Digital Commons Network^™

Evolution Of Alu Subfamily Structure In The Saimiri Lineage Of New World Monkeys, Jasmine N. Baker, Jerilyn A. Walker, John A. Vanchiere, Kacie R. Phillippe, Corey P. St Romain, Paulina Gonzalez-Quiroga, Michael W. Denham, Jackson R. Mierl, Miriam K. Konkel, Mark A. Batzer

Faculty Publications

© The Author 2017. Squirrel monkeys, Saimiri, are commonly found in zoological parks and used in biomedical research. S. Boliviensis is the most common species for research; however, there is little information about genome evolution within this primate lineage. Here, we reconstruct the Alu element sequence amplification and evolution in the genus Saimiri at the time of divergence within the family Cebidae lineage. Alu elements are the most successful SINE (Short Interspersed Element) in primates. Here, we report 46 Saimiri lineage specific Alu subfamilies. Retrotransposition activity involved subfamilies related to AluS, AluTa10, and AluTa15. Many subfamilies are simultaneously active within …

Alu Insertion Polymorphisms As Evidence For Population Structure In Baboons, Cody J. Steely, Jerilyn A. Walker, Vallmer E. Jordan, Thomas O. Beckstrom, Cullen L. Mcdaniel, Corey P. St Romain, Emily C. Bennett, Arianna Robichaux, Brooke N. Clement, Muthuswamy Raveendran, Kim C. Worley, Jane Phillips-Conroy, Clifford J. Jolly, Jeff Rogers, Miriam K. Konkel, Mark A. Batzer, Yue Liu, Shwetha Murali, Tauras P. Vilgalys, Jerilyn A. Walker

Faculty Publications

© The Author 2017. Male dispersal from the natal group at or near maturity is a feature of most baboon (Papio) species. It potentially has profound effects upon population structure and evolutionary processes, but dispersal, especially for unusually long distances, is not readily documented by direct field observation. In this pilot study, we investigate the possibility of retrieving baboon population structure in yellow (Papio cynocephalus) and kinda (Papio kindae) baboons from the distribution of variation in a genome-wide set of 494 Alu insertion polymorphisms, made available via the recently completed Baboon Genome Analysis Consortium. Alu insertion variation in a mixed …

Phylogenomics Using Formalin-Fixed And 100+ Year-Old Intractable Natural History Specimens, Sara Ruane, Christopher C. Austin

Faculty Publications

© 2017 John Wiley & Sons Ltd Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here, we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections. We successfully extracted DNA and sequenced ultraconserved elements ((Formula presented.) = 2318 loci) …

Plant Genotype And Induced Defenses Affect The Productivity Of An Insect-Killing Obligate Viral Pathogen, Ikkei Shikano, Elizabeth M. Mccarthy, Bret D. Elderd, Kelli Hoover

Faculty Publications

© 2017 Elsevier Inc. Plant-mediated variations in the outcomes of host-pathogen interactions can strongly affect epizootics and the population dynamics of numerous species, including devastating agricultural pests such as the fall armyworm. Most studies of plant-mediated effects on insect pathogens focus on host mortality, but few have measured pathogen yield, which can affect whether or not an epizootic outbreak occurs. Insects challenged with baculoviruses on different plant species and parts can vary in levels of mortality and yield of infectious stages (occlusion bodies; OBs). We previously demonstrated that soybean genotypes and induced anti-herbivore defenses influence baculovirus infectivity. Here, we used …

Cannibalism And Infectious Disease: Friends Or Foes?, Benjamin G. Van Allen, Forrest P. Dillemuth, Andrew J. Flick, Matthew J. Faldyn, David R. Clark, Volker H.W. Rudolf, Bret D. Elderd

Faculty Publications

© 2017 by The University of Chicago. Cannibalism occurs in a majority of both carnivorous and noncarnivorous animal taxa from invertebrates to mammals. Similarly, infectious parasites are ubiquitous in nature. Thus, interactions between cannibalism and disease occur regularly. While some adaptive benefits of cannibalism are clear, the prevailing view is that the risk of parasite transmission due to cannibalism would increase disease spread and, thus, limit the evolutionary extent of cannibalism throughout the animal kingdom. In contrast, surprisingly little attention has been paid to the other half of the interaction between cannibalism and disease, that is, how cannibalism affects parasites. …

