Systems Biology Commons^™

Global Intron Retention Mediated Gene Regulation During Cd4+ T Cell Activation., Ting Ni, Wenjing Yang, Miao Han, Yubo Zhang, Ting Shen, Hongbo Nie, Zhihui Zhou, Yalei Dai, Yanqin Yang, Poching Liu, Kairong Cui, Zhouhao Zeng, Yi Tian, Bin Zhou, Gang Wei, Keji Zhao, Weiqun Peng, Jun Zhu

Genomics and Precision Medicine Faculty Publications

T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Using strand-specific RNA-seq, we observed that intron retention is prevalent in polyadenylated transcripts in resting CD4(+) T cells and is significantly reduced upon T cell activation. Several lines of evidence suggest that intron-retained transcripts are less stable than fully spliced transcripts. Strikingly, the decrease in intron retention (IR) levels correlate with the increase in steady-state mRNA levels. Further, the majority of the genes upregulated in activated T cells are accompanied by a significant reduction in IR. Of these 1583 genes, 185 genes are predominantly regulated at …

A Dynamical Systems Model Of Progesterone Receptor Interactions With Inflammation In Human Parturition, Douglas Brubaker, Mark R. Chance, Sam Mesiano

Faculty Scholarship

Background: Progesterone promotes uterine relaxation and is essential for the maintenance of pregnancy. Withdrawal of progesterone activity and increased inflammation within the uterine tissues are key triggers for parturition. Progesterone actions in myometrial cells are mediated by two progesterone receptor (PR) isoforms, PR-A and PR-B, that function as ligand-activated transcription factors. PR-B mediates relaxatory actions of progesterone, in part, by decreasing myometrial cell responsiveness to pro-inflammatory stimuli. These same pro-inflammatory stimuli promote the expression of PR-A which inhibits the anti-inflammatory activity of PR-B. Competitive interaction between the progesterone receptors then augments myometrial responsiveness to pro-inflammatory stimuli. The interaction between PR-B …

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by discussing our …

Nasp: An Accurate, Rapid Method For The Identification Of Snps In Wgs Datasets That Supports Flexible Input And Output Formats, Jason Sahl, Darrin Lemmer, Jason Travis, James Schupp, John Gillece, Maliha Aziz, +Several Additional Authors

Environmental and Occupational Health Faculty Publications

Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces similar, and often better, results in comparison with other pipelines, but is much more …

Computational Labeling, Partitioning, And Balancing Of Molecular Networks, Biaobin Jiang

Open Access Dissertations

Recent advances in high throughput techniques enable large-scale molecular quantification with high accuracy, including mRNAs, proteins and metabolites. Differential expression of these molecules in case and control samples provides a way to select phenotype-associated molecules with statistically significant changes. However, given the significance ranking list of molecular changes, how those molecules work together to drive phenotype formation is still unclear. In particular, the changes in molecular quantities are insufficient to interpret the changes in their functional behavior. My study is aimed at answering this question by integrating molecular network data to systematically model and estimate the changes of molecular functional …

Opn-A Induces Muscle Inflammation By Increasing Recruitment And Activation Of Pro-Inflammatory Macrophages., Gina M Many, Yasuyuki Yokosaki, Kitipong Uaesoontrachoon, Peter P Nghiem, Luca Bello, Sherry Dadgar, Ying Yin, Jesse M Damsker, Heather B Cohen, Joe N Kornegay, Marcas M Bamman, David M Mosser, Kanneboyina Nagaraju, Eric P Hoffman

Genomics and Precision Medicine Faculty Publications

New Findings

• What is the central question of this study? What is the functional relevance of OPN isoform expression in muscle pathology?
• What is the main finding and its importance? The full‐length human OPN‐a isoform is the most pro‐inflammatory isoform in the muscle microenvironment, acting on macrophages and myoblasts in an RGD‐integrin‐dependent manner. OPN‐a upregulates expression of tenascin‐C (TNC), a known Toll‐like receptor 4 (TLR4) agonist. Blocking TLR4 signalling inhibits the pro‐inflammatory effects of OPN‐a, suggesting that a potential mechanism of OPN action is by promoting TNC–TLR4 signalling.

