Newsletter: October 2006


	In This Issue: A Message From the Director Focus on Research Recent Publications & Presentations Service Laboratory Update Education and Outreach Affymetrix Gene Chip Symposium Teacher Symposium Seminars Grants and Fellowships International Collaborations Center News		A Message from the Director The Center for Integrated BioSystems (CIB) fosters collaborations among life scientists at USU concentrating on plant, animal and microbial genomics, and metabolic characterization and cellular communications. The CIB is a fusion of intellectual strength, laboratory services and biotechnology education and training, all of which provide the scientific community with practical solutions to specific problems. At the Center we have an active research program concentrating on such areas as gene expression during stress in alfalfa, metagenomics of microbes in crop soils, metabolomics, molecular events of animal fertilization and metagenomics of extreme environments in Utah. We want to welcome you to visit our Center and learn more about our activities. This newsletter will bring you up-to-date information about the CIB on a bimonthly basis and we welcome your suggestions and participations to improve the quality of this publication. 2006 has been an especially successful year for the Center. We have submitted 24 research proposals to various agencies and our success level has been more than 60%. Our service laboratories have been upgraded to offer new and improved equipment such as our new mass spectrophotometer. Our education and training programs reached a new level of success both nationally and internationally, and we aim at reaching higher levels of success in coming years.
	A note from the Editors The Utah State University Center for Integrated BioSystems is located amidst the Rocky Mountains in Cache Valley, Utah. This newsletter is produced by the Education Office of the Center. Complimentary hard copies are available by contacting the Education Office at 435-797-3504 or by email, krashid@cc.usu.edu Editorial Board: Kamal Rashid, Bart Weimer, Ken White, Pam Garcia, Ken Olsen		Focus on Research Metabolomics of alcohol utilization in yeast. The genetic details of alcohol metabolism and how it alters the expression of genes in S. cerevisiae is being studied. The metabolomics studies of this biotransformation include gene expression, proteomics, and metabolite analysis. Data will be assembled from these different sources to identify genes and pathways related to activities determining the metabolic mechanisms for optimization of product formation. This information will enable the genetic modification of yeast for maximal bioconversions of agricultural products. Recent Publications and Presentations Rashid, K.R. and Weimer, B.C. 2006. Academia's Response to the Growing Biopharma's wrkforce Needs. Biotrends. Volume 2, Issue 3. Ganesan, B. P., Dobrowolski, P., and. Weimer, B. C. 2006. Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis. App. Environ. Microbiol. 72:4264-73. Weimer, B. C. (Editor). Improving the flavour of cheese. Woodhead/CRC Press, Cambridge, England. Weimer, B. C. and Ganesan, B.P. Amino acid metabolism and cheese flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead/CRC Press, Cambridge, England. Weimer, B. C., Ganesan, B.P., and Chen, D.C. Functional genomics and flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead/CRC Press, Cambridge, England. Rashid, K.R. and Weimer, B.C. 2006.Academia's Response to the Growing Biopharma's Workforce Needs. Biotrends. Volume 2, Issue 3. Ganesan, B. P., Dobrowolski, P., and. Weimer, B. C. 2006. Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis. App. Environ. Microbiol. 72:4264-73. Weimer, B. C. (Editor). Improving the flavour of cheese. Woodhead/CRC Press, Cambridge, England. Weimer, B. C. and Ganesan, B.P. Amino acid metabolism and cheese flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead/CRC Press, Cambridge, England. Weimer, B. C., Ganesan, B.P., and Chen, D.C. Functional genomics and flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead/CRC Press, Cambridge, England. Li, G-P., Bunch, T.D., White, K.L., Rickords, L, Liu, J. and B.R. Sessions. 