Source: MISSISSIPPI STATE UNIV submitted to
INSTITUTE FOR GENOMICS, BIOCOMPUTING & BIOTECHNOLOGY
Sponsoring Institution
State Agricultural Experiment Station
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
1002406
Grant No.
(N/A)
Project No.
MIS-201010
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jan 20, 2014
Project End Date
Jan 20, 2019
Grant Year
(N/A)
Project Director
Peterson, DA, G..
Recipient Organization
MISSISSIPPI STATE UNIV
(N/A)
MISSISSIPPI STATE,MS 39762
Performing Department
LSBI / IGBB
Non Technical Summary
TheInstitute for Genomics, Biocomputing & Biotechnology(IGBB) atMississippi State University(MS State) was founded in 2011 to increase the ability of Mississippi scientists to lead and participate in high-throughput, multi-disciplinary projects focused on understanding the biomolecular interactions underlying the diversity, value, health, and sustainability of species of agricultural, medical, bioenergy, and/or ecological importance. The IGBB serves the university by providing MS State researchers and their collaborators access to a team of highly-skilled professionals trained in cutting-edge genomics, proteomics, and high performance biocomputing principles and techniques. Through in-house instrumentation and commercial/academic partnerships, the IGBB team generates DNA sequence, transcriptomic, metabolomic, and proteomic data. The IGBB team works with researchers to analyze data using state-of-the-art software including programs/pipelines developed by IGBB computational scientists. Moreover, as one of the five member institutes of MS State's High Performance Computing Collaboratory (HPC2), the IGBB utilizes HPC2supercomputing power to efficiently derive biological knowledge from large, diverse datasets. In addition to the aforementioned activities, the IGBB administration works to optimize the scientific and economic impact of the university through the development of multidisciplinary research/grant-writing teams and by making strategic investments in infrastructure and personnel. The primary goal of the IGBB is to foster research synergies that ultimately improve the scientific standing and economic status of Mississippi State University and the state of Mississippi.
Animal Health Component
40%
Research Effort Categories
Basic
45%
Applied
45%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2010612104010%
2011719108010%
3043899104010%
3114010104010%
2124030108010%
2123130103010%
3114050108010%
7121510100010%
7123710100010%
7224030108010%
Goals / Objectives
The mission of the IGBB is to foster research synergies that ultimately improve the scientific standing and economic status of Mississippi State University. Specific goals of the IGBB include:(1) Conducting scientific research that meets the needs of society and further enhances the unique strengths of MS State;(2) Attracting and retaining outstanding faculty and students at MS State;(3) Offering researchers at MS State and elsewhere the opportunity to collaborate with the IGBB's genomics, proteomics, and computational biology experts;(4) Helping principal investigators leverage the experience and expertise of the IGBB to make their research programs more productive, increase the number and scientific impact of their publications, and enhance their ability to procure extramural funding;(5) Supporting educational activities that enhance the abilities of students and faculty to succeed in the multi-disciplinary fields of computational biology, genomics, and biotechnology.
Project Methods
IGBB research projects are conducted using a variety of methods, techniques, and instrumentation. The tools most commonly used in our research include the following:(1) Illumina DNA sequencing - The IGBB owns an Illumina MiSeq sequencer and has access to Illumina HiSeq instruments. Sequencing is performed as part of externally-funded research projects and as a service to Mississippi State faculty/staff on a fee-per-service basis. Illumina DNA and RNA-Seq data is stored, manipulated, and analyzed using the supercomputers in MS State's High Performance Computing Collaboratory (HPC2) of which the IGBB is a member center. Public, commercial, and in-house scripts are used in sequence analysis. (2) Mass Spectrometry - The IGBB has both gel-based and liquid based mass spectrometry systems which it uses to identify proteins, discover and characterize protein post-translational modifications, conduct quantitative proteomics, perform qualitative and quantitative comparison of the protein complements of different tissues/stages/organisms, integrate proteomic and nucleic acids data (e.g., proteogenomic mapping), and perform functional annotation of proteins using Gene Ontology (GO) standards and procedures. For liquid-based proteomics, the IGBB's proteomics staff uses a Waters Nano ESI Q-TOF (model Xevo G2-S) mass spectrometer and LTQ Orbitrap Velos and standard LTQ mass spectrometers fitted with upstream HPLC sample purification systems. Gel-based proteomics is conducted using the IGBB's MALDI TOF TOF mass spectrometer. Recently, we have also begun to perform metabolomic research using the Waters Xevo G2-S.(3) Computational Biology - The IGBB is one of five member centers of MS State's High Performance Computing Collaboratory (HPC2: http://www.hpc.msstate.edu/). The HPC2 is governed by an Operations Board (Ops Board) composed of the directors of the five member institutes (voting members) and the Associate Vice President for Research (non-voting member). Dr. Peterson is the IGBB's representative on the Ops Board.All IGBB faculty/staff/affiliates have access to the various supercomputers located in the HPC Building. The HPC2 and all of its computers are managed and maintained by the HPC2's Computing Office. The HPC2 has ranked in 18 of the past 32 Top500 supercomputing lists since June 1996. In June 2010, the HPC2 computer Talon (IBM iDataPlex cluster with 3,072 processor cores, six-core Intel Xeon processors, more than six terabytes of RAM, and a Voltaire, Inc., high-speed quad data rate InfiniBand network) was ranked the 18th fastest supercomputer at any U.S. academic location and the 331st most powerful computer in the world. Talon has a proven peak performance of more than 34 trillion calculations per second. Other resources include a 10-teraflop 2048 processor AMD Opteron cluster, a 384 processor Intel Xeon cluster with InfiniBand interconnect, a 512 processor SGI ORIGIN 3900, a 128 processor SGI ORIGIN 3800, a 64 processor SGI ORIGIN 3800, and numerous additional special purpose machines. Data storage capabilities include a 250 terabyte high performance disk system and a 2 petabyte near-line storage system.The HPC2 recently purchased a Cray cluster which has been named "Shadow." Shadow will be 10 times faster than the Talon while using a fraction of the energy.Genome assembly, which is notoriously RAM intensive, is performed using the shared memory machines Atlas and Skybolt. Each machine has 512 GB RAM, 16 compute cores, and 2.3 TB of local storage.High-end visualization needs are met by an immersive reconfigurable CAVE virtual reality environment driven by a 4 node visualization cluster. An access grid node allows for state-of-the-art video teleconferencing and remote collaboration.The network infrastructure backbone consists of both 10-Gigabit Ethernet and Gigabit Ethernet, with an extensive Gigabit Ethernet network for desktop connectivity. Internet connectivity is provided via Mississippi State University's 10-Gigabit Ethernet campus backbone. Campus connectivity to the Internet at large is via a 1 Gigabit connection. Mississippi State University is a charter member of the Internet2 Consortium, and currently utilizes a 1 Gigabit connection to the Louisiana Optical Network Initiative (LONI) regional network for connectivity to Internet2/NewNet and the National LambdaRail (NLR) via a 10 Gigabit connection.A number of different molecular analysis programs are currently loaded on the HPC2 supercomputers. Examples of commonly used programs include the following:abyss -> Abyss - v1.3.2 Genome Assembler ( MaxK = 96 )abyss-k64 -> Abyss - v1.3.2 Genome Assembler ( MaxK = 64 )allpaths -> Allpaths LG - short read genome assembleramber10 -> Amber10 Molecular Dynamics Simulator, from UCSFamber10test -> Amber10 Molecular Dynamics Simulator, from UCSFamber8 -> Amber8 Molecular Dynamics Simulator, from UCSFamos -> AMOS - Genome Sequence Assemblybioperl -> BioPerl 1.6.0blast -> Blast - NCBI Blast - Biological Sequencer - v2.2.25blast-24 -> Blast - NCBI Blast - Biological Sequencer - v2.2.24blastcl3 -> BLAST Client3blat -> Blast-Like Alignment Toolbowtie -> Bowtie - short read alignercap3 -> CAP3 - sequence assembly programcelera -> Celera - Celera genome assemblerfastx -> Fastx - tools for Short-Reads FASTA/FASTQhmmer -> HMMER3 - sequence search algorithm based on hidden Markov modelsiprscan -> InterProScan - Protein signature tooliprscan -> InterProScan - signature recognition searchlammps -> lammps - Molecular Dynamics Simulator (lmp_openmpi)mpiblast -> MpiBlast - Parallel NCBI BLASTmummer -> MUMmer 3.0 - whole genome alignmentmuscle -> MUSCLE - multiple sequence alignmentnseg ->removal of tandem and low-complexity repeatsnwchem -> NWChem Computational Chemistry Packagepaup -> PAUP - phylogenetic inference algorithmperl-64 -> perl - 64-bitpiler -> PILER - ab initio repeat discoverypython -> Python - Python scripting languager -> R - Statistics and Differential Equations Packagerasmol -> Rasmol - molecular graphics visualisationrecon -> RECON - ab initio repeat discoveryrepeatmasker -> RepeatMasker - homology-based repeat discoveryrepeatmodeler -> RepeatModeler - repeat ID and modelingrepeatscout -> RepeatScout - ab initio repeat discoveryrmblast -> RepeatMasker compatible BLASTtreefinder -> TreeFinder - computes phylogenetic trees from nucleotide sequence datavelvet -> Velvet - Genome sequence assemblervienna -> ViennaRNA - RNA Secondary Structure Prediction and Comparisonxtandem -> X! Tandem - match tandem mass spectra with peptide sequences

Progress 01/20/14 to 01/20/19

Outputs
Target Audience:The target audience for our research is diverse and includes plant and animal breeders, evolutionary biologists, plant and animal pathologists, pest/pathogen management personnel, farmers and ranchers, medical researchers and practicing doctors, computational biologists and bioinformaticians, ecologists, toxicologists, virologists, food scientists, entomologists, nematologists, and veterinary scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?• The IGBB was the chief sponsor and host of the 15th Annual Mid-South Computational Biology and Bioinformatics Society (MCBIOS) meeting. The highly attended meeting was held in Starkville on March 29-31. Many IGBB-associated faculty and their students/postdocs participated in the meeting via oral and poster presentations. • The IGBB continued its active role in the University & Industry Consortium (UIC). The UIC is a group working to increase partnerships between agricultural, food, and biotechnology companies and land-grant institutions. The UIC began more than 20 years ago with Mississippi State serving as a founding member. The UIC provides opportunities for students and faculty to interact and develop research and educational collaborations with leaders in industry and academia. • The IGBB supported participation of research faculty, research associates, and students in a number of national and international scientific meetings. • The IGBB hosted a student from the public high school known as the Mississippi School for Mathematics & Science. The student learned the principles of virology from Dr. Nina Aboughanem, an IGBB faculty member. • The IGBB hosted several vendor shows and equipment demonstrations. • The IGBB helped Dr. Nina Aboughanem apply for and successfully obtain promotion to associate research professor. How have the results been disseminated to communities of interest?Results have been disseminated to the scientific community through peer-reviewed publications, book chapters, scientific meetings/presentations, faculty exchange programs, and the IGBB website (www.igbb.msstate.edu). In addition, DNA sequence and gene expression data were disseminated through AgBase (www.agbase.msstate.edu), CrocGenomes (www.crocgenomes.org), CottonGen (www.cottongen.org), VetBioBase (http://vetbiobase.igbb.msstate.edu), and the National Center for Biotechnology Information (NCBI; www.ncbi.nlm.nih.gov). What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Below is a list of our major project goals (1-5). Each goal is followed by accomplishments (each delineated by a bullet) made over the course of the last year that advanced that goal. (1) Conducting scientific research that meets the needs of society and further enhances the unique strengths of MS State. • The IGBB employed 20.5 people (FTE) during the period in question. In doing so, the IGBB helped strengthen MS State and the local/state economies. • The IGBB's total expenditures were $2.06 M. • IGBB accounting records indicate that the IGBB Service Center accounted for $285,054 in service work, a 50% increase from the $189,000 of FY17. • IGBB scientists published IGBB scientists published eight technique/tool development papers in FY18 including methods for cryopreservation of animal tissues, techniques for producing safer and/or more effective vaccines for humans and animals, a program for detecting color variations in butterfly wings, and an algorithm for efficiently visualizing massive next generation DNA sequence data sets. • The IGBB was awarded a contract with the U.S. Army Corps of Engineers (USACE) Engineering Research and Development Center (ERDC) in Vicksburg, MS. Through this contract the IGBB will conduct sequencing and computational biology research on aquatic toxicology in collaboration with the ERDC's ecology team. (2) Attracting and retaining outstanding faculty and students at MS State. • The IGBB employs Drs. Tibor Pechan, Nina Aboughanem, and George Popescu as research faculty. In this fiscal year Dr. Aboughanem was promoted from assistant research professor to associate research professor. In late 2018, the IGBB hired soil microbiologist, Dr. Shankar Shanmugam, as a new research assistant professor. He will start in January 2019. • The IGBB invested in the research programs of several MSU departmental faculty including Drs. Renita Horton (Ag and Bio Engineering - sickle cell anemia and heart disease), Diana Outlaw (Biological Sciences, malaria), Erdogan Memili and Jean Feugang (Animal and Dairy Sciences - livestock fertility), Din-Pow Ma (Biochemistry - cotton transcriptomics), Peter Allen and Federico Hoffmann (Aquaculture and Biochemistry, respectively - alligator gar genomics), and Shien Lu (Biochemistry - antifungal bacteria). • The IGBB has provided opportunities for five graduate students to earn their Ph.D. degrees. These students are funded through extramural awards to the IGBB. • The IGBB has continued to invest in purchase and maintenance of state-of-the-art equipment as a means of creating research opportunities and attracting/retaining faculty. In FY18 the IGBB purchased the service contracts for their LTQ Orbitrap Velos mass spectrometer and an Illumina MiSeq DNA sequencer. In FY18 the IGBB purchased an Oxford Nanopore GridIONx5 DNA sequencer. (3) Offering researchers at MS State and elsewhere the opportunity to collaborate with the IGBB's genomics, proteomics, and computational biology experts. • Records showed that the IGBB conducted 108 separately invoiced service projects. • Service Center records show that service jobs were submitted by 25 different MSU PIs representing eight different departments. • Additionally, work was done for one researcher at Millsaps College, two U.S. Forest Service labs, two USDA-ARS labs, and the toxicology group of the U.S. Army Corps of Engineers. • Service Center and computer usage records indicate that the institute conducted collaborative research with 40 different MSU PIs representing nine different academic departments. (4) Helping principal investigators leverage the experience and expertise of the IGBB to make their research programs more productive, increase the number and scientific impact of their publications, and enhance their ability to procure extramural funding. • Several new local/state/federal grants (net value = $1,194,508) were obtained by IGBB scientists. • Ninety-eight peer-reviewed manuscripts were published by IGBB-affiliated scientists during the fiscal year. • During the fiscal year IGBB faculty/staff/affiliates published 99 peer-reviewed papers. Fifteen of these have SCOPUS 2- year citation indices > 4. (5) Supporting educational activities that enhance the abilities of students and faculty to succeed in the multidisciplinary fields of computational biology, genomics, and biotechnology. • See Opportunities for Training and Professional Development below.