Digital Commons Network^™

Regional Impact Of Submarine Canyons During Seasonal Upwelling, Thomas Connolly, Barbara Hickey

Faculty Publications

A numerical model of the northern California Current System along the coasts of Washington and British Columbia is used to quantify the impact of submarine canyons on upwelling from the continental slope onto the shelf. Comparisons with an extensive set of observations show that the model adequately represents the seasonal development of near-bottom density, as well as along-shelf currents that are critical in governing shelf-slope exchange. Additional model runs with simplified coastlines and bathymetry are used to isolate the effects of submarine canyons. Near submarine canyons, equatorward flow over the outer shelf is correlated with dense water at canyon heads …

Statistics Based Modeling Of Wind Speed And Wind Direction In Real Time Optimal Guidance Strategies Via Ornstein-Uhlenbeck Stochastic Processes, Kamran Turkoglu

Faculty Publications

No abstract provided.

Can Crude Oil Toxicity On Phytoplankton Be Predicted Based On Toxicity Data On Benzo(A)Pyrene And Naphthalene?, Koray Ozhan, Sibel Bargu

Faculty Publications

Polycyclic aromatic hydrocarbons (PAHs), which are major components of crude oil, are responsible in large part for the toxicity of crude oil to phytoplankton. This study addressed the following question. Can reliable predictions of the aquatic toxicity of crude oil, a multi-component mixture, be described from toxicity data on individual PAH compounds? Naphthalene, the most abundant PAH compound, and benzo(a)pyrene, a highly toxic PAH compound, were selected as model compounds to quantify toxicity of crude oil on two phytoplankton species, Ditylum brightwellii and Heterocapsa triquetra, by analyzing the effects of different concentrations of these PAHs on growth rate. EC50 values …

Resistant Starch From High Amylose Maize (Ham-Rs2) And Dietary Butyrate Reduce Abdominal Fat By A Different Apparent Mechanism, Kirk Vidrine, Jianping Ye, Roy J. Martin, Kathleen L. Mccutcheon, Anne M. Raggio, Christine Pelkman, Holiday A. Durham, June Zhou, Reshani N. Senevirathne, Cathy Williams, Frank Greenway, John Finley, Zhanguo Gao, Felicia Goldsmith, Michael J. Keenan

Faculty Publications

Objective Obesity is a health concern. Resistant starch (RS) type 2 from high-amylose maize (HAM-RS2) and dietary sodium butyrate (SB) reduce abdominal fat in rodents. RS treatment is associated with increased gut hormones peptide YY (PYY) and glucagon-like peptide 1 (GLP-1), but it is not known if SB increases these hormones. Design and Methods This was investigated in a 2 × 2 rat study with HAM-RS2 (0 or 28% weight) and dietary sodium butyrate (0 and 3.2%) resulting in isocaloric treatments: energy control (EC), sodium butyrate (SB), HAM-RS2 (RS), and the combination (SBRS). Results RS and SB reduced abdominal fat …

Resistant Starch From High Amylose Maize (Ham-Rs2) And Dietary Butyrate Reduce Abdominal Fat By A Different Apparent Mechanism, Kirk Vidrine, Jianping Ye, Roy J. Martin, Kathleen L. Mccutcheon, Anne M. Raggio, Christine Pelkman, Holiday A. Durham, June Zhou, Reshani N. Senevirathne, Cathy Williams, Frank Greenway, John Finley, Zhanguo Gao, Felicia Goldsmith, Michael J. Keenan

Faculty Publications

Objective Obesity is a health concern. Resistant starch (RS) type 2 from high-amylose maize (HAM-RS2) and dietary sodium butyrate (SB) reduce abdominal fat in rodents. RS treatment is associated with increased gut hormones peptide YY (PYY) and glucagon-like peptide 1 (GLP-1), but it is not known if SB increases these hormones. Design and Methods This was investigated in a 2 × 2 rat study with HAM-RS2 (0 or 28% weight) and dietary sodium butyrate (0 and 3.2%) resulting in isocaloric treatments: energy control (EC), sodium butyrate (SB), HAM-RS2 (RS), and the combination (SBRS). Results RS and SB reduced abdominal fat …

