INTERDEPARTMENTAL GENETICS and GENOMICS Iowa State University

2014

Genetics graduate major changes name effective October 2014 After several years of discussion which began with Fred Janzen who was Chair of IG in 2006 and finalized during Chris Tuggle’s tour as Chair in 2013, the program submitted documentation to the Board of Regents to change the major from GENETICS to GENETICS and GENOMICS. This change was approved October 23, 2014. Faculty voted in November to refer to the program as Interdepartmental Genetics and Genomics (IG2 or IG2). It is also likely that we will have to change the catalog designation to something other than GENET. Students presently enrolled in the program will be able to choose which major they prefer on their POSC and diplomas.

(photo) Aileen Keating, Animal Science, genetics graduate student Ben Hale (Animal Science/Ross) and Dr. Jackson Nteeba (Animal Science/Keating Lab/Genetics 2014) participate in a 5K run for the Society for the Study of Reproduction in Grand Rapids, Michigan in July 2014.

(Photo) Melissa Herrmann (Lamont Lab/Animal Science) with her poster for the Avian Immunology Research Group Meeting at the University of Geulph, in Ontario, Canada (July 16-19, 2014). Melissa received the Houghton Trust Travel Grant and funding from the Dr. Sui Tong Chan Fung Endowment. Her poster is entitled, “TLR4, MD-2, and MyD88 RNA expression levels in peripheral leukocytes after LPS stimulus in adult, male broiler, Fayoumi, and Leghorn chickens.” Melissa Herrmann, Kelsey Casebere, Michael Kaiser, Susan J. Lamont.

(photo) Susan Carpenter, Animal Science, and her graduate student, Chijioke (“CJ”) Umunnakwe (Genetics, Ph.D. expected Fall 2014) biked RAGRAI XLII this summer (Register’s Great Annual Bike Ride Across Iowa) including the Karras Loop (100 miles). The goal is to dip your back tire in the Missouri River (Rock Valley, Iowa) on Sunday morning and your front tire in the Mississippi River (Guttenberg, Iowa) on Saturday afternoon. And of course to party from one end of the state to the other with the other 10,000 riders and approximately 5,000 support crew.

(photos) September 2014 sCYvenger Hunt before the football game in Ames. During a 11 mile run Jonathan Wendel, EEOB, (left side of photo, back) and friends including Fred Janzen, EEOB (left side of photo, front) visited with 15 of the 31 Cy’s about Ames.

The 31 6-foot Cy statues produced as part of the CyclONE City project are displayed around Ames. Take the tour: http://www.youtube.com/watch?v=ywIY2AQwly0&feature=youtu.be

NEWS

EVE WURTELE and LI LING LAB, Genetics Development and Cell Biology. Matthew Crispin will complete his Ph.D. in genetics Fall 2014. Arendsee Z, Li Ling, and Wurtele ES* (2014) Coming of age: The species-specific (orphan) genes of

plant. Trends in Plant Science, doi: 10.1016/j.tplants.2014.07.003 (*corresponding authors). Li Ling, and Wurtele ES* (2014) The QQS orphan gene of Arabidopsis modulates carbon allocation

in soybean. Plant Biotechnology Journal, doi:10.1111/pbi.12238 (*corresponding authors). Crispin Matthew C, Hur M. Park T, Kim YM, Widrlechneer MP, Wurtele ES (2013). Identification

and biosynthesis of acylphloroglucinols In Hypericum gentianoides. Physiologia Plantarum 148: 354-370.

Crispin Matthew C, Wurtele ES (2013). Use of metabolomics and transcriptomics to gain insights into the regulation and biosynthesis of medicinal compounds: Hypericum as a model. In: Chandra S; Lata H; and Varma A, eds. Biotechnology for Medicinal Plants. Chapter 17, Springer 395-411.