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Abdelhamed H, Lawrence ML, Waldbieser G (2019) Complete genome sequence data of multidrug-resistant Aeromonas veronii strain MS-18-37. Data in Brief 23: 103689.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Abdelhamed H, Ozdemir O, Ibrahim I, Lawrence M, Karsi A (2019) Antibacterial activities of trans-cinnamaldehyde, caprylic acid, and ?-resorcylic acid against catfish pathogens. Aquaculture 504: 334-344.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Adl SM, Bass D, Lane CE, Lukea J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, C�rdenas P, ?epi?ka I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q (2019) Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology 66(1): 4-119.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Akgul A, Nho SW, Kalindamar S, Tekedar HC, Abdalhamed H, Lawrence ML, Karsi A (2018) Universal stress proteins contribute Edwardsiella ictaluri virulence in catfish. Frontiers in Microbiology 9(NOV): 2931.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Bookwalter JD, Riggins JJ, Dean JFD, Mastro VC, Schimleck LR, Sullivan BT, Gandhi KJK (2019) Colonization and Development of Sirex noctilio (Hymenoptera: Siricidae) in Bolts of a Native Pine Host and Six Species of Pine Grown in the Southeastern United States. Journal of Entomological Science 54(1): 1-18.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Brauer EK, Popescu GV, Singh DK, Calvi�o M, Gupta K, Gupta B, Chakravarthy S, Popescu SC (2018) Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to Pseudomonas syringae. PLoS Biology 16(12): e2005956.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Cai L, Jeremic D, Lim H, Kim Y (2019) ?-Cyclodextrins as sustained-release carriers for natural wood preservatives. Industrial Crops and Products 130: 42-48.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: De Abrew Abeysundara P, Dhowlaghar N, Nannapaneni R (2019) Influence of cold stress on the survival of Listeria monocytogenes Bug600 and ScottA in lethal alkali, acid and oxidative stress. LWT 100: 40-47.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Dhakal J, Sharma CS, Nannapaneni R, McDaniel CD, Kim T, Kiess A (2019) Effect of chlorine-induced sublethal oxidative stress on the biofilm-forming ability of salmonella at different temperatures, nutrient conditions, and substrates. Journal of Food Protection 82(1): 78-92.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Durfey CL, Swistek SE, Liao SF, Crenshaw MA, Clemente HJ, Thirumalai RVKG, Steadman CS, Ryan PL, Willard ST, Feugang JM (2019) Nanotechnology-based approach for safer enrichment of semen with best spermatozoa. Journal of Animal Science and Biotechnology 10(1): 14.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Gastal GDA, Aguiar FLN, Ishak GM, Cavinder CA, Willard ST, Ryan PL, Feugang JM, Gastal EL (2019) Effect of cryopreservation techniques on proliferation and apoptosis of cultured equine ovarian tissue. Theriogenology 126: 88-94.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Glasa M, Predaj?a L, Sihelsk� N, `oltys K, Ruiz-Garc�a AB, Olmos A, Wetzel T, Sabanadzovic S (2018) Grapevine virus T is relatively widespread in Slovakia and Czech Republic and genetically diverse. Virus Genes 54(5): 737-741.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Glasa M, Predaj?a L, Wetzel T, Rheinpfalz DLR, `oltys K, Sabanadzovic S (2019) First report of grapevine rupestris vein feathering virus in grapevine in slovakia. Plant Disease 103(1): 170.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Grover CE, Arick MA, 2nd, Thrash A, Conover JL, Sanders WS, Peterson DG, Frelichowski JE, Scheffler JA, Scheffler BE, Wendel JF (2019) Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing. Genome Biology and Evolution 11(1): 53-71.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Han L, Li L, Wen F, Zhong L, Zhang T, Wan XF (2019) Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus. Bioinformatics (Oxford, England) 35(1): 77-87.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Horacek TM, Yildirim ED, Kelly E, White AA, Shelnutt KP, Riggsbee K, Olfert MD, Morrell JS, Mathews AE, Mosby TT, Kidd T, Kattelmann K, Greene G, Franzen-Castle L, Colby S, Byrd-Bredbenner C, Brown O (2018) Development and validation of a simple convenience store SHELF audit. International Journal of Environmental Research and Public Health 15(12): 2676.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Jiang J, Smith HN, Ren D, Mudiyanselage SDD, Dawe AL, Wang L, Wang Y (2018) Potato spindle tuber viroid modulates its replication through a direct interaction with a splicing regulator. Journal of Virology 92(20): e01004.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kosikova M, Li L, Radvak P, Ye Z, Wan XF, Xie H (2018) Imprinting of Repeated Influenza A/H3 Exposures on Antibody Quantity and Antibody Quality: Implications for Seasonal Vaccine Strain Selection and Vaccine Performance. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 67(10): 1523-1532.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Li L, Bowman AS, DeLiberto TJ, Killian ML, Krauss S, Nolting JM, Torchetti MK, Ramey AM, Reeves AB, Stallknecht DE, Webby RJ, Wan XF (2018) Genetic evidence supports sporadic and independent introductions of subtype H5 low-pathogenic avian influenza A viruses from wild birds to domestic poultry in North America. Journal of Virology 92(19): e00913.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Li L, DeLiberto TJ, Killian ML, Torchetti MK, Wan XF (2018) Evolutionary pathway for the 2017 emergence of a novel highly pathogenic avian influenza A(H7N9) virus among domestic poultry in Tennessee, United States. Virology 525: 32-39.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Nho SW, Abdelhamed H, Paul D, Park S, Mauel MJ, Karsi A, Lawrence ML (2018) Taxonomic and functional metagenomic profile of sediment from a commercial catfish pond in Mississippi. Frontiers in Microbiology 9(NOV): 02855.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Omer AR, Henderson JE, Falconer L, Kr?ger R, Allen PJ (2019) Economic costs of using tailwater recovery systems for maintaining water quality and irrigation. Journal of Environmental Management 235: 186-193.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Tak�? T, `amajov� O, Vadovi? P, Pechan T, `amaj J (2019) Shot-gun proteomic analysis on roots of arabidopsis pld?1 mutants suggesting the involvement of PLD?1 in mitochondrial protein import, vesicular trafficking and glucosinolate biosynthesis. International Journal of Molecular Sciences 20(1): 82.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Teimouri Jervekani M, Karimmojeni H, Razmjo J, Tseng TM (2018) Common sage (Salvia officinalis L.) tolerance to herbicides. Industrial Crops and Products 121: 46-53.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Thompson SK, Kutchy NA, Kwok S, Rosyada ZNA, Imumorin IG, Purwantara B, Memili E (2018) REVIEW: Sperm: Comparative morphology and function related to altered reproductive strategies and fertility in mammals. Professional Animal Scientist 34(6): 558-565.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Van Belleghem SM, Baquero M, Papa R, Salazar C, McMillan WO, Counterman BA, Jiggins C, Martin SH (2018) Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography. Molecular Ecology 27(19): 3852-3872.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Viana AGA, Martins AMA, Pontes AH, Fontes W, Castro MS, Ricart CAO, Sousa MV, Kaya A, Topper E, Memili E, Moura AA (2018) Proteomic landscape of seminal plasma associated with dairy bull fertility. Scientific Reports 8(1): 16323.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Wang X, Kiess AS, Peebles ED, Wamsley KGS, Zhai W (2018) Effects of Bacillus subtilis and zinc on the growth performance, internal organ development, and intestinal morphology of male broilers with or without subclinical coccidia challenge. Poultry Science 97(11): 3947-3956.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Wilson AE, Sparks DL, Knott KK, Willard S, Brown A (2018) Implementing solid phase microextraction (SPME) as a tool to detect volatile compounds produced by giant pandas in the environment. PLoS One 13(12): e0208618.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: You W, Yang Z, Guo G, Wan XF, Ji G (2019) Prediction of DNA-binding proteins by interaction fusion feature representation and selective ensemble. Knowledge-Based Systems 163: 598-610.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Ravichandran A, Geng M, Hull KG, Li J, Romo D, Lu SE, Albee A, Nutter C, Gordon DM, Ghannoum MA, Lockless SW, Smith L (2019) A novel actin binding drug with in vivo efficacy. Antimicrobial Agents and Chemotherapy 63(1): e01585-18.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Schuler GA, Brown MW (2019) Description of Armaparvus languidus n. gen. n. sp. Confirms Ultrastructural Unity of Cutosea (Amoebozoa, Evosea). Journal of Eukaryotic Microbiology 66(1): 158-166.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Schuler GA, Tice AK, Pearce RA, Foreman E, Stone J, Gammill S, Willson JD, Reading C, Silberman JD, Brown MW (2018) Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade. Protist 169(6): 853-874.
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Siegert CM, Clay NA, Tang JD, Garrigues LG, Riggins JJ (2018) Indirect effects of bark beetle-generated dead wood on biogeochemical and decomposition processes in a pine forest. Oecologia: in press.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Singh G, Sinha S, Bandyopadhyay KK, Lawrence M, Paul D (2018) Triauxic growth of an oleaginous red yeast Rhodosporidium toruloides on waste 'extract' for enhanced and concomitant lipid and ?-carotene production. Microbial cell factories 17(1): 182.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Zhang X, Sun H, Cunningham FL, Li L, Hanson-Dorr K, Hopken MW, Cooley J, Long LP, Baroch JA, Li T, Schmit BS, Lin X, Olivier AK, Jarman RG, DeLiberto TJ, Wan XF (2018) Tissue tropisms opt for transmissible reassortants during avian and swine influenza A virus co-infection in swine. PLoS Pathogens 14(12): e1007417.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Target audiences include scientists interested in conducting genomics, transcriptomics, proteomics, and metabolomics research; computational biologists; plant and animal breeders; microbiologists; agricultural scientists; farmers; ranchers; food safety scientists; veterinarians; evolutionary biologists; pathologists and forensic biologists; forest and wood products biologists; aquaculture and fisheries experts; entomologists; and human health scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?• The IGBB continued its active role in the University & Industry Consortium (UIC). The UIC is a group working to increase partnerships between agricultural, food, and biotechnology companies and land-grant institutions. The UIC began more than 20 years ago with Mississippi State serving as a founding member. The UIC provides opportunities for students and faculty to interact and develop research and educational collaborations with leaders in industry and academia. • The IGBB supported participation of research faculty, research associates, and students in a number of national and international scientific meetings. • The IGBB hosted a student from the public high school known as the Mississippi School for Mathematics & Science. The student learned the principles of virology from Dr. Nina Aboughanem, an IGBB faculty member. • The IGBB hosted several vendor shows and equipment demonstrations. • The IGBB helped Dr. Nina Aboughanem apply for promotion to associate research professor. No other IGBB faculty/staff members were eligible for promotion during FY17. How have the results been disseminated to communities of interest?Results have been disseminated to the scientific community through peer-reviewed publications, scientific meetings/presentations, faculty exchange programs, and the IGBB website (www.igbb.msstate.edu). In addition, DNA sequence and gene expression data were disseminated through AgBase (www.agbase.msstate.edu), CrocGenomes (www.crocgenomes.org), CottonGen (www.cottongen.org), VetBioBase (http://vetbiobase.igbb.msstate.edu), and the National Center for Biotechnology Information (NCBI; www.ncbi.nlm.nih.gov). What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period we plan to focus on expandingthe IGBB's computational biology expertise.Training and research plans will be adapted and modified as necessary.

