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Adaptation To Ephemeral Habitat May Overcome Natural Barriers And Severe Habitat Fragmentation In A Fire-Dependent Species, The Bachman's Sparrow (Peucaea Aestivalis), Blain Cerame, James A. Cox, Robb T. Brumfield, James W. Tucker, Sabrina S. Taylor Jan 2014

Adaptation To Ephemeral Habitat May Overcome Natural Barriers And Severe Habitat Fragmentation In A Fire-Dependent Species, The Bachman's Sparrow (Peucaea Aestivalis), Blain Cerame, James A. Cox, Robb T. Brumfield, James W. Tucker, Sabrina S. Taylor

Faculty Publications

Bachman's Sparrow (Peucaea aestivalis) is a fire-dependent species that has undergone range-wide population declines in recent decades. We examined genetic diversity in Bachman's Sparrows to determine whether natural barriers have led to distinct population units and to assess the effect of anthropogenic habitat loss and fragmentation. Genetic diversity was examined across the geographic range by genotyping 226 individuals at 18 microsatellite loci and sequencing 48 individuals at mitochondrial and nuclear genes. Multiple analyses consistently demonstrated little genetic structure and high levels of genetic variation, suggesting that populations are panmictic. Based on these genetic data, separate management units/subspecies designations or translocations …

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The Influence Of The Complex Topography And Dynamic History Of The Montane Neotropics On The Evolutionary Differentiation Of A Cloud Forest Bird (Premnoplex Brunnescens, Furnariidae), Eugenio Valderrama, Jorge L. Pérez-Emán, Robb T. Brumfield, Andrés M. Cuervo, Carlos Daniel Cadena Jan 2014

The Influence Of The Complex Topography And Dynamic History Of The Montane Neotropics On The Evolutionary Differentiation Of A Cloud Forest Bird (Premnoplex Brunnescens, Furnariidae), Eugenio Valderrama, Jorge L. Pérez-Emán, Robb T. Brumfield, Andrés M. Cuervo, Carlos Daniel Cadena

Faculty Publications

Aim: To examine the effect of geographical barriers and habitat dynamics related to climatic oscillations on the phylogeography of a widespread passerine of Neotropical cloud forests, the spotted barbtail (Premnoplex brunnescens). Location: Neotropical humid forests of montane areas in lower Central America and South America. Methods: We sequenced two mitochondrial genes and one nuclear intron from specimens collected across the distribution of P. brunnescens. Phylogenetic relationships were inferred using Bayesian and maximum-likelihood methods. Groups with maximum differentiation were estimated with spatial analysis of molecular variance (SAMOVA). We estimated timing of differentiation and relationships among groups with a species-tree approach and …

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Computational Redesign Of Bacterial Biotin Carboxylase Inhibitors Using Structure-Based Virtual Screening Of Combinatorial Libraries, Michal Brylinski, Grover L. Waldrop Jan 2014

Computational Redesign Of Bacterial Biotin Carboxylase Inhibitors Using Structure-Based Virtual Screening Of Combinatorial Libraries, Michal Brylinski, Grover L. Waldrop

Faculty Publications

As the spread of antibiotic resistant bacteria steadily increases, there is an urgent need for new antibacterial agents. Because fatty acid synthesis is only used for membrane biogenesis in bacteria, the enzymes in this pathway are attractive targets for antibacterial agent development. Acetyl-CoA carboxylase catalyzes the committed and regulated step in fatty acid synthesis. In bacteria, the enzyme is composed of three distinct protein components: biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase. Fragment-based screening revealed that amino-oxazole inhibits biotin carboxylase activity and also exhibits antibacterial activity against Gram-negative organisms. In this report, we redesigned previously identified lead inhibitors to …

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Engineering Behavior And Characterization Of Biomass Ashes Using Geotechnical Measurement Techniques, Francisco Javier Grau Sacoto Jan 2014

Engineering Behavior And Characterization Of Biomass Ashes Using Geotechnical Measurement Techniques, Francisco Javier Grau Sacoto

LSU Master's Theses

Biomass, the organic material derived from plants or animals in a biological process, has rapidly become a topic of worldwide interest. The need to find new types of renewable energy sources has led to the use of natural materials as an economic, sustainable and environmental alternative. Biomass can be used to produce biofuel after a conversion process. The combustion of biomass matter –which is mainly produced in industrial plants- becomes biomass ash, which contains macronutrients and micronutrients. Currently, the recycling potential is wasted and most of the biomass ash is dumped without control or just disposed in landfills. The main …

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Louisiana Agriculture Winter, 2014 Jan 2014

Louisiana Agriculture Winter, 2014

Louisiana Agriculture

No abstract provided.

