Life Sciences Commons^™

The Digital Society, Place

PLACE Historical Documents

This document explains the PLACE theme at Linfield College for 2016-2018 (The Digital Society).

Identification Of Pathway-Specific Serum Biomarkers Of Response To Glucocorticoid And Infliximab Treatment In Children With Inflammatory Bowel Disease, Christopher R. Heier, Alyson A. Fiorillo, Ellen Chaisson, Heather A. Gordish-Dressman, Yetrib Hathout, Jesse M. Damsker, Eric P. Hoffman, Laurie S. Conklin

Genomics and Precision Medicine Faculty Publications

Objective:

Serum biomarkers may serve to predict early response to therapy, identify relapse, and facilitate drug development in inflammatory bowel disease (IBD). Biomarkers are particularly important in children, in whom achieving early remission and minimizing procedures are especially beneficial.

Methods:

We profiled protein and micro RNA (miRNA) in serum from patients pre- and post-therapy, to identify molecular markers of pharmacodynamic effect. Serum was obtained from children with IBD before and after treatment with either corticosteroids (prednisone; n=12) or anti-tumor necrosis factor-α biologic (infliximab; n=7). Over 1,100 serum proteins were assayed using aptamer-based SOMAscan proteomics, and 22 miRNAs analyzed …

Muscle Myeloid Type I Interferon Gene Expression May Predict Therapeutic Responses To Rituximab In Myositis Patients., Kanneboyina Nagaraju, Svetlana Ghimbovschi, Sree Rayavarapu, Aditi Phadke, Lisa G. Rider, Eric P. Hoffman, Frederick Miller

Genomics and Precision Medicine Faculty Publications

Objective. To identify muscle gene expression patterns that predict rituximab responses and assess the effects of rituximab on muscle gene expression in PM and DM.

Methods. In an attempt to understand the molecular mechanism of response and non-response to rituximab therapy, we performed Affymetrix gene expression array analyses on muscle biopsy specimens taken before and after rituximab therapy from eight PM and two DM patients in the Rituximab in Myositis study. We also analysed selected muscle-infiltrating cell phenotypes in these biopsies by immunohistochemical staining. Partek and Ingenuity pathway analyses assessed the gene pathways and networks.

Results. Myeloid type I IFN …

2017 Barley Variety Sowing Guide For Western Australia, Blakely Paynter, Georgia Trainor

Bulletins 4000 -

This variety guide is designed as a reference to help determine which barley variety to grow in your region. It provides market feedback, relative grain yield comparisons, disease ratings, agronomic information and herbicide tolerance ratings for all malt and food barley varieties segregated in Western Australia (WA) and selected feed varieties (Tables 1-9; Figures 1-7).

Methane Emissions From Global Rice Fields: Magnitude, Spatiotemporal Patterns, And Environmental Controls, Bowen Zhang, Hanqin Tian, Wei Ren, Bo Tao, Chaoqun Lu, Jia Yang, Kamaljit Banger, Shufen Pan

Plant and Soil Sciences Faculty Publications

Given the importance of the potential positive feedback between methane (CH₄) emissions and climate change, it is critical to accurately estimate the magnitude and spatiotemporal patterns of CH₄ emissions from global rice fields and better understand the underlying determinants governing the emissions. Here we used a coupled biogeochemical model in combination with satellite-derived contemporary inundation area to quantify the magnitude and spatiotemporal variation of CH₄ emissions from global rice fields and attribute the environmental controls of CH₄ emissions during 1901–2010. Our study estimated that CH₄ emissions from global rice fields varied from 18.3 ± …

How Did The Deepwater Horizon Oil Spill Impact Deep-Sea Ecosystems?, Charles R. Fisher, Paul A. Montagna, Tracey Sutton

Marine & Environmental Sciences Faculty Articles

Approximately 90% of the volume of the Gulf of Mexico is contained in water deeper than 200 m, a region where the Deepwater Horizon (DWH) blowout had more impact on ecosystems than any previous oil spill. The remoteness and relative inaccessibility of the deep sea makes documenting even acute impacts to the animals that live in this realm difficult. This article reviews Natural Resource Damage Assessment studies and follow-up work funded as part of the Gulf of Mexico Research Initiative that targeted deepwater pelagic and benthic fauna. Oil was incorporated into the pelagic food web, and a reduction in planktonic …

