Digital Commons Network^™

Fast Magic-Angle-Spinning 19F Spin Exchange Nmr For Determining Nanometer 19F-19F Distances In Proteins And Pharmaceutical Compounds, Matthias Roos, Tuo Wang, Alexander A. Shcherbakov, Mei Hong

Faculty Publications

© 2018 American Chemical Society. Internuclear distances measured using NMR provide crucial constraints of three-dimensional structures but are often restricted to about 5 Å due to the weakness of nuclear-spin dipolar couplings. For studying macromolecular assemblies in biology and materials science, distance constraints beyond 1 nm will be extremely valuable. Here we present an extensive and quantitative analysis of the feasibility of 19F spin exchange NMR for precise and robust measurements of interatomic distances up to 1.6 nm at a magnetic field of 14.1 T, under 20-40 kHz magic-angle spinning (MAS). The measured distances are comparable to those achievable from …

Trauma-Focused Interventions: A Clinical Practice Analysis, Jose Carbajal

Faculty Publications

This paper presents a systematic review of trauma-treatment interventions, which have different theoretical perspectives on trauma etiology and its application. The empirical findings of these trauma treatment therapies are presented. The extant literature identifies five therapies as the most-effective treatment modalities for PTSD: cognitive therapy (CT), cognitive-behavioral therapy (CBT), cognitive processing therapy (CPT), prolonged exposure (PE) therapy, and eye movement desensitization and reprocessing (EMDR) therapy. They are all validated with some nuances on treatment approach and effectiveness. However, to use these five interventions, practitioners need to consider and apply the research findings that indicate which intervention is best for which …

Solution Self-Assemblies Of Sequence-Defined Ionic Peptoid Block Copolymers, Garrett L. Sternhagen, Sudipta Gupta, Yueheng Zhang, Vijay John, Gerald J. Schneider, Donghui Zhang

Faculty Publications

© 2018 American Chemical Society. A series of amphiphilic ionic peptoid block copolymers where the total number (1 or 3) and position of ionic monomers along the polymer chain are precisely controlled have been synthesized by the submonomer method. Upon dissolution in water at pH = 9, the amphiphilic peptoids self-assemble into small spherical micelles having hydrodynamic radius in ∼5-10 nm range and critical micellar concentration (CMC) in the 0.034-0.094 mg/mL range. Small-angle neutron scattering (SANS) analysis of the micellar solutions revealed unprecedented dependence of the micellar structure on the number and position of ionic monomers along the chain. It …

Long-Term Irrigation Affects The Dynamics And Activity Of The Wheat Rhizosphere Microbiome, Dmitri V. Mavrodi, Olga Mavrodi, Liam D.H. Elbourne, Sasha Tetu, Robert F. Bonsall, James Parejko, Mingming Yang, Ian T. Paulsen, David M. Weller, Linda S. Thomashow

Faculty Publications

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat …

Dietary Inflammatory Index And Type 2 Diabetes Mellitus In Adults: The Diabetes Mellitus Survey Of Mexico City, Edgar Denova-Gutiérrez, Paloma Muñoz-Aguirre, Nitin Shivappa, James R. Hébert, Lizbeth Tolentino-Mayo, Carolina Batis, Simón Barquera

Faculty Publications

Diet and inflammation are both associated with type 2 diabetes mellitus (T2DM). In the present study, we aimed to assess the relation between the dietary inflammatory index (DII) and the presence of T2DM in Mexican adults participating in the Diabetes Mellitus Survey administered in Mexico City (DMS-MC). The study involved 1174 subjects (48.5% men) between 20–69 years of age. A validated semi-quantitative food frequency questionnaire was employed to evaluate dietary intake and to compute DII. The DII is based on scientific evidence about the association between dietary compounds and six established inflammatory biomarkers. Multivariate logistic regression models were used to …

