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Mapping And Analysis Of Caenorhabditis Elegans Transcription Factor Sequence Specificities, Kamesh Narasimhan, Samuel A. Lambert, Ally Yang, Jeremy Riddell, Sanie Mnaimneh, Hong Zheng, Mihai Albu, Hamed S. Najafabadi, John S. Reece-Hoyes, Juan Fuxman Bass, Albertha J. M. Walhout, Matthew T. Weirauch, Timothy R. Hughes 2015 University of Toronto

Mapping And Analysis Of Caenorhabditis Elegans Transcription Factor Sequence Specificities, Kamesh Narasimhan, Samuel A. Lambert, Ally Yang, Jeremy Riddell, Sanie Mnaimneh, Hong Zheng, Mihai Albu, Hamed S. Najafabadi, John S. Reece-Hoyes, Juan Fuxman Bass, Albertha J. M. Walhout, Matthew T. Weirauch, Timothy R. Hughes

Program in Systems Biology Publications and Presentations

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (~40%). These data highlight ...


An Analysis Of Dna Methylation In Human Adipose Tissue Reveals Differential Modification Of Obesity Genes Before And After Gastric Bypass And Weight Loss, Miles C. Benton, Alice Johnstone, David Eccles, Brennan Harmon, Mark T. Hayes, Rod A. Lea, Lyn Griffiths, Eric P. Hoffman, Richard S. Stubbs, Donia Macartney-Coxson 2015 George Washington University

An Analysis Of Dna Methylation In Human Adipose Tissue Reveals Differential Modification Of Obesity Genes Before And After Gastric Bypass And Weight Loss, Miles C. Benton, Alice Johnstone, David Eccles, Brennan Harmon, Mark T. Hayes, Rod A. Lea, Lyn Griffiths, Eric P. Hoffman, Richard S. Stubbs, Donia Macartney-Coxson

Integrative Systems Biology Faculty Publications

Background

Environmental factors can influence obesity by epigenetic mechanisms. Adipose tissue plays a key role in obesity-related metabolic dysfunction, and gastric bypass provides a model to investigate obesity and weight loss in humans.

Results

Here, we investigate DNA methylation in adipose tissue from obese women before and after gastric bypass and significant weight loss. In total, 485,577 CpG sites were profiled in matched, before and after weight loss, subcutaneous and omental adipose tissue. A paired analysis revealed significant differential methylation in omental and subcutaneous adipose tissue. A greater proportion of CpGs are hypermethylated before weight loss and increased methylation ...


Mcnamara 201412 Nih Scap Innocentive Challenge Solution - T-Bow Rainbow T-Cells And Tumor Cells Spatial Multiplexing Gene Expression Reporter System – Plus Supplement Plus Posters - 20141228s, George McNamara 2014 M.D. Anderson Cancer Center

Mcnamara 201412 Nih Scap Innocentive Challenge Solution - T-Bow Rainbow T-Cells And Tumor Cells Spatial Multiplexing Gene Expression Reporter System – Plus Supplement Plus Posters - 20141228s, George Mcnamara

George McNamara

McNamara 201412 NIH SCAP InnoCentive Challenge Solution - T-Bow Rainbow T-cells and Tumor Cells Spatial Multiplexing Gene Expression Reporter System – plus supplement plus posters - 20141228S

The download is my/Cooper lab solution (submission) to the 2014 NIH Single Cell Analysis Program (SCAP) InnoCentive Challenge, "Follow That Cell". I submitted the Solution on 20141215Mon (with 20 minutes to spare). The Challenge web page is

https://www.innocentive.com/ar/challenge/9933618

Our Solution is to revolutionize live cell transcriptional reporter assays. Specifically, we propose to multiplex five promoter response elements to drive expression of different color fluorescent proteins that would bind to ...


High Rates Of Hiv Seroconversion In Pregnant Women And Low Reported Levels Of Hiv Testing Among Male Partners In Southern Mozambique: Results From A Mixed Methods Study, Caroline De Schacht, Heather J. Hoffman, Nedio Mabunda, Carlota Lucas, Catharina L. Alons, Ana Madonela, Adolfo Vubil, Orlando C. Ferreira, Nurbai Calu, Iolanda S. Santos, Ilesh V. Jani, Laura Guay 2014 George Washington University

High Rates Of Hiv Seroconversion In Pregnant Women And Low Reported Levels Of Hiv Testing Among Male Partners In Southern Mozambique: Results From A Mixed Methods Study, Caroline De Schacht, Heather J. Hoffman, Nedio Mabunda, Carlota Lucas, Catharina L. Alons, Ana Madonela, Adolfo Vubil, Orlando C. Ferreira, Nurbai Calu, Iolanda S. Santos, Ilesh V. Jani, Laura Guay

Integrative Systems Biology Faculty Publications

Introduction

Prevention of acute HIV infections in pregnancy is required to achieve elimination of pediatric HIV. Identification and support for HIV negative pregnant women and their partners, particularly serodiscordant couples, are critical. A mixed method study done in Southern Mozambique estimated HIV incidence during pregnancy, associated risk factors and factors influencing partner's HIV testing.

