Digital Commons Network^™

Northern Eurasia Future Initiative (Nefi): Facing The Challenges And Pathways Of Global Change In The Twenty-First Century, Pavel Ya. Groisman, Herman Shugart, David Kicklighter, Geoffrey Henebry, Nadezhda Tchebakova, Shamil Maksyutov, Erwan Monier, Garik Gutman, Sergey Gulev, Jiaguo Qi, Alexander Prishchepov, Elena Kukavskaya, Boris Porfiriev, Alexander I. Shiklomanov, Tatiana Loboda, Nikolay Shiklomanov, Son Nghiem, Kathleen Bergen, Jana Albrechtova, Jiquan Chen, Maria Shahgedanova, Anatoly Shvidenko, Nina Speranskaya, Amber Soja

Faculty Publications

During the past several decades, the Earth system has changed significantly, especially across Northern Eurasia. Changes in the socio-economic conditions of the larger countries in the region have also resulted in a variety of regional environmental changes that can have global consequences. The Northern Eurasia Future Initiative (NEFI) has been designed as an essential continuation of the Northern Eurasia Earth Science Partnership Initiative (NEESPI), which was launched in 2004. NEESPI sought to elucidate all aspects of ongoing environmental change, to inform societies and, thus, to better prepare societies for future developments. A key principle of NEFI is that these developments …

Perchlorate-Coupled Carbon Monoxide (Co) Oxidation: Evidence For A Plausible Microbe-Mediated Reaction In Martian Brines, Marisa R. Myers, Gary M. King

Faculty Publications

© 2017 Myers and King. The presence of hydrated salts on Mars indicates that some regions of its surface might be habitable if suitable metabolizable substrates are available. However, several lines of evidence have shown that Mars' regolith contains only trace levels of the organic matter needed to support heterotrophic microbes. Due to the scarcity of organic carbon, carbon monoxide (CO) at a concentration of about 700 parts per million (about 0.4 Pa) might be the single most abundant readily available substrate that could support near-surface bacterial activity. Although a variety of electron acceptors can be coupled to CO oxidation, …

Classifying Cancer Genome Aberrations By Their Mutually Exclusive Effects On Transcription, Jonathan B. Dayton, Stephen R. Piccolo

Faculty Publications

Background

Malignant tumors are typically caused by a conglomeration of genomic aberrations—including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemotherapies and targeted drug treatments are effective against tumors that harbor certain genomic aberrations. However, predictive aberrations (biomarkers) have not been identified for many tumor types and treatments. One way to address this problem is to examine the downstream, transcriptional effects of genomic aberrations and to identify characteristic patterns. Even though two tumors harbor different genomic aberrations, the transcriptional effects of those aberrations may be similar. These patterns could be used to inform treatment …

Complete Mitochondrial Genomes Of Three Neotropical Sleeper Gobies: Eleotris Amblyopsis, E. Picta And Hemieleotris Latifasciata (Gobiiformes: Eleotridae), Fernando Alda, Alexandria J. Adams, W. Owen Mcmillan, Prosanta Chakrabarty

Faculty Publications

© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. We report the first complete mitochondrial genomes of three species of eleotrid fishes from the Pacific and Atlantic watersheds of Panama: Eleotris amblyopsis, E. picta, and Hemieleotris latifasciata. The three species have similar mitochondrial genomes with identical gene order; however, there are differences in the length of control region, 16S rRNA, and in seven of the tRNAs. In addition, ATP8 is one codon shorter in E. picta than in E. amblyopsis or H. latifasciata. We infer a phylogeny for Gobiiformes based on all mitochondrial protein-coding …

Relationship Between Physical Activity And Stress Among Junior High School Students In The Physical Education Environment, David C. Barney, Frank Pleban, Terrance Lewis