2006. Denuding and Centrifugation of Maturing Bovine Oocytes Alters Oocyte Spindle Integrity and the Ability of Cytoplasm to Support Parthenogenetic and Nuclear Transfer Embryo Development. Mole. Reprod. Devel. 73:446-451. Vanderwall, DK, Woods, GL, Roser, JF, Schlafer, DH, Sellon, DC, Tester, DF, and White, KL. 2006. Equine Cloning: Applications and Outcomes. Reprod. Fertil. Devel. 18:91-98. White, K.L., Passipieri, M, Bunch, TD, Campbell, KD and Pate, BJ. 2006. Effects of Arginine-Glycine-Aspartic Acid (RGD) Containing Snake Venom Peptides on Parthenogenetic Development and In Vitro Fertilization of Bovine Oocytes. Mole. Reprod. Devel. In Press. Sessions, BR, Aston, KI, Davis, AP, Pate, BJ and KL White. 2006. Effects of Amino Acid Substitutions in and Around the Arginine-Glycine-Aspartic Acid (RGD) Sequence on Fertilization and Parthenogenetic Development in Mature Bovine Oocytes. Mole. Reprod. Devel. 73:651-657. Aston, K.I., Li, G.P., Hicks, B.A., Sessions, B.R., Pate, B.J., Hammon, D.S., Bunch, T.D., and White, K.L. 2005. The Developmental Competence Of Bovine Nuclear Transfer Embryos Derived From Cow Versus Heifer Cytoplasts. Anim. Reprod. Sci. In Press. Aston, K.I., Li, G.P., Hicks, B.A., Sessions, B.R., Pate, B.J., Hammon, D., Bunch, T.D. and White, K.L. 2006. Effect of the Time Interval Between Fusion and Activation on Nuclear State and Development In Vitro and In Vivo of Bovine Somatic Cell Nuclear Transfer Embryos. Reproduction, 131:1-8. Wang, L., White, K.L., Reed, W.A. and K.D. Campbell. 2005. Dynamic Changes To The Inositol 1,4,5-Trisphosphate And Ryanodine Receptors During Maturation Of Bovine Oocytes. Cloning and Stem Cells, 7(4):306-320. Meerdo, L.N., Reed, W.A. and K.L. White. 2005. Telomere to Centromere Ratio of Bovine Clones, Embryos, Gametes, Fetal Cells, and Adult Cells. Cloning and Stem Cells, 7(1):61-72. Li, G-P., Liu, Y., White, K.L. and T.D. Bunch. 2005. Cytogenetic analysis of diploidy in cloned bovine embryos using an improved air-dry karyotyping method. Theriogenology 63: 2434-2444
			Service Laboratory Up-Dates The CIB offers Affymetrix GeneChip microarray services. Affymetrix GeneChips have been widely recognized as leaders in gene expression analysis. Highly reproducible, accurate and reliable, GeneChips are used around the world for a broad and expanding list of applications. This technology allows researchers to study expression for any number of genes in any model organism. For more information on service please contact: Ninglin Yin, CIB Genomics Group Leader at usudna@cc.usu.edu or 435-797-8218
Education and Outreach Updates Proteomics Graduate Training Course Ten graduate students from across campus attended the one-day training course on proteomics on June 27. The course included a brief introduction to the tools used in the proteomics study as well as hands-on laboratory work. Students learned what tools and materials are needed and how to set up their own proteomics study. Course instructors were Dr. Dong Chen, proteomics group leader and Kum Park, research associate at the CIB. Bioinformatics Graduate Training Course Forty-two faculty, graduate students and researchers from Utah State University and USDA labs on Campus participated in the one-day intensive training course on bioinformatics offered by the Center. This course presented insights into capabilities varying from sequence analyses with public resources and databases to statistical analysis of “-omics” data. Resources available at the CIB were showcased, as a hands-on way to use informatics in understanding biology. The course instructors were Drs. Bala Ganesan, CIB; John Stevens, Computer Science; and Paul Clifton, Biology The Sixth Annual Biotechnology Summer Academy The Sixth Annual Biotechnology Summer Academy held July 10-14, 2006 was a great success. Forty-three high school students participated in this year’s program. Seven of those were returning students participating in the first Advanced Summer