Digital Commons Network^™

Lea Proteins During Water Stress: Not Just For Plants Anymore, Steven C. Hand, Michael A. Menze, Mehmet Toner, Leaf Boswell, Daniel Moore

Faculty Publications

Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins that were first identified in land plants. Intracellular accumulation is tightly correlated with acquisition of desiccation tolerance, and data support their capacity to stabilize other proteins and membranes during drying, especially in the presence of sugars like trehalose. Exciting reports now show that LEA proteins are not restricted to plants; multiple forms are expressed in desiccation-tolerant animals from at least four phyla. We evaluate here the expression, subcellular localization, biochemical properties, and potential functions of LEA proteins in animal species during water stress. LEA proteins are intrinsically unstructured in aqueous solution, …

Detecting Toxic Diatom Blooms From Ocean Color And A Regional Ocean Model, Clarissa R. Anderson, Raphael M. Kudela, Claudia R. Benitez-Nelson, Emily Sekula-Wood, Christopher T. Burrell, Yi Chao, Gregg Langlois, Jo Goodman, David A. Siegel

Faculty Publications

[1] An apparent link between upwelling‐related physical signatures, macronutrients, and toxic diatom blooms in the various “hotspots” throughout California has motivated attempts to forecast harmful algal blooms (HABs) as a function of select environmental variables. Empirical models for predicting toxic Pseudo‐nitzschia blooms in one such region, the Santa Barbara Channel (SBC), are tested in a nowcast mode using predictions based on merging data from MODIS ocean color geophysical products and the Regional Ocean Modeling System (ROMS) applied to the Southern California Bight. Thresholds for each model generate event forecasts. Spatially‐explicit, monthly HAB maps are compared to shipboard observations and California …

Improving Tree-Thinking One Learnable Skill At A Time, Kristy Lynn Halverson

Faculty Publications

Representations are a critical way to communicate scientific knowledge. Systematists biologists are acknowledged as expert tree thinkers who can both read and build phylogenetic trees (e.g., cladograms) accurately. The purpose of this study was to identify the core skills essential to help college students overcome tree-thinking challenges. In this study, I used pre/posttests, interviews, weekly reflective journal entries, field notes from course observations, and student responses to coursework to learn how upper-level college biology students developed representational competence with phylogenetic trees. I identified essential core skills by investigating students' tree-thinking progression over the course of the semester. Three major patterns …

A New Emoia Samoensis Group Lizard (Squamata: Scincidae) From The Cook Islands, South-Central Pacific, George R. Zug, Alison M. Hamilton, Christopher C. Austin

Faculty Publications

The first published report of a large treeskink from Rarotonga, Cook Islands, appeared in 1988. The first museum voucher specimen was collected in 1984. Although this skink seems likely to be a recent arrival to the island of Rarotonga, it represents a unique member of the Emoia samoensis species group. We compare this population with other members of the E. samoensis group and describe the population as Emoia tuitarere n. sp., distinguished by a suite of external characters including SVL, number of dorsal scale rows, and number of subdigital lamellae of the fourth toe. We provide preliminary definitions for the …

Analysis Of Common And Specific Mechanisms Of Liver Function Affected By Nitrotoluene Compounds, Youping Deng, Sharon A. Meyer, Xin Guan, Barbara Lynn Escalon, Junmei Ai, Mitchell S. Wilbanks, Ruth Welti, Natàlia Garcia-Reyero, Edward J. Perkins

Faculty Publications

Background: Nitrotoluenes are widely used chemical manufacturing and munitions applications. This group of chemicals has been shown to cause a range of effects from anemia and hypercholesterolemia to testicular atrophy. We have examined the molecular and functional effects of five different, but structurally related, nitrotoluenes on using an integrative systems biology approach to gain insight into common and disparate mechanisms underlying effects caused by these chemicals.

Methodology/Principal Findings: Sprague-Dawley female rats were exposed via gavage to one of five concentrations of one of five nitrotoluenes [2,4,6-trinitrotoluene (TNT), 2-amino-4,6-dinitrotoluene (2ADNT) 4-amino-2,6-dinitrotoulene (4ADNT), 2,4-dinitrotoluene (2,4DNT) and 2,6-dinitrotoluene (2,6DNT)] with necropsy …

Isolation Of A Rickettsial Pathogen From A Non-Hematophagous Arthropod, Chutima Thepparit, Piyanate Sunyakumthorn, Mark L. Guillotte, Vsevolod L. Popov, Lane D. Foil, Kevin R. Macaluso