Faculty Publications

The study purpose was to explore grade level differences (7^th, 8^th, and 9^th) among junior high school students’ perception of participation in physical education class on individual environmental stress. Physical activity’s role as a stress reduction tool has been well documented. However, physical activity as a stressful event in the school and physical education environment has been less established; particularly in junior high school students. Study participants were comprised of 872 junior high school students, 585 males (67%) and 287 females (33%), enrolled in four junior high schools. Stratified by grade, 315 7^{th …}

Material State Awareness For Composites Part Ii: Precursor Damage Analysis And Quantification Of Degraded Material Properties Using Quantitative Ultrasonic Image Correlation (Quic), Subir Patra, Sourav Banerjee

Faculty Publications

Material state awareness of composites using conventional Nondestructive Evaluation (NDE) method is limited by finding the size and the locations of the cracks and the delamination in a composite structure. To aid the progressive failure models using the slow growth criteria, the awareness of the precursor damage state and quantification of the degraded material properties is necessary, which is challenging using the current NDE methods. To quantify the material state, a new offline NDE method is reported herein. The new method named Quantitative Ultrasonic Image Correlation (QUIC) is devised, where the concept of microcontinuum mechanics is hybrid with the experimentally …

Context-Dependent Chemosensory Signaling, Aggression And Neural Activation Patterns In Gravid Female African Cichlid Fish, Karen E. Field, Karen P. Maruska

Faculty Publications

© 2017. Published by The Company of Biologists Ltd . Social animals must constantly assess their environment to make appropriate behavioral decisions. The use of various sensory modalities is imperative in this process and it is hypothesized that the highly conserved brain nuclei comprising the social decisionmaking network (SDMN) integrates social information with an animal's internal state to elicit behavioral responses. Here, we used the highly social African cichlid fish, Astatotilapia burtoni, to investigate whether reproductively receptive (gravid) females show contextual chemosensory signaling, social behaviors and neural activation patterns within the SDMN. We exposed gravid females to different social contexts: …

Global Awakening Of Cryptic Biosynthetic Gene Clusters In Burkholderia Thailandensis, Ashish Gupta, Renesh Bedre, Sudarshan Singh Thapa, Afsana Sabrin, Guannan Wang, Maheshi Dassanayake, Anne Grove

Faculty Publications

© 2017 American Chemical Society. Many bacteria encode biosynthetic proteins that produce a vast array of natural products. These compounds are often synthesized during host invasion as they function as virulence factors. In addition, such secondary metabolites have yielded numerous molecular scaffolds with pharmaceutical and clinical importance. The gene clusters that encode proteins responsible for synthesis of these compounds are typically silenced or "cryptic" under laboratory growth conditions, hampering discovery of novel lead compounds. We report here that MftR is a global repressor of secondary metabolite synthesis in Burkholderia thailandensis and that urate functions as a physiologically relevant inducer of …

Characterization Of Pathogenic Vibrio Parahaemolyticus From The Chesapeake Bay, Maryland, Arlene J. Chen, Nur A. Hasan, Bradd J. Haley, Elisa Taviani, Mitch Tarnowski, Kathy Brohawn, Crystal N. Johnson, Rita R. Colwell, Anwar Huq

Faculty Publications

Vibrio parahaemolyticus is the leading cause of bacterial gastroenteritis associated with seafood consumption in the United States. Here we investigated the presence of virulence factors and genetic diversity of V. parahaemolyticus isolated from water, oyster, and sediment samples from the Chesapeake Bay, Maryland. Of more than 2,350 presumptive Vibrio collected, more than half were confirmed through PCR as V. parahaemolyticus, with 10 encoding both tdh and trh and 6 encoding only trh. Potentially pathogenic V. parahaemolyticus were then serotyped with O1:KUT and O3:KUT predominant. Furthermore, pulsed-field gel electrophoresis was performed and the constructed dendrogram displayed high diversity, as did results …

Sexual Recombination And Increased Mutation Rate Expedite Evolution Of Escherichia Coli In Varied Fitness Landscapes, George Peabody, Hao Li, Katy Kao

