IGBB News & Research Highlights
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November 14, 2016
Adapted from article by Vanessa W. Beeson, Agriculture & Natural Resources Marketing, Mississippi State University
The unexpected findings of a two-nation research team including a Mississippi State scientist are featured in a recent edition of a leading academic journal.
Genetic adaptations of hummingbirds to life at high altitudes where oxygen is less available are the focus of the recent report in SCIENCE authored by Federico G. Hoffmann, in collaboration with academic partners in the U.S. and Denmark.
Hoffmann is an assistant professor in the university’s Department of Biochemistry, Molecular Biology and Plant Pathology and an affiliate of the Institute for Genomics, Biocomputing & Biotechnology. Hoffman said the team’s findings could have further implications in the field of evolutionary biology.
“This work helps us to better understand that there are multiple ways in which evolution solves problems,” the specialist in bioinformatics said.
The research project was funded by grants from the U.S. National Institutes of Health, National Science Foundation and Danish Council for Independent Research. The article may be read here.
Hoffman’s colleagues included Chandrasekhar Natarajan and Jay F. Storz from the University of Nebraska-Lincoln, Roy E. Weber and Angela Fago from Aarhus University in Denmark, and Christopher C. Witt from the University of New Mexico.
SCIENCE, a peer-reviewed publication of the American Association for the Advancement of Science, is devoted to the weekly presentation of research papers “that are most influential in their fields or across fields, and that will significantly advance scientific understanding.” For more, visit the Science website.
Hoffman explained that the team successfully gained insight into the evolutionary process of natural selection by studying hummingbirds and several other avian species that live at both low and high altitudes. Weighing less than a nickel but having the highest metabolic rate of any vertebrate, hummingbirds have adapted over time to surviving in mountainous regions.
A Texas Tech University doctoral graduate, he said the research “shows that we can predict how species with similar starting points are going to adapt to each environment. If the starting points are dissimilar, the process of natural selection becomes much more difficult to predict.”
In their study featured in the journal’s Oct. 21 issue, Hoffman describes how team members focused on hemoglobin in 28 pairs of high- and low-altitude lineages of bird species to determine how different species evolve. Hemoglobin is a red blood cell protein that carries oxygen throughout a body.
While hemoglobin from species adapted for life at high altitudes had a higher affinity for oxygen, researchers found that genetic paths leading to those hemoglobin adaptations varied. Using computational methods, they were able to travel back in time 100 million years by reconstructing protein present in the birds’ ancestors.
Jeffrey F.D. Dean, professor and head of the Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, said the study is significant and a “powerful piece of work that contributes to our fundamental understanding of evolutionary biology.”
“By focusing on a key component in adaptation – hemoglobin and its role as an oxygen carrier – Dr. Hoffmann and his colleagues were able to infer the ancestral form of this protein despite the random nature of the evolutionary process,” Dean said.
Hoffmann also is part of the research team at the MSU-based Mississippi Agricultural and Forestry Experiment Station. He is an alumnus of the Universidad de la Republica Uruguay, with bachelor’s and master’s degrees completed, respectively, in biology and zoology.
His post-doctoral fellowships in molecular evolution and bioinformatics were completed at the University of Nebraska-Lincoln and Instituto Carlos Chagas, Brazil’s equivalent to the National Institutes of Health in the U.S.
July 8, 2016
The IGBB is pleased to welcome two new individuals to its ranks.
Dr. George Popescu (left) has been hired as an IGBB research assistant professor. He is the first IGBB faculty member whose primary discipline is computer science. Dr. Popescu received his B.S. and M.S. in electrical engineering in his home country of Romania before moving to the U.S. He obtained a Ph.D. in electrical and computer engineering from Rutgers University, and did postdoctoral research in bioinformatics at Yale University. "Our research at the IGBB has become increasingly focused on bioinformatics and computational biology," notes Dr. Daniel G. Peterson, IGBB director. "We have been looking to grow our computational research endeavors and are thrilled to have George join the IGBB team. He adds tremendous depth to the institute and has an impressive record of conducting inovative research in collaboration with biologists."
Dr. Ramey "Cal" Youngblood (right) joins the IGBB as a research associate. Dr. Youngblood will be stationed in Stoneville, MS where he will work closely with the USDA ARS's Genomics & Bioinformatics Research Unit (GBRU). The IGBB and the GBRU have built a synergistic relationship based on their shared interest in crop genomics, and Dr. Youngblood's presence at the GBRU will strengthen the GBRU/IGBB partnership. Dr. Youngblood is a recent Ph.D. graduate of MSU's Department of Animal & Dairy Sciences. He conducted his dissertation research under the guidance of Dr. Peter Ryan, MSU Associate Provost. "We are extremely excited to have Cal joining the IGBB team," notes Peterson. "Cal has a wide range of skills and a proven track record." Dr. Youngblood will primarily conduct genomics research on plants and animals of importance to Mississippi.