Although osteopontin (OPN) is an important mediator of muscle remodelling in health …

Comparison Of Soil Phosphorus Concentration In Farm Restored And Reference Wetlands In Lake County, Il, Catherine L. Pease

DePaul Discoveries

The soil in the Midwest is fertile for agriculture use and therefore a lot of the wetlands have been turned into farmland. Wetlands can act as a sink for excess nutrients such as phosphorus. In part due to their value for nutrient storage, restoration of wetlands has become more frequent, including restoration of wetlands on former farmland. I am interested in phosphorus and the potential of wetlands to either store or release phosphorus. I compared differences in soil reactive phosphorus of restored and reference wetlands. This study compares Prairie Wolf Slough (PWS), a restored wetland, to two reference wetlands, both …

Diversity And Distribution Of Diatom Endosymbionts In Amphistegina Spp. (Foraminifera) Based On Molecular And Morphological Techniques, Kwasi H. Barnes

USF Tampa Graduate Theses and Dissertations

Diatoms associated with foraminifers of the genus Amphistegina were assessed using a combination of morphological and molecular techniques. These included: 1) microscopic identification of diatoms cultured from the host, 2) sequencing of portions of the small subunit of the ribosomal RNA gene (18S) and the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase [i.e., RubisCO] gene (rbcL) from DNA extracted directly from the Amphistegina hosts and also from diatoms cultured from these hosts, and 3) denaturing gradient gel electrophoresis (DGGE) profiles of rbcL and internal transcribed spacer 1 (ITS1) PCR amplicons from DNA extracted directly from …

Histological And Molecular Analysis Of A Progressive Diffuse Intrinsic Pontine Glioma And Synchronous Metastatic Lesions: A Case Report., Javad Nazarian, Gary E Mason, Cheng Ying Ho, Eshini Panditharatna, Madhuri Kambhampati, Louis Gilbert Vezina, Roger J. Packer, Eugene I Hwang

Genomics and Precision Medicine Faculty Publications

There is no curative treatment for patients with diffuse intrinsic pontine glioma (DIPG). However, with the recent availability of biopsy and autopsy tissue, new data regarding the biologic behavior of this tumor have emerged, allowing greater molecular characterization and leading to investigations which may result in improved therapeutic options. Treatment strategies must address both primary disease sites as well as any metastatic deposits, which may be variably sensitive to a particular approach.In this case report, we present a patient with DIPG treated with irradiation and serial investigational agents. The clinical, pathological and molecular phenotypes of both the progressive primary tumor …

Global Attractors And Random Attractors Of Reaction-Diffusion Systems, Junyi Tu

USF Tampa Graduate Theses and Dissertations

The dissertation studies about the existence of three different types of attractors of three multi-component reaction-diffusion systems. These reaction-diffusion systems play important role in both chemical kinetics and biological pattern formation in the fast-growing area of mathematical biology.

In Chapter 2, we prove the existence of a global attractor and an exponential attractor for the solution semiflow of a reaction-diffusion system called Boissonade equations in the L² phase space. We show that the global attractor is an (H, E) global attractor with the L^∞ and H² regularity and that the Hausdorff dimension and the …

Distribution Of Short-Tailed Shrews (Mammalia: Soricidae: Blarina) In Missouri, Russell S. Pfau, Aaron P. Figueroa

The Prairie Naturalist

Three species of short-tailed shrews (genus Bla- rina) occur throughout the eastern one-half of the United States and southern Canada. B. brevicauda is the most widely distributed, ranging from the Atlantic ocean to the western Great Plains. B. carolinensis occurs throughout the southeastern U.S., and B. hylophaga is found in the southern plains states. The current understanding of the geographic distributions of these species is based primarily on morphol- ogy; size is the primary characteristic used for identifica- tion with B. brevicauda the largest and B. carolinensis the smallest.

The only states in which all three species have been reported …

Notes: Comparisons Of Catch Between Two Bait Types With An Emphasis On Pallid Stur- Geon, Thad W. Huenemann, Kirk D. Steffensen

The Prairie Naturalist

Trotline sampling has been a common practice used by commercial and recreational anglers to target specific fish species (e.g. Ictaluridae and Acipenseridae), while biologists have used them as a management tool to monitor and evaluate fish populations (Graham 1997, Vokoun and Rabeni 1999, Arterburn and Berry 2002, Steffensen et al. 2011). Different trotline configurations have been evaluated to determine which combination of hook type and bait produces higher catch rates for catfish species (Johnson 1987, Arterburn and Berry 2002) but this information is lacking for sturgeon species. For example, Arterburn and Berry (2002) concluded that channel catfish (Ictalurus punctatus) were …

