Systems Biology Commons^™

Updated Manuscript Submission Guidelines For The Prairie Naturalist, Christopher N. Jacques, Troy W. Grovenburg, Jonathan A. Jenks

The Prairie Naturalist

These guidelines present updated policies and procedures for submitting scientific manuscripts for consideration for publication in The Prairie Naturalist (PNAT). These guidelines incorporate substantial changes that have occurred following a change in Editorial staff during January 2009, and update the online “Suggestions for Contributors” guidelines provided on the PNAT website (http://www.sdstate.edu/nrm/organizations/gpnss/tpn/index.cfm); these instructions supersede all previous guidelines.

Tables and appendices are included for common word expressions with superfluous wording (Table 1), examples of correct format and style guidelines for tables accompanying manuscripts (Table 2, Appendix A), guidance in properly preparing Research notes (Appendix B) and citing literature (Appendix …

Interior Least Tern Powerline Collision On The Lower Platte River, Lauren R. Dinan, Joel G. Jorgensen, Mary Bomberger Brown

The Prairie Naturalist

Collisions with electrical powerlines are a well-known documented cause of avian mortality (Avian Power Line Interaction Committee [APLIC] 1994, Savereno et al. 1996). Mortality caused by collisions with powerlines can be an important concern for many bird species, but is a serious conservation problem for threatened and endangered species because any mortality can have biological and legal ramifications (Janss 2000). Loss of individuals, particularly breeding adults, from an already small population may impede a species’ recovery by reducing reproduction and recruitment into the breeding population. The death of an individual from a threatened or endangered species as a result of …

Walleye Trophic Position Before And After A Gizzard Shad Extirpation, Bethany J. Bethke, Justin A. Vandehey, Mark J. Fincel, Brian D.S. Graeb, Mark T. Porath

The Prairie Naturalist

Walleye (Sander vitreus) are an ecologically and recreationally important sport fish species. Reduced growth and condition in walleye can occur when prey availability is limited. In two Nebraska reservoirs, walleye consumed gizzard shad (Dorosoma cepedianum) as their primary prey until a winterkill extirpated the gizzard shad in 2001. Because of the winterkill, walleye in the two reservoirs had to change to alternative prey items. Our objective was to determine if stable isotope analysis on archived walleye scales can be used to detect a known food web shift in two reservoir food webs. We quantified the changes …

Avian Diversity And Habitat Use On Wetland Reserve Program Lands In The Lower Missouri River Valley, Eric C. Hopps

The Prairie Naturalist

A primary objective of the Wetland Reserve Program (WRP) is to provide habitat for migratory birds throughout all seasons of the year. Comprehensive avian assessments are lacking and limit our ability to evaluate the benefits of the WRP to continental bird populations. I investigated avian species occurrence on WRP lands within the Lower Missouri River Valley (LMRV), Nebraska, USA, from March 2010 to February 2011. Ten WRP habitat types are described based on plant community assemblages and observed hydrological regimes. Estimates of avian species richness were greatest in lowland forest (n = 115), lowland woodland (n = 83) and upland …

Of Gardens, Microorganisms, And Long Island Sound, Judy Preston

Wrack Lines

How healthy soil can make an environmental difference.

"I happened to turn over a large rounded stone in my garden to find a mesmerizing world of organisms that had, just moments earlier, been going about their business before being exposed to the sunlit world, and me."

Extensive And Prolonged Restoration Of Dystrophin Expression With Vivo-Morpholino-Mediated Multiple Exon Skipping In Dystrophic Dogs, Toshifumi Yokota, Akinori Nakamura, Tetsuya Nagata, Takashi Saito, Masanori Kobayashi, Yoshitsugu Aoki, Yusuke Echigoya, Terence A. Partridge, Eric P. Hoffman, Shinichi Takeda