The Aspergillus Flavus Spermidine Synthase (Spds) Gene, Is Required For Normal Development, Aflatoxin Production, And Pathogenesis During Infection Of Maize Kernels., Rajtilak Majumdar, Matthew D. Lebar, Brian M. Mack, Rakesh Minocha, Subhash C. Minocha, Carol H. Carter-Wientjes, Christine M. Sickler, Kanniah Rajasekaran, Jeffrey W. Cary

Faculty Publications

Aspergillus flavus is a soil-borne saprophyte and an opportunistic pathogen of both humans and plants. This fungus not only causes disease in important food and feed crops such as maize, peanut, cottonseed, and tree nuts but also produces the toxic and carcinogenic secondary metabolites (SMs) known as aflatoxins. Polyamines (PAs) are ubiquitous polycations that influence normal growth, development, and stress responses in living organisms and have been shown to play a significant role in fungal pathogenesis. Biosynthesis of spermidine (Spd) is critical for cell growth as it is required for hypusination-mediated activation of eukaryotic translation initiation factor 5A (eIF5A), and …

Does Body Size Affect Fitness The Same Way In Males And Females? A Test Of Multiple Fitness Components, Ashlee N. Smith, Mark C. Belk

Faculty Publications

Body size generally has an important relationship with fitness, whereby larger body size leads to an increase in fitness through competition, reproductive output and survivorship. However, the traits through which body size increases fitness often differ between the sexes. We tested for the effects of body size on fitness in both sexes using three separate experiments on competitive ability, reproductive output and starvation resistance in the burying beetle Nicrophorus marginatus. Results varied between sexes as follows: (1) larger body size increased competitive ability differentially between sexes; (2) female body size, but not male body size, significantly affected reproductive output …

Analysis Of Lineage-Specific Alu Subfamilies In The Genome Of The Olive Baboon, Papio Anubis, Cody J. Steely, Jasmine N. Baker, Jerilyn A. Walker, Charles D. Loupe, Mark A. Batzer, Jeffrey Rogers, R. Alan Harris, Muthuswamy Raveendran, Yue Liu, Shwetha Murali, Tauras P. Vilgalys, Jerilyn A. Walker, Miriam K. Konkel, Vallmer E. Jordan

Faculty Publications

© 2018 The Author(s). Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome …

Descriptive Density Models Of Scyphozoan Jellyfish In The Northern Gulf Of Mexico, Katrina T. Aleksa, Redwood W. Nero, Jerry D. Wiggert, William M. Graham

Faculty Publications

Jellyfish play an important role in the food web of many coastal environments but are generally considered a nuisance to scientific fieldwork and industrial and economic trades. A better understanding of how jellyfish densities and distributions are affected by environmental parameters could elucidate population trends and provide assistance in ecological research and undesirable human interactions. In this study, abundance data for scyphozoan medusae, Chrysaora sp. and Aurelia spp., were extracted from Southeast Area Monitoring and Assessment Program trawling surveys for the northern Gulf of Mexico (nGoM) during the summer and fall months. Both in situ and satellite oceanographic measurements were …

Satellite Estimation Of Coastal Pco2 And Air-Sea Flux Of Carbon Dioxide In The Northern Gulf Of Mexico, S. E. Lohrenz, W. J. Cai, S. Chakraborty, W. J. Huang, X. Guo, R. He, Z. Xue, K. Fennel, S. Howden, H. Tian

Faculty Publications

Satellite approaches for estimation of the partial pressure of CO2 (pCO2) and air-sea flux of CO2 in coastal regions offer the potential to reduce uncertainties in coastal carbon budgets and improve understanding of spatial and temporal patterns and the factors influencing them. We used satellite-derived products in combination with an extensive data set of ship-based observations to develop an unprecedented multi-year time-series of pCO2 and air-sea flux of CO2 in the northern Gulf of Mexico for the period 2006–2010. A regression tree algorithm was used to relate satellite-derived products for chlorophyll, sea surface temperature, and dissolved and detrital organic matter …

Cdk1-Dependent Phosphoinhibition Of A Formin-F-Bar Interaction Opposes Cytokinetic Contractile Ring Formation, Alaina H. Willet, K. Adam Bohnert, Kathleen L. Gould

