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Taxonomy And Systematics Of The Herichthyins (Cichlidae: Tribe Heroini), With The Description Of Eight New Middle American Genera, Caleb D. Mcmahan, Wilfredo A. Matamoros, Kyle R. Piller, Prosanta Chakrabarty Aug 2015

Taxonomy And Systematics Of The Herichthyins (Cichlidae: Tribe Heroini), With The Description Of Eight New Middle American Genera, Caleb D. Mcmahan, Wilfredo A. Matamoros, Kyle R. Piller, Prosanta Chakrabarty

Faculty Publications

In recent years great strides have been made for improving our understanding of the evolutionary relationships among neotropical cichlids, particularly within the clade Heroini and its crown clade the herichthyins. Most phylogenetic studies have largely converged on congruent topologies for relationships among species and major lineages within the herichthyins. One major aspect missing from previous studies of these cichlids is a formal taxonomic revision, including the redefining of genera. Based on analysis of 52 species and three mitochondrial and two nuclear loci, we generate a Bayesian phylogeny for the herichthyin cichlids, and formally revise the taxonomy for genera within this …


Investigation Of Stilbenoids As Potential Therapeutic Agents For Rotavirus Gastroenteritis, Judith M. Ball, Fabricio Medina-Bolivar, Katelyn D. Defrates, Emily Hambleton, Megan E. Hurlburt, Lingling Fang, Tianhong Yang, Luis Nopo-Olazabal, Richard L. Atwill, Pooj Ghai, Rebecca D. Parr Aug 2015

Investigation Of Stilbenoids As Potential Therapeutic Agents For Rotavirus Gastroenteritis, Judith M. Ball, Fabricio Medina-Bolivar, Katelyn D. Defrates, Emily Hambleton, Megan E. Hurlburt, Lingling Fang, Tianhong Yang, Luis Nopo-Olazabal, Richard L. Atwill, Pooj Ghai, Rebecca D. Parr

Faculty Publications

Rotavirus (RV) infections cause severe diarrhea in infants and young children worldwide. Vaccines are available but cost prohibitive for many countries and only reduce severe symptoms. Vaccinated infants continue to shed infectious particles, and studies show decreased efficacy of the RV vaccines in tropical and subtropical countries where they are needed most. Continuing surveillance for new RV strains, assessment of vaccine efficacy, and development of cost effective antiviral drugs remain an important aspect of RV studies. This study was to determine the efficacy of antioxidant and anti-inflammatory stilbenoids to inhibit RV replication. Peanut (A. hypogaea) hairy root cultures were induced …


Effects Of Hydrogen Peroxide On Different Toxigenic And Atoxigenic Isolates Of Aspergillus Flavus, Jake C. Fountain, Brian T. Scully, Zhi Yuan Chen, Scott E. Gold, Anthony E. Glenn, Hamed K. Abbas, R. Dewey Lee, Robert C. Kemerait, Baozhu Guo Aug 2015

Effects Of Hydrogen Peroxide On Different Toxigenic And Atoxigenic Isolates Of Aspergillus Flavus, Jake C. Fountain, Brian T. Scully, Zhi Yuan Chen, Scott E. Gold, Anthony E. Glenn, Hamed K. Abbas, R. Dewey Lee, Robert C. Kemerait, Baozhu Guo

Faculty Publications

Drought stress in the field has been shown to exacerbate aflatoxin contamination of maize and peanut. Drought and heat stress also produce reactive oxygen species (ROS) in plant tissues. Given the potential correlation between ROS and exacerbated aflatoxin production under drought and heat stress, the objectives of this study were to examine the effects of hydrogen peroxide (H2O2)-induced oxidative stress on the growth of different toxigenic (+) and atoxigenic (−) isolates of Aspergillus flavus and to test whether aflatoxin production affects the H2O2 concentrations that the isolates could survive. Ten isolates were tested: NRRL3357 (+), A9 (+), AF13 (+), Tox4 …


How Diverse Detrital Environments Influence Nutrient Stoichiometry Between Males And Females Of The Co-Occurring Container Mosquitoes Aedes Albopictus, Ae. Aegypti, And Culex Quinquefasciatus, Donald A. Yee, Michael G. Kaufman, Nnaemeka F. Ezeakacha Aug 2015

