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The Equitable Contributions Of Environment, Management And Restoration Status On Grassland Diversity And Composition, RaeAnn C. Powers 2014 University of Nebraska - Lincoln

The Equitable Contributions Of Environment, Management And Restoration Status On Grassland Diversity And Composition, Raeann C. Powers

Dissertations and Theses in Biological Sciences

Plant composition is controlled by a combination of environmental, biotic, historical and management factors. Although there has been much focus on restoring grassland diversity, it is unclear which factors and/or interactions of factors are constraining diversity in grasslands and the relative influences of different factors. We measured soil fertility, soil texture, grazing intensity, fire frequency and plant cover in 694 plots, located within 33 remnant and restored fields in managed grasslands in the central Great Plains. Using univariate (general linear model) and multivariate (PERMANOVA) analyses, we identified significant factors and their relative contributions to plant richness, evenness, floristic quality ...


High Hiv Incidence In The Postpartum Period Sustains Vertical Transmission In Settings With Generalized Epidemics: A Cohort Study In Southern Mozambique, Caroline De Schacht, Nedia Mabunda, Orlando C. Ferreira Jr., Nalia Ismael, Nurbai Calu, Iolanda Santos, Heather J. Hoffman, Catharina Alons, Laura Guay, Ilesh V. Jani 2014 Himmelfarb Health Sciences Library, The George Washington University

High Hiv Incidence In The Postpartum Period Sustains Vertical Transmission In Settings With Generalized Epidemics: A Cohort Study In Southern Mozambique, Caroline De Schacht, Nedia Mabunda, Orlando C. Ferreira Jr., Nalia Ismael, Nurbai Calu, Iolanda Santos, Heather J. Hoffman, Catharina Alons, Laura Guay, Ilesh V. Jani

Integrative Systems Biology Faculty Publications

Introduction: Acute infection with HIV in the postpartum period results in a high risk of vertical transmission through breastfeeding. A study was done to determine the HIV incidence rate and associated risk factors among postpartum women in Southern Mozambique, where HIV prevalence among pregnant women is 21%.

Methods: A prospective cohort study was conducted in six rural health facilities in Gaza and Maputo provinces from March 2008 to July 2011. A total of 1221 women who were HIV-negative on testing at delivery or within two months postpartum were recruited and followed until 18 months postpartum. HIV testing, collection of dried ...


Expression Pattern And Biochemical Properties Of Zebrafish N-Acetylglutamate Synthase, Ljubica Caldovic, Nantaporn Haskins, Amy Mumo, Himani Majumdar, Mary Pinter, Mendel Tuchman, Alison Krufka 2014 Himmelfarb Health Sciences Library, The George Washington University

Expression Pattern And Biochemical Properties Of Zebrafish N-Acetylglutamate Synthase, Ljubica Caldovic, Nantaporn Haskins, Amy Mumo, Himani Majumdar, Mary Pinter, Mendel Tuchman, Alison Krufka

Integrative Systems Biology Faculty Publications

The urea cycle converts ammonia, a waste product of protein catabolism, into urea. Because fish dispose ammonia directly into water, the role of the urea cycle in fish remains unknown. Six enzymes, N-acetylglutamate synthase (NAGS), carbamylphosphate synthetase III, ornithine transcarbamylase, argininosuccinate synthase, argininosuccinate lyase and arginase 1, and two membrane transporters, ornithine transporter and aralar, comprise the urea cycle. The genes for all six enzymes and both transporters are present in the zebrafish genome. NAGS (EC 2.3.1.1) catalyzes the formation of N-acetylglutamate from glutamate and acetyl coenzyme A and in zebrafish is partially inhibited by L-arginine. NAGS ...


Transcription Factor Binding To Caenorhabditis Elegans First Introns Reveals Lack Of Redundancy With Gene Promoters, Juan I. Fuxman Bass, Alex M. Tamburino, Akihiro Mori, Nathan Beittel, Matthew T. Weirauch, John S. Reece-Hoyes, Albertha J. M. Walhout 2014 University of Massachusetts Medical School

Transcription Factor Binding To Caenorhabditis Elegans First Introns Reveals Lack Of Redundancy With Gene Promoters, Juan I. Fuxman Bass, Alex M. Tamburino, Akihiro Mori, Nathan Beittel, Matthew T. Weirauch, John S. Reece-Hoyes, Albertha J. M. Walhout

Program in Systems Biology Publications and Presentations

Gene expression is controlled through the binding of transcription factors (TFs) to regulatory genomic regions. First introns are longer than other introns in multiple eukaryotic species and are under selective constraint. Here we explore the importance of first introns in TF binding in the nematode Caenorhabditis elegans by combining computational predictions and experimentally derived TF-DNA interaction data. We found that first introns of C. elegans genes, particularly those for families enriched in long first introns, are more conserved in length, have more conserved predicted TF interactions and are bound by more TFs than other introns. We detected a significant positive ...