Faculty Publications

© 2018 Willet et al. In Schizosaccharomyces pombe, cytokinesis requires the assembly and constriction of an actomyosin-based contractile ring (CR). A single essential formin, Cdc12, localizes to the cell middle upon mitotic onset and nucleates the F-actin of the CR. Cdc12 medial recruitment is mediated in part by its direct binding to the F-BAR scaffold Cdc15. Given that Cdc12 is hyperphosphorylated in M phase, we explored whether Cdc12 phosphoregulation impacts its association with Cdc15 during mitosis. We found that Cdk1, a major mitotic kinase, phosphorylates Cdc12 on six N-terminal residues near the Cdc15-binding site, and phosphorylation on these sites inhibits …

Modeling Of First-Order Photobleaching Kinetics Using Krylov Subspace Spectral Methods, Somayyeh Sheikholeslami, James V. Lambers

Faculty Publications

We solve the first order 2-D reaction–diffusion equations which describe binding-diffusion kinetics using the photobleaching scanning profile of a confocal laser scanning microscope, approximated by a Gaussian laser profile. We show how to solve the first-order photobleaching kinetics partial differential equations (PDEs) using a time-stepping method known as a Krylov subspace spectral (KSS) method. KSS methods are explicit methods for solving time-dependent variable-coefficient partial differential equations. They approximate Fourier coefficients of the solution using Gaussian quadrature rules in the spectral domain. In this paper, we show how a KSS method can be used to obtain not only an approximate numerical …

Characterizing The Phylogenetic Specialism-Generalism Spectrum Of Mammal Parasites, A. W. Park, M. J. Farrell, J. P. Schmidt, S. Huang, T. A. Dallas, P. Pappalardo, J. M. Drake, P. R. Stephens, R. Poulin, C. L. Nunn, T. J. Davies

Faculty Publications

© 2018 The Author(s) Published by the Royal Society. All rights reserved. The distribution of parasites across mammalian hosts is complex and represents a differential ability or opportunity to infect different host species. Here, we take a macroecological approach to investigate factors influencing why some parasites show a tendency to infect species widely distributed in the host phylogeny (phylogenetic generalism) while others infect only closely related hosts. Using a database on over 1400 parasite species that have been documented to infect up to 69 terrestrialmammal host species,we characterize the phylogenetic generalism of parasites using standard effect sizes for three metrics: …

Public Knowledge Of Monarchs And Support For Butterfly Conservation, Jerrod Penn, Hannah Penn, Wuyang Hu

Faculty Publications

© 2018 by the authors. Pollinator populations in North America are in decline, including the iconic monarch butterfly. In order to determine if public knowledge of monarchs informs opinions on butterfly conservation, we surveyed the public to assess their knowledge of monarchs. We also asked participants about their attitudes towards general butterfly conservation and if they believe that butterfly gardens contribute to conservation. Respondents generally had some knowledge of monarchs but were unaware of monarch population declines and the necessity of milkweed to their life cycle. Respondent knowledge was correlated with more positive attitudes about butterfly conservation. Furthermore, membership in …

Limit-Feeding Dairy Heifers: More Efficient Feeding Can Lead To Reduced Costs, Peter S. Erickson

Faculty Publications

No abstract provided.

Biomarkers Of Rehabilitation Therapy Vary According To Stroke Severity, Erin Burke Quinlan, Lucy Dodakian, Jill See, Alison Mckenzie, Jill Campbell Stewart Pt,Phd, Steven C. Cramer

Faculty Publications

Biomarkers that capture treatment effects could improve the precision of clinical decision making for restorative therapies. We examined the performance of candidate structural, functional, and angiogenesis-related MRI biomarkers before and after a 3-week course of standardized robotic therapy in 18 patients with chronic stroke and hypothesized that results vary significantly according to stroke severity. Patients were 4.1 ± 1 months poststroke, with baseline arm Fugl-Meyer scores of 20–60. When all patients were examined together, no imaging measure changed over time in a manner that correlated with treatment-induced motor gains. However, when also considering the interaction with baseline motor status, treatment-induced …

