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Antarctic Microbial Mats: A Modern Analog For Archean Lacustrine Oxygen Oases, Dawn Y. Sumner, Ian Hawes, Tyler J. Mackey, Anne D. Jungblut, Peter T. Doran Oct 2015

Antarctic Microbial Mats: A Modern Analog For Archean Lacustrine Oxygen Oases, Dawn Y. Sumner, Ian Hawes, Tyler J. Mackey, Anne D. Jungblut, Peter T. Doran

Faculty Publications

© 2015 Geological Society of America. The evolution of oxygenic photosynthesis was the most important geochemical event in Earth history, causing the Great Oxidation Event (GOE) ~2.4 b.y. ago. However, evidence is mixed as to whether O2 production occurred locally as much as 2.8 b.y. ago, creating O2 oases, or initiated just prior to the GOE. The biogeochemical dynamics of possible O2 oases have been poorly constrained due to the absence of modern analogs. However, cyanobacteria in microbial mats in a perennially anoxic region of Lake Fryxell, Antarctica, create a 1-2 mm O2-containing layer in the upper mat during summer, …

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Genomic Approaches To Understanding Population Divergence And Speciation In Birds, David P.L. Toews, Leonardo Campagna, Scott A. Taylor, Christopher N. Balakrishnan, Daniel T. Baldassarre, Petra E. Deane-Coe, Michael G. Harvey, Daniel M. Hooper, Darren E. Irwin, Caroline D. Judy, Nicholas A. Mason, John E. Mccormack, Kevin G. Mccracken, Carl H. Oliveros, Rebecca J. Safran, Elizabeth S.C. Scordato, Katherine Faust Stryjewski, Anna Tigano, J. Albert C. Uy, Benjamin M. Winger Oct 2015

Genomic Approaches To Understanding Population Divergence And Speciation In Birds, David P.L. Toews, Leonardo Campagna, Scott A. Taylor, Christopher N. Balakrishnan, Daniel T. Baldassarre, Petra E. Deane-Coe, Michael G. Harvey, Daniel M. Hooper, Darren E. Irwin, Caroline D. Judy, Nicholas A. Mason, John E. Mccormack, Kevin G. Mccracken, Carl H. Oliveros, Rebecca J. Safran, Elizabeth S.C. Scordato, Katherine Faust Stryjewski, Anna Tigano, J. Albert C. Uy, Benjamin M. Winger

Faculty Publications

© 2016 American Ornithologists' Union. The widespread application of high-throughput sequencing in studying evolutionary processes and patterns of diversification has led to many important discoveries. However, the barriers to utilizing these technologies and interpreting the resulting data can be daunting for first-time users. We provide an overview and a brief primer of relevant methods (e.g., whole-genome sequencing, reduced-representation sequencing, sequence-capture methods, and RNA sequencing), as well as important steps in the analysis pipelines (e.g., loci clustering, variant calling, whole-genome and transcriptome assembly). We also review a number of applications in which researchers have used these technologies to address questions related …

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Geauxdock: A Novel Approach For Mixed-Resolution Ligand Docking Using A Descriptor-Based Force Field, Yun Ding, Ye Fang, Wei P. Feinstein, Jagannathan Ramanujam, David M. Koppelman, Juana Moreno, Michal Brylinski, Mark Jarrell Oct 2015

Geauxdock: A Novel Approach For Mixed-Resolution Ligand Docking Using A Descriptor-Based Force Field, Yun Ding, Ye Fang, Wei P. Feinstein, Jagannathan Ramanujam, David M. Koppelman, Juana Moreno, Michal Brylinski, Mark Jarrell

Faculty Publications

© 2015 Wiley Periodicals, Inc. Molecular docking is an important component of computer-aided drug discovery. In this communication, we describe GeauxDock, a new docking approach that builds on the ideas of ligand homology modeling. GeauxDock features a descriptor-based scoring function integrating evolutionary constraints with physics-based energy terms, a mixed-resolution molecular representation of protein-ligand complexes, and an efficient Monte Carlo sampling protocol. To drive docking simulations toward experimental conformations, the scoring function was carefully optimized to produce a correlation between the total pseudoenergy and the native-likeness of binding poses. Indeed, benchmarking calculations demonstrate that GeauxDock has a strong capacity to identify …

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Lsu Research Fall 2015, Louisiana State University And Agricultural & Mechanical College Oct 2015

Lsu Research Fall 2015, Louisiana State University And Agricultural & Mechanical College

Research Magazine

LSU Research is published annually by the Office of Research & Economic Development, Louisiana State University.