Faculty Publications

Rickettsial diversity is intriguing in that some species are transmissible to vertebrates, while others appear exclusive to invertebrate hosts. Of particular interest is Rickettsia felis, identifiable in both stored product insect pests and hematophagous disease vectors. To understand rickettsial survival tactics in, and probable movement between, both insect systems will explicate the determinants of rickettsial pathogenicity. Towards this objective, a population of Liposcelis bostrychophila, common booklice, was successfully used for rickettsial isolation in ISE6 (tick-derived cells). Rickettsiae were also observed in L. bostrychophila by electron microscopy and in paraffin sections of booklice by immunofluorescence assay using anti-R. felis polyclonal antibody. …

Mapping Copy Number Variation By Population-Scale Genome Sequencing, Ryan E. Mills, Klaudia Walter, Chip Stewart, Robert E. Handsaker, Ken Chen, Can Alkan, Alexej Abyzov, Seungtai Chris Yoon, Kai Ye, R. Keira Cheetham, Asif Chinwalla, Donald F. Conrad, Yutao Fu, Fabian Grubert, Iman Hajirasouliha, Fereydoun Hormozdiari, Lilia M. Iakoucheva, Zamin Iqbal, Shuli Kang, Jeffrey M. Kidd, Miriam K. Konkel, Joshua Korn, Ekta Khurana, Deniz Kural, Hugo Y.K. Lam, Jing Leng, Ruiqiang Li, Yingrui Li, Chang Yun Lin, Ruibang Luo, Xinmeng Jasmine Mu, James Nemesh, Heather E. Peckham, Tobias Rausch

Faculty Publications

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined …

Effects Of Androgen Receptor And Androgen On Gene Expression In Prostate Stromal Fibroblasts And Paracrine Signaling To Prostate Cancer Cells, Matthew J. Tanner, R. Charles Welliver, Mengqian Chen, Michael Shtutman, Alejandro Godoy, Gary Smith, Badar M. Mian, Ralph Buttyan

Faculty Publications

The androgen receptor (AR) is expressed in a subset of prostate stromal cells and functional stromal cell AR is required for normal prostate developmental and influences the growth of prostate tumors. Although we are broadly aware of the specifics of the genomic actions of AR in prostate cancer cells, relatively little is known regarding the gene targets of functional AR in prostate stromal cells. Here, we describe a novel human prostate stromal cell model that enabled us to study the effects of AR on gene expression in these cells. The model involves a genetically manipulated variant of immortalized human WPMY-1 …

Metals Affect The Structure And Activity Of Human Plasminogen Activator Inhibitor-1. I. Modulation Of Stability And Protease Inhibition, Lawrence C. Thompson, Sumit Goswami, David S. Ginsberg, Duane E. Day, Ingrid M. Verhamme, Cynthia B. Peterson

Faculty Publications

Human plasminogen activator inhibitor type 1 (PAI-1) is a serine protease inhibitor with a metastable active conformation. Under physiological conditions, half of the inhibitor transitions to a latent state within 1-2 h. The interaction between PAI-1 and the plasma protein vitronectin prolongs this active lifespan by ∼50%. Previously, our group demonstrated that PAI-1 binds to resins using immobilized metal affinity chromatography (Day, U.S. Pat. 7,015,021 B2, March 21, 2006). In this study, the effect of these metals on function and stability was investigated by measuring the rate of the transition from the active to latent conformation. All metals tested showed …

Metals Affect The Structure And Activity Of Human Plasminogen Activator Inhibitor-1. Ii. Binding Affinity And Conformational Changes, Lawrence C. Thompson, Sumit Goswami, Cynthia B. Peterson

Faculty Publications

Human plasminogen activator inhibitor type 1 (PAI-1) is a serine protease inhibitor with a metastable active conformation. The lifespan of the active form of PAI-1 is modulated via interaction with the plasma protein, vitronectin, and various metal ions. These metal ions fall into two categories: Type I metals, including calcium, magnesium, and manganese, stabilize PAI-1 in the absence of vitronectin, whereas Type II metals, including cobalt, copper, and nickel, destabilize PAI-1 in the absence of vitronectin, but stabilize PAI-1 in its presence. To provide a mechanistic basis for understanding the unusual modulation of PAI-1 structure and activity, the binding characteristics …

The Nlrp3 Inflammasome Instigates Obesity-Induced Inflammation And Insulin Resistance, Bolormaa Vandanmagsar, Yun Hee Youm, Anthony Ravussin, Jose E. Galgani, Krisztian Stadler, Randall L. Mynatt, Eric Ravussin, Jacqueline M. Stephens, Vishwa Deep Dixit

