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Temperature Responses Of Carbon Monoxide And Hydrogen Uptake By Vegetated And Unvegetated Volcanic Cinders, Caitlin E. King, Gary M. King Aug 2012

Temperature Responses Of Carbon Monoxide And Hydrogen Uptake By Vegetated And Unvegetated Volcanic Cinders, Caitlin E. King, Gary M. King

Faculty Publications

Ecosystem succession on a large deposit of volcanic cinders emplaced on Kilauea Volcano in 1959 has resulted in a mosaic of closed-canopy forested patches and contiguous unvegetated patches. Unvegetated and unshaded surface cinders (Bare) experience substantial diurnal temperature oscillations ranging from moderate (16°C) to extreme (55°C) conditions. The surface material of adjacent vegetated patches (Canopy) experiences much smaller fluctuations (14-25°C) due to shading. To determine whether surface material from these sites showed adaptations by carbon monoxide (CO) and hydrogen (H2) consumption to changes in ambient temperature regimes accompanying succession, we measured responses of CO and H2 uptake to short-term variations …

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Conversion Of Human 5-Lipoxygenase To A 15-Lipoxygenase By A Point Mutation To Mimic Phosphorylation At Serine-663, Nathaniel C. Gilbert, Zhe Rui, David B. Neau, Maria T. Waight, Sue G. Bartlett, William E. Boeglin, Alan R. Brash, Marcia E. Newcomer Aug 2012

Conversion Of Human 5-Lipoxygenase To A 15-Lipoxygenase By A Point Mutation To Mimic Phosphorylation At Serine-663, Nathaniel C. Gilbert, Zhe Rui, David B. Neau, Maria T. Waight, Sue G. Bartlett, William E. Boeglin, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

The enzyme 5-lipoxygenase (5-LOX) initiates biosynthesis of the proinflammatory leukotriene lipid mediators and, together with 15-LOX, is also required for synthesis of the anti-inflammatory lipoxins. The catalytic activity of 5-LOX is regulated through multiple mechanisms, including Ca 2+-targeted membrane binding and phosphorylation at specific serine residues. To investigate the consequences of phosphorylation at S663, we mutated the residue to the phosphorylation mimic Asp, providing a homogenous preparation suitable for catalytic and structural studies. The S663D enzyme exhibits robust 15-LOX activity, as determined by spectrophotometric and HPLC analyses, with only traces of 5-LOX activity remaining; synthesis of the anti-inflammatory lipoxin A4 …

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Multiple Independent Origins Of Mitochondrial Control Region Duplications In The Order Psittaciformes, Erin E. Schirtzinger, Erika S. Tavares, Lauren A. Gonzales, Jessica R. Eberhard, Cristina Y. Miyaki, Juan J. Sanchez, Alexis Hernandez, Heinrich Müeller, Gary R. Graves, Robert C. Fleischer, Timothy F. Wright Aug 2012

Multiple Independent Origins Of Mitochondrial Control Region Duplications In The Order Psittaciformes, Erin E. Schirtzinger, Erika S. Tavares, Lauren A. Gonzales, Jessica R. Eberhard, Cristina Y. Miyaki, Juan J. Sanchez, Alexis Hernandez, Heinrich Müeller, Gary R. Graves, Robert C. Fleischer, Timothy F. Wright

Faculty Publications

Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and …

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Improving The Scalability Of Parallel N-Body Applications With An Event-Driven Constraint-Based Execution Model, Chirag Dekate, Matthew Anderson, Maciej Brodowicz, Hartmut Kaiser, Bryce Adelstein-Lelbach, Thomas Sterling Aug 2012

Improving The Scalability Of Parallel N-Body Applications With An Event-Driven Constraint-Based Execution Model, Chirag Dekate, Matthew Anderson, Maciej Brodowicz, Hartmut Kaiser, Bryce Adelstein-Lelbach, Thomas Sterling

Faculty Publications

The scalability and efficiency of graph applications are significantly constrained by conventional systems and their supporting programming models. Technology trends such as multicore, manycore, and heterogeneous system architectures are introducing further challenges and possibilities for emerging application domains such as graph applications. This paper explores the parallel execution of graphs that are generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The workloads are expressed using the semantics of an exascale computing execution model called ParalleX. For comparison, results using conventional execution model semantics are also presented. We find improved load balancing during runtime and automatic parallelism discovery by using …

