Digital Commons Network^™

The Effects Of Tether Placement On Antibody Stability On Surfaces, Thomas A. Knotts, Rebecca W. Grawe

Faculty Publications

Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. …

Judicial Fact-Finding In An Age Of Rapid Change: Creative Reforms From Abroad, Allison Orr Larsen

Faculty Publications

No abstract provided.

Effect Of Cohorts On Student Retention In Engineering, Patricia Backer, Cindy Kato

Faculty Publications

Project Succeed is a campus-wide initiative funded by the U.S. Department of Education. Its focus is to improve the 5-year graduation and retention rates and close the achievement gap for Under-Represented Minorities (URMs) across all majors at San José State University (SJSU). There are three major goals: strengthen SJSU’s core academic performance in retention and graduation; provide an improved supportive environment for URM students; and enhance the delivery and integration of academic and co-curricular support services. For Fall 2015, newly matriculated students in the College of Business, College of Engineering, and Child and Adolescent Development Department (CHAD) were assigned schedules …

Microbial Extracellular Polymeric Substances (Epss) In Ocean Systems, Alan W. Decho, Tony Gutierrez

Faculty Publications

Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured ‘biofilm’ communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called ‘marine snow.’ Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range …

Rapid Reversible Borane To Boryl Hydride Exchange By Metal Shuttling On The Carborane Cluster Surface, Bennett J. Eleazer, Mark D. Smith, Alexey A. Popov, Dmitry V. Peryshkov

Faculty Publications

In this work, we introduce a novel concept of a borane group vicinal to a metal boryl bond acting as a supporting hemilabile ligand in exohedrally metalated three-dimensional carborane clusters. The (POBOP)Ru(Cl)(PPh3) pincer complex (POBOP ¼ 1,7-OP(i-Pr)2-m-2-carboranyl) features extreme distortion of the two-center-two-electron Ru–B bond due to the presence of a strong three-centertwo-electron B–H/Ru vicinal interaction. Replacement of the chloride ligand with a hydride afforded the (POBOP)Ru(H)(PPh3) pincer complex, which possesses B–Ru, B–H/Ru, and Ru–H bonds. This complex was found to exhibit a rapid exchange between hydrogen atoms of the borane and the terminal hydride through metal center shuttling between …

Predicting Cryptic Links In Host-Parasite Networks, Tad Dallas, Andrew W. Park, John M. Drake

Faculty Publications

Networks are a way to represent interactions among one (e.g., social networks) or more (e.g., plant-pollinator networks) classes of nodes. The ability to predict likely, but unobserved, interactions has generated a great deal of interest, and is sometimes referred to as the link prediction problem. However, most studies of link prediction have focused on social networks, and have assumed a completely censused network. In biological networks, it is unlikely that all interactions are censused, and ignoring incomplete detection of interactions may lead to biased or incorrect conclusions. Previous attempts to predict network interactions have relied on known properties of network …

Predicting The Impacts Of Mississippi River Diversions And Sea-Level Rise On Spatial Patterns Of Eastern Oyster Growth Rate And Production, Hongqing Wang, Qin Chen, Megan K. La Peyre, Kelin Hu, Jerome F. La Peyre

Faculty Publications

© 2017 There remains much debate regarding the perceived tradeoffs of using freshwater and sediment diversions for coastal restoration in terms of balancing the need for wetland restoration versus preserving eastern oyster (Crassostrea virginica) production. Further complicating the issue, climate change-induced sea-level rise (SLR) and land subsidence are also expected to affect estuarine water quality. In this study, we developed a process-based numerical modeling system that couples hydrodynamic, water quality, and oyster population dynamics. We selected Breton Sound Estuary (BSE) (∼2740 km2) in the eastern Mississippi River Deltaic Plain since it is home to several of the largest public oyster …

Optimizing Sediment Diversion Operations: Working Group Recommendations For Integrating Complex Ecological And Social Landscape Interactions, Natalie S. Peyronnin, Rex H. Caffey, James H. Cowan, Dubravko Justic, Alexander S. Kolker, Shirley B. Laska, Alex Mccorquodale, Earl Melancon, John A. Nyman, Robert R. Twilley, Jenneke M. Visser, John R. White, James G. Wilkins

