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Faculty Publications

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Articles 1111 - 1140 of 2622

Full-Text Articles in Life Sciences

Cognitive Phenotypes And The Evolution Of Animal Decisions, Tamra C. Mendelson, Courtney L. Fitzpatrick, Mark E. Hauber, Charles H. Pence, Rafael L. Rodríguez, Rebecca J. Safran, Caitlin A. Stern, Jeffrey R. Stevens Jan 2016

Cognitive Phenotypes And The Evolution Of Animal Decisions, Tamra C. Mendelson, Courtney L. Fitzpatrick, Mark E. Hauber, Charles H. Pence, Rafael L. Rodríguez, Rebecca J. Safran, Caitlin A. Stern, Jeffrey R. Stevens

Faculty Publications

Despite the clear fitness consequences of animal decisions, the science of animal decision making in evolutionary biology is underdeveloped compared with decision science in human psychology. Specifically, the field lacks a conceptual framework that defines and describes the relevant components of a decision, leading to imprecise language and concepts. The ‘judgment and decision-making’ (JDM) framework in human psychology is a powerful tool for framing and understanding human decisions, and we apply it here to components of animal decisions, which we refer to as ‘cognitive phenotypes’. We distinguish multiple cognitive phenotypes in the context of a JDM framework and highlight empirical …

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Modeling Animal Behavior In A Changing Environment, Shandelle M. Henson, James M. Cushing, James L. Hayward Jan 2016

Modeling Animal Behavior In A Changing Environment, Shandelle M. Henson, James M. Cushing, James L. Hayward

Faculty Publications

No abstract provided.

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Synergistic Growth In Bacteria Depends On Substrate Complexity, Yi-Jie Deng, Shiao Y. Wang Jan 2016

Synergistic Growth In Bacteria Depends On Substrate Complexity, Yi-Jie Deng, Shiao Y. Wang

Faculty Publications

Both positive and negative interactions among bacteria take place in the environment. We hypothesize that the complexity of the substrate affects the way bacteria interact with greater cooperation in the presence of recalcitrant substrate. We isolated lignocellulolytic bacteria from salt marsh detritus and compared the growth, metabolic activity and enzyme production of pure cultures to those of three-species mixed cultures in lignocellulose and glucose media. Synergistic growth was common in lignocellulose medium containing carboxyl methyl cellulose, xylan and lignin but absent in glucose medium. Bacterial synergism promoted metabolic activity in synergistic mixed cultures but not the maximal growth rate (μ). …

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Data For Henson Et Al. 2016, Shandelle Henson, James Hayward, J Cushing, Gordon Atkins, Sumiko Weir, Ashley Reichert, Wayanne Watson, Wadenerson Saint Martin, Amanda Sandler Jan 2016

Data For Henson Et Al. 2016, Shandelle Henson, James Hayward, J Cushing, Gordon Atkins, Sumiko Weir, Ashley Reichert, Wayanne Watson, Wadenerson Saint Martin, Amanda Sandler

Faculty Publications

These data are archived for the paper "Adaptation to short-term ENSO fluctuations may provide tipping points for populations subjected to long-term climate change" by Henson et al., submitted. Additional files: Supplementary Figure 1 | Sample plots on Violet Point, Protection Island National Wildlife Refuge, Washington, USA. The larger colony extends throughout much of the spit.

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Powerful Association Test Combining Rare Variant And Gene Expression Using Family Data From Genetic Analysis Workshop 19, Yen Yi Ho, Weihua Guan, Michael O'Connell, Saonli Basu Jan 2016

Powerful Association Test Combining Rare Variant And Gene Expression Using Family Data From Genetic Analysis Workshop 19, Yen Yi Ho, Weihua Guan, Michael O'Connell, Saonli Basu