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Tracking The Emergence Of A New Breed Using 49,034 Snp In Sheep, James W. Kijas, James E. Miller, Tracy Hadfield, Russell Mcculloch, Elsa Garcia-Gamez, Laercio R. Neto, Noelle Cockett Jul 2012

Tracking The Emergence Of A New Breed Using 49,034 Snp In Sheep, James W. Kijas, James E. Miller, Tracy Hadfield, Russell Mcculloch, Elsa Garcia-Gamez, Laercio R. Neto, Noelle Cockett

Faculty Publications

Domestic animals are unique in that they have been organised into managed populations called breeds. The strength of genetic divergence between breeds may vary dependent on the age of the breed, the scenario under which it emerged and the strength of reproductive isolation it has from other breeds. In this study, we investigated the Gulf Coast Native breed of sheep to determine if it contains lines of animals that are sufficiently divergent to be considered separate breeds. Allele sharing and principal component analysis (PCA) using nearly 50,000 SNP loci revealed a clear genetic division that corresponded with membership of either …

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Fission Yeast Dma1 Requires Ring Domain Dimerization For Its Ubiquitin Ligase Activity And Mitotic Checkpoint Function, Alyssa E. Johnson, Scott E. Collier, Melanie D. Ohi, Kathleen L. Gould Jul 2012

Fission Yeast Dma1 Requires Ring Domain Dimerization For Its Ubiquitin Ligase Activity And Mitotic Checkpoint Function, Alyssa E. Johnson, Scott E. Collier, Melanie D. Ohi, Kathleen L. Gould

Faculty Publications

In fission yeast (Schizosaccharomyces pombe), the E3 ubiquitin ligase Dma1 delays cytokinesis if chromosomes are not properly attached to the mitotic spindle.Dma1contains a C-terminal RING domain, and we have found that the Dma1 RING domain forms a stable homodimer. Although the RING domain is required for dimerization, residues in the C-terminal tail are also required to help form or stabilize the dimeric structure because mutation of specific residues in this region disrupts Dma1 dimerization. Further analyses showed that Dma1 dimerization is required for proper localization at spindle pole bodies and the cell division site, E3 ligase activity, and mitotic checkpoint …

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Comparison Of Therapeutic Dosimetric Data From Passively Scattered Proton And Photon Craniospinal Irradiations For Medulloblastoma, Rebecca M. Howell, Annelise Giebeler, Wendi Koontz-Raisig, Anita Mahajan, Carol J. Etzel, Anthony M. D'Amelio, Kenneth L. Homann, Wayne D. Newhauser Jul 2012

Comparison Of Therapeutic Dosimetric Data From Passively Scattered Proton And Photon Craniospinal Irradiations For Medulloblastoma, Rebecca M. Howell, Annelise Giebeler, Wendi Koontz-Raisig, Anita Mahajan, Carol J. Etzel, Anthony M. D'Amelio, Kenneth L. Homann, Wayne D. Newhauser

Faculty Publications

Background: For many decades, the standard of care radiotherapy regimen for medulloblastoma has been photon (megavoltage x-rays) craniospinal irradiation (CSI). The late effects associated with CSI are well-documented in the literature and are in-part attributed to unwanted dose to healthy tissue. Recently, there is growing interest in using proton therapy for CSI in pediatric and adolescent patients to reduce this undesirable dose. Previous comparisons of dose to target and non-target organs from conventional photon CSI and passively scattered proton CSI have been limited to small populations (n ≤ 3) and have not considered the use of age-dependent target volumes in …

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Insights Into Salt Tolerance From The Genome Of Thellungiella Salsuginea, Hua Jun Wu, Zhonghui Zhang, Jun Yi Wang, Dong Ha Oh, Maheshi Dassanayake, Binghang Liu, Quanfei Huang, Hai Xi Sun, Ran Xia, Yaorong Wu, Yi Nan Wang, Zhao Yang, Yang Liu, Wanke Zhang, Huawei Zhang, Jinfang Chu, Cunyu Yan, Shuang Fang, Jinsong Zhang, Yiqin Wang, Fengxia Zhang, Guodong Wang, Sang Yeol Lee, John M. Cheeseman, Bicheng Yang, Bo Li, Jiumeng Min, Linfeng Yang, Jun Wang, Chengcai Chu, Shou Yi Chen, Hans J. Bohnert, Jian Kang Zhu Jul 2012

