Biology Commons^™

Developmental Functions Of Mir156-Regulated Squamosa Promoter Binding Protein-Like (Spl) Genes In Arabidopsis Thaliana, Mingli Xu, Tieqiang Hu, Jianfei Zhao, Mee-Yeon Park, Keith W. Earley, Gang Wu, Li Yang, R. Scott Poethig

Faculty Publications

Correct developmental timing is essential for plant fitness and reproductive success. Two important transitions in shoot development—the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition—are mediated by a group of genes targeted by miR156, SQUAMOSA PROMOTER BINDING PROTEIN (SBP) genes. To determine the developmental functions of these genes in Arabidopsis thaliana, we characterized their expression patterns, and their gain-of-function and loss-of-function phenotypes. Our results reveal that SBP-LIKE (SPL) genes in Arabidopsis can be divided into three functionally distinct groups: 1) SPL2, SPL9, SPL10, SPL11, SPL13 and SPL15 contribute to both the juvenile-to-adult vegetative transition …

Structural Characterization Of Tick Cement Cones Collected From In Vivo And Artifical Membrane Blood-Fed Lone Star Ticks (Ambylomma Americanum), Rebekah Bullard, Paige Allen, Chien-Chung Chao, Jessica Douglas, Pradipta K. Das, Sarah E. Morgan, Wei-Mei Ching, Shahid Karim

Faculty Publications

The Lone Star tick, Amblyomma americanum, is endemic to the southeastern United States and capable of transmitting pathogenic diseases and causing non-pathogenic conditions. To remain firmly attached to the host, the tick secretes a proteinaceous matrix termed the cement cone which hardens around the tick’s mouthparts to assist in the attachment of the tick as well as to protect the mouthparts from the host immune system. Cement cones collected from ticks on a host are commonly contaminated with host skin and hair making analysis of the cone difficult. To reduce the contamination found in the cement cone, we have adapted …

Sources And Transformations Of Dissolved Lignin Phenols And Chromophoric Dissolved Organic Matter In Otsuchi Bay, Japan, Chia-Jung Lu, Ronald Benner, Cedric Fichot, Hideki Fukuda, Youhei Yamashita, Hiroshi Ogawa

Faculty Publications

Dissolved lignin phenols and optical properties of dissolved organic matter (DOM) were measured to investigate the sources and transformations of terrigenous DOM (tDOM) in Otsuchi Bay, Japan. Three rivers discharge into the bay, and relatively high values of syringyl:vanillyl phenols (0.73 ± 0.07) and cinnamyl:vanillyl phenols (0.33 ± 0.10) indicated large contributions of non-woody angiosperm tissues to lignin and tDOM. The physical mixing of river and seawater played an important role in controlling the concentrations and distributions of lignin phenols and chromophoric DOM (CDOM) optical properties in the bay. Lignin phenol concentrations and the CDOM absorption coefficient at 350 nm, …

Assessment Of Tick Antioxidant Responses To Exogenous Oxidative Stressors And Insight Into The Role Of Catalase In The Reproductive Fitness Of The Gulf Coast Tick, Amblyomma Maculatum, D. Kumar, K. Budachetri, V.C. Meyers, Shahid Karim

Faculty Publications

As obligate blood‐sucking ectoparasites, to avoid tissue damage, ticks must neutralize the reactive oxygen species (ROS) generated from uptake and digestion of a bloodmeal. Consequently, ticks utilize a battery of antioxidant molecules, including catalase (CAT), an enzyme that converts hydrogen peroxide (H₂O₂) into water and oxygen. Here, we investigated the tick antioxidant machinery by exogenous injection of sublethal doses of H₂O₂ or paraquat. The relative transcript levels of selected Amblyomma maculatum antioxidant targets in tissues were determined by quantitative reverse transcriptase PCR following treatment. The results showed 2–16‐fold increases in target antioxidant gene …

Rickettsia Parkeri Colonization In Ambylomma Maculatum: The Role Of Superoxide Dismutases, Gary Crispell, Khemraj Budachetri, Shahid Karim

Faculty Publications

Background

The Gulf Coast tick (Amblyomma maculatum) is an arthropod vector of Rickettsia parkeri, the causative agent of American boutonneuse fever and an infectious agent of public health significance. In this study, we evaluated the biological significance of the superoxide dismutases (SODs) of A. maculatum in hematophagy and R. parkeri colonization within the tick host.