Methods

Between April 2008 and November 2011, a prospective cohort of 1230 HIV negative pregnant women was followed during pregnancy. A structured questionnaire, HIV testing, and collection of dried blood spots were done at 2–3 scheduled visits. HIV incidence rates were calculated by repeat ...


Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood 2014 University of Tennessee - Knoxville

Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood

Doctoral Dissertations

Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous ...


Whole Exome Sequencing In Family Trios Reveals De Novo Mutations In Pura As A Cause Of Severe Neurodevelopmental Delay And Learning Disability, David Hunt, Richard J. Leventer, Cas Simons, Ryan J. Taft, Kathryn J. Swoboda, Mary Gawne-Cain, The DDD Study, Wellcome Trust Sanger Institute, Cambridge, UK, Alex C. Magee, Perter D. Turnpenny, Diana Baralle 2014 Princess Anne Hospital, Southampton, UK

Whole Exome Sequencing In Family Trios Reveals De Novo Mutations In Pura As A Cause Of Severe Neurodevelopmental Delay And Learning Disability, David Hunt, Richard J. Leventer, Cas Simons, Ryan J. Taft, Kathryn J. Swoboda, Mary Gawne-Cain, The Ddd Study, Wellcome Trust Sanger Institute, Cambridge, Uk, Alex C. Magee, Perter D. Turnpenny, Diana Baralle

Integrative Systems Biology Faculty Publications

Background De novo mutations are emerging as an important cause of neurocognitive impairment, and whole exome sequencing of case-parent trios is a powerful way of detecting them. Here, we report the findings in four such trios.

Methods The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. Three of our patients were ascertained from the first 1133 children to have been investigated through this large-scale study. Case 4 was a phenotypically isolated case recruited into an undiagnosed rare disorders sequencing study.

Results Protein-altering de novo mutations in PURA ...


The Cedar Point Experience, 40 Years Of Field Based, Experiential Learning, Jon Garbisch 2014 University of Nebraska-Lincoln

The Cedar Point Experience, 40 Years Of Field Based, Experiential Learning, Jon Garbisch

DBER Speaker Series

The Cedar Point Experience was born in the summer of 1975. At the urging of several biology faculty UNL leased the Goodall Cedar Point Girlscout Camp and offered a broad range of field based courses exploiting the local environment as their classroom. These instructors also had a strong interest in the area as a base for their own research. Today the UNL Cedar Point Biological Station with a few additional buildings can support around 100 people with full service dining, housing, classroom and lab space.

The instructional model has remained unchanged for the past 40 years. Field based or place ...


Affinity Proteomics Within Rare Diseases: A Bio‐Nmd Study For Blood Biomarkers Of Muscular Dystrophies, Brucu Ayoglu, Amina Chaouch, Hans Lochmuller, Luisa Politano, Enrico Bertini, Sebahattin Cirak, +17 additional authors 2014 George Washington University

Affinity Proteomics Within Rare Diseases: A Bio‐Nmd Study For Blood Biomarkers Of Muscular Dystrophies, Brucu Ayoglu, Amina Chaouch, Hans Lochmuller, Luisa Politano, Enrico Bertini, Sebahattin Cirak, +17 Additional Authors

Integrative Systems Biology Faculty Publications

Despite the recent progress in the broad‐scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO‐NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we ...


Hear After: Matters Of Life And Death In David Tudor’S Electronic Music, You Nakai 2014 New York University

Hear After: Matters Of Life And Death In David Tudor’S Electronic Music, You Nakai

communication +1

In David Tudor’s electronic music, home-brew modular devices were carefully connected together to form complex feedback networks wherein all components—including the composer/performer himself—could only partially ‘influence’ one another. Once activated, the very instability of mismatched connections between the components triggered a cascade of signals and signal modulations, so that the work “composed itself,” and took “a life of its own.” Due to this self-producing, perpetuating nature of his works, Tudor insisted on what he called “the view from inside,” focusing more on the internal observation of his devices and sound than in materials external to the ...