Life In The Cold: An Investigation Of Polar Regions, Briar Bragdon, Ashley Breault, Bailey Bush, Jennifer Gamble, Rebecca Hudak, Emily Johnston, Kaitlyn Kennedy, Alexandria Makucewicz, Sharlene Maynard, Erin Mohr, Gwen Pelletier, Halie Pruitt, Abigail Rhodes, Peter Swan, Markus Frederich

Marine Sciences Student Projects

Polar areas provide unique environments that, though they may seem extreme and uninhabitable, are flourishing with life. These areas around the North and South poles include deep oceans, shallow shelf regions, tundra, mountain ranges and vast glaciers. With the increasing effects of global climate change, a basic knowledge of polar regions is crucial to understand future impacts and implications. The purpose of this book is to give a broad background of polar biology, and also provide details on specific examples through case studies. Topics included throughout this book are: Ice, Life in Polar Regions, Species Interactions, and Anthropogenic Impacts.

The …

Book Reviews: A Chorus Of Cranes: The Cranes Of North America And The World. Paul A. Johnsgard (With Photographs By Thomas D. Mangelsen, And Drawings And Maps By Paul A. Johnsgard)., John G. Sidle

The Prairie Naturalist

Once again, naturalist and author Paul A. Johnsgard invites us to dance and chorus with cranes, and to appreciate their beauty and links to another species, Homo sapiens. A Chorus of Cranes is about natural history but also is a plea for conservation, which is a common foreword, prologue, preface, and/or epilogue of many wildlife books. It is vintage Paul Johnsgard text from preface to epilogue, words that emerge after a long wade through countless papers and reports, and a prolonged career of observation and reflection in the field. He has beckoned us before to cherish cranes and the natural …

Missing The Point, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! I hope summer finds you well and enjoying the Great Plains in some way, whether that be getting your hands dirty with field work, a reprieve from the office, anxiously awaiting the crappie bite at your favorite lake, or taking a much needed vacation. For those who enjoy cooler temperatures, summer heat and humidity are challenging and even the most seasoned field biologists among us are tested when fighting the conditions doing what we are passionate about. I personally prefer the fall and winter seasons, though also look forward to summer because it offers me a break …

Varmints And Victims: Predator Control In The Ameri- Can West. Frank Van Nuys., Phil Mastrangelo

The Prairie Naturalist

Having recently retired after 30+ years working in the field of human-wildlife conflicts, including predator conflicts with livestock, I looked forward to reading Varmints and Victims: Predator Control in the American West by Frank Van Nuys. As a wildlife biologist with an interest in the history of wildlife management in North America, I was further intrigued by the subject matter selected by Van Nuys.

In the book’s introduction, Van Nuys explains how the issue of mountain lion (Puma concolor) management in his home state of South Dakota sparked his interest in further exploring the history of predators and their management …

The Science Of Open Spaces: Theory And Practice For Conserving Large, Complex Systems. Charles G. Curtin., Michelle L. Hellman, Caleb P. Roberts, Hannah Birge, Zachary Warren, Craig R. Allen

The Prairie Naturalist

The phrase “open spaces,” may bring to mind expansive tracts of prairie, rangeland, or even desert, stretching lonely and unchanged to the horizon. Open spaces also could conjure open oceans or interstitial rural lands between urbanized hubs, dotted with farms, fields, and woodlands. In an abstract sense, open spaces could represent gaps in human understanding or blank spaces on a map. In his book The Science of Open Spaces, landscape ecologist Charles Curtin combines all these perspectives, expanding the definition of “open spaces” to multi-layered and multi-scaled complex systems that are “greater than the sum of their parts.” He populates …

Mink Predation Of Brown Trout In A Black Hills Stream, Jake Davis, Jerry W. Wilhite, Steven R. Chipps

The Prairie Naturalist

In the early 2000’s, declines in the brown trout (Salmo trutta) fishery in Rapid Creek, South Dakota, caused concern for anglers and fisheries managers. We conducted a radio telemetry study in 2010 and 2011 to identify predation mortality associated with mink, using hatchery-reared (2010) or wild (2011) brown trout. Estimated predation rates by mink (Mustela vison) on radio-tagged brown trout were 30% for hatchery fish and 32% for wild fish. Size frequency analysis revealed that the size distribution of brown trout lost to predation was similar to that of other, radio-tagged brown trout. In both years, a higher proportion of …