Faculty Publications

Sexual recombination and mutation rate are theorized to play different roles in adaptive evolution depending on the fitness landscape; however, direct experimental support is limited. Here we examine how these factors affect the rate of adaptation utilizing a “genderless” strain of Escherichia coli capable of continuous in situ sexual recombination. The results show that the populations with increased mutation rate, and capable of sexual recombination, outperform all the other populations. We further characterize two sexual and two asexual populations with increased mutation rate and observe maintenance of beneficial mutations in the sexual populations through mutational sweeps. Furthermore, we experimentally identify …

Deep Experimental Profiling Of Microrna Diversity, Deployment, And Evolution Across The Drosophila Genus, Jaaven Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hossain Mondal, Matthew Decruz, Adam Siepel, Eric C. Lai

Faculty Publications

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death …

No Consistent Evidence For Advancing Or Delaying Trends In Spring Phenology On The Tibetan Plateau, Xufeng Wang, Jingfeng Xiao, Xin Li, Guodong Cheng, Mingguo Ma, Tao Che, Shaoying Wang, Jinkui Wu

Faculty Publications

Vegetation phenology is a sensitive indicator of climate change and has significant effects on the exchange of carbon, water, and energy between the terrestrial biosphere and the atmosphere. The Tibetan Plateau, the Earth's “third pole,” is a unique region for studying the long‐term trends in vegetation phenology in response to climate change because of the sensitivity of its alpine ecosystems to climate and its low‐level human disturbance. There has been a debate whether the trends in spring phenology over the Tibetan Plateau have been continuously advancing over the last two to three decades. In this study, we examine the trends …

Homogenization Techniques For Population Dynamics In Strongly Heterogeneous Landscapes, Brian P. Yurk, Christina A. Cobbold

Faculty Publications

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction–diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic …

Using Milk Urea Nitrogen To Calculate Urine And Urinary Nitrogen Output, Peter S. Erickson

Faculty Publications

No abstract provided.

Dinoflagellate Cysts Track Eutrophication In The Northern Gulf Of Mexico, Andrea M. Price, Melissa M. Baustian, R. Eugene Turner, Nancy N. Rabalais, Gail L. Chmura

Faculty Publications

We examined organic-walled dinoflagellate cysts from one 210Pb-dated sediment core and 39 surface sediment samples from the northern Gulf of Mexico to determine the relationship between nutrient enrichment and cyst assemblages in this region characterized by oxygen deficiency. The core spans from 1962 to 1997 and its sampling location is directly influenced by the Mississippi River plume. Surface sediments were collected in 2006, 2007, 2008, and 2014 and represent approximately 1 to 4 years of accumulation. A total of 57 cyst taxa were recorded, and four heterotrophic taxa in particular were found to increase in the top section (1986–1997) of …

Utilizing Undf In Dairy Cow Diets: A New Way Of Looking At Forage Fiber, Peter S. Erickson

Faculty Publications

No abstract provided.

Comparison Of Ecosystem Processes In A Woodland And Prairie Pond With Different Hydroperiods, Daniel J. Hornbach, Mark C. Hove, Mira W. Ensley-Field, Matthew R. Glasenapp, Ian A. Goodbar, J. Douglas Harman, Benjamin D. Huber, Emily A. Kangas, Kira X. Liu, Molly Stark-Ragsdale, Long K. Tran

Faculty Publications

Shallow lakes and ponds constitute a significant number of water bodies worldwide. Many are heterotrophic, indicating that they are likely net contributors to global carbon cycling. Climate change is likely to have important impacts on these waterbodies. In this study, we examined two small Minnesota ponds; a permanent woodland pond and a temporary prairie pond. The woodland pond had lower levels of phosphorus and phytoplankton than the prairie pond. Using the open water oxygen method, we found the prairie pond typically had a higher level of gross primary production (GPP) and respiration (R) than the woodland pond, although the differences …