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A Comparative Study On The Risks Of Radiogenic Second Cancers And Cardiac Mortality In A Set Of Pediatric Medulloblastoma Patients Treated With Photon Or Proton Craniospinal Irradiation, Rui Zhang, Rebecca M. Howell, Phillip J. Taddei, Annelise Giebeler, Anita Mahajan, Wayne D. Newhauser Jan 2014

A Comparative Study On The Risks Of Radiogenic Second Cancers And Cardiac Mortality In A Set Of Pediatric Medulloblastoma Patients Treated With Photon Or Proton Craniospinal Irradiation, Rui Zhang, Rebecca M. Howell, Phillip J. Taddei, Annelise Giebeler, Anita Mahajan, Wayne D. Newhauser

Faculty Publications

Purpose: To compare the risks of radiogenic second cancers and cardiac mortality in 17 pediatric medulloblastoma patients treated with passively scattered proton or field-in-field photon craniospinal irradiation (CSI). Material/methods: Standard of care photon or proton CSI treatment plans were created for all 17 patients in a commercial treatment planning system (TPS) (Eclipse version 8.9; Varian Medical Systems, Palo Alto, CA) and prescription dose was 23.4 or 23.4 Gy (RBE) to the age specific target volume at 1.8 Gy/fraction. The therapeutic doses from proton and photon CSI plans were estimated from TPS. Stray radiation doses were determined from Monte Carlo simulations …

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Artemisia Extracts Activate Pparγ, Promote Adipogenesis, And Enhance Insulin Sensitivity In Adipose Tissue Of Obese Mice, Allison J. Richard, Thomas P. Burris, David Sanchez-Infantes, Yongjun Wang, David M. Ribnicky, Jacqueline M. Stephens Jan 2014

Artemisia Extracts Activate Pparγ, Promote Adipogenesis, And Enhance Insulin Sensitivity In Adipose Tissue Of Obese Mice, Allison J. Richard, Thomas P. Burris, David Sanchez-Infantes, Yongjun Wang, David M. Ribnicky, Jacqueline M. Stephens

Faculty Publications

Objective: Studies have shown that the inability of adipose tissue to properly expand during the obese state or respond to insulin can lead to metabolic dysfunction. Artemisia is a diverse group of plants that has a history of medicinal use. The aim of this study was to examine the ability of ethanolic extracts of Artemisia scoparia (SCO) and Artemisia santolinifolia (SAN) to modulate adipocyte development in cultured adipocytes and white adipose tissue (WAT) function invivo using a mouse model of diet-induced obesity. Method: Adipogenesis was assessed using Oil Red O staining and immunoblotting. A nuclear receptor specificity assay was used …

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Spatiotemporal Expression Of Trpm4 In The Mouse Cochlea, Mayumi Sakuraba, Junko Murata, Ryoichi Teruyama, Kazusaku Kamiya, Junji Yamaguchi, Hideyuki Okano, Yasuo Uchiyama, Katsuhisa Ikeda Jan 2014

Spatiotemporal Expression Of Trpm4 In The Mouse Cochlea, Mayumi Sakuraba, Junko Murata, Ryoichi Teruyama, Kazusaku Kamiya, Junji Yamaguchi, Hideyuki Okano, Yasuo Uchiyama, Katsuhisa Ikeda

Faculty Publications

The present study was conducted to elucidate the presence of the transient receptor potential cation channel subfamily M member 4, TRPM4, in the mouse inner ear. TRPM4 immunoreactivity (IR) was found in the cell body of inner hair cells (IHCs) in the organ of Corti in the apical side of marginal cells of the stria vascularis, in the apical portion of the dark cells of the vestibule, and in a subset of the type II neurons in the spiral ganglion. Subsequently, changes in the distribution and expression of TRPM4 in the inner ear during embryonic and postnatal developments were also …