Genomics and Precision Medicine Faculty Publications

Duchenne muscular dystrophy (DMD) is a severe and the most prevalent form of muscular dystrophy, characterized by rapid progression of muscle degeneration. Antisense-mediated exon skipping is currently one of the most promising therapeutic options for DMD. However, unmodified antisense oligos such as morpholinos require frequent (weekly or bi-weekly) injections. Recently, new generation morpholinos such as vivo-morpholinos are reported to lead to extensive and prolonged dystrophin expression in the dystrophic mdx mouse, an animal model of DMD. The vivo-morpholino contains a cell-penetrating moiety, octa-guanidine dendrimer. Here, we sought to test the efficacy of multiple exon skipping of exons 6–8 with vivo-morpholinos …

Monitoring Standing Herbage Of The Sands And Choppy Sands Ecological Vegetation Types In The Nebraska Sandhills, Daniel W. Uresk

Great Plains Research: A Journal of Natural and Social Sciences (through 2013)

A modified Robel pole with white and gray alternating bands (2.54 cm) was used to measure vegetation on sands and choppy sands ecological types in the Sandhills of Nebraska. Objectives were to determine the relationship between visual obstruction readings (VOR) and clipped standing herbage, develop guidelines for monitoring standing herbage, and provide sample size estimates. Visual obstruction measurements of standing herbage were linear, and regression coefficients were significant (P< 0.001) for 125 transects (R² = 0.60, SE = 496 kg/ha). Clipped standing herbage ranged from 293 to 4389 kg/ha with a mean of 1,559 kg/ha. A minimum of four transects (20 stations/transect with four …

Deletion Of Galectin-3 Exacerbates Microglial Activation And Accelerates Disease Progression And Demise In A Sod1 G93a Mouse Model Of Amyotrophic Lateral Sclerosis, Bruce J. Lerman, Eric P. Hoffman, Margaret L. Sutherland, Khaled Bouri, Daniel K. Hsu, Jeffrey D. Rothstein, Susan M. Knoblach

Genomics and Precision Medicine Faculty Publications

Galectins are pleiotropic carbohydrate-binding lectins involved in inflammation, growth/differentiation, and tissue remodeling. The functional role of galectins in amyotrophic lateral sclerosis (ALS) is unknown. Expression studies revealed increases in galectin-1 mRNA and protein in spinal cords from SOD1 ^G93A mice, and in galectin-3 and -9 mRNAs and proteins in spinal cords of both SOD1^G93A mice and sporadic ALS patients. As the increase in galectin-3 appeared in early presymptomatic stages and increased progressively through to end stage of disease in the mouse, it was selected for additional study, where it was found to be mainly expressed by microglia. Galectin-3 antagonists …

The Breathing Of The Bays, Jamie Vaudrey, Margaret (Peg) A. Van_Patten (Editor)

Wrack Lines

Bays in Long Island Sound and beyond have natural rhythms like breathing. Stress can impact the health of these natural ecosystems. While Long Island Sound has been examined for the extent of hypoxia in the summer, small embayments have not been examined carefully. In this article, two researchers investigate the oxygen, or lack of, in small bays of Long Island Sound.

The Crayfish (Decapoda: Cambaridae) Subgenus Hiaticambarus: Undescribed Diversity And Life History Characteristics Of Selected Members, Danny Jones

All Dissertations

A taxonomic study of the crayfish species Cambarus (Hiaticambarus) longirostris was conducted. Multivariate and univariate statistical analyses of morphometric data and examination of morphological characters revealed the existence of four undescribed species from populations previously considered to belong to C. longirostris; these were located on the southern extents of the range of C. longirostris. Three of these new species were morphologically similar to the group of species containing C. coosawattae, C. chasmodactylus, C. elkensis, C. longirostris, C. longulus, and C. manningi, while one was morphologically similar to the C. fasciatus, C. …

Systems Biology Approaches To Probe Gene Regulation In Bacteria, Diogo F. Troggian Veiga

Dissertations and Theses (Open Access)

Mechanisms that allow pathogens to colonize the host are not the product of isolated genes, but instead emerge from the concerted operation of regulatory networks. Therefore, identifying components and the systemic behavior of networks is necessary to a better understanding of gene regulation and pathogenesis. To this end, I have developed systems biology approaches to study transcriptional and post-transcriptional gene regulation in bacteria, with an emphasis in the human pathogen Mycobacterium tuberculosis (Mtb).