***************************************************

ROGER WISE LAB, Plant Pathology and Microbiology NSF-PGRP / ERA-CAPS project funded (2.5 million here + 3 million to ERA-CAPS partners = $5.5 million total. http://www.news.iastate.edu/news/2014/05/08/wisensf Host targets of fungal effectors as keys to durable disease resistance http://www.nsf.gov/awardsearch/showAward?AWD_ID=1339348&HistoricalAwards=false http://eracaps.org/joint-calls/era-caps-funded-projects/era-caps-first-call-%E2%80%93-2012/functional-characterisation-and Antony Chapman, Genetics graduate student, will work on this project. Presentation of “Suppression of host cell death by a broadly conserved fungal effector” at 21st Triennial North American Barley Researchers Workshop http://www.nabrw.umn.edu/nabrw-home/workshop-program/ , June 29 to July 2, 2014, University of Minnesota and at Networks in Immunity April 1-3, 2014 University of California, Davis.

March 2014 New Phytologist Cover Article: http://onlinelibrary.wiley.com/doi/10.1111/nph.2014.201.issue-4/issuetoc Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. Courtesy of Weihui Xu, (Xu et al. pp 1396-1412). Dr. Wise hosted two high school biology teachers as part of NSF-sponsored Research Experience for Teachers (RETs): iTAG Barley: Classroom Activities on Inheritance of Traits and Genes: In the past three years, we have created a self-sustaining, inquiry-based curriculum comprising lab and classroom activities to help students make the connection from genotype to phenotype, which is the core foundation for modern genomics projects. To date, the iTAG Barley outreach module has been used successfully in thirty high school biology classes -- greater than 700 students, of which 50% were from underrepresented and underserved groups.

Segregating plants from the Informative & Spectacular Subset (ISS) of the Oregon Wolfe doubled haploid barley (OWB) population are easily grown on a lighted window bench in the classroom. These lines originate from a wide cross and have exceptionally diverse and dramatic phenotypes, making this an ideal population for teaching concepts in plant development, phenotypic diversity, genetics, and/or genomics.

iTAG Barley is aligned to the National Science Standards; thus, can be adapted to any state standards. Students observe the spikes for seed-coat color, 2-row vs. 6-row (encoded by Vrs, a domestication trait), hooded vs. non-hooded (Kap: encoded by BKn3 of the Knox gene family - a homoeotic mutation where the awn is replaced by another floret), and long awn vs. short awn (encoded by Lks1; epistatic to Kap); thus, gaining experience in phenotype observation. These phenotypes are then discussed in the context of developmental mutations, grain domestication, and cellular pathways. Students perform PCR of the Vrs and BKn3 genes using DNA they isolate from the segregating plants, and size fractionate the products on agarose gels. Inquiry based activities are used to present concepts of co-segregation of genes with biological phenotypes. Teachers conduct pre- and post content-based survey of iTAG concepts. Results of the assessment are incorporated into publications and presented at NSTA and ASPB conference.

Kevin Natukunda is a Ph.D

student using zebrafish as a model system for human gastrointestinal (GI) motility disorders in Dr. Julie Kuhlman’s lab (Genetics Development and Cell Biology). Gastrointestinal (GI) motility requires the proper regulation, and coordination of the neurons of the enteric nervous system, the smooth muscle cells, and a specialized group of cells called the interstitial cells of Cajal (ICCs). The interstitial cells of Cajal (ICC) may play a central role in the normal function of GI motility because of their proposed role as pacemakers within the GI tract. A reduction in number or absence of these cells has been associated with some GI tract disorders. However, less is known about the regulation of number, differentiation and function of ICC. Kevin is studying the molecular mechanisms that coordinate GI motility, and in particular the interstitial cells of Cajal (ICC) and their role in pacemaking. The ultimate goal is to gain a better understanding of the development and function of these cells, and how they interface with the enteric nervous system to regulate motility.

GRADUATE STUDENT PROFESSIONAL TRAVEL 2014

Vikas Belamkar, Agronomy (Cannon Lab). International Plant & Animal Genome XXIII, January 10, 2015, San Diego, California. "Mining plant collections using phenotyping and high-throughput sequencing for accelerated crop improvement - A case study of the native American bean Apios americana.

Regina McGrane, Plant Pathology and Microbiology (Beattie Lab). North Central Branch American Society of Microbiology 74th Annual Meeting, October 10, 2014. Oral presentation: "Pseudomonas syringae regulate swarming and virulence in response to light through photosensory proteins", at University of Wisconsin-Superior.