Stellaris Fish Workshop Gadph And Dapi Z-Series, George McNamara 2013 The University of Texas

Stellaris Fish Workshop Gadph And Dapi Z-Series, George Mcnamara

George McNamara

Stellaris FISH workshop GADPH and DAPI Z-series at MD Anderson Cancer Center, Houston, TX.

The zip file contains raw and GPU deconvolved image data from a workshop Biosearch Technologies conducted for MDACC researchers in December 2013. Image data was acquired on a Leica DMI6000 microscope with Lumencor SOLA light engine, DAPI and Cy5 filter cubes, Hamamatsu ORCA FLASH4.0 sCMOS camera (500 ms exposure time per plane for Quasar 670).

Pixel size 100 nm XY.

Z-step size 200 nm.

32 planes (power of 2 is optimal for GPU deconvolution). With 500 ms exposure time, the Quasar 670 GADPH FISH probes ...


Conditional Expression Of Tgf-Β1 In Skeletal Muscles Causes Endomysial Fibrosis And Myofibers Atrophy, Jigna Narola, Sachchida Nand Pandey, Adam Glick, Yi-Wen Chen 2013 Himmelfarb Health Sciences Library, The George Washington University

Conditional Expression Of Tgf-Β1 In Skeletal Muscles Causes Endomysial Fibrosis And Myofibers Atrophy, Jigna Narola, Sachchida Nand Pandey, Adam Glick, Yi-Wen Chen

Integrative Systems Biology Faculty Publications

To study the effects of transforming growth factor beta 1 (TGF-β1) on fibrosis and failure of regeneration of skeletal muscles, we generated a tet-repressible muscle-specific TGF-β1transgenic mouse in which expression of TGF-β1 is controlled by oral doxycycline. The mice developed muscle weakness and atrophy after TGF-β1 over-expression. We defined the group of mice that showed phenotype within 2 weeks as early onset (EO) and the rest as late onset (LO), which allowed us to further examine phenotypic differences between the groups. While only mice in the EO group showed significant muscle weakness, pathological changes including endomysial fibrosis and smaller ...


Leica Microscope Gpu Deconvolution Stellaris Fish Dataset #1, George McNamara 2013 The University of Texas

Leica Microscope Gpu Deconvolution Stellaris Fish Dataset #1, George Mcnamara

George McNamara

McNamara 20131101Fri Leica widefield microscope CUDA Deconvolution Stellaris FISH probe cultured cells dataset #1.zip

A text file in the zip archive has experiment details. I am posting this online so that researchers - whether academic or commercial - can evaluate the acquired data, the Bruce and Butte 2013 Optics Express ( http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-21-4-4766 ) deconvolution result (note: I may not have used optimal settings), and to compare these deconvolution results to other methods. If anyone generates alternative spatial deconvolution output, such as from: * SVI Huygens * Media Cy AutoQuant * Agard's ER-Decon (Arigovindan 2013 PNAS) * Vicidomini SGP ...


The Envenoming Pandemic And The Misguided Views Of Snakes: Developing Sustainable Relationships Between Native Poisonous Snakes Of India And The Citizens Of Maharashtra Through The Use Of The Irula Model., Destiny Villanueva 2013 California Polytechnic State University

The Envenoming Pandemic And The Misguided Views Of Snakes: Developing Sustainable Relationships Between Native Poisonous Snakes Of India And The Citizens Of Maharashtra Through The Use Of The Irula Model., Destiny Villanueva

Animal Science

Due to its vast population and general negative consensus regarding snakes, India is notorious for having more snakebite incidents than any other country. Snakes are simultaneously revered and feared in Indian religion and culture. This stigma is perpetuated through propaganda, family beliefs, and innate fears of snakes.These stigmas are more pronounced within rural areas, such as the region of Mahad within the state of Maharshtra. Envenoming is endemic in these areas, and others like them. The World Health Organization identified envenoming as one of the most neglected tropical diseases of the 21st century (Nature India, 2013). Additionally, both nonvenomous ...