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An Integrated Map Of Structural Variation In 2,504 Human Genomes, Peter H. Sudmant, Tobias Rausch, Eugene J. Gardner, Robert E. Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus His Yang Fritz, Miriam K. Konkel, Ankit Malhotra, Adrian M. Stütz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark J.P. Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y.K. Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong Sep 2015

An Integrated Map Of Structural Variation In 2,504 Human Genomes, Peter H. Sudmant, Tobias Rausch, Eugene J. Gardner, Robert E. Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus His Yang Fritz, Miriam K. Konkel, Ankit Malhotra, Adrian M. Stütz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark J.P. Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y.K. Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong

Faculty Publications

© 2015 Macmillan Publishers Limited. All rights reserved. Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified …

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Ecological Networks In Stored Grain: Key Postharvest Nodes For Emerging Pests, Pathogens, And Mycotoxins, John F. Hernandez Nopsa, Gregory J. Daglish, David W. Hagstrum, John F. Leslie, Thomas W. Phillips, Caterina Scoglio, Sara Thomas-Sharma, Gimme H. Walter, Karen A. Garrett Sep 2015

Ecological Networks In Stored Grain: Key Postharvest Nodes For Emerging Pests, Pathogens, And Mycotoxins, John F. Hernandez Nopsa, Gregory J. Daglish, David W. Hagstrum, John F. Leslie, Thomas W. Phillips, Caterina Scoglio, Sara Thomas-Sharma, Gimme H. Walter, Karen A. Garrett

Faculty Publications

Wheat is at peak quality soon after harvest. Subsequently, diverse biota use wheat as a resource in storage, including insects and mycotoxin-producing fungi. Transportation networks for stored grain are crucial to food security and provide a model system for an analysis of the population structure, evolution, and dispersal of biota in networks. We evaluated the structure of rail networks for grain transport in the United States and Eastern Australia to identify the shortest paths for the anthropogenic dispersal of pests and mycotoxins, as well as the major sources, sinks, and bridges for movement. We found important differences in the risk …

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A Global Reference For Human Genetic Variation, Adam Auton, Gonçalo R. Abecasis, David M. Altshuler, Richard M. Durbin, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Peter Donnelly, Evan E. Eichler, Paul Flicek, Stacey B. Gabriel, Richard A. Gibbs, Eric D. Green, Matthew E. Hurles, Bartha M. Knoppers, Jan O. Korbel, Eric S. Lander, Charles Lee, Hans Lehrach, Elaine R. Mardis, Gabor T. Marth, Gil A. Mcvean, Deborah A. Nickerson, Jeanette P. Schmidt, Stephen T. Sherry, Jun Wang, Richard K. Wilson, Eric Boerwinkle, Harsha Doddapaneni, Yi Han, Viktoriya Korchina, Christie Kovar, Sandra Lee, Donna Muzny Sep 2015

A Global Reference For Human Genetic Variation, Adam Auton, Gonçalo R. Abecasis, David M. Altshuler, Richard M. Durbin, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Peter Donnelly, Evan E. Eichler, Paul Flicek, Stacey B. Gabriel, Richard A. Gibbs, Eric D. Green, Matthew E. Hurles, Bartha M. Knoppers, Jan O. Korbel, Eric S. Lander, Charles Lee, Hans Lehrach, Elaine R. Mardis, Gabor T. Marth, Gil A. Mcvean, Deborah A. Nickerson, Jeanette P. Schmidt, Stephen T. Sherry, Jun Wang, Richard K. Wilson, Eric Boerwinkle, Harsha Doddapaneni, Yi Han, Viktoriya Korchina, Christie Kovar, Sandra Lee, Donna Muzny

Faculty Publications

© 2015 Macmillan Publishers Limited. All rights reserved. The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto …

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Evidence For The Convergence Model: The Emergence Of Highly Pathogenic Avian Influenza (H5n1) In Viet Nam, Sumeet Saksena, Jefferson Fox, Michael Epprecht, Chinh C. Tran, Duong H. Nong, James H. Spencer, Lam Nguyen, Melissa L. Finucane, Vien D. Tran, Bruce A. Wilcox Sep 2015

Evidence For The Convergence Model: The Emergence Of Highly Pathogenic Avian Influenza (H5n1) In Viet Nam, Sumeet Saksena, Jefferson Fox, Michael Epprecht, Chinh C. Tran, Duong H. Nong, James H. Spencer, Lam Nguyen, Melissa L. Finucane, Vien D. Tran, Bruce A. Wilcox

Faculty Publications

Building on a series of ground breaking reviews that first defined and drew attention to emerging infectious diseases (EID), the 'convergence model' was proposed to explain the multifactorial causality of disease emergence. The model broadly hypothesizes disease emergence is driven by the co-incidence of genetic, physical environmental, ecological, and social factors. We developed and tested a model of the emergence of highly pathogenic avian influenza (HPAI) H5N1 based on suspected convergence factors that are mainly associated with land-use change. Building on previous geospatial statistical studies that identified natural and human risk factors associated with urbanization, we added new factors to …

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Influence Of Solvent On Poly(2-(Dimethylamino)Ethyl Methacrylate) Dynamics In Polymer-Concentrated Mixtures: A Combined Neutron Scattering, Dielectric Spectroscopy, And Calorimetric Study, Guido Goracci, Arantxa Arbe, Angel Alegría, Victoria García Sakai, Svemir Rudić, Gerald J. Schneider, Wiebke Lohstroh, Fanni Juranyi, Juan Colmenero Sep 2015

Influence Of Solvent On Poly(2-(Dimethylamino)Ethyl Methacrylate) Dynamics In Polymer-Concentrated Mixtures: A Combined Neutron Scattering, Dielectric Spectroscopy, And Calorimetric Study, Guido Goracci, Arantxa Arbe, Angel Alegría, Victoria García Sakai, Svemir Rudić, Gerald J. Schneider, Wiebke Lohstroh, Fanni Juranyi, Juan Colmenero

Faculty Publications

© 2015 American Chemical Society. We have investigated the dynamical processes-α-relaxation, local motions of the side-groups, and methyl group rotations-in poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) in the dry state and in mixtures (at 70 wt% polymer concentration) with tetrahydrofuran (THF) and water, to address the question as to how these polymer motions are affected by plasticizers interacting in different ways with the polymer. Differential scanning calorimetry, dielectric spectroscopy, and neutron scattering techniques on labeled samples (with deuterated solvents to isolate the signal of the polymer component) have been combined. The α-relaxation is drastically affected, with similar shifts of the glass-transition temperature for …

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Monitoring The Photocleaving Dynamics Of Colloidal Microrna-Functionalized Gold Nanoparticles Using Second Harmonic Generation, Raju R. Kumal, Corey R. Landry, Mohammad Abu-Laban, Daniel J. Hayes, Louis H. Haber Sep 2015

Monitoring The Photocleaving Dynamics Of Colloidal Microrna-Functionalized Gold Nanoparticles Using Second Harmonic Generation, Raju R. Kumal, Corey R. Landry, Mohammad Abu-Laban, Daniel J. Hayes, Louis H. Haber

Faculty Publications

© 2015 American Chemical Society. Photoactivated drug delivery systems using gold nanoparticles provide the promise of spatiotemporal control of delivery that is crucial for applications ranging from regenerative medicine to cancer therapy. In this study, we use second harmonic generation (SHG) spectroscopy to monitor the light-activated controlled release of oligonucleotides from the surface of colloidal gold nanoparticles. MicroRNA is functionalized to spherical gold nanoparticles using a nitrobenzyl linker that undergoes photocleaving upon ultraviolet irradiation. The SHG signal generated from the colloidal nanoparticle sample is shown to be a sensitive probe for monitoring the photocleaving dynamics in real time. The photocleaving …

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Sugar-Based Polyamides: Self-Organization In Strong Polar Organic Solvents, Cornelia Rosu, Paul S. Russo, William H. Daly, Rafael Cueto, John A. Pople, Roger A. Laine, Ioan I. Negulescu Sep 2015