How Diverse Detrital Environments Influence Nutrient Stoichiometry Between Males And Females Of The Co-Occurring Container Mosquitoes Aedes Albopictus, Ae. Aegypti, And Culex Quinquefasciatus, Donald A. Yee, Michael G. Kaufman, Nnaemeka F. Ezeakacha

Faculty Publications

Allocation patterns of carbon and nitrogen in animals are influenced by food quality and quantity, as well as by inherent metabolic and physiological constraints within organisms. Whole body stoichiometry also may vary between the sexes who differ in development rates and reproductive allocation patterns. In aquatic containers, such as tree holes and tires, detrital inputs, which vary in amounts of carbon and nitrogen, form the basis of the mosquito-dominated food web. Differences in development times and mass between male and female mosquitoes may be the result of different reproductive constraints, which could also influence patterns of nutrient allocation. We examined …


Genotype-By-Sequencing Of The Plant-Pathogenic Fungi Pyrenophora Teres And Sphaerulina Musiva Utilizing Ion Torrent Sequence Technology, Jared M. Leboldus, Kasia Kinzer, Jonathan Richards, Zhu Ya, Changhui Yan, Timothy L. Friesen, Robert Brueggeman Aug 2015

Genotype-By-Sequencing Of The Plant-Pathogenic Fungi Pyrenophora Teres And Sphaerulina Musiva Utilizing Ion Torrent Sequence Technology, Jared M. Leboldus, Kasia Kinzer, Jonathan Richards, Zhu Ya, Changhui Yan, Timothy L. Friesen, Robert Brueggeman

Faculty Publications

Genetic and genomics tools to characterize host-pathogen interactions are disproportionately directed to the host because of the focus on resistance. However, understanding the genetics of pathogen virulence is equally important and has been limited by the high cost of denovo genotyping of species with limited marker data. Non-resource-prohibitive methods that overcome the limitation of genotyping are now available through genotype-by-sequencing (GBS). The use of a two-enzyme restriction-associated DNA (RAD)-GBS method adapted for Ion Torrent sequencing technology provided robust and reproducible high-density genotyping of several fungal species. A total of 5783 and 2373 unique loci, 'sequence tags', containing 16441 and 9992 …


Point Of No Return From Water Loss In Coptotermes Formosanus (Isoptera: Rhinotermitidae), Bal K. Gautam, Gregg Henderson Aug 2015

Point Of No Return From Water Loss In Coptotermes Formosanus (Isoptera: Rhinotermitidae), Bal K. Gautam, Gregg Henderson

Faculty Publications

Describing desiccation stages based on the physical appearance of termites has not been evaluated previously. Formosan subterranean termites were studied to determine the rate of water loss, singly and in groups, in the laboratory. The stages of water loss are described based on changes in physical appearance and percent total body water loss evaluated at 2- to 8-h time intervals up to 32 h.Workers in groups lost water slower than individual worker trials. Weight loss was linear over time for worker groups and individuals, as was individual soldier only trials. Water loss in individual workers was significantly faster than in …


Infectious Disease And Red Wolf Conservation: Assessment Of Disease Occurrence And Associated Risks, Kristin E. Brzeski, Rebecca B. Harrison, William T. Waddell, Karen N. Wolf, David R. Rabon, Sabrina S. Taylor Aug 2015

Infectious Disease And Red Wolf Conservation: Assessment Of Disease Occurrence And Associated Risks, Kristin E. Brzeski, Rebecca B. Harrison, William T. Waddell, Karen N. Wolf, David R. Rabon, Sabrina S. Taylor

Faculty Publications

Infectious diseases pose a significant threat to global biodiversity and may contribute to extinction. As such, establishing baseline disease prevalence in vulnerable species where disease could affect persistence is important to conservation. We assessed potential disease threats to endangered red wolves (Canis rufus) by evaluating regional (southeastern United States) disease occurrences in mammals and parasite prevalence in red wolves and sympatric coyotes (Canis latrans) in North Carolina. Common viral pathogens in the southeast region, such as canine distemper and canine parvovirus, and numerous widespread endoparasites could pose a threat to the red Wolf population. The most prevalent parasites in red …