Principles And Practices Fostering Inclusive Excellence: Lessons From The Howard Hughes Medical Institute’S Capstone Institutions, P. M. Dibartolo, L. Gregg-Jolly, D. Gross, C. A. Manduca, E. Iverson, D. B. Cooke Iii, G. K. Davis, C. Davidson, P. E. Hertz, L. Hibbard, S. K. Ireland, C. Mader, A. Pai, S. Raps, Kathleen King Siwicki, J. E. Swartz

Biology Faculty Works

Best-practices pedagogy in science, technology, engineering, and mathematics (STEM) aims for inclusive excellence that fosters student persistence. This paper describes principles of inclusivity across 11 primarily undergraduate institutions designated as Capstone Awardees in Howard Hughes Medical Institute’s (HHMI) 2012 competition. The Capstones represent a range of institutional missions, student profiles, and geographical locations. Each successfully directed activities toward persistence of STEM students, especially those from traditionally underrepresented groups, through a set of common elements: mentoring programs to build community; research experiences to strengthen scientific skill/identity; attention to quantitative skills; and outreach/bridge programs to broaden the student pool. This paper grounds …

Review Of "A Primer Of Human Genetics" By G. Gibson, John B. Jenkins

Biology Faculty Works

No abstract provided.

Year-Round Measures Of Planktonic Metabolism Reveal Net Autotrophy In Surface Waters Of A Great Lakes Estuary, Angela L. Defore, Anthony D. Weinke, Morgan M. Lindback, Bopaiah A. Biddanda

Open Access Publishing Support Funded Articles

During 2009 and 2010, we quantified monthly changes in plankton metabolism and environmental variables in the surface waters of Muskegon Lake, a Great Lakes estuary connected to Lake Michigan. Muskegon Lake’s mean (±SE) annual gross plankton primary production (GPP) and respiration (R) rates were 46 ± 9 and 23 ± 4 mg C l−1 yr−1, respectively. GPP:R ratios of 0.6 to +4.8 with a yearly mean of 2.0 ± 0.3 indicated that the surface water of Muskegon Lake was net autotrophic during all but the winter months under ice cover, when it was in a near carbon balance to slightly …

Market Integration And Price Transmission In The World Rice Export Markets, Bo Chen, Sayed H. Saghaian

Agricultural Economics Faculty Publications

This paper investigates market integration and asymmetric price transmission in the world rice export markets. Using monthly rice prices from Thailand, Vietnam, and United States, we employ the Johansen test and estimate the threshold vector error correction model (TVECM). Our main findings are that export prices in the three countries are cointegrated, with Thailand and the United States the price leaders, and that the Vietnamese price adjusts faster to long-run equilibrium when it is above its equilibrium level with Thai and U.S. prices. These results suggest market integration and competition rather than collusion are prevalent in world rice markets. Policy …

The Relationship Between Basic Psychological Need Satisfaction, Behavioral Regulation, And Participation In Crossfit, Melissa J. Davies, Lyndsie Coleman, Megan Babkes Stellino

College of the Pacific Faculty Articles

CrossFit can be described as a relatively new fitness training method that is based on a variety of high-intensity weight training, body weight movements, and cardiovascular exercise. Given the recent rise in CrossFit establishments, the purpose of this study was to explore the relationships between basic need satisfaction (autonomy, relatedness, competence), behavioral regulation toward CrossFit, and actual participation behaviors within the framework of Self-Determination Theory. CrossFit participants (N = 206; Mage = 37.6 years), majority Caucasian (76%), females (58%), who reported attending three (n = 91; 44.2%) and five (n = 78; 37.9%) CrossFit sessions per week completed online surveys …