Faculty Publications

Background: Genetic association studies aim to test for disease or trait association with genetic variants, either throughout the human genome or in regions of interest. However, for most diseases and traits, the combined effects of associated genetic variants explain only a small proportion of the genetic variation. This "missing heritability" may be a result of the small effects of common variants considered in the genetic association studies. Rare variants may also play an important role in understanding the missing heritability of complex traits. Method: We propose a novel weight-adjustment approach to combine gene expression into rare variant analysis. Results from …

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Natural History, Phenology, And Stream Use Of Hyla Plicata From The Arroyo Los Axolotes, State Of Mexico, Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith, A. Hernandez Ruiz, R. Montoya Ayala Jan 2016

Natural History, Phenology, And Stream Use Of Hyla Plicata From The Arroyo Los Axolotes, State Of Mexico, Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith, A. Hernandez Ruiz, R. Montoya Ayala

Faculty Publications

No abstract provided.

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Amphibians And Reptiles Of The State Of Nuevo Leon, Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith, A. Cruz Jan 2016

Amphibians And Reptiles Of The State Of Nuevo Leon, Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith, A. Cruz

Faculty Publications

No abstract provided.

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Amphibians And Reptiles Of The State Of Coahuila, Mexico, With Comparison With Adjoining States, J. A. Lemos-Espinal, Geoffrey R. Smith Jan 2016

Amphibians And Reptiles Of The State Of Coahuila, Mexico, With Comparison With Adjoining States, J. A. Lemos-Espinal, Geoffrey R. Smith

Faculty Publications

No abstract provided.

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Failure Of A Heterologous Recombinant Sca5/Ompb Protein-Based Vaccine To Elicit Effective Protective Immunity Against Rickettsia Rickettsii Infections In C3h/Hen Mice, Sean P. Riley, Marissa M. Cardwell, Yvonne G. Chan, Ludovic Pruneau, Fabio Del Piero, Juan J. Martinez Dec 2015

Failure Of A Heterologous Recombinant Sca5/Ompb Protein-Based Vaccine To Elicit Effective Protective Immunity Against Rickettsia Rickettsii Infections In C3h/Hen Mice, Sean P. Riley, Marissa M. Cardwell, Yvonne G. Chan, Ludovic Pruneau, Fabio Del Piero, Juan J. Martinez

Faculty Publications

Spotted fever group (SFG) rickettsial species are obligate intracellular tick-borne pathogens that are responsible for important human diseases. Previous reports have demonstrated the feasibility of using recombinant surface cell antigen Sca5/OmpB to elicit protective immunity against homologous challenges using murine models of Mediterranean spotted fever and Rocky Mountain spotted fever. In addition, the feasibility of generating cross-protective immunity against related rickettsial species has also been established, but the molecular basis for these phenomena was not explored. Here, we demonstrate that vaccination of C3H/HeN mice with a recombinant OmpB domain derived from Rickettsia conorii induced high titer humoral immune responses that …

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Dollfustrema Durum N. Sp. And Heterobucephalopsis Perardua N. Sp. (Digenea: Bucephalidae) From The Giant Moray Eel, Gymnothorax Javanicus (Bleeker) (Anguilliformes: Muraenidae), And Proposal Of The Heterobucephalopsinae N. Subfam, Matthew J. Nolan, Stephen S. Curran, Terrence L. Miller, Scott C. Cutmore, Cinzia Cantacessi, Thomas H. Cribb Dec 2015

Dollfustrema Durum N. Sp. And Heterobucephalopsis Perardua N. Sp. (Digenea: Bucephalidae) From The Giant Moray Eel, Gymnothorax Javanicus (Bleeker) (Anguilliformes: Muraenidae), And Proposal Of The Heterobucephalopsinae N. Subfam, Matthew J. Nolan, Stephen S. Curran, Terrence L. Miller, Scott C. Cutmore, Cinzia Cantacessi, Thomas H. Cribb