Impacts
What was accomplished under these goals? Below is a list of our major project goals (1-5). Each goal is followed by accomplishments (each delineated by a bullet) made over the course of the last year that advanced that goal. (1) Conducting scientific research that meets the needs of society and further enhances the unique strengths of MS State. • The IGBB employed 19.5 people (FTE) during the period in question. In doing so, the IGBB helped strengthen MS State and the local/state economies. • The IGBB's total expenditures were $2.45 M. This is a $900K increase from FY16. • IGBB accounting records indicate that the IGBB Service Center brought in $189,000, a $39,000 increase from FY16. • Three technique/tool development publications were published in FY17. (2) Attracting and retaining outstanding faculty and students at MS State. • The IGBB employs Drs. Tibor Pechan, Nina Aboughanem, George Popescu, and Kurt Showmaker as research faculty. In this fiscal year Dr. Aboughanem, with the support of the IGBB director, submitted her application from assistant research professor to associate research professor. • The IGBB invested in the research programs of several MSU departmental faculty including Drs. Renita Horton (Ag and Bio Engineering - sickle cell anemia and heart disease), Erdogan Memili and Jean Feugang (Animal and Dairy Sciences - livestock fertility), Peter Allen and Federico Hoffmann (Aquaculture and Biochemistry, respectively - alligator gar genomics), and Shien Lu (Biochemistry - antifungal bacteria). • The IGBB has provided opportunities for five graduate students to earn their Ph.D. degrees. These students are funded through extramural awards to the IGBB. • The IGBB has continued to invest in purchase and maintenance of state-of-the-art equipment as a means of creating research opportunities and attracting/retaining faculty. In FY17 the IGBB purchased the service contracts for their LTQ Orbitrap Velos mass spectrometer and an Illumina MiSeq DNA sequencer. • In FY17 the IGBB purchased high performance computing storage devices, a floor centrifuge, several microcentrifuges, and multiple 2D gel devices. Purchase of an Oxford Nanopore GridIon DNA sequencer is in the works. (3) Offering researchers at MS State and elsewhere the opportunity to collaborate with the IGBB's genomics, proteomics, and computational biology experts. • Service Center and computer usage records indicate that the institute conducted collaborative research with 40 different MSU PIs representing ten different academic departments. • Records showed that the IGBB conducted service activities for investigators at three different USDA units, the US Army Corps of Engineers, and the U.S. Forest Service. (4) Helping principal investigators leverage the experience and expertise of the IGBB to make their research programs more productive, increase the number and scientific impact of their publications, and enhance their ability to procure extramural funding. • According to MS State Sponsored Programs records, 15 proposals were submitted through the IGBB. • Several new local/state/federal grants (net value = $1.0 M) submitted by the IGBB or with the IGBB as a collaborating unit were awarded to MSU faculty. • Ninety-two peer-reviewed manuscripts were published by IGBB-affiliated scientists during the fiscal year. • During the fiscal year IGBB-associated researchers IGBB faculty/staff/affiliates published one paper in each of the following journals: SCIENCE (IF = 33.611), NATURE REVIEWS MICROBIOLOGY (IF = 24.727), SYSTEMATIC BIOLOGY (IF = 8.225), and GENOME RESEARCH (IF = 11.351). • The IGBB continues to produced more Nature and Science papers than any other unit on MS State's campus. • Based on analysis using the SCOPUS database, 3.30% of all 728 IGBB peer-reviewed publications fall within the 99th percentile in terms of citation impact. 14.70% are in the 90th percentile or greater. (5) Supporting educational activities that enhance the abilities of students and faculty to succeed in the multidisciplinary fields of computational biology, genomics, and biotechnology. See Opportunities for Training and Professional Development below.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Abdelhamed H, Ibrahim I, Baumgartner W, Lawrence ML, Karsi A (2017) Characterization of histopathological and ultrastructural changes in channel catfish experimentally infected with virulent Aeromonas hydrophila. Frontiers in Microbiology 8: 1519. doi:10.3389/fmicb.2017.01519
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Abdelhamed H, Ibrahim I, Nho SW, Banes MM, Wills RW, Karsi A, Lawrence ML (2017) Evaluation of three recombinant outer membrane proteins, OmpA1, Tdr, and TbpA, as potential vaccine antigens against virulent Aeromonas hydrophila infection in channel catfish (Ictalurus punctatus). Fish and Shellfish Immunology 66: 480-486. doi:10.1016/j.fsi.2017.05.043
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Abdelhamed H, Lu J, Lawrence ML, Karsi A (2016) Ferric hydroxamate uptake system contributes to Edwardsiella ictaluri virulence. Microbial Pathogenesis 100: 195-200. doi:10.1016/j.micpath.2016.09.018
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Abdelhamed H, Lu J, Lawrence ML, Karsi A (2016) Involvement of tolQ and tolR genes in Edwardsiella ictaluri virulence. Microbial Pathogenesis 100: 90-94. doi:10.1016/j.micpath.2016.09.011
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Abdelhamed H, Nho SW, Turaga G, Banes MM, Karsi A, Lawrence ML (2016) Protective efficacy of four recombinant fimbrial proteins of virulent Aeromonas hydrophila strain ML09-119 in channel catfish. Veterinary Microbiology 197: 8-14. doi:10.1016/j.vetmic.2016.10.026
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Aboagye DL, Allen PJ (2017) Effects of acute and chronic hypoxia on acidbase regulation, hematology, ion, and osmoregulation of juvenile American paddlefish. Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology. 10.1007/s00360-017-1104-7:10.1007/s00360-017-1104-7: 1-12. doi:10.1007/s00360-017-1104-7
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert ML, Sabanadzovic S, Sanfacon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Orton RJ, Smith DB, Gorbalenya AE, Davison AJ (2017) 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Archives of Virology 162(5): 1441-1446. doi:10.1007/s00705-016-3215-y
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfacon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ (2017) Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017). Archives of Virology 162(8): 2505-2538. doi:10.1007/s00705-017-3358-5
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Allen PJ, Haukenes A, Lochmann SE (2017) Similarity of osmoregulatory capacity in coastal and inland alligator gar. Comparative Biochemistry and Physiology -Part A : Molecular and Integrative Physiology 209: 16-24. doi:10.1016/j.cbpa.2017.04.003
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bednarova A, Hanna M, Durham I, VanCleave T, England A, Chaudhuri A, Krishnan N (2017) Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. Frontiers in Molecular Neuroscience 10: 135. doi:10.3389/fnmol.2017.00135
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bednarova A, Hanna ME, Rakshit K, O'Donnell JM, Krishnan N (2017) Disruption of dopamine homeostasis has sexually dimorphic effects on senescence characteristics of Drosophila melanogaster. European Journal of Neuroscience 45(6): 816-825. doi:10.1111/ejn.13525
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bertram MR, Hamer SA, Hartup BK, Snowden KF, Medeiros MC, Outlaw DC, Hamer GL (2016) A novel Haemosporida clade at the rank of genus in North American cranes (Aves: Gruiformes). Molecular Phylogenetics and Evolution 109: 73-79. doi:10.1016/j.ympev.2016.12.025
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bertram MR, Hamer SA, Hartup BK, Snowden KF, Medeiros MC, Outlaw DC, Hamer GL (2017) A novel Haemosporida clade at the rank of genus in North American cranes (Aves: Gruiformes). Molecular Phylogenetics and Evolution 109: 73-79. doi:10.1016/j.ympev.2016.12.025
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bhatty M, Tan W, Basco M, Pruett S, Nanduri B (2017) Binge alcohol consumption 18 h after induction of sepsis in a mouse model causes rapid overgrowth of bacteria, a cytokine storm, and decreased survival. Alcohol 63: 9-17. doi:10.1016/j.alcohol.2016.11.007
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Brockmeier EK, Hodges G, Hutchinson TH, Butler E, Hecker M, Tollefsen KE, Garcia-Reyero N, Kille P, Becker D, Chipman K, Colbourne J, Collette TM, Cossins A, Cronin M, Graystock P, Gutsell S, Knapen D, Katsiadaki I, Lange A, Marshall S, Owen SF, Perkins EJ, Plaistow S, Schroeder A, Taylor D, Viant M, Ankley G, Falciani F (2017) The role of omics in the application of adverse outcome pathways for chemical risk assessment. Toxicological Sciences 158(2): 252-262. doi:10.1093/toxsci/kfx097
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Clay NA, Little N, Riggins JJ (2017) Inoculation of ophiostomatoid fungi in loblolly pine trees increases the presence of subterranean termites in fungal lesions. Arthropod-Plant Interactions 11(2): 213-219. doi:10.1007/s11829-016-9473-5
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Deng P, Foxfire A, Xu J, Baird SM, Jia J, Delgado KH, Shin R, Smith L, Lu SE (2017) The Siderophore Product Ornibactin Is Required for the Bactericidal Activity of Burkholderia contaminans MS14. Applied and Environmental Microbiology 83(8): doi:10.1128/AEM.00051-17
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Escher BI, Hackerm�ller J, Polte T, Scholz S, Aigner A, Altenburger R, Bohme A, Bopp SK, Brack W, Busch W, Chadeau-Hyam M, Covaci A, Eisentrager A, Galligan JJ, Garcia-Reyero N, Hartung T, Hein M, Herberth G, Jahnke A, Kleinjans J, Kluver N, Krauss M, Lamoree M, Lehmann I, Luckenbach T, Miller GW, Muller A, Phillips DH, Reemtsma T, Rolle-Kampczyk U, Schuurmann G, Schwikowski B, Tan YM, Trump S, Walter-Rohde S, Wambaugh JF (2017) From the exposome to mechanistic understanding of chemical-induced adverse effects. Environment International 99: 97-106. doi:10.1016/j.envint.2016.11.029
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Fast KM, Walstrom VW, Outlaw DC (2016) Haemosporidian Prevalence and Parasitemia In the Tufted Titmouse (Baeolophus bicolor). Journal of Parasitology 102(6): 636-642. doi:10.1645/15-935
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Fenner J, Seltzer J, Peyton S, Sullivan H, Tolson P, Walsh RP, Hill J, Counterman BA (2017) Demographic Variation of Wolbachia Infection in the Endangered Mitchell's Satyr Butterfly. Insects 8(2): doi:10.3390/insects8020050
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Feugang JM (2017) Novel agents for sperm purification, sorting, and imaging. Molecular Reproduction and Development 84(9): 832-841. doi:10.1002/mrd.22831
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Fleming D, Krishnan N, Musser F (2017) Polygalacturonase gene expression and enzymatic activity in salivary glands of laboratory reared and wild populations of Lygus lineolaris (Hemiptera: Miridae). European Journal of Entomology 114(1): 16-24. doi:10.14411/eje.2017.003
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Gastal GD, Alves BG, Alves KA, Souza ME, Vieira AD, Varela AS, Jr., Figueiredo JR, Feugang JM, Lucia T, Jr., Gastal EL (2017) Ovarian fragment sizes affect viability and morphology of preantral follicles during storage at 4 degrees C. Reproduction 153(5): 577-587. doi:10.1530/REP-16-0621
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Gastal GDA, Aguiar FLN, Alves BG, Alves KA, de Tarso SGS, Ishak GM, Cavinder CA, Feugang JM, Gastal EL (2017) Equine ovarian tissue viability after cryopreservation and in vitro culture. Theriogenology 97: 139-147. doi:10.1016/j.theriogenology.2017.04.029
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Gastal GDA, Hamilton A, Alves BG, de Tarso SGS, Feugang JM, Banz WJ, Apgar GA, Nielsen CK, Gastal EL (2017) Ovarian features in white-tailed deer (Odocoileus virginianus) fawns and does. PLoS One 12(5): e0177357. doi:10.1371/journal.pone.0177357
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gawryluk RM, Kamikawa R, Stairs CW, Silberman JD, Brown MW, Roger AJ (2016) The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian. Current Biology 26(20): 2729-2738. doi:10.1016/j.cub.2016.08.025
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Geisen S, Mitchell EAD, Wilkinson DM, Adl S, Bonkowski M, Brown MW, Fiore-Donno AM, Heger TJ, Jassey VEJ, Krashevska V, Lahr DJG, Marcisz K, Mulot M, Payne R, Singer D, Anderson OR, Charman DJ, Ekelund F, Griffiths BS, Ronn R, Smirnov A, Bass D, Belbahri L, Berney C, Blandenier Q, Chatzinotas A, Clarholm M, Dunthorn M, Feest A, Fernandez LD, Foissner W, Fournier B, Gentekaki E, Hajek M, Helder J, Jousset A, Koller R, Kumar S, La Terza A, Lamentowicz M, Mazei Y, Santos SS, Seppey CVW, Spiegel FW, Walochnik J, Winding A, Lara E (2017) Soil protistology rebooted: 30 fundamental questions to start with. Soil Biology and Biochemistry 111: 94-103. doi:10.1016/j.soilbio.2017.04.001
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Glasa M, Predajna L, Soltys K, Sihelska N, Nagyova A, Wetzel T, Sabanadzovic S (2017) Analysis of grapevine rupestris stem pitting-associated virus in Slovakia reveals differences in intra-host population diversity and naturally occurring recombination events. Plant Pathology Journal 33(1): 34-42. doi:10.5423/PPJ.OA.07.2016.0158
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hartshorn JA, Ray Fisher J, Riggins JJ, Stephen FM (2017) Molecular identification of Deladenus proximus Bedding, 1974 (Tylenchida: Neotylenchidae), a parasite of Sirex nigricornis (Hymenoptera: Siricidae). Nematology 19(1): 15-20. doi:10.1163/15685411-00003029
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hassan M, Di Bello PL, Keller KE, Martin RR, Sabanadzovic S, Tzanetakis IE (2017) A new, widespread emaravirus discovered in blackberry. Virus Research 235: 1-5. doi:10.1016/j.virusres.2017.04.006
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hofstatter PG, Tice AK, Kang S, Brown MW, Lahr DJ (2016) Evolution of bacterial recombinase A (recA) in eukaryotes explained by addition of genomic data of key microbial lineages. Proceedings of the Royal Society B: Biological Sciences 283(1840): pii: 20161453. doi:10.1098/rspb.2016.1453
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Horton RE (2017) Microfluidics for investigating vaso-occlusions in sickle cell disease. Microcirculation 24(5): e12373. doi:10.1111/micc.12373
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Howe K, Salehi S, Hartford Bailey R, Brooks JP, Wills R, Lawrence ML, Karsi A (2017) Supplemental invasion of Salmonella from the perspective of Salmonella enterica serovars Kentucky and Typhimurium. BMC Microbiology 17(1): 88. doi:10.1186/s12866-017-0989-3
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hughes MA, Riggins JJ, Koch FH, Cognato AI, Anderson C, Formby JP, Dreaden TJ, Ploetz RC, Smith JA (2017) No rest for the laurels: symbiotic invaders cause unprecedented damage to southern USA forests. Biological Invasions 19(7): 2143-2157. doi:10.1007/s10530-017-1427-z
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kenzig AR, Butler JR, Priddy LB, Lacy KR, Elder SH (2017) A biomechanical comparison of conventional dynamic compression plates and string-of-pearls" locking plates using cantilever bending in a canine Ilial fracture model. BMC Veterinary Research 13(1): doi:10.1186/s12917-017-1139-8
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kordon AO, Scott MA, Ibrahim I, Abdelhamed H, Ahmed H, Baumgartner W, Karsi A, Pinchuk LM (2016) Identification of Langerhans-like cells in the immunocompetent tissues of channel catfish, Ictalurus punctatus. Fish and Shellfish Immunology 58: 253-258. doi:10.1016/j.fsi.2016.09.033
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kumru S, Tekedar HC, Gulsoy N, Waldbieser GC, Lawrence ML, Karsi A (2017) Comparative analysis of the Flavobacterium columnare genomovar I and II genomes. Frontiers in Microbiology 8(JUL): doi:10.3389/fmicb.2017.01375
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kutchy NA, Velho A, Menezes ESB, Jacobsen M, Thibaudeau G, Wills RW, Moura A, Kaya A, Perkins A, Memili E (2017) Testis specific histone 2B is associated with sperm chromatin dynamics and bull fertility-a pilot study. Reproductive Biology and Endocrinology 15(1): doi:10.1186/s12958-017-0274-1
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Lei J, Priddy LB, Lim JJ, Koob TJ (2017) Dehydrated Human Amnion/Chorion Membrane (dHACM) Allografts as a Therapy for Orthopedic Tissue Repair. Techniques in Orthopaedics 32(3): 149-157. doi:10.1097/BTO.0000000000000229
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Luo J, Ferguson L, Smith DR, Woolums AR, Epperson WB, Wan XF (2017) Serological evidence for high prevalence of Influenza D Viruses in Cattle, Nebraska, United States, 20032004. Virology 501: 88-91. doi:10.1016/j.virol.2016.11.004
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Martin BE, Bowman AS, Li L, Nolting JM, Smith DR, Hanson LA, Wan XF (2017) Detection of antigenic variants of subtype H3 swine influenza A viruses from clinical samples. Journal of Clinical Microbiology 55(4): 1037-1045. doi:10.1128/JCM.02049-16
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Menezes EB, de Oliveira RV, van Tilburg MF, Barbosa EA, Nascimento NV, Velho ALMCS, Moreno FB, Moreira RA, Monteiro-Moreira ACO, Carvalho GMC, Ramos AF, Memili E, Moura AA (2017) Proteomic analysis of seminal plasma from locally-adapted Curraleiro P�-Duro bulls (Bos taurus): identifying biomarkers involved in sperm physiology in endangered animals for conservation of biodiversity. Animal Reproduction Science 183: 86-101. doi:10.1016/j.anireprosci.2017.05.014
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Miao Q, Deng P, Saha S, Jenkins JN, Hsu CY, Abdurakhmonov IY, Buriev ZT, Pepper A, Ma DP (2017) Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line. PLoS One 12(6): e0179381. doi:10.1371/journal.pone.0179381
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Mwima R, Gidudu A, Mazimwe A, Ligmann-Zielinska A, Majalija S, Khaitsa M, Kabasa JD, Bergholz P (2017) Spatially explicit uncertainty modeling of zoonotic pathogen distribution: a case of Listeria monocytogenes in New York State, USA. Applied Geomatics 9(1): 27-41. doi:10.1007/s12518-016-0177-4
