Using the Acropora digitifera genome to understand coral responses to environmental change.
Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T, Fujiyama A, Miller DJ, Satoh N.
Nature. 2011 Jul 24. doi: 10.1038/nature10249. [Epub ahead of print]
Despite the enormous ecological and economic importance of coral reefs, the keystone organisms in their establishment, the scleractinian corals, increasingly face a range of anthropogenic challenges including ocean acidification and seawater temperature rise. To understand better the molecular mechanisms underlying coral biology, here we decoded the approximately 420-megabase genome of Acropora digitifera using next-generation sequencing technology. This genome contains approximately 23,700 gene models. Molecular phylogenetics indicate that the coral and the sea anemone Nematostella vectensis diverged approximately 500 million years ago, considerably earlier than the time over which modern corals are represented in the fossil record (∼240 million years ago). Despite the long evolutionary history of the endosymbiosis, no evidence was found for horizontal transfer of genes from symbiont to host. However, unlike several other corals, Acropora seems to lack an enzyme essential for cysteine biosynthesis, implying dependency of this coral on its symbionts for this amino acid. Corals inhabit environments where they are frequently exposed to high levels of solar radiation, and analysis of the Acropora genome data indicates that the coral host can independently carry out de novo synthesis of mycosporine-like amino acids, which are potent ultraviolet-protective compounds. In addition, the coral innate immunity repertoire is notably more complex than that of the sea anemone, indicating that some of these genes may have roles in symbiosis or coloniality. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. The coral genome provides a platform for understanding the molecular basis of symbiosis and responses to environmental changes.
PLoS and Mendeley, the popular reference manager and academic social network, have teamed up to create a Binary Battle contest to build the best apps that make science more open using PLoS and/or Mendeley’s APIs (Application Programming Interface). There’s $16,000 in prize money to be won plus other cool gifts and the opportunity to get your entries in front of a panel of influential judges from technology, media and science that include:
We have two APIs for you to mine in this competition. The PLoS Search API allows anyone to build their own applications for the web, desktop or mobile devices using PLoS content. The Mendeley API opens up a database of over 80 million research papers, usage statistics, reader demographics, social tags, and related research recommendations. Since Mendeley got this competition up and running before PLoS joined the party, you can see what some people have already made using their API. It’s also worth knowing that Mendeley are organizing two simultaneous Hackathons at their NY and London offices on Saturday June 11-Sunday June 12, 2011.
Here’s the lowdown on the amazing prizes:
Entries will be judged on criteria such as: activity; popularity/usefulness; whether it increases collaboration and/or transparency and how cool is it (does it make our jaws drop!). Please note, we can not accept entries from PLoS or Mendeley staff or their immediate families, their investors or board members. To get started, developers need to get a key from PLoS, Mendeley or both. Don’t forget, the last day to submit your app is September 30th 2011.
JP Morgan Buys Into FPGA Supercomputing
One of the largest financial institutions in the world is using FPGA-based supercomputing for analyzing some of its largest and most complex credit derivative portfolios. JP Morgan, along with Maxeler Technologies, has built and deployed a state-of-the art HPC system capable of number-crunching the company's collateralized debt obligation (CDO) portfolio in near real-time. Read More...
The Next Step in Human Brain Simulation
Can the human brain devise a system capable of understanding itself? That's been something brain simulation researchers have been working toward for nearly a decade. With recent advances in supercomputing capabilities and modeling techniques, the question may soon be answered. Read More...
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NEW YORK (GenomeWeb News) – Individuals with sporadic schizophrenia tend to carry more new, potentially deleterious, genetic changes than individuals in the general population, according to an exome sequencing study of schizophrenia-affected families that appeared online in Nature Genetics yesterday.
"The occurrence of de novo mutations, as observed in this study, may in part explain the high worldwide incidence of schizophrenia," co-senior author Guy Rouleau, a researcher at the University of Montreal and director of its CHU Sainte-Justine Research Center, said in a statement.
A bioinformatics startup is giving users a free taste of its wares in hopes of eventually realizing commercial success.
The company, Sequilab, recently launched a free web portal of the same name that offers access to publicly available online bioinformatics tools for sequence analysis, as well as social-networking capabilities to improve collaborations between research groups.
Access is currently free for all users, but the Sequilab team is considering ways to "monetize" the website, including a premium version of the software that would include advanced features, as well as an ad-supported model, CEO Dan Melvin told BioInform.
"What we are trying to do is build the community now and then when it reaches a specific size of user base, that's when we would [go] commercial," Melvin said.
: Next generation sequencing (NGS) is widely used in metagenomic and transcriptomic analyses in biodiversity. The ease of data generation provided by NGS platforms has allowed researchers to perform these analyses on their particular study systems. In particular the 454 platform has become the preferred choice for PCR amplicon based biodiversity surveys because it generates the longest sequence reads. Nevertheless, the handling and organization of massive amounts of sequencing data poses a major problem for the research community, particularly when multiple researchers are involved in data acquisition and analysis. An integrated and user-friendly tool, which performs quality control, read trimming, PCR primer removal, and data organization is desperately needed, therefore, to make data interpretation fast and manageable. We developed CANGS DB (Cleaning and Analyzing Next Generation Sequences DataBase) a flexible, stand alone and user-friendly integrated database tool. CANGS DB is specifically designed to organize and manage the massive amount of sequencing data arising from various NGS projects. CANGS DB also provides an intuitive user interface for sequence trimming and quality control, taxonomy analysis and rarefaction analysis. Our database tool can be easily adapted to handle multiple sequencing projects in parallel with different sample information, amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians. Furthermore, CANGS DB is especially suited for projects where multiple users need to access the data. CANGS DB is available at http://code.google.com/p/cangsdb/. CANGS DB provides a simple and user-friendly solution to process, store and analyze 454 sequencing data. Being a local database that is accessible through a user-friendly interface, CANGS DB provides the perfect tool for collaborative amplicon based biodiversity surveys without requiring prior bioinformatics skills. PMID: 21718534 [PubMed -as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/21718534
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Abstract
Linear amplification for deep sequencing (LADS) is an amplification method that produces representative libraries for Illumina next-generation sequencing within 2 d. The method relies on attaching two different sequencing adapters to blunt-end repaired and A-tailed DNA fragments, wherein one of the adapters is extended with the sequence for the T7 RNA polymerase promoter. Ligated and size-selected DNA fragments are transcribed in vitro with high RNA yields. Subsequent cDNA synthesis is initiated from a primer complementary to the first adapter, ensuring that the library will only contain full-length fragments with two distinct adapters. Contrary to the severely biased representation of AT-or GC-rich fragments in standard PCR-amplified libraries, the sequence coverage in T7-amplified libraries is indistinguishable from that of nonamplified libraries. Moreover, in contrast to amplification-free methods, LADS can generate sequencing libraries from a few nanograms of DNA, which is essential for all applications in which the starting material is limited.
http://www.ncbi.nlm.nih.gov/pubmed/21720315
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