Digital Commons Network^™

Updating Models For Restoration And Management Of Fiery Ecosystems, Jennifer M. Fill, William J. Platt, Shane M. Welch, Jayme L. Waldron, Timothy A. Mousseau

Faculty Publications

© 2015 Elsevier B.V. Scientific models that guide restoration/management protocols should be reviewed periodically as new data become available. We examine ecological concepts used to guide restoration of pine savannas and woodlands, historically prominent but now rare habitats in the southern North American Coastal Plain. For many decades, pine savanna management has been guided predominantly by a biome-centric succession model. Pine savannas have been considered early-successional communities that, in the absence of fire, transition rapidly toward closed-canopy hardwood forests. Recurrent fires have been viewed as exogenous disturbances that maintain savanna ecosystems as a sub-climax, blocking succession to an equilibrium steady …

Size-Controlled Large-Diameter And Few-Walled Carbon Nanotube Catalysts For Oxygen Reduction, Xianliang Wang, Qing Li, Hengyu Pan, Ye Lin, Yujie Ke, Haiyang Sheng, Mark T. Swihart, Gang Wu

Faculty Publications

We demonstrate a new strategy for tuning the size of large-diameter and few-walled nitrogen-doped carbon nanotubes (N-CNTs) from 50 to 150 nm by varying the transition metal (TM = Fe, Co, Ni or Mn) used to catalyze graphitization of dicyandiamide. Fe yielded the largest tubes, followed by Co and Ni, while Mn produced a clot-like carbon morphology. We show that morphology is correlated with electrocatalytic activity for the oxygen reduction reaction (ORR). A clear trend of Fe > Co > Ni > Mn for the ORR catalytic activity was observed, in both alkaline media and more demanding acidic media. The Fe-derived N-CNTs exhibited …

Equation Of Motion Coupled Cluster Methods For Electron Attachment And Ionization Potential In Polyacenes, Kiran Bhaskaran-Nair, Karol Kowalski, Mark Jarrell, Juana Moreno, William A. Shelton

Faculty Publications

Polyacenes have attracted considerable attention due to their various applications in organic optoelectronic materials. This study focuses on linear polyacenes and their electron affinity (EA) and ionization potential (IP) properties. We have employed our recent implementation of EA/IP equation of motion coupled cluster singles and doubles (EA/IP-EOMCCSD) methods which are accurate, computationally efficient and are capable of treating large systems employing reasonable basis sets size. The EA/IP results obtained for naphthalene, anthracene, tetracene, pentacene, hexacene and heptacene are in a good agreement with experiment. Comparison between quality of excitation energies obtained from IP-EOMCCSD and EE-EOMCCSD formalisms were also studied.

Linkages Among Fluorescent Dissolved Organic Matter, Dissolved Amino Acids And Lignin-Derived Phenols In River-Influenced Ocean Margins, Youhei Yamashita, Cédric G. Fichot, Yuan Shen, Rudolf Jaffé, Ronald Benner

Faculty Publications

Excitation emission matrix (EEM) fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC) is commonly used to investigate the dynamics of dissolved organic matter (DOM). However, a lack of direct comparisons with known biomolecules makes it difficult to substantiate the molecular composition of specific fluorescent components. Here, coincident surface-water measurements of EEMs, dissolved lignin, and total dissolved amino acids (TDAA) acquired in the northern Gulf of Mexico were used to investigate the relationships between specific fluorescent components and DOM biomolecules. Two terrestrial humic-like components identified by EEM-PARAFAC using samples obtained from river to offshore waters were strongly linearly correlated with dissolved …

Innovation Levers In Diagnostic Patents, Colleen Chien

Faculty Publications

No abstract provided.

Structural Characterization Of A Newly Identified Component Of Α-Carboxysomes: The Aaa+ Domain Protein Csocbbq, Markus Sutter, Evan W. Roberts, Raul C. Gonzalez, Cassandra Bates, Salma Dawoud, Kimberly Landry, Gordon C. Cannon, Sabine Heinhorst, Cheryl A. Kerfeld

Faculty Publications

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO₂ within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysome …

Gene-Expression Patterns In Peripheral Blood Classify Familial Breast Cancer Susceptibility, Stephen R. Piccolo, Irene L. Andrulis, Adam L. Cohen, Thomas Connor, Philip J. Moos, Avrum E. Spira, Saundra S. Buys, W. Evan Johnson, Andrea H. Bild