Insights Into Salt Tolerance From The Genome Of Thellungiella Salsuginea, Hua Jun Wu, Zhonghui Zhang, Jun Yi Wang, Dong Ha Oh, Maheshi Dassanayake, Binghang Liu, Quanfei Huang, Hai Xi Sun, Ran Xia, Yaorong Wu, Yi Nan Wang, Zhao Yang, Yang Liu, Wanke Zhang, Huawei Zhang, Jinfang Chu, Cunyu Yan, Shuang Fang, Jinsong Zhang, Yiqin Wang, Fengxia Zhang, Guodong Wang, Sang Yeol Lee, John M. Cheeseman, Bicheng Yang, Bo Li, Jiumeng Min, Linfeng Yang, Jun Wang, Chengcai Chu, Shou Yi Chen, Hans J. Bohnert, Jian Kang Zhu

Faculty Publications

Thellungiella salsuginea, a close relative of Arabidopsis, represents an extremophile model for abiotic stress tolerance studies. We present the draft sequence of the T. salsuginea genome, assembled based on ∼134-fold coverage to seven chromosomes with a coding capacity of at least 28,457 genes. This genome provides resources and evidence about the nature of defense mechanisms constituting the genetic basis underlying plant abiotic stress tolerance. Comparative genomics and experimental analyses identified genes related to cation transport, abscisic acid signaling, and wax production prominent in T. salsuginea as possible contributors to its success in stressful environments.

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Tfiiic Localizes Budding Yeast Etc Sites To The Nuclear Periphery, Shin Ichiro Hiraga, Sotirios Botsios, David Donze, Anne D. Donaldson Jul 2012

Tfiiic Localizes Budding Yeast Etc Sites To The Nuclear Periphery, Shin Ichiro Hiraga, Sotirios Botsios, David Donze, Anne D. Donaldson

Faculty Publications

Chromatin function requires specific three-dimensional architectures of chromosomes. We investigated whether Saccharomyces cerevisiae extra TFIIIC (ETC) sites, which bind the TFIIIC transcription factor but do not recruit RNA polymerase III, show specific intranuclear positioning. We show that six of the eight known S. cerevisiae ETC sites localize predominantly at the nuclear periphery, and that ETC sites retain their tethering function when moved to a new chromosomal location. Several lines of evidence indicate that TFIIIC is central to the ETC peripheral localization mechanism. Mutating or deleting the TFIIIC-binding consensus ablated ETC -site peripheral positioning, and inducing degradation of the TFIIIC subunit …

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Mapping The Biosphere: Exploring Species To Understand The Origin, Organization And Sustainability Of Biodiversity, Q. D. Wheeler, S. Knapp, D. W. Stevenson, J. Stevenson, S. D. Blum, B. M. Boom, G. G. Borisy, J. L. Buizer, M. R. De Carvalho, A. Cibrian, M. J. Donoghue, V. Doyle, E. M. Gerson, C. H. Graham, P. Graves, S. J. Graves, R. P. Guralnick, A. L. Hamilton, J. Hanken, W. Law, D. L. Lipscomb, T. E. Lovejoy, H. Miller, J. S. Miller, S. Naeem, M. J. Novacek, L. M. Page, N. I. Platnick, H. Porter-Morgan, P. H. Raven, M. A. Solis, A. G. Valdecasas, S. Van Der Leeuw Jul 2012

Mapping The Biosphere: Exploring Species To Understand The Origin, Organization And Sustainability Of Biodiversity, Q. D. Wheeler, S. Knapp, D. W. Stevenson, J. Stevenson, S. D. Blum, B. M. Boom, G. G. Borisy, J. L. Buizer, M. R. De Carvalho, A. Cibrian, M. J. Donoghue, V. Doyle, E. M. Gerson, C. H. Graham, P. Graves, S. J. Graves, R. P. Guralnick, A. L. Hamilton, J. Hanken, W. Law, D. L. Lipscomb, T. E. Lovejoy, H. Miller, J. S. Miller, S. Naeem, M. J. Novacek, L. M. Page, N. I. Platnick, H. Porter-Morgan, P. H. Raven, M. A. Solis, A. G. Valdecasas, S. Van Der Leeuw

Faculty Publications

The time is ripe for a comprehensive mission to explore and document Earth's species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is …

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Radiation Reaction: General Approach And Applications, Especially To Electrodynamics, R. F. O'Connell Jul 2012

Radiation Reaction: General Approach And Applications, Especially To Electrodynamics, R. F. O'Connell