Fixed Versus Random Sampling Designs In Small South Dakota Glacial Lakes, Bradley J. Smith, Nathan S. Kruger, Nicholas S. Voss, Brian G. Blackwell

The Prairie Naturalist

Choice of sampling design is fundamental when planning surveys to monitor fisheries resources. However, little is known about the impact that different sampling designs may have on commonly collected fish population metrics used to index relative abundance, size structure, and diversity in small (<200 ha) glacial lakes. To address this issue, we sampled three small glacial lakes in eastern South Dakota with modified fyke nets and gill nets at fixed sites used by South Dakota Game, Fish and Parks and a complement of nets at randomized sites. Catch per unit effort (CPUE), proportional size distribution (PSD), and PSD-preferred (PSD-P) were compared between fixed and random designs for each species and gear by lake while Bray-Curtis distances were calculated between sample designs for each gear type in each lake. Precision of CPUE estimates for routinely indexed species were calculated for both gears used by each sampling design. No consistent bias in calculated population metrics was detected between sampling designs for any species collected with either gear type in the three lakes. Sampling precision of CPUE estimates were low for both gears and study designs; though randomized sites tended to yield lower precision. Power analyses indicated that current levels of sampling effort are insufficient to detect differences in CPUE or PSD/PSD-P between fixed and random sampling designs. In addition to being small, study lakes had relatively homogenous habitat allowing for effective sampling resulting in similar values of CPUE and PSD/PSD-P for both fixed and random study designs, and high assemblage overlap. We conclude that fixed sampling sites provide adequate representation of fish communities in small glacial lakes and are sufficient for monitoring temporal changes in these small, but numerous, systems.

Assessing Genetic Variation Of Rocky Mountain Bighorn Sheep At Elk Mountain, Brynn L. Parr, Rebeca L. Juarez, Jonathan A. Jenks

The Prairie Naturalist

The bighorn sheep (Ovis canadensis canadensis) herd occupying the Elk Mountain Region of South Dakota and Wyoming was established in 2001 with 20 individuals. An additional 7 ewes were released in 2004. The population increased to approximately 120 individuals in 2009, but subsequently declined to an estimated 80 individuals. Because of the low population size used to establish the herd and relative isolation of the Elk Mountain Region, potential factors associated with the population decline included reduced genetic diversity. Our objectives were to: 1) assess genetic diversity, 2) measure effective population size (Ne), and 3) compare the genetic diversity of …

Resource Selection By Black-Backed Woodpeckers (Picoides Arcticus) And American Three-Toed Woodpeckers (P. Dorsalis) In South Dakota And Wyoming, Sean R. Mohren, Mark A. Rumble, Chadwick P. Lehman, Stanley H. Anderson

The Prairie Naturalist

Black-backed woodpeckers (Picoides arcticus, [BBWO]) and American three-toed woodpeckers (P. dorsalis, [ATTW]) are uncommon inhabitants of conifer forests and are sympatric in some areas, including the Black Hills. Both species exhibit genetic characteristics associated with isolated populations, are species of special management concern, and for which data are lacking concerning populations and habitats. We developed resource selection models of forest vegetation within 500 m radius plots (78.5 ha) for BBWOs and ATTWs to provide forest managers with stand-level information to estimate how forest management might affect habitat for these species in the Black Hills. Relative probability of selection by BBWOs …

Keys To Lichens Of North America, Revised And Expand- Ed. Irwin M. Brodo (Photographs By Sylvia Duran Sharnoff And Stephen Sharnoff; Drawings By Susan Laurie-Bourque)., Caleb A. Morse

The Prairie Naturalist

It would be hard to overestimate the importance of the 2001 publication of Lichens of North America (hereafter LNA) by Irwin Brodo, Silvia Duran Sharnoff, and Stephen Sharnoff (Brodo et al. 2001). Beautifully illustrated, LNA included both an excellent overview to lichenology—including such diverse topics as chemistry, ecology, ethnolichenology, and specimen preparation—and descriptions of more than 800 of the common and charismatic lichens of North Ameri- ca. It is the rare book that provides a good introduction to the discipline, while serving as an essential tool for lichenologists. LNA is frequently cited in journals as an authoritative source on spot …