Faculty Publications

The emergence of chronic inflammation during obesity in the absence of overt infection or well-defined autoimmune processes is a puzzling phenomenon. The Nod-like receptor (NLR) family of innate immune cell sensors, such as the nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3 (Nlrp3, but also known as Nalp3 or cryopyrin) inflammasome are implicated in recognizing certain nonmicrobial originated 'danger signals' leading to caspase-1 activation and subsequent interleukin-1β 2 (IL-1β 2) and IL-18 secretion. We show that calorie restriction and exercise-mediated weight loss in obese individuals with type 2 diabetes is associated with a reduction in adipose tissue expression of Nlrp3 as well …

Neighborhood Stressors And Race/Ethnic Differences In Hypertension Prevalence (The Multi-Ethnic Study Of Atherosclerosis), Mahasin S. Mujahid, Ana V. Diez Roux, Richard C. Cooper, Steven Shea, David R. Williams

Faculty Publications

BackgroundThe reasons for racial/ethnic disparities in hypertension (HTN) prevalence in the United States are poorly understood.MethodsUsing data from the Multi-Ethnic Study of Atherosclerosis (MESA), we investigated whether individual- and neighborhood-level chronic stressors contribute to these disparities in cross-sectional analyses. The sample consisted of 2,679 MESA participants (45-84 years) residing in Baltimore, New York, and North Carolina. HTN was defined as systolic or diastolic blood pressure 140 or 90mmHg, or taking antihypertensive medications. Individual-level chronic stress was measured by self-reported chronic burden and perceived major and everyday discrimination. A measure of neighborhood (census tract) chronic stressors (i.e., physical disorder, violence) was …

High-Throughput Cryopreservation Of Spermatozoa Of Blue Catfish (Ictalurus Furcatus): Establishment Of An Approach For Commercial-Scale Processing, E. Hu, Huiping Yang, Terrence R. Tiersch

Faculty Publications

Hybrid catfish created by crossing of female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) are being used increasingly in foodfish aquaculture because of their fast growth and efficient food conversion. However, the availability of blue catfish males is limited, and their peak spawning is at a different time than that of the channel catfish. As such, cryopreservation of sperm of blue catfish could improve production of hybrid catfish, and has been studied in the laboratory and tested for feasibility in a commercial dairy bull cryopreservation facility. However, an approach for commercially relevant production of cryopreserved blue catfish …

Education And Levels Of Salivary Cortisol Over The Day In Us Adults, Jennifer B. Dowd, Nalini Ranjit, D. Phuong Do, Elizabeth A. Young, James S. House, George A. Kaplan

Faculty Publications

Background - Dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis is hypothesized to be an important pathway linking socioeconomic position and chronic disease.

Purpose - This paper tests the association between education and the diurnal rhythm of salivary control.

Methods - Up to 8 measures of cortisol (mean of 5.38 per respondent) over two days were obtained from 311 respondents aged 18-70, drawn from 2001-2002 Chicago Community Adult Health Study. Multi-level models with linear splines were used to estimate waking level, rates of cortisol decline, and area-under-the-curve over the day, by categories of education.

Results - Lower education (0-11 years) was associated …

Comparative And Demographic Analysis Of Orang-Utan Genomes, Devin P. Locke, Ladeana W. Hillier, Wesley C. Warren, Kim C. Worley, Lynne V. Nazareth, Donna M. Muzny, Shiaw Pyng Yang, Zhengyuan Wang, Asif T. Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D. Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A. Fulton, Robert S. Fulton, Joanne O. Nelson, Vincent Magrini, Craig Pohl, Tina A. Graves, Chris Markovic, Andy Cree, Huyen H. Dinh, Jennifer Hume, Christie L. Kovar, Gerald R. Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P. Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen

Faculty Publications

Orang-utan- is derived from a Malay term meaning man of the forest- and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly …

The Crime Of Aggression And Humanitarian Intervention On Behalf Of Women, Beth Van Schaack

Faculty Publications

This article is part of a larger project to analyze the rarely-considered gender aspects of the crime of aggression and to explore whether or not the amendments adding the crime of aggression to the Statute of the International Criminal Court (ICC) represent an advancement for women. This piece focuses on the potential for the new provisions to chill bona fide exercises of humanitarian intervention given that (1) the crime is expansively drafted to potentially cover all uses of sovereign force, (2) delegates rejected efforts by the United States to include an express exception for military operations launched to prevent the …

Spatiotemporal Analyses Of Soil Moisture From Point To Footprint Scale In Two Different Hydroclimatic Regions, Champa Joshi, Binayak P. Mohanty, Jennifer M. Jacobs, Amor V. M. Ines