Erosion And Accretion On A Mudflat: The Importance Of Very Shallow-Water Effects, Benwei Shi, James R. Cooper, Paula D. Pratolongo, Shu Gao, T. J. Bouma, Gaocong Li, Chunyan Li, S. L. Yang, Ya Ping Wang

Faculty Publications

Understanding erosion and accretion dynamics during an entire tidal cycle is important for assessing their impacts on the habitats of biological communities and the long-term morphological evolution of intertidal mudflats. However, previous studies often omitted erosion and accretion during very shallow-water stages (VSWS, water depths < 0.20 m). It is during these VSWS that bottom friction becomes relatively strong and thus erosion and accretion dynamics are likely to differ from those during deeper flows. In this study, we examine the contribution of very shallow-water effects to erosion and accretion of the entire tidal cycle, based on measured and modeled time-series of bed-level changes. Our field experiments revealed that the VSWS accounted for only 11% of the duration of the entire tidal cycle, but erosion and accretion during these stages accounted for 35% of the bed-level changes of the entire tidal cycle. Predicted cumulative bed-level changes agree much better with measured results when the entire tidal cycle is modeled than when only the conditions at water depths of >0.2 m (i.e., probe submerged) are considered. These findings suggest that the magnitude of bed-level changes during VSWS should not be neglected when modeling morphodynamic processes. Our results are useful in understanding the mechanisms of micro-topography formation and destruction that often occur at VSWS, and also improve our understanding and modeling ability of coastal morphological …

Species Are Not Most Abundant In The Centre Of Their Geographic Range Or Climatic Niche, Tad Dallas, Robin R. Decker, Alan Hastings

Faculty Publications

© 2017 John Wiley & Sons Ltd/CNRS The pervasive idea that species should be most abundant in the centre of their geographic range or centre of their climatic niche is a key assumption in many existing ecological hypotheses and has been declared a general macroecological rule. However, empirical support for decreasing population abundance with increasing distance from geographic range or climatic niche centre (distance–abundance relationships) remains fairly weak. We examine over 1400 bird, mammal, fish and tree species to provide a thorough test of distance–abundance relationships, and their associations with species traits and phylogenetic relationships. We failed to detect consistent …

Editorial: Special Thematic Issue On Inland Aquatic Ecosystems, Hongchen Jiang, Yongqin Liu, Gary King

Faculty Publications

No abstract provided.

Pyruvate Dehydrogenase Complex (Pdc) Subunits Moonlight As Interaction Partners Of Phosphorylated Stat5 In Adipocytes And Adipose Tissue, Allison J. Richard, Hardy Hang, Jacqueline M. Stephens

Faculty Publications

© 2017 by The American Society for Biochemistry and Molecular Biology, Inc. STAT5 proteins play a role in adipocyte development and function, but their specific functions are largely unknown. To this end, we used an unbiased MS-based approach to identify novel STAT5-interacting proteins. We observed that STAT5A bound the E1 and E2 subunits of the pyruvate dehydrogenase complex (PDC). Whereas STAT5A typically localizes to the cytosol or nucleus, PDC normally resides within the mitochondrial matrix where it converts pyruvate to acetyl-CoA. We employed affinity purification and immunoblotting to validate the interaction between STAT5A and PDC subunits in murine and human …

Swim Bladder Morphology Changes With Female Reproductive State In The Mouth-Brooding African Cichlid Astatotilapia Burtoni, Julie M. Butler, Sarah M. Whitlow, Anwei P. Gwan, Prosanta Chakrabarty, Karen P. Maruska

