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 The Genomic Sciences Laboratory (GSL) was established in 2008 by the College of Agriculture and Life Sciences at North Carolina State University to provide researchers and students with the necessary infrastructure and equipment to conduct genomic, proteomic and metabolomics research at NC State University.
Formed from the merger of the Genome Research Laboratory (GRL) and the Metabolomics & Proteomics Laboratory (MPL), the lab provides the NCSU community with high-throughput DNA sequencing and fingerprinting, equipment to perform functional genomic assays, protein identification and characterization as well as metabolomics, biochemical profiling and target compound analyses.
The GSL is committed to an expanded portfolio of capabilities. And, the lab is committed to positioning the NCSU community at the forefront of genomic sciences. 
Read more about some recent GSL projects: Nucleotide polymorphisms  Meloidogyne spp. (root-knot nematodes) are one of the most damaging pathogens on crop species worldwide. Nearly every agricultural commodity is susceptible to root-knot nematodes (RKN), but each species of RKN and sometimes isolates of a single species differ in the plant hosts that it can infect. In order to identify factors that contribute to plant host range, Dr. Jennifer Schaff (GSL, NC State) in collaboration with Dr. Valerie Williamson (Dept. of Nematology, UC Davis) have taken advantage of the recently completed RKN genomic sequence (released by Professors Charles Opperman and David Bird, NC State) and the genetic map (produced by Dr. Williamson’s lab) of Meloidogyne hapla to look for single nucleotide polymorphisms between M. hapla lines that differ in their ability to infect a wild potato.
 One run on the 454 FLX system yielded 125 MB of data, 503,980 reads of 250 bases average length which resulted in an approximate 2.3x coverage of M. hapla. Over 99% of these reads mapped to the genomic reference sequence, and we discovered over 57,000 potential polymorphisms between isolates of M. hapla that were used to produce the mapping population, over 21,000 of those are potential SNPs. We are currently in the process of verifying these polymorphisms.
Aspergillus speciation and aspergillosis diagnosis  Our very own Norm Glassbrook, working with Dr. Gary Payne (Center for Integrated Fungal Research, Dept of Plant Pathology) has been studying low molecular weight biochemical profiles and protein profiles from a cross section of Aspergillus and other fungal species.
 Amongst his project aims has been the detection and speciation of Aspergillus field isolates and clinical speciation of infections from aspergillosis sufferers. As things stand, his approaches rapidly lead to the identification of over 500 proteins from Aspergillus, and their sequence identities definitively identify the Aspergillus species.
He has also undertaken protein profiling to identify secreted proteins that may be involved in the host-pathogen interaction between Aspergillus flavus and maize. These analytical methodologies developed for the study have been successfully used in the GSL for the analysis of protein from a wide range of organisms - bacteria, fungi, plants, nematodes, insects and fish - for other researchers on the NC State campus. Norm's work forms part of his PhD dissertation which he defends in December, in Wales (of all places). Update: That'd be Dr Norm.
T4-related Phage Genomes  Bacterial viruses (bacteriophages) are the most abundant biological entities on earth, with an estimated number of more than 1030. Although the genomic sequence diversity of phages is significant, only relatively few complete genomes are deposited in public databases.
 Dr. Eric Miller (CALS Department of Microbiology) working with staff members Dr.Jenn Schaff and Megan Ulmer recently set about the task of simultaneously sequencing 16 isolated, but poorly characterized, T4-type phages (isolates that infect E. coli, Acinetobacter, Aeromonas, and Vibrio) at the GSL.
Collaborators Jim Karam (Tulane Medical Center), Jim Nolan (Georgia Gwinnett College) and Miller provided phage genomic DNA for processing. Separate phage DNA libraries were prepared and sequenced on a single Roche LR70 plate using a gasket system that divides the plate into 16 tracks. While the biggest challenge was template sizing for some of the more “testy” phage genomes, complete dsDNA genome sequences, which range in size from 87 kbp to 247 kbp, were obtained at 15 to 20-fold coverage. Most were completely closed, while others were resolved to just a few large contigs.  At about $1,000 per genome, with advances likely to drop the price, comparative genomics of phages can ensue at a cost that is within reach of most research labs and most university teaching programs. The phage sequences will be annotated and deposited at GenBank and at the Phage Genome Browser.
