Systems Biology Commons^™

Research Notes Vs. Research Articles, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! I hope this email finds you well, winding down another academic year, and looking forward to the summer field season. Warm temperatures, peak foliage, and heightened anticipation of the start of another field season are upon us following a long winter season and unusually wet spring for many of us across the Great Plains. Here in westcentral Illinois, wild turkeys are gobbling, neotropical migrants are singing and establishing breeding territories, and white-tailed deer are within days of giving birth to the next generation of fawns. Granted, there are many outdoor activities to participate in, though oppressive heat …

Contributions Of Stocked And Naturally Reproduced Rainbow Trout In The Deerfield Reservoir System, Jacob L. Davis, Jerry W. Wilhite, Greg Simpson, Michael E. Barnes, Kaite N. Bertrand, David W. Willis

The Prairie Naturalist

Deerfield Reservoir in the Black Hills of South Dakota and its tributary system are managed as hatchery supplemented rainbow trout (Oncorhynchus mykiss) fisheries. Three genetically unique strains of rainbow trout (Shasta, Erwin and McConaughy) are stocked into the system. Recently, juvenile rainbow trout of unknown origin were collected in the tributary system above Deerfield Reservoir, indicating potential natural reproduction. Understanding the genetic origins and ability of these rainbow trout to contribute to the fishery is essential in determining the proper management strategy for these waters. Our objectives were to 1) evaluate the genetic origins of potentially naturally reproduced rainbow trout …

Notes: Nesting Patterns Of Red-Tailed Hawks And Great-Horned Owls In South-Cen- Tral Kansas, William Langley

The Prairie Naturalist

Red-tailed hawks (Buteo jamaicensis) and great-horned owls (Bubo virginianus) can influence the nesting behavior of each other through direct competition for nesting sites. For instance, owls begin nesting before hawks and, thus, can use nests from the previous year and prevent hawks from occupying those sites (Orians and Kuhl- man 1956, Gilmer et al. 1983, Minor et al. 1993). However, both species sometimes kill the nestlings of the other (Craig- head and Craighead 1956, Bosakowski et al. 1989).

The objective of my study was to investigate nesting patterns of these two raptors at the edge of the tallgrass prairie over …

Dux4 Differentially Regulates Transcriptomes Of Human Rhabdomyosarcoma And Mouse C2c12 Cells, Vishakha Sharma, Naoe Harafuji, Alexandra Belayew, Yi-Wen Chen

Genomics and Precision Medicine Faculty Publications

Facioscapulohumeral muscular dystrophy (FSHD) is linked to the deletion of the D4Z4 arrays at chromosome 4q35. Recent studies suggested that aberrant expression of double homeobox 4 (DUX4) from the last D4Z4 repeat causes FSHD. The aim of this study is to determine transcriptomic responses to ectopically expressed DUX4 in human and mouse cells of muscle lineage. We expression profiled human rhabdomyosarcoma (RD) cells and mouse C2C12 cells transfected with expression vectors of DUX4 using the Affymetrix Human Genome U133 Plus 2.0 Arrays and Mouse Genome 430 2.0 Arrays, respectively. A total of 2267 and 150 transcripts were identified to be …

Human Cytomegalovirus Inhibits Apoptosis By Proteasome-Mediated Degradation Of Bax At Endoplasmic Reticulum-Mitochondrion Contacts, Aiping Zhang, Richard L. Hildreth, Anamaris M. Colberg-Poley

Genomics and Precision Medicine Faculty Publications

Human cytomegalovirus (HCMV) encodes the UL37 exon 1 protein (pUL37x1), which is the potent viral mitochondrion-localized inhibitor of apoptosis (vMIA), to increase survival of infected cells. HCMV vMIA traffics from the endoplasmic reticulum (ER) to ER subdomains, which are physically linked to mitochondria known as mitochondrion-associated membranes (MAM), and to mitochondria. The antiapoptotic function of vMIA is thought to primarily result from its ability to inhibit Bax-mediated permeabilization of the outer mitochondrial membrane (OMM). Here, we establish that vMIA retargets Bax to the MAM as well as to the OMM from immediate early through late times of infection. However, MAM …

A Pedagogical Simulation Of The Spatial Distribution Of Carbon Flux Dynamics In Peat Soils, Alan Gilmer

Conference Papers

No abstract provided.