Members Of The Conserved Deda Family Are Likely Membrane Transporters And Are Required For Drug Resistance In Escherichia Coli, Sujeet Kumar, William T. Doerrler

Faculty Publications

Bacterial resistance to antibiotics and biocides is an increasing public health problem. Genes encoding integral membrane proteins belonging to the DedA family are present in most bacterial genomes, including Escherichia coli. An E. coli strain lacking partially redundant DedA family genes yqjA and yghB (strain BC202) displays temperature sensitivity and cell division defects. These phenotypes can be corrected by overexpression of mdfA, anNa+-K+/H+ antiporter of the major facilitator superfamily. We show that BC202 is hypersensitive to several biocides and cationic compounds that are known substrates of several multidrug resistance transporters, including MdfA, EmrE, and AcrB. The introduction of deletions of …

Oncostatin M Is Produced In Adipose Tissue And Is Regulated In Conditions Of Obesity And Type 2 Diabetes, David Sanchez-Infantes, Ursula A. White, Carrie M. Elks, Ron F. Morrison, Jeffrey M. Gimble, Robert V. Considine, Anthony W. Ferrante, Eric Ravussin, Jacqueline M. Stephens

Faculty Publications

Context: Adipose tissue is a highly active endocrine organ that secretes many factors that affect other tissues and whole-body metabolism. Adipocytes are responsive to several glycoprotein 130 (gp130) cytokines, some of which have been targeted as potential antiobesity therapeutics. Objective: Oncostatin M (OSM) is a gp130 family member known to inhibit adipocyte differentiation in vitro, but its effects on other adipocyte properties are not characterized. The expression of OSM in white adipose tissue (WAT) has not been evaluated in the context of obesity. Thus, our objective was to examine the expression of adipose tissue OSM in obese animals and humans. …

Virulence And Biotype Analyses Of Hessian Fly (Diptera: Cecidomyiidae) Populations From Texas, Louisiana, And Oklahoma, Sandra Garcés-Carrera, Allen Knutson, Haiyan Wang, Kristopher L. Giles, Fangneng Huang, R. Jeffrey Whitworth, C. Michael Smith, Ming Shun Chen

Faculty Publications

Hessian fly, Mayetiola destructor (Say, 1817), is a major pest of wheat, and is controlled mainly through deploying fly-resistant wheat cultivars. The challenge for the plant resistance approach is that virulence of Hessian fly populations in the field is dynamic, and wheat cultivars may lose resistance within 6 - 8 yr. To ensure continuous success of host plant resistance, Hessian fly populations in the field need to be constantly monitored to determine which resistance genes remain effective in different geographic regions. This study investigated five Hessian fly populations collected from Texas, Louisiana, and Oklahoma, where infestation by Hessian fly has …

Effects Of Biological Control On Long-Term Population Dynamics: Identifying Unexpected Outcomes, James R. Reilly, Bret D. Elderd

Faculty Publications

Attempts to control natural systems through management have often met with success but have also led to unexpected and often undesirable outcomes. Unfortunately, the ultimate result of such management programmes may not be apparent until long after the control efforts have begun. This is particularly true for forest-defoliating species that exhibit long-period cycles such as the invasive gypsy moth Lymantria dispar, which causes widespread damage in some years but is rare in other years. We studied the effects of two commonly employed biocontrol agents on gypsy moth dynamics using a series of field-tested and empirically parameterized mathematical models, which allowed …

Quantitative Genetics Of Response To Novelty And Other Stimuli By Infant Rhesus Macaques (Macaca Mulatta) Across Three Behavioral Assessments, G. L. Fawcett, A. M. Dettmer, D. Kay, M. Raveendran, James Dee Higley, N. D. Ryan, J. L. Cameron, J. Rogers