Forage News [2016-09], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• Dr. Chris Teutsch Accepts Forage Extension Specialist Position in Princeton, KY
• UK and USDA Specialists to speak at KFGC Field Day
• Forage News Quote of the Month: "You Can Observe a Lot Just by Watching"
• 16th Kentucky Grazing Conference Schedule Announced
• Difficulty with Alfalfa Establishment in 2016
• Featured Publication: Wildlife Benefits of Switchgrass Production in Kentucky (AGR-221)
• Considerations in Selecting a Cool Season Cereal Variety
• KFGC Award Nominations
• KFGC Board Nominations

Rapid Museum, Gary Barwin

The Goose

Poetry by Gary Barwin

Subscription And Organization Information [September 2016]

Nebraska Bird Review

The Nebraska Bird Review is published quarterly by the Nebraska Ornithologists' Union, Inc., as its official journal, and is sent to members not in arrears of dues. Annual subscription rates (on a calendar-year basis only): $25 in the United States and $35 in all other countries, payable in advance. Single copies are $7 each, postpaid, in the United States and $9 elsewhere. Send orders for back issues to Anita Breckbill, NOU Librarian, c/o Music Library, WMB 30, University of Nebraska, Lincoln, NE 68588-0101.

Memberships in the NOU (on a calendar-year basis only): Active Household (one or more people) $25; Sustaining …

A Documented Occurrence Of Black Rail (Laterallus Jamaicensis) In Nebraska, Cody Mcgregor, Eric Bruster, Mary Bomberger Brown, Lauren R. Dinan, Joel G. Jorgensen

Nebraska Bird Review

Black Rails (Laterallus jamaicensis) are the smallest of the rails found in North America. Even though they are broadly distributed in coastal tidal and inland freshwater marshes, they are rarely seen and consequently are poorly known. They prefer areas of moist soil interspersed with scattered small pools of shallow water surrounded by fine-stemmed rushes, grasses, and sedges for use during migratory stopover and nesting. All populations of Black Rail have declined precipitously over the past century due to the draining of marshes and wetlands and demands on water resources. In 2011, the U.S. Fish and Wildlife Service initiated …

How Did The Deepwater Horizon Oil Spill Affect Coastal And Continental Shelf Ecosystems Of The Gulf Of Mexico?, Steven Murawski, John E. Fleeger, William F. Patterson Iii, Chuanmin Hu, Kendra L. Daly, Isabel C. Romero, Gerardo Toro-Farmer

Marine Science Faculty Publications

The Deepwater Horizon (DWH) oil spill originated at the base of the continental shelf in the northern Gulf of Mexico (GoM), but large quantities of the oil were transported to the shelf (≤200 m water depth) and into coastal waters (herein defined as ≤15 km from the coast). Water-column effects were generally limited to the period of the ongoing oil releases, although, due to an extensive oil sedimentation event (“dirty blizzard”), effects on the benthos have the potential to be chronic, especially in soft sediments. Impacts on phytoplankton, zooplankton, and ichthyoplankton were relatively short-lived, and the abundance and species composition …

A Hybrid Method To Estimate Suspended Particle Sizes From Satellite Measurements Over Bohai Sea And Yellow Sea, Deyong Sun, Zhongfeng Qiu, Chuanmin Hu, Shengqiang Wang, Lin Wang, Lufei Zheng, Tian Peng, Yijun He

Marine Science Faculty Publications

Particle-size distribution (PSD), a measure of particle concentrations at different sizes, is of great importance to the understanding of many biogeochemical processes in coastal marine ecosystems. Here, a hybrid method, including analytical, semianalytical, and empirical steps, is developed to estimate PSD through the median diameter of suspended particles ( ). Four cruise surveys were conducted to measure optical scattering properties, particle concentrations, spectral reflectance, and particle-size distributions (obtained with a LISST instrument covering a size range of 2.5–500 μm) in coastal waters of Bohai Sea, Yellow Sea, and Jiangsu coastal region. Based on the Mie scattering theory, is closely related …