First, I developed a network response method to identify parts of the Mtb global transcriptional regulatory network utilized by the pathogen to counteract phagosomal stresses …

Platelets Induce Apoptosis During Sepsis In A Contact-Dependent Manner That Is Inhibited By Gpiib/Iiia Blockade, Matthew Sharron, Claire E. Hoptay, Andrew A. Wiles, Lindsay M. Garvin, Mayya Geha, Angela S. Benton, Kanneboyina Nagaraju, Robert J. Freishtat

Genomics and Precision Medicine Faculty Publications

Purpose

End-organ apoptosis is well-described in progressive sepsis and Multiple Organ Dysfunction Syndrome (MODS), especially where platelets accumulate (e.g. spleen and lung). We previously reported an acute sepsis-induced cytotoxic platelet phenotype expressing serine protease granzyme B. We now aim to define the site(s) of and mechanism(s) by which platelet granzyme B induces end-organ apoptosis in sepsis.

Methods

End-organ apoptosis in murine sepsis (i.e. polymicrobial peritonitis) was analyzed by immunohistochemistry. Platelet cytotoxicity was measured by flow cytometry following 90 minute ex vivo co-incubation with healthy murine splenocytes. Sepsis progression was measured via validated preclinical murine sepsis score.

Measurements and Main Results …

Conditional Over-Expression Of Pitx1 Causes Skeletal Muscle Dystrophy In Mice, Sachchida Nand Pandey, Jennifer Cabotage, Rongye Shi, Manjusha Dixit, Margaret L. Sutherland, Jian Liu, Stephanie Muger, Scott Q. Harper, Kanneboyina Nagaraju, Yi-Wen Chen

Genomics and Precision Medicine Faculty Publications

Paired-like homeodomain transcription factor 1 (PITX1) was specifically up-regulated in patients with facioscapulohumeral muscular dystrophy (FSHD) by comparing the genome-wide mRNA expression profiles of 12 neuromuscular disorders. In addition, it is the only known direct transcriptional target of the double homeobox protein 4 (DUX4) of which aberrant expression has been shown to be the cause of FSHD. To test the hypothesis that up-regulation of PITX1 contributes to the skeletal muscle atrophy seen in patients with FSHD, we generated a tet-repressible muscle-specific Pitx1 transgenic mouse model in which expression of PITX1 in skeletal muscle can be controlled by oral administration of …

Il-6 Signaling Blockade Increases Inflammation But Does Not Affect Muscle Function In The Mdx Mouse, Mathew A. Kostek, Kanneboyina Nagaraju, Emidio E. Pistilli, Arpana Sali, San-Huei Lai, Brad Gordon, Yi-Wen Chen

Genomics and Precision Medicine Faculty Publications

No abstract provided.

Systematics Of Harrisia (Cactaceae), Alan R. Franck

USF Tampa Graduate Theses and Dissertations

The genus Harrisia Britton (Cactaceae) comprises species of columnar cacti that are united by a unique seed morphology. The species range in form from prostrate shrubs to large trees and are native to South America and the Caribbean region. Harrisia is placed in an unresolved position within subtribe Trichocereinae of tribe Cereeae of subfamily Cactoideae. Relationships among the species within Harrisia are also poorly understood. In this study, several species of Harrisia were sequenced for as many as seven different regions of nuclear and plastid DNA. Species in the Caribbean were also examined with amplified fragment length polymorphisms. The morphology …

Monitoring Standing Herbage Of Mid-Grass Prairie On The Fort Pierre National Grassland, South Dakota, Daniel W. Uresk