Faculty Publications

Primate behavior is influenced by both heritable factors and environmental experience during development. Previous studies of rhesus macaques (Macaca mulatta) examined the effects of genetic variation on expressed behavior and related neurobiological traits (heritability and/or genetic association) using a variety of study designs. Most of these prior studies examined genetic effects on the behavior of adults or adolescent rhesus macaques, not in young macaques early in development. To assess environmental and additive genetic variation in behavioral reactivity and response to novelty among infants, we investigated a range of behavioral traits in a large number (N = 428) of pedigreed infants …

Fetal Baboon Sex-Specific Outcomes In Adipocyte Differentiation At 0.9 Gestation In Response To Moderate Maternal Nutrient Reduction, Y. D. Tchoukalova, R. Krishnapuram, U. A. White, D. Burk, X. Fang, M. J. Nijland, P. W. Nathanielsz

Faculty Publications

Objective:To investigate in vitro adipocyte differentiation in baboon fetuses in response to reduced maternal nutrition.Design:Cross-sectional comparison of adipocyte differentiation in normally grown fetuses and fetuses of pregnant baboons fed 70% of the control global diet from 30 days of pregnancy to term.Subjects:The subjects comprised control (CTR) fetuses (five female and five male) of mothers fed ad libitum and fetuses of mothers fed 70% of the global diet consumed by CTR (maternal nutrient reduction (MNR), five female and five male fetuses). The expression of genes/proteins involved in adipogenesis (PPARγ, FABP4 and adiponectin) and brown adipose tissue development (UCP1, TBX15 and COXIV) …

Contributions Of Adipose Tissue Architectural And Tensile Properties Toward Defining Healthy And Unhealthy Obesity, Denise E. Lackey, David H. Burk, Mohamed R. Ali, Rouzbeh Mostaedi, William H. Smith, Jiyoung Park, Philipp E. Scherer, Shundra A. Seay, Colin S. Mccoin, Paolo Bonaldo, Sean H. Adams

Faculty Publications

The extracellular matrix (ECM) plays an important role in the maintenance of white adipose tissue (WAT) architecture and function, and proper ECM remodeling is critical to support WAT malleability to accomodate changes in energy storage needs. Obesity and adipocyte hypertrophy place a strain on the ECM remodeling machinery, which may promote disordered ECM and altered tissue integrity and could promote proinflammatory and cell stress signals. To explore these questions, new methods were developed to quantify omental and subcutaneous WAT tensile strength and WAT collagen content by three-dimensional confocal imaging, using collagen VI knockout mice as a methods validation tool. These …

Modulation Of Leukocyte Infiltration And Phenotype In Microporous Tissue Engineering Scaffolds Via Vector Induced Il-10 Expression, R. Michael Gower, Ryan M. Boehler, Samira M. Azarin, Christine F. Ricci, Joshua N. Leonard, Lonnie D. Shea

Faculty Publications

Biomaterial scaffolds are central to many tissue engineering strategies as they create a space for tissue growth and provide a support for cell adhesion and migration. However, biomaterial implantation results in unavoidable injury resulting in an inflammatory response, which can impair integration with the host and tissue regeneration. Toward the goal of reducing inflammation, we investigated the hypothesis that a lentiviral gene therapy-based approach to localized and sustained IL-10 expression at a scaffold could modulate the number, relative proportions, and cytokine production of infiltrating leukocyte populations. Flow cytometry was used to quantify infiltration of six leukocyte populations for 21 days …

Genomics Of Plant Abiotic Stress Tolerance, Dong Ha Oh, Maheshi Dassanayake, Hyewon Hong, Suja George, Seol Ki Paeng, Anna Kropornika, Ray A. Bressan, Sang Yeol Lee, Dae Jin Yun, Hans J. Bohnert

Faculty Publications

© 2014 by John Wiley & Sons, Inc. Genome sequences and RNA-seq data provide unparalleled views into the genetic basis that underlies plant phenotypes. This chapter outlines a paradigm shift in plant biology originating from the relative ease of generating sequences, and points to tools that have enabled global transcript analyses (RNA-seq), replacing arduous microarray hybridization experiments and laborious quantitative RT-PCR platform designs. Soon, it can be envisioned that one may replace individual transcript assays by measuring how the entire transcriptome responds globally to a manipulation or mutation. The chapter advances a position that the knowledge of genome content and …