Faculty Publications

Background: Women with a family history of breast cancer face considerable uncertainty about whether to pursue standard screening, intensive screening, or prophylactic surgery. Accurate and individualized risk-estimation approaches may help these women make more informed decisions. Although highly penetrant genetic variants have been associated with familial breast cancer (FBC) risk, many individuals do not carry these variants, and many carriers never develop breast cancer. Common risk variants have a relatively modest effect on risk and show limited potential for predicting FBC development. As an alternative, we hypothesized that additional genomic data types, such as gene-expression levels, which can reflect …

Deepsat - A Learning Framework For Satellite Imagery, Saikat Basu, Sangram Ganguly, Supratik Mukhopadhyay, Robert Dibiano, Manohar Karki, Ramakrishna Nemani

Faculty Publications

Satellite image classification is a challenging problem that lies at the crossroads of remote sensing, computer vision, and machine learning. Due to the high variability inherent in satellite data, most of the current object classification approaches are not suitable for handling satellite datasets. The progress of satellite image analytics has also been inhibited by the lack of a single labeled highresolution dataset with multiple class labels. The contributions of this paper are twofold - (1) first, we present two new satellite datasets called SAT-4 and SAT-6, and (2) then, we propose a classification framework that extracts features from an input …

Resonant Interneurons Can Increase Robustness Of Gamma Oscillations., Tikidji-Hamburyan Ra, Martínez Jj, White Ja, Canavier Cc

Faculty Publications

No abstract provided.

Short-Term Effects Of Herbicides And A Prescribed Fire On Restoration Of A Shrub-Encroached Pine Savanna, William J. Platt, Alex K. Entrup, Emily K. Babl, Cody Coryell-Turpin, Viet Dao, James A. Hebert, Claire D. Labarbera, Jené F.L. Noto, Similoluwa O. Ogundare, Lucas K. Stamper, Nabin Timilsina

Faculty Publications

© 2015 Society for Ecological Restoration. Shrub encroachment occurring worldwide in savannas and grasslands has commonly been hypothesized to result from anthropogenically altered environments. Two disturbance-based approaches to restoration have involved: (1) application of selective herbicides to reduce density/cover of shrubs; (2) reinstatement of natural fire regimes to generate environmental conditions favoring herbaceous species. We studied short-term responses of native shrubs, vines, and grasses in a Louisiana pine savanna to herbicides followed by a prescribed fire and fire alone. Plots established in the summer, 2013, were hand-sprayed in the fall with Imazapyr and Triclopyr, Triclopyr alone, or no herbicide, then …

Fetal Programming In Meat Production, Min Du, Bo Wang, Xing Fu, Qiyuan Yang, Mei Jun Zhu

Faculty Publications

© 2015 Elsevier Ltd. Nutrient fluctuations during the fetal stage affects fetal development, which has long-term impacts on the production efficiency and quality of meat. During the early development, a pool of mesenchymal progenitor cells proliferate and then diverge into either myogenic or adipogenic/fibrogenic lineages. Myogenic progenitor cells further develop into muscle fibers and satellite cells, while adipogenic/fibrogenic lineage cells develop into adipocytes, fibroblasts and resident fibro-adipogenic progenitor cells. Enhancing the proliferation and myogenic commitment of progenitor cells during fetal development enhances muscle growth and lean production in offspring. On the other hand, promoting the adipogenic differentiation of adipogenic/fibrogenic progenitor …

Functional Conservation In The Siamese-Related Family Of Cyclin-Dependent Kinase Inhibitors In Land Plants, Narender Kumar, Hirofumi Harashima, Shweta Kalve, Jonathan Bramsiepe, Kai Wang, Bulelani L. Sizani, Laura L. Bertrand, Matthew C. Johnson, Christopher Faulk, Renee Dale, L. Alice Simmons, Michelle L. Churchman, Keiko Sugimoto, Naohiro Kato, Maheshi Dasanayake, Gerrit Beemster, Arp Schnittger, John C. Larkin

Faculty Publications

© 2015 American Society of Plant Biologists. All rights reserved. The best-characterized members of the plant-specific SIAMESE-RELATED (SMR) family of cyclin-dependent kinase inhibitors regulate the transition from the mitotic cell cycle to endoreplication, also known as endoreduplication, an altered version of the cell cycle in which DNA is replicated without cell division. Some other family members are implicated in cell cycle responses to biotic and abiotic stresses. However, the functions of most SMRs remain unknown, and the specific cyclin- dependent kinase complexes inhibited by SMRs are unclear. Here, we demonstrate that a diverse group of SMRs, including an SMR from …

Cellular And Molecular Remodeling Of Inguinal Adipose Tissue Mitochondria By Dietary Methionine Restriction, Yuvraj N. Patil, Kelly N. Dille, David H. Burk, Cory C. Cortez, Thomas W. Gettys