Joonbae Seo, Biomedical Sciences (Singh Lab). Society for Neuroscience, November 15, 2014. "Loss of Survival Motor Neuron 1 (SMN1) gene coupled with the skipping of SMN2 exon 7 causes spinal muscular atrophy \(SMA\), a leading genetic cause of infant mortality"

Mercy Kabahuma, Plant Pathology and Microbiology (Lauter Lab). ASA, CSSA & SSSA International Annual Meeting, November 2, 2014 in Long Beach, California. "Ureides are manufactured predominantly in legume root nodules and are the primary form of organic Nitrogen transported to the shoots in common bean."

Damarius Fleming, Animal Science (Lamont and Reecy Labs). 10th World Congress on Genetics Applied to Livestock Production (WCGALP), August 18, 2014. Vancouver, British Columbia, Canada. "A Tale Of Two Birds: SNP discovery and genomic architecture of highly inbred Leghorn and Fayoumi chicken breeds using whole genome resequencing."

Martha Ibore, Biochemistry, Biophysics and Molecular Biology (MacIntosh Lab). Molecular and Cellular Biology of the Soybean 15th Biennial Conference, August 3, 2014, Minneapolis, Minnesota. "Effects of Aphis glycines (soybean aphids) on growth of Helicoverpa zea (Corn earworms) on soybean." This study enhanced our understanding of multiple pest interactions and how soybean aphids affect the performance on corn earworms on soybean.

Lydia Hardie, Animal Science (D. Spurlock Lab): 10th World Congress on Genetics Applied to Livestock Production, August 17, 2014. "Genetic Basis of Digestibility in Nursery Pigs under PRRSV Infection".

Bo Chen, Genetics Development and Cell Biology (Spalding Lab): Plant Biology 2014, July 12-16, Portland, Oregon. "Investigating the function and regulation of CIA5/CCM1 in Chlamydomonas reinhardtii".

Soujanya Akella, Genetics Development and Cell Biology (Spalding Lab): Plant Biology, 2014, July 12-16, Portland, Oregon. "Mapping the Locus of an air dier-suppressor Mutation in Chlamydomonas reinhardtii".

Jerry Chavez, Animal Science (Carpenter Lab): Society for the Advancement of Chicanos/Hispanics and Native Americans in the Sciences, October 16-18, 2014. Los Angeles, CA. "Functional Analysis of Rev Binding Region 2, a Structural Element of the EIAV Rev Responsive Element".

Angelica Bjorkquist, Animal Science (Lamont Lab): 10th World Congress on Genetics Applied to Livestock Production, August 17, 2014. "QTL revealed for body composition traits during heat stress in an advanced intercross line of chickens." Vancouver, BC, Canada.

Kaylee Rowland, Animal Science (D. Spurlock Lab): 10th World Congress on Genetics Applied to Livestock Production, August 17, 2014, Vancouver, BC, CANADA. "Parameter Estimates of Average Daily Feed Consumption and Association with CCKAR Genotypes in White and Brown Egg-Type Laying Hens".

Laura Schultz, GDCB (McGrail Lab): Zebrafish Disease Models 7, Madison, Wisconsin, June 2014.

Melissa Herrmann, Animal Science (Lamont Lab): 10th World Congress of Genetics Applied to Livestock Production Conference, August 17-22, 2014, Vancouver, British Columbia, Canada. "SSC4 WUR Genotype and Vaccination Effect on Nursery Pigs Co-infected with PRRSV and PCV2b.”

Ellis Powell, Animal Science (Tuggle Lab). ISAG Conference, July 2014, Xian China. “Function of NK

Cells in pigs with severe combined immune deficiency (SCID) caused by natural mutations in the Artemis genes.

(photo, right) Linda visiting CY on Duff Avenue.

IG STUDENTS GRADUATING Fall 2013 through Summer 2014

David Hessel, Plant Pathology and Microbiology/Lauter Lab. Deciphering the genetic architecture of native resistance and tolerance to western corn rootworm larval feeding.

Katrin Hollinger, Ph.D., Animal Science/Selsby Lab. Evaluating the PGC-1 alpha pathway and a new preclinical model to advance treatment options for dystrophinopathies.