Erratum: Peg3 Mutational Effects On Reproduction And Placenta-Specific Gene Families (Plos One (2014) 9:1 Doi: 10.1371/Annotation/8de03ec5-E62c-4135-87ee- 4928475090a8), Joomyeong Kim, Wesley D. Frey, Hongzhi He, Hana Kim, Muhammad B. Ekram, Arundhati Bakshi, Mohammad Faisal, Bambarendage P.U. Perera, An Ye, Ryoichi Teruyama

Faculty Publications

No abstract provided.

Aphid Amino Acid Transporter Regulates Glutamine Supply To Intracellular Bacterial Symbionts, Daniel R.G. Price, Honglin Feng, James D. Baker, Selvan Bavan, Charles W. Luetje, Alex C.C. Wilson

Faculty Publications

Endosymbiotic associations have played a major role in evolution. However, the molecular basis for the biochemical interdependence of these associations remains poorly understood. The aphid-Buchnera endosymbiosis provides a powerful system to elucidate how these symbioses are regulated. In aphids, the supply of essential amino acids depends on an ancient nutritional symbiotic association with the gamma-proteobacterium Buchnera aphidicola. Buchnera cells are densely packed in specialized aphid bacteriocyte cells. Here we confirm that five putative amino acid transporters are highly expressed and/or highly enriched in Acyrthosiphon pisum bacteriocyte tissues. When expressed in Xenopus laevis oocytes, two bacteriocyte amino acid transporters displayed significant …

Species Coexistence And The Dynamics Of Phenotypic Evolution In Adaptive Radiation, Joseph A. Tobias, Charlie K. Cornwallis, Elizabeth P. Derryberry, Santiago Claramunt, Robb T. Brumfield, Nathalie Seddon

Faculty Publications

Interactions between species can promote evolutionary divergence of ecological traits and social signals, a process widely assumed to generate species differences in adaptive radiation. However, an alternative view is that lineages typically interact when relatively old, by which time selection for divergence is weak and potentially exceeded by convergent selection acting on traits mediating interspecific competition. Few studies have tested these contrasting predictions across large radiations, or by controlling for evolutionary time. Thus the role of species interactions in driving broad-scale patterns of trait divergence is unclear. Here we use phylogenetic estimates of divergence times to show that increased trait …

Morphogenesis And Propagation Of Complex Cracks Induced By Thermal Shocks, Blaise Bourdin, Jean Jacques Marigo, Corrado Maurini, Paul Sicsic

Faculty Publications

We study the genesis and the selective propagation of complex crack networks induced by thermal shock or drying of brittle materials. We use a quasistatic gradient damage model to perform large-scale numerical simulations showing that the propagation of fully developed cracks follows Griffith criterion and depends only on the fracture toughness, while crack morphogenesis is driven by the material's internal length. Our numerical simulations feature networks of parallel cracks and selective arrest in two dimensions and hexagonal columnar joints in three dimensions, without any hypotheses on cracks geometry, and are in good agreement with available experimental results. © 2014 American …

Changing Microspatial Patterns Of Sulfate-Reducing Microorganisms (Srm) During Cycling Of Marine Stromatolite Mats, Alexandru I. Petrisor, Sandra Szyjka, Tomohiro Kawaguchi, Pieter T. Visscher, Robert Sean Norman, Alan W. Decho

Faculty Publications

Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing “non-lithifying” (Type-1) and “lithifying” (Type-2) mats. Our results revealed three major trends: (1) Molecular typing using the dsrA probe revealed a shift in the SRM community composition between Type-1 and Type-2 mats. Fluorescence in-situ hybridization (FISH) coupled to confocal scanning-laser microscopy (CSLM)-based image analyses, and ³⁵SO₄²⁻-silver foil patterns showed that SRM were present in surfaces of …