Faculty Publications

This paper presents time stability analyses of soil moisture at different spatial measurement support scales (point scale and airborne remote sensing (RS) footprint scale 800 m × 800 m) in two different hydroclimatic regions. The data used in the analyses consist of in situ and passive microwave remotely sensed soil moisture data from the Southern Great Plains Hydrology Experiments 1997 and 1999 (SGP97 and SGP99) conducted in the Little Washita (LW) watershed, Oklahoma, and the Soil Moisture Experiments 2002 and 2005 (SMEX02 and SMEX05) in the Walnut Creek (WC) watershed, Iowa. Results show that in both the regions soil properties …

Tests Of Integrin Transmembrane Domain Homo-Oligomerization During Integrin Ligand Binding And Signaling, Wei Wang, Jieqing Zhu, Timothy A. Springer, Bing Hao Luo

Faculty Publications

Integrin transmembrane (TM) and/or cytoplasmic domains play a critical role in integrin bidirectional signaling. Although it has been shown that TM and/or cytoplasmic α and β domains associate in the resting state and separation of these domains is required for both inside-out and outside-in signaling, the role of TM homomeric association remains elusive. Formation of TM homo-oligomers was observed in micelles and bacterial membranes previously, and it has been proposed that homomeric association is important for integrin activation and clustering. This study addresses whether integrin TM domains form homo-oligomers in mammalian cell membranes using cysteine scanning mutagenesis. Our results show …

Dma1 Ubiquitinates The Sin Scaffold, Sid4, To Impede The Mitotic Localization Of Plo1 Kinase, Alyssa E. Johnson, Kathleen L. Gould

Faculty Publications

Proper cell division requires strict coordination between mitotic exit and cytokinesis. In the event of a mitotic error, cytokinesis must be inhibited to ensure equal partitioning of genetic material. In the fission yeast, Schizosaccharomyces pombe, the checkpoint protein and E3 ubiquitin ligase, Dma1, delays cytokinesis by inhibiting the septation initiation network (SIN) when chromosomes are not attached to the mitotic spindle. To elucidate the mechanism by which Dma1 inhibits the SIN, we screened all SIN components as potential Dma1 substrates and found that the SIN scaffold protein, Sid4, is ubiquitinated in vivo in a Dma1-dependent manner. To investigate the role …

Loose Ligands And Available Iron In The Ocean, Ronald Benner

Faculty Publications

No abstract provided.

The Structure Of Human 5-Lipoxygenase, Nathaniel C. Gilbert, Sue G. Bartlett, Maria T. Waight, David B. Neau, William E. Boeglin, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

The synthesis of both proinflammatory leukotrienes and anti-inflammatory lipoxins requires the enzyme 5-lipoxygenase (5-LOX). 5-LOX activity is short-lived, apparently in part because of an intrinsic instability of the enzyme. We identified a 5-LOX-specific destabilizing sequence that is involved in orienting the carboxyl terminus, which binds the catalytic iron. Here, we report the crystal structure at 2.4 angstrom resolution of human 5-LOX stabilized by replacement of this sequence.

Changing The Culture Of Science Education At Research Universities, W. A. Anderson, U. Banerjee, C. L. Drennan, S. C.R. Elgin, I. R. Epstein, J. Handelsman, G. F. Hatfull, R. Losick, D. K. O'Dowd, B. M. Olivera, S. A. Strobel, G. C. Walker, I. M. Warner

Faculty Publications

No abstract provided.

Child Work And Labour Among Orphaned And Abandoned Children In Five Low And Middle Income Countries, Rachel Whetten, Lynne Messer, Jan Ostermann, Kathryn Whetten, Brian Wells Pence, Megan Buckner, Nathan Thielman, Karen O’Donnell, The Positive Outcomes For Orphans (Pofo) Research Team

Faculty Publications

Background

The care and protection of the estimated 143,000,000 orphaned and abandoned children (OAC) worldwide is of great importance to global policy makers and child service providers in low and middle income countries (LMICs), yet little is known about rates of child labour among OAC, what child and caregiver characteristics predict child engagement in work and labour, or when such work infers with schooling. This study examines rates and correlates of child labour among OAC and associations of child labour with schooling in a cohort of OAC in 5 LMICs.

Methods

The Positive Outcomes for Orphans (POFO) study employed a …

The Making Of Differences: Theological Discourse On The Unity Of The Church, Guillermo C. Hansen

Faculty Publications

No abstract provided.