Spatial Extinction Date Estimation: A Novel Method For Reconstructing Spatiotemporal Patterns Of Extinction And Identifying Potential Zones Of Rediscovery, Colin J. Carlson, Kevin R. Burgio, Tad Dallas, Alexander L. Bond

Faculty Publications

1. The estimation of extinction dates from limited and incomplete sighting records

is a key challenge in conservation (when experts are uncertain whether a species has

gone extinct) and historical ecology (when the date and mechanism of extinction is

controversial).

2. We introduce a spatially-explicit method of interpolating extinction date estima8 tors, allowing users to estimate spatiotemporal surfaces of population persistence 9 from georeferenced sighting data of variable quality.

3. We present the R package spatExtinct, which produces spatially-explicit extinction date surfaces from geolocated sightings, including options for custom randomization schemes to improve accuracy with limited datasets. We use simulations …

Comparative Assessment Of Strategies To Identify Similar Ligand-Binding Pockets In Proteins, Rajiv Gandhi Govindaraj, Michal Brylinski

Faculty Publications

© 2018 The Author(s). Background: Detecting similar ligand-binding sites in globally unrelated proteins has a wide range of applications in modern drug discovery, including drug repurposing, the prediction of side effects, and drug-target interactions. Although a number of techniques to compare binding pockets have been developed, this problem still poses significant challenges. Results: We evaluate the performance of three algorithms to calculate similarities between ligand-binding sites, APoc, SiteEngine, and G-LoSA. Our assessment considers not only the capabilities to identify similar pockets and to construct accurate local alignments, but also the dependence of these alignments on the sequence order. We point …

Comparison Of Workload For University Core Courses Taught In Regular Semester And Time-Compressed Term Formats, Lyndell Lutes, Randall Davies

Faculty Publications

This study compared student workload and perceived value of coursework assigned for a matching set of semester and term general education courses at Brigham Young University. Statistically significant differences in workloads were found between most semester and term courses. While term workloads were slightly lighter in general, both could be called “university lite,” in that students did not spend the expected two hours outside of class per hour in class. Math and physics courses came closest to meeting the expected workloads, which tended to remain constant between semesters and terms. Differences in the value students reported for homework varied significantly …

Environmentally Persistent Free Radicals: Insights On A New Class Of Pollutants, Eric P. Vejerano, Guiying Rao, Lavrent Khachatryan, Stephania A. Cormier, Slawo Lomnicki

Faculty Publications

© 2018 American Chemical Society. Environmentally persistent free radicals, EPFRs, exist in significant concentration in atmospheric particulate matter (PM). EPFRs are primarily emitted from combustion and thermal processing of organic materials, in which the organic combustion byproducts interact with transition metal-containing particles to form a free radical-particle pollutant. While the existence of persistent free radicals in combustion has been known for over half-a-century, only recently that their presence in environmental matrices and health effects have started significant research, but still in its infancy. Most of the experimental studies conducted to understand the origin and nature of EPFRs have focused primarily …

Jak/Stat3 Regulated Global Gene Expression Dynamics During Late-Stage Reprogramming Process, Ling Wang, Zongliang Jiang, Delun Huang, Jingyue Duan, Chang Huang, Shannon Sullivan, Kaneha Vali, Yexuan Yin, Ming Zhang, Jill Wegrzyn, Xiuchun Cindy Tian, Young Tang

Faculty Publications

© 2018 The Author(s). Background: The generation of induced pluripotent stem cells (iPSCs) has underdefined mechanisms. In addition, leukemia inhibitory factor (LIF) activated Janus kinase/signal transducer and activator of transcription 3 (JAK/STAT3) pathway is the master regulator for naïve-state pluripotency achievement and maintenance. However, the regulatory process to attain naïve pluripotent iPSCs is not well understood. Results: We performed transcriptome analysis to dissect the genomic expression during mouse iPSC induction, with or without blocking the JAK/STAT3 activity. We describe JAK/STAT3 signaling-specific biological events such as gametogenesis, meiotic/mitotic cell cycle, and DNA repair, and JAK/STAT3-dependent expression of key transcription factors such …