Faculty Publications

Radiation reaction (but, more generally, fluctuations and dissipation) occurs when a system interacts with a heat bath, a particular case being the interaction of an electron with the radiation field. We have developed a general theory for the case of a quantum particle in a general potential (but, in more detail, an oscillator potential) coupled to an arbitrary heat bath at arbitrary temperature, and in an external time-dependent c-number field. The results may be applied to a large variety of problems in physics but we concentrate by showing in detail the application to the blackbody radiation heat bath, giving an …

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Controlling A Master Switch Of Adipocyte Development And Insulin Sensitivity: Covalent Modifications Of Pparγ, Z. Elizabeth Floyd, Jacqueline M. Stephens Jul 2012

Controlling A Master Switch Of Adipocyte Development And Insulin Sensitivity: Covalent Modifications Of Pparγ, Z. Elizabeth Floyd, Jacqueline M. Stephens

Faculty Publications

Adipocytes are highly specialized cells that play a central role in lipid homeostasis and the maintenance of energy balance. Obesity, an excessive accumulation of adipose tissue, is a major risk factor for the development of Type 2 diabetes mellitus (T2DM), cardiovascular disease, and hypertension. A variety of studies suggest that obesity and T2DM can be linked to a breakdown in the regulatory mechanisms that control the expression and transcriptional activity of PPARγ. PPARγ is a nuclear hormone receptor that functions as a master switch in controlling adipocyte differentiation and development. Also important in controlling glucose homeostasis and insulin sensitivity, PPARγ …

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Genome-Wide Studies Of The Multi-Zinc Finger Drosophila Suppressor Of Hairy-Wing Protein In The Ovary, Alexey A. Soshnev, Bing He, Ryan M. Baxley, Nan Jiang, Craig M. Hart, Kai Tan, Pamela K. Geyer Jul 2012

Genome-Wide Studies Of The Multi-Zinc Finger Drosophila Suppressor Of Hairy-Wing Protein In The Ovary, Alexey A. Soshnev, Bing He, Ryan M. Baxley, Nan Jiang, Craig M. Hart, Kai Tan, Pamela K. Geyer

Faculty Publications

The Drosophila Suppressor of Hairy-wing [Su(Hw)] protein is a globally expressed, multi-zinc finger (ZnF) DNA-binding protein. Su(Hw) forms a classic insulator when bound to the gypsy retrotransposon and is essential for female germline development. These functions are genetically separable, as exemplified by Su(Hw)f that carries a defective ZnF10, causing a loss of insulator but not germline function. Here, we completed the first genome-wide analysis of Su(Hw)-binding sites (SBSs) in the ovary, showing that tissue-specific binding is not responsible for the restricted developmental requirements for Su(Hw). Mapping of ovary Su(Hw)f SBSs revealed that female fertility requires binding to only one third …

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Can A Semiochemical-Based Trapping Method Diminish Damage Levels Caused By Rhabdoscelus Obscurus (Coleoptera: Curculionidae)?, G. V.P. Reddy, P. Shi, C. R. Mann, D. M.H. Mantanona, Z. Dong Jul 2012

Can A Semiochemical-Based Trapping Method Diminish Damage Levels Caused By Rhabdoscelus Obscurus (Coleoptera: Curculionidae)?, G. V.P. Reddy, P. Shi, C. R. Mann, D. M.H. Mantanona, Z. Dong

Faculty Publications

The New Guinea sugarcane weevil, Rhabdoscelus obscurus (Boisduval) (Coleoptera: Curculionidae), is an important pest of palms, ornamental nurseries, and sugarcane in the Pacific Islands. Without effective control methods, R. obscurus populations can cause major or complete loss of palm production in Guam and other Micronesian Islands. Moreover, R. obscurus has inflicted severe attacks on coconut trees on Guam. The role of monitoring is important in judging the dynamics of R. obscurus and recording area wide population trends. There is no precise research information available on the trap catch threshold levels relative to the damage caused by R. obscurus. Here we …

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Larval Mosquito Habitat Utilization And Community Dynamics Of Aedes Albopictus And Aedes Japonicus (Diptera: Culicidae), Kristen Bartlett-Healy, Isik Unlu, Peter Obenauer, Tony Hughes, Sean Healy, Taryn Crepeau, Ary Farajollahi, Banu Kesavaraju, Dina Fonseca, George Schoeler, Randy Gaugler, Daniel Strickman Jul 2012