Vbp15, A Novel Anti-Inflammatory And Membrane-Stabilizer, Improves Muscular Dystrophy Without Side Effects, Christopher R. Heier, Jesse M. Damsker, Qing Yu, Blythe C. Dillingham, Tony Huynh, Heather A. Gordish-Dressman, Jyoti K. Jaiswal, Eric P. Hoffman, Kanneboyina Nagaraju, +15 additional authors 2013 Himmelfarb Health Sciences Library, The George Washington University

Vbp15, A Novel Anti-Inflammatory And Membrane-Stabilizer, Improves Muscular Dystrophy Without Side Effects, Christopher R. Heier, Jesse M. Damsker, Qing Yu, Blythe C. Dillingham, Tony Huynh, Heather A. Gordish-Dressman, Jyoti K. Jaiswal, Eric P. Hoffman, Kanneboyina Nagaraju, +15 Additional Authors

Integrative Systems Biology Faculty Publications

No abstract provided.


Transformations In Matter And Energy: Student Learning And Inquiry To Inform Teaching, Jenny Dauer 2013 University of Nebraska - Lincoln

Transformations In Matter And Energy: Student Learning And Inquiry To Inform Teaching, Jenny Dauer

DBER Speaker Series

Learning progressions are descriptions of increasing levels of sophistication of student reasoning about a topic based on empirical evidence. Our learning progression framework about student explanations of carbon-transforming processes (e.g. photosynthesis, cellular respiration) describes how student’s interconnected and mutually supporting ideas and practices are deeply embedded in discourse at all levels of achievement. My research is in two areas: 1) applying the learning progression framework for student explanations of carbon-transforming processes to describe the most productive pathways for student learning, 2) extending the research to student reasoning during inquiry activities about carbon-transforming processes. One finding is that students ...


An Exploration Of Heat Tolerance In Mice Utilizing Mrna And Microrna Expression Analysis, Islam Aminul, Patricia A. Deuster, Joseph M. Devaney, Svetlana Ghimbovschi, Yifan Chen 2013 Himmelfarb Health Sciences Library, The George Washington University

An Exploration Of Heat Tolerance In Mice Utilizing Mrna And Microrna Expression Analysis, Islam Aminul, Patricia A. Deuster, Joseph M. Devaney, Svetlana Ghimbovschi, Yifan Chen

Integrative Systems Biology Faculty Publications

Background

Individuals who rapidly develop hyperthermia during heat exposure (heat-intolerant) are vulnerable to heat associated illness and injury. We recently reported that heat intolerant mice exhibit complex alterations in stress proteins in response to heat exposure. In the present study, we further explored the role of genes and molecular networks associated with heat tolerance in mice.

Methodology

Heat-induced physiological and biochemical changes were assessed to determine heat tolerance levels in mice. We performed RNA and microRNA expression profiling on mouse gastrocnemius muscle tissue samples to determine novel biological pathways associated with heat tolerance.

Principal Findings

Mice (n = 18) were assigned ...


Individual Differences In Emotion-Cognition Interactions: Emotional Valence Interacts With Serotonin Transporter Genotype To Influence Brain Systems Involved In Emotional Reactivity And Cognitive Control, Melanie Stollstorff, Yuko Munakata, Arielle P.C. Jensen, Ryan M. Guild, Harry R. Smolker, Joseph M. Devaney, Marie T. Banich 2013 Himmelfarb Health Sciences Library, The George Washington University

Individual Differences In Emotion-Cognition Interactions: Emotional Valence Interacts With Serotonin Transporter Genotype To Influence Brain Systems Involved In Emotional Reactivity And Cognitive Control, Melanie Stollstorff, Yuko Munakata, Arielle P.C. Jensen, Ryan M. Guild, Harry R. Smolker, Joseph M. Devaney, Marie T. Banich

Integrative Systems Biology Faculty Publications

The serotonin transporter gene (5-HTTLPR) influences emotional reactivity and attentional bias toward or away from emotional stimuli, and has been implicated in psychopathological states, such as depression and anxiety disorder. The short allele is associated with increased reactivity and attention toward negatively-valenced emotional information, whereas the long allele is associated with increased reactivity and attention towardpositively-valenced emotional information. The neural basis for individual differences in the ability to exert cognitive control over these bottom-up biases in emotional reactivity and attention is unknown, an issue investigated in the present study. Healthy adult participants were divided into two groups, either homozygous ...