Faculty Publications

© 2015 Elsevier Inc. Dietary methionine restriction (MR) produces a coordinated series of biochemical and physiological responses that improve biomarkers of metabolic health, increase energy expenditure, limit fat accretion and improve overall insulin sensitivity. Inguinal white adipose tissue (IWAT) is a primary target and site of action where the diet initiates transcriptional programs linked to enhancing both synthesis and oxidation of lipid. Using a combination of ex vivo approaches to assess dietary effects on cell morphology and function, we report that dietary MR produced a fourfold increase in multilocular, UCP1-expressing cells within this depot in conjunction with significant increases in …

Lithologic Discontinuity Assessment In Soils Via Portable X-Ray Fluorescence Spectrometry And Visible Near-Infrared Diffuse Reflectance Spectroscopy, David C. Weindorf, Somsubhra Chakraborty, Abdalsamad Abdalsatar, Ali Aldabaa, Laura Pau Lette, Giuseppe Corti, Stefania Cocco, Erika Michéli, Dandan Wang, Bin Li, Titus Man, Aakriti Sharma, Taylor Person

Faculty Publications

Lithologic discontinuity identification can be arduous and erroneous in instances where distinct morphological differences between parent materials are absent. Often, investigators must wait for laboratory data to help differentiate parent materials via physicochemical properties. This study used visible near-infrared diffuse reflectance spectroscopy (VisNIR DRS) and portable X-ray fluorescence (PXRF) spectrometry for establishing parent material differentia more quickly. Ten pedons containing 135 samples were scanned in situ in the United States, Italy, and Hungary, morphologically described by trained pedologists, then sampled for standard laboratory characterization. Compared with laboratory data and/or morphologically described discontinuities, PXRF data were associated with large, abrupt changes …

Darwin’S Dice: The Idea Of Chance In The Thought Of Charles Darwin, Charles H. Pence

Faculty Publications

No abstract provided.

Recent Advances In The Use Of Mass Spectrometry To Examine Structure/Function Relationships In Photosystem Ii, Terry M. Bricker, Manjula P. Mummadisetti, Laurie K. Frankel

Faculty Publications

© 2015 Elsevier B.V. All rights reserved. Tandem mass spectrometry often coupled with chemical modification techniques, is developing into increasingly important tool in structural biology. These methods can provide important supplementary information concerning the structural organization and subunit make-up of membrane protein complexes, identification of conformational changes occurring during enzymatic reactions, identification of the location of posttranslational modifications, and elucidation of the structure of assembly and repair complexes. In this review, we will present a brief introduction to Photosystem II, tandem mass spectrometry and protein modification techniques that have been used to examine the photosystem. We will then discuss a …

Changes In Habitat Use At Rain Forest Edges Through Succession: A Case Study Of Understory Birds In The Brazilian Amazon, Luke L. Powell, Gustavo Zurita, Jared D. Wolfe, Erik I. Johnson, Philip C. Stouffer

Faculty Publications

Primary tropical rain forests are being rapidly perforated with new edges via roads, logging, and pastures, and vast areas of secondary forest accumulate following abandonment of agricultural lands. To determine how insectivorous Amazonian understory birds respond to edges between primary rain forest and three age classes of secondary forest, we radio-tracked two woodcreepers (Glyphorynchus spirurus, N = 17; Xiphorhynchus pardalotus, N = 18) and a terrestrial antthrush (Formicarius colma, N = 19). We modeled species-specific response to distance to forest edge (a continuous variable) based on observations at varying distances from the primary-secondary forest interface. All species avoided 8-14-yr-old secondary …

Abundance, Stable Isotopic Composition, And Export Fluxes Of Doc, Poc, And Dic From The Lower Mississippi River During 2006-2008, Yihua Cai, Laodong Guo, Xuri Wang, George Aiken

Faculty Publications

Sources, abundance, isotopic compositions, and export fluxes of dissolved inorganic carbon (DIC), dissolved and colloidal organic carbon (DOC and COC), and particulate organic carbon (POC), and their response to hydrologic regimes were examined through monthly sampling from the Lower Mississippi River during 2006–2008. DIC was the most abundant carbon species, followed by POC and DOC. Concentration and δ¹³C of DIC decreased with increasing river discharge, while those of DOC remained fairly stable. COC comprised 61 ± 3% of the bulk DOC with similar δ¹³C abundances but higher percentages of hydrophobic organic acids than DOC, suggesting its …

Amp-Activated Protein Kinase Stimulates Warburg-Like Glycolysis And Activation Of Satellite Cells During Muscle Regeneration, Xing Fu, Mei Jun Zhu, Mike V. Dodson, Min Du