Effects Of Tectonics And Large Scale Climatic Changes On The Evolutionary History Of Hyalomma Ticks, Arthur F. Sands, Dmitry A. Apanaskevich, Sonja Matthee, Ivan G. Horak, Alan Harrison, Shahid Karim, Mohammad K. Mohammad, Kosta Y. Mumcuoglu, Rupika S. Rajakaruna, Maria M. Santos-Silva, Joshua Kamani, Conrad A. Matthee

Faculty Publications

Hyalomma Koch, 1844 are ixodid ticks that infest mammals, birds and reptiles, to which 27 recognized species occur across the Afrotropical, Palearctic and Oriental regions. Despite their medical and veterinary importance, the evolutionary history of the group is enigmatic. To investigate various taxonomic hypotheses based on morphology, and also some of the mechanisms involved in the diversification of the genus, we sequenced and analysed data derived from two mtDNA fragments, three nuclear DNA genes and 47 morphological characters. Bayesian and Parsimony analyses based on the combined data (2242 characters for 84 taxa) provided maximum resolution and strongly supported the monophyly …

Genetic Dissection Of Seedling Stage Salinity Tolerance In Rice Using Introgression Lines Of A Salt Tolerant Landrace Nona Bokra, Venkata Ramana Rao Puram, John Ontoy, Steven Linscombe, Prasanta K. Subudhi

Faculty Publications

Salinity is an important abiotic stress affecting rice production worldwide. Development of salt tolerant varieties is the most feasible approach for improving rice productivity in salt affected soils. In rice, seedling stage salinity tolerance is crucial for better crop establishment. Quantitative trait loci (QTL) mapping using introgression lines (ILs) is useful for identification and simultaneous transfer of desirable alleles into elite genetic background. In the present study, 138 ILs derived from the cross between a high yielding elite salt susceptible japonica rice cultivar Jupiter and a salt tolerant indica landrace Nona Bokra were evaluated for salt tolerance at seedling stage …

Effect Of Metabolic Status On Conceptus–Maternal Interactions On Day 19 In Dairy Cattle: Ii. Effects On The Endometrial Transcriptome, Stefan Bauersachs, Constantine A. Simintiras, Roger G. Sturmey, Stefan Krebs, Jochen Bick, Helmut Blum, Eckhard Wolf, Pat Lonergan, Niamh Forde

Faculty Publications

The aim of this study was to test the hypothesis that the metabolic stresses associated with lactation alter the ability of the endometrium to respond appropriately to the conceptus by examining endometrial gene expression on day 19 of pregnancy. Immediately after calving, primiparous Holstein cows with similar production and fertility estimated breeding values were randomly divided into two groups and either dried off (i.e. never milked) immediately or milked twice daily. Approximately 65–75 days postpartum, grade 1 blastocysts recovered from superovulated Holstein heifer donors (n = 5) were transferred (1 per recipient) into lactating (n = 11) and nonlactating (n …

Amblyomma Maculatum Secis Binding Protein 2 And Putative Selenoprotein P Are Indispensable For Pathogen Replication And Tick Fecundity, Khemraj Budachetri, Gary Crispell, Shahid Karim

Faculty Publications

Selenium, a vital trace element, is incorporated into selenoproteins to produce selenocysteine. Our previous studies have revealed an adaptive co-evolutionary process that has enabled the spotted fever-causing tick-borne pathogen Rickettsia parkeri to survive by manipulating an antioxidant defense system associated with selenium, which includes a full set of selenoproteins and other antioxidants in ticks. Here, we conducted a systemic investigation of SECIS binding protein 2 (SBP2) and putative selenoprotein P (SELENOP) by transcript silencing in adult female Gulf-coast ticks (Amblyomma maculatum). Knockdown of the SBP2 and SELENOP genes depleted the respective transcript levels of these tick selenogenes, and …