Faculty Publications

© 2017. Published by The Company of Biologists Ltd. Journal of Experimental Biology. Mouth brooding is an extreme form of parental care in which the brooding parent carries the developing young in their buccal cavity for the duration of development. Brooding fish need to compensate for the brood weight on the anterior portion of their body. For fishes with a compartmentalized swim bladder, gas distribution between the chambers may aid in regulating buoyancy during brooding. To test this hypothesis, we took radiographs of Astatotilapia burtoni to compare the swim bladder morphology of gravid, mouth-brooding and recovering females. Following spawning, females …

Intramyocellular Lipid Droplet Size Rather Than Total Lipid Content Is Related To Insulin Sensitivity After 8 Weeks Of Overfeeding, Jeffrey D. Covington, Darcy L. Johannsen, Paul M. Coen, David H. Burk, Diana N. Obanda, Philip J. Ebenezer, Charmaine S. Tam, Bret H. Goodpaster, Eric Ravussin, Sudip Bajpeyi

Faculty Publications

© 2017 The Obesity Society Objective: Intramyocellular lipid (IMCL) is inversely related to insulin sensitivity in sedentary populations, yet no prospective studies in humans have examined IMCL accumulation with overfeeding. Methods: Twenty-nine males were overfed a high-fat diet (140% caloric intake, 44% from fat) for 8 weeks. Measures of IMCL, whole-body fat oxidation from a 24-hour metabolic chamber, muscle protein extracts, and muscle ceramide measures were obtained before and after the intervention. Results: Eight weeks of overfeeding did not increase overall IMCL. The content of smaller lipid droplets peripherally located in the myofiber decreased, while increases in larger droplets correlated …

Gradients In Wall Mechanics And Polysaccharides Along Growing Inflorescence Stems, Pyae Phyo, Tuo Wang, Sarah N. Kiemle, Hugh O’Neill, Sai Venkatesh Pingali, Mei Hong, Daniel J. Cosgrove

Faculty Publications

© 2017 American Society of Plant Biologists. All Rights Reserved. At early stages of Arabidopsis (Arabidopsis thaliana) flowering, the inflorescence stem undergoes rapid growth, with elongation occurring predominantly in the apical; 4 cm of the stem. We measured the spatial gradients for elongation rate, osmotic pressure, cell wall thickness, and wall mechanical compliances and coupled these macroscopic measurements with molecular-level characterization of the polysaccharide composition, mobility, hydration, and intermolecular interactions of the inflorescence cell wall using solid-state nuclear magnetic resonance spectroscopy and small-angle neutron scattering. Force-extension curves revealed a gradient, from high to low, in the plastic and elastic compliances …

Species Identification Of Vagrant Empidonax Flycatchers In Northeastern North America Via Non-Invasive Dna Sequencing, Nathan R. Goldberg, Nicholas A. Mason

Faculty Publications

Vagrant individuals from cryptic species complexes pose a persistent challenge for accurate species identification, hindering our understanding of vagrancy in these taxa. Here, we used non-invasive sampling of fecal matter to sequence the ND2 mitochondrial gene of 2 vagrant western flycatchers observed in northeastern North America. The DNAsequence data we recovered from these vagrants fell within a clade of known Empidonax difficillis (Pacific-slope Flycatcher) haplotypes. Our work provides robust records of 2 vagrant Pacific-slope Flycatchers in the northeastern US. These findings illustrate the power of non-invasive sampling for species identification of vagrants from cryptic species complexes.

The Phylogeny Of Heliconia (Heliconiaceae) And The Evolution Of Floral Presentation, William J.D. Iles, Chodon Sass, Laura Lagomarsino, Gracie Benson-Martin, Heather Driscoll, Chelsea D. Specht

Faculty Publications

© 2016 Elsevier Inc. Heliconia (Heliconiaceae, order Zingiberales) is among the showiest plants of the Neotropical rainforest and represent a spectacular co-evolutionary radiation with hummingbirds. Despite the attractiveness and ecological importance of many Heliconia, the genus has been the subject of limited molecular phylogenetic studies. We sample seven markers from the plastid and nuclear genomes for 202 samples of Heliconia. This represents ca. 75% of accepted species and includes coverage of all taxonomic subgenera and sections. We date this phylogeny using fossils associated with other families in the Zingiberales; in particular we review and evaluate the Eocene fossil Ensete oregonense. …