Measurement Issues With Couple-And Family-Level Data, Dean M. Busby, Franklin O. Poulsen

Faculty Publications

Early in my (D.B.) training as a family therapist, I did some co-therapy with a clinical psychology student who wanted to learn how to work with couples. The couple we were working with was quite volatile, and it was not uncommon for the dialogue between the spouses to get heated. While it was challenging enough to keep the interactions between the partners moving in a productive direction, my co-therapist was quite uncomfortable with conflict and would emotionally "check out" of the session as soon as things became intense. Each time a session was challenging and conflict became intense, my co-therapist …

A Field Guide To Genomics Research, Andrea H. Bild, Jeffrey T. Chang, W. Evan Johnson, Stephen R. Piccolo

Faculty Publications

High-throughput technologies are enabling scientists to profile genomes, transcriptomes, proteomes, and metabolomes at an unprecedented scale [1]. All this “-omics” research (let's call it genomics for simplicity) is exciting—and game changing—but it's also fraught with dangers for the tenderfoot. Here, we've put together a brief “field guide” for those wishing to visit the genomics frontier, in which we use caricatures to illustrate various pitfalls that can beset those who inhabit this new territory. By documenting the behaviors of these common types, we hope to guide researchers in their quest to apply sound practices when designing genomics experiments and analyzing …

Energy Input Is Primary Controller Of Methane Bubbling In Subarctic Lakes, Martin Wik, Brett F. Thornton, David Bastviken, Sally Macintyre, Ruth K. Varner, Patrick M. Crill

Faculty Publications

Emission of methane (CH4) from surface waters is often dominated by ebullition (bubbling), a transport mode with high‐spatiotemporal variability. Based on new and extensive CH4 ebullition data, we demonstrate striking correlations (r2 between 0.92 and 0.997) when comparing seasonal bubble CH4 flux from three shallow subarctic lakes to four readily measurable proxies of incoming energy flux and daily flux magnitudes to surface sediment temperature (r2 between 0.86 and 0.94). Our results after continuous multiyear sampling suggest that CH4 ebullition is a predictable process, and that heat flux into the lakes is the dominant driver of gas production and release. Future …

Sixteen Years Of Collaborative Learning Through Active Sense-Making In Physics (Clasp) At Uc Davis, Wendell Potter, David Webb, Cassandra Paul, Emily West, Mark Bowen, Brenda Weiss, Lawrence Coleman, Charles De Leone

Faculty Publications

This paper describes our large reformed introductory physics course at UC Davis, which bioscience students have been taking since 1996. The central feature of this course is a focus on sense-making by the students during the five hours per week discussion/labs in which the students take part in activities emphasizing peer-peer discussions, argumentation, and presentations of ideas. The course differs in many fundamental ways from traditionally taught introductory physics courses. After discussing the unique features of CLASP and its implementation at UC Davis, various student outcome measures are presented showing increased performance by students who took the CLASP course compared …

Using Infrared-Triggered Cameras To Monitor Activity Of Forest Carnivores, Matthew E. Symmank, Christopher E. Comer, James C. Kroll

Faculty Publications

The activity patterns of 4 forest predator species were monitored, using infrared-triggered cameras, within a 1318-ha study area in East Texas. We recorded 161 photographic capture events in 1925 trap-nights over 17 weeks. Photographic capture events included 18 Lynx rufus (Bobcat), 109 Procyon lotor (Raccoon), 21 Didelphis virginiana (Virginia Opossum), and 13 Canis latrans (Coyote). We developed an easily replicated method of measuring time on a percent scale to compare activity data over several months, accounting for changes in sunrise and sunset times. Bobcat activity was 38.9% crepuscular and 22.1% diurnal. The activity of the other 3 species was mostly …

New Host And Location Record For The Bat Bug Cimex Adjunctus Barber 1939, With A Summary Of Previous Records, M. E. Grilliot, J. L. Hunt, C. G. Sims, Chris E. Comer