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Syntheses And Functionalizations Of Porphyrin Macrocycles, Maria Da G.H. Vicente, Kevin M. Smith Jan 2014

Syntheses And Functionalizations Of Porphyrin Macrocycles, Maria Da G.H. Vicente, Kevin M. Smith

Faculty Publications

Porphyrin macrocycles have been the subject of intense study in the last century because they are widely distributed in nature, usually as metal complexes of either iron or magnesium. As such, they serve as the prosthetic groups in a wide variety of primary metabolites, such as hemoglobins, myoglobins, cytochromes, catalases, peroxidases, chlorophylls, and bacteriochlorophylls; these compounds have multiple applications in materials science, biology and medicine. This article describes current methodology for preparation of simple, symmetrical model porphyrins, as well as more complex protocols for preparation of unsymmetrically substituted porphyrin macrocycles similar to those found in nature. The basic chemical reactivity …

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Radiocarbon Distribution And The Effect Of Legacy In Lakes Of The Mcmurdo Dry Valleys, Antarctica, Peter T. Doran, Fabien Kenig, Jennifer Lawson Knoepfle, Jill A. Mikucki, W. Berry Lyons Jan 2014

Radiocarbon Distribution And The Effect Of Legacy In Lakes Of The Mcmurdo Dry Valleys, Antarctica, Peter T. Doran, Fabien Kenig, Jennifer Lawson Knoepfle, Jill A. Mikucki, W. Berry Lyons

Faculty Publications

The water of the ice-covered lakes of the McMurdo Dry Valleys is derived primarily from glacial melt streams and to a lesser extent permafrost seeps and subglacial outflow. The result is a mixture of radiocarbon ages that reflect both the end-member water source and the biogeochemical processing of waters as they migrate to the lake-water column. Samples were collected from various locations within perennially ice-covered Antarctic lakes and the streams that feed them, and they were analyzed for radiocarbon abundance of organic and inorganic carbon. Stream gradient and length were shown to affect the degree of equilibration of water with …

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Syntaxin Of Plant Proteins Syp123 And Syp132 Mediate Root Hair Tip Growth In Arabidopsis Thaliana, Mie Ichikawa, Tomoko Hirano, Kazuhiko Enami, Taylor Fuselier, Naohiro Kato, Chian Kwon, Boris Voigt, Paul Schulze-Lefert, František Baluška, Masa H. Sato Jan 2014

Syntaxin Of Plant Proteins Syp123 And Syp132 Mediate Root Hair Tip Growth In Arabidopsis Thaliana, Mie Ichikawa, Tomoko Hirano, Kazuhiko Enami, Taylor Fuselier, Naohiro Kato, Chian Kwon, Boris Voigt, Paul Schulze-Lefert, František Baluška, Masa H. Sato

Faculty Publications

Root hairs are fast-growing tubular protrusions on root epidermal cells that play important roles in water and nutrient uptake in plants. The tip-focused polarized growth of root hairs is accomplished by the secretion of newly synthesized materials to the tip via the polarized membrane trafficking mechanism. Here, we report the function of two different types of plasma membrane (PM) Qa-SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors), SYP123 and SYP132, in the growth of root hair in Arabidopsis. We found that SYP123, but not SYP132, localizes in the tip region of root hairs by recycling between the brefeldin A (BFA)-sensitive endosomes …

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Split Luciferase Complementation Assay To Detect Regulated Protein-Protein Interactions In Rice Protoplasts In A Large-Scale Format, Yukichi Fujikawa, Takahiro Nakanishi, Hiroko Kawakami, Kanako Yamasaki, Masa H. Sato, Hiroyuki Tsuji, Makoto Matsuoka, Naohiro Kato Jan 2014

Split Luciferase Complementation Assay To Detect Regulated Protein-Protein Interactions In Rice Protoplasts In A Large-Scale Format, Yukichi Fujikawa, Takahiro Nakanishi, Hiroko Kawakami, Kanako Yamasaki, Masa H. Sato, Hiroyuki Tsuji, Makoto Matsuoka, Naohiro Kato