Chesapeake Bay Nitrogen Fluxes Derived From A Land-Estuarine Ocean Biogeochemical Modeling System: Model Description, Evaluation, And Nitrogen Budgets, Yang Feng, Marjorie A.M. Friedrichs, John Wilkin, Hanqin Tian, Qichun Yang, Eileen E. Hofmann, Jerry D. Wiggert, Raleigh R. Hood Aug 2015

Chesapeake Bay Nitrogen Fluxes Derived From A Land-Estuarine Ocean Biogeochemical Modeling System: Model Description, Evaluation, And Nitrogen Budgets, Yang Feng, Marjorie A.M. Friedrichs, John Wilkin, Hanqin Tian, Qichun Yang, Eileen E. Hofmann, Jerry D. Wiggert, Raleigh R. Hood

Faculty Publications

The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land-estuarine-ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within-estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite-derived data, and a simulation using environmental conditions for 2001–2005 was conducted to quantify the Chesapeake Bay nitrogen …


Reliability Of Oscillometric Central Hemodynamic Responses To An Orthostatic Challenge, Lee Stoner, Chantel Bonner, Daniel Credeur, Danielle Lambrick, James Faulkner, Daniel Wadsworth, Michelle A. Williams Aug 2015

Reliability Of Oscillometric Central Hemodynamic Responses To An Orthostatic Challenge, Lee Stoner, Chantel Bonner, Daniel Credeur, Danielle Lambrick, James Faulkner, Daniel Wadsworth, Michelle A. Williams

Faculty Publications

Background: Monitoring central hemodynamic responses to an orthostatic challenge may provide important insight into autonomic nervous system function. Oscillometric pulse wave analysis devices have recently emerged, presenting clinically viable options for investigating central hemodynamic properties. The purpose of the current study was to determine whether oscillometric pulse wave analysis can be used to reliably (between-day) assess central blood pressure and central pressure augmentation (augmentation index) responses to a 5 min orthostatic challenge (modified tilt-table).

Methods: Twenty healthy adults (26.4 y (SD 5.2), 55% F, 24.7 kg/m2 (SD 3.8)) were tested on 3 different mornings in the fasted …


A Multiple Endpoint Analysis Of The Effects Of Chronic Exposure To Sediment Contaminated With Deepwater Horizon Oil On Juvenile Southern Flounder And Their Associated Microbiomes, Nancy J. Brown-Peterson, Michelle Krasnec, Ryan Takeshita, Caitlin N. Ryan, Kimberly J. Griffitt, Claire Lay, Gregory D. Mayer, Keith M. Bayha, William E. Hawkins, Jeffrey Morris, Robert J. Griffitt Aug 2015

A Multiple Endpoint Analysis Of The Effects Of Chronic Exposure To Sediment Contaminated With Deepwater Horizon Oil On Juvenile Southern Flounder And Their Associated Microbiomes, Nancy J. Brown-Peterson, Michelle Krasnec, Ryan Takeshita, Caitlin N. Ryan, Kimberly J. Griffitt, Claire Lay, Gregory D. Mayer, Keith M. Bayha, William E. Hawkins, Jeffrey Morris, Robert J. Griffitt

Faculty Publications

Exposure to oiled sediments can negatively impact the health of fish species. Here, we examine the effects of chronic exposure of juvenile southern flounder, Paralichthys lethostigma, to a sediment-oil mixture. Oil:sediment mixtures are persistent over time and can become bioavailable following sediment perturbation or resuspension. Juvenile flounder were exposed for 32 days under controlled laboratory conditions to five concentrations of naturally weathered Macondo MC252 oil mixed into uncontaminated, field-collected sediments. The percent composition of individual polycyclic aromatic hydrocarbons (PAHs) of the weathered oil did not change after mixing with the sediment. Spiked exposure sediments contained 0.04–395 mg/kg tPAH50 (sum of …


Analyzing The Expression Profile Of Areb/Abf And Dreb/Cbf Genes Under Drought And Salinity Stresses In Grape (Vitis Vinifera L.), Hana Zandkarimi, Ali Ebadi, Seyed Alireza Salami, Houshang Alizade, Niranjan Baisakh Jul 2015

Analyzing The Expression Profile Of Areb/Abf And Dreb/Cbf Genes Under Drought And Salinity Stresses In Grape (Vitis Vinifera L.), Hana Zandkarimi, Ali Ebadi, Seyed Alireza Salami, Houshang Alizade, Niranjan Baisakh