Comparative genomics indeed, with a capital “C”.
The Magnaporthe grisea secretome  Magnaporthe grisea is a pathogenic fungus that causes rice blast disease worldwide. We have recently been working with Dr Ralph Dean (Center for Integrated Fungal Research, Dept of Plant Pathology) in an attempt to characterize the secreted proteome during appressorium formation. One of the major goals of CIFR is to perform a comprehensive molecular dissection of the mechanisms regulating early events of the host-pathogen recognition process, including the induction of a specialized infection cell, the appressorium, as well as host response genes.
Proteins secreted by the fungus are probable candidates for being effectors that are potentially recognized by determinants of resistance or susceptibility in host plants. To date, we have identified around 70 secreted proteins. Dr Dean's Website
Pasteuria penetrans  Pasteuria penetrans is an endospore producing, Gram-positive bacterium that is an obligate parasite of root-knot nematodes (Meloidogyne spp.), which are themselves obligate parasites of plants. This bacterium has been associated with nematode-suppressing soils and also shown to have tremendous potential for the biological control of root-knot nematodes. However, the fastidious nature of the organism and the lack of ability to perform forward genetic experiments have hindered progress on the culturing, host range expansion and mass production techniques....that is until now!
 Working with Dr Charlie Opperman (Plant Pathology; Center for the Biology of Nematode Parasitism) and Dr Keith Davies (Rothamsted Research, United Kingdom), we have obtained a draft genome sequence of this organism. This, along with the recently completed Meloidogyne hapla genome, allows us to conduct experiments investigating global gene expression, proteomics and metabolomics of this parasitic interaction.
Our findings are to be presented at the 5th International Congress on Nematology in Brisbane in July.
Center for the Biology of Nematode Parasitism Website. Dr Davies' Website.
(GxE) interactions  Dr Laura Reed, working with Dr Greg Gibson (former William Neal Reynolds Distinguished Professor of Genetics at NCSU), has spent the last few months undertaking a metabolomics study in the GSL.
Laura has been developing Drosophila as a model system for the high-throughput study of complex metabolic disease resulting from genotype by environment (GxE) interactions. The focus of her work is 'Metabolic Syndrome', a constellation of energy metabolism linked symptoms, which has a very high prevalence in developed countries, and is thought to arise as a result of environment (diet) interacting with genotype. Dr. Gibson's Website.
Tick gene expression  Kevin Donohue, of Dr Michael Roe's group (Entomology) is studying gene expression in the tick synganglion throughout reproduction and development.
They had planned to sequence approximately 20,000 ESTs by Sanger methods, an approach that would have taken several months and $70,000. Using the GSL's GS FLX, we generated over 113 megabases of sequence from 532,000 reads at a total cost of only $14,000. This represents 6 fold more data than was originally envisaged. Kevin presented his results to the 6th International Conference on Ticks and Tick Borne Pathogens in Buenos Aires in September, and successfully defended his PhD October. Congrats! Dr Roe's home page
"JOB5" Sequenced  In collaboration with Dr Michael Hyman (Microbiology), we have obtained a full genome sequence of organism "JOB5".
Coverage to 23X was obtained with one and a half plates of long reads on the Roche GS FLX at a total cost of around $14,000. This organism is the first to be entirely sequenced on the NCSU campus. We are currently using this genomic information to empower proteomic studies of this organism, specifically the expression levels of proteins in the presence of different substrates. Dr Hyman intends to obtain full genome sequences for another two microorganisms this year. Update - May 2008: S1B1 draft sequence obtained. Update - October 2008: G2B2 and ELW1 draft sequences obtained. Dr Hyman's home page
Join the GSL Community Membership has its advantages. To facilitate access to the expanded scope of our laboratory, we have developed this dual-purpose web portal.
Members and guests will find a dynamic source of information relevant to the genomic sciences. Our registered partners will have access to one-stop plate submissions, an equipment sign-up calendar, secure discussion forums, and the ability to add resource links and news.