Interactive Effects Of Nitrogen And Phosphorus On Soil Microbial Communities In A Tropical Forest, Lei Liu, Tao Zhang, Frank S. Gilliam, Per Gundersen, Wei Zhang, Hao Chen, Jiangming Mo

Biological Sciences Faculty Research

Elevated nitrogen (N) deposition in humid tropical regions may exacerbate phosphorus (P) deficiency in forests on highly weathered soils. However, it is not clear how P availability affects soil microbes and soil carbon (C), or how P processes interact with N deposition in tropical forests. We examined the effects of N and P additions on soil microbes and soil C pools in a N-saturated old-growth tropical forest in southern China to test the hypotheses that (1) N and P addition will have opposing effects on soil microbial biomass and activity, (2) N and P addition will alter the composition of …

Mir-411 Is Up-Regulated In Fshd Myoblasts And Suppresses Myogenic Factors, Naoe Harafuji, Peter Schneiderat, Maggie C. Walter, Yi-Wen Chen

Genomics and Precision Medicine Faculty Publications

Background

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant muscle disorder, which is linked to the contraction of the D4Z4 array at chromosome 4q35. Recent studies suggest that this shortening of the D4Z4 array leads to aberrant expression of double homeobox protein 4 (DUX4) and causes FSHD. In addition, misregulation of microRNAs (miRNAs) has been reported in muscular dystrophies including FSHD. In this study, we identified a miRNA that is differentially expressed in FSHD myoblasts and investigated its function.

Methods

To identify misregulated miRNAs and their potential targets in FSHD myoblasts, we performed expression profiling of both miRNA and mRNA …

Pro-Asthmatic Cytokines Regulate Unliganded And Ligand-Dependent Glucocorticoid Receptor Signaling In Airway Smooth Muscle, Aihua Hu, Maureen B. Josephson, Barry L. Diener, Gustavo Nino, Shuyun Xu, Chinmay Paranjape, Jordan S. Orange, Michael M. Grunstein

Genomics and Precision Medicine Faculty Publications

To elucidate the regulation of glucocorticoid receptor (GR) signaling under pro-asthmatic conditions, cultured human airway smooth muscle (HASM) cells were treated with proinflammatory cytokines or GR ligands alone and in combination, and then examined for induced changes in ligand-dependent and -independent GR activation and downstream signaling events. Ligand stimulation with either cortisone or dexamethsone (DEX) acutely elicited GR translocation to the nucleus and, comparably, ligand-independent stimulation either with the Th2 cytokine, IL-13, or the pleiotropic cytokine combination, IL-1β/TNFα, also acutely evoked GR translocation. The latter response was potentiated by combined exposure of cells to GR ligand and cytokine. Similarly, treatment …

Reproductive Isolation In The Elegans-Group Of Caenorhabditis, Scott Everet Baird, Sara Rose Seibert

Biological Sciences Faculty Publications

Reproductive isolation is the basis of the Biological Species Definition and can be a driving force of speciation. Theoretical studies have provided models of how reproductive isolation can arise within individual species. Genetic tests of these models are limited to populations in which reproductive isolation is present but not complete. Here, reproductive isolation in the Elgans-Group of the nematode genus Caenorhabditis is reviewed. Pre-mating barriers, assortative fertilization and post-zygotic barriers all have been observed in this clade. In some combinations of species, fertile F1 hybrids can be obtained. Therefore, the Elegans-Group of Caenorhabditis is poised to become an important experimental …

Nuclear Envelope Laminopathies: Evidence For Developmentally Inappropriate Chromatin-Nuclear Envelope Interactions, Jelena Perovanovic, Jyoti K. Jaiswal, Nikola Markovic, Eric P. Hoffman

Genomics and Precision Medicine Faculty Publications

Background

During terminal differentiation of cells, there is typically a transition of the nuclear envelope from the Lamin B protein to Lamin A/C proteins. This is commensurate with exit from the cell cycle, and maintenance of the transcriptional programs associated with the terminally differentiated cells. Dominant missense mutations in Lamin A/C cause a broad spectrum of human genetic disorders, where specific point mutations are associated with defects in specific organs or tissues. We have previously presented a model where Lamin A/C mutations disrupt developmentally appropriate interactions between chromatin and the nuclear envelope and lead to poor coordination of E2F cell …

Dux4 Expression In Fshd Muscle Cells: How Could Such A Rare Protein Cause A Myopathy?, Alexandra Tassin, Dalila Laoudj-Chenivesse, Celine Vanderplanck, Marietta Barro, Sebastien Charron, Eugenie Ansseau, Yi-Wen Chen, Jacques Mercier, Frederique Coppee, Alexandra Belayew

Genomics and Precision Medicine Faculty Publications

Facioscapulohumeral muscular dystrophy (FSHD) is one of the most frequent hereditary muscle disorders. It is linked to contractions of the D4Z4 repeat array in 4q35. We have characterized the double homeobox 4 (DUX4) gene in D4Z4 and its mRNA transcribed from the distal D4Z4 unit to a polyadenylation signal in the flanking pLAM region. It encodes a transcription factor expressed in FSHD but not healthy muscle cells which initiates a gene deregulation cascade causing differentiation defects, muscle atrophy and oxidative stress.PITX1 was the first identified DUX4 target and encodes a transcription factor involved in muscle atrophy. DUX4 was …