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Nanduri B, Shack LA, Rai AN, Epperson WB, Baumgartner W, Schmidt TB, Edelmann MJ (2016) Use of focused ultrasonication in activity-based profiling of deubiquitinating enzymes in tissue. Analytical Biochemistry 515: 9-13. doi:10.1016/j.ab.2016.09.016
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Navarro B, Loconsole G, Giampetruzzi A, Aboughanem-Sabanadzovic N, Ragozzino A, Ragozzino E, Di Serio F (2017) Identification and characterization of privet leaf blotch-associated virus, a novel idaeovirus. Molecular Plant Pathology 18(7): 925-936. doi:10.1111/mpp.12450
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Noonan J, Williams WP, Shan X (2017) Investigation of antimicrobial peptide genes associated with fungus and insect resistance in maize. International Journal of Molecular Sciences 18(9): 1938. doi:10.3390/ijms18091938
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Ogunola OF, Hawkins LK, Mylroie E, Kolomiets MV, Borrego E, Tang JD, Williams WP, Warburton ML (2017) Characterization of the maize lipoxygenase gene family in relation to aflatoxin accumulation resistance. PLoS One 12(7): doi:10.1371/journal.pone.0181265
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Outlaw DC, Harvey JA, Drovetski SV, Voelker G (2016) Diversity and distribution of avian haemosporidians in sub-Saharan Africa: an inter-regional biogeographic overview. Parasitology 144(4): 394-402. doi:10.1017/S0031182016001979
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Peebles ED, Barbosa TM, Cummings TS, Dickson J, Womack SK, Gerard PD (2017) Comparative effects of in ovo versus subcutaneous administration of the Marek's disease vaccine and pre-placement holding time on the post-hatch performance of Ross 708 broilers1,2,3. Poultry Science 96(5): 1071-1077. doi:10.3382/ps/pew392
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Popescu SC, Brauer EK, Dimlioglu G, Popescu GV (2017) Insights into the Structure, Function, and Ion-Mediated Signaling Pathways Transduced by Plant Integrin-Linked Kinases. Frontiers in Plant Science 8: 376. doi:10.3389/fpls.2017.00376
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Postler TS, Clawson AN, Amarasinghe GK, Basler CF, Bavari S, Benko M, Blasdell KR, Briese T, Buchmeier MJ, Bukreyev A, Calisher CH, Chandran K, Charrel R, Clegg CS, Collins PL, Juan Carlos T, Derisi JL, Dietzgen RG, Dolnik O, Durrwald R, Dye JM, Easton AJ, Emonet S, Formenty P, Fouchier RAM, Ghedin E, Gonzalez JP, Harrach B, Hewson R, Horie M, Jiang D, Kobinger G, Kondo H, Kropinski AM, Krupovic M, Kurath G, Lamb RA, Leroy EM, Lukashevich IS, Maisner A, Mushegian AR, Netesov SV, Nowotny N, Patterson JL, Payne SL, PaWeska JT, Peters CJ, Radoshitzky SR, Rima BK, Romanowski V, Rubbenstroth D, Sabanadzovic S, Sanfacon H, Salvato MS, Schwemmle M, Smither SJ, Stenglein MD, Stone DM, Takada A, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang LF, Varsani A, Whitfield AE, Zerbini FM, Kuhn JH (2017) Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials. Systems Biology 66(3): 463-473. doi:10.1093/sysbio/syw096
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Reddy S, Turaga G, Abdelhamed H, Banes MM, Wills RW, Lawrence ML (2017) Listeria monocytogenes PdeE, a phosphodiesterase that contributes to virulence and has hydrolytic activity against cyclic mononucleotides and cyclic dinucleotides. Microbial Pathogenesis 110: 399-408. doi:10.1016/j.micpath.2017.07.020
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Reichley SR, Waldbieser GC, Lawrence ML, Griffin MJ (2017) Complete genome sequence of Edwardsiella hoshinae ATCC 35051. Genome Announcements 5(6): doi:10.1128/genomeA.01605-16
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Reichley SR, Waldbieser GC, Soto E, Lawrence ML, Griffin MJ (2017) Complete Genome Sequence of Edwardsiella ictaluri Isolate RUSVM-1 Recovered from Nile Tilapia (Oreochromis niloticus) in the Western Hemisphere. Genome Announcements 5(24): doi:10.1128/genomeA.00390-17
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Reichley SR, Waldbieser GC, Tekedar HC, Lawrence ML, M.J. G (2016) Complete genome sequence of Edwardsiella piscicida isolate S11-285 recovered from channel catfish (Ictalurus punctatus) in Mississippi, USA. Genome Announcements 4(6): e01259-01216. doi:10.1128/genomeA.01259-16
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN, 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ, Jr., Green RE (2017) Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research 27(5): 686-696. doi:10.1101/gr.213595.116
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Ricklefs RE, Medeiros M, Ellis VA, Svensson-Coelho M, Blake JG, Loiselle BA, Soares L, Fecchio A, Outlaw D, Marra PP, Latta SC, Valki?nas G, Hellgren O, Bensch S (2017) Avian migration and the distribution of malaria parasites in New World passerine birds. Journal of Biogeography 44(5): 1113-1123. doi:10.1111/jbi.12928
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Salehi S, Howe K, Lawrence ML, Brooks JP, Hartford Bailey R, Karsi A (2017) Salmonella enterica serovar Kentucky flagella are required for broiler skin adhesion and Caco-2 cell invasion. Applied and Environmental Microbiology 83(2): doi:10.1128/AEM.02115-16
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Schroeder AL, Martinovic-Weigelt D, Ankley GT, Lee KE, Garcia-Reyero N, Perkins EJ, Schoenfuss HL, Villeneuve DL (2017) Prior knowledge-based approach for associating contaminants with biological effects: A case study in the St. Croix River basin, MN, WI, USA. Environmental Pollution 221: 427-436. doi:10.1016/j.envpol.2016.12.005
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Shaak SG, Counterman BA (2017) High warning colour polymorphism in Heliconius hybrid zone roosts. Ecological Entomology 42(3): 315-324. doi:10.1111/een.12386
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Shahid MS, Aboughanem-Sabanadzovic N, Sabanadzovic S, Tzanetakis IE (2017) Genomic characterization and population structure of a badnavirus infecting blackberry. Plant Disease 101(1): 110-115. doi:10.1094/PDIS-04-16-0527-RE
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Shanmugam SG, Magbanua ZV, Williams MA, Jangid K, Whitman WB, Peterson DG, Kingery WL (2017) Bacterial Diversity Patterns Differ in Soils Developing in Sub-tropical and Cool-Temperate Ecosystems. Microbial Ecology 73(3): 556-569. doi:10.1007/s00248-016-0884-8
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Shields-Menard SA, AmirSadeghi M, Green M, Womack E, Sparks DL, Blake J, Edelmann M, Ding X, Sukhbaatar B, Hernandez R, Donaldson JR, French T (2017) The effects of model aromatic lignin compounds on growth and lipid accumulation of Rhodococcus rhodochrous. International Biodeterioration and Biodegradation 121: 79-90. doi:10.1016/j.ibiod.2017.03.023
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Showmaker KC, Arick MA, Hsu CY, Martin BE, Wang X, Jia J, Wubben MJ, Nichols RL, Allen TW, Peterson DG, Lu SE (2017) The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1. Standards in Genomic Sciences 12(1): doi:10.1186/s40793-017-0253-3
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Simmonds P, Adams MJ, Benko M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AM, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A, Zerbini FM (2017) Consensus statement: Virus taxonomy in the age of metagenomics. Nature Reviews Microbiology 15(3): 161-168. doi:10.1038/nrmicro.2016.177
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Skrobot F, III, Diehl SV, Borazjani H (2017) Mycotoxin production by Stachybotrys chartarum on water-damaged building materials. BioResources 12(3): 6490-6503. doi:10.15376/biores.12.3.6490-6503
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sokale AO, Zhai W, Pote LM, Williams CJ, Peebles ED (2017) Effects of coccidiosis vaccination administered by in ovo injection on the hatchability and hatching chick quality of broilers1,2,3. Poultry Science 96(3): 541-547. doi:10.3382/ps/pew370
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sokale AO, Zhai W, Pote LM, Williams CJ, Peebles ED (2017) Immunology, health, and disease: Effects of coccidiosis vaccination administered by in ovo injection on the hatchability and hatching chick quality of broilers. Poultry Science 96(3): 541-547. doi:10.3382/ps/pew370
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sun H, Kaplan BS, Guan M, Zhang G, Ye J, Long LP, Blackmon S, Yang CK, Chiang MJ, Xie H, Zhao N, Cooley J, Smith DF, Liao M, Cardona C, Li L, Wang GP, Webby R, Wan XF (2017) Pathogenicity and transmission of a swine influenza A(H6N6) virus. Emerging Microbes and Infections 6(4): e17. doi:10.1038/emi.2017.3
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Takac T, Samajova O, Pechan T, Luptovciak I, Samaj J (2017) Feedback microtubule control and microtubule-actin cross-talk in arabidopsis revealed by integrative proteomic and cell biology analysis of KATANIN 1 mutants. Molecular and Cellular Proteomics 16(9): 1591-1609. doi:10.1074/mcp.M117.068015
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Tekedar HC, Karsi A, Reddy JS, Nho SW, Kalindamar S, Lawrence ML (2017) Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512. Frontiers in Microbiology 8: 588. doi:10.3389/fmicb.2017.00588
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Tekedar HC, Kumru S, Kalindamar S, Karsi A, Waldbieser GC, Sonstegard T, Schroeder SG, Liles MR, Griffin MJ, Lawrence ML (2017) Draft genome sequences of three Aeromonas hydrophila isolates from catfish and tilapia. Genome Announcements 5(3): doi:10.1128/genomeA.01509-16
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Thekke-Veetil T, Khadgi A, Johnson D, Burrack H, Sabanadzovic S, Tzanetakis IE (2017) First report of Raspberry leaf mottle virus in Blackberry in the United States. Plant Disease 101(1): 265. doi:10.1094/PDIS-07-16-1014-PDN
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tice AK, Shadwick LL, Fiore-Donno AM, Geisen S, Kang S, Schuler GA, Spiegel FW, Wilkinson KA, Bonkowski M, Dumack K, Lahr DJ, Voelcker E, Clauss S, Zhang J, Brown MW (2016) Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group. Biology Direct 11(1): 69. doi:10.1186/s13062-016-0171-0
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gomez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE (2017) Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). Journal of Biomolecular Techniques 28(1): 31-39. doi:10.7171/jbt.17-2801-004
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Tomasco IH, Boullosa N, Hoffmann FG, Lessa EP (2017) Molecular adaptive convergence in the ?-globin in subterranean octodontid rodents. Gene 628: 275-280. doi:10.1016/j.gene.2017.07.057
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ulyshen MD, Diehl SV, Jeremic D (2016) Termites and flooding affect microbial communities in decomposing wood. International Biodeterioration and Biodegradation 115: 83-89. doi:10.1016/j.ibiod.2016.07.017
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Van Belleghem SM, Rastas P, Papanicolaou A, Martin SH, Arias CF, Supple MA, Hanly JJ, Mallet J, Lewis JJ, Hines HM, Ruiz M, Salazar C, Linares M, Moreira GRP, Jiggins CD, Counterman BA, McMillan WO, Papa R (2017) Complex modular architecture around a simple toolkit of wing pattern genes. Nature Ecology and Evolution 1(3): 52. doi:10.1038/s41559-016-0052
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Walstrom VW, Outlaw DC (2017) Distribution and Prevalence of Haemosporidian Parasites in the Northern Cardinal (Cardinalis cardinalis). Journal of Parasitology 103(1): 63-68. doi:10.1645/14-693
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang C, Liu H, Luo J, Chen L, Li M, Su W, Zhao N, Liu S, Xie L, Jia Y, Ding H, Wan X, He H (2017) HA Triggers the Switch from MEK1 SUMOylation to Phosphorylation of the ERK Pathway in Influenza A Virus-Infected Cells and Facilitates Its Infection. Frontiers in Cellular and Infection Microbiology 7: 27. doi:10.3389/fcimb.2017.00027
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang T, Feugang JM, Crenshaw MA, Regmi N, Blanton JR, Liao SF (2017) A Systems Biology Approach Using Transcriptomic Data Reveals Genes and Pathways in Porcine Skeletal Muscle Affected by Dietary Lysine. International Journal of Molecular Sciences 18(4): doi:10.3390/ijms18040885
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ward L, Lindsey S, Martin JM, Nicodemus M, Memili E (2016) REVIEW: Challenges and opportunities in rising feral horse populations. Professional Animal Scientist 32(6): 717-724. doi:10.15232/pas.2015-01415
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Welch ME, Colosimo G, Pasachnik SA, Malone CL, Hilton J, Long J, Getz AH, Alberts AC, Gerber GP (2017) Molecular variation and population structure in critically endangered Turks and Caicos Rock Iguanas: identifying intraspecific conservation units and revising subspecific taxonomy. Conservation Genetics 18(2): 479-493. doi:10.1007/s10592-016-0922-6
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wichmann IA, Zavala K, Hoffmann FG, Vandewege MW, Corvalan AH, Amigo JD, Owen GI, Opazo JC (2016) Evolutionary history of the reprimo tumor suppressor gene family in vertebrates with a description of a new reprimo gene lineage. Gene 591(1): 245-254. doi:10.1016/j.gene.2016.07.036
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wren JD, Toby I, Hong H, Nanduri B, Kaundal R, Dozmorov MG, Thakkar S (2016) Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 17(Suppl 13): 356. doi:10.1186/s12859-016-1213-4
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wright AA, Nandula VK, Grier L, Showmaker KC, Bond JA, Peterson DG, Ray JD, Shaw DR (2016) Characterization of Fenoxaprop-P-ethyl Resistant Echinochloa colona from Mississippi. Weed Science 64: 588-595. doi:10.1614/WS-D-16-00024.1
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Xie H, Li L, Ye Z, Li X, Plant EP, Zoueva O, Zhao Y, Jing X, Lin Z, Kawano T, Chiang MJ, Finch CL, Kosikova M, Zhang A, Zhu Y, Wan XF (2017) Differential Effects of Prior Influenza Exposures on H3N2 Cross-reactivity of Human Postvaccination Sera. Clinical Infectious Diseases 65(2): 259-267. doi:10.1093/cid/cix269
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Xing S, Meng X, Zhou L, Mujahid H, Zhao C, Zhang Y, Wang C, Peng Z (2016) Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm. PLoS One 11(12): e0168467. doi:10.1371/journal.pone.0168467
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Xu Y, Ramey AM, Bowman AS, DeLiberto TJ, Killian ML, Krauss S, Nolting JM, Torchetti MK, Reeves AB, Webby RJ, Stallknecht DE, Wan XF (2017) Low-Pathogenic Influenza A Viruses in North American Diving Ducks Contribute to the Emergence of a Novel Highly Pathogenic Influenza A(H7N8) Virus. Journal of Virology 91(9): e02208-02216. doi:10.1128/JVI.02208-16
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Zavala K, Vandewege MW, Hoffmann FG, Opazo JC (2017) Evolution of the ?-adrenoreceptors in vertebrates. General and Comparative Endocrinology 240: 129-137. doi:10.1016/j.ygcen.2016.10.005
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Zhao Y, Jackson V, Ciaramella MA, Lolley AT, Allen PJ, Schilling M (2017) Impact of marination, pre-harvest salt acclimation and sodium chloride concentration on the sensory acceptability of freshwater prawn, Macrobrachium rosenbergii. Aquaculture Research 48(5): 2096-2101. doi:10.1111/are.13044


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Target audiences include scientists interested in conducting genomics, transcriptomics, proteomics, and metabolomicsresearch; computational biologists; plant and animal breeders; microbiologists; agricultural scientists; farmers; ranchers; foodsafety scientists; veterinarians; evolutionary biologists; pathologists and forensic biologists; forest and wood products biologists; aquaculture and fisheries experts; entomologists; and human health scientists. Changes/Problems:The size of the IGBB faculty has grown during the last fiscal year. Consequently, the decision was made to convert a small conference room in the IGBB lab building (Pace Building) into wet lab space. The estimated cost for this renovation is $25,000. What opportunities for training and professional development has the project provided?• The IGBB co-sponsored the 2016 Southeastern Pneumococcal Symposiumwhich was held at Mississippi State University. • The IGBB continued its active role in the University & Industry Consortium (UIC). The UIC is a group working to increase partnerships between agricultural, food, and biotechnology companies and land-grant institutions. The UIC began more than 20 years ago with Mississippi State serving as a founding member. The UIC provides opportunities for students and faculty to interact and develop research and educational collaborations with leaders in industry and academia. •The IGBB sent computational biologyresearch associate Tony Arickto the Plant & Animal Genome Conference(San Diego, CA) and the ESnet CrossConnects Bioinformatics Conference (Lawrence Berkeley Nat'l Laboratory, Berkeley, CA). •The IGBB funded participation of postdoctoral associate Dinum Pererain theMid-South Computational Biology & Bioinformatics Society meeting (Memphis, TN). •The IGBB supported participation of research associate professor Dr. Tibor Pechan in the 64th Conference on Mass Spectrometry & Allied Topics in San Antonio, TXand the 2nd International Plant Proteomics Organization (IPPO)World Congress in Bratislava, Slovakia. •The IGBB hosted a student from the public high school known as the Mississippi School for Mathematics & Science. The student learned the principles of virology from Dr. Nina Aboughanem, an IGBB faculty member. • Dr. Daniel Peterson, IGBB Director, gave invited seminars for students and faculty atmeetings in Orleans, France and Goiana, Brazil. •The IGBB hosted several vendor shows and equipmentdemonstrations. How have the results been disseminated to communities of interest?Results have been disseminated to the scientific community through peer-reviewed publications, scientificmeetings/presentations, faculty exchange programs, and the IGBB website (www.igbb.msstate.edu). In addition, DNAsequence and gene expression data were disseminated through AgBase (www.agbase.msstate.edu), CrocGenomes(www.crocgenomes.org), CottonGen (www.cottongen.org), VetBioBase (http://vetbiobase.igbb.msstate.edu) and the NationalCenter for Biotechnology Information (NCBI; www.ncbi.nlm.nih.gov). What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period we plan to expand the IGBB's local user base through distribution of a professional annualreport, presentations at academic department meetings, and through our website. Training and researchplans will be adapted and modified as necessary.