Faculty Publications

Two new species of bucephalid trematode (Platyhelminthes: Digenea) are described from the giant moray eel, Gymnothorax javanicus (Anguilliformes: Muraenidae), from off Lizard Island, Australia. We used a combined morphological and molecular-based approach targeting the internal transcribed spacer 2 (ITS2) of the ribosomal DNA (rDNA) and the D1–D3 region of the large subunit (28S) of rDNA to circumscribe the species. Dollfustrema durum n. sp. is distinguished from seven congeners in having 5–6 rows of enlarged body spines circling the anterior portion of the rhynchus. From the remaining 10 species, D. durum n. sp. differs in body length, and in having a …

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Differences In Patterns Of Reproductive Allocation Between The Sexes In Nicrophorus Orbicollis, Ashlee N. Smith, J. Curtis Creighton, Mark C. Belk Nov 2015

Differences In Patterns Of Reproductive Allocation Between The Sexes In Nicrophorus Orbicollis, Ashlee N. Smith, J. Curtis Creighton, Mark C. Belk

Faculty Publications

Organisms are selected to maximize lifetime reproductive success by balancing the costs of current reproduction with costs to future survival and fecundity. Males and females typically face different reproductive costs, which makes comparisons of their reproductive strategies difficult. Burying beetles provide a unique system that allows us to compare the costs of reproduction between the sexes because males and females are capable of raising offspring together or alone and carcass preparation and offspring care represent the majority of reproductive costs for both sexes. Because both sexes perform the same functions of carcass preparation and offspring care, we predict that they …

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Linkages Among Fluorescent Dissolved Organic Matter, Dissolved Amino Acids And Lignin-Derived Phenols In River-Influenced Ocean Margins, Youhei Yamashita, Cédric G. Fichot, Yuan Shen, Rudolf Jaffé, Ronald Benner Nov 2015

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

Faculty Publications

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

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Gene-Expression Patterns In Peripheral Blood Classify Familial Breast Cancer Susceptibility, Stephen R. Piccolo, Irene L. Andrulis, Adam L. Cohen, Thomas Connor, Philip J. Moos, Avrum E. Spira, Saundra S. Buys, W. Evan Johnson, Andrea H. Bild Nov 2015

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

Faculty Publications

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

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Loss Of Glycosaminoglycan Receptor Binding After Mosquito Cell Passage Reduces Chikungunya Virus Infectivity, Dhiraj Acharya, Amber M. Paul, John F. Anderson, Faqing Huang, Fengwei Bai Oct 2015

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

Faculty Publications

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

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Sedentary Behavior In Preschoolers: How Many Days Of Accelerometer Monitoring Is Needed?, Wonwoo Byun, Michael W. Beets, Russell R. Pate Oct 2015

Sedentary Behavior In Preschoolers: How Many Days Of Accelerometer Monitoring Is Needed?, Wonwoo Byun, Michael W. Beets, Russell R. Pate

Faculty Publications

The reliability of accelerometry for measuring sedentary behavior in preschoolers has not been determined, thus we determined how many days of accelerometry monitoring are necessary to reliably estimate daily time spent in sedentary behavior in preschoolers. In total, 191 and 150 preschoolers (three to five years) wore ActiGraph accelerometers (15-s epoch) during the in-school (≥4 days) and the total-day (≥6 days) period respectively. Accelerometry data were summarized as time spent in sedentary behavior (min/h) using three different cutpoints developed for preschool-age children (

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An Insight Into The Functional Role Of Thioredoxin Reductase, A Selenoprotein, In Maintaining Normal Native Microbiota In The Gulf Coast Tick (Ambylomma Maculatum), Khemraj Budachetri, Shahid Karim Oct 2015

An Insight Into The Functional Role Of Thioredoxin Reductase, A Selenoprotein, In Maintaining Normal Native Microbiota In The Gulf Coast Tick (Ambylomma Maculatum), Khemraj Budachetri, Shahid Karim

Faculty Publications

Tick selenoproteins have been associated with antioxidant activity in ticks. Thioredoxin reductase (TrxR), also a selenoprotein, belongs to the pyridine nucleotide‐disulphide oxidoreductase family of proteins and is an important antioxidant. Molecular interactions between native microbiota and tick hosts have barely been investigated to date. In this study, we determined the functional role of TrxR in tick feeding and in maintenance of the native microbial community. TrxR transcript levels remained high and microbial load was reduced throughout tick attachment to the vertebrate host. RNA interference (RNAi) showed that depletion of TrxR activity did not interfere with tick haematophagy or phenotype but …