Sugar-Based Polyamides: Self-Organization In Strong Polar Organic Solvents, Cornelia Rosu, Paul S. Russo, William H. Daly, Rafael Cueto, John A. Pople, Roger A. Laine, Ioan I. Negulescu

Faculty Publications

© 2015 American Chemical Society. Periodic patterns resembling spirals were observed to form spontaneously upon unassisted cooling of d-glucaric acid- and d-galactaric acid-based polyamide solutions in N-methyl-N-morpholine oxide (NMMO) monohydrate. Similar observations were made in d-galactaric acid-based polyamide/ionic liquid (IL) solutions. The morphologies were investigated by optical, polarized light and confocal microscopy assays to reveal pattern details. Differential scanning calorimetry was used to monitor solution thermal behavior. Small- and wide-angle X-ray scattering data reflected the complex and heterogeneous nature of the self-organized patterns. Factors such as concentration and temperature were found to influence spiral dimensions and geometry. The distance between …

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Genome-Wide Transcriptome Analysis Of Cotton (Gossypium Hirsutum L.) Identifies Candidate Gene Signatures In Response To Aflatoxin Producing Fungus Aspergillus Flavus, Renesh Bedre, Kanniah Rajasekaran, Venkata Ramanarao Mangu, Luis Eduardo Sanchez Timm, Deepak Bhatnagar, Niranjan Baisakh Sep 2015

Genome-Wide Transcriptome Analysis Of Cotton (Gossypium Hirsutum L.) Identifies Candidate Gene Signatures In Response To Aflatoxin Producing Fungus Aspergillus Flavus, Renesh Bedre, Kanniah Rajasekaran, Venkata Ramanarao Mangu, Luis Eduardo Sanchez Timm, Deepak Bhatnagar, Niranjan Baisakh

Faculty Publications

Aflatoxins are toxic and potent carcinogenic metabolites produced from the fungi Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive preharvest and postharvest conditions. United States federal regulations restrict the use of aflatoxin contaminated cottonseed at >20 ppb for animal feed. Several strategies have been proposed for controlling aflatoxin contamination, and much success has been achieved by the application of an atoxigenic strain of A. flavus in cotton, peanut and maize fields. Development of cultivars resistant to aflatoxin through overexpression of resistance associated genes and/or knocking down aflatoxin biosynthesis of A. flavus will be an effective strategy for …

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Comparative Effectiveness Of Potential Elicitors Of Plant Resistance Against Spodoptera Frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) In Four Crop Plants, John W. Gordy, B. Rogers Leonard, David Blouin, Jeffrey A. Davis, Michael J. Stout Sep 2015

Comparative Effectiveness Of Potential Elicitors Of Plant Resistance Against Spodoptera Frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) In Four Crop Plants, John W. Gordy, B. Rogers Leonard, David Blouin, Jeffrey A. Davis, Michael J. Stout

Faculty Publications

© 2015 Gordy et al. Feeding by insect herbivores activates plant signaling pathways, resulting in the enhanced production of secondary metabolites and other resistance-related traits by injured plants. These traits can reduce insect fitness, deter feeding, and attract beneficial insects. Organic and inorganic chemicals applied as a foliar spray, seed treatment, or soil drench can activate these plant responses. Azelaic acid (AA), benzothiadiazole (BTH), gibberellic acid (GA), harpin, and jasmonic acid (JA) are thought to directly mediate plant responses to pathogens and herbivores or to mimic compounds that do. The effects of these potential elicitors on the induction of plant …

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Climate Extremes Dominating Seasonal And Interannual Variations In Carbon Export From The Mississippi River Basin, Hanqin Tian, Wei Ren, Jia Yang, Bo Tao, Wei Jun Cai, Steven E. Lohrenz, Charles S. Hopkinson, Mingliang Liu, Qichun Yang, Chaoqun Lu, Bowen Zhang, Kamaljit Banger, Shufen Pan, Ruoying He, Zuo Xue Sep 2015