Larval Mosquito Habitat Utilization And Community Dynamics Of Aedes Albopictus And Aedes Japonicus (Diptera: Culicidae), Kristen Bartlett-Healy, Isik Unlu, Peter Obenauer, Tony Hughes, Sean Healy, Taryn Crepeau, Ary Farajollahi, Banu Kesavaraju, Dina Fonseca, George Schoeler, Randy Gaugler, Daniel Strickman

Faculty Publications

Aedes albopictus (Skuse) and Ae. japonicus (Theobald) are important container-inhabiting mosquitoes that transmit disease agents, outcompete native species, and continue to expand their range in the United States. Both species deposit eggs in natural and artificial containers and thrive in peridomestic environments. The goal of our study was to examine the types and characteristics of containers that are most productive for these species in the northeastern United States. In total, 306 containers were sampled in urban, suburban, and rural areas of New Jersey. Multiple biotic and abiotic factors were recorded in an attempt to identify variables associated with the productivity …

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Spheres, Jülichs High-Flux Neutron Backscattering Spectrometer At Frm Ii, Joachim Wuttke, Alfred Budwig, Matthias Drochner, Hans Kämmerling, Franz Joseph Kayser, Harald Kleines, Vladimir Ossovyi, Luis Carlos Pardo, Michael Prager, Dieter Richter, Gerald J. Schneider, Harald Schneider, Simon Staringer Jul 2012

Spheres, Jülichs High-Flux Neutron Backscattering Spectrometer At Frm Ii, Joachim Wuttke, Alfred Budwig, Matthias Drochner, Hans Kämmerling, Franz Joseph Kayser, Harald Kleines, Vladimir Ossovyi, Luis Carlos Pardo, Michael Prager, Dieter Richter, Gerald J. Schneider, Harald Schneider, Simon Staringer

Faculty Publications

SPHERES is a third-generation neutron backscattering spectrometer, located at the 20MW German neutron source FRM II and operated by the Jülich Centre for Neutron Science. It offers an energy resolution (fwhm) better than 0.65 μeV, a dynamic range of ± 31 μeV, and a signal-to-noise ratio of up to 1750:1. © 2012 American Institute of Physics.

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Assessment Of The Mass, Length, Center Of Mass, And Principal Moment Of Inertia Of Body Segments In Adult Males Of The Brown Anole (Anolis Sagrei) And Green, Or Carolina, Anole (Anolis Carolinensis), Pierre Legreneur, Dominique G. Homberger, Vincent Bels Jul 2012

Assessment Of The Mass, Length, Center Of Mass, And Principal Moment Of Inertia Of Body Segments In Adult Males Of The Brown Anole (Anolis Sagrei) And Green, Or Carolina, Anole (Anolis Carolinensis), Pierre Legreneur, Dominique G. Homberger, Vincent Bels

Faculty Publications

This study provides a morphometric data set of body segments that are biomechanically relevant for locomotion in two ecomorphs of adult male anoles, namely, the trunk-ground Anolis sagrei and the trunk-crown Anolis carolinensis. For each species, 10 segments were characterized, and for each segment, length, mass, location of the center of mass, and radius of gyration were measured or calculated, respectively. The radii of gyration were computed from the moments of inertia by using the double swing pendulum method. The trunk-ground A. sagrei has relatively longer and stockier hindlimbs and forelimbs with smaller body than A. carolinensis. These differences between …

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Salt Stress Induced Variation In Dna Methylation Pattern And Its Influence On Gene Expression In Contrasting Rice Genotypes, Ratna Karan, Teresa Deleon, Hanamareddy Biradar, Prasanta K. Subudhi Jun 2012

Salt Stress Induced Variation In Dna Methylation Pattern And Its Influence On Gene Expression In Contrasting Rice Genotypes, Ratna Karan, Teresa Deleon, Hanamareddy Biradar, Prasanta K. Subudhi

Faculty Publications

Background: Salinity is a major environmental factor limiting productivity of crop plants including rice in which wide range of natural variability exists. Although recent evidences implicate epigenetic mechanisms for modulating the gene expression in plants under environmental stresses, epigenetic changes and their functional consequences under salinity stress in rice are underexplored. DNA methylation is one of the epigenetic mechanisms regulating gene expression in plant's responses to environmental stresses. Better understanding of epigenetic regulation of plant growth and response to environmental stresses may create novel heritable variation for crop improvement. Methodology/Principal Findings: Methylation sensitive amplification polymorphism (MSAP) technique was used to …

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Structure Of A Calcium-Dependent 11r-Lipoxygenase Suggests A Mechanism For Ca2+ Regulation, Priit Eek, Reet Järving, Ivar Järving, Nathaniel C. Gilbert, Marcia E. Newcomer, Nigulas Samel Jun 2012