Impacts
What was accomplished under these goals? Below is a list of our major project goals (1-5). Each goal is followed by accomplishments (each delineated by a bullet) made over the course of the last year that advanced that goal. (1) Conducting scientific research that meets the needs of society and further enhances the unique strengths of MS State. • The IGBB employed, in full or part, 20 people during the period in question. In doing so, the IGBB helped strengthen MS State and the local/state economies. • The IGBB's total expenditures were $1.55 M. Though there have been ups and downs, the general economic benefits of the IGBB have increased from about $500,000 in expenditures in 2007 to > $1.5 M in FY16. • IGBB accounting records indicate that the IGBB Service Center brought in $150,000. • Five technique/tool development publications were published in FY16. (2) Attracting and retaining outstanding faculty and students at MS State. • The IGBB recruited Drs. George Popescu and Kurt Showmaker into research assistant professor roles. •The IGBB was instrumental in attracting Drs. Lauren Priddy to the university. Dr. Priddy is a tenure-track faculty member in the Department of Agricultural & Biological Engineering. Her focus is on the molecular processes involved in bone regeneration. • The IGBB has provided opportunities for three graduate students to earntheir Ph.D. degrees. These students are funded through extramural awards to the IGBB. • The IGBB has continued to invest in purchase and maintenance of state-of-the-art equipment as a means of creating research opportunities and attracting/retaining faculty. In FY16 the IGBB purchased the service contracts for their LTQ Orbitrap Velos mass spectrometer ($44,749) and an Illumina MiSeq DNA sequencer ($15,965). In addition, the IGBB paid $17,160to repair its GE Healthcare Typhoon Phosphoimager. • In FY16 the IGBB spent $179K on new equipment. Items include a newquantitative RT-PCR machine, a Wes protein analysis system, a fragment analyzer, a SageELF, a plate reader, anda mixer mill. (3) Offering researchers at MS State and elsewhere the opportunity to collaborate with the IGBB's genomics, proteomics, and computational biology experts. • Internal records revealed that IGBB employees were engaged in research projects with 30 different MS State PIs representing nine academic departments. Fourteen MSU faculty members utilize the High Performance Computing Collaboratory supercomputers through their affiliation with the IGBB. • Records showed that the IGBB conducted service activities for investigators at three differentUSDA units,Global Biologics (a biotech company),theUS Army Corps of Engineers, and the U.S. Forest Service. (4) Helping principal investigators leverage the experience and expertise of the IGBB to make their research programs more productive, increase the number and scientific impact of their publications, and enhance their ability to procure extramural funding. • According to MS State Sponsored Programs records, 9 proposals were submitted through the IGBB. • Six new local/state/federal grants submitted by the IGBB or with the IGBB as a collaborating unit were awarded to MSU faculty (net value = $1.36 M). • Seventy-eight peer-reviewed manuscripts were published by IGBB-affiliated scientists during the fiscal year. • During the fiscal year IGBB-associated researcherspublished five papers in journals with Thomson ReutersImpact Factors greater than 6; one paper in Nature (IF =41.456), one in Plant Physiology (IF = 6.841), one inEnvironmental Microbiology (IF = 6.201), one in Cell Reports(IF = 7.207), and one in Molecular Biology & Evolution (IF =14.308). • The IGBB continues to produced more Nature and Science papers than any other unit on MS State's campus. (5) Supporting educational activities that enhance the abilities of students and faculty to succeed in the multidisciplinary fields of computational biology, genomics, and biotechnology. See Opportunities for Training and Professional Development below.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang T, Zhao M, Rotgans BA, Ni G, Dean JF, Nahrung HF,Cummins SF (2016) Proteomic analysis of the venom and venom sac of the woodwasp, Sirex noctilio - Towards understanding its biological impact. Journal of Proteomics 146: 195-206.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tice AK, Silberman JD, Walthall AC, Le KN, Spiegel FW,Brown MW (2016) Sorodiplophrys stercorea: Another Novel Lineage of Sorocarpic Multicellularity. Journal of Eukaryotic Microbiology 63(5): 623-628.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kumar P, He Y, Singh R, Davis RF, Guo H, Paterson AH, Peterson DG, Shen X, Nichols RL,Chee PW (2016) Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton. BMC Genomics 17: 567.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hartshorn JA, Haavik LJ, Allison JD, Meeker JR, Johnson W, Galligan LD, Chase KD, Riggins JJ,Stephen FM (2016) Emergence of adult female Sirex nigricornis F. and Sirex noctilio F. (Hymenoptera: Siricidae) coincides with a decrease in daily minimum and maximum temperature. Agricultural and Forest Entomology 18(3): 206-213.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ramee SW,Allen PJ (2016) Freshwater influences on embryos, hatching and larval survival of euryhaline Gulf killifish Fundulus grandis and potential constraints on habitat distribution. Journal of Fish Biology 89(2): 1466-1472.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Noguchi F, Tanifuji G, Brown MW, Fujikura K, Takishita K (2016) Complex evolution of two types of cardiolipin synthase in the eukaryotic lineage stramenopiles. Molecular Phylogenetics and Evolution 101: 133-141.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Fleming DE, Krishnan N, Catchot AL, Musser FR (2016) Susceptibility to insecticides and activities of glutathione S-transferase and esterase in populations of Lygus lineolaris (Hemiptera: Miridae) in Mississippi. Pest Management Science 72(8): 1595-1603.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Salehi S, Howe K, Brooks J, Lawrence ML, Bailey RH,Karsi A (2016) Identification of Salmonella enterica serovar Kentucky genes involved in attachment to chicken skin. BMC Microbiology 16(1): 168.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Brauer EK, Ahsan N, Dale R, Kato N, Coluccio AE, Pineros MA, Kochian LV, Thelen JJ, Popescu SC (2016) The Raf-like Kinase ILK1 and the High Affinity K+ Transporter HAK5 Are Required for Innate Immunity and Abiotic Stress Response. Plant Physiology 171(2): 1470-1484.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Rai AN, Thornton JA, Stokes J, Sunesara I, Swiatlo E, Nanduri B (2016) Polyamine transporter in Streptococcus pneumoniae is essential for evading early innate immune responses in pneumococcal pneumonia. Scientific Reports -UK 6: 26964.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang X, Farnell YZ, Peebles ED, Kiess AS, Wamsley KG, Zhai W (2016) Effects of prebiotics, probiotics, and their combination on growth performance, small intestine morphology, and resident Lactobacillus of male broilers. Poultry Science 95(6): 1332-1340.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kaya A, Memili E (2016) Sperm macromolecules associated with bull fertility. Animal Reproduction Science 169: 88-94.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Garcia-Reyero N, Escalon L, Prats E, Faria M, Soares AM, Raldua D (2016) Targeted Gene Expression in Zebrafish Exposed to Chlorpyrifos-Oxon Confirms Phenotype-Specific Mechanisms Leading to Adverse Outcomes. Bulletin of Environmental Contamination and Toxicology 96(6): 707-713.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Garcia-Reyero N (2016) Advancing Ecotoxicology in the US Southern States. Bulletin of Environmental Contamination and Toxicology 96(6): 705-706.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ciaramella MA, Nair MN, Suman SP, Allen PJ,Schilling MW (2016) Differential abundance of muscle proteome in cultured channel catfish (Ictalurus punctatus) subjected to ante-mortem stressors and its impact on fillet quality. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 20: 10-18.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Takac T, Vadovic P, Pechan T, Luptovciak I, Samajova O,Samaj J (2016) Comparative proteomic study of Arabidopsis mutants mpk4 and mpk6. Scientific Reports 6: 28306.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ferguson L, Olivier AK, Genova S, Epperson WB, Smith DR, Schneider L, Barton K, McCuan K, Webby RJ,Wan XF (2016) Pathogenesis of Influenza D Virus in Cattle. Journal of Virology 90(12): 5636-5642.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hamann E, Gruber-Vodicka H, Kleiner M, Tegetmeyer HE, Riedel D, Littmann S, Chen J, Milucka J, Viehweger B, Becker KW, Dong X, Stairs CW, Hinrichs KU, Brown MW, Roger AJ, Strous M (2016) Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature 534(7606): 254-258.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Giejdasz K, Fliszkiewicz M, Bednarova A,Krishan N (2016) Reproductive potential and nesting effects of Osmia rufa (Syn. Bicornis) female (Hymenoptera: Megachilidae). Journal of Apiculture Science 60(1): 75-85.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Culpepper III CM, Allen PJ (2016) Aquaculture Techniques for Crappie, Pomoxis spp., Culture. Journal of the World Aquaculture Society 47(3): 314-326.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhai W, Peebles ED, Wang X, Gerard PD, Olanrewaju HA, Mercier Y (2016) Effects of dietary lysine and methionine supplementation on Ross 708 male broilers from 21 to 42 d of age (III): Serum metabolites, hormones, and their relationship with growth performance. Journal of Applied Poultry Research 25(2): 223-231.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhai W, Schilling MW, Jackson V, Peebles ED, Mercier Y (2016) Effects of dietary lysine and methionine supplementation on Ross 708 male broilers from 21 to 42 days of age (II): Breast meat quality. Journal of Applied Poultry Research 25(2): 212-222.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhai W, Peebles ED, Schilling MW, Mercier Y (2016) Effects of dietary lysine and methionine supplementation on Ross 708 male broilers from 21 to 42 d of age (I): Growth performance, meat yield, and cost effectiveness. Journal of Applied Poultry Research 25(2): 197-211.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Shahid MS, Tzanetakis IE, Aboughanem-Sabanadzovic N, Sabanadzovic S (2016) An integrating Badnavirus infects blackberry. Acta Horticulturae 1133: 507-510.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Lv Y, Liang Z, Ge M, Qi W, Zhang T, Lin F, Peng Z, Zhao H (2016) Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.). BMC Genomics 17(1): 350.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Williams CL, Dill-McFarland KA, Vandewege MW, Sparks DL, Willard ST, Kouba AJ, Suen G, Brown AE (2016) Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca). Frontiers in Microbiology 7: 661.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bass D, Silberman JD, Brown MW, Pearce RA, Tice AK, Jousset A, Geisen S, Hartikainen H (2016) Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists. Environmental Microbiology 18(5): 1604-1619.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Alugubelly N, Hercik K, Kibler P, Nanduri B, Edelmann MJ (2016) Analysis of differentially expressed proteins in Yersinia enterocolitica-infected HeLa cells. Biochimica et Biophysica Acta-Proteins and Proteomics 1864(5): 562-569.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Clarke SR, Riggins JJ, Stephen FM (2016) Forest management and southern pine beetle outbreaks: A historical perspective. Forest Science 62(2): 166-180.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Popescu SC (2016) Protein networks - A driving force for discovery in plant science. Current Plant Biology 5: 1.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Eyun SI, Moriyama H, Hoffmann FG, Moriyama EN (2016) Molecular Evolution and Functional Divergence of Trace Amine-Associated Receptors. PLoS One 11(3): e0151023.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Aplasca AC, Iverson JB, Welch ME, Colosimo G, Hekkala ER (2016) Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata. PeerJ 4: e1793.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Warnock JN, Mohammadi-Aragh MJ (2016) Case study: use of problem-based learning to develop students' technical and professional skills. European Journal of Engineering Education 41(2): 142-153.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Sabanadzovic S, Wintermantel WM, Valverde RA, McCreight JD, Aboughanem-Sabanadzovic N (2016) Cucumis melo endornavirus: Genome organization, host range and co-divergence with the host. Virus Research 214: 49-58.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mangum LH, Crow JA, Stokes JV, Howell GE, III, Ross MK, Pruett SB, Chambers JE (2016) Exposure to p,p'-DDE Alters Macrophage Reactivity and Increases Macrophage Numbers in Adipose Stromal Vascular Fraction. Toxicological Sciences 150(1): 169-177.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Xu Y, Bailey E, Spackman E, Li T, Wang H, Long LP, Baroch JA, Cunningham FL, Lin X, Jarman RG, DeLiberto TJ, Wan XF (2016) Limited Antigenic Diversity in Contemporary H7 Avian-Origin Influenza A Viruses from North America. Scientific Reports 6: 20688.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Vidal-Dorsch DE, Bay SM, Moore S, Layton B, Mehinto AC, Vulpe CD, Brown-Augustine M, Loguinov A, Poynton H, Garcia-Reyero N, Perkins EJ, Escalon L, Denslow ND, Cristina CD, Doan T, Shukradas S, Bruno J, Brown L, Van AG, Jackman P, Bauer M (2016) Ecotoxicogenomics: Microarray interlaboratory comparability. Chemosphere 144: 193-200.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Haines JM, Thomason JM, Seage EC, Wills RW, Bulla C, Lunsford KV, Mackin AJ (2016) In vitro and in vivo assessment of platelet function in healthy dogs during administration of a low-dose aspirin regimen. American Journal of Veterinary Research 77(2): 174-185.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Warnock J, Mohammadi-Aragh MJ (2016) Case study: use of problem-based learning to develop students' technical and professional skills. European Journal of Engineering Education 41(2): 142-153.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Panek T, Zadrobilkova E, Walker G, Brown MW, Gentekaki E, Hroudova M, Kang S, Roger AJ, Tice AK, Vlcek C, Cepicka I (2016) First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. Molecular Phylogenetics and Evolution 98: 41-51.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Brown LR, Gunnell SM, Cassella AN, Keller LE, Scherkenbach LA, Mann B, Brown MW, Hill R, Fitzkee NC, Rosch JW, Tuomanen EI, Thornton JA (2016) AdcAII of Streptococcus pneumoniae Affects Pneumococcal Invasiveness. PLoS One 11(1): e0146785.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mylroie JE, Ozkan S, Shivaji R, Windham GL, Alpe MN, Williams WP (2016) Identification and Quantification of a Toxigenic and Non-Toxigenic Aspergillus flavus Strain in Contaminated Maize Using Quantitative Real-Time PCR. Toxins 8(1): pii: E15.