Ethanol-Induced Stress Response Of Staphylococcus Aureus, Jasmine M. Pando, Richard F. Pfeltz, Jesus A. Cuaron, Vijayaraj Nagarajan, Mukti N. Mishra, Nathaniel J. Torres, Mohamed O. Elasri, Brian J. Wilkinson, John E. Gustafson

Faculty Publications

Transcriptional profiles of 2 unrelated clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates were analyzed following 10% (v/v) ethanol challenge (15 min), which arrested growth but did not reduce viability. Ethanol-induced stress (EIS) resulted in differential gene expression of 1091 genes, 600 common to both strains, of which 291 were upregulated. With the exception of the downregulation of genes involved with osmotic stress functions, EIS resulted in the upregulation of genes that contribute to stress response networks, notably those altered by oxidative stress, protein quality control in general, and heat shock in particular. In addition, genes involved with …

Application Of An Advanced Maximum Likelihood Estimation Restoration Method For Enhanced-Resolution And Contrast In Second-Harmonic Generation Microscopy, Mayandi Sivaguru, Mohammad M. Kabir, Manas Ranjan Gartia, David S.C. Biggs, Barghav S. Sivaguru, Vignesh A. Sivaguru, Glenn A. Fried, Gang Logan Liu, Sakthivel Sadayappan, Kimani C. Toussaint

Faculty Publications

Second-harmonic generation (SHG) microscopy has gained popularity because of its ability to perform submicron, label-free imaging of noncentrosymmetric biological structures, such as fibrillar collagen in the extracellular matrix environment of various organs with high contrast and specificity. Because SHG is a two-photon coherent scattering process, it is difficult to define a point spread function (PSF) for this modality. Hence, compared to incoherent two-photon processes like two-photon fluorescence, it is challenging to apply the various PSF-engineering methods to improve the spatial resolution to be close to the diffraction limit. Using a synthetic PSF and application of an advanced maximum likelihood estimation …

Connecting The Dots: Stopover Strategies Of An Intercontinental Migratory Songbird In The Context Of The Annual Cycle, Kristina Paxton, Frank R. Moore

Faculty Publications

The phases of the annual cycle for migratory species are inextricably linked. Yet, less than five percent of ecological studies examine seasonal interactions. In this study, we utilized stable hydrogen isotopes to geographically link individual black-and-white warblers (Mniotilta varia) captured during spring migration with breeding destinations to understand a migrant's stopover strategy in the context of other phases of the annual cycle. We found that stopover strategy is not only a function of a bird's current energetic state, but also the distance remaining to breeding destination and a bird's time-schedule, which has previously been linked to habitat conditions experienced …

The Role Of Efferent Reduction Of Cochlear Compression In The Detection Of Tones In Noise, Shaum Bhagat, Anusha Yellamsetty

Faculty Publications

Stimulation of medial olivocochlear (MOC) efferent neurons reduces basilar membrane (BM) sensitivity and increases the slope of BM input-output (I/O) functions in animal models. Decreased compression of I/O functions associated with activation of MOC efferent neurons may assist in extending the neural response to the tone above that of noise, leading to an improvement in masked thresholds. To evaluate this hypothesis, the distortion-product otoacoustic emission (DPOAE) I/O function, a proxy measure of BM compression, was examined in conditions with presentation of contralateral noise. DPOAE I/O functions were measured at f2 frequencies of 1000 and 2000 Hz in 16 normal-hearing adults. …

Assessing The Vegetative Diversity Of An East Texas Golf Course Using Principles Of Landscape Ecology, Brian P. Oswald, Penny G. Lanham, Hans M. Williams, David Kulhavy

Faculty Publications

The objectives of this study was to determine the vegetative diversity and the effects of the edge between fairways (introduced patches) and out-of-bounds areas (remnant patches) to determine if such management activities influence plant diversity. This study was conducted at the Pineywoods Country Club in the Pineywoods Region of East Texas near Nacogdoches, TX, USA by assessing the spatial distribution of these matrices and patches and their influence on edge effect composition and structure in the matrix; and, if species diversity and composition differed between these edges and interior of the matrices. Nested plots were placed along transects and canopy …