The Proton Pump Inhibitor Lansoprazole Improves The Skeletal Phenotype In Dystrophin Deficient Mdx Mice, Arpana Sali, Gina M. Many, Heather Gordish-Dressman, Jack Van der Meulen, Aditi Phadke, Christopher F. Spurney, Avital Cnaan, Eric P. Hoffman, Kanneboyina Nagaraju 2013 Himmelfarb Health Sciences Library, The George Washington University

The Proton Pump Inhibitor Lansoprazole Improves The Skeletal Phenotype In Dystrophin Deficient Mdx Mice, Arpana Sali, Gina M. Many, Heather Gordish-Dressman, Jack Van Der Meulen, Aditi Phadke, Christopher F. Spurney, Avital Cnaan, Eric P. Hoffman, Kanneboyina Nagaraju

Integrative Systems Biology Faculty Publications

Background

In Duchenne muscular dystrophy (DMD), loss of the membrane stabilizing protein dystrophin results in myofiber damage. Microinjury to dystrophic myofibers also causes secondary imbalances in sarcolemmic ion permeability and resting membrane potential, which modifies excitation-contraction coupling and increases proinflammatory/apoptotic signaling cascades. Although glucocorticoids remain the standard of care for the treatment of DMD, there is a need to investigate the efficacy of other pharmacological agents targeting the involvement of imbalances in ion flux on dystrophic pathology.

Methodology/Principal Findings

We designed a preclinical trial to investigate the effects of lansoprazole (LANZO) administration, a proton pump inhibitor, on the ...


Omigapil Treatment Decreases Fibrosis And Improves Respiratory Rate In Dy2j Mouse Model Of Congenital Muscular Dystrophy, Qing Yu, Arpana Sali, Jack Van der Meulen, Brittany K. Creeden, Heather Gordish-Dressman, Anne Rutkowski, Sree Rayavarapu, Kitipong Uaesoontrachoon, Tony Huynh, Kanneboyina Nagaraju, Christopher F. Spurney 2013 Himmelfarb Health Sciences Library, The George Washington University

Omigapil Treatment Decreases Fibrosis And Improves Respiratory Rate In Dy2j Mouse Model Of Congenital Muscular Dystrophy, Qing Yu, Arpana Sali, Jack Van Der Meulen, Brittany K. Creeden, Heather Gordish-Dressman, Anne Rutkowski, Sree Rayavarapu, Kitipong Uaesoontrachoon, Tony Huynh, Kanneboyina Nagaraju, Christopher F. Spurney

Integrative Systems Biology Faculty Publications

No abstract provided.


Daily Supplementation Of D-Ribose Shows No Therapeutic Benefits In The Mhc-I Transgenic Mouse Model Of Inflammatory Myositis, William Coley, Sree Rayavarapu, Jack H. Van der Meulen, Ayyappa S. Duba, Kanneboyina Nagaraju 2013 Himmelfarb Health Sciences Library, The George Washington University

Daily Supplementation Of D-Ribose Shows No Therapeutic Benefits In The Mhc-I Transgenic Mouse Model Of Inflammatory Myositis, William Coley, Sree Rayavarapu, Jack H. Van Der Meulen, Ayyappa S. Duba, Kanneboyina Nagaraju

Integrative Systems Biology Faculty Publications

Background

Current treatments for idiopathic inflammatory myopathies (collectively called myositis) focus on the suppression of an autoimmune inflammatory response within the skeletal muscle. However, it has been observed that there is a poor correlation between the successful suppression of muscle inflammation and an improvement in muscle function. Some evidence in the literature suggests that metabolic abnormalities in the skeletal muscle underlie the weakness that continues despite successful immunosuppression. We have previously shown that decreased expression of a purine nucleotide cycle enzyme, adenosine monophosphate deaminase (AMPD1), leads to muscle weakness in a mouse model of myositis and may provide a mechanistic ...


Idiopathic Inflammatory Myopathies: Pathogenic Mechanisms Of Muscle Weakness, Sree Rayavarapu, William Coley, Travis B. Kinder, Kanneboyina Nagaraju 2013 Himmelfarb Health Sciences Library, The George Washington University

Idiopathic Inflammatory Myopathies: Pathogenic Mechanisms Of Muscle Weakness, Sree Rayavarapu, William Coley, Travis B. Kinder, Kanneboyina Nagaraju

Integrative Systems Biology Faculty Publications

Idiopathic inflammatory myopathies (IIMs) are a heterogenous group of complex muscle diseases of unknown etiology. These diseases are characterized by progressive muscle weakness and damage, together with involvement of other organ systems. It is generally believed that the autoimmune response (autoreactive lymphocytes and autoantibodies) to skeletal muscle-derived antigens is responsible for the muscle fiber damage and muscle weakness in this group of disorders. Therefore, most of the current therapeutic strategies are directed at either suppressing or modifying immune cell activity. Recent studies have indicated that the underlying mechanisms that mediate muscle damage and dysfunction are multiple and complex. Emerging evidence ...


