. Finally, gaps were filled using the GapCloser32 tool. The resulting assemblies consisted of between 210,080 and 315,526 genomic sequences (depending on species), with an average depth of coverage of 17 to 18. Estimated genome size was approximately ~2Gb in all four bats, whereas contiguity (as assessed by the N50 statistic) ranged from 16,292bp (M. lyra genomic sequences) to 27,140bp (E. helvum). Homology-based gene prediction analyses using the genBlastG33 tool recovered 20,424 gene models for R. ferrumequinum, 20,043 for M. lyra, 20,455 for E. helvum and 20,357 for P. parnellii, in line with published gene content values for other mammals34. The completeness/contiguity of the gene representation was evaluated using the CEGMA (Core Eukaryotic Genes Mapping Approach) pipeline35, 36 and found ranging across species between 61.29% to 77.02% and 90.32% to 96.77% for complete and partial genes, respectively. These compared well to the published M. lucifugus genome; when we analysed that genome using CEGMA the comparable completeness/contiguity scores for complete and partial genes were in the middle of this range (62.9% and 91.5%, respectively).

To identify genes adequate for systematic phylogenetic-based analyses of convergent sequence evolution, we next filtered the above predictions for single-copy orthologous protein-coding genes conserved across the Eutheria. This was achieved by performing reciprocal blast searches against a database consisting of the gene models for the four bats, and using as queries the human sequences of 11,185 genes reported as 1-to-1 or apparent 1-to-1 orthologues between the human and Myotis genomes in Ensembl databases (http://www.ensembl.org/, release 63). In total we determined 7,612 1-to-1 orthologous genes, from which the longest coding sequences (CDSs) were then retrieved from Ensembl for the 18 additional mammalian genomes (Supplementary Table 1).

Coding gene sequences (CDS) of individual loci were built and aligned as codons using a modified version of transAlign37 incorporating MAFFT38, such that all sequences remained in the correct reading frame. Any ambiguously aligned sites, and codons with excessive numbers of gaps, were removed from each gene alignment using Gblocks39 under the following options: t = c b1 = $b1 b2 = $b1 b3 = 1 b4 = 6 b5 = h, where b1 = 70% of the sequences sampled in the data set.

In order to avoid potential biases due to either sequencing or assembly errors, for all phylogenetic and molecular evolution analyses, we chose to focus on only a subset of the identified genes. Specifically, we restricted our downstream analyses on data sets, which after filtering out of ambiguous sites showed no missing data in any of the sampled bats. The exception to this rule was P. vampyrus, which, because of its comparatively lower genome coverage, was missing in around 2% of CDS alignments. All final CDS alignments used in our analyses were characterized by a minimum length of 450bp (or 150 codons/amino acids) and included a minimum of six bat species, the dolphin Tursiops truncatus and the additional following mammals as outgroups: Canis familiaris, Equus caballus, Bos taurus, Mus musculus and Homo sapiens. Of the 2,326 loci examined, 642 were also included in the analysis of ref. 20.

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Genome-wide signatures of convergent evolution in echolocating mammals

1000 Subs Kit Update - Genome and Foxhound - Marsoc and Force Recon
The second video in our 1000 subs kit updates. Still more content to come.

By: IllestAirsoft

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1000 Subs Kit Update - Genome and Foxhound - Marsoc and Force Recon - Video

Hatsune Miku--Orange Genome - Vocaloid
Hatsune Miku--Daidai Genome - Vocaloid [????] ???? [?????]

By: Tiranodragon X

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Hatsune Miku--Orange Genome - Vocaloid - Video

9am, Tuesday 3 September

Release of a High Density SNP Genotyping Chip for the Sheep Genome

An international team has developed a powerful new tool that can be used to test a sheeps genetics and predict its productivity and meat quality.

FarmIQ in conjunction with Illumina and the International Sheep Genomics Consortium (ISGC) are today announcing completion of the Ovine Infinium HD SNP BeadChip.

This new chip is capable of identifying up to 600,000 points across the sheep genome (otherwise known as single nucleotide polymorphisms or SNPs). It is one of the first high-density chips developed for sheep and follows the release in January 2009 of the OvineSNP50 BeadChip, which can identify over 50,000 points.

FarmIQ commissioned the HD Chip as part of its mission to add value to red meat by improving linkages between animals meat yield and quality, and what happens on the farm and in the processing plant.

During testing since May, the HD Chip has been used to test 5000 animals from a range of breeds and has proved very accurate and robust, says John McEwan of AgResearch, who led the chip design work with Rudi Brauning.

Development of the HD Chip started with sequencing of the whole genome (gene map) for 75 individual sheep by Kim Worley and Richard Gibbss team at the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). DNA samples and measurements were also taken from 12,000 New Zealand lamb carcasses. The sheep tested represent a broad range of breeds.

Teams at AgResearch, BCM-HGSC, the Department of Primary Industries Victoria, USDA and CSIRO then collaborated to finalise the identification of more than 20 million sheep gene sequence variants.

John McEwan says the new HD chip is more than an expanded version of the OvineSNP50 chip and it will dramatically increase the power to identify key genes. The HD chip includes 53,000 of the DNA variants that are known to affect proteins and therefore determine the animals measurable traits.