Faculty Publications

© 2014 Fujikawa et al. Background: The rice interactome, in which a network of protein-protein interactions has been elucidated in rice, is a useful resource to identify functional modules of rice signal transduction pathways. Protein-protein interactions occur in cells in two ways, constitutive and regulative. While a yeast-based high-throughput method has been widely used to identify the constitutive interactions, a method to detect the regulated interactions is rarely developed for a large-scale analysis. Results: A split luciferase complementation assay was applied to detect the regulated interactions in rice. A transformation method of rice protoplasts in a 96-well plate was first …

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Social Status Differences Regulate The Serotonergic System Of A Cichlid Fish, Astatotilapia Burtoni, Jasmine L. Loveland, Natalie Uy, Karen P. Maruska, Russ E. Carpenter, Russell D. Fernald Jan 2014

Social Status Differences Regulate The Serotonergic System Of A Cichlid Fish, Astatotilapia Burtoni, Jasmine L. Loveland, Natalie Uy, Karen P. Maruska, Russ E. Carpenter, Russell D. Fernald

Faculty Publications

© 2014. Published by The Company of Biologists Ltd. Serotonin (5-HT) inhibits aggression and modulates aspects of sexual behaviour in many species, but the mechanisms responsible are not well understood. Here, we exploited the social dominance hierarchy of Astatotilapia burtoni to understand the role of the serotonergic system in long-term maintenance of social status. We identified three populations of 5-HT cells in dorsal and ventral periventricular pretectal nuclei (PPd, PPv), the nucleus of the paraventricular organ (PVO) and raphe. Dominant males had more 5-HT cells than subordinates in the raphe, but the size of these cells did not differ between …

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Folate In Demethylation: The Crystal Structure Of The Rat Dimethylglycine Dehydrogenase Complexed With Tetrahydrofolate, Zigmund Luka, Svetlana Pakhomova, Lioudmila V. Loukachevitch, Marcia E. Newcomer, Conrad Wagner Jan 2014

Folate In Demethylation: The Crystal Structure Of The Rat Dimethylglycine Dehydrogenase Complexed With Tetrahydrofolate, Zigmund Luka, Svetlana Pakhomova, Lioudmila V. Loukachevitch, Marcia E. Newcomer, Conrad Wagner

Faculty Publications

Dimethylglycine dehydrogenase (DMGDH) is a mammalian mitochondrial enzyme which plays an important role in the utilization of methyl groups derived from choline. DMGDH is a flavin containing enzyme which catalyzes the oxidative demethylation of dimethylglycine in vitro with the formation of sarcosine (N-methylglycine), hydrogen peroxide and formaldehyde. DMGDH binds tetrahydrofolate (THF) in vivo, which serves as an acceptor of formaldehyde and in the cell the product of the reaction is 5,10-methylenetetrahydrofolate instead of formaldehyde. To gain insight into the mechanism of the reaction we solved the crystal structures of the recombinant mature and precursor forms of rat DMGDH and DMGDH-THF …

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Crystal Structure Of The Histone Lysine Specific Demethylase Lsd1 Complexed With Tetrahydrofolate, Zigmund Luka, Svetlana Pakhomova, Lioudmila V. Loukachevitch, M. Wade Calcutt, Marcia E. Newcomer, Conrad Wagner Jan 2014

Crystal Structure Of The Histone Lysine Specific Demethylase Lsd1 Complexed With Tetrahydrofolate, Zigmund Luka, Svetlana Pakhomova, Lioudmila V. Loukachevitch, M. Wade Calcutt, Marcia E. Newcomer, Conrad Wagner

Faculty Publications

An important epigenetic modification is the methylation/demethylation of histone lysine residues. The first histone demethylase to be discovered was a lysine-specific demethylase 1, LSD1, a flavin containing enzyme which carries out the demethylation of di- and monomethyllysine 4 in histone H3. The removed methyl groups are oxidized to formaldehyde. This reaction is similar to those performed by dimethylglycine dehydrogenase and sarcosine dehydrogenase, in which protein-bound tetrahydrofolate (THF) was proposed to serve as an acceptor of the generated formaldehyde. We showed earlier that LSD1 binds THF with high affinity which suggests its possible participation in the histone demethylation reaction. In the …