Faculty Publications

© 2015 by The American Society for Biochemistry and Molecular Biology, Inc. Satellite cells are the major myogenic stem cells residing inside skeletal muscle and are indispensable for muscle regeneration. Satellite cells remain largely quiescent but are rapidly activated in response to muscle injury, and the derived myogenic cells then fuse to repair damaged muscle fibers or form new muscle fibers. However, mechanisms eliciting metabolic activation, an inseparable step for satellite cell activation following muscle injury, have not been defined. We found that a non-canonical Sonic Hedgehog (Shh) pathway is rapidly activated in response to muscle injury, which activates AMPK …

Changes In Litter Quality Caused By Simulated Nitrogen Deposition Reinforce The N-Induced Suppression Of Litter Decay, Linda T. A. Van Diepen, Serita D. Frey, Christopher M. Sthultz, Eric W. Morrison, Rakesh Minocha, Anne Pringle

Faculty Publications

Rates of nitrogen (N) deposition are increasing in industrialized and rapidly developing nations. Simulated N deposition suppresses plant litter decay rates, in particular for low quality (high lignin) litter. Litter quality is a primary driver of litter decomposition; however, it is not clear how changes in litter quality caused by long-term ecosystem exposure to chronic N additions interact with altered soil N-availability to influence litter decay dynamics. To document the effects of simulated N deposition on litter quality, we conducted a meta-analysis of available litter nutrient data from simulated N deposition experiments in temperate forests. To directly test whether changes …

“Adulthood” By Whose Definition?: The Complexity Of Emerging Adults’ Conceptions Of Adulthood, Larry J. Nelson, Stephanie S. Luster

Faculty Publications

The beginning of adulthood may well be the most nebulous transition of the life course. It is fair to say that no clear-cut universal marker indicates the beginning of adulthood, leading to widespread cultural and individual diversity in the beliefs of you people aged 18–29 regarding what it means to be an adult and how the transition into adulthood should occur. This chapter examines this complexity. The authors review the literature exploring the conceptions of adulthood of young people begging at age 18 and continuing through the third decade; examining how these conceptions have been linked to beliefs, behaviors, and …

A Nonlinear Splitting Algorithm For Systems Of Partial Differential Equations With Self-Diffusion, Matthew Beauregard, Joshua L. Padgett, Rana D. Parshad

Faculty Publications

Systems of reaction-diffusion equations are commonly used in biological models of food chains. The populations and their complicated interactions present numerous challenges in theory and in numerical approximation. In particular, self-diffusion is a nonlinear term that models overcrowding of a particular species. The nonlinearity complicates attempts to construct efficient and accurate numerical approximations of the underlying systems of equations. In this paper, a new nonlinear splitting algorithm is designed for a partial differential equation that incorporates self diffusion. We present a general model that incorporates self-diffusion and develop a numerical approximation. The numerical analysis of the approximation provides criteria for …

Improving Healthspan Via Changes In Gut Microbiota And Fermentation, Michael J. Keenan, Maria L. Marco, Donald K. Ingram, Roy J. Martin

Faculty Publications

Dietary resistant starch impact on intestinal microbiome and improving healthspan is the topic of this review. In the elderly population, dietary fiber intake is lower than recommended. Dietary resistant starch as a source of fiber produces a profound change in gut microbiota and fermentation in animal models of aging. Dietary resistant starch has the potential for improving healthspan in the elderly through multiple mechanisms as follows: (1) enhancing gut microbiota profile and production of short-chain fatty acids, (2) improving gut barrier function, (3) increasing gut peptides that are important in glucose homeostasis and lipid metabolism, and (4) mimicking many of …

Loss Of Glycosaminoglycan Receptor Binding After Mosquito Cell Passage Reduces Chikungunya Virus Infectivity, Dhiraj Acharya, Amber M. Paul, John F. Anderson, Faqing Huang, Fengwei Bai

Faculty Publications

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that can cause fever and chronic arthritis in humans. CHIKV that is generated in mosquito or mammalian cells differs in glycosylation patterns of viral proteins, which may affect its replication and virulence. Herein, we compare replication, pathogenicity, and receptor binding of CHIKV generated in Vero cells (mammal) or C6/36 cells (mosquito) through a single passage. We demonstrate that mosquito cell-derived CHIKV (CHIKV_mos) has slower replication than mammalian cell-derived CHIKV (CHIKV_vero), when tested in both human and murine cell lines. Consistent with this, CHIKV_mos infection in both cell lines …

Identification Of The Substrate Access Portal Of 5-Lipoxygenase, Sunayana Mitra, Sue G. Bartlett, Marcia E. Newcomer