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High Density SNP Genotyping Chip for the Sheep Genome

Public release date: 4-Sep-2013 [ | E-mail | Share ]

Contact: Kay Branz kbranz@benaroyaresearch.org 206-342-6903 Immune Tolerance Network

SeattleSep. 4, 2013

The National Institutes of Health (NIH) awarded Benaroya Research Institute at Virginia Mason (BRI) a $1.9 million grant to find marks in the human genome which can explain why some white blood cells cause damage to the spinal cord and brain in multiple sclerosis (MS). This is the first study to look for molecular changes in the genome of specific immune cells responsible for the devastation caused by MS. The broad-based study will determine the function of these cells, how they are generated and how they can be regulated in system models of MS and in humans.

"We want to understand the factors that make these cells target the spinal cord and brain to cause disease," says Estelle Bettelli, PhD, BRI Assistant Member and co-principal investigator of the study. Dr. Bettelli and other scientists have identified different types of T cells which they believe are potent inducers of MS and other autoimmune diseases. She has also developed system models to study different forms of multiple sclerosis.

"With Dr. Bettelli's research advances and with the new technological innovations in genome research, we can look at specific marks present in the genome of these cells and understand how they are generated and how they can be controlled," says co-principal investigator Steven Ziegler, PhD, Director of the BRI Immunology Research Program. Dr. Ziegler has used whole genome studies to investigate these cell types in healthy individuals. "We can then see how the genomic marks affect the cells in model systems of MS and how they operate in humans cells with and without the disease. We can also see how these cells behave once the patient receives treatment and if various treatments make the cells act differently."

"It is important to know how and when these cells are formed in the body to determine how to inhibit their harmful function," says Dr. Bettelli. "It is becoming clear that MS is not a unique disease entity but can present itself in different clinical forms and variants. Several factors, including the cell types involved, are believed to dictate the clinical progression of MS. The understanding of how and which cell populations of the immune system participate in the autoimmune attack is very important for determining current treatments and designing new therapeutics tailored to the different forms of MS. We hope to find ways to significantly inhibit these dangerous cells with new targeted medicines with fewer side effects.

"This work highlights a key mechanism for understanding and modifying the immune cells that cause autoimmune diseases like MS," says BRI Director Gerald Nepom, MD, PhD. "It is an exciting example of the power of merging new genomic technologies with state-of-the-art immunology research to address a major clinical need."

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Other scientists collaborating in this effort are Jane Buckner, MD, BRI Associate Director, Damien Chaussabel, PhD, BRI Director of Systems Immunology, Mariko Kita, MD, BRI Affiliate Investigator and Director of the Virginia Mason Multiple Sclerosis Center, and John Stamatoyannopoulos, MD, Associate Professor of Genome Sciences and Medicine, University of Washington.

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First study to investigate the human genome in multiple sclerosis

Public release date: 3-Sep-2013 [ | E-mail | Share ]

Contact: Benjamin Thompson b.thompson@sgm.ac.uk 44-758-468-9611 Society for General Microbiology

The use of whole bacterial genome sequencing will allow scientists to inexpensively track how bovine tuberculosis (TB) is transmitted from farm to farm, according to research presented this week at the Society of General Microbiology Autumn Conference.

Bovine TB is primarily a disease of cattle, caused by the bacterium Mycobacterium bovis. The disease is hugely expensive, costing the Government over 91 million in England in 2010/11.

Researchers from the University of Glasgow, working in collaboration with the Agri-Food and Biosciences Institute and the Department of Agriculture and Rural Development, Northern Ireland, sequenced the genomes of 147 M. bovis samples, collected over a decade of outbreaks in Northern Ireland. By combining the genomic sequences of the bacteria with information about when and where the sample was isolated, in addition to data on the movement of cattle from farm to farm, the researchers were able to build a detailed forensic map of bovine TB spread.

The results showed that, even on a scale of few kilometres, M. bovis samples from neighbouring farms were more closely genetically related than geographically distant farms that had had cattle moved between them. This finding confirms that, while long distance spread via cattle movements plays a role, local transmission mechanisms appear to drive the spread of the disease, although the researchers are unable to determine what these are at the present time.

Hannah Trewby, who is presenting this work says, "The inclusion of whole genome information in our data will give us unprecedented insight into how bovine TB spreads, and will help us to develop better control methods for the disease."

The role of infected wild badgers in spreading bovine TB remains controversial. This work will help to clarify the role that badgers may have in spreading the disease and continue to build a sound scientific evidence base on which control measures can be built.

Professor Rowland Kao, the Principle Investigator of the project, explains, "Our results suggests that the establishment and local persistence of the pathogen in cattle has a distinct spatial signature -- we believe that explaining this signature is the key to quantifying the role that badgers play in the persistence of bovine TB in Britain and Ireland. While we do not yet have sufficient data to be definitive, it is clear that whole genome sequencing of the bacterium will play an important part in solving this puzzle. Given the extensive collection of samples already collected from cattle and badgers, we are optimistic that this approach will help accumulating the right scientific evidence over the coming years to tackle this important problem."

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Whole genome sequencing provides researchers with a better understanding of bovine TB outbreaks