Structure Of A Calcium-Dependent 11r-Lipoxygenase Suggests A Mechanism For Ca2+ Regulation, Priit Eek, Reet Järving, Ivar Järving, Nathaniel C. Gilbert, Marcia E. Newcomer, Nigulas Samel

Faculty Publications

Lipoxygenases (LOXs) are a key part of several signaling pathways that lead to inflammation and cancer. Yet, the mechanisms of substrate binding and allosteric regulation by the various LOX isoforms remain speculative. Here we report the 2.47-Å resolution crystal structure of the arachidonate 11R-LOX from Gersemia fruticosa, which sheds new light on the mechanism of LOXcatalysis. Our crystallographic and mutational studies suggest that the aliphatic tail of the fatty acid is bound in a hydrophobic pocket with two potential entrances. We speculate that LOXs share a common T-shaped substrate channel architecture that gives rise to the varying positional specificities. A …

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A Novel Ascaroside Controls The Parasitic Life Cycle Of The Entomopathogenic Nematode Heterorhabditis Bacteriophora, Jaime H. Noguez, Elizabeth S. Conner, Yue Zhou, Todd A. Ciche, Justin R. Ragains, Rebecca A. Butcher Jun 2012

A Novel Ascaroside Controls The Parasitic Life Cycle Of The Entomopathogenic Nematode Heterorhabditis Bacteriophora, Jaime H. Noguez, Elizabeth S. Conner, Yue Zhou, Todd A. Ciche, Justin R. Ragains, Rebecca A. Butcher

Faculty Publications

Entomopathogenic nematodes survive in the soil as stress-resistant infective juveniles that seek out and infect insect hosts. Upon sensing internal host cues, the infective juveniles regurgitate bacterial pathogens from their gut that ultimately kill the host. Inside the host, the nematode develops into a reproductive adult and multiplies until unknown cues trigger the accumulation of infective juveniles. Here, we show that the entomopathogenic nematode Heterorhabditis bacteriophora uses a small-molecule pheromone to control infective juvenile development. The pheromone is structurally related to the dauer pheromone ascarosides that the free-living nematode Caenorhabditis elegans uses to control its development. However, none of the …

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Further Evidence For The Likely Completeness Of The Library Of Solved Single Domain Protein Structures, Jeffrey Skolnick, Hongyi Zhou, Michal Brylinski Jun 2012

Further Evidence For The Likely Completeness Of The Library Of Solved Single Domain Protein Structures, Jeffrey Skolnick, Hongyi Zhou, Michal Brylinski

Faculty Publications

Recent studies questioned whether the Protein Data Bank (PDB) contains all compact, single domain protein structures. Here, we show that all quasi-spherical, QS, random protein structures devoid of secondary structure are in the PDB and are excellent templates for all native PDB proteins up to 250 residues. Because QS templates have a similar global contour as native, TASSER can refine 98% (90%) of those whose TM-score is 0.4 (0.35) to structures greater than or equal to the 0.5 TM-score threshold (0.74 (0.64) mean TM-score) for CATH/SCOP assignment. On the basis of this and the fact that, at a TM-score of …

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Effect Of Low Temperature Thermal Treatment On Soils Contaminated With Pentachlorophenol And Environmentally Persistent Free Radicals, Albert Leo N.Dela Cruz, Robert L. Cook, Slawomir M. Lomnicki, Barry Dellinger Jun 2012

Effect Of Low Temperature Thermal Treatment On Soils Contaminated With Pentachlorophenol And Environmentally Persistent Free Radicals, Albert Leo N.Dela Cruz, Robert L. Cook, Slawomir M. Lomnicki, Barry Dellinger

Faculty Publications

The effect of low temperature thermal treatment on soils from a former Superfund wood-treating site contaminated with pentachlorophenol (PCP) and the environmentally persistent free radical (EPFR), pentachlorophenoxyl, was determined. The pentachlorophenoxyl EPFRs' and the PCP molecules' chemical behavior were simultaneously monitored at temperatures ranging from 25 to 300 °C via electron paramagnetic resonance (EPR) spectroscopy and GC-MS analysis, respectively. Two types of thermal treatment were employed: a closed heating (oxygen-starved condition) where the soil was heated under vacuum and an open heating system (oxygen-rich conditions), where the soil was heated in ambient air. EPR analyses for closed heating indicated the …