Permaculture Design: On The Practice Of Radical Imagination, Katja Rothe 2014 Berlin University of Arts

Permaculture Design: On The Practice Of Radical Imagination, Katja Rothe

communication +1

Permaculture design is a concept that aims at transforming not only agriculture, but also city planning, architecture, development, etc. In short it aims to change human habitats. It is part of a new ecological paradigm that is currently spreading in popularity from the urban gardening movement to various other alternative movements such as the slow movement, sustainable architecture, etc. Permaculture design defines itself as building on systems theory (as formulated in particular by Howard Thomas Odum and Christopher Alexander). However I would like to propose that the afterlife of systems theory as expressed in the concept of permaculture, first developed ...


Predation Risk, Elk, And Aspen: Comment, Robert L. Beschta, Cristina Eisenberg, John W. Laundre, William J. Ripple, Thomas P. Rooney 2014 Wright State University - Main Campus

Predation Risk, Elk, And Aspen: Comment, Robert L. Beschta, Cristina Eisenberg, John W. Laundre, William J. Ripple, Thomas P. Rooney

Biological Sciences Faculty Publications

No abstract provided.


Rapid Identification Of A Novel Complex I Mt-Nd2 M.10134c>A Mutation In A Leigh Syndrome Patient, David K. Miller, Minal J. Menezes, Cas Simons, Lisa G. Riley, Sandra T. Cooper, Sean M. Grimmond, David R. Thorburn, John Christodoulou, Ryan J. Taft 2014 University of Queensland

Rapid Identification Of A Novel Complex I Mt-Nd2 M.10134c>A Mutation In A Leigh Syndrome Patient, David K. Miller, Minal J. Menezes, Cas Simons, Lisa G. Riley, Sandra T. Cooper, Sean M. Grimmond, David R. Thorburn, John Christodoulou, Ryan J. Taft

Integrative Systems Biology Faculty Publications

Leigh syndrome (LS) is a rare progressive multi-system neurodegenerative disorder, the genetics of which is frequently difficult to resolve. Rapid determination of the genetic etiology of LS in a 5-year-old girl facilitated inclusion in Edison Pharmaceutical’s phase 2B clinical trial of EPI-743. SNP-arrays and high-coverage whole exome sequencing were performed on the proband, both parents and three unaffected siblings. Subsequent multi-tissue targeted high-depth mitochondrial sequencing was performed using custom long-range PCR amplicons. Tissue-specific mutant load was also assessed by qPCR. Complex I was interrogated by spectrophotometric enzyme assays and Western Blot. No putatively causal mutations were identified in nuclear-encoded ...


Development Of An Experimental And Computational Platform For Enhanced Characterization Of Modified Peptides And Proteins In Environmental Proteomics, Ritin Sharma 2014 University of Tennessee - Knoxville

Development Of An Experimental And Computational Platform For Enhanced Characterization Of Modified Peptides And Proteins In Environmental Proteomics, Ritin Sharma

Doctoral Dissertations

Over the last decade, mass spectrometry based proteomics has been established as the front-runner in systems-level protein expression studies. However, with the field progressing into research of more and more complex samples, novel challenges have been raised with respect to efficient protein extraction and computational matching. In this dissertation, various aspects in the proteomics workflow, including experimental and computational approaches, have been developed, optimized and systematically evaluated. In this work, some of the critical factors with respect to proteomics sample preparation, like available biomass, detergent removal methods, and intact protein fractionation to achieve deeper proteome measurements were evaluated. The presented ...


Aquaponics And Basil Plant Density, Danika L. MacMaster, Brook Murphy, Dudley Burton 2014 CSU-Sacramento

Aquaponics And Basil Plant Density, Danika L. Macmaster, Brook Murphy, Dudley Burton

STAR (STEM Teacher and Researcher) Program Posters

Aquaponics is the use of water from a fish tank to provide nutrients to plants in a soil-less environment. The rocks cultivate the bacteria that turns the ammonia into nitrates that the plants need, and the plant bed functions as a filter for the fish tank. In this study, with the guidance of Doctor Dudley Burton, Doctor Brook Murphy, we researched the optimal plant density for basil in an Aquaponics system. We attempted to control or measure all the other variables to consider, as to isolate the variable of distance between plants. The water flow was spread through the plant ...