Faculty Publications

Expression patterns of four candidate AREB/ABF genes and four DREB/CBF genes were evaluated in leaf and root tissues of five grape varieties ('Qalati', 'Kaj Angoor', 'Sabz Angoor', 'Siahe Zarghan', 'Bidane Safid') with differential response to drought stress. Among the AREB/ABF genes, AREB1 and ABF2 showed up-regulation in response to drought stress in leaf and root tissues of all varieties while AREB2 and ABF1 showed downregulation in both leaf and root tissues of the sensitive variety 'Bidane Sefid' in response to drought and salt stress. Among the DREB/CBF genes, CBF4 was the most responsive to drought stress in both leaf and …


The Adaptive Change Of Hla-Drb1 Allele Frequencies Caused By Natural Selection In A Mongolian Population That Migrated To The South Of China, Hao Sun, Zhaoqing Yang, Keqin Lin, Shuyuan Liu, Kai Huang, Xiuyun Wang, Jiayou Chu, Xinyu Huang Jul 2015

The Adaptive Change Of Hla-Drb1 Allele Frequencies Caused By Natural Selection In A Mongolian Population That Migrated To The South Of China, Hao Sun, Zhaoqing Yang, Keqin Lin, Shuyuan Liu, Kai Huang, Xiuyun Wang, Jiayou Chu, Xinyu Huang

Faculty Publications

Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another …


Fruit And Vegetable Consumption, Fat Intake, And Physical Activity Participation In Relation To Socio-Demographic Factors Among Medically Underserved Adults, Amir Alakaam, Jennifer Lemacks Jul 2015

Fruit And Vegetable Consumption, Fat Intake, And Physical Activity Participation In Relation To Socio-Demographic Factors Among Medically Underserved Adults, Amir Alakaam, Jennifer Lemacks

Faculty Publications

Fruit and vegetable intake as well as physical activity participation in Mississippi is consistently lower than recommendations. We conducted a cross-sectional study to examine fruit and vegetables consumption, fat intake, and moderate-intensity physical activity participation and how these variables relate to socio-demographic factors among medically underserved adults in south Mississippi. Fruit and vegetable consumption and fat intake along with physical activity participation and socio-demographic characteristics was collected from a sample of 161 (48 male and 113 female) adults in south Mississippi. A majority (81.9%) of participants reported consuming less than five servings of fruits and vegetables per day and 54% …


Phytochrome Diversity In Green Plants And The Origin Of Canonical Plant Phytochromes, Fay Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka Shu Wong, Kathleen M. Pryer, Sarah Mathews Jul 2015

Phytochrome Diversity In Green Plants And The Origin Of Canonical Plant Phytochromes, Fay Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka Shu Wong, Kathleen M. Pryer, Sarah Mathews

Faculty Publications

© 2015 Macmillan Publishers Limited. All rights reserved. Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within …


Quantum Mechanics, Strong Emergence And Ontological Non-Reducibility, Rodolfo Gambini, Lucía Lewowicz, Jorge Pullin Jul 2015

Quantum Mechanics, Strong Emergence And Ontological Non-Reducibility, Rodolfo Gambini, Lucía Lewowicz, Jorge Pullin

Faculty Publications

We show that a new interpretation of quantum mechanics, in which the notion of event is defined without reference to measurement or observers, allows to construct a quantum general ontology based on systems, states and events. Unlike the Copenhagen interpretation, it does not resort to elements of a classical ontology. The quantum ontology in turn allows us to recognize that a typical behavior of quantum systems exhibits strong emergence and ontological non-reducibility. Such phenomena are not exceptional but natural, and are rooted in the basic mathematical structure of quantum mechanics.