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hebrard C, Peterson DG, Willems G, Delaunay A, Jesson B, Lefebvre M, Barnes S, Maury S (2016) Epigenomics and bolting tolerance in sugar beet genotypes. Journal of Experimental Botany 67(1): 207-225.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Aboughanem-Sabanadzovic N, Tzanetakis IE, Lawrence A, Stephenson RC, Sabanadzovic S (2016) A Novel Ilarvirus Is Associated with Privet Necrotic Ringspot Disease in the Southern United States. Phytopathology 106(1): 87-93.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ramee S, Green C, Allen PJ (2016) Effects of Low Salinities on Osmoregulation, Growth, and Survival of Juvenile Gulf Killifish. North American Journal of Aquaculture 78(1): 8-19.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Deng P, Wang X, Baird SM, Lu SE (2015) Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato. Standards in Genomic Sciences 10: 117.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Moorthy SM, Chandrakanth N, Krishan N (2015) Inheritance of heat stable esterase in near isogenic lines and functional classification of esterase in silkworm Bombyx mori. Invertebrate Survival Journal 13: 1-10.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Pechanova O, Pechan T (2015) Maize-Pathogen Interactions: An Ongoing Combat from a Proteomics Perspective. International Journal of Molecular Sciences 16(12): 28429-28448.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Buza TM, Jack SW, Kirunda H, Khaitsa ML, Lawrence ML, Pruett S, Peterson DG (2015) ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases. Database 2015: bav110.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Showmaker KC, Bednarova A, Gresham C, Hsu CY, Peterson DG, Krishnan N (2016) Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PLoS One 11(1): e0147197.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Campanini EB, Vandewege MW, Pillai NE, Tay BH, Jones JL, Venkatesh B, Hoffmann FG (2015) Early Evolution of Vertebrate Mybs: An Integrative Perspective Combining Synteny, Phylogenetic, and Gene Expression Analyses. Genome Biology and Evolution 7(11): 3009-3021.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: White SJ, McClung DM, Wilson JG, Roberts BN, Donaldson JR (2015) Influence of pH on bile sensitivity amongst various strains of Listeria monocytogenes under aerobic and anaerobic conditions. Journal of Medical Microbiology 64(11): 1287-1296.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ohno KM, Clausen CA, Green III F, Diehl SV (2015) Insights into the mechanism of copper-tolerance in Fibroporia radiculosa: The biosynthesis of oxalate. International Biodeterioration and Biodegration 105: 90-96.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Zhang YD, Zheng J, Liang ZK, Liang YL, Peng ZH, Wang CL (2015) Verification and evaluation of grain QTLs using RILs from TD70 x Kasalath in rice. Genetics and Molecular Research 14(4): 14882-14892.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Zhao N, Martin BE, Yang CK, Luo F, Wan XF (2015) Association analyses of large-scale glycan microarray data reveal novel host-specific substructures in influenza A virus binding glycans. Scientific Reports 5: 15778.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Faria M, Garcia-Reyero N, Padros F, Babin PJ, Sebastian D, Cachot J, Prats E, Arick IM, Rial E, Knoll-Gellida A, Mathieu G, Le BF, Escalon BL, Zorzano A, Soares AM, Raldua D (2015) Zebrafish Models for Human Acute Organophosphorus Poisoning. Scientific Reports 5: 15591.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Rai AN, Epperson WB, Nanduri B (2015) Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. Bioinformatics and Biology Insights 9(Suppl 2): 13-23.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sotero-Caio CG, Volleth M, Hoffmann FG, Scott L, Wichman HA, Yang F, Baker RJ (2015) Integration of molecular cytogenetics, dated molecular phylogeny, and model-based predictions to understand the extreme chromosome reorganization in the Neotropical genus Tonatia (Chiroptera: Phyllostomidae). BMC Evolutionary Biology 15: 220.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kook I, Henley C, Meyer F, Hoffmann FG, Jones C (2015) Bovine herpesvirus 1 productive infection and immediate early transcription unit 1 promoter are stimulated by the synthetic corticosteroid dexamethasone. Virology 484: 377-385.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Standish JR, Tomaso-Peterson M, Allen TW, Sabanadzovic S, Aboughanem-Sabanadzovic N (2015) Occurrence of qoi fungicide resistance in Cercospora sojina from Mississippi Soybean. Plant Disease 99(10): 1347-1352.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Stewart HA, Bosworth B, Petrie-Hanson L, Martin JA, Allen PJ (2015) Effects of chronic upper temperature regimes on growth of two geographical strains of channel and hybrid catfish. Aquaculture Research 46(10): 2407-2417.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Supple MA, Papa R, Hines HM, McMillan WO, Counterman BA (2015) Divergence with gene flow across a speciation continuum of Heliconius butterflies. BMC Evolutionary Biology 15: 204.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Xie H, Wan XF, Ye Z, Plant EP, Zhao Y, Xu Y, Li X, Finch C, Zhao N, Kawano T, Zoueva O, Chiang MJ, Jing X, Lin Z, Zhang A, Zhu Y (2015) H3N2 Mismatch of 2014-15 Northern Hemisphere Influenza Vaccines and Head-to-head Comparison between Human and Ferret Antisera derived Antigenic Maps. Scientific Reports 5: 15279.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Su W, Wang C, Luo J, Zhao Y, Wu Y, Chen L, Zhao N, Li M, Xing C, Liu H, Zhang H, Chang YF, Li T, Ding H, Wan X, He H (2015) Testing the Effect of Internal Genes Derived from a Wild-Bird-Origin H9N2 Influenza A Virus on the Pathogenicity of an A/H7N9 Virus. Cell Reports 12(11): 1831-1841.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ferguson L, Eckard L, Epperson WB, Long LP, Smith D, Huston C, Genova S, Webby R, Wan XF (2015) Influenza D virus infection in Mississippi beef cattle. Virology 486: 28-34.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Altinok I, Capkin E, Karsi A (2015) Succinate dehydrogenase mutant of Listonella anguillarum protects rainbow trout against vibriosis. Vaccine 33(42): 5572-5577.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sun H, Cunningham FL, Harris J, Xu Y, Long LP, Hanson-Dorr K, Baroch JA, Fioranelli P, Lutman MW, Li T, Pedersen K, Schmit BS, Cooley J, Lin X, Jarman RG, DeLiberto TJ, Wan XF (2015) Dynamics of virus shedding and antibody responses in influenza A virus-infected feral swine. Journal of General Virology 96(9): 2569-2578.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nho SW, Abdelhamed H, Reddy S, Karsi A, Lawrence ML (2015) Identification of high-risk Listeria monocytogenes serotypes in lineage I (serotype 1/2a, 1/2c, 3a and 3c) using multiplex PCR. Journal of Applied Microbiology 119(3): 845-852.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Warburton ML, Tang JD, Windham GL, Hawkins LK, Murray SC, Xu W, Boykin D, Perkins A, Williams WP (2015) Genome-wide association mapping of Aspergillus flavus and aflatoxin accumulation resistance in maize. Crop Science 55(5): 1857-1867.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Target audiences include faculty interested in conducting genomics, transcriptomics, proteomics, and metabolomics research; computational biologists; plant and animal breeders; microbiologists; agricultural scientists; farmers; ranchers; food safety scientists; veterinarians; evolutionary biologists;pathologists and forensic biologists; and human health scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?• The IGBB hosted campus visits/workshops from several biotech companies including Pacific Biosciences, BioNano Genomics, and ProteinSimple. • The IGBB continued its active role in the University & Industry Consortium (UIC). The UIC is a group working to increase partnerships between agricultural, food, and biotechnology companies and land-grant institutions. The UIC began more than 20 years ago with Mississippi State serving as a founding member. The UIC provides opportunities for students and faculty to interact and develop research and educational collaborations with leaders in industry and academia. • The IGBB hosted another visit by Dr. Tomas Takac from Palacky University in the Czech Republic. Dr. Takac has had a very fruitful collaboration with IGBB faculty member Dr. Tibor Pechan. Later in the year, Dr. Takac returned the favor by hosting a visit by Dr. Pechan to the Czech Republic/Slovakia. • The IGBB sent research associate Jo-Ann Ding to the annual meeting of the American Society for Plant Biologists. Until recently, Ms. Ding was in charge of mass spectrometry at the IGBB's Service Center. • The IGBB funded participation by postdoctoral associate Shane Sanders and research associate Kurt Showmaker in the Plant & Animal Genome Conference and the Mid-South Computational Biology & Bioinformatics Society meeting. The IGBB also funded Mr. Showmakers participation in two nematode-specific research meetings. • The IGBB trained Pakistani cotton scientists Rubab Naqvi and Muhammed Farooq through Borlaug Fellowships. Ms. Naqvi and Mr. Farooq learned the basics of high performance computing and computational biology during their time at the IGBB. They will apply these computational techniques to their cotton research programs which are aimed at controling the spread of cotton leaf curl virus in Pakistan. • The IGBB hosted a student from the public high school known as the Mississippi School for Mathematics & Science. The student learned the principles of virology from Dr. Nina Aboughanem, an IGBB faculty member. • Dr. Daniel Peterson, IGBB Director, gave an invited seminar for students and faculty at a meeting in Vienna, Austria. In addition, Dr. Peterson traveled to Iguassu Falls, Brazil to discuss research collaborations with Brazilian crop scientists. How have the results been disseminated to communities of interest?Results have been disseminated to the scientific community through peer-reviewed publications, scientific meetings/presentations, faculty exchange programs, and the IGBB website (www.igbb.msstate.edu). In addition, DNA sequence and gene expression data were disseminated through AgBase (www.agbase.msstate.edu), CrocGenomes (www.crocgenomes.org), CottonGen (www.cottongen.org), VetBioBase (http://vetbiobase.igbb.msstate.edu) and the National Center for Biotechnology Information (NCBI; www.ncbi.nlm.nih.gov). What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period we plan to expand the IGBB's local user base through distribution of a professional annual report, presentations at academic department meetings, and through our new, imrproved website. Training and research plans will be adapted and modified as necessary.

Impacts
What was accomplished under these goals? Below is a list of our major project goals (1-5). Each goal is followed by accomplishments (each delineated by a bullet) made over the course of the last year that advanced that goal. (1) Conducting scientific research that meets the needs of society and further enhances the unique strengths of MS State. • The IGBB employed, in full or part, 17 people during the period in question. In doing so, the IGBB helped strengthen MS State and the local/state economies. • The IGBB's total expenditures were $1.69 M. Though there have been ups and downs, the general economic benefits of the IGBB have increased from about $500,000 in expenditures in 2007 to > $1.5 M in 2015. • IGBB accounting records indicate that the IGBB Service Center brought in $43,939. • Nine technique/tool development publications were published in FY14. Tools and techniques developed through IGBB research include (a) new software for more accurate DNA sequence alignment, (b) a cross-linking technique for determining protein:protein interactions, (c) a technique for generating influenza vaccine candidates, and (d) a plasmid for gene mutation in Listeria, (e) a microRNA database for domestic animals, and (f) a new means of detecting influenza infections. (2) Attracting and retaining outstanding faculty and students at MS State. • The IGBB was instrumental in attracting Drs. Jonas King and Sorina Popescu to the university. Drs. King and Popescu are tenure-track faculty members in the Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology. Dr. King's research focuses on insects and their roles as disease vectors. Dr. Popescu uses gene editing techniques to conduct functional genomics research in crop plants. These faculty may not have come to MS State had the IGBB not provided them with high performance computing support (equivalent to $20K per year). • The IGBB helped recruit Dr. Te-Ming (Paul) Tseng, an expert in weed molecular biology and genetics, to MS State. Dr. Tseng is a tenure-track faculty member in the Department of Plant & Soil Sciences. The IGBB donated roughly $50K worth of supplies and equipment to help recruit Dr. Tseng to MS State. • The IGBB has provided opportunities for one graduate student to earn an M.S. degree and three graduate students to earn their Ph.D. degrees. These students are funded through extramural awards to the IGBB. • The IGBB has continued to invest in purchase and maintenance of state-of-the-art equipment as a means of creating research opportunities and attracting/retaining faculty. In 2015 the IGBB purchased the service contracts for their LTQ Orbitrap Velos mass spectrometer ($32,246) and their Illumina MiSeq DNA sequencer ($15,500). The IGBB is in the process of purchasing a new quantitative RT-PCR machine. (3) Offering researchers at MS State and elsewhere the opportunity to collaborate with the IGBB's genomics, proteomics, and computational biology experts. • Internal records revealed that IGBB employees were engaged in research projects with 32 different MS State PIs representing multiple academic units. • Records showed that the IGBB conducted service activities for investigators at the USDA, US Army Corps of Engineers, the US Forest Service, and the University of Georgia. (4) Helping principal investigators leverage the experience and expertise of the IGBB to make their research programs more productive, increase the number and scientific impact of their publications, and enhance their ability to procure extramural funding. • According to MS State Sponsored Programs records, 8 proposals were submitted through the IGBB. • Six new local/state/federal grants submitted by the IGBB or with the IGBB as a collaborating unit were awarded to MSU faculty (net value = $1,583,335). • Fifty-five peer-reviewed manuscripts were published by IGBB-affiliated scientists. • Papers by IGBB faculty included several with ISI Impact Factors > 8.0. Specifically, one paper was published in Nature Biotechnology (IF = 39.08), three papers were published in Science (IF = 31.477), and two in Molecular Biology & Evolution (IF = 14.308), and one in Genome Biology (IF = 10.465). • The IGBB continues to produced more Nature and Science papers than any other unit on MS State's campus. (5) Supporting educational activities that enhance the abilities of students and faculty to succeed in the multidisciplinary fields of computational biology, genomics, and biotechnology. See Opportunities for Training and Professional Development below.