Isotopes From Fecal Material Provides Evidence Of Recent Diet Of Prairie Deer Mice, John W. Doudna, Brent J. Danielson

The Prairie Naturalist

Prairie deer mice are important predators in many agricultural systems, and through their diet they can help to regulate pest insect and weed populations. Our objective was to test whether fecal material is an effective means of detailing the foraging ecology of small mammals. We conducted three studies to evaluate the efficacy of this technique: 1) field-collected fecal material from unknown deer mice from late winter to early spring, 2) fecal material collected in an enclosure with mice fed a mix of C3 and C4 plant seeds, and 3) fecal material from tagged female mice in the field. We detected …

Book Review: Better Birding: Tips, Tools, And Concepts For The Field. George L. Armistead And Brian L. Sullivan., Stephen J. Dinsmore

The Prairie Naturalist

George Armistead and Brian Sullivan have written a book whose aim is to provide birders with a solid foundation upon which to develop better birding skills. They advocate a more holistic approach to bird identification than simply looking at a set of predetermined field marks. To that end, their approach combines traditional field identification approaches with behavioral and habitat cues, as well as natural history, to broaden bird identification skills. This is not the first book to make a case for looking at bird identification more broadly, although their specific approach seems unique. The authors offer constructive criticism of “traditional” …

Ocean Acidification And Predator-Prey Relations: Correlating Disruption Of Predator Avoidance With Chemosensory Deficits, Alexandra Fw Sidun, William G. Wright

Student Scholar Symposium Abstracts and Posters

One of the most destructive effects of global climate change is the increased carbon sequestering and consequential acidification of our world’s oceans. The impacts of ocean acidification on marine organisms are still relatively unknown, especially effects on behavioral ecology. Avoiding predation has emerged from recent behavioral ecology literature as a critical feature in the life history of a wide array of animal species; experiments on marine fishes suggest acidic water compromises their predator-avoidance abilities. Recent assays in our lab suggest predator-induced behavior is reduced by weakly acidic water. These experiments do not address the potential factor of generalized malaise caused …

Compost Land Management And Soil Carbon Sequestration, Kylene A. Hohman

Senior Honors Projects, 2010-2019

Extensive fossil fuel burning has released carbon dioxide into the atmosphere. Under proper ecological conditions plants convert atmospheric carbon dioxide into stable soil organic matter, a natural and efficient means of mitigating climate change. In the symbiotic relationship between mycorrhizae and plants, mycorrhizae provide plants with essential nutrients in exchange for carbon sugars leaked from the plants. Mycorrhizae convert carbon sugars to an exudate called glomalin, a protein that assists in developing soil aggregates composed of sand, silt, and clay. These aggregates, called humus, store carbon for hundreds of years under healthy ecological conditions. Compost prompts soil microbes to aerobically …

Germline Defects Caused By Smed-Boule Rna-Interference Reveal That Egg Capsule Deposition Occurs Independently Of Fertilization, Ovulation, Mating, Or The Presence Of Gametes In Planarian Flatworms, Jessica Kathryne Steiner, Junichi Tasaki, Labib Rouhana

Biological Sciences Faculty Publications

Few animals are known to lay eggs in the absence of ovulation or copulation, as it is presumably energetically wasteful and subjected to negative selection. Characterization of Smed-boule, a member of the DAZ family of germline RNA-binding proteins, revealed that egg capsule (or capsule) production and deposition occurs independently of the presence of gametes in the planarian flatworm Schmidtea mediterranea. Reduction of Smed-boule expression by RNA-interference (RNAi) causes ablation of spermatogonial stem cells and the inability of ovarian germline stem cells to undergo oogenesis. Although animals subjected to Smed-boule RNAi lose their gametes and become sterile, they continue …

The Mayfly Newsletter, Peter M. Grant

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Mycodb, A Global Database Of Plant Response To Mycorrhizal Fungi, V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy C. Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook Milligan, John C. Moore, Thomas H. Pendergast Iv, Bridget J. Piculell, Blake Ramsby, Suzanne Simard, Shubha Shrestha, James Umbanhowar, Wolfgang Viechtbauer, Lawrence Walters, Gail W. T. Wilson, Peter C. Zee, Jason D. Hoeksema

Biological Sciences Faculty Publications

Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis …

The Frugal Innovator: Creating Change On A Shoestring Budget, Charles Leadbeater

Asian Management Insights

The world needs innovation that is lean, simple, clean and social.