Oxidized And Reduced [2fe-2s] Clusters From An Iron(I) Synthon, Megan E. Reesbeck, Meghan M. Rodriguez, William W. Brennessel, Brandon Q. Mercado, David Vinyard, Patrick L. Holland Jul 2015

Oxidized And Reduced [2fe-2s] Clusters From An Iron(I) Synthon, Megan E. Reesbeck, Meghan M. Rodriguez, William W. Brennessel, Brandon Q. Mercado, David Vinyard, Patrick L. Holland

Faculty Publications

© 2015 SBIC. Abstract Synthetic [2Fe-2S] clusters are often used to elucidate ligand effects on the reduction potentials and spectroscopy of natural electron-transfer sites, which can have anionic Cys ligands or neutral His ligands. Current synthetic routes to [2Fe-2S] clusters are limited in their feasibility with a range of supporting ligands. Here, we report a new synthetic route to synthetic [2Fe-2S] clusters, through oxidation of an iron(I) source with elemental sulfur. This method yields a neutral diketiminate-supported [2Fe-2S] cluster in the diiron(III)-oxidized form. The oxidized [2Fe-2S] cluster can be reduced to a mixed valent iron(II)-iron(III) compound. Both the diferric and …


A Novel Glp1 Receptor Interacting Protein Atp6ap2 Regulates Insulin Secretion In Pancreatic Beta Cells, Feihan F. Dai Jul 2015

A Novel Glp1 Receptor Interacting Protein Atp6ap2 Regulates Insulin Secretion In Pancreatic Beta Cells, Feihan F. Dai

Faculty Publications

GLP1 activates its receptor, GLP1R, to enhance insulin secretion. The activation and transduction of GLP1R requires complex interactions with a host of accessory proteins, most of which remain largely unknown. In this study, we used membrane-based split ubiquitin yeast two-hybrid assays to identify novel GLP1R interactors in both mouse and human islets. Among these, ATP6ap2 (ATPase H-transporting lysosomal accessory protein 2) was identified in both mouse and human islet screens. ATP6ap2 was shown to be abundant in islets including both alpha and beta cells. When GLP1R and ATP6ap2 were co-expressed in beta cells, GLP1R was shown to directly interact with …


Urban Evolution: The Role Of Water, Sujay S. Kaushal, William H. Mcdowell, Wilfred M. Wollheim, Tamara A. Newcomer Johnson, Paul M. Mayer, Kenneth T. Belt, Michael J. Pennino Jul 2015

Urban Evolution: The Role Of Water, Sujay S. Kaushal, William H. Mcdowell, Wilfred M. Wollheim, Tamara A. Newcomer Johnson, Paul M. Mayer, Kenneth T. Belt, Michael J. Pennino

Faculty Publications

The structure, function, and services of urban ecosystems evolve over time scales from seconds to centuries as Earth’s population grows, infrastructure ages, and sociopolitical values alter them. In order to systematically study changes over time, the concept of “urban evolution” was proposed. It allows urban planning, management, and restoration to move beyond reactive management to predictive management based on past observations of consistent patterns. Here, we define and review a glossary of core concepts for studying urban evolution, which includes the mechanisms of urban selective pressure and urban adaptation. Urban selective pressure is an environmental or societal driver contributing to …


High Yield Non-Detergent Isolation Of Photosystem I-Light-Harvesting Chlorophyll Ii Membranes From Spinach Thylakoids: Implications For The Organization Of The Ps I Antennae In Higher Plants, Adam J. Bell, Laurie K. Frankel, Terry M. Bricker Jul 2015

High Yield Non-Detergent Isolation Of Photosystem I-Light-Harvesting Chlorophyll Ii Membranes From Spinach Thylakoids: Implications For The Organization Of The Ps I Antennae In Higher Plants, Adam J. Bell, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

© 2015 by The American Society for Biochemistry and Molecular Biology, Inc. Styrene-maleic acid copolymer was used to effect a non-detergent partial solubilization of thylakoids from spinach. A high density membrane fraction, which was not solubilized by the copolymer, was isolated and was highly enriched in the Photosystem (PS) I-light-harvesting chlorophyll (LHC) II supercomplex and depleted of PS II, the cytochrome b6/f complex, and ATP synthase. The LHC II associated with the supercomplex appeared to be energetically coupled to PS I based on 77 K fluorescence, P700 photooxidation, and PS I electron transport light saturation experiments. The chlorophyll (Chl) a/b …


Alternative Preprocessing Of Rna-Sequencing Data In The Cancer Genome Atlas Leads To Improved Analysis Results, Mumtahena Rahman, Laurie K. Jackson, W. Evan Johnson, Dean Y. Li, Andrea H. Bild, Stephen R. Piccolo Jul 2015