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Tools For The Identification Of Bioactives Impacting The Metabolic Syndrome: Screening Of A Botanical Extract Library Using Subcutaneous And Visceral Human Adipose-Derived Stem Cell-Based Assays, Benjamin M. Buehrer, David J. Duffin, Y. Renee Lea-Currie, David Ribnicky, Ilya Raskin, Jacqueline M. Stephens, William T. Cefalu, Jeffrey M. Gimble Jun 2012

Tools For The Identification Of Bioactives Impacting The Metabolic Syndrome: Screening Of A Botanical Extract Library Using Subcutaneous And Visceral Human Adipose-Derived Stem Cell-Based Assays, Benjamin M. Buehrer, David J. Duffin, Y. Renee Lea-Currie, David Ribnicky, Ilya Raskin, Jacqueline M. Stephens, William T. Cefalu, Jeffrey M. Gimble

Faculty Publications

Plant extracts continue to represent an untapped source of renewable therapeutic compounds for the treatment and prevention of illnesses including chronic metabolic disorders. With the increase in worldwide obesity and its related morbidities, the need for identifying safe and effective treatments is also rising. As such, use of primary human adipose-derived stem cells represents a physiologically relevant cell system to screen for bioactive agents in the prevention and treatment of obesity and its related complications. By using these cells in a primary screen, the risk and cost of identifying artifacts due to interspecies variation and immortalized cell lines is eliminated. …

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Vitronectin Inhibits Neutrophil Apoptosis Through Activation Of Integrin-Associated Signaling Pathways, Hong Beom Bae, Jaroslaw W. Zmijewski, Jessy S. Deshane, Degui Zhi, Lawrence C. Thompson, Cynthia B. Peterson, David D. Chaplin, Edward Abraham Jun 2012

Vitronectin Inhibits Neutrophil Apoptosis Through Activation Of Integrin-Associated Signaling Pathways, Hong Beom Bae, Jaroslaw W. Zmijewski, Jessy S. Deshane, Degui Zhi, Lawrence C. Thompson, Cynthia B. Peterson, David D. Chaplin, Edward Abraham

Faculty Publications

Vitronectin is present in large concentrations in serum and the extracellular matrix. Although vitronectin is known to modulate neutrophil adhesion and chemotaxis, and to contribute to neutrophil-associated proinflammatory processes, a role in apoptosis has not been demonstrated. In thepresent studies,wefound that neutrophils demonstrated more rapid progression to spontaneous or TNF-related apoptosisinducing ligand-induced apoptosis when incubated under vitronectinfree conditions thanwhen vitronectinwas present. The ability of native vitronectin to delay neutrophil apoptosis was not recapitulated by the vitronectin somatomedin B domain. In contrast, inclusion of the cyclo[Arg-Gly-Asp-D-Phe-Val] peptide in cultures containing vitronectin resulted in enhanced neutrophil apoptosis, showing that the vitronectin RGD …

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Imprinting Control Region (Icr) Of The Peg3 Domain, Joomyeong Kim, Muhammad B. Ekram, Hana Kim, Mohammad Faisal, Wesley D. Frey, Jennifer M. Huang, Kim Ngoc Tran, Michelle M. Kim, Sungryul Yu Jun 2012

Imprinting Control Region (Icr) Of The Peg3 Domain, Joomyeong Kim, Muhammad B. Ekram, Hana Kim, Mohammad Faisal, Wesley D. Frey, Jennifer M. Huang, Kim Ngoc Tran, Michelle M. Kim, Sungryul Yu

Faculty Publications

The imprinting and transcription of the 500 kb genomic region surrounding the mouse Peg3 is predicted to be regulated by the Peg3-differentially methylated region (DMR). In the current study, this prediction was tested using a mutant mouse line lacking this potential imprinting control region (ICR). At the organismal level, paternal and maternal transmission of this knockout (KO) allele caused either reduced or increased growth rates in the mouse, respectively. In terms of the imprinting control, the paternal transmission of the KO allele resulted in bi-allelic expression of the normally maternally expressed Zim2, whereas the maternal transmission switched the transcriptionally dominant …

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Food Deprivation Explains Effects Of Mouthbrooding On Ovaries And Steroid Hormones, But Not Brain Neuropeptide And Receptor Mrnas, In An African Cichlid Fish, Brian P. Grone, Russ E. Carpenter, Malinda Lee, Karen P. Maruska, Russell D. Fernald Jun 2012