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Evolutionary And Ecological Characterization Of Mayaro Virus Strains Isolated During An Outbreak, Venezuela, 2010, Albert J. Auguste, Jonathan Liria, Naomi L. Forrester, Dileyvic Giambalvo, Moncada Maria, Kanya C. Long, Dulce Morón, Nuris De Manzione, Robert B. Tesh, Eric S. Halsey, Tadeusz J. Kochel, Rosa Hernandez, Juan-Carlos Navarro, Scott C. Weaver Oct 2015

Evolutionary And Ecological Characterization Of Mayaro Virus Strains Isolated During An Outbreak, Venezuela, 2010, Albert J. Auguste, Jonathan Liria, Naomi L. Forrester, Dileyvic Giambalvo, Moncada Maria, Kanya C. Long, Dulce Morón, Nuris De Manzione, Robert B. Tesh, Eric S. Halsey, Tadeusz J. Kochel, Rosa Hernandez, Juan-Carlos Navarro, Scott C. Weaver

Faculty Publications

In 2010, an outbreak of febrile illness with arthralgic manifestations was detected at La Estación village, Portuguesa State, Venezuela. The etiologic agent was determined to be Mayaro virus (MAYV), a reemerging South American alphavirus. A total of 77 cases was reported and 19 were confirmed as seropositive. MAYV was isolated from acute-phase serum samples from 6 symptomatic patients. We sequenced 27 complete genomes representing the full spectrum of MAYV genetic diversity, which facilitated detection of a new genotype, designated N. Phylogenetic analysis of genomic sequences indicated that etiologic strains from Venezuela belong to genotype D. Results indicate that MAYV is …

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Altered Activation Of Protein Kinase Pkr And Enhanced Apoptosis In Dystonia Cells Carrying A Mutation In Pkr Activator Protein Pact, Lauren S. Vaughn, D. Cristopher Bragg, Nutan Sharma, Sarah Camargos, Francisco Cardoso, Rekha C. Patel Sep 2015

Altered Activation Of Protein Kinase Pkr And Enhanced Apoptosis In Dystonia Cells Carrying A Mutation In Pkr Activator Protein Pact, Lauren S. Vaughn, D. Cristopher Bragg, Nutan Sharma, Sarah Camargos, Francisco Cardoso, Rekha C. Patel

Faculty Publications

PACT is a stress-modulated activator of the interferon-induced double-stranded RNA-activated protein kinase (PKR). Stress-induced phosphorylation of PACT is essential for PACT's association with PKR leading to PKR activation. PKR activation leads to phosphorylation of translation initiation factor eIF2α inhibition of protein synthesis and apoptosis.Arecessively inherited form of early-onset dystonia DYT16 has been recently identified to arise due to a homozygous missense mutation P222L in PACT. To examine if the mutant P222L protein alters the stress-response pathway, we examined the ability of mutant P222L to interact with and activate PKR. Our results indicate that the substitution mutant P222L activates PKR more …

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Precise Repair Of Mping Excision Sites Is Facilitated By Target Site Duplication Derived Microhomology, David M. Gilbert, M. Catherine Bridges, Ashley E. Strother, Courtney E. Burckhalter, James M. Burnette Iii, C. Nathan Hancock Sep 2015

Precise Repair Of Mping Excision Sites Is Facilitated By Target Site Duplication Derived Microhomology, David M. Gilbert, M. Catherine Bridges, Ashley E. Strother, Courtney E. Burckhalter, James M. Burnette Iii, C. Nathan Hancock