Dux4 Differentially Regulates Transcriptomes Of Human Rhabdomyosarcoma And Mouse C2c12 Cells, Vishakha Sharma, Naoe Harafuji, Alexandra Belayew, Yi-Wen Chen 2013 Himmelfarb Health Sciences Library, The George Washington University

Dux4 Differentially Regulates Transcriptomes Of Human Rhabdomyosarcoma And Mouse C2c12 Cells, Vishakha Sharma, Naoe Harafuji, Alexandra Belayew, Yi-Wen Chen

Integrative Systems Biology Faculty Publications

Facioscapulohumeral muscular dystrophy (FSHD) is linked to the deletion of the D4Z4 arrays at chromosome 4q35. Recent studies suggested that aberrant expression of double homeobox 4 (DUX4) from the last D4Z4 repeat causes FSHD. The aim of this study is to determine transcriptomic responses to ectopically expressed DUX4 in human and mouse cells of muscle lineage. We expression profiled human rhabdomyosarcoma (RD) cells and mouse C2C12 cells transfected with expression vectors of DUX4 using the Affymetrix Human Genome U133 Plus 2.0 Arrays and Mouse Genome 430 2.0 Arrays, respectively. A total of 2267 and 150 transcripts were identified ...


Evaluating Wetland Restoration Performance Through A Case Study On The University Of Maine Campus, Andrew L. Tomes 2013 The University of Maine

Evaluating Wetland Restoration Performance Through A Case Study On The University Of Maine Campus, Andrew L. Tomes

Honors College

Federal statutes require wetlands that are disturbed or destroyed by human activity to be restored or replaced. However, restoration projects are often unsuccessful, resulting in a continued loss of wetland area and function. This project focuses on a wetland restoration project undertaken by the University of Maine to compensate for construction impacts that took place over the period of 1980-2010. Three sites were involved in the study, of which two were direct restoration and a third compensatory mitigation to offset impacts that could not be restored. All sites were graded to restore wetland hydrology and then revegetated by seeding and ...


Development And Application Of Mass Spectrometry-Based Proteomics To Generate And Navigate The Proteomes Of The Genus Populus, Paul Edward Abraham 2013 University of Tennessee, Knoxville

Development And Application Of Mass Spectrometry-Based Proteomics To Generate And Navigate The Proteomes Of The Genus Populus, Paul Edward Abraham

Doctoral Dissertations

Historically, there has been tremendous synergy between biology and analytical technology, such that one drives the development of the other. Over the past two decades, their interrelatedness has catalyzed entirely new experimental approaches and unlocked new types of biological questions, as exemplified by the advancements of the field of mass spectrometry (MS)-based proteomics. MS-based proteomics, which provides a more complete measurement of all the proteins in a cell, has revolutionized a variety of scientific fields, ranging from characterizing proteins expressed by a microorganism to tracking cancer-related biomarkers. Though MS technology has advanced significantly, the analysis of complicated proteomes, such ...


Human Cytomegalovirus Inhibits Apoptosis By Proteasome-Mediated Degradation Of Bax At Endoplasmic Reticulum-Mitochondrion Contacts, Aiping Zhang, Richard L. Hildreth, Anamaris M. Colberg-Poley 2013 Himmelfarb Health Sciences Library, The George Washington University

Human Cytomegalovirus Inhibits Apoptosis By Proteasome-Mediated Degradation Of Bax At Endoplasmic Reticulum-Mitochondrion Contacts, Aiping Zhang, Richard L. Hildreth, Anamaris M. Colberg-Poley

Integrative Systems Biology Faculty Publications

Human cytomegalovirus (HCMV) encodes the UL37 exon 1 protein (pUL37x1), which is the potent viral mitochondrion-localized inhibitor of apoptosis (vMIA), to increase survival of infected cells. HCMV vMIA traffics from the endoplasmic reticulum (ER) to ER subdomains, which are physically linked to mitochondria known as mitochondrion-associated membranes (MAM), and to mitochondria. The antiapoptotic function of vMIA is thought to primarily result from its ability to inhibit Bax-mediated permeabilization of the outer mitochondrial membrane (OMM). Here, we establish that vMIA retargets Bax to the MAM as well as to the OMM from immediate early through late times of infection. However, MAM ...


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