Climate Extremes Dominating Seasonal And Interannual Variations In Carbon Export From The Mississippi River Basin, Hanqin Tian, Wei Ren, Jia Yang, Bo Tao, Wei Jun Cai, Steven E. Lohrenz, Charles S. Hopkinson, Mingliang Liu, Qichun Yang, Chaoqun Lu, Bowen Zhang, Kamaljit Banger, Shufen Pan, Ruoying He, Zuo Xue

Faculty Publications

Knowledge about the annual and seasonal patterns of organic and inorganic carbon (C) exports from the major rivers of the world to the coastal ocean is essential for our understanding and potential management of the global C budget so as to limit anthropogenic modification of global climate. Unfortunately our predictive understanding of what controls the timing, magnitude, and quality of C export is still rudimentary. Here we use a process-based coupled hydrologic/ecosystem biogeochemistry model (the Dynamic Land Ecosystem Model) to examine how climate variability and extreme events, changing land use, and atmospheric chemistry have affected the annual and seasonal patterns …

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Can We Identify Genes With Increased Phylogenetic Reliability?, V P. Doyle, R E. Young, G J. Naylor, J M. Brown, V P. Doyle Sep 2015

Can We Identify Genes With Increased Phylogenetic Reliability?, V P. Doyle, R E. Young, G J. Naylor, J M. Brown, V P. Doyle

Faculty Publications

Topological heterogeneity among gene trees is widely observed in phylogenomic analyses and some of this variation is likely caused by systematic error in gene tree estimation. Systematic error can be mitigated by improving models of sequence evolution to account for all evolutionary processes relevant to each gene or identifying those genes whose evolution best conforms to existing models. However, the best method for identifying such genes is not well established. Here, we ask if filtering genes according to their clock-likeness or posterior predictive effect size (PPES, an inference-based measure of model violation) improves phylogenetic reliability and congruence. We compared these …

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Can We Identify Genes With Increased Phylogenetic Reliability?, V P. Doyle, R E. Young, G J. Naylor, J M. Brown, V P. Doyle Sep 2015

Can We Identify Genes With Increased Phylogenetic Reliability?, V P. Doyle, R E. Young, G J. Naylor, J M. Brown, V P. Doyle

Faculty Publications

Topological heterogeneity among gene trees is widely observed in phylogenomic analyses and some of this variation is likely caused by systematic error in gene tree estimation. Systematic error can be mitigated by improving models of sequence evolution to account for all evolutionary processes relevant to each gene or identifying those genes whose evolution best conforms to existing models. However, the best method for identifying such genes is not well established. Here, we ask if filtering genes according to their clock-likeness or posterior predictive effect size (PPES, an inference-based measure of model violation) improves phylogenetic reliability and congruence. We compared these …

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Switch Between Morphospecies Of Pocillopora Corals, David A. Paz-García, Michael E. Hellberg, Francisco J. García-De-León, Eduardo F. Balart Sep 2015

Switch Between Morphospecies Of Pocillopora Corals, David A. Paz-García, Michael E. Hellberg, Francisco J. García-De-León, Eduardo F. Balart

Faculty Publications

© 2015 by The University of Chicago. All rights reserved. Pocillopora corals are the main reef builders in the eastern tropical Pacific. The validity of Pocillopora morphospecies remains under debate because of disagreements between morphological and genetic data. To evaluate the temporal stability of morphospecies in situ, we monitored the shapes of individual colonies in three communities in the southern Gulf of California for 44 months. Twenty-three percent of tagged colonies of Pocillopora damicornis changed to Pocillopora inflata morphology during this time. This switch in identity coincided with a shift to a higher frequency of storms and lower water turbidity …

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The Human Shoulder Suspension Apparatus: A Causal Explanation For Bilateral Asymmetry And A Fresh Look At The Evolution Of Human Bipedality, Michelle L. Osborn, Dominique G. Homberger Sep 2015

The Human Shoulder Suspension Apparatus: A Causal Explanation For Bilateral Asymmetry And A Fresh Look At The Evolution Of Human Bipedality, Michelle L. Osborn, Dominique G. Homberger