Alternative Preprocessing Of Rna-Sequencing Data In The Cancer Genome Atlas Leads To Improved Analysis Results, Mumtahena Rahman, Laurie K. Jackson, W. Evan Johnson, Dean Y. Li, Andrea H. Bild, Stephen R. Piccolo

Faculty Publications

Motivation: The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides ‘Level 3’ data, which have been processed using a pipeline specific to that resource. However, we have found using experimentally derived data that this pipeline produces gene-expression values that vary considerably across biological replicates. In addition, some RNA-Sequencing analysis tools require integer-based read counts, which are not provided with the Level 3 data. As an alternative, we have reprocessed the data for 9264 tumor and 741 normal samples across 24 cancer types using the Rsubread package. We have also collated corresponding clinical data for these …


Directional Dominance On Stature And Cognition In Diverse Human Populations, Peter K. Joshi, Tonu Esko, Hannele Mattsson, Niina Eklund, Ilaria Gandin, Teresa Nutile, Anne U. Jackson, Claudia Schurmann, Albert V. Smith, Weihua Zhang, Yukinori Okada, Alena Stančáková, Jessica D. Faul, Wei Zhao, Traci M. Bartz, Maria Pina Concas, Nora Franceschini, Stefan Enroth, Veronique Vitart, Stella Trompet, Xiuqing Guo, Daniel I. Chasman, Jeffrey R. O'Connel, Tanguy Corre, Suraj S. Nongmaithem, Yuning Chen, Massimo Mangino, Daniela Ruggiero, Michela Traglia, Aliki Eleni Farmaki, Tim Kacprowski, Andrew Bjonnes, Ashley Van Der Spek Jul 2015

Directional Dominance On Stature And Cognition In Diverse Human Populations, Peter K. Joshi, Tonu Esko, Hannele Mattsson, Niina Eklund, Ilaria Gandin, Teresa Nutile, Anne U. Jackson, Claudia Schurmann, Albert V. Smith, Weihua Zhang, Yukinori Okada, Alena Stančáková, Jessica D. Faul, Wei Zhao, Traci M. Bartz, Maria Pina Concas, Nora Franceschini, Stefan Enroth, Veronique Vitart, Stella Trompet, Xiuqing Guo, Daniel I. Chasman, Jeffrey R. O'Connel, Tanguy Corre, Suraj S. Nongmaithem, Yuning Chen, Massimo Mangino, Daniela Ruggiero, Michela Traglia, Aliki Eleni Farmaki, Tim Kacprowski, Andrew Bjonnes, Ashley Van Der Spek

Faculty Publications

Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of …


Exposure To Deepwater Horizon Crude Oil Burnoff Particulate Matter Induces Pulmonary Inflammation And Alters Adaptive Immune Response, Sridhar Jaligama, Zaili Chen, Jordy Saravia, Nikki Yadav, Slawomir M. Lomnicki, Tammy R. Dugas, Stephania A. Cormier Jul 2015

Exposure To Deepwater Horizon Crude Oil Burnoff Particulate Matter Induces Pulmonary Inflammation And Alters Adaptive Immune Response, Sridhar Jaligama, Zaili Chen, Jordy Saravia, Nikki Yadav, Slawomir M. Lomnicki, Tammy R. Dugas, Stephania A. Cormier

Faculty Publications

© 2015 American Chemical Society. The "in situ burning" of trapped crude oil on the surface of Gulf waters during the 2010 Deepwater Horizon (DWH) oil spill released numerous pollutants, including combustion-generated particulate matter (PM). Limited information is available on the respiratory impact of inhaled in situ burned oil sail particulate matter (OSPM). Here we utilized PM collected from in situ burn plumes of the DWH oil spill to study the acute effects of exposure to OSPM on pulmonary health. OSPM caused dose-and time-dependent cytotoxicity and generated reactive oxygen species and superoxide radicals in vitro. Additionally, mice exposed to OSPM …


Macromolecular Crystallography For Synthetic Abiological Molecules: Combining Xmdff And Phenix For Structure Determination Of Cyanostar Macrocycles, Abhishek Singharoy, Balasubramanian Venkatakrishnan, Yun Liu, Christopher G. Mayne, Semin Lee, Chun Hsing Chen, Adam Zlotnick, Klaus Schulten, Amar H. Flood Jul 2015