Reconstruction Of Piñon-Juniper Forest Structure To Examine Historic Wildlife Habitat Characteristics In The Davis Mountains, Usa, Brian P. Oswald, John R. Lanham, James C. Kroll, Mohammed M. Bataineh, Yanli Zhang

Faculty Publications

Changes in piñon-juniper (Pinus spp., Juniperus spp.) communities across the southwestern United States have often decreased ecological diversity of the understory and increases of exotic species. Reconstructing age and establishment patterns provides essential understanding to guide treatments and management for anthropogenically-altered forests. The goal of this study was to determine how patterns of piñon and juniper growth in the Davis Mountains, Texas, varied over time and how this pattern influenced wildlife habitat of several indicator species. Establishment patterns and basal area growth progression were identified, canopy cover estimates regressed from pre-developed canopy regression equations to re-construct historic forest stand …

Stable Isotope Analyses Of Feather Amino Acids Identify Penguin Migration Strategies At Ocean Basin Scales, Michael J. Polito, Jefferson T. Hinke, Tom Hart, Mercedes Santos, Leah A. Houghton, Simon R. Thorrold

Faculty Publications

No abstract provided.

Estimating Parasite Host Range, Tad Dallas, Shan Huang, Charles Nunn, Andrew W. Park, John M. Drake

Faculty Publications

© 2017 The Author(s) Published by the Royal Society. All rights reserved. Estimating the number of host species that a parasite can infect (i.e. host range) provides key insights into the evolution of host specialism and is a central concept in disease ecology. Host range is rarely estimated in real systems, however, because variation in species relative abundance and the detection of rare species makes it challenging to confidently estimate host range. We applied a non-parametric richness indicator to estimate host range in simulated and empirical data, allowing us to assess the influence of sampling heterogeneity and data completeness. After …

Epigenetic Response Of Imprinted Domains During Carcinogenesis, Corey L. Bretz, Ingeborg M. Langohr, Joomyeong Kim

Faculty Publications

© 2017 The Author(s). Background: Imprinted domains have been identified as targets for aberrant DNA methylation during carcinogenesis, but it remains unclear when these epigenetic alterations occur and how they contribute to tumor progression. Epigenetic instability at key cis-regulatory elements within imprinted domains can concomitantly activate proto-oncogenes and turn off tumor suppressor genes. Thus, to further characterize the epigenetic response of imprinted domains during carcinogenesis, we compared the stability of DNA methylation at a variety of cis-regulatory elements within imprinted domains in two fundamentally different mouse tumors, benign and malignant, induced by the KrasG12D mutation. Results: We report that imprinted …

A Recent Project Shows That The Microbial Carbon Pump Is A Primary Mechanism Driving Ocean Carbon Uptake, Jing M. Chen, Louis Legendre, Ronald Benner

Faculty Publications

No abstract provided.

Altered Sensitivity To Social Gaze In The Fmr1 Premutation And Pragmatic Language Competence, Jessica Klusek, Joseph Schmidt, Amanda J. Fairchild, Ann Porter, Jane E. Roberts

Faculty Publications

Background: The FMR1 premutation affects 1:291 women and is associated with a range of cognitive, affective, and physical health complications, including deficits in pragmatic language (i.e., social language). This study investigated attention to eye gaze as a fundamental social-cognitive skill that may be impaired in the FMR1 premutation and could underlie pragmatic deficits. Given the high prevalence of the FMR1 premutation, efforts to define its phenotype and mechanistic underpinnings have significant public health implications. Methods: Thirty-five women with the FMR1 premutation and 20 control women completed an eye-tracking paradigm that recorded time spent dwelling within the eye region in response …

Synthesis And Characterization Of Pt(Ii) Complexes With Pyridyl Ligands: Elongated Octahedral Ion Pairs And Other Factors Influencing 1H Nmr Spectra, Nerissa A. Lewis, Svetlana Pakhomova, Patricia A. Marzilli, Luigi G. Marzilli