For Dr. Popescu's description of his research objectives, see below:
DR. GEORGE POPESCU
My research focuses on the use of computational approaches to study biological networks and processes in order to understand evolution and dynamics at the molecular and cellular levels. Using system analysis methods, I seek to analyze the properties of biochemical networks, infer plant protein interactions, and to study the dynamics of signaling networks. My research interest is in developing high-throughput assays for performing large-scale genome and proteome analyses and in designing novel computational modeling and simulation tools for genomics and proteomics studies. One of my key contributions is the discovery of the complex structure of the MAPK signaling networks. I am now pursuing a system analysis approach that combines high-throughput experimental data, mathematical and computational modeling for a comprehensive study of cellular signaling networks.
My recent research has focused on gaining a predictive understanding of cellular decisions during a plant's response to stress. Using high-throughput assays I have recently identified key proteins involved in plant's response to biotic and abiotic stressors, including peptidases, trafficking proteins, and transcription factors involved in immune responses. By developing models of cellular circuits responsive to plant stress factors. I am uncovering the cellular functions of these key cellular components and exploring their roles in redox and immune response pathways.
Another direction of my research concentrates on generating new computational methods for the analysis of genome methylation patterns and the study of chromosomal variations leading to developmental diseases. I have discovered small copy number variations in the human genome and mapped large deletions and duplications associated with developmental diseases. These discoveries were enabled by the genomics tools I have developed: efficient genome sampling methods, whole-genome tilling microarrays, and analytical tools for genomics data analysis.
I am now designing methods for inference of gene regulatory networks by integrating expression variation, transcription factor binding and interactome data with predictions from comparative analysis of conserved sequences of several plant genomes. I am working on developing new analytical tools to infer cis-regulatory networks from conserved sequences, to identify control structures (network motifs) from genomics and proteomics data and to study perturbation of cellular dynamics associated with copy number variations. Looking forward, I would like to focus my research on the study of cellular networks in order to understand their structure, dynamics and evolution.
May 17, 2016
By Sasha Steinberg
STARKVILLE, Miss.—Nearly 60 senior research scientists, postdoctoral fellows and undergraduate and graduate students from Mississippi, Alabama, Georgia and Tennessee institutions of higher learning are gathering Thursday-Friday [May 19-20] at Mississippi State for the 2016 Southeastern Pneumococcal Symposium.
Bringing together nearly one quarter of all of the major pneumococcal research laboratories in the U.S., this year's two-day scientific conference is designed to facilitate discussion and foster new collaborations between labs in an effort to increase funding opportunities for the institutions involved.
Topics of discussion will include host-pathogen interactions, epidemiology, antimicrobial therapies, bacterial physiology, vaccine research and polymicrobial infections.
Occurring in the respiratory tract, pneumococcus is a spherical bacterium that is the most common cause of bacterial pneumonia and also is associated with pericarditis, meningitis and other infectious diseases.
Serving as keynote speaker for this year's symposium is David Briles. A world-renowned Streptococcus pneumoniae biology and pathogenesis researcher, he also is the symposium's founder.
In addition to the American Society for Microbiology, support for this year's event is provided by the university's Institute for Genomics, Biotechnology & Biocomputing, College of Arts & Sciences and its Department of Biological Sciences, and the College of Veterinary Medicine and its Center of Biomedical Research Excellence.
For more information on the MSU-hosted 2016 Southeastern Pneumococcal Symposium, contact biological sciences assistant professor Justin Thornton at 662-325-8020 or firstname.lastname@example.org.
MSU is Mississippi's leading university (see www.msstate.edu).
The image shows Streptococcus pneumoniae in spinal fluid (FA stain; digitally colorized). Photo Credit/Content Providers(s): CDC/Dr. M.S. Mitchell - This media comes from the Centers for Disease Control and Prevention's Public Health Image Library (PHIL).
Ulyshen MD, Diehl SV,Jeremic D (2016) Termites and flooding affect microbial communities in decomposing wood. International Biodeterioration and Biodegradation 115: 83-89.IMPACT FACTOR: 2.131PMID: DOI: 10.1016/j.ibiod.2016.07.017
Adams MJ, Lefkowitz EJ, King AM, 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 (2016) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016). Archives of Virology 161(10): 2921-2949.IMPACT FACTOR: 2.39PMID: 27424026DOI: 10.1007/s00705-016-2977-6
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.IMPACT FACTOR: 3.888PMID: 27389852DOI: 10.1016/j.jprot.2016.07.002
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.IMPACT FACTOR: 3.217PMID: 26940948DOI: 10.1111/jeu.12311
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.IMPACT FACTOR: 3.986PMID: 27503539DOI: 10.1186/s12864-016-2954-1[All Publications]