Macromolecular Crystallography For Synthetic Abiological Molecules: Combining Xmdff And Phenix For Structure Determination Of Cyanostar Macrocycles, Abhishek Singharoy, Balasubramanian Venkatakrishnan, Yun Liu, Christopher G. Mayne, Semin Lee, Chun Hsing Chen, Adam Zlotnick, Klaus Schulten, Amar H. Flood

Faculty Publications

© 2015 American Chemical Society. Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multimolecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that biomacromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar …


Redesigning Photosynthesis To Sustainably Meet Global Food And Bioenergy Demand, Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, Ralph Bock, Roberta Croce, Maureen R. Hanson, Julian M. Hibberd, Stephen P. Long, Thomas A. Moore, James Moroney, Krishna K. Niyogi, Martin A.J. Parry, Pamela P. Peralta-Yahya, Roger C. Prince, Kevin E. Redding, Martin H. Spalding, Klaas J. Van Wijk, Wim F.J. Vermaas, Susanne Von Caemmerer, Andreas P.M. Weber, Todd O. Yeates, Joshua S. Yuan, Xin Guang Zhu Jul 2015

Redesigning Photosynthesis To Sustainably Meet Global Food And Bioenergy Demand, Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, Ralph Bock, Roberta Croce, Maureen R. Hanson, Julian M. Hibberd, Stephen P. Long, Thomas A. Moore, James Moroney, Krishna K. Niyogi, Martin A.J. Parry, Pamela P. Peralta-Yahya, Roger C. Prince, Kevin E. Redding, Martin H. Spalding, Klaas J. Van Wijk, Wim F.J. Vermaas, Susanne Von Caemmerer, Andreas P.M. Weber, Todd O. Yeates, Joshua S. Yuan, Xin Guang Zhu

Faculty Publications

© 2015, National Academy of Sciences. All rights reserved. The world's crop productivity is stagnating whereas population growth, rising affluence, and mandates for biofuels put increasing demands on agriculture. Meanwhile, demand for increasing cropland competes with equally crucial global sustainability and environmental protection needs. Addressing this looming agricultural crisis will be one of our greatest scientific challenges in the coming decades, and success will require substantial improvements at many levels. We assert that increasing the efficiency and productivity of photosynthesis in crop plants will be essential if this grand challenge is to be met. Here, we explore an array of …


Optimum 3d Matrix Stiffness For Maintenance Of Cancer Stem Cells Is Dependent On Tissue Origin Of Cancer Cells, Esmaiel Jabbari, Samaneh K. Sarvestani, Leily Daneshian, Seyedsina Moeinzadeh Jul 2015

Optimum 3d Matrix Stiffness For Maintenance Of Cancer Stem Cells Is Dependent On Tissue Origin Of Cancer Cells, Esmaiel Jabbari, Samaneh K. Sarvestani, Leily Daneshian, Seyedsina Moeinzadeh

Faculty Publications

Introduction

The growth and expression of cancer stem cells (CSCs) depend on many factors in the tumor microenvironment. The objective of this work was to investigate the effect of cancer cells’ tissue origin on the optimum matrix stiffness for CSC growth and marker expression in a model polyethylene glycol diacrylate (PEGDA) hydrogel without the interference of other factors in the microenvironment.

Methods

Human MCF7 and MDA-MB-231 breast carcinoma, HCT116 colorectal and AGS gastric carcinoma, and U2OS osteosarcoma cells were used. The cells were encapsulated in PEGDA gels with compressive moduli in the 2-70 kPa range and optimized cell seeding density …


Evaluating The Validity Of Self-Reported Smoking In Mexican Adolescents, María Del Carmen Valladolid-López, Tonatiuh Barrientos-Gutiérrez, Luz Myriam Reynales-Shigematsu, Jim Thrasher, Ingris Peláez-Ballestas, Eduardo Lazcano-Ponce, Mauricio Hernández-Ávila Jul 2015

Evaluating The Validity Of Self-Reported Smoking In Mexican Adolescents, María Del Carmen Valladolid-López, Tonatiuh Barrientos-Gutiérrez, Luz Myriam Reynales-Shigematsu, Jim Thrasher, Ingris Peláez-Ballestas, Eduardo Lazcano-Ponce, Mauricio Hernández-Ávila

Faculty Publications

Objectives We aimed to evaluate the validity of the self-reported smoking indicator used in the Global Youth Tobacco Survey (GYTS).