Faculty Publications

© 2017 by the authors. Future conditions of coastal Louisiana are highly uncertain due to the dynamic nature of deltas, climate change, tropical storms, and human reliance on natural resources and ecosystem services. Managing a system in which natural and socio-economic components are highly integrated is inherently difficult. Sediment diversions are a unique restoration tool that would reconnect the Mississippi River to its deltaic plain to build and sustain land. Diversions are innately adaptable as operations can be modified over time. An expert working group was formed to explore how various operational strategies may affect the complex interactions of coastal …

Continuous Ethanol Production From Synthesis Gas By Clostridium Ragsdalei In A Trickle-Bed Reactor, Mamatha Devarapalli, Randy S. Lewis, Hasan K. Atiyeh

Faculty Publications

A trickle-bed reactor (TBR) when operated in a trickle flow regime reduces liquid resistance to mass transfer because a very thin liquid film is in contact with the gas phase and results in improved gas–liquid mass transfer compared to continuous stirred tank reactors (CSTRs). In the present study, continuous syngas fermentation was performed in a 1-L TBR for ethanol production by Clostridium ragsdalei. The effects of dilution and gas flow rates on product formation, productivity, gas uptakes and conversion efficiencies were examined. Results showed that CO and H2 conversion efficiencies reached over 90% when the gas flow rate was maintained …

Preferential Binding Effects On Protein Structure And Dynamics Revealed By Coarse-Grained Monte Carlo Simulation, Ras B. Pandey, D.L. Jacobs, Barry L. Farmer

Faculty Publications

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (R_g) of the …

Strong Linkages Between Surface And Deep-Water Dissolved Organic Matter In The East/Japan Sea, Tae-Hoon Kim, Guebuem Kim, Yuan Shen, Ronald Benner

Faculty Publications

Vertical and horizontal distributions of total dissolved amino acids (TDAAs), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON) were measured in the East/Japan Sea (EJS). The euphotic zone of this sea is N-limited, and the N : P ratio is ∼ 13 below 200 m depth. Elevated TDAA concentrations (137 ± 34 nM) and DOC-normalized yields (0.8 ± 0.2 % of DOC) were observed in deep waters ( ≥  1000 m) of the EJS and compared with those in the deep North Pacific Ocean. Significantly high TDAA concentrations and yields were observed in a region of deep-water formation, indicating …

Long-Term Carbon And Nitrogen Dynamics At Spruce Revealed Through Stable Isotopes In Peat Profiles, Erik A. Hobbie, Janet Chen, Paul J. Hanson, Colleen M. Iversen, Karis J. Mcfarlane, Nathan R. Thorp, Kirsten S. Hofmockel

Faculty Publications

Peatlands encode information about past vegetation dynamics, climate, and microbial processes. Here, we used δ15N and δ13C patterns from 16 peat profiles to deduce how the biogeochemistry of the Marcell S1 forested bog in northern Minnesota responded to environmental and vegetation change over the past  ∼ 10000 years. In multiple regression analyses, δ15N and δ13C correlated strongly with depth, plot location, C∕N, %N, and each other. Correlations with %N, %C, C∕N, and the other isotope accounted for 80% of variance for δ15N and 38% of variance for δ13C, reflecting N and C losses. In contrast, correlations with depth and topography …

On The Origin Of Energy: Metaphors And Manifestations As Resources For Conceptualizing And Measuring The Invisible, Imponderable, Benedikt Harrer

Faculty Publications

This article explores the origins of metaphorical language to describe energy by reviewing the historical development of the concept by physicists since the early 19th century. In addition to examples of historical and contemporary use of metaphors in academic writing, observable manifestations of energy are identified as the origin of energy “forms.” The historical- philosophical review and presentation of examples from contemporary physics literature contribute a disciplinary foundation to recent claims about the productiveness of physics learners’ use of metaphors and indicators to describe energy.