Biotechnology Academy. The students enjoyed their time at Utah State University during this short but intensive week. Exposure to research programs, as well as the expertise of the faculty and staff members, was very enlightening for them. We received positive feedback from both parents and students. The program achieved its objective in attracting a group of talented high school students and introducing them to the quality of research and education at Utah State University. Gene Expression and Microarray Analysis Training Program An intensive training course covering the main areas of microarray technology was offered on August 1-4, 2006. The course focused on microbial as well as plant gene expression and emphasized theory, sample preparations, labeling, fluorescent imaging, microarray data analysis, and data mining. Hands-on laboratory sessions covered microarray tools, kits, reagents and services, experimental design, labeling cDNA synthesis, sample preparation, microarray reaction, microarray detection, data analysis and modeling and Affymetrix demonstrations. Up-coming Training Courses: Protein Purification: Isolation and Characterization, September 19-22, 2006 Microbial Fermentation: Development and Scale-up, October 17-20, 2006 Techniques in Animal Cell Culture and Scale-Up Strategies, November 14-17, 2006 For more details about the training programs please check our web site: http://www.biosystems.usu.edu/education/ Undergraduate Student Support Programs The Center offers undergraduate research fellowships and internships to students who are actively pursuing life science or agricultural degrees at USU. These programs are crafted to be relevant to the students’ stated goals within the research activities of the Center. For more information and how to apply contact Dr. Afifa Sabir, program coordinator, at afifa@cc.usu.edu. Affymetrix Gene Chip Symposium On August 21, a half-day symposium was organized for the recipients of the Affymetrix chips from the CIB in conjunction with the VPR’s office. The purpose of the symposium was to allow USU PIs to share data and experiences from the use of the Affymetrix platform. The program consisted of a short presentation from each group followed by a panel discussion on experimental design, data analysis, methodologies, pitfalls and more. It was a great success. Go Aggies ! The Sixth Annual Biotechnology Teacher Symposium All Utah science, health and agriculture educators teaching grades 7-12 who are interested in increasing their knowledge of biotechnology and want to learn exciting new experiments to use in their own classrooms are encouraged to apply. All principals and counselors are welcome too! Time: November 6, 2006 Location: Center for Integrated Biotechnology, Utah State University Space is limited, so please apply early. CIB Seminars Fall 2006
Fall Seminars Date		Location	Speaker	Affiliation	Institution
	Monday, September 11, 2006	CIB 103	Dr. Ashok Kolaskar	Professor, Biotechnology & Bioinformatics	University of Pune - India
	Thursday, September 14, 2006	LIB 154	Dr. Andy Benson	Associate Professor	University of Nebraska - Lincoln
	Thursday, September 21, 2006	LIB 154	Dr. Bart Weimer	Director	Center for Integrated BioSystems, USU
	Thursday, September 28, 2006	LIB 154	Dr. Krishna Shenai	USTAR Professor	Electrical and Computer Engineering Department, USU
	Wednesday, October 04 2006	LIB 154	Dr. David York	USTAR Professor	The Center for Advanced Nutrition
	Thursday, October 12, 2006 at 12:00 Noon	ENGR 104	Dr. Terry Hazen	Professor	Lawrence Berkley National Laboratory
	Thursday, November 02, 2006	LIB 154	Dr. Patrick Chain	Biomedical Scientist Biosciences Directorate	Lawrence Livermore National Laboratory
	Thursday, November 9, 2006	LIB 154	Dr. Loren Israelsen	Executive Director	Utah Natural Products Alliance
	Thursday, November 30,2006	LIB 154	Dr. Bonnie Baxter	Associate Professor	Westminster College
Grants and Fellowships 2006 Grants received
	Funding Agency:	USDA/CSREES
	Title:	Functional Genomics in Nature
	Term:	1 July 2006 – 30 June 2007
	Investigators:	Bart Weimer, Kamal Rashid