Setting 43 middle and high-school classrooms from 26 schools were selected from Mexico City and Cuernavaca, Morelos.

Participants A total of 1257 students provided both a questionnaire and a urine sample.

Primary and secondary outcome Sensitivity and specificity of self-reported smoking compared to urinary cotinine. Validity indices were evaluated by subgroups of gender, social acceptability of smoking (ie, smoking parents or friends) and smoking frequency.

Results Sensitivity and specificity for current smoking were 93.2% and 81.7%, respectively. Validity indices remained …


Deep Characterization Of The Microbiomes Of Calophya Spp. (Hemiptera: Calophyidae) Gall-Inducing Psyllids Reveals The Absence Of Plant Pathogenic Bacteria And Three Dominant Endosymbionts, Will A. Overholt, Rodrigo Diaz, Erin Rosskopf, Stefan J. Green, William A. Overholt Jul 2015

Deep Characterization Of The Microbiomes Of Calophya Spp. (Hemiptera: Calophyidae) Gall-Inducing Psyllids Reveals The Absence Of Plant Pathogenic Bacteria And Three Dominant Endosymbionts, Will A. Overholt, Rodrigo Diaz, Erin Rosskopf, Stefan J. Green, William A. Overholt

Faculty Publications

© This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Bacteria associated with sap-feeding insect herbivores include not only symbionts that may increase their hosts' fitness but also harmful plant pathogens. Calophya spp. gall-inducing psyllids (Hemiptera: Calophyidae) are being investigated for their potential as biological control agents of the noxious weed, Brazilian peppertree (Schinus terebinthifolia), in Florida. Although there are no examples of plant pathogen transmission by …


Demographic Comparison Of Sweetpotato Weevil Reared On A Major Host, Ipomoea Batatas, And An Alternative Host, I. Triloba, Gadi V.P. Reddy, Hisn Chi Jul 2015

Demographic Comparison Of Sweetpotato Weevil Reared On A Major Host, Ipomoea Batatas, And An Alternative Host, I. Triloba, Gadi V.P. Reddy, Hisn Chi

Faculty Publications

In this study, we collected life table data for the sweetpotato weevil, Cylas formicarius, grown on Ipomoea batatas and Ipomoea triloba, and analyzed them using an age-stage, two-sex life table. We also demonstrated the growth potential of C. formicarius on these two host plants by using population projection. These data will be useful to the growers to the selection or eradication of host plants in an integrated control strategy for C. formicarius for the entire area of the targeted areas. We found that C. formicarius developed faster on I. batatas than on I. triloba. The developmental times of the larval …


Erratum: Biological Evidence Supports An Early And Complex Emergence Of The Isthmus Of Panama (Proceedings Of The National Academy Of Sciences Of The United States Of America (2015) 112:19 (6110-6115) Doi: 10.1073/Pnas.1423853112), Christine D. Bacon, Daniele Silvestro, Carlos Jaramillo, Brian Tilston Smith, Prosanta Chakrabarty, Alexandre Antonelli Jul 2015

Erratum: Biological Evidence Supports An Early And Complex Emergence Of The Isthmus Of Panama (Proceedings Of The National Academy Of Sciences Of The United States Of America (2015) 112:19 (6110-6115) Doi: 10.1073/Pnas.1423853112), Christine D. Bacon, Daniele Silvestro, Carlos Jaramillo, Brian Tilston Smith, Prosanta Chakrabarty, Alexandre Antonelli

Faculty Publications

No abstract provided.


Connecting Self-Efficacy And Nature Of Science Shifts In Undergraduate Research Experiences, Gina Quan Jul 2015

Connecting Self-Efficacy And Nature Of Science Shifts In Undergraduate Research Experiences, Gina Quan

Faculty Publications

Undergraduate research can support students’ more central participation in physics. We present analysis of one way this participation may shift: changes in their beliefs about the Nature of Science coupled to changes in a sense of ability to contribute to authentic research. Students in the study worked with faculty and graduate student research mentors on research projects and also participated in a seminar where they learned about research and reflected on their experiences. In videotaped interviews, we asked students to describe their experiences in research. Students developed nuanced views about how the research process works coupled to shifts in their …