Faculty Publications

A key difference between the Tourist and Stowaway families of miniature inverted repeat transposable elements (MITEs) is the manner in which their excision alters the genome. Upon excision, Stowaway-like MITEs and the associated Mariner elements usually leave behind a small duplication and short sequences from the end of the element. These small insertions or deletions known as “footprints” can potentially disrupt coding or regulatory sequences. In contrast, Tourist-like MITEs and the associated PIF/Pong/Harbinger elements generally excise precisely, returning the genome to its original state. The purpose of this study was to determine the mechanisms underlying these …

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Testosterone Might Not Be Necessary To Support Female Aggression In Incubating Northern Cardinals, M. Susan Devries, Caitlin P. Winters, Jodie M. Jawor Sep 2015

Testosterone Might Not Be Necessary To Support Female Aggression In Incubating Northern Cardinals, M. Susan Devries, Caitlin P. Winters, Jodie M. Jawor

Faculty Publications

Testosterone's (T) influence on male aggression has been well established in many vertebrate species, but the impact of T on female aggressive behaviour is poorly understood. Among birds, a link between T and female aggression is plausible, as females of many species exhibit a seasonal peak in T concentrations at the onset of breeding when social instability is greatest and they may have circulating T through much of the breeding season. However, investigations examining the relationship between T and female aggression are few and have yielded conflicting results, with experimentally or endogenously elevated T supporting aggressive behaviour in females of …

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Functional, Sub-100 Nm Polymer Nanoparticles Via Thiol-Ene Miniemulsion Photopolymerization, Douglas Amato, Dahlia Amato, Alex S. Flynt, Derek L. Patton Aug 2015

Functional, Sub-100 Nm Polymer Nanoparticles Via Thiol-Ene Miniemulsion Photopolymerization, Douglas Amato, Dahlia Amato, Alex S. Flynt, Derek L. Patton

Faculty Publications

In this work, sub-100 nm crosslinked polythioether nanoparticles were synthesized via thiol–ene photopolymerization in miniemulsion using high-energy homogenization. The effects of the miniemulsion formulation and homogenization parameters – including inhibitor concentration, surfactant concentration, organic weight fraction, ultrasonication time and amplitude – on nanoparticle size and size distribution were investigated. Thiol–ene nanoparticles with a mean particle diameter of 46 nm were obtained under optimized conditions for the current system at 2.5 wt% organic fraction and 20 mM surfactant concentration. In an effort to demonstrate potential utility of thiol–ene nanoparticles, we exploit the step-growth radical mechanism of thiol–ene photopolymerization under non-stoichiometric conditions …

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Nanotechnology In The Real World: Redeveloping The Nanomaterial Consumer Products Inventory, Marina E. Vance, Todd Kuiken, Eric P. Vejerano, Sean P. Mcginnis, Michael F. Hochella Jr., David Rejeski, Matthew S. Hull Aug 2015

Nanotechnology In The Real World: Redeveloping The Nanomaterial Consumer Products Inventory, Marina E. Vance, Todd Kuiken, Eric P. Vejerano, Sean P. Mcginnis, Michael F. Hochella Jr., David Rejeski, Matthew S. Hull

Faculty Publications

To document the marketing and distribution of nano-enabled products into the commercial marketplace, the Woodrow Wilson International Center for Scholars and the Project on Emerging Nanotechnologies created the Nanotechnology Consumer Products Inventory (CPI) in 2005. The objective of this present work is to redevelop the CPI by leading a research effort to increase the usefulness and reliability of this inventory. We created eight new descriptors for consumer products, including information pertaining to the nanomaterials contained in each product. The project was motivated by the recognition that a diverse group of stakeholders from academia, industry, and state/federal government had become highly …

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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 hostparasite 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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The Effect Of Training In Minimalist Running Shoes On Running Economy, Sarah T. Ridge, Tyler Standifird, Jessica Rivera, A. Wayne Johnson, Ulrike H. Mitchell, Iain Hunter Aug 2015

The Effect Of Training In Minimalist Running Shoes On Running Economy, Sarah T. Ridge, Tyler Standifird, Jessica Rivera, A. Wayne Johnson, Ulrike H. Mitchell, Iain Hunter