The Prairie Naturalist

Monitoring vegetation with a modified Robel pole on the Fort Pierre National Grassland was evaluated for combined shallow clay and loamy overflow ecological sites (dominated by warm-season grasses), and for clayey ecological sites (dominated by cool-season grasses). My objectives were to 1) develop a relationship between visual obstruction readings (VOR) and standing herbage, 2) provide guidelines for vegetation monitoring, and 3) evaluate vegetation monitoring during the growing season for clayey ecological sites. The relationship between visual obstruction readings and standing herbage was linear and regression coefficients were highly significant (P < 0.001) for both ecological types. Cluster analyses for shallow clay and loamy overflow ecological sites grouped the VOR and standing herbage (kg•ha-1) into 4 resource categories. Monitoring with 4 transects will provide adequate information to estimate standing herbage within 259 ha (1 section). Three resource categories (VOR + herbage) for clayey ecological sites were defined by cluster analyses. Monitoring with 4 transects was determined to provide reliable estimates of standing herbage. July validation of vegetation with the developed clayey ecological site model will provide reliable monitoring of standing herbage from July through November for this ecological site.

Germination Response Of Prairie Dropseed And Hairy Goldaster To Stratification And Temperature, Aurora R. Roemmich, Jack L. Bulter, Gary E. Larson, E. Brent Turnipseed

The Prairie Naturalist

The unique vegetation assemblage of the Black Hills in conjunction with the frequent occurrence of natural and anthropogenic disturbances emphasizes the need to use locally adapted native species in a wide variety of restoration efforts. However, a general lack of information regarding germination and propagation requirements for most native plant species has restricted their usage. A better understanding of dormancy and germination patterns for native species will increase their availability and affordability. We selected two common native species, hairy goldaster (Heterotheca villosa) and prairie dropseed (Sporobolus heterolepis), to determine their optimum germination conditions. We hand-harvested seeds during 2007–2009 for use …

Five New Records Of Ants (Hymenoptera: Formicidae) For Nebraska, Kristine T. Nemec, James C. Trager, Elizabeth Manley, Craig R. Allen

The Prairie Naturalist

Ants are ubiquitous and influential organisms in terrestrial ecosystems. About 1,000 ant species occur in North America, where they are found in nearly every habitat (Fisher and Cover 2007). Ants are critical to ecological processes and structure. Ants affect soils via tunneling activity (Baxter and Hole 1967), disperse plant seeds (Lengyel et al. 2009), prey upon a variety of insects and other invertebrates (Way and Khoo 1992, Folgarait 1998), are often effective primary consumers through their prodigious consumption of floral and especially extrafloral nectar, and honeydew (Tobin 1994), and serve as prey for invertebrates (Gotelli 1996, Gastreich 1999) and vertebrates …

Distribution And Diversity Of Ant Genera From Selected Ecoregions Across Nebraska, Jessica Jurzenski, Marc Albrecht, W. Wyatt Hoback

The Prairie Naturalist

We documented distribution and diversity of ant genera in four of the six-level III ecoregions across Nebraska. We sampled ants using bait cards, pitfall traps, and by opportunistic sampling, including direct collection and in carrion-baited pitfall traps. We identified 22 genera from five subfamilies, which were further classified into six functional groups. In common with other Great Plains states, Formica Linnaeus and Lasius Fabricius occurred most frequently in our samples, and overall ant genus-level richness was comparable to surrounding states. We compared genera similarity using Jaccard’s similarity index within and between the High Plains (western-most) and Western Corn Belt Plains …

My Manuscript Needs Revision: Now What?, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! Hopefully by now you have read my previous editorial notes about the transformation of The Prairie Naturalist (Journal) during the past few years and the work the Editorial Staff continues to do to provide a quality publication venue for the Journal’s membership and prospective authors. During my tenure as Editor-in-Chief (Editor), I have had the good fortune of working with many authors and a truly dedicated Editorial Staff. Most topics for editorials come to me relatively easily, though admittedly I found myself scratching my head when thinking about a topic for this editorial. After much pensive thought, …