Publications

  • Type: Books Status: Published Year Published: 2015 Citation: Ricke SC, Donaldson JR, Phillips CA [Eds] (2015) Food Safety: Emerging Issues, Technologies and Systems. Elsevier. Boston.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Abdelhamed H, Lawrence ML, Karsi A (2015) A novel suicide plasmid for efficient gene mutation in Listeria monocytogenes. Plasmid 81: 1-8.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Aboughanem-Sabanadzovic N, Sabanadzovic S (2015) First report of Grapevine leafroll-associated virus 2 infecting muscadine (Vitis rotundifolia) and summer grape (Vitis aestivalis) in the United States. Plant Disease 99(1): 163.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H (2015) Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Blake JA, Christie KR, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Dietze H, Lewis SS, Mungall CJ, Munoz-Torres MC, Feuermann M, Gaudet P, Basu S, Chisholm RL, Dodson RJ, Fey P, Mi H, Thomas PD, Muruganujan A, Poudel S, Hu J, Aleksander SA, McIntosh BK, Renfro DP, Siegele DA, Attrill H, Brown NH, Tweedie S, Lomax J, Osumi-Sutherland D, Parkinson H, Roncaglia P, Lovering RC, Talmud PJ, Humphries SE, Denny P, Campbell NH, Foulger RE, Chibucos MC, Gwinn Giglio M, Chang HY, Finn R, Fraser M, Mitchell A, Nuka G, Pesseat S, Sangrador A, Scheremetjew M, Young SY, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman GT, Wang SJ, Petri V, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Demeter J, Dwight SS, Engel SR, Hitz BC, Inglis DO, Lloyd P, Miyasato SR, Paskov K, Roe G, Simison M, Nash RS, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Argasinska J, Arighi C, Auchincloss A, Axelsen K, Argoud-Puy G, Bateman A, Bely B, Blatter MC, Bonilla C, Bougueleret L, Boutet E, Breuza L, Bridge A, Britto R, Casals C, Cibrian-Uhalte E, Coudert E, Cusin I, Duek-Roggli P, Estereicher A, Famiglietti L, Gane P, Garmiri P, Gos A, Gruaz-Gumowski N, Hatton-Ellis E, Hinz U, Hulo C, Huntley R, Jungo F, Keller G, Laiho K, Lemercier P, Lieberherr D, MacDougall A, Magrane M, Martin M, Masson P, Mutowo P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Shypitsyna A, Stutz A, Sundaram S, Tognolli M, Wu C, Xenarios I, Chan J, Kishore R, Sternberg PW, Van Auken K, Muller HM, Done J, Li Y, Howe D, Westerfield M (2015) Gene Ontology Consortium: going forward. Nucleic Acids Research 43(Database issue): D1049-D1056.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Burdick Sanchez NC, Carroll JA, Donaldson JR, Buntyn JO, Schmidt TB (2015) Exogenous administration of lipids to steers alters aspects of the innate immune response to endotoxin challenge. Innate Immunity 21(5): 512-22.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Chong AY, Kojima KK, Jurka J, Ray DA, Smit AF, Isberg SR, Gongora J (2014) Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes. Retrovirology 11(1): 71.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Collier SD, Branton SL, Evans JD, Leigh SA, Wan XF, Cooksey AM, Olanrewaju HA, Pharr GT (2015) Proteomic analysis of Mycoplasma gallisepticum vaccine strain F. International Journal of Poultry Science 14(1): 1-12.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Dogan S, Vargovic P, Oliveira R, Belser LE, Kaya A, Moura A, Sutovsky P, Parrish J, Topper E, Memili E (2015) Sperm protamine-status correlates to the fertility of breeding bulls. Biology of Reproduction 92(4): 92.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Donaldson JR, Hercik K, Rai AN, Reddy S, Lawrence ML, Nanduri B, Edelmann M (2015) Listeria and-OMICS approaches for understanding its biology. In: Food Safety: Emerging Issues, Technologies and Systems. Elsevier. Boston. pp 135-158.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Dumpala PR, Peterson BC, Lawrence ML, Karsi A (2015) Identification of Differentially Abundant Proteins of Edwardsiella ictaluri during Iron Restriction. PLoS One 10(7): e0132504.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Edelmann MJ, Shack LA, Naske CD, Walters KB, Nanduri B (2014) SILAC-based quantitative proteomic analysis of human lung cell response to copper oxide nanoparticles. PLoS One 9(12): e114390.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Garcia-Reyero N (2015) Are adverse outcome pathways here to stay? Environmental Science & Technology 49(1): 3-9.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutierrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW, Jr., Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldon T, Paten B, Ray DA (2014) Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346(6215): 1254449.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Gust KA, Nanduri B, Rawat A, Wilbanks MS, Ang CY, Johnson DR, Pendarvis K, Chen X, Quinn MJ, Jr., Johnson MS, Burgess SC, Perkins EJ (2015) Systems toxicology identifies mechanistic impacts of 2-amino-4,6-dinitrotoluene (2A-DNT) exposure in Northern Bobwhite. BMC Genomics 16 587.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hanna ME, Bednarova A, Rakshit K, Chaudhuri A, O'Donnell JM, Krishnan N (2015) Perturbations in dopamine synthesis lead to discrete physiological effects and impact oxidative stress response in Drosophila. Journal of Insect Physiology 73 11-9.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hawkins LK, Mylroie JE, Oliveira DA, Smith JS, Ozkan S, Windham GL, Williams WP, Warburton ML (2015) Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance. PLoS One 10(6): e0126185.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Herrera F, Aboughanem-Sabanadzovic N, Valverde RA (2015) A begomovirus associated with yellow vein symptoms of Oxalis debilis. European Journal of Plant Pathology 142 203-209.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Huang X, Jennings SF, Bruce B, Buchan A, Cai L, Chen P, Cramer CL, Guan W, Hilgert UK, Jiang H, Li Z, McClure G, McMullen DF, Nanduri B, Perkins A, Rekepalli B, Salem S, Specker J, Walker K, Wunsch D, Xiong D, Zhang S, Zhang Y, Zhao Z, Moore JH (2015) Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. BioData Mining 8: 7.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S, Lyons E, McCarthy FM, Isberg SR, Higgins DP, Chong AY, John JS, Glenn TC, Ray DA, Gongora J (2014) Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC. PLoS One 9(12): e114631.
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  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Garcia-Reyero N, Thornton C, Hawkins AD, Escalon L, Kennedy AJ, Steevens JA, Willett KL (2015) Assessing the exposure to nanosilver and silver nitrate on fathead minnow gill gene expression and mucus production. Environmental Nanotechnology, Monitoring and Management 4(17): 58-66.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Marsico TD, Sauby KE, Brooks CP, Welch ME, Ervin GN (2015) Phylogeographic evidence for a Florida panhandle-peninsula discontinuity in the distribution of Melitara prodenialis Walker (Lepidoptera: Pyralidae), a native cactus-boring moth. Insect Conservation and Diversity 8(4): 377-388.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Martin BE, Jia K, Sun H, Ye J, Hall C, Ware D, Wan XF (2015) Detection of influenza antigenic variants directly from clinical samples using polyclonal antibody based proximity ligation assays. Virology 476 151-8.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Martin JL, Knapp CR, Gerber GP, Thorpe RS, Welch ME (2015) Phylogeography of the endangered lesser antillean iguana, iguana delicatissima: a recent diaspora in an archipelago known for ancient herpetological endemism. Journal of Heredity 106(3): 315-21.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Moyle RG, Hosner PA, Jones AW, Outlaw DC (2015) Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): novel results from fresh source material. Molecular Phylogenetics and Evolution 82(Pt A): 87-94.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kumar S, Driskell EA, Cooley AJ, Jia K, Blackmon S, Wan XF, Uhl EW, Saliki JT, Sanchez S, Krimer PM, Hogan RJ (2015) Fatal Canid Herpesvirus 1 Respiratory Infections in 4 Clinically Healthy Adult Dogs. Veterinary Pathology 52(4): 681-687.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu Y, Baird SM, Qiao J, Du Y, Lu SE (2015) SecG is required for antibiotic activities of Pseudomonas sp. YL23 against Erwinia amylovora and Dickeya chrysanthemi. Journal of Basic Microbiology 55(5): 617-24.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Narayanan LA, Edelmann MJ (2014) Ubiquitination as an efficient molecular strategy employed in salmonella infection. Frontiers in Immunology 5: 558.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Natarajan C, Hoffmann FG, Lanier HC, Wolf CJ, Cheviron ZA, Spangler ML, Weber RE, Fago A, Storz JF (2015) Intraspecific Polymorphism, Interspecific Divergence, and the Origins of Function-Altering Mutations in Deer Mouse Hemoglobin. Molecular Biology and Evolution 32(4): 978-97.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nho SW, Abdelhamed H, Reddy S, Karsi A, Lawrence ML (2015) Identification of high-risk Listeria monocytogenes serotypes in lineage I (serotype 1/2a, 1/2c, 3a and 3c) using multiplex PCR. Journal of Applied Microbiology 119(3): 845-52.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Omar-Ali A, Hohn C, Allen PJ, Rodriguez J, Petrie-Hanson L (2015) Tissue PAH, blood cell and tissue changes following exposure to water accommodated fractions of crude oil in alligator gar, Atractosteus spatula. Marine Environmental Research 108 33-44.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Opazo JC, Lee AP, Hoffmann FG, Toloza-Villalobos J, Burmester T, Venkatesh B, Storz JF (2015) Ancient Duplications and Expression Divergence in the Globin Gene Superfamily of Vertebrates: Insights from the Elephant Shark Genome and Transcriptome. Molecular Biology and Evolution 32(7): 1684-94.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Outlaw RK, Counterman B, Outlaw DC (2015) Differential patterns of molecular evolution among Haemosporidian parasite groups. Parasitology 142(4): 612-22.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu C-R (2015) An integrated approach to sequence-independent local alignment of protein binding sites. IEEE-ACM Transactions on Computational Biology and Bioinformatics 12(2): 298-308.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Perera D, Barnes DJ, Baldwin BS, Reichert NA (2015) Mutagenesis of in vitro cultures of Miscanthus x giganteus cultivar Freedom and detecting polymorphisms of regenerated plants using ISSR markers. Industrial Crops and Products 65 110-6.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Perera D, Barnes DJ, Baldwin BS, Reichert NA (2015) Direct and indirect in vitro regeneration of Miscanthus � giganteus cultivar Freedom: Effects of explant type and medium on regeneration efficiency. In Vitro Cellular & Developmental Biology-Plant 51(3): 294-302.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Pirim H, Eksioglu B, Perkins AD (2015) Clustering high throughput biological data with B-MST, a minimum spanning tree based heuristic. Computers in Biology and Medicine 62: 94-102.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang RL, Bencic DC, Garcia-Reyero N, Perkins EJ, Villeneuve DL, Ankley GT, Biales AD (2014) Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PLoS One 9(12): e114178.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang XQ, Showmaker KC, Yu XQ, Bi T, Hsu CY, Baird SM, Peterson DG, Li XD, Lu SE (2014) Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens. Genome Announcements 2(5): pii: e00991-14.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Warburton ML, Tang JD, Windham GL, Hawkins LK, Murray SC, Xu W, Boykin D, Perkins A, Williams WP (2015) Genome-wide association mapping of aspergillus flavus and aflatoxin accumulation resistance in maize. Crop Science 55(5): 1857-67.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wasielewski O, Wojciechowicz T, Giejdasz K, Krishnan N (2015) Enhanced UV-B radiation during pupal stage reduce body mass and fat content, while increasing deformities, mortality and cell death in female adults of solitary bee Osmia bicornis. Insect Science 22(4): 512-520.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ramakodi MP, Singh B, Wells JD, Guerrero F, Ray DA (2015) A 454 sequencing approach to dipteran mitochondrial genome research. Genomics 105(1): 53-60.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ricklefs RE, Outlaw DC, Svensson-Coelho M, Medeiros MC, Ellis VA, Latta S (2014) Species formation by host shifting in avian malaria parasites. Proceedings of the National Academy of Sciences of the United States of America 111(41): 14816-21.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Shields-Menard SA, Amirsadeghi M, Sukhbaatar B, Revellame E, Hernandez R, Donaldson JR, French WT (2015) Lipid accumulation by Rhodococcus rhodochrous grown on glucose. Journal of Industrial Microbiology & Biotechnology 42(5): 693-699.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Su W, Wang C, Luo J, Zhao Y, Wu Y, Chen L, Zhao N, Li M, Xing C, Liu H, Zhang H, Chang YF, Li T, Ding H, Wan X, He H (2015) Testing the Effect of Internal Genes Derived from a Wild-Bird-Origin H9N2 Influenza A Virus on the Pathogenicity of an A/H7N9 Virus. Cell Reports 12(11): 1831-41.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H (2014) Early mesozoic coexistence of amniotes and hepadnaviridae. PLoS Genetics 10(12): e1004559.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Suh A, Churakov G, Ramakodi MP, Platt RN, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J (2015) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution 7(1): 205-17.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sun H, Cunningham FL, Harris J, Xu Y, Long LP, Hanson-Dorr K, Baroch JA, Fioranelli P, Lutman MW, Li T, Pedersen K, Schmit BS, Cooley J, Lin X, Jarman RG, DeLiberto TJ, Wan XF (2015) Dynamics of virus shedding and antibody responses in influenza A virus-infected feral swine. Journal of General Virology 96(9): 2569-78.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Takac T, Samajova O, Vadovic P, Pechan T, Kosutova P, Ovecka M, Husickova A, Komis G, Samaj J (2014) Proteomic and biochemical analyses show a functional network of proteins involved in antioxidant defense of the Arabidopsis anp2anp3 double mutant. Journal of Proteome Research 13(12): 5347-61.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Xu Y, Cao H, Liu H, Sun H, Martin B, Zhao Y, Wang Q, Deng G, Xue J, Zong Y, Zhu J, Wen F, Long LP, Wong SS, Zhao N, Fu X, Liao M, Hu G, Webby R, Gao GF, Wan XF (2015) Identification of the source of A (H10N8) virus causing human infection. Infection Genetics and Evolution 30 159-63.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ye J, Wen F, Xu Y, Zhao N, Long L, Sun H, Yang J, Cooley J, Todd PG, Webby R, Wan XF (2015) Error-prone pcr-based mutagenesis strategy for rapidly generating high-yield influenza vaccine candidates. Virology 482 234-43.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Odeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Nunez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farre M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Hastad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alstrom P, Fjeldsa J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Jarvis ED, Gilbert MT, Wang J (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346(6215): 1311-1320.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM, Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG, Thaxton P, Jones DC, Wang Q, Xu X, Zhang H, Wu H, Zhou L, Mei G, Chen S, Tian Y, Xiang D, Li X, Ding J, Zuo Q, Tao L, Liu Y, Li J, Lin Y, Hui Y, Cao Z, Cai C, Zhu X, Jiang Z, Zhou B, Guo W, Li R, Chen ZJ (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33(5): 531-537.