Li Ting, Ph.D., Genetics Development and Cell Biology/Bing Yang Lab. Function and application of TAL effectors.

Jill Madden, Ph.D., Ph.D., Animal Science/Keating Lab. Investigation of mechanisms of follicle depletion and the ovarian protective response to ovotoxicant exposure.

Jackson Nteeba, Ph.D., Animal Science/Keating Lab. Impact of metabolic perturbation on ovarian function.

Diveena Vijayendran, Ph.D., Entomology/Bonning Lab. Aphid small RNAs and viruses.

Xia Zhang, Ph.D. Ecology Evolution and Organismal Biology/Serb Lab. Decoding heterogeneous big data in an integrative way.

Rebecca Weeks, Ph.D, Genetics Development and Cell Biology/Vollbrecht Lab. Inflorescence branching in maize: A quantitative genetics approach to identifying key players in the inflorescence development pathway.

Daolin Cheng, Ph.D., Biochemistry Biophysics and Molecular Biology/Nikolau Lab. Wax ester biosynthetic pathway.

Shikha Parsai, M.S., Ecology Evolution and Organismal Biology/Bronikowski Lab. Molecular evolution of the p53 network in reptiles.

Nicole Cray, M.S., Veterinary Pathology/Whitley Lab. Effects of diets containing digestion-resistant starch on Wnt pathway control of proliferation and differentiation of the colorectal mucosa.

Caitlin Farris, M.S., Genetics Development and Cell Biology/Kuhlman/Trimarchi Labs. Starting small: Transcriptomics with single and small populations of cells.

Aarthi Putarjunan, Ph.D., Genetics Development and Cell Biology/Rodermel Lab. Genetic regulation of chloroplast biogenesis in Arabidopsis.

New 2014 Graduate Students

IG recruited 21 new students for Fall 2014. Domestic students completed undergraduate degrees at Buena Vista University (Iowa), Missouri Western State, Stevenson University (Maryland), University of Missouri-Columbia, Truman State (Missouri), University of Rhode Island, University of California-Los Angeles, University of Texas at San Antonio, Northern New Mexico College, Tuskegee University (Alabama), University of Wisconsin-Stevens Point, University of Colorado Boulder, Grinnell College (Iowa), and University of Nebraska at Lincoln.

International students are from India, Russia, Brazil, Pakistan, Malaysia, and Indonesia. Thirteen students are participating in rotations and 8 students are direct admits.

New IG Faculty

Four new faculty joined the IG program this fall: Marna Yandeau-Nelson (GDCB), Ludovico Cademartiri (MSE), Michelle Graham (AGRON), and Asheesh Singh (AGRON).

Dr. Yandeau-Nelson received her B.S. in Biology from Drake University in 1998 and her Ph.D. in Genetics (Schnable Lab) in 2005 from Iowa State University. Her graduate thesis work characterized meiotic recombination in maize. As a postdoctoral scholar at Penn State University from 2005-2008, her work focused on the genetics of starch biosynthesis in maize. In 2009, she returned to Iowa State University as an Associate Scientist and Graduate Faculty in the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, and the NSF-Engineering Research Center for Biorenewable Chemicals (CBiRC). She joined the faculty of the Genetics, Development, and Cell Biology Department in 2014. http://www.gdcb.iastate.edu/marna-d-yandeau-nelson/

Research in the Yandeau-Nelson group is focused on the dissection of genetic networks that underlie metabolic processes, and to understand how natural genetic variation in or manipulation of these networks impact how organisms respond to environmental cues. In a collaborative and inter-disciplinary effort with Nick Lauter (USDA), Basil Nikolau (BBMB, ISU) and Craig Abel (USDA), the team has recently been funded by NSF-IOS. In this project maize silks are being used as the model system to dissect the genetic and metabolic networks responsible for the synthesis of plant cuticle lipids, and to understand the protective capacities that these surface lipids confer against environmental stresses. The Yandeau-Nelson group also contributes to the Center for Biorenewable Chemicals headquartered at ISU and in that context, the group addresses how the fatty acid biosynthetic pathway can be utilized in genetically tractable microbes to produce precursors for the emerging biorenewable chemicals industry.