Juvenile Winter Flounder (Pseudopleuronectes Americanus) And Summer Flounder (Paralichthys Dentatus) Utilization Of Southern New England Nurseries: Comparisons Among Estuarine, Tidal River, And Coastal Lagoon Shallow-Water Habitats, David L. Taylor, Jason Mcnamee, John Lake, Carissa L. Gervasi, Danial G. Palance

Arts & Sciences Faculty Publications

This study evaluated the relative importance of the Narragansett Bay estuary (RI and MA, USA), and associated tidal rivers and coastal lagoons, as nurseries for juvenile winter flounder, Pseudopleuronectes americanus, and summer flounder, Paralichthys dentatus. Winter flounder (WF) and summer flounder (SF) abundance and growth were measured from May to October (2009–2013) and served as indicators for the use and quality of shallow-water habitats (water depth < 1.5–3.0 m). These bioindicators were then analyzed with respect to physiochemical conditions to determine the mechanisms underlying intraspecific habitat selection. WF and SF abundances were greatest in late May and June (maximum monthly mean = 4.9 and 0.55 flounder/m2 for WF and SF, respectively) and were significantly higher in the tidal rivers relative to the bay and lagoons. Habitat-related patterns in WF and SF abundance were primarily governed by their preferences for oligohaline (0.1–5 ppt) and mesohaline (6–18 ppt) waters, but also their respective avoidance of hypoxic conditions (< 4 mg DO/L) and warm water temperatures (>25 °C). Flounder habitat usage was also positively related to sediment organic content, which may be due to these substrates having sufficiently high prey densities. WF growth rates (mean = 0.25 ± 0.14 mm/day) …

Insights Into The Molecular Roles Of Heparan Sulfate Proteoglycans (Hspgs-Syndecans) In Autocrine And Paracrine Growth Factor Signaling In The Pathogenesis Of Hodgkin's Lymphoma, Rajendra Ghardbaran

Publications and Research

Syndecans (SDC, SYND) comprise a group of four structurally related type 1 transmembrane heparan sulfate proteoglycans (HSPGs) that play important roles in tumorigenic processes. SDCs exert signaling via their protein cores and their conserved transmembrane and cytoplasmic domains or by forming complexes with growth factors (GFs). In classical Hodgkin's lymphoma (cHL), a lymphoid neoplasm of predominantly B cell origin, SDC1 and SDC4 are the active SDCs, and a number of GF (vascular endothelial growth factor, fibroblast growth factor, etc.) signaling pathways have been studied. However, despite extensive pre-clinical and clinical research on SDC-mediated GF signaling in many cancer types, there …

Ectopic Expression Of A Cyanobacterial Flavodoxin In Creeping Bentgrass Impacts Plant Development And Confers Broad Abiotic Stress Tolerance, Zhigang Li, Shuangrong Yuan, Haiyan Jia, Fangyuan Gao, Qian Hu, Dongfa Sun, Hong Luo

Publications

Flavodoxin (Fld) plays a pivotal role in photosynthetic microorganisms as an alternative electron carrier flavoprotein under adverse environmental conditions. Cyanobacterial Fld has been demonstrated to be able to substitute ferredoxin (Fd) of higher plants in most electron transfer processes under stressful conditions. We have explored the potential of Fld for use in improving plant stress response in creeping bentgrass (Agrostis stolonifera L.). Overexpression of Fld altered plant growth and development. Most significantly, transgenic (TG) plants exhibited drastically enhanced performance under oxidative, drought and heat stress as well as nitrogen (N) starvation, which was associated with higher water retention and …

Optimizing Gdna Purification And Qpcr Techniques For Specific Detection And Enumeration Of Probiotic Bacteria, Katelynn C. Lee, Jennifer Vanderkelen, Christopher Kitts

STAR Program Research Presentations

Probiotics are live microorganisms, like bacteria and yeast, which are thought to provide health benefits when ingested. Large manufacturers produce blends of probiotics for supplementing the diets of agriculturally important animals. Commercial probiotic products are labeled with the number of cells present at the time of manufacture. Our assignment was to develop an assay which can be used to quantify the number of specific lactic acid bacteria present in certain probiotic products, thus verifying the number reported on the product labels. This quantification process involves isolating genomic DNA (gDNA) from the given samples and then running the DNA through a …