Incorporating Flaxseed (Linum Usitatissimum) Oil Into Queso Blanco At Different Stages Of The Cheese Manufacturing Process, Cristhiam Gurdian, Vondel Reyes, Emmanuel Kyereh, Franklin Bonilla, Cesar Galindo, Alexander Chouljenko, Kevin Mis Solval, Charles Boeneke, Joan M. King, Subramaniam Sathivel

Faculty Publications

The objective of this study was to evaluate the physicochemical and microbial properties of queso blanco (QB) with flaxseed oil (FO) incorporated at different stages of the cheese manufacturing process. Whole milk was homogenized, coagulated with citric acid, salted with NaCl, and the resulting curds were pressed. Then QBFO was produced by incorporating FO during homogenization (QBFO-H), coagulation (QBFO-C), or salting (QBFO-S). The cheeses were stored at 8 °C for 30 days. Significantly lower lipid oxidation in QB was observed when FO was added during coagulation or salting compared to homogenization. However, lipid oxidation values of QBFO-H did not exceed …

Comparison Of Five Methods For Parameter Estimation Under Taylor's Power Law, Peijian Shi, David A. Ratkowsky, Ningtao Wang, Yang Li, Lei Zhao, Gadi V.P. Reddy, Bai Lian Li

Faculty Publications

Taylor's power law (TPL) can be applied to the mean-variance relationship for various quantities, e.g., population densities over space and time, biomass of plants in the growth processes, developmental rates and growth rates of arthropods at different temperatures, etc. When TPL holds in the grouped data (e.g., the biomass of plants at different investigation times with limited replicates at each investigation), we must consider the heterocedasticity when carrying out the parameter estimation for a given mathematical model. We propose two new target functions based on TPL and attempt to more accurately estimate the model parameter(s). By capturing the mean-variance relationship, …

Twenty Years Later: An Update To The Birds Of The Biological Dynamics Of Forest Fragments Project, Amazonas, Brazil, Cameron L. Rutt, Vitek Jirinec, Erik I. Johnson, Mario Cohn-Haft, Claudeir F. Vargas, Philip C. Stouffer

Faculty Publications

Although species lists from throughout Amazonia have become available, relatively complete inventories based on longterm work remain rare. Longitudinal comparisons at well-studied sites provide the best opportunities for describing communities and identifying changes in regional avifaunas. Within central Amazonia, no region has received as much consistent ornithological coverage as the terra firme forests north of Manaus, Brazil, at the Biological Dynamics of Forest Fragments Project (BDFFP). Here we provide an updated list of the area, including notes on all species added between 1997 and 2017. We recorded 21 species new for the site, most of which (>75%) are birds …

Effect Of Lactation On Conceptus-Maternal Interactions At The Initiation Of Implantation In Cattle: I. Effects On The Conceptus Transcriptome And Amino Acid Composition Of The Uterine Luminal Fluid, Niamh Forde, Constantine A. Simintiras, Roger G. Sturmey, Alexander Graf, Eckhard Wolf, Helmut Blum, Pat Lonergan

Faculty Publications

Approximately 65-75 days postpartum (dpp), the estrous cycles of nonlactating (dried off immediately postpartum: n = 12) and lactating (n = 13) Holstein Friesian cows were synchronized and on day 7 a single blastocyst derived from superovulated nulliparous Holstein Friesian heifers was transferred to each cow. A control group of nulliparous heifers (n = 8) were synchronized, inseminated to a standing heat, and slaughtered on the same day as nonlactating and lactating recipients (day 19; estrus = day 0). The uterine horn ipsilateral to the corpus luteum was flushed with 10 ml phosphate-buffered saline and the conceptus, and uterine luminal …