Faculty Publications

© 2015 Wiley Periodicals, Inc. The combination of large mastoid processes and clavicles is unique to humans, but the biomechanical and evolutionary significance of their special configuration is poorly understood. As part of the newly conceptualized shoulder suspension apparatus, the mastoid processes and clavicles are shaped by forces exerted by the musculo-fascial components of the cleidomastoid and clavotrapezius muscles as they suspend the shoulders from the head. Because both skeletal elements develop during infancy in tandem with the attainment of an upright posture, increased manual dexterity, and the capacity for walking, we hypothesized that the same forces would have shaped …

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Environmental Gradients And The Evolution Of Successional Habitat Specialization: A Test Case With 14 Neotropical Forest Sites, Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H.S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander Defrancesco, Juan M. Dupuy, Bryan Finegan, Eugenio González-Jiménez, Jefferson S. Hall, Kyle E. Harms, José Luis Hernández-Stefanoni, Peter Hietz, Deborah Kennard, Timothy J. Killeen, Susan G. Laurance Sep 2015

Environmental Gradients And The Evolution Of Successional Habitat Specialization: A Test Case With 14 Neotropical Forest Sites, Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H.S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander Defrancesco, Juan M. Dupuy, Bryan Finegan, Eugenio González-Jiménez, Jefferson S. Hall, Kyle E. Harms, José Luis Hernández-Stefanoni, Peter Hietz, Deborah Kennard, Timothy J. Killeen, Susan G. Laurance

Faculty Publications

© 2015 British Ecological Society. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late-successional stages in wet forest. We applied a robust multinomial classification model to samples of primary and secondary forest trees from 14 Neotropical lowland forest sites spanning a …

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Developmental Changes In Hypoxic Exposure And Responses To Anoxia In Drosophila Melanogaster, Viviane Callier, Steven C. Hand, Jacob B. Campbell, Taylor Biddulph, Jon F. Harrison Sep 2015

Developmental Changes In Hypoxic Exposure And Responses To Anoxia In Drosophila Melanogaster, Viviane Callier, Steven C. Hand, Jacob B. Campbell, Taylor Biddulph, Jon F. Harrison

Faculty Publications

© 2015. Published by The Company of Biologists Ltd. Holometabolous insects undergo dramatic morphological and physiological changes during ontogeny. In particular, the larvae of many holometabolous insects are specialized to feed in soil, water or dung, inside plant structures, or inside other organisms as parasites where they may commonly experience hypoxia or anoxia. In contrast, holometabolous adults usually are winged and live with access to air. Here, we show that larval Drosophila melanogaster experience severe hypoxia in their normal laboratory environments; third instar larvae feed by tunneling into a medium without usable oxygen. Larvae move strongly in anoxia for many …

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Nonparametric Estimation Of Interspecific Spatio-Temporal Niche Separation Between Two Lady Beetles (Coleoptera: Coccinellidae) In Bt Cotton Fields, Zeng Bin Lu, Pei Jian Shi, Gadi V.P. Reddy, Lin Mao Li, Xing Yuan Men, Feng Ge Sep 2015

Nonparametric Estimation Of Interspecific Spatio-Temporal Niche Separation Between Two Lady Beetles (Coleoptera: Coccinellidae) In Bt Cotton Fields, Zeng Bin Lu, Pei Jian Shi, Gadi V.P. Reddy, Lin Mao Li, Xing Yuan Men, Feng Ge

Faculty Publications

Predaceous lady beetles are important natural enemies of many insect pests in agro-ecosystem. The altered agricultural practices associated with widespread adoption of Bt cotton may have potential effects on the spatio-temporal patterns of predaceous lady beetles, as the composition and abundance of nontarget sucking pests have been changed in Bt cotton fields. In the current study, the spatio-temporal patterns of two important lady beetles, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae) and Propylea japonica (Thunberg) (Coleoptera: Coccinellidae), were surveyed in Bt cotton fields. A nonparametric method associated with Monte Carlo tests was used to address and test whether niche segregation occurred between …

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Sequence Analysis And Characterization Of Active Human Alu Subfamilies Based On The 1000 Genomes Pilot Project, Miriam K. Konkel, Jerilyn A. Walker, Ashley B. Hotard, Megan C. Ranck, Catherine C. Fontenot, Jessica Storer, Chip Stewart, Gabor T. Marth, Mark A. Batzer Sep 2015