Modeled Co2 Emissions From Coastal Wetland Transitions To Other Land Uses: Tidal Marshes, Mangrove Forests, And Seagrass Beds, Catherine E. Lovelock, James W. Fourqurean, James T. Morris

Faculty Publications

The sediments of coastal wetlands contain large stores of carbon which are vulnerable to oxidation once disturbed, resulting in high levels of CO2 emissions that may be avoided if coastal ecosystems are conserved or restored. We used a simple model to estimate CO2 emissions from mangrove forests, seagrass beds, and tidal marshes based on known decomposition rates for organic matter in these ecosystems under either oxic or anoxic conditions combined with assumptions of the proportion of sediment carbon being deposited in either oxic or anoxic environments following a disturbance of the habitat. Our model found that over 40 years after …

Across-Proteome Modeling Of Dimer Structures For The Bottom-Up Assembly Of Protein-Protein Interaction Networks, Surabhi Maheshwari, Michal Brylinski

Faculty Publications

© 2017 The Author(s). Background: Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide interaction space at molecular level. Although a growing body of research shows that protein docking can, in principle, be used to predict biologically relevant interactions, the accuracy of the across-proteome identification of interacting partners and the selection of near-native complex structures still need to be improved. Results: In this study, we developed a new method to discover and model protein interactions employing an exhaustive all-to-all docking strategy. …

Cardiovascular Risk Status Of Afro-Origin Populations Across The Spectrum Of Economic Development: Findings From The Modeling The Epidemiologic Transition Study, Lara R. Dugas, Terrence E. Forrester, Jacob Plange-Rhule, Pascal Bovet, Estelle V. Lambert, Ramon A. Durazo-Arvizu, Guichan Cao, Richard S. Cooper, Rasha Khatib, Laura Tonino, Walter Riesen, Wolfgang Korte, Stephanie Kliethermes, Amy Luke

Faculty Publications

Background: Cardiovascular risk factors are increasing in most developing countries. To date, however, very little standardized data has been collected on the primary risk factors across the spectrum of economic development. Data are particularly sparse from Africa. Methods: In the Modeling the Epidemiologic Transition Study (METS) we examined population-based samples of men and women, ages 25-45 of African ancestry in metropolitan Chicago, Kingston, Jamaica, rural Ghana, Cape Town, South Africa, and the Seychelles. Key measures of cardiovascular disease risk are described. Results: The risk factor profile varied widely in both total summary estimates of cardiovascular risk and in the magnitude …

Reproductive Dynamics Of Gulf Menhaden (Brevoortia Patronus) In The Northern Gulf Of Mexico: Effects On Stock Assessments, Nancy J. Brown-Peterson, Robert T. Leaf, Amy M. Schueller, Michael J. Andres

Faculty Publications

Gulf menhaden (Brevoortia patronus) produce one of the largest U.S. fisheries, yet information on reproductive dynamics of the stock is sparse. Males and females reach 50% maturity at 140.8 and 137.2 mm fork length, respectively and recruit into the commercial fishery at this size. Analysis of fishery-dependent data from 1964 through 2014 indicated that somatic condition was lower during the late 1980s and late 2000s and that reproductively active fish from 2014 were significantly larger and had greater gonadosomatic index values than those from 1964 through 1970. Histological analysis performed on fish from 2014 through 2016 revealed spawning-capable …

Cytosolic Delivery Of Doxorubicin From Liposomes To Multidrug-Resistant Cancer Cells Via Vaporization Of Perfluorocarbon Droplets, Jacob B. Williams, Clara M. Buchanan, Ghaleb A. Husseini, William G. Pitt

Faculty Publications

A common mechanism of multidrug resistance is the upregulation of efflux pumps in the cancer cells that can more rapidly export unwanted materials (e.g. cancer drugs) out of the cell, compared to sensitive cancer cells. This research seeks to overcome this mechanism by vaporizing a perfluoropentane emulsion droplet inside of a drug-containing liposome (eLiposome) that was endocytosed into a cancer cell. Folate attached to the eLiposome facilitates uptake into the cell as observed by confocal microscopy. Ultrasound was examined as a trigger to initiate the vaporization of the perfluoropentane droplet and release doxorubicin from folated eLiposomes (feLD). Two seconds of …

Cytosolic Delivery Of Doxorubicin From Liposomes To Multidrug-Resistant Cancer Cells Via Vaporization Of Perfluorocarbon Droplets, Jacob B. Williams, Clara M. Buchanan, Ghaleb Husseini, William G. Pitt

Faculty Publications

A common mechanism of multidrug resistance is the upregulation of efflux pumps in the cancer cells that can more rapidly export unwanted materials (e.g. cancer drugs) out of the cell, compared to sensitive cancer cells. This research seeks to overcome this mechanism by vaporizing a perfluoropentane emulsion droplet inside of a drug-containing liposome (eLiposome) that was endocytosed into a cancer cell. Folate attached to the eLiposome facilitates uptake into the cell as observed by confocal microscopy. Ultrasound was examined as a trigger to initiate the vaporization of the perfluoropentane droplet and release doxorubicin from folated eLipsosomes (feLD). Two seconds of …