Faculty Publications

The purpose of this study was to examine the effect of minimalist running shoes on oxygen uptake during running before and after a 10-week transition from traditional to minimalist running shoes. Twenty-five recreational runners (no previous experience in minimalist running shoes) participated in submaximal VO2 testing at a self-selected pace while wearing traditional and minimalist running shoes. Ten of the 25 runners gradually transitioned to minimalist running shoes over 10 weeks (experimental group), while the other 15 maintained their typical training regimen (control group). All participants repeated submaximal VO2 testing at the end of 10 weeks. Testing included a 3 …

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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 …

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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 …

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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 …

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Anion-Responsive Metallopolymer Hydrogels For Healthcare Applications, Jiuyang Zhang, Jing Yan, Parasmani Pageni, Yi Yan, Adam Wirth, Yun-Ping Chen, Yali Qiao, Qian Wang, Alan W. Decho, Chuanbing Tang Jul 2015

Anion-Responsive Metallopolymer Hydrogels For Healthcare Applications, Jiuyang Zhang, Jing Yan, Parasmani Pageni, Yi Yan, Adam Wirth, Yun-Ping Chen, Yali Qiao, Qian Wang, Alan W. Decho, Chuanbing Tang

Faculty Publications

Metallopolymers combine a processable, versatile organic polymeric skeleton with functional metals, providing multiple functions and methodologies in materials science. Taking advantage of cationic cobaltocenium as the key building block, organogels could be simply switched to hydrogels via a highly efficient ion exchange. With the unique ionic complexion ability, cobaltocenium moieties provide a robust soft substrate for recycling antibiotics from water. The essential polyelectrolyte nature offers the metallopolymer hydrogels to kill multidrug resistant bacteria. The multifunctional characteristics of these hydrogels highlight the potential for metallopolymers in the field of healthcare and environmental treatment.

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An Insight Into The Sialome Of The Lone Star Tick, Ambylomma Americanum, With A Glimpse On Its Time Dependent Gene Expression, Shahid Karim, José M.C. Ribeiro Jul 2015

An Insight Into The Sialome Of The Lone Star Tick, Ambylomma Americanum, With A Glimpse On Its Time Dependent Gene Expression, Shahid Karim, José M.C. Ribeiro

Faculty Publications

Hard ticks feed for several days or weeks on their hosts. Blood feeding is assisted by tick saliva, which is injected in the host skin regularly, alternating with blood ingestion. Tick saliva contains hundreds or thousands of different peptides and other bioactive compounds that assist feeding by inhibiting their hosts’ blood clotting, platelet aggregation, vasoconstriction, as well as pain and itching. Immunomodulatory and antimicrobial peptides are also found in tick saliva. Molecular characterization of tick salivary compounds, or its sialome (from the Greek sialos = saliva), helps identification of possible antigens that might confer anti-tick immunity, as well as identifying …

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Inferring Pathway Dysregulation In Cancers From Multiple Types Of Omic Data, Shelley M. Macneil, William E. Johnson, Dean Y. Li, Stephen R. Piccolo, Andrea H. Bild Jun 2015

Inferring Pathway Dysregulation In Cancers From Multiple Types Of Omic Data, Shelley M. Macneil, William E. Johnson, Dean Y. Li, Stephen R. Piccolo, Andrea H. Bild

Faculty Publications

Although in some cases individual genomic aberrations may drive disease development in isolation, a complex interplay among multiple aberrations is common. Accordingly, we developed Gene Set Omic Analysis (GSOA), a bioinformatics tool that can evaluate multiple types and combinations of omic data at the pathway level. GSOA uses machine learning to identify dysregulated pathways and improves upon other methods because of its ability to decipher complex, multigene patterns. We compare GSOA to alternative methods and demonstrate its ability to identify pathways known to play a role in various cancer phenotypes. Software implementing the GSOA method is freely available from https://bitbucket.org/srp33/gsoa …

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