Food Deprivation Explains Effects Of Mouthbrooding On Ovaries And Steroid Hormones, But Not Brain Neuropeptide And Receptor Mrnas, In An African Cichlid Fish, Brian P. Grone, Russ E. Carpenter, Malinda Lee, Karen P. Maruska, Russell D. Fernald

Faculty Publications

Feeding behavior and reproduction are coordinately regulated by the brain via neurotransmitters, circulating hormones, and neuropeptides. Reduced feeding allows animals to engage in other behaviors important for fitness, including mating and parental care. Some fishes cease feeding for weeks at a time in order to provide care to their young by brooding them inside the male or female parent's mouth. Maternal mouthbrooding is known to impact circulating hormones and subsequent reproductive cycles, but neither the full effects of food deprivation nor the neural mechanisms are known. Here we ask what effects mouthbrooding has on several physiological processes including gonad and …

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The Evolution Of Reproductive Structures In Seed Plants: A Re-Examination Based On Insights From Developmental Genetics, Sarah Mathews, Elena M. Kramer Jun 2012

The Evolution Of Reproductive Structures In Seed Plants: A Re-Examination Based On Insights From Developmental Genetics, Sarah Mathews, Elena M. Kramer

Faculty Publications

The study of developmental genetics is providing insights into how plant morphology can and does evolve, and into the fundamental nature of specific organs. This new understanding has the potential to revise significantly the way we think about seed plant evolution, especially with regard to reproductive structures. Here, we have sought to take a step in bridging the divide between genetic data and critical fields such as paleobotany and systematics. We discuss the evidence for several evolutionarily important interpretations, including the possibility that ovules represent meristematic axes with their own type of lateral determinate organs (integuments) and a model that …

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The Tegula Tango: A Coevolutionary Dance Of Interacting, Positively Selected Sperm And Egg Proteins, Michael E. Hellberg, Alice B. Dennis, Patricia Arbour-Reily, Jan E. Aagaard, Willie J. Swanson Jun 2012

The Tegula Tango: A Coevolutionary Dance Of Interacting, Positively Selected Sperm And Egg Proteins, Michael E. Hellberg, Alice B. Dennis, Patricia Arbour-Reily, Jan E. Aagaard, Willie J. Swanson

Faculty Publications

Reproductive proteins commonly show signs of rapid divergence driven by positive selection. The mechanisms driving these changes have remained ambiguous in part because interacting male and female proteins have rarely been examined. We isolate an egg protein the vitelline envelope receptor for lysin (VERL) from Tegula, a genus of free-spawning marine snails. Like VERL from abalone, Tegula VERL is a major component of the VE surrounding the egg, includes a conserved zona pellucida (ZP) domain at its C-terminus, and possesses a unique, negatively charged domain of about 150 amino acids implicated in interactions with the positively charged lysin. Unlike for …

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Ecology And Management Of Bark Beetles (Coleoptera: Curculionidae: Scolytinae) In Southern Pine Forests, T. D. Schowalter Jun 2012

Ecology And Management Of Bark Beetles (Coleoptera: Curculionidae: Scolytinae) In Southern Pine Forests, T. D. Schowalter

Faculty Publications

Bark beetles (Coleoptera: Curculionidae: Scolytinae) have been an important historic and current factor affecting pine forest production in the southern United States. Although tree mortality to bark beetles often detracts from forest management goals, the natural role of bark beetles is canopy opening, thinning, and diversification of stand structure and composition, effects that contribute to some ecosystem services in forests managed for multiple uses. Strategies to prevent bark beetle outbreaks exploit their sensitivity to host tree spacing and reliance on pheromones to attract sufficient numbers to overwhelm tree defenses. Tree species selection at planting or through selective thinning can favor …

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The Bayou Lafourche Oral History Project: Understanding Environmental Change And Religious Identity In Louisiana, Michael Pasquier, Jennifer Cramer Jun 2012

The Bayou Lafourche Oral History Project: Understanding Environmental Change And Religious Identity In Louisiana, Michael Pasquier, Jennifer Cramer

Faculty Publications

The article discusses the Bayou Lafourche Oral History Project, which studied the relation between environmental changes and religion in Bayou Lafourche, a river in South Louisiana. Topics include the role of oral history in community history, the work of Louisiana State University (LSU) students in the project, and the use of audiorecording devices. Also discussed are the role of Roman Catholic devotion to Our Lady of Prompt Succor in the community, the 1965 experience of Hurricane Betsy, and the indexing of interviews from the project.

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