Lower Doses Of Fructose Extend Lifespan In Caenorhabditis Elegans, Jolene Zheng, Chenfei Gao, Mingming Wang, Phuongmai Tran, Nancy Mai, John W. Finley, Steven B. Heymsfield, Frank L. Greenway, Zhaoping Li, David Heber, Jeffrey H. Burton, William D. Johnson, Roger A. Laine

Faculty Publications

© 2017, Copyright © Taylor & Francis Group, LLC. Epidemiological studies indicate that the increased consumption of sugars including sucrose and fructose in beverages correlate with the prevalence of obesity, type-2 diabetes, insulin resistance, hyperinsulinemia, hypertriglyceridemia, and hypertension in humans. A few reports suggest that fructose extends lifespan in Saccharomyces cerevisiae. In Anopheles gambiae, fructose, glucose, or glucose plus fructose also extended lifespan. New results presented here suggest that fructose extends lifespan in Caenorhabditis elegans (C. elegans) wild type (N2). C. elegans were fed standard laboratory food source (E. coli OP50), maintained in liquid culture. Experimental groups received additional glucose …

Genetic Bottlenecks In Pristis Sawfishes In Northern Australian Waters, Nicole M. Phillips, Annemarie Fearing, David L. Morgan

Faculty Publications

Northern Australia has been identified as the last stronghold for the dwarf sawfish Pristis clavata, green sawfish P. zijsron, and largetooth sawfish P. pristis, making these populations key in global conservation efforts for each species. This research assesses the levels of genetic diversity in these 3 sawfishes in Australian waters, testing for the presence of population bottlenecks using data at microsatellite loci. Levels of observed heterozygosity in each species from the west coast of Australia and the north-eastern Gulf of Carpentaria were generally high. M ratio tests suggest that assemblages of P. zijsron and P. pristis on …

Gender Disparities In Midlife Hypertension: A Review Of The Evidence On The Arab Region, Christelle Akl, Chaza Akik, Hala Ghattas Ph.D., Carla Makhlouf Obermeyer

Faculty Publications

Objective

While gender differences in hypertension and increased prevalence rates among women at midlife have been documented in multiple settings, the evidence on the Arab world has not been systematically examined. This review summarizes the evidence related to gender disparities in midlife hypertension in this region.

Methods

We searched MEDLINE and Social Sciences Citation Index (SSCI) databases for studies, published between January 2000 and August 2015, on hypertension in the 22 countries of the Arab region. We abstracted information on the prevalence of hypertension among women and men, in general populations during midlife.

Results

Nineteen studies provided data on the …

Redox-Sensitive Marr Homologue Bifr From Burkholderia Thailandensis Regulates Biofilm Formation, Ashish Gupta, Stanley M. Fuentes, Anne Grove

Faculty Publications

© 2017 American Chemical Society. Biofilm formation by pathogenic Burkholderia species is a serious complication as it renders the bacteria resistant to antibiotics and host defenses. Using B. thailandensis, we report here a novel redox-sensitive member of the multiple antibiotic resistance regulator (MarR) protein family, BifR, which represses biofilm formation. BifR is encoded as part of the emrB-bifR operon; emrB-bifR is divergent to ecsC, which encodes a putative LasA protease. In Pseudomonas aeruginosa, LasA has been implicated in virulence by contributing to cleavage of elastase. BifR repressed the expression of ecsC and emrB-bifR, and expression was further repressed under oxidizing …

Crude Oil Impairs Immune Function And Increases Susceptibility To Pathogenic Bacteria In Southern Flounder, Keith M. Bayha, Natalie Ortell, Caitlin Ryan, Kimberly J. Griffitt, Michelle Krasnec, Johnny Sena, Thiruvangan Ramaraj, Ryan Takeshita, Gregory D. Mayer, Faye Schilkey, Robert J. Griffitt