Progress 01/20/14 to 09/30/14

Outputs
Target Audience: Target audiences include faculty interested in conducting genomics, transcriptomics, and proteomics research; computational biologists; plant and animal breeders; microbiologists; agricultural scientists; farmers; ranchers; food safety scientists; veterinarians; pathologists and forensic biologists; and human health scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Opportunities for Training and Professional Development • The IGBB co-sponsored MS State's "Darwin Week" including a concert by Baba Brinkmann, a rap artist who performs a show promoting scientific literacy and evolutionary principles. • The IGBB/MS State helped host the University & Industry Consortium (UIC) meeting in Jackson, Mississippi in April 2014. The UIC is a group working to increase partnerships between agricultural, food, and biotechnology companies and land-grant institutions. The UIC began more than 20 years ago with Mississippi State serving as a founding member. The UIC provides opportunities for students and faculty to interact and develop research and educational collaborations with leaders in industry and academia. • The IGBB hosted a month long visit by Dr. Tomas Takac from Palacky University in the Czech Republic. Dr. Takac has had a very fruitful collaboration with IGBB faculty member Dr. Tibor Pechan. Later in the year, Dr. Takac returned the favor by hosting a visit by Dr. Pechan to the Czech Republic/Slovakia. • The IGBB sent research associate Jo-Ann Ding to the annual meeting of the American Society for Mass Spectrometry. Ms. Ding is in charge of the mass spectrometry at IGBB's Service Center. • The IGBB funded participation by postdoctoral associate Shane Sanders in the Plant & Animal Genome Conference and the Mid-South Computational Biology & Bioinformatics Society meeting. • The IGBB trained Dr. Imran Amin through a Borlaug Fellowship. Dr. Amin, a scientist at the National Institute for Biotechnology and Genetic Engineering in Faisalabad, Pakistan, learned basics of high performance computing and computational biology during his time at the IGBB. He will apply these computational techniques to his research program which is aimed at controling the spread of cotton leaf curl virus in Pakistan. • The IGBB is currently hosting a student from the public high school known as the Mississippi School for Mathematics & Science. The student has been learning the principles of virology from Dr. Nina Aboughanem, an IGBB faculty member. • Dr. Daniel Peterson, IGBB Director, gave seminars for students and faculty at meetings in Riga, Latvia and Wuhan, China. How have the results been disseminated to communities of interest? Results have been disseminated to the scientific community through peer-reviewed publications, scientific meetings/presentations, faculty exchange programs, and the IGBB website (www.igbb.msstate.edu). In addition, DNA sequence and gene expression data were disseminated through AgBase (www.agbase.msstate.edu), CrocGenomes (www.crocgenomes.org), CottonGen (www.cottongen.org), and the National Center for Biotechnology Information (NCBI; www.ncbi.nlm.nih.gov). What do you plan to do during the next reporting period to accomplish the goals? During the next reporting period we plan to expand the IGBB's local user base through advertising (e-mails and flyers), YouTube videos, and presentations at academic department meetings. Training and research plans will be adapted and modified as necessary.

Impacts
What was accomplished under these goals? Below is a list of our major project goals (1-5). Each goal is followed by accomplishments (each delineated by a bullet) made over the course of the last year that advanced that goal. (1) Conducting scientific research that meets the needs of society and further enhances the unique strengths of MS State. • The IGBB employed, in full or part, 17 people during the period in question. In doing so, the IGBB helped strengthen MS State and the local/state economies. • The IGBB’s total expenditures were $2.34 M. Though there have been ups and downs, the general economicbenefits of the IGBB have increased from about $500,000 in expenditures in 2007 to $2.34 M in 2014. • IGBB accounting records indicate that the IGBB Service Center brought in $32,534. • Seven technique/tool development publications were published in FY14. Tools and techniques developed through IGBB research include (a) A mathematical model for better development of flu vaccines, (b) a novel anti-fungal compound, (c) an algorithm for better dating molecular divergence events, and (d) a data-mining algorithm for improving gene annotation. (2) Attracting and retaining outstanding faculty and students at MS State. • The IGBB was instrumental in attracting Dr. Matthew Brown to the university. Dr. Brown, a tenure-track faculty member in the Department of Biological Sciences, is an expert in protist evolution and taxonomy. Dr. Brown has a record of producing numerous high impact publications. It is unlikely that Dr. Brown would have come to MS State had the IGBB not provided him with high performance computing support (equivalent to $20K per year). • The IGBB helped recruit Dr. Yuhua Farnell, an expert in Circadian rhythms, to MS State. Dr. Farnell is a tenure-track faculty member in the Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology. Of note, the IGBB provided summer salary for Dr. Farnell to serve as an IGBB genomics consultant. • The IGBB played a role in recruiting Dr. Jeffrey Dean to MS State. Dr. Dean is the new head of the Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology. Dr. Dean, formerly of the University of Georgia, collaborated with the IGBB for many years before making the move to MS State. • The IGBB has provided opportunities for three graduate students to earn their Ph.D. degrees. These students are funded through extramural awards to the IGBB. • The IGBB has continued to invest in purchase and maintenance of state-of-the-art equipment as a means of creating research opportunities and attracting/retaining faculty. In 2014 the IGBB purchased the service contracts for their (a) MALDI, $25,000, (b) LTQ Orbitrap Velos, $32,246.40, (c) Waters Xevo G2-S, $12,365, and (d) Illumina MiSeq DNA sequencer, $15,500. (3) Offering researchers at MS State and elsewhere the opportunity to collaborate with the IGBB's genomics, proteomics, and computational biology experts. • Internal records revealed that IGBB employees were engaged in research projects with 23 different MS State PIs representing seven academic units. • Records showed that the IGBB conducted service activities for investigators at five external institutions; specifically, the University of Arkansas Medical Sciences Center, North Carolina State University, the University of Southern Mississippi, the Slovak Academy of Sciences, and the USDA. (4) Helping principal investigators leverage the experience and expertise of the IGBB to make their research programs more productive, increase the number and scientific impact of their publications, and enhance their ability to procure extramural funding. • According to MS State Sponsored Programs records, 17 proposals were submitted through the IGBB. • Seven new local/state/federal grants submitted by the IGBB or with the IGBB as a collaborating unit were awarded to MSU faculty (net value = $811 K). • Forty peer-reviewed manuscripts were published by IGBB-affiliated scientists. • Papers by IGBB faculty included several with ISI Impact Factors > 8.0. Specifically, one paper was published in Genome Research (IF = 13.852), one in Current Biology (IF = 9.916), and one in Molecular Biology & Evolution (IF = 14.308). • The IGBB has produced more Nature and Science papers than any other unit on MS State's campus. (5) Supporting educational activities that enhance the abilities of students and faculty to succeed in the multi-disciplinary fields of computational biology, genomics, and biotechnology. See Opportunities for Training and Professional Development below.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ (2014) A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Curr Biol 24(11): 1176-86.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Tang JD, Diehl SV (2014) Omics and the future of sustainable biomaterials. ACS Symposium Series 1158: 59-79.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu WG, Melkonian M, Archibald JM (2014) Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics 15: 374.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2014 Citation: Watson PM, Sorrell SC, Brown MW (2014) Ptolemeba n. gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea, Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba. J Eukaryot Microbiol.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Xu J, Deng P, Showmaker KC, Wang H, Baird SM, Lu SE (2014) The pqqC gene is essential for antifungal activity of Pseudomonas kilonensis JX22 against Fusarium oxysporum f. sp. lycopersici. FEMS Microbiol Lett 353(2): 98-105.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Yang J, Grunewald S, Xu Y, Wan XF (2014) Quartet-based methods to reconstruct phylogenetic networks. BMC Syst Biol 8: 21.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Arroyo JI, Hoffmann FG, Opazo JC (2014) Evolution of the relaxin/insulin-like gene family in anthropoid primates. Genome Biol Evol 6(3): 491-9.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Asters MC, Williams WP, Perkins AD, Mylroie JE, Windham GL, Shan X (2014) Relating significance and relations of differentially expressed genes in response to Aspergillus flavus infection in maize. Sci Rep 4: 4815.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Beato MS, Xu Y, Long LP, Capua I, Wan XF (2014) Antigenic and genetic evolution of low-pathogenicity avian influenza viruses of subtype H7N3 following heterologous vaccination. Clin Vaccine Immunol 21(5): 603-12.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Berninger JP, Martinovic-Weigelt D, Garcia-Reyero N, Escalon L, Perkins EJ, Ankley GT, Villeneuve DL (2014) Using transcriptomic tools to evaluate biological effects across effluent gradients at a diverse set of study sites in Minnesota, USA. Environ Sci Technol 48(4): 2404-12.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Buza T, Arick M, Wang H, Peterson DG (2014) Computational prediction of disease microRNAs in domestic animals. BMC Res Notes 7(1): 403.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Cheng K, Escalon BL, Robert J, Chinchar VG, Garcia-Reyero N (2014) Differential transcription of fathead minnow immune-related genes following infection with frog virus 3, an emerging pathogen of ectothermic vertebrates. Virology 456-457: 77-86.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Colosimo G, Knapp CR, Wallace LE, Welch ME (2014) Inferred vs Realized Patterns of Gene Flow: An Analysis of Population Structure in the Andros Island Rock Iguana. PLoS One 9(9): e106963.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Dahal N, Abdelhamed H, Karsi A, Lawrence ML (2014) Tissue persistence and vaccine efficacy of tricarboxylic acid cycle and one-carbon metabolism mutant strains of Edwardsiella ictaluri. Vaccine 32(31): 3971-6.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Dahal N, Abdelhamed H, Lu J, Karsi A, Lawrence ML (2014) Effect of multiple mutations in tricarboxylic acid cycle and one-carbon metabolism pathways on Edwardsiella ictaluri pathogenesis. Vet Microbiol 169(1-2): 107-12.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Eme L, Sharpe SC, Brown MW, Roger AJ (2014) On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks. Cold Spring Harb Perspect Biol 6(8): pii: a016139.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Feng Z, Baroch JA, Long LP, Xu Y, Cunningham FL, Pedersen K, Lutman MW, Schmit BS, Bowman AS, DeLiberto TJ, Wan XF (2014) Influenza A subtype H3 viruses in feral swine, United States, 2011-2012. Emerg Infect Dis 20(5): 843-6.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P (2014) De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. PLoS One 9(5): e96855.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ganji S, Jenkins JN, Wubben MJ (2014) Molecular characterization of the reniform nematode C-type lectin gene family reveals a likely role in mitigating environmental stresses during plant parasitism. Gene 537(2): 269-78.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Garcia-Reyero N, Kennedy AJ, Escalon BL, Habib T, Laird JG, Rawat A, Wiseman S, Hecker M, Denslow N, Steevens JA, Perkins EJ (2014) Differential effects and potential adverse outcomes of ionic silver and silver nanoparticles in vivo and in vitro. Environ Sci Technol 48(8): 4546-55.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Garcia-Reyero N, Escalon BL, Prats E, Stanley JK, Thienpont B, Melby NL, Baron E, Eljarrat E, Barcelo D, Mestres J, Babin PJ, Perkins EJ, Raldua D (2014) Effects of BDE-209 contaminated sediments on zebrafish development and potential implications to human health. Environ Int 63: 216-23.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Garcia-Reyero N, Kennedy AJ, Escalon BL, Habib T, Laird JG, Rawat A, Wiseman S, Hecker M, Denslow N, Steevens JA, Perkins EJ (2014) Differential Effects and Potential Adverse Outcomes of Ionic Silver and Silver Nanoparticles in Vivo and in Vitro. Environ Sci Technol 48(8): 4546-55.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Garcia-Reyero N, Tingaud-Sequeira A, Cao M, Zhu Z, Perkins EJ, Hu W (2014) Endocrinology: Advances through omics and related technologies. Gen Comp Endocrinol 203: 262-73.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Garcia-Reyero N, Ekman DR, Habib T, Villeneuve DL, Collette TW, Bencic DC, Ankley GT, Perkins EJ (2014) Integrated approach to explore the mechanisms of aromatase inhibition and recovery in fathead minnows (Pimephales promelas). Gen Comp Endocrinol 203: 193-202.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Garcia-Reyero N, Escalon BL, Prats E, Stanley K, Thienpont B, Melby NL, Baron E, Eljarrat E, Barcelo D, Mestres J, Babin PJ, Perkins EJ, Raldua D (2014) Effects of BDE-209 contaminated sediments on zebrafish development and potential implications to human health. Environ Int 63: 216-23.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gaudry MJ, Storz JF, Butts GT, Campbell KL, Hoffmann FG (2014) Repeated evolution of chimeric fusion genes in the beta-globin gene family of laurasiatherian mammals. Genome Biol Evol 6(5): 1219-34.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Guo H, Wang X, Gundlach H, Mayer KF, Peterson DG, Scheffler BE, Chee PW, Paterson AH (2014) Extensive and Biased Intergenomic Non-Reciprocal DNA Exchanges Shaped a Nascent Polyploid Genome, Gossypium (Cotton). Genetics 197(4): 1153-63.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Johnson JB, Roberts JH, King TL, Edwards JW, Ford WM, Ray DA (2014) Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales. Acta Theriologica 59(2): 223-31.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Kudryavtsev A, Brown MW, Tice A, Spiegel FW, Pawlowski J, Anderson OR (2014) A revision of the order Pellitida Smirnov et al., 2011 (Amoebozoa, Discosea) based on ultrastructural and molecular evidence, with description of Endostelium crystalliferum n. sp. Protist 165(2): 208-29.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Lee N, Horstemeyer MF, Rhee H, Nabors B, Liao J, Williams LN (2014) Hierarchical multiscale structure-property relationships of the red-bellied woodpecker (Melanerpes carolinus) beak. J R Soc Interface 11(96): 20140274.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Magbanua ZV, Arick M, Buza T, Hsu CY, Showmaker KC, Chouvarine P, Deng P, Peterson DG, Lu S (2014) Transcriptomic dissection of the rice - Burkholderia glumae interaction. BMC Genomics 15: 755.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Mali I, Vandewege MW, Davis SK, Forstner MR (2014) Magnitude of the freshwater turtle exports from the US: long term trends and early effects of newly implemented harvest management regimes. PLoS One 9(1): e86478.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Myles V, Liao J, Warnock JN (2014) Cyclic pressure and angiotensin II influence the biomechanical properties of aortic valves. J Biomech Eng 136(1): 011011.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Nallamilli BR, Edelmann MJ, Zhong X, Tan F, Mujahid H, Zhang J, Nanduri B, Peng Z (2014) Global analysis of lysine acetylation suggests the involvement of protein acetylation in diverse biological processes in rice (Oryza sativa). PLoS One 9(2): e89283.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Outlaw DC, Ricklefs RE (2014) Species limits in avian malaria parasites (Haemosporida): how to move forward in the molecular era. Parasitology 141(10): 1223-32.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Paul D, Magbanua Z, Arick M, French T, Bridges SM, Burgess SC, Lawrence ML (2014) Genome Sequence of the Oleaginous Yeast Rhodotorula glutinis ATCC 204091. Genome Announc 2(1) pii: e00046-14.
  • Type: Book Chapters Status: Published Year Published: 2014 Citation: Peterson DG (2014) Evolution of Plant Genome Analysis. In: Advances in Botanical Research, Volume 69, Genomes of Herbaceous Land Plants. Edited by: Paterson AH. Academic Press. Amsterdam. pp 13-46.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Pittman JR, Buntyn JO, Posadas G, Nanduri B, Pendarvis K, Donaldson JR (2014) Proteomic analysis of cross protection provided between cold and osmotic stress in Listeria monocytogenes. J Proteome Res 13(4): 1896-904.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Platt RN, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA (2014) Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats. Mol Biol Evol 31(6): 1536-45.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Pramod S, Perkins AD, Welch ME (2014) Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome. J Genet 93(2): 431-42.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Reddy S, Lawrence ML (2014) Virulence characterization of Listeria monocytogenes. Methods Mol Biol 1157: 157-65.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Smekalova V, Luptovciak I, Komis G, Samajova O, Ovecka M, Doskocilova A, Takac T, Vadovic P, Novak O, Pechan T, Ziemann A, Kosutova P, Samaj J (2014) Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation and cell division plane orientation. New Phytol 203(4): 1175-93.