Genotypic Diversity Effects On Biomass Production In Native Perennial Bioenergy Cropping Systems, Geoffrey P. Morris, Zhenbin Hu, Paul P. Grabowski, Justin O. Borevitz, Marie-Anne De Graaff, R. Michael Miller, Julie D. Jastrow

Biology Faculty Publications and Presentations

The perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) on perennial biomass cropping systems in two experiments conducted over 2008–2014 at a 5.4-ha fertile field site in northeastern Illinois, USA. We varied levels of switchgrass and big bluestem genotypic diversity using various local and nonlocal cultivars – under low or high species diversity, with or without nitrogen inputs – and …

A Phylum-Level Phylogenetic Classification Of Zygomycete Fungi Based On Genome-Scale Data, Merlin M. White

Biology Faculty Publications and Presentations

Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support themonophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, …

Nebline, September 2016

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: 4-H Youth Showcase Projects, Develop Skills at the Super Fair

Food & Health

Farm & Acreage

Pests & Wildlife

Horticulture

Early Childhood

4-H & Youth

Extension Calendar

and other extension news and events

Short-Interval Cortical Inhibition And Intracortical Facilitation During Submaximal Voluntary Contractions Changes With Fatigue, Sandra K. Hunter, Chris J. Mcneil, Jane E. Butler, Simon C. Gandevia, Janet L. Taylor

Exercise Science Faculty Research and Publications

This study determined whether short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) change during a sustained submaximal isometric contraction. On 2 days, 12 participants (6 men, 6 women) performed brief (7-s) elbow flexor contractions before and after a 10-min fatiguing contraction; all contractions were performed at the level of integrated electromyographic activity (EMG) which produced 25 % maximal unfatigued torque. During the brief 7-s and 10-min submaximal contractions, single (test) and paired (conditioning–test) transcranial magnetic stimuli were applied over the motor cortex (5 s apart) to elicit motor-evoked potentials (MEPs) in biceps brachii. SICI and ICF were elicited on separate …

Establishing Birdsfoot Trefoil In The Mountain West, Joe E. Brummer, Jennifer W. Macadam, Glenn Shewmaker, M. Anowarul Isllam

All Current Publications

This bulletin describes birdsfoot trefoil in the Mountain West, and why it should be considered for planting. It includes cultivar selection and seeding rate, establishment considerations, and interseeding methods. Its high nutritive value and ruminant-friendly tannins will support livestock production without risk of bloat, while it fixes nitrogen to increase production in the entire pasture.

Voles [Microtus Spp.], Ryan Davis

All Current Publications

This fact sheet focuses on the meadow vole and includes a description, how to identify voles, their biology, activity and damage, and how to manage them.

Sequoia Pitch Moth In Pines, Ryan S. Davis, Katie Wagner

All Current Publications

This fact sheet focuses on the sequoia pitch moth (SPM) (Sesiidae: Synanthedon sequoiae). It includes how to identify, life cycle, damage, and management.

Summaries Of Arkansas Cotton Research 2015, Derrick M. Oosterhuis

Arkansas Agricultural Experiment Station Research Series

No abstract provided.

Hydrodynamic Performance Of Aquatic Flapping: Efficiency Of Underwater Flight In The Manta, Frank E. Fish, Christian M. Schreiber, Keith W. Moored, Geng Liu, Haibo Dong, Hilary Bart-Smith

Biology Faculty Publications

The manta is the largest marine organism to swim by dorsoventral oscillation (flapping) of the pectoral fins. The manta has been considered to swim with a high efficiency stroke, but this assertion has not been previously examined. The oscillatory swimming strokes of the manta were examined by detailing the kinematics of the pectoral fin movements swimming over a range of speeds and by analyzing simulations based on computational fluid dynamic potential flow and viscous models. These analyses showed that the fin movements are asymmetrical up- and downstrokes with both spanwise and chordwise waves interposed into the flapping motions. These motions …