Faculty Publications

Exposure to crude oil or its individual constituents can have detrimental impacts on fish species, including impairment of the immune response. Increased observations of skin lesions in northern Gulf of Mexico fish during the 2010 Deepwater Horizon oil spill indicated the possibility of oil-induced immunocompromisation resulting in bacterial or viral infection. This study used a full factorial design of oil exposure and bacterial challenge to examine how oil exposure impairs southern flounder (Paralichthys lethostigma) immune function and increases susceptibility to the bacteria Vibrio anguillarum, a causative agent of vibriosis. Fish exposed to oil prior to bacterial challenge …

Reduced Vagal Tone In Women With The Premutation Is Associated With Mrna But Not Depression Or Anxiety, Jessica Klusek, Giuseppe Lafauci, Tatyana Adayev, W Ted Brown, Flora Tassone, Jane E. Roberts

Faculty Publications

BACKGROUND: Autonomic dysfunction is implicated in a range of psychological conditions, including depression and anxiety. The () premutation is a common genetic mutation that affects ~1:150 women and is associated with psychological vulnerability. This study examined cardiac indicators of autonomic function among women with the premutation and control women as potential biomarkers for psychological risk that may be linked to . METHODS: Baseline inter-beat interval and respiratory sinus arrhythmia (a measure of parasympathetic vagal tone) were measured in 35 women with the premutation and 28 controls. The women completed anxiety and depression questionnaires. genetic indices (i.e., CGG repeat, quantitative FMRP, …

Species Differences In Egocentric Navigation: The Effect Of Burrowing Ecology On A Spatial Cognitive Trait In Mice, Jason N. Bruck, Noah A. Allen, Kelsey E. Brass, Brian A. Horn, Polly Campbell

Faculty Publications

© 2017 The Association for the Study of Animal Behaviour Efficient navigation is a critical component of fitness for most animals. While most species use a combination of allocentric (external) and egocentric (internal) cues to navigate through their environment, subterranean environments present a unique challenge in that visually mediated allocentric cues are unavailable. The relationship between egocentric spatial cognition and species differences in ecology is surprisingly understudied. We used a maze-learning task to test for differences in egocentric navigation between two closely related species of mice, the eastern house mouse, Mus musculus musculus, and the mound-building mouse, Mus spicilegus. The …

Why Is Family Medicine Different?, F. Matthew Mihelic, Gregory H. Blake

Faculty Publications

An understanding of the role and function of Family Medicine in the healthcare system can provide important insights for Enterprise Architecture. It is often stated that the thought process utilized by Family Medicine physicians is different from that of specialty physicians, but heretofore there has been little or no analysis of what that difference is. This article examines that difference from the perspective of the complex adaptive system that is healthcare today, and shows how it is that Family Medicine physicians perform the vital function of decreasing the entropy or disorder in the patient care system via decision loops, as …

Hard Real-Time Closed-Loop Electrophysiology With The Real-Time Experiment Interface (Rtxi)., Patel Ya, George A, Dorval Ad, White Ja, Christini Dj, Butera Rj

Faculty Publications

No abstract provided.

Predicting Cryptic Links In Host-Parasite Networks, Tad Dallas, Andrew W. Park, John M. Drake

Faculty Publications

© 2017 Dallas et al. Networks are a way to represent interactions among one (e.g., social networks) or more (e.g., plant-pollinator networks) classes of nodes. The ability to predict likely, but unobserved, interactions has generated a great deal of interest, and is sometimes referred to as the link prediction problem. However, most studies of link prediction have focused on social networks, and have assumed a completely censused network. In biological networks, it is unlikely that all interactions are censused, and ignoring incomplete detection of interactions may lead to biased or incorrect conclusions. Previous attempts to predict network interactions have relied …

Multiple Lhcii Antennae Can Transfer Energy Efficiently To A Single Photosystem I, Inge Bos, Kaitlyn M. Bland, Lijin Tian, Roberta Croce, Laurie K. Frankel, Herbert Van Amerongen, Terry M. Bricker, Emilie Wientjes

Faculty Publications

© 2017 Elsevier B.V. Photosystems I and II (PSI and PSII) work in series to drive oxygenic photosynthesis. The two photosystems have different absorption spectra, therefore changes in light quality can lead to imbalanced excitation of the photosystems and a loss in photosynthetic efficiency. In a short-term adaptation response termed state transitions, excitation energy is directed to the light-limited photosystem. In higher plants a special pool of LHCII antennae, which can be associated with either PSI or PSII, participates in these state transitions. It is known that one LHCII antenna can associate with the PsaH site of PSI. However, membrane …