Faculty Publications

© 2015 American Chemical Society. The overproduction of inflammatory lipid mediators derived from arachidonic acid contributes to asthma and cardiovascular diseases, among other pathologies. Consequently, the enzyme that initiates the synthesis of pro-inflammatory leukotrienes, 5-lipoxygenase (5-LOX), is a target for drug design. The crystal structure of 5-LOX revealed a fully encapsulated active site; thus the point of substrate entry is not known. We asked whether a structural motif, a "cork" present in 5-LOX but absent in other mammalian lipoxygenases, might be ejected to allow substrate access. Our results indicate that reduction of cork volume facilitates access to the active site. …

Ethanol Enhances Arsenic-Induced Cyclooxygenase-2 Expression Via Both Nfat And Nf-Κb Signalings In Colorectal Cancer Cells, Lei Wang, John Andrew Hitron, James T.F. Wise, Young Ok Son, Ram Vinod Roy, Donghern Kim, Jin Dai, Poyil Pratheeshkumar, Zhuo Zhang, Mei Xu, Jia Luo, Xianglin Shi

Faculty Publications

Arsenic is a known carcinogen to humans, and chronic exposure to environmental arsenic is a worldwide health concern. As a dietary factor, ethanol carries a well-established risk for malignancies, but the effects of co-exposure to arsenic and ethanol on tumor development are not well understood. In the present study, we hypothesized that ethanol would enhance the function of an environmental carcinogen such as arsenic through increase in COX-2 expression. Our in vitro results show that ethanol enhanced arsenic-induced COX-2 expression. We also show that the increased COX-2 expression associates with intracellular ROS generation, up-regulated AKT signaling, with activation of both …

Characterization Of The Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction In Solution And Determination Of Binding Energy Hot Spots, Yan Wang, Huili Yao, Yuan Cheng, Scott Lovell, Kevin P. Battaile, C. Russell Midaugh, Mario Rivera

Faculty Publications

© 2015 American Chemical Society. Mobilization of iron stored in the interior cavity of BfrB requires electron transfer from the [2Fe-2S] cluster in Bfd to the core iron in BfrB. A crystal structure of the Pseudomonas aeruginosa BfrB:Bfd complex revealed that BfrB can bind up to 12 Bfd molecules at 12 structurally identical binding sites, placing the [2Fe-2S] cluster of each Bfd immediately above a heme group in BfrB [Yao, H., et al. (2012) J. Am. Chem. Soc., 134, 13470-13481]. We report here a study aimed at characterizing the strength of the P. aeruginosa BfrB:Bfd association using surface plasmon resonance …

Dual Mode Of Action Of Bt Proteins: Protoxin Efficacy Against Resistant Insects, Bruce E. Tabashnik, Min Zhang, Jeffrey A. Fabrick, Yidong Wu, Meijing Gao, Fangneng Huang, Jizhen Wei, Jie Zhang, Alexander Yelich, Gopalan C. Unnithan, Alejandra Bravo, Mario Soberón, Yves Carrière, Xianchun Li

Faculty Publications

Transgenic crops that produce Bacillus thuringiensis (Bt) proteins for pest control are grown extensively, but insect adaptation can reduce their effectiveness. Established mode of action models assert that Bt proteins Cry1Ab and Cry1Ac are produced as inactive protoxins that require conversion to a smaller activated form to exert toxicity. However, contrary to this widely accepted paradigm, we report evidence from seven resistant strains of three major crop pests showing that Cry1Ab and Cry1Ac protoxins were generally more potent than the corresponding activated toxins. Moreover, resistance was higher to activated toxins than protoxins in eight of nine cases evaluated in this …

Breach Avoidance Or Treaty Avoidance?: The Problem Of Over-Compliance And U.S. Ratification Of The Basel Convention On Hazardous Wastes, Tseming Yang, C. Scott Fulton

Faculty Publications

Over the past two decades, the failure of the United States to ratify a string of global multilateral environmental agreements has become a significant source of frustration for environmentalists and diplomats. The common perception is that Washington politics is to blame. The problem has even led to scholarly suggestions that any new climate agreement coming out of the Paris negotiations later this year could be entered into by the U.S. as an Executive Agreement rather than a Senate-approved treaty.

Delay has been uniquely serious, however, with respect to the 1989 Basel Convention on Hazardous Wastes. Signed under the elder President …

A Generalized Force-Modified Potential Energy Surface For Mechanochemical Simulations, Gopinath Subramanian, Nithin Mathew, Jeff Leiding

Faculty Publications

We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G- level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules are blueshifted …