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The Carbon Concentrating Mechanism In Chlamydomonas Reinhardtii: Finding The Missing Pieces, Nadine Jungnick, Yunbing Ma, Bratati Mukherjee, Julie C. Cronan, Dequantarius J. Speed, Susan M. Laborde, David J. Longstreth, James V. Moroney Jan 2014

The Carbon Concentrating Mechanism In Chlamydomonas Reinhardtii: Finding The Missing Pieces, Nadine Jungnick, Yunbing Ma, Bratati Mukherjee, Julie C. Cronan, Dequantarius J. Speed, Susan M. Laborde, David J. Longstreth, James V. Moroney

Faculty Publications

The photosynthetic, unicellular green alga, Chlamydomonas reinhardtii, lives in environments that often contain low concentrations of CO2 and HCO3-, the utilizable forms of inorganic carbon (Ci). C. reinhardtii possesses a carbon concentrating mechanism (CCM) which can provide suitable amounts of Ci for growth and development. This CCM is induced when the CO2 concentration is at air levels or lower and is comprised of a set of proteins that allow the efficient uptake of Ci into the cell as well as its directed transport to the site where Rubisco fixes CO2 into biomolecules. While several components of the CCM have been …

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The Arabidopsis Siamese-Related Cyclin-Dependent Kinase Inhibitors Smr5 And Smr7 Regulate The Dna Damage Checkpoint In Response To Reactive Oxygen Species, Dalong Yi, Claire Lessa Alvim Kamei, Toon Cools, Sandy Vanderauwera, Naoki Takahashi, Yoko Okushima, Thomas Eekhout, Kaoru Okamoto Yoshiyama, John Larkin, Hilde Van Den Daele, Phillip Conklin, Anne Britt, Masaaki Umeda, Lieven De Veylder Jan 2014

The Arabidopsis Siamese-Related Cyclin-Dependent Kinase Inhibitors Smr5 And Smr7 Regulate The Dna Damage Checkpoint In Response To Reactive Oxygen Species, Dalong Yi, Claire Lessa Alvim Kamei, Toon Cools, Sandy Vanderauwera, Naoki Takahashi, Yoko Okushima, Thomas Eekhout, Kaoru Okamoto Yoshiyama, John Larkin, Hilde Van Den Daele, Phillip Conklin, Anne Britt, Masaaki Umeda, Lieven De Veylder

Faculty Publications

Whereas our knowledge about the diverse pathways aiding DNA repair upon genome damage is steadily increasing, little is known about the molecular players that adjust the plant cell cycle in response to DNA stress. By a meta-analysis of DNA stress microarray data sets, three family members of the SIAMESE/SIAMESE-RELATED (SIM/SMR) class of cyclin-dependent kinase inhibitors were discovered that react strongly to genotoxicity. Transcriptional reporter constructs corroborated specific and strong activation of the three SIM/SMR genes in the meristems upon DNA stress, whereas overexpression analysis confirmed their cell cycle inhibitory potential. In agreement with being checkpoint regulators, SMR5 and SMR7 knockout …

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Molecular And Biogeochemical Evidence For Methane Cycling Beneath The Western Margin Of The Greenland Ice Sheet, Markus Dieser, Erik L.J.E. Broemsen, Karen A. Cameron, Gary M. King, Amanda Achberger, Kyla Choquette, Birgit Hagedorn, Ron Sletten, Karen Junge, Brent C. Christner Jan 2014

Molecular And Biogeochemical Evidence For Methane Cycling Beneath The Western Margin Of The Greenland Ice Sheet, Markus Dieser, Erik L.J.E. Broemsen, Karen A. Cameron, Gary M. King, Amanda Achberger, Kyla Choquette, Birgit Hagedorn, Ron Sletten, Karen Junge, Brent C. Christner