Methods

An RNA interference approach was used to measure the functional roles of tick SODs (Cu/Zn-SOD and Mn-SOD) in R. parkeri colonization of the tick vector. Total microbial load, R. parkeri infection rate, and compensatory mechanisms by tick genes were …

Destruction Of Opportunistic Pathogens Via Polymer Nanoparticle-Mediated Release Of Plant-Based Antimicrobial Payloads, Dahlia N. Amato, Douglas V. Amato, Olga V. Mavrodi, Dwaine A. Braasch, Susan E. Walley, Jessica R. Douglas, Dmitri V. Mavrodi, Derek L. Patton

Faculty Publications

The synthesis of antimicrobial thymol/carvacrol‐loaded polythioether nanoparticles (NPs) via a one‐pot, solvent‐free miniemulsion thiol‐ene photopolymerization process is reported. The active antimicrobial agents, thymol and carvacrol, are employed as “solvents” for the thiol‐ene monomer phase in the miniemulsion to enable facile high capacity loading (≈50% w/w), excellent encapsulation efficiencies (>95%), and elimination of all postpolymerization purification processes. The NPs serve as high capacity reservoirs for slow‐release and delivery of thymol/carvacrol‐combination payloads that exhibit inhibitory and bactericidal activity (>99.9% kill efficiency at 24 h) against gram‐positive and gram‐negative bacteria, including both saprophytic (Bacillus subtilis ATCC 6633 and Escherichia coli …

Integrative Analysis Reveals Clinical Phenotypes And Oncogenic Potentials Of Long Non-Coding Rnas Across 15 Cancer Types, Ze-Lin Wang, Bin Li, Stephen R. Piccolo, Xiao-Qin Zhang, Jun-Hao Li, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu

Faculty Publications

Long non-coding RNAs (lncRNAs) have been shown to contribute to tumorigenesis. However, surprisingly little is known about the comprehensive clinical and genomic characterization of lncRNAs across human cancer. In this study, we conducted comprehensive analyses for the expression profile, clinical outcomes, somatic copy number alterations (SCNAs) profile of lncRNAs in ~7000 clinical samples from 15 different cancer types. We identified significantly differentially expressed lncRNAs between tumor and normal tissues from each cancer. Notably, we characterized 47 lncRNAs which were extensively dysregulated in at least 10 cancer types, suggesting a conserved function in cancer development. We also analyzed the associations between …

The Removal Kinetics Of Dissolved Organic Matter And The Optical Clarity Of Groundwater, Francis H. Chapelle, Yuan Shen, Eric W. Strom, Ronald Benner

Faculty Publications

Concentrations of dissolved organic matter (DOM) and ultraviolet/visible light absorbance decrease systematically as groundwater moves through the unsaturated zones overlying aquifers and along flowpaths within aquifers. These changes occur over distances of tens of meters (m) implying rapid removal kinetics of the chromophoric DOM that imparts color to groundwater. A one-compartment input-output model was used to derive a differential equation describing the removal of DOM from the dissolved phase due to the combined effects of biodegradation and sorption. The general solution to the equation was parameterized using a 2-year record of dissolved organic carbon (DOC) concentration changes in groundwater at …

Case-Oriented Pathways Analysis In Pancreatic Adenocarcinoma Using Data From A Sleeping Beauty Transposon Mutagenesis Screen, Yen Yi Ho, Timothy K. Starr, Rebecca S. Larue, David A. Largaespada

Faculty Publications

Background: Mutation studies of pancreatic ductal adenocarcinoma (PDA) have revealed complicated heterogeneous genomic landscapes of the disease. These studies cataloged a number of genes mutated at high frequencies, but also report a very large number of genes mutated in lower percentages of tumors. Taking advantage of a well-established forward genetic screening technique, with the Sleeping Beauty (SB) transposon, several studies produced PDA and discovered a number of common insertion sites (CIS) and associated genes that are recurrently mutated at high frequencies. As with human mutation studies, a very large number of genes were found to be altered by transposon insertion …

Does Habitat Restoration Increase Coexistence Of Native Stream Fishes With Introduced Brown Trout: A Case Study On The Middle Provo River, Utah, Usa, Mark C. Belk, Eric J. Billman, Craig Ellsworth, Brock R. Mcmillan

Faculty Publications

Restoration of altered or degraded habitats is often a key component in the conservation plan of native aquatic species, but introduced species may influence the response of the native community to restoration. Recent habitat restoration of the middle section of the Provo River in central Utah, USA, provided an opportunity to evaluate the effect of habitat restoration on the native fish community in a system with an introduced, dominant predator—brown trout (Salmo trutta). To determine the change in distribution of fish species and community composition, we surveyed 200 m of each of the four study reaches both before …

Integrative Analyses Reveal Signaling Pathways Underlying Familial Breast Cancer Susceptibility, Stephen R. Piccolo, Laura M. Hoffman, Thomas Conner, Gajendra Shrestha, Adam L. Cohen, Jeffrey R. Marks, Leigh A. Neumayer, Cori A. Agarwal, Mary C. Beckerle, Irene L. Andrulis, Avrum E. Spira, Philip J. Moos, Saundra S. Buys, William Evan Johnson, Andrea H. Bild