Dr. Ludovico Cademartiri’s latest research looks at flexible one-dimensional nanostructures; creates materials solutions to enable a better understanding of seed germination, plant development, and soil erosion; and is exploring the extension of the topological properties of polymers to crystals and nanomaterials. Dr. Cademartiri began at ISU in the Department of Materials Science and Engineering in 2012. He has a Ph.D. in interdisciplinary chemistry from the University of Toronto, Canada. http://l.cademartirilab.net/

Dr. C. plays with Lego’s for Science: http://www.wired.co.uk/news/archive/2014-07/14/growing-plants-in-lego He recently received the Beckman Young Investigator Award from the Arnold and Mabel Backman Foundation.

Asheesh Singh, Agronomy, works with soybean breeding and genetics research. His lab’s efforts are targeted towards cultivar and germplasm development and conducting applied and basic research on soybean in areas of phenomics, genomics, biotic (Diseases, Insects, Nematode) and abiotic stress tolerance. http://faculty.agron.iastate.edu/singhak/ Dr. Singh works to improve and exploit genetic diversity for trait improvements, understanding the underlying physiolgical mechanisms that govern yield and stress response, understand and eluciadate gene and trait interactions and gene networks particularly for biotic and abiotic stress response, and gene mapping (linkage and association), genomic selection. In order to feed the growing population, food production needs to nearly double by 2050 (FAO, 2009). This increase in production will likely have to come from a similar agriculture field footprint, and in an increasingly variable environment. In order to achieve this goal of increased production, we need to develop strategic approaches and utilize optimum tools. Increased production will come from maximizing yield/unit land, yield protection against biotic and abiotic stress, sustainability (minimize input resources without compromising production, while being environmentally conscious), and superior quality.

Michelle Graham, Agronomy, works in the Corn Insects and Crop Genetics section of the United States Department of Agriculture (USDA-ARS) Agricultural Research Service. Recent projects include functional and structural genetic analysis of soybean and other legumes; identifying genetic pathways involved in iron efficiency of soybean, and R-gene clusters for Phytophthora Sojae resistance: cloning Rps Genes. http://www.ars.usda.gov/pandp/people/people.htm?personid=39096

Sampling of Student Publications Ott Alina, Yang Y, Bhattacharyya M, Horner H T, Palmer R G, Sandhu D. (2013). Molecular Mapping of D1, D2 and ms5 Revealed Linkage between the Cotyledon Color Locus D2 and the Male-Sterile Locus ms5 in Soybean. Plants 2(3), 441-454. Vikas Belamkar, Nathan T. Weeks, Arvind K. Bharti, Andrew D. Farmer, Michelle A. Graham, and Steven B. Cannon. BMC Genomics 2014, 15:950. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress.

Boddicker, N., Bjorkquist, A, Rowland, R., Lunney, J., Reecy, J., and Dekkers, J. 4 Mar. 2014. Genome-wide association and genomic prediction for host response to Porcine Reproductive and Respiratory Syndrome infection. Genetics Selection and Evolution. Keil JM, Seo Joonbae, Howell MD, Hsu WH, Singh RN, Didonato CJ (2014) A short antisense oligonucleotide ameliorates symptoms of severe mouse models of spinal muscular atrophy. Molecular Therapy-Nucleic Acids, 3, e174. Seo Joonbae*, Howell MD*, Singh NN, Singh RN (2013) Spinal muscular atrophy: An update on therapeutic progress. Biochim Biophys Acta 1832:2180-2190 (*these authors contributed equally to this work). Vikas Belamkar, Alex Wenger, Scott Kalberer, Gautam Bhattacharya, William Blackmon and Steven Cannon. Evaluation of phenotypic variation in a collection of Apios americana: An edible tuberous legume. In press at Crop Science (doi: 10.2135/cropsci2014.04.0281). Research featured in WIRED Magazine, June 2014, article, “How We Can Tame Overlooked Wild Plants to Feed the World”, by Hillary Rosner, http://www.wired.com/2014/06/potato-bean/ Roy, Rahul and Diane C. Bassham (2014). “Root growth movements: Waving and skewing.” Plant Sci 221-222C: 42-47. Renny-Byfield, S., Gallagher, Joe P., Grover, C.E., Szadkowski, E. Page, J. T. Udall, J. A., Wang X., Paterson, A.H., Wendel, Jonathan F. (2014). Ancient duplicats in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biology and Evolution 6(3), 559-571. doi: 10. 1093/gbe/evu037. Grover, C.E., Zhu X., Grupp, K.K.Jareczek, J.J., Gallagher, Joe P., Szadkowski, E., Seijo, J.G., Wendel, Jonathan F (2014). Molecular confirmation of species status for the allopolypoid cotton species, Gossypium ekmanianum Wittmack. Genetic Resources and Crop Evolution. Doi: 10. 1007/s10722-014-0138-x.