Sequence Analysis And Characterization Of Active Human Alu Subfamilies Based On The 1000 Genomes Pilot Project, Miriam K. Konkel, Jerilyn A. Walker, Ashley B. Hotard, Megan C. Ranck, Catherine C. Fontenot, Jessica Storer, Chip Stewart, Gabor T. Marth, Mark A. Batzer

Faculty Publications

© The Author(s) 2015. The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent fromthe human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent …

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Production Of Inbred Larvae Through Self-Fertilization Using Oocytes And Cryopreserved Sperm From The Same Individuals After Sex Reversal In Eastern Oyster Crassostrea Virginica, Huiping Yang, Yan Wang, Ximing Guo, Terrence R. Tiersch Sep 2015

Production Of Inbred Larvae Through Self-Fertilization Using Oocytes And Cryopreserved Sperm From The Same Individuals After Sex Reversal In Eastern Oyster Crassostrea Virginica, Huiping Yang, Yan Wang, Ximing Guo, Terrence R. Tiersch

Faculty Publications

The eastern oyster Crassostrea virginica can change sex which makes self-fertilization possible if sperm can be cryopreserved. In this study, small (~1 year old) and large (~2-3 years old) oysters were biopsied for sperm collection. Survival of the biopsied oysters after 1 year was 50% for small oysters and 17% for large oysters. Oocytes were collected from sex-reversed females, and self-fertilized with cryopreserved sperm. Of the 24 cryopreserved samples, 14 individuals had ≤1% fertility when crossed with oocytes from unrelated females, indicating that the cryopreserved sperm had reduced fertility. The other 10 individuals had a fertility of 39 ± 25% …

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The Challenges Of Resolving A Rapid, Recent Radiation: Empirical And Simulated Phylogenomics Of Philippine Shrews, Thomas C. Giarla, Jacob A. Esselstyn Sep 2015

The Challenges Of Resolving A Rapid, Recent Radiation: Empirical And Simulated Phylogenomics Of Philippine Shrews, Thomas C. Giarla, Jacob A. Esselstyn

Faculty Publications

Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses have the potential to mitigate these difficulties. Here, we attempt to resolve phylogenetic relationships among eight shrew species (genus Crocidura) from the Philippines, a phylogenetic problem that has proven intractable with small (< 10 loci) data sets. We sequenced hundreds of ultraconserved elements and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a maximally supported and fully resolved tree. In contrast, the coalescent-based approaches produced similar topologies, but each had several poorly supported nodes. Using simulations, we demonstrate that the concatenated tree could be positively misleading. Our simulations also show that the tree shape we tend to infer, which involves a series of short internal branches, is difficult to resolve, even if substitution models are known and multiple individuals per species are sampled. As such, the low support we obtained for backbone relationships in our coalescent-based inferences reflects a real and appropriate lack of certainty. Our results illuminate the challenges of estimating a bifurcating tree in a rapid and recent radiation, providing a rare empirical example of a nearly simultaneous series of speciation events in a terrestrial animal lineage as it spreads across an oceanic archipelago.

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Scalemic And Racemic Imprinting With A Chiral Crosslinker, Britney Hebert, Danielle S. Meador, David A. Spivak Aug 2015

Scalemic And Racemic Imprinting With A Chiral Crosslinker, Britney Hebert, Danielle S. Meador, David A. Spivak

Faculty Publications

© 2015 Elsevier B.V. The development of molecularly imprinted chiral stationary phases has traditionally been limited by the need for a chiral pure template. Paradoxically, availability of a chiral pure template largely defeats the purpose of developing a chiral stationary phase. To solve this paradox, imprinting of scalemic and racemic template mixtures was investigated using both chiral (N-α-bismethacryloyl-. l-alanine) and achiral (N,O-bisacrylamide ethanolamine) crosslinkers. Imprinting of scalemic mixtures provided polymers capable of partial separation of Boc-tyrosine enantiomers with virtually the same results when using either the chiral or achiral crosslinker. However, the chiral crosslinker was required for chiral differentiation by …

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Genetic Divergence Of An Avian Endemic On The Californian Channel Islands, Amy G. Wilson, Yvonne Chan, Sabrina S. Taylor, Peter Arcese Aug 2015