Faculty Publications

© 2014 International Society for Microbial Ecology All rights reserved. Microbial processes that mineralize organic carbon and enhance solute production at the bed of polar ice sheets could be of a magnitude sufficient to affect global elemental cycles. To investigate the biogeochemistry of a polar subglacial microbial ecosystem, we analyzed water discharged during the summer of 2012 and 2013 from Russell Glacier, a land-terminating outlet glacier at the western margin of the Greenland Ice Sheet. The molecular data implied that the most abundant and active component of the subglacial microbial community at these marginal locations were bacteria within the order …

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Myo-Inositol And Phytate Are Toxic To Formosan Subterranean Termites (Isoptera: Rhinotermitidae), Lucas Veillon, Jared Bourgeois, Amanda Leblanc, Gregg Henderson, Brian D. Marx, Syed Muniruzzaman, Roger A. Laine Jan 2014

Myo-Inositol And Phytate Are Toxic To Formosan Subterranean Termites (Isoptera: Rhinotermitidae), Lucas Veillon, Jared Bourgeois, Amanda Leblanc, Gregg Henderson, Brian D. Marx, Syed Muniruzzaman, Roger A. Laine

Faculty Publications

© 2014 Entomological Society of America. Several rare and common monosaccharides were screened for toxic effects on the Formosan subterranean termite, Coptotermes formosanus Shiraki, with the aim of identifying environmentally friendly termiticides. myo-Inositol and phytic acid, which are nontoxic to mammals, were identified as potential termite control compounds. Feeding bioassays with termite workers, where both compounds were supplied on filter paper in concentrations from 160.2 to 1,281.7μg/mm3, showed concentration-dependent toxicity within 2 wk. Interestingly myo-inositol was nontoxic when administered to termites in agar (40 mg/ml) in the absence of a cellulosic food source, an unexplained phenomenon. In addition, decreased populations …

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Strong Natural Selection On Juveniles Maintains A Narrow Adult Hybrid Zone In A Broadcast Spawner, Carlos Prada, Michael E. Hellberg Jan 2014

Strong Natural Selection On Juveniles Maintains A Narrow Adult Hybrid Zone In A Broadcast Spawner, Carlos Prada, Michael E. Hellberg

Faculty Publications

© 2014 by The University of Chicago. Natural selection can maintain and help form species across different habitats, even when dispersal is high. Selection against inferior migrants (immigrant inviability) acts when locally adapted populations suffer high mortality on dispersal to unsuitable habitats. Habitat-specific populations undergoing divergent selection via immigrant inviability should thus show (1) a change in the ratio of adapted to nonadapted individuals among age/size classes and (2) a cline (defined by the environmental gradient) as selection counterbalances migration. Here we examine the frequencies of two depthsegregated lineages in juveniles and adults of a Caribbean octocoral, Eunicea flexuosa. Distributions …

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Evaluating Summary Statistics Used To Test For Incomplete Lineage Sorting: Mito-Nuclear Discordance In The Reef Sponge Callyspongia Vaginalis, Melissa B. Debiasse, Bradley J. Nelson, Michael E. Hellberg Jan 2014

Evaluating Summary Statistics Used To Test For Incomplete Lineage Sorting: Mito-Nuclear Discordance In The Reef Sponge Callyspongia Vaginalis, Melissa B. Debiasse, Bradley J. Nelson, Michael E. Hellberg

Faculty Publications

Conflicting patterns of population differentiation between the mitochondrial and nuclear genomes (mito-nuclear discordance) have become increasingly evident as multilocus data sets have become easier to generate. Incomplete lineage sorting (ILS) of nucDNA is often implicated as the cause of such discordance, stemming from the large effective population size of nucDNA relative to mtDNA. However, selection, sex-biased dispersal and historical demography can also lead to mito-nuclear discordance. Here, we compare patterns of genetic diversity and subdivision for six nuclear protein-coding gene regions to those for mtDNA in a common Caribbean coral reef sponge, Callyspongia vaginalis, along the Florida reef tract. We …

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Latitudinal Variation Of Freeze Tolerance In Intertidal Marine Snails Of The Genus Melampus (Gastropoda: Ellobiidae), A. B. Dennis, S. H. Loomis, M. E. Hellberg Jan 2014