Whilst membership is open primarily to the North Carolina State University research community, other partners and collaborators will be considered on an individual basis by the GSL Director.
GSL featured in: nature | methods ; and, GS FLX is "Method of the Year "
Nature Methods - 5, 11 - 14 (2008) The year of sequencing In 2007, the next-generation sequencing technologies have come into their own with an impressive array of successful applications. In the toxicology building of North Carolina State University in Raleigh, Nigel Deighton, head of a small genome research facility, and a few others unpack the facility's first next-generation sequencing machine, a 454 GS FLX, on loan from Roche Diagnostics for three months. They train for a few days, nebulize a colleague's bacterial DNA and PCR-amplify "the living daylights out of it," Deighton recalls. They load the bead-bound PCR products onto a plate with holes that are not visible to the naked eye, pop the plate into the machine and close the drawbridge-like door...
The next day, Deighton scrolls through graphs from the newly sequenced bacterial genomes. On its first test run, the GS FLX gave sixfold coverage of each genome, with read lengths of around 250 bases. "That's not bad, for the first go," Deighton says... READ THE ENTIRE ARTICLE
 ...there is exciting, important, impact-making work being done at the College of Agriculture and Life Sciences. When it comes to innovation and change, for the College the future is now.
Johnny Wynne, Dean, CALS
The GSL is located on Centennial Campus.
North Carolina State University's Centennial Campus is a research and advanced technology community where university, industry and government partners interact in multidisciplinary programs directed toward the solution of contemporary problems.In this "knowledge enterprise zone," clusters of activity break down traditional, artificial barriers to create, integrate, and apply advancements in knowledge. The resulting synergy leads to: - technological innovation and transfer;
- real-world teaching and learning;
- sound business investment; and,
- greater quality of life for North Carolina and beyond.
The unique master plan for this environmentally sensitive, mixed-use, academic village responds to the professional, educational and recreational needs of the University's faculty, staff and student body, as well as those of corporate and government affiliates whose presence on Centennial Campus adds to its vigor and effectiveness. Centennial Campus is providing a new dimension of excellence for the 21st century in the performance of North Carolina State University's land-grant mission of teaching, research and service to the people of North Carolina.
Centennial Campus named "Research Science Park of the Year" North Carolina State University's Centennial Campus has been named the top Research Science Park of the Year. The Association of University Research Parks (AURP) made the announcement at its annual awards luncheon.
"NC State is about unique partnerships – creating student opportunities, research and economic development," said Chancellor James Oblinger. "Centennial Campus epitomizes the work of NC State. It's no surprise that Centennial Campus has become a national model for university research parks." Located on a 1,334-acre site adjacent to NC State's main campus, Centennial Campus houses more than 130 companies, government agencies, and NC State research and academic units advancing technologies ranging from semiconductors to genomics tools. More than 1,600 corporate and government employees work alongside a thousand-plus faculty, staff, post-docs, and students. Major partners include ABB, Red Hat, the Iams Company, Ericsson IPI, the U.S. Department of Agriculture, GlaxoSmithKline, MeadWestVaco and Talecris Biotherapeutics.  These partnerships allow corporate and government entities to tap into NC State's strengths in cutting-edge research and client-driven training programs across multidisciplinary fields such as information and communications technologies, bioscience and biotechnology, advanced materials, and education.
Centennial Campus had a record year for new businesses last year, adding 17. Centennial Campus is based on a "knowledge enterprise zone, which creates synergy leading to innovation and transfer, and improved quality of life for North Carolina and beyond," said David Winwood, associate vice chancellor for technology development and innovation at NC State. "We are honored to be the recipient of the AURP 2007 Science Research Park Award."  Centennial Campus was selected from among finalists that included bwtech@UMBC Research and Technology Park in Baltimore, and Sandia Science and Technology Park in Albuquerque, N.M. AURP cited Centennial Campus for accomplishments in innovation and technology partnership creation for economic development.
 "Congratulations to Centennial Campus on winning the Science Research Park of the Year Award," said AURP President Mike Bowman. "Centennial Campus exemplifies the new model of research science parks, in which strategically planned mixed-use campus expansions create innovation, partnerships, and a high quality of life for their community and the nation." |