Genetic Divergence Of An Avian Endemic On The Californian Channel Islands, Amy G. Wilson, Yvonne Chan, Sabrina S. Taylor, Peter Arcese

Faculty Publications

The Californian Channel Islands are near-shore islands with high levels of endemism, but extensive habitat loss has contributed to the decline or extinction of several endemic taxa. A key parameter for understanding patterns of endemism and demography in island populations is the magnitude of inter-island dispersal. This paper estimates the extent of migration and genetic differentiation in three extant and two extinct populations of Channel Island song sparrows (Melospiza melodia graminea). Inter-island differentiation was substantial (G''ST: 0.14-0.37), with San Miguel Island having the highest genetic divergence and lowest migration rates. Santa Rosa and Santa Cruz Island populations were less diverged …

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Molecular Approaches For Improving Desiccation Tolerance: Insights From The Brine Shrimp Artemia Franciscana, Steven C. Hand, Michael A. Menze Aug 2015

Molecular Approaches For Improving Desiccation Tolerance: Insights From The Brine Shrimp Artemia Franciscana, Steven C. Hand, Michael A. Menze

Faculty Publications

© 2015, Springer-Verlag Berlin Heidelberg. Main conclusion: We have evaluated the endogenous expression and molecular properties of selected Group 3 LEA proteins fromArtemia franciscana, and the capacity of selected Groups 1 and 3 proteins transfected into various desiccation-sensitive cell lines to improve tolerance to drying. Organisms inhabiting both aquatic and terrestrial ecosystems frequently are confronted with the problem of water loss for multiple reasons—exposure to hypersalinity, evaporative water loss, and restriction of intracellular water due to freezing of extracellular fluids. Seasonal desiccation can become severe and lead to the production of tolerant propagules and entry into the state of anhydrobiosis …

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Co-Extinction In A Host-Parasite Network: Identifying Key Hosts For Network Stability, Tad Dallas, Emily Cornelius Aug 2015

Co-Extinction In A Host-Parasite Network: Identifying Key Hosts For Network Stability, Tad Dallas, Emily Cornelius

Faculty Publications

Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one …

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Externally And Internally Functionalized Copper(Ii) Β-Diketonate Molecular Squares, Jackson K. Cherutoi, Jace D. Sandifer, Uttam R. Pokharel, Frank R. Fronczek, Svetlana Pakhomova, Andrew W. Maverick Aug 2015

Externally And Internally Functionalized Copper(Ii) Β-Diketonate Molecular Squares, Jackson K. Cherutoi, Jace D. Sandifer, Uttam R. Pokharel, Frank R. Fronczek, Svetlana Pakhomova, Andrew W. Maverick

Faculty Publications

© 2015 American Chemical Society. Five functionalized bis(β-diketones) and their Cu(II) molecular squares are described. The new bis(β-diketones), m-pbhxH2 (3), 5-MeO-m-pbaH2 (4), 5-BuO-m-pbaH2 (5), 2-MeO-m-pbaH2 (6), and 2-MeO-m-pbprH2 (7), were prepared by reaction of the corresponding aldehydes with phospholenes, as we previously reported for m-pbaH2 (1) and m-pbprH2 (2). Ligand 3 has long alkyl chains in its β-diketone moieties, while ligands 4-7 have alkoxy substituents on their aromatic rings. When treated with Cu2+, the new bis(β-diketones) 3, 4, 5, and 7 afford molecular squares, Cu4(m-pbhx)4 (10), Cu4(5-MeO-m-pba)4 (11), Cu4(5-BuO-m-pba)4 (12), and Cu4(2-MeO-m-pbpr)4 (13), respectively. Two of the new …

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The Origin And Evolution Of Phototropins, Fay Wei Li, Carl J. Rothfels, Michael Melkonian, Juan C. Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane K.S. Wong, Sarah Mathews, Kathleen M. Pryer Aug 2015

The Origin And Evolution Of Phototropins, Fay Wei Li, Carl J. Rothfels, Michael Melkonian, Juan C. Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane K.S. Wong, Sarah Mathews, Kathleen M. Pryer

Faculty Publications

© 2015 Li, Rothfels, Melkonian, Villarreal, Stevenson, Graham, Wong, Mathews and Pryer. Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but …

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