Latitudinal Variation Of Freeze Tolerance In Intertidal Marine Snails Of The Genus Melampus (Gastropoda: Ellobiidae), A. B. Dennis, S. H. Loomis, M. E. Hellberg

Faculty Publications

Low temperatures limit the poleward distribution of many species such that the expansion of geographic range can only be accomplished via evolutionary innovation. We have tested for physiological differences among closely related species to determine whether their poleward latitudinal ranges are limited by tolerance to cold. We measured lower temperature tolerance (LT50) among a group of intertidal pulmonate snails from six congeneric species and nine locales. Differences in tolerance are placed in the context of a molecular phylogeny based on one mitochondrial (cytochrome oxidase subunit I) and two nuclear (histone 3 and a mitochondrial phosphate carrier protein) markers. Temperate species …

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The Hoosier Cavefish, A New And Endangered Species (Amblyopsidae, Amblyopsis) From The Caves Of Southern Indiana, Prosanta Chakrabarty, Jacques A. Prejean, Matthew L. Niemiller Jan 2014

The Hoosier Cavefish, A New And Endangered Species (Amblyopsidae, Amblyopsis) From The Caves Of Southern Indiana, Prosanta Chakrabarty, Jacques A. Prejean, Matthew L. Niemiller

Faculty Publications

We describe a new species of amblyopsid cavefish (Percopsiformes: Amblyopsidae) in the genus Amblyopsis from subterranean habitats of southern Indiana, USA. The Hoosier Cavefish, Amblyopsis hoosieri sp. n., is distinguished from A. spelaea, its only congener, based on genetic, geographic, and morphological evidence. Several morphological features distinguish the new species, including a much plumper, Bibendumlike wrinkled body with rounded fins, and the absence of a premature stop codon in the gene rhodopsin. This is the first new cavefish species described from the United States in 40 years and exemplifies how molecular data can alert us to the presence of otherwise …

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Specimen Collection: An Essential Tool, L. A. Rocha, A. Aleixo, G. Allen, F. Almeda, C. C. Baldwin, M. V.L. Barclay, J. M. Bates, A. M. Bauer, F. Benzoni, C. M. Berns, M. L. Berumen, D. C. Blackburn, S. Blum, F. Bolaños, R. C.K. Bowie, R. Britz, R. M. Brown, C. D. Cadena, K. Carpenter, L. M. Ceríaco, P. Chakrabarty, G. Chaves, J. H. Choat, K. D. Clements, B. B. Collette, A. Collins, J. Coyne, J. Cracraft, T. Daniel, M. R. De Carvalho, K. De Queiroz, F. Di Dario, R. Drewes Jan 2014

Specimen Collection: An Essential Tool, L. A. Rocha, A. Aleixo, G. Allen, F. Almeda, C. C. Baldwin, M. V.L. Barclay, J. M. Bates, A. M. Bauer, F. Benzoni, C. M. Berns, M. L. Berumen, D. C. Blackburn, S. Blum, F. Bolaños, R. C.K. Bowie, R. Britz, R. M. Brown, C. D. Cadena, K. Carpenter, L. M. Ceríaco, P. Chakrabarty, G. Chaves, J. H. Choat, K. D. Clements, B. B. Collette, A. Collins, J. Coyne, J. Cracraft, T. Daniel, M. R. De Carvalho, K. De Queiroz, F. Di Dario, R. Drewes

Faculty Publications

No abstract provided.

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Hepatitis E Antibodies In Laboratory Rabbits From 2 Us Vendors, Leslie Birke, Stephania A. Cormier, Dahui You, Rhett W. Stout, Christian Clement, Merlin Johnson, Hilary Thompson Jan 2014

Hepatitis E Antibodies In Laboratory Rabbits From 2 Us Vendors, Leslie Birke, Stephania A. Cormier, Dahui You, Rhett W. Stout, Christian Clement, Merlin Johnson, Hilary Thompson

Faculty Publications

We tested laboratory rabbits from 2 US vendors for antibodies against hepatitis E virus (HEV); Seroprevalences were 40% and 50%. Retrospective analysis of an ocular herpes simplex 1 experiment demonstrated that HEV seropositivity had no effect on experiment outcome. HEV probably is widespread in research rabbits, but effects on research remain unknown.