Faculty Publications

In June 2009, 14 Rafinesque’s big-eared bats (Corynorhinus rafinesquii) were collected from an abandoned house near Shepherd, San Jacinto County, Texas. Three individuals harbored bat bugs which were subsequently identified as Cimex adjunctus Barber 1939. This is the first record of this species from C. rafinesquii. In August 2013, 10 C. rafinesquii were collected from a maternity colony in Drew County in southeastern Arkansas. Four of the bats harbored bat bugs, which were identified as C. adjunctus. This is the first record of this bat bug from Arkansas. A summary of previous state and host records of the insect is …

Instream Woody Debris And Riparian Forest Characteristics In The Sabine River, Texas, Matthew W. Mcbroom, Michael Ringer, Yanli Zhang

Faculty Publications

We examined instream large woody debris (LWD) dynamics on the Sabine River, TX. All wood >10 cm in diameter and >2 m long was measured on four river meanders (meander wavelengths) below the dam on Toledo Bend Reservoir. We determined LWD species, degree of decay, bank orientation, jam association, and stage contact. We also measured riparian vegetation characteristics on each meander. LWD volumes were significantly greater at the site immediately below Toledo Bend Dam, due to the relatively steeper channel gradient and higher rates of channel erosion. Based on mass balance estimates, between 11 and 21% of total annual recruitment …

Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell

Faculty Publications

We formulate low Mach number fluctuating hydrodynamic equations appropriate for modeling diffusive mixing in isothermal mixtures of fluids with different density and transport coefficients. These equations eliminate the fast isentropic fluctuations in pressure associated with the propagation of sound waves by replacing the equation of state with a local thermodynamic constraint. We demonstrate that the low Mach number model preserves the spatio-temporal spectrum of the slower diffusive fluctuations. We develop a strictly conservative finite-volume spatial discretization of the low Mach number fluctuating equations in both two and three dimensions. We construct several explicit Runge-Kutta temporal integrators that strictly maintain the …

Coastal Trapped Waves, Alongshore Pressure Gradients, And The California Undercurrent, Thomas Connolly, Barbara Hickey, Igor Shulman, Richard Thomson

Faculty Publications

The California Undercurrent (CUC), a poleward-flowing feature over the continental slope, is a key transport pathway along the west coast of North America and an important component of regional upwelling dynamics. This study examines the poleward undercurrent and alongshore pressure gradients in the northern California Current System (CCS), where local wind stress forcing is relatively weak. The dynamics of the undercurrent are compared in the primitive equation Navy Coastal Ocean Model and a linear coastal trapped wave model. Both models are validated using hydrographic data and current-meter observations in the core of the undercurrent in the northern CCS. In the …

A Picture Is Worth A Thousand Words: Chinese College Students’ Self-Presentation On Social Networking Sites, Qinghua Yang, Zongchao Li

Faculty Publications

Social media have provided new means of self-presentation. Because individuals are able to post notes, pictures, and videos, social media users can construct their personal images on social networking sites (SNSs) and build links with their various communities. This study aims to find out how Chinese college students perceive other users' online self-presentations and how they conduct their own self-presentations through posting pictures on SNSs. Using photo-elicitation as the primary methodology, the authors conducted two.focus groups with male and female participants respectively. With grounded theory as the framework, the qualitative data show gender differences in the attitudes towards extreme self-presentation, …

A Method For Evaluating Library Liaison Activities In Small Academic Libraries, Jonathan Miller

Faculty Publications

This article presents a practical method for formative, self-reflective assessment of the liaison activities of individual librarians and to evaluate liaison activities in general. Many libraries evaluate their liaison programs, but few evaluate the effectiveness of individual librarians’ efforts within the program.

Librarians of Rollins College redefined and re-branded their liaison program as “Your Librarian.” As part of this effort, the author surveyed the faculty and assessed the program and the effectiveness of individual librarians. The author outlines the liaison responsibilities, the survey instrument, and how the results are analyzed and used in a process of continuous reflective improvement for …