Demonstration Of Versatile Whispering-Gallery Micro-Lasers For Remote Refractive Index Sensing, Lei Wan, Hengky Chandrahalim, Jian Zhou

Faculty Publications

We developed chip-scale remote refractive index sensors based on Rhodamine 6G (R6G)-doped polymer micro-ring lasers. The chemical, temperature, and mechanical sturdiness of the fused-silica host guaranteed a flexible deployment of dye-doped polymers for refractive index sensing. The introduction of the dye as gain medium demonstrated the feasibility of remote sensing based on the free-space optics measurement setup. Compared to the R6G-doped TZ-001, the lasing behavior of R6G-doped SU-8 polymer micro-ring laser under an aqueous environment had a narrower spectrum linewidth, producing the minimum detectable refractive index change of 4 x 10⁻⁴ RIU. The maximum bulk refractive index sensitivity (BRIS) …

Flux And Seasonality Of Dissolved Organic Matter From The Northern Dvina (Severnaya Dvina) River, Russia, Sarah Ellen Johnston, Natalia Shorina, Ekaterina Bulygina, Taisya Vorobjeva, Anna Chupakova, Sergey I. Klimov, Anne M. Kellerman, Francois Guillemette, Alexander I. Shiklomanov, David C. Podgorski, Robert G. M. Spencer

Faculty Publications

Pan‐Arctic riverine dissolved organic carbon (DOC) fluxes represent a major transfer of carbon from land‐to‐ocean, and past scaling estimates have been predominantly derived from the six major Arctic rivers. However, smaller watersheds are constrained to northern high‐latitude regions and, particularly with respect to the Eurasian Arctic, have received little attention. In this study, we evaluated the concentration of DOC and composition of dissolved organic matter (DOM) via optical parameters, biomarkers (lignin phenols), and ultrahigh resolution mass spectrometry in the Northern Dvina River (a midsized high‐latitude constrained river). Elevated DOC, lignin concentrations, and aromatic DOM indicators were observed throughout the year …

Tuberculosis During Pregnancy In The United States: Racial/Ethnic Disparities In Pregnancy Complications And In-Hospital Death, Erika M. Dennis, Yun Hao, Mabella Tamambang, Tasha N. Roshan, Knubian J. Gatlin, Hanane Bghigh, Oladimeji T. Ogunyemi, Fatoumata Diallo, Kiara K. Spooner, Jason L. Salemi, Omonike A. Olaleye, Kashif Z. Khan, Muktar H. Aliyu, Hamisu M. Salihu

Faculty Publications

Background: Despite decades of efforts to eliminate tuberculosis (TB) in the United States (US), TB still contributes to adverse ill health, especially among racial/ethnic minorities. According to the Centers for Disease Control and Prevention, in 2016, about 87% of the TB cases reported in the US were among racial and ethnic minorities. The objective of this study is to explore the risks for pregnancy complications and in-hospital death among mothers diagnosed with TB across racial/ethnic groups in the US. Methods: This retrospective cohort study utilized National Inpatient Sample data for all inpatient hospital discharges in the US. We analyzed pregnancy-related …

Participatory And Collaborative Evaluation Strategies To Support Data-Informed Decisions And Management, Christine Marie Bishop, Isaac Karikari, Betty Walton, Stephanie Moynihan

Faculty Publications

Surveys were completed by local stakeholders who had been recruited from local communities and regions by the Indiana System of Care Planning Team. Periodic collection of System of Care Implementation Survey (SOCIS) information identified strengths and ongoing challenges.