	Funding Agency:	Juvenile Diabetes Research Foundation
	Title:	Impact of Type I Diabetes on the Mitochondrial Proteome
	Term:	1 September 2006 – 30 August 2008
	Investigators:	Bart Weimer, Dong Chen, Daryll DeWald

	Funding Source:	Monsanto, Inc.
	Title:	Biotechnology Summer Academy for High School Students
	Investigators:	Kamal Rashid, Afifa Sabir

	Funding Agency:	George S. and Dolores Doré Eccles Foundation
	Title:	Advanced Biotechnology Summer Academy for High School Students
	Investigators:	Bart Weimer, Daryll DeWald, Kamal Rashid, Afifa Sabir
CIB Seed Grants awarded for FY2006-2007.
	Title:	Bioinformatic Profiling of Responses to Utah Urban Air – A Multidisciplinary Study
	Term:	1 July 2006 – 30 June 2007
	Investigators:	Roger Coulombe (PI), Randy Martin (Co-PI), and Philip Silva (Co-PI)

	Title:	Investigating Genes Involved in Embryonic Skin Development by Characterizing the AP-2γ Mutant Skin Phenotype
	Term:	1 July 2006 – 30 June 2007
	Investigators:	Quinton Winger (PI), Brian Gowen (Co-PI), and Ramona Skirpstunas (Co-PI)
E.L. and Inez Waldron Biotechnology Endowment Fund Graduate students engaged in genomic or proteomic research are encouraged to apply for scholarship awards from the E.L. and Inez Waldron Endowment Fund for the USU Biotechnology Center. In 2005 the following graduate students received Waldron awards from CIB:
	Name:	Sanghamitra Mitra
	Title:	Understanding the catalytic mechanism of MetAP genes or gene products in bacteria and yeast
	Conference:	American Society of Biochemistry and Molecular Biology Annual Meeting, San Francisco, CA, 1-5 April 2006

	Name:	Miguel A. Pabón
	Title:	The FeFe and VFe proteins from Azotobacter vinelandii: Structural Features Revealed by Homology Modeling
	Conference:	Gordon Research Conference, Iron-Sulfur Enzymes Meeting, 11-16 June 2006

	Name:	Ravi Rai
	Title:	Regioselective Staudinger reaction for the synthesis of N-1 modified Aminoglycosides
	Conference:	231st ACS National Meeting, Atlanta, GA, 26-30 March 2006

	Name:	Sakara Tunsophon
	Title:	Mechanism of 1,25-dihydroxyvitamin D3 mediated signal transduction through membrane receptors in intestinal epithelial cells
	Conference:	88th Endocrine Society Annual Meeting, Boston, MA, 24-27 June 2006
For information about 2006 funding please contact CIB grant specialist Katherine McConkie at katherine.mcconkie@usu.edu
International Collaborations Dominican Republic Utah State University (USU) and the Government of the Dominican Republic (DR) entered into a Technical Cooperation Agreement on August 26, 2005 with the objective of establishing the structural basis of cooperation for jointly executing programs in biotechnology, which will provide the means for commercializing technology, training Dominican students and professors, and developing sustainable capacity in biotechnology in public higher education institutions in the DR. In November 2005, four Dominican scientists, hosted by the Center for Integrated BioSystems (CIB), traveled to USU to become familiar with the biotechnology programs and laboratories at USU. Following their visit, three staff members from the CIB went to the DR to work with their Dominican counterparts in evaluating current biotechnology programs at both public and private institutions. They identified areas of strength and the principal constraints to improving biotechnology in the DR. During the course of the assessment, the team visited nine public and private entities in the DR and found that the scientists were very interested in promoting and using biotechnology techniques in their daily work. The joint team also found the potential to build capacity for biotechnology to be very high. In January 2006, recommendations were made to the government for development of a national plan for biotechnology. Since then, between April and June 2006, two Dominican scientists, Drs. David Terrero and Marisol de Castro, have come to the CIB to work and collaborate with USU researchers. It is hoped that the collaborative efforts will lead to joint research programs and continued training opportunities for other Dominican scientists China USU officials traveled to the People’s Republic of China on May 7-17, 2006 to sign two agreements fostering collaborative research and academic exchange with Chinese universities. Included in the agreements was the establishment of a satellite facility for Utah State’s Center for Integrated BioSystems at Xiamen University. The USU delegation, led by President Stan Albrecht, met with officials in China’s Ministry of Science and Technology in Beijing and at the Northwest Sci-Tech University of Forestry and Agriculture in central China’s Shaanxi province, in addition to personnel at Xiamen University in the coastal Fujian province. Other USU officials on the trip included First Lady Joyce Albrecht, Brent Miller, vice president for research, Noelle Cockett, vice president for USU Extension and dean of the College of Agriculture, Bart Weimer, director, CIB, and Dong Chen, research assistant professor, CIB. Thailand Training Program Strategies for Stem Cell Research and Nuclear Transfer Techniques December 1-3, 2006 Singapore Training Program (Link to Singapore Web Announcement) Scale-Up Strategies for mammalian and Microbial Bioprocessing: A Hands-on Approach: December 11-15, 2006
Center News
Dr. Ken White Dr. Ken White, professor of reproductive physiology with the Department of Animal, Dairy and Vet Sciences has joined the Center as associate director for research. We want to give him a warm welcome.
Dr. Daryll DeWald Dr. Daryll DeWald accepted the position of department head, Department of Biology effective July 1, 2006. We congratulate him for his new post and want to thank him for his significant contributions to the Center as associate director of research.
Anne Martin Anne Martin joined the Center on May 15th, 2006 as Business Assistant
Sarah Morrill Sarah Morrill joined the Center on September 13, 2006 as Staff Assistant II. Welcome Anne and Sarah. Congratulations to Giovanni Rompato and his wife for the arrival of the new addition to the family, Francesca.