Faculty Publications

© 2017 American Chemical Society. Our goal is to develop convenient methods for obtaining trans-[PtII(4-Xpy)2Cl2] complexes applicable to 4-substituted pyridines (4-Xpy) with limited volatility and water solubility, properties typical of 4-Xpy, with X being a moiety targeting drug delivery. Treatment of cis-[PtII(DMSO)2Cl2] (DMSO = dimethyl sulfoxide) with 4-Xpy in acetonitrile allowed isolation of a new series of simple trans-[PtII(4-Xpy)2Cl2] complexes. A side product with very downfield H2/6 signals led to our synthesis of a series of new [PtII(4-Xpy)4]Cl2 salts. For both series in CDCl3, the size of the H2/6 δ[coordinated minus "free" 4-Xpy H2/6 shift] decreased as 4-Xpy donor ability …

Reproductive And Metabolic State Differences In Olfactory Responses To Amino Acids In A Mouth Brooding African Cichlid Fish, Alexandre A. Nikonov, Julie M. Butler, Karen E. Field, John Caprio, Karen P. Maruska

Faculty Publications

© 2017. Published by The Company of Biologists Ltd | Journal of Experimental Biology. Olfaction mediates many crucial life-history behaviors such as prey detection, predator avoidance, migration and reproduction. Olfactory function can also be modulated by an animal's internal physiological and metabolic states. While this is relatively well studied in mammals, little is known about how internal state impacts olfaction in fishes, the largest and most diverse group of vertebrates. Here we apply electroolfactograms (EOGs) in the African cichlid fish Astatotilapia burtoni to test the hypothesis that olfactory responses to food-related cues (i.e. L-amino acids; alanine and arginine) vary with …

Temperature-Modulated Expression Of Allometric Respiration Strategies Supports A Metabolic Scaling Rule, Chet F. Rakocinski, Kelsey Burns Gillam

Faculty Publications

A model based on the mass-specific oxygen consumption rate of the tolerant polychaete, Capitella telata, related meaningfully to a novel metabolic scaling rule as applied to the infaunal size spectrum. Depending on temperature, C. telataexpressed divergent oxyregulating or oxyconforming strategies relative to oxygen availability. A non-linear response surface fitted to the allometric exponents of a family of V_O2 curves for 12 treatment combinations of DO saturation and temperature was used to project oxygen consumption rates across the infaunal size spectrum. Plasticity in respiration strategies was evident, based on four simulated dynamic 32 d oxygen-temperature exposure scenarios and …

Alternative Healthy Eating Index 2010, Dietary Inflammatory Index And Risk Of Mortality: Results From The Whitehall Ii Cohort Study And Meta-Analysis Of Previous Dietary Inflammatory Index And Mortality Studies, Nitin Shivappa, James R. Hébert, Mika Kivimaki, Tasnime Akbaraly

Faculty Publications

We aimed to examine the association between the Alternative Healthy Eating Index updated in 2010 (AHEI-2010), the Dietary Inflammatory Index (DIITM) and risk of mortality in the Whitehall II study. We also conducted a meta-analysis on the DII-based results from previous studies to summarise the overall evidence. Data on dietary behaviour assessed by self-administered repeated FFQ and on mortality status were available for 7627 participants from the Whitehall II cohort. Cox proportional hazards regression models were performed to assess the association between cumulative average of AHEI-2010 and DII scores and mortality risk. During 22 years of follow-up, 1001 participants died …

Listeria Occurrence In Poultry Flocks: Detection And Potential Implications, Michael J. Rothrock Jr., Morgan L. Davis, Aude Locatelli, Aaron Bodie, Tori G. Mcintosh, Janet R. Donaldson, Steven C. Ricke

Faculty Publications

Foodborne pathogens such as Salmonella, Campylobacter, Escherichia coli, and Listeria are a major concern within the food industry due to their pathogenic potential to cause infection. Of these, Listeria monocytogenes, possesses a high mortality rate (approximately 20%) and is considered one of the most dangerous foodborne pathogens. Although the usual reservoirs for Listeria transmission have been extensively studied, little is known about the relationship between Listeria and live poultry production. Sporadic and isolated cases of listeriosis have been attributed to poultry production and Listeria spp. have been isolated from all stages of poultry production and processing. Farm studies …

Capturing Plasmon-Molecule Dynamics In Dye Monolayers On Metal Nanoparticles Using Classical Electrodynamics With Quantum Embedding, Holden T. Smith, Tony E. Karam, Louis H. Haber, Kenneth Lopata