Community Assembly Of The Ferns Of Florida, Emily B. Sessa, Sally M. Chambers, Daijiang Li, Lauren Trotta, Lorena Endara, J. Gordon Burleigh, Benjamin Baiser

Faculty Publications

© 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America. Premise of the Study: Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. Methods: We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional …

Transcriptomics Reveal Transgenerational Effects In Purple Sea Urchin Embryos: Adult Acclimation To Upwelling Conditions Alters The Response Of Their Progeny To Differential Pco2 Levels, Juliet M. Wong, Kevin M. Johnson, Morgan W. Kelly, Gretchen E Hofmann

Faculty Publications

© 2018 John Wiley & Sons Ltd Understanding the mechanisms with which organisms can respond to a rapidly changing ocean is an important research priority in marine sciences, especially in the light of recent predictions regarding the pace of ocean change in the coming decades. Transgenerational effects, in which the experience of the parental generation can shape the phenotype of their offspring, may serve as such a mechanism. In this study, adult purple sea urchins, Strongylocentrotus purpuratus, were conditioned to regionally and ecologically relevant pCO2 levels and temperatures representative of upwelling (colder temperature and high pCO2) and nonupwelling (average temperature …

Cd Obesity-Prone Rats, But Not Obesity-Resistant Rats, Robustly Ferment Resistant Starch Without Increased Weight Or Fat Accretion, Diana Obanda, Ryan Page, Justin Guice, Anne M. Raggio, Claudia Husseneder, Brian Marx, Rhett W. Stout, David A. Welsh, Christopher M. Taylor, Meng Luo, Eugene E. Blanchard, Zach Bendiks, Diana Coulon, Michael J. Keenan

Faculty Publications

© 2018 The Obesity Society Objective: This study used CD obesity-prone (OP) and obesity-resistant (OR) rats to examine how weight gain and fat accretion relate to fermentation levels and microbiota composition after feeding resistant starch (RS). Methods: After feeding OP rats and OR rats a high-fat (HF) diet for 4 weeks, rats were stratified into three groups: they were fed either an HF diet (group 1: HF-HF) or were switched to a low-fat (LF) diet (group 2: HF-LF) or an LF diet supplemented with 20% RS by weight for 4 weeks (group 3: HF-LFRS). Energy intake, body weight, fermentation variables, …

Cd Obesity-Prone Rats, But Not Obesity-Resistant Rats, Robustly Ferment Resistant Starch Without Increased Weight Or Fat Accretion, Diana Obanda, Ryan Page, Justin Guice, Anne M. Raggio, Claudia Husseneder, Brian Marx, Rhett W. Stout, David A. Welsh, Christopher M. Taylor, Meng Luo, Eugene E. Blanchard, Zach Bendiks, Diana Coulon, Michael J. Keenan

Faculty Publications

© 2018 The Obesity Society Objective: This study used CD obesity-prone (OP) and obesity-resistant (OR) rats to examine how weight gain and fat accretion relate to fermentation levels and microbiota composition after feeding resistant starch (RS). Methods: After feeding OP rats and OR rats a high-fat (HF) diet for 4 weeks, rats were stratified into three groups: they were fed either an HF diet (group 1: HF-HF) or were switched to a low-fat (LF) diet (group 2: HF-LF) or an LF diet supplemented with 20% RS by weight for 4 weeks (group 3: HF-LFRS). Energy intake, body weight, fermentation variables, …

First Impressions—The Potential Of Altering Initial Host-Virus Interactions For Rational Design Of Herpesvirus Vaccine Vectors, Paul J.F. Rider, Farhana Musarrat, Rafiq Nabi, Shan Naidu, Konstantin G. Kousoulas

Faculty Publications

© 2018, Springer International Publishing AG, part of Springer Nature. Purpose of Review: The earliest host-virus interactions occur during virus attachment and entry into cells. These initial steps in the virus lifecycle influence the outcome of infection beyond delivery of the viral genome into the cell. Herpesviruses alter host signaling pathways and processes during attachment and entry to facilitate virus infection and modulate innate immune responses. We suggest in this review that understanding these early events may inform the rational design of therapeutic and prevention strategies for herpesvirus infection, as well as the engineering of viral vectors for immunotherapy purposes. …