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Metacom: An R Package For The Analysis Of Metacommunity Structure, Tad Dallas Jan 2014

Metacom: An R Package For The Analysis Of Metacommunity Structure, Tad Dallas

Faculty Publications

Metacommunity theory is an extension of metapopulation theory with the goal of understanding how ecological communities vary through space and time. One off-shoot of metacommunity theory deals with understanding how community structure varies along biotic or environmental gradients. The Elements of Metacommunity Structure framework is a three-tiered analysis of metacommunity structure that enables the user to identify metacommunity properties that arise in site-by-species incidence matrices. These properties can then be related to underlying variables that influence species distributions. The EMS framework is now implemented in metacom, an open source R package that allows for the analysis and plotting of metacommunities. …

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Copper Binding In Isca Inhibits Iron-Sulphur Cluster Assembly In Escherichia Coli, Guoqiang Tan, Zishuo Cheng, Yilin Pang, Aaron P. Landry, Jianghui Li, Jianxin Lu, Huangen Ding Jan 2014

Copper Binding In Isca Inhibits Iron-Sulphur Cluster Assembly In Escherichia Coli, Guoqiang Tan, Zishuo Cheng, Yilin Pang, Aaron P. Landry, Jianghui Li, Jianxin Lu, Huangen Ding

Faculty Publications

© 2014 John Wiley & Sons Ltd. Among the iron-sulphur cluster assembly proteins encoded by gene cluster iscSUA-hscBA-fdx in Escherichia coli, IscA has a unique and strong iron binding activity and can provide iron for iron-sulphur cluster assembly in proteins in vitro. Deletion of IscA and its paralogue SufA results in an E. coli mutant that fails to assemble [4Fe-4S] clusters in proteins under aerobic conditions, suggesting that IscA has a crucial role for iron-sulphur cluster biogenesis. Here we report that among the iron-sulphur cluster assembly proteins, IscA also has a strong and specific binding activity for Cu(I) in vivo …

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The N-Terminal Domain Of Human Dna Helicase Rtel1 Contains A Redox Active Iron-Sulfur Cluster, Aaron P. Landry, Huangen Ding Jan 2014

The N-Terminal Domain Of Human Dna Helicase Rtel1 Contains A Redox Active Iron-Sulfur Cluster, Aaron P. Landry, Huangen Ding

Faculty Publications

© 2014 Aaron P. Landry and Huangen Ding. Human telomere length regulator Rtel1 is a superfamily II DNA helicase and is essential for maintaining proper length of telomeres in chromosomes. Here we report that the N-terminal domain of human Rtel1 (RtelN) expressed in Escherichia coli cells produces a protein that contains a redox active iron-sulfur cluster with the redox midpoint potential of -248 ± 10 mV (pH 8.0). The iron-sulfur cluster in RtelN is sensitive to hydrogen peroxide and nitric oxide, indicating that reactive oxygen/nitrogen species may modulate the DNA helicase activity of Rtel1 via modification of its iron-sulfur cluster. …

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Developing Ethread Pipeline Using Saga-Pilot Abstraction For Large-Scale Structural Bioinformatics, Anjani Ragothaman, Sairam Chowdary Boddu, Nayong Kim, Wei Feinstein, Michal Brylinski, Shantenu Jha, Joohyun Kim Jan 2014

Developing Ethread Pipeline Using Saga-Pilot Abstraction For Large-Scale Structural Bioinformatics, Anjani Ragothaman, Sairam Chowdary Boddu, Nayong Kim, Wei Feinstein, Michal Brylinski, Shantenu Jha, Joohyun Kim

Faculty Publications

While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function. However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. To leverage its utility, we have developed a pipeline for eThread - a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. We employ a pilot-based approach that supports seamless data and task-level parallelism and manages …

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Ematchsite: Sequence Order-Independent Structure Alignments Of Ligand Binding Pockets In Protein Models, Michal Brylinski Jan 2014

Ematchsite: Sequence Order-Independent Structure Alignments Of Ligand Binding Pockets In Protein Models, Michal Brylinski

Faculty Publications

© 2014 Michal Brylinski. Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing …

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