Measurement Of Particle Size Distribution In A Swine Building, Sheryll B. Jerez, Yuanhui Zhang, X Wang

Faculty Publications

The majority of the research in animal buildings has been on measured concentrations of contaminants that the workers and animals are exposed to; emission measurements have only gained attention in recent years due to potential federal regulations on air quality emissions from animal feeding operations (AFOs). The contribution of AFOs to ambient PM10 and PM2.5 entails reliable measurement of particle size distribution. The objective of this study was to measure and compare the size distribution of particulate matter (PM) at multiple locations inside and at the exhausts of a wean‐to‐finish commercial swine building. The particle size distribution was measured by …

Spatial And Temporal Distributions Of Dust And Ammonia Concentrations In A Swine Building, Sheryll B. Jerez, Yuanhui Zhang, X Wang

Faculty Publications

Pollutants, especially dust, are rarely uniformly distributed within ventilated air spaces due to non‐uniform flow fields, particle inertia, gravitational settling, and diffusion. Thus, selecting suitable sampling locations for representative sampling is a challenge. The objective of this study was to determine the spatial and temporal distributions of dust and ammonia concentrations(NH3) in a swine building. Results of this study are useful in the design of sampling strategies that require limited sampling locations and in studying pollutant transport. This study was conducted in a commercial swine building in Illinois. The total suspended particulate (TSP) matter and ammonia concentrations were measured at …

Spread Of Plague Among Black-Tailed Prairie Dogs Is Associated With Colony Spatial Characteristics, Christopher Frey, Tammi L. Johnson, Jack Cully Jr., Sharon K. Collinge, Chris Ray, Brett Sandercock

Faculty Publications

Sylvatic plague (Yersinia pestis) is an exotic pathogen that is highly virulent in black-tailed prairie dogs (Cynomys ludovicianus) and causes widespread colony losses and individual mortality rates >95%. We investigated colony spatial characteristics that may influence inter-colony transmission of plague at 3 prairie dog colony complexes in the Great Plains. The 4 spatial characteristics we considered include: colony size, Euclidean distance to nearest neighboring colony, colony proximity index, and distance to nearest drainage (dispersal) corridor. We used multi-state mark–recapture models to determine the relationship between these colony characteristics and probability of plague transmission among prairie dog colonies. Annual mapping of …

Involving The Public In Restoring The Role Of Fire In The Longleaf Pine Ecosystem Of Upland Island Wilderness, Brian P. Oswald, Ike Mcwhorter, Penny Whisenant

Faculty Publications

The 13,250-acre Upland Island Wilderness (UIW) in Texas was established in 1984 and is managed by the United States Forest Service (USFS). Historically, portions of it consisted of open and diverse longleaf pine (Pinus palustris) ecosystems which depend on frequent, low-intensity surface fires. As in many other relatively small wilderness areas, the vegetation and fuel conditions in the UIW underwent extensive changes after wilderness designation. Lightning-caused wildfires were no longer allowed to burn with the frequency or intensity that characterized the natural fire regime. This has resulted in an increase of shade-tolerant trees and shrubs, heavy accumulations of …

Anthocyanins, Phenolics, And Antioxidant Capacity Of Vaccinium L. In Texas, Usa, Wei Yuan, Lijing Zhou, Guangrui Deng, Ping Wang, David Creech, Shiyou Li

Faculty Publications

Berries of Vaccinium spp. have long been an important source of food and pharmaceutical ingredients and are considered to have high antioxidant potential. Growing blueberries in Texas, United States is a substantial industry, but there is no report on their antioxidant capacity, total phenolics, and anthocyanins. This study evaluates antioxidant capacity and contents of total phenolics and anthocayanins in both fruits and leaves of 19 genotypes including five commercial cultivars and 11 selections of rabbiteye blueberry (V. ashei) and southern highbush (V. corymbosum hybrids), and three native species (V. darrowii, V. arboreum, and V. fuscatum) grown in Nacogdoches, Texas. Significant …

Preparation And Characterization Of A Standardized Anticonvulsant Ginseng Rb Extract From Panax Quinquefolius L., Xiao-Yuan Lian, Zhizhen Zhang

Faculty Publications

A ginseng Rb extract (GRbE) containing three major ingredients of ginsenoside Rb1 (G-Rb1), ginsenoside Rb3 (G-Rb3) and ginsenoside Rd (G-Rd) has been shown to have anticonvulsant and neuroprotective activity. As such, sufficient characterization and standardization of this active GRbE are demanded to facilitate an ongoing preclinical investigation on its potential for the treatment of epilepsy. In the investigation, the methods for generating the active GRbE and isolating G-Rb1, G-Rb3, and G-Rd in large scale from Panax quinquefolius are described. The chemical profile of GRbE was characterized by identifying the structure of the individual ingredients using NMR, and the concentration of …