Faculty Publications

© 2017 American Chemical Society. A multiscale hybrid quantum/classical approach using classical electrodynamics and a collection of discrete three-level quantum systems is used to simulate the coupled dynamics and spectra of a malachite green monolayer adsorbed to the surface of a spherical gold nanoparticle (NP). This method utilizes finite difference time domain (FDTD) to describe the plasmonic response of the NP within the main FDTD framework and a three-level quantum description for the molecule via a Maxwell/Liouville framework. To avoid spurious self-excitation, each quantum molecule has its own auxiliary FDTD subregion embedded within the main FDTD grid. The molecular parameters …

A Lab-On-Chip Phosphate Analyzer For Long-Term In Situ Monitoring At Fixed Observatories: Optimization And Performance Evaluation In Estuarine And Oligotrophic Coastal Waters, Maxime Grand, Geraldine Clinton-Bailey, Alexander Beaton, Allison Schaap, Thomas Johengen, Mario Tamburri, Douglas Connelly, Matthew Mowlem, Eric Achterberg

Faculty Publications

The development of phosphate sensors suitable for long-term in situdeployments in natural waters, is essential to improve our understanding of the distribution, fluxes, and biogeochemical role of this key nutrient in a changing ocean. Here, we describe the optimization of the molybdenum blue method for in situ work using a lab-on-chip (LOC) analyzer and evaluate its performance in the laboratory and at two contrasting field sites. The in situ performance of the LOC sensor is evaluated using hourly time-series data from a 56-day trial in Southampton Water (UK), as well as a month-long deployment in the subtropical oligotrophic waters of …

Evaluation Of Fitting And Adjustment Methods For Taper And Volume Prediction Of Black Pine In Turkey, Ramazan Özçelik, Quang V. Cao

Faculty Publications

A modified form (Cao, Q.V. South. J. Appl. For. 33[2]:58–61, 2009) of the taper model of T.A. Max and H.E. Burkhart (For. Sci. 22[3]:283–289, 1976) was used in this study to predict taper and volume of black pine. A total of 16 methods were evaluated, including 4 fitting methods (optimized for taper, cumulative volume, taper and cumulative volume, and taper and total volume) and 4 adjustment strategies (unadjusted, adjusted to match dbh, predicted total volume, and dbh and predicted total volume). Results showed that adjustment did not improve the performance of the taper model. Also for this data set, the …

Novel Species-Specific Glycoprotein On The Surface Of Mytilus Edulis And M. Trossulus Eggs, Fiona M. Harper, Kasandra J. Riley, R. D. Rawson

Faculty Publications

Protein–protein interactions play a central role in the gamete attraction, binding, and fusion stages of gamete interactions and fertilization for broadcast spawning species, such as marine mussels in the Mytilus edulis species complex. Although assortative gamete interaction has been implicated in the level of reproductive isolation among the three species in this complex, the molecular basis of these interactions has not been elucidated. Using mass spectrometry peptide sequencing, cDNA sequencing, and bioinformatics approaches, we have investigated species-level variation in the proteins expressed on the surface of mussel eggs. We herein describe an extracellular protein, MESP-1, from the surface of the …

The Relationship Of Plasma Trans Fatty Acids With Dietary Inflammatory Index Among Us Adults, Mohsen Mazidi, Hong-Kai Gao, Nitin Shivappa, Michael David Wirth, James R. Hébert, Andre Pascal Kengne

Faculty Publications

Background: It has been suggested that trans fatty acids (TFAs) play an important role in cardiovascular diseases. We investigated the association between plasma TFAs and the dietary inflammatory index (DII) ™ in US adults.

Methods: National Health and Nutrition Examination Survey (NHANES) participants with data on plasma TFAs measured from 1999 to 2010 were included. Energy-adjusted-DII ™ (E-DII ™) expressed per 1000 kcal was calculated from 24-h dietary recalls. All statistical analyses accounted for the survey design and sample weights.

Results: Of the 5446 eligible participants, 46.8% (n = 2550) were men. The mean age of the population was 47.1 …