Highlights From The Functional Single Nucleotide Polymorphisms Associated With Human Muscle Size And Strength Or Famuss Study, Linda S. Pescatello, Joseph M. Devaney, Monica J. Hubal, Paul D. Thompson, Eric P. Hoffman

Genomics and Precision Medicine Faculty Publications

The purpose of the Functional Single Nucleotide Polymorphisms Associated with Human Muscle Size and Strength study or FAMuSS was to identify genetic factors that dictated the response of health-related fitness phenotypes to resistance exercise training (RT). The phenotypes examined were baseline muscle strength and muscle, fat, and bone volume and their response to RT. FAMuSS participants were 1300 young (24 years), healthy men (42%) and women (58%) that were primarily of European-American descent. They were genotyped for ~500 polymorphisms and completed the Paffenbarger Physical Activity Questionnaire to assess energy expenditure and time spent in light, moderate, and vigorous intensity habitual …

Systems Biology In Animal Breeding: Identifying Relationships Among Markers, Genes, And Phenotypes [Breeding And Genetics Symposium], John B. Cole, Ronald M. Lewis, C. Maltecca, S. Newman, K. M. Olson, R. G. Tait

Department of Animal Science: Faculty Publications

The Breeding and Genetics Symposium titled “Systems Biology in Animal Breeding: Identifying relationships among markers, genes, and phenotypes” was held at the Joint Annual Meeting of the American Society of Animal Science and the American Dairy Science Association in Phoenix, Arizona, July 15-19, 2012. The primary goal of the symposium was to demonstrate the use of high-density SNP genotypes to determine the complex regulatory relationships among genotypes and phenotypes but also to present methods for studying complex relationships among phenotypes. Case studies from mammalian and avian species were included to emphasize the broad applicability of these methods.

Progress Towards A Phylogeny Of World Tachinidae. Year 1, John O. Stireman Iii, James E. O'Hara, Michael C. Moulton, Pierfilippo Cerretti, Isaac S. Winkler

Biological Sciences Faculty Publications

D eveloping a structural phylogenetic framework for the family Tachinidae has been an interest of mine since I first started working on tachinids as a graduate student. It was then that I developed a new phylogenetic perspective with which to view the world, and many of the questions I wanted to ask of tachinids depended on some level of phylogenetic knowledge of them. I was surprised at the time that no one had attempted a broad quantitative phylogenetic analysis of the family, and a publication from my thesis work on the Exoristinae (Stireman 2002) became the first such study that …

Food Limitation As A Potentially Emerging Contributor To The Asian Vulture Crisis, Fakhar -I- Abbas, Thomas P. Rooney, Jibran Haider, Afsar Mian

Biological Sciences Faculty Publications

It was believed that the reason for decline in Asian vulture population is the drug, Diclofenac sodium (DFS), used in livestock. Even after declaring the DFS use banned by the government, apparent decrease in the population of vultures was reported. Alternate hypothesis was suggested that food limitation may be a cause of Asian vulture crisis in Pakistan. Very recent shifts in livestock utilization observed in Pakistan may present a significant barrier to vulture recovery. Increased livestock utilization is translated to fewer carcasses. Since 2005, no livestock carcasses were found in 1650 km transect in the habitat of vultures. Carcasses recorded …

Game-Based Curricula In Biology Classes: Multi-Level Assessment Of Science Learning, Troy D. Sadler, William L. Romine, Parker E. Stuart

Biological Sciences Faculty Publications

Video games played on computers, game consoles, tablets and smart phones have become a very popular medium in our society. A growing body of scholarship suggests that video games can support substantial learning (for reviews see Gee, 2007; Honey & Hilton, 2011; Squire, 2011). Research has documented ways in which games engage students deeply in thinking, learning, and collaboration (Gee, 2005). Evidence suggests that games can support development of critical thinking (Squire, 2006), creativity (Annetta, Cheng, & Holmes, 2010), and mastery and application of target concepts (Squire, 2011).

To 'Die Hel' And Back. Expeditions Of The Phylogeny Of World Tachinidae Project. Part I: Western Cape, South Africa, Pierfilippo Cerretti, James E. O'Hara, John O. Stireman Iii, Isaac S. Winkler, Ashley H. Kirk-Spriggs

Biological Sciences Faculty Publications

The “Phylogeny of World Tachinidae” project kicked off with an operational meeting in June 2012 at the Canadian National Collection of Insects (CNC) in Ottawa. Goals were discussed, work plans prepared, and of course the destinations and timing of major field expeditions were debated. During our three years of National Science Foundation funding we hope to gather fresh material for molecular analysis from all biogeographic regions of the world.