Pace Jordon, Lee N, Naik HS, Ganapathysubramanian B, Lübberstedt Thomas (2014) Analysis of Maize (Zea mays L.) Seedling Roots with the High-Throughput Image Analysis Tool ARIA (Automatic Root Image Analysis). PLoS ONE 9(9): e108255. doi:10.1371/journal.pone.0108255

Wang, X., Chen, J., Xie, Z., Liu, Sanzhen., Trevor Nolan, Huaxun Ye, Mingcai Zhang, Hongqing Guo, Patrick S. Schnable, Zhaohu Li, and Yin Yanhai (2014). Histone Lysine Methyltranferase SDG8 is involved in Brassinosteroid-Regulated Gene Expression in Arabidopsis thaliana. Molecular Plant, 7(8), 1303-1315. Doi: 10.1093/mp/ssu-56.

Ambrosio L., Morriss S, Riaz Ayesha, Bailey R, Ding J. Gustavo C. MacIntosh (2014). Phylogenetic Analyses and Characterization of RNase X25 from Drosophila melanogaster suggest a Conserved Housekeeping Role and Additional Functions for RNase T2 Enzymes in Protostomes. PLoS ONE 9(8): e105444. Doi: 10. 1371/journal.pone.0105444.

(photo) Jessica Hohenstein, Biochemistry Biophysics and Molecular Biology (MacIntosh Lab) attended Plant Biology, July 12-16, 2014, Portland, Oregon and Molecular and Cellular Biology of the Soybean 15th Biennial Conference, August 3-6, 2014, Minneapolis, MN. Poster title: "Plant defenses and soybean aphid counter-defenses: an exploitation of phytohormone signaling." Jessica won best poster award at the Soybean Conference.

Genetics and Toxicology were represented at SACNAS 2014 in Los Angles, California. Society for the Advancement of Chicano/Latino and Native Americans in the Sciences. Daniela Flores (EEOB/Janzen), Jerry Chavez (Animal Science/Carpenter) and Gustavo MacIntosh, BBMB, met with interested students during the Career Fair.

Photos: Many of the Cy photos were taken by John Hsieh, a graduate student in Bioinformatics and Computational Biology.

IG faculty members Roger Wise (Plant Path & Micro), Steven Whitham (Plant Path & Micro), Madan Bhattacharyya (Agronomy), and Thomas Baum (Plant Path & Micro) attended the XVI International Congress on Molecular Plant-Microbe Interactions in Greece in July 2014.

(photo) Gustavo MacIntosh, BBMB, rode from Ames to Fort Frances, Canada, with the Ames-Canada Cycling Adventure Team. The team had 4 people and a support driver that carried their gear on a truck and scouted routes and overnight stops. They rode ~700 miles in 12 days, and on day #13 they crossed to Canada. They had to endure some strong winds, heavy storms, bad roads, and long climbs, but there were also tailwind days, beautiful landscapes, sun and fast descents. The trip took them through rural Iowa, Wisconsin bluffs, the Twin Cities, and

the forests of northern Minnesota. Gustavo was the team mechanic, and had to take care of all the flats (only 6, not so bad). They had a fantastic experience.

Student Publications continued. Boddicker, N., Bjorkquist, Angelica, Rowland, R., Lunney, J., Reecy, James and Dekkers, Jack. 4 March 2014. Genome-wide association and genomic prediction for host response to Porcine Reproductive and Respiratory Syndrome infection. Genetics Selection and Evolution. New structures going up at Welch and Lincoln Way in Ames.