Faculty Publications

The signaling events that drive familial breast cancer (FBC) risk remain poorly understood. While the majority of genomic studies have focused on genetic risk variants, known risk variants account for at most 30% of FBC cases. Considering that multiple genes may influence FBC risk, we hypothesized that a pathway‐based strategy examining different data types from multiple tissues could elucidate the biological basis for FBC. In this study, we performed integrated analyses of gene expression and exome‐sequencing data from peripheral blood mononuclear cells and showed that cell adhesion pathways are significantly and consistently dysregulated in women who develop FBC. The dysregulation …

Predicting Dissolved Lignin Phenol Concentrations In The Coastal Ocean From Chromophoric Dissolved Organic Matter (Cdom) Absorption Coefficients, Cédric G. Fichot, Ronald Benner, Karl Kaiser, Yuan Shen, Rainer M. W. Amon, Hiroshi Ogawa, Chua-Jung Lu

Faculty Publications

Dissolved lignin is a well-established biomarker of terrigenous dissolved organic matter (DOM) in the ocean, and a chromophoric component of DOM. Although evidence suggests there is a strong linkage between lignin concentrations and chromophoric dissolved organic matter (CDOM) absorption coefficients in coastal waters, the characteristics of this linkage and the existence of a relationship that is applicable across coastal oceans remain unclear. Here, 421 paired measurements of dissolved lignin concentrations (sum of nine lignin phenols) and CDOM absorption coefficients [ag(λ)] were used to examine their relationship along the river-ocean continuum (0–37 salinity) and across contrasting coastal oceans (sub-tropical, temperate, high-latitude). …

Costs Of Resistance And Infection By A Generalist Pathogen, Tad Dallas, Mathieu Holtackers, John M. Drake

Faculty Publications

Pathogen infection is typically costly to hosts, resulting in reduced fitness. However, pathogen exposure may also come at a cost even if the host does not become infected. These fitness reductions, referred to as “resistance costs”, are inducible physiological costs expressed as a result of a trade-off between resistance to a pathogen and aspects of host fitness (e.g., reproduction). Here, we examine resistance and infection costs of a generalist fungal pathogen (Metschnikowia bicuspidata) capable of infecting a number of host species. Costs were quantified as reductions in host lifespan, total reproduction, and mean clutch size as a function …

Road-Edge Effects On Herpetofauna In A Lowland Amazonian Rainforest, Ross J. Maynard, Nathalie C. Aall, Daniel Saenz, Paul S. Hamilton, Matthew Kwiatkowski

Faculty Publications

The impact of roads on the flora and fauna of Neotropical rainforest is perhaps the single biggest driver of habitat modification and population declines in these ecosystems. We investigated the road-edge effect of a low-use dirt road on amphibian and reptile abundance, diversity, and composition within adjacent lowland Amazonian rainforest at San José de Payamino, Ecuador. The road has been closed to vehicle traffic since its construction in 2010. Thus, effects from vehicle mortality, vehicle-related pollution, and road noise were not confounding factors. Herpetofauna were surveyed using both visual encounter surveys and drift fences with pitfall and funnel traps at …

Habitat Use And Avoidance By Foraging Red-Cockaded Woodpeckers In East Texas, John N. Macey, Brent Burt, Daniel Saenz, Richard N. Conner

Faculty Publications

Picoides borealis (Red-cockaded Woodpecker) is an endangered bird endemic to the Pinus (pine) ecosystems of the southeastern US. Mature pine savannahs with a minimal midstory and lush herbaceous groundcover represent high-quality habitat. This study examines the foraging-habitat patterns of Red-cockaded Woodpeckers in East Texas. We present a logistic regression model that best differentiates between foraged and non-foraged habitat. Increases in hardwood-midstory basal area have the greatest negative impact on the probability of Red-cockaded Woodpeckers selecting a habitat patch for foraging. Five additional variables negatively impact foraging probability: shrub height, diameter at breast height (DBH) of pine midstory, canopy closure, density …

Spatial Distribution Of Earthworms In An East Texas Forest Ecosystem, Melissa A. Bozarth, Kenneth W. Farrish, George A. Damoff, James Van Kley, J. Leon Young

Faculty Publications

Earthworms were collected and identified in different ecological habitats of the Stephen F. Austin Experimental Forest (SFAEF) in the Piney Woods Ecoregion (PWE) of Texas. Earthworm spatial distribution data were collected over four distinct ecological habitats with a range of soil conditions and vegetative cover. A total of 128 sampling plots were surveyed in two different, broadly defined locations (mesic slope = 68 plots, dry-mesic upland = 60 plots). Using multivariate classification/ordination (TWINSPAN) and detrended correspondence analysis (DCA) of overstory vegetation data, these two locations were further divided into four distinct habitats: dry-mesic mixed upland, transitional zone, mesic slope and …

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 …

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.

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

Faculty Publications

No abstract provided.

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.

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 …

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 …

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 …

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 (CHIKV_mos) has slower replication than mammalian cell-derived CHIKV (CHIKV_vero), when tested in both human and murine cell lines. Consistent with this, CHIKV_mos infection in both cell lines …

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 …

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 …

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 …

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 …

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 …

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 …