Eccentric Muscle Challenge Shows Osteopontin Polymorphism Modulation Of Muscle Damage., Whitney L. Barfield, Kitipong Uaesoontrachoon, Chung-Sheih Wu, Stephen Lin, Yue Chen, Paul C. Wang, Yasmine Kanaan, Vernon Bond, Eric P. Hoffman 2014 George Washington University

Eccentric Muscle Challenge Shows Osteopontin Polymorphism Modulation Of Muscle Damage., Whitney L. Barfield, Kitipong Uaesoontrachoon, Chung-Sheih Wu, Stephen Lin, Yue Chen, Paul C. Wang, Yasmine Kanaan, Vernon Bond, Eric P. Hoffman

Integrative Systems Biology Faculty Publications

A promoter polymorphism of the osteopontin (OPN) gene (rs28357094) has been associated with multiple inflammatory states, severity of Duchenne muscular dystrophy (DMD) and muscle size in healthy young adults. We sought to define the mechanism of action of the polymorphism, using allele-specific in vitroreporter assays in muscle cells, and a genotype-stratified intervention in healthy controls. In vitro reporter constructs showed the G allele to respond to estrogen treatment, whereas the T allele showed no transcriptional response. Young adult volunteers (n = 187) were enrolled into a baseline study, and subjects with specific rs28357094 genotypes enrolled into an eccentric muscle challenge ...


A Quantitative Analysis Of Kalandars And Captive Bears In Pakistan, Thomas P. Rooney, Kendra C. Millam 2014 Wright State University - Main Campus

A Quantitative Analysis Of Kalandars And Captive Bears In Pakistan, Thomas P. Rooney, Kendra C. Millam

Biological Sciences Faculty Publications

In 2013, the Bioresource Research Centre (Islamabad, Pakistan) conducted a comprehensive census of the remaining dancing and bear-baiting bears in Pakistan. This involved locating and counting the actual involved bears and bear keepers (kalandars), collecting detailed socio-economic data from the bear-keepers, and identifying attitudes and key drivers behind this livelihood. This report summarizes the findings from the census, reveals relationships in the data that are not immediately apparent, and identifies potential leverage points for ongoing campaign efforts.


Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz 2014 University of Massachusetts Medical School

Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz

Biochemistry and Molecular Pharmacology Publications and Presentations

The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator ...


White-Tailed Deer Are A Biotic Filter During Community Assembly, Reducing Species And Phylogenetic Diversity, Danielle R. Begley-Miller, Andrew L. Hipp, Bethany H. Brown, Marlene Hahn, Thomas P. Rooney 2014 Wright State University - Main Campus

White-Tailed Deer Are A Biotic Filter During Community Assembly, Reducing Species And Phylogenetic Diversity, Danielle R. Begley-Miller, Andrew L. Hipp, Bethany H. Brown, Marlene Hahn, Thomas P. Rooney

Biological Sciences Faculty Publications

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H′), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed ...


Increased 5-Hydroxymethylcytosine And Decreased 5-Methylcytosine Are Indicators Of Global Epigenetic Dysregulation In Diffuse Intrinsic Pontine Glioma, Sama Ahsan, Eric H. Raabe, Michael C. Haffner, Ajay Vaghasia, Katherine E. Warren, Martha Quezado, Leomar Y. Ballester, Javad Nazarian, Charles G. Eberhart, Fausto J. Rodriguez 2014 Johns Hopkins University

Increased 5-Hydroxymethylcytosine And Decreased 5-Methylcytosine Are Indicators Of Global Epigenetic Dysregulation In Diffuse Intrinsic Pontine Glioma, Sama Ahsan, Eric H. Raabe, Michael C. Haffner, Ajay Vaghasia, Katherine E. Warren, Martha Quezado, Leomar Y. Ballester, Javad Nazarian, Charles G. Eberhart, Fausto J. Rodriguez

Integrative Systems Biology Faculty Publications

Introduction

Diffuse intrinsic pontine glioma (DIPG) is a malignant pediatric brain tumor associated with dismal outcome. Recent high-throughput molecular studies have shown a high frequency of mutations in histone-encoding genes (H3F3A and HIST1B) and distinctive epigenetic alterations in these tumors. Epigenetic alterations described in DIPG include global DNA hypomethylation. In addition to the generally repressive methylcytosine DNA alteration, 5-hydroxymethylation of cytosine (5hmC) is recognized as an epigenetic mark associated with active chromatin. We hypothesized that in addition to alterations in DNA methylation, that there would be changes in 5hmC. To test this hypothesis, we performed immunohistochemical studies to compare epigenetic ...


Comparative Phylogeography, Phylogenetics, And Population Genomics Of East African Montane Small Mammals, Terrence Constant Demos 2014 City University of New York, Graduate Center

Comparative Phylogeography, Phylogenetics, And Population Genomics Of East African Montane Small Mammals, Terrence Constant Demos

Dissertations and Theses, 2014-Present

The Eastern Afromontane region of Africa is characterized by striking levels of endemism and species richness which rank it as a global biodiversity hotspot for diverse plants and animals including mammals, but has been poorly sampled and little studied to date. Using mtDNA and multi-locus nDNA sequence data, genome-wide RAD-Seq SNP data, and morphological data, I identify major cryptic biogeographic patterns within and between 11 co-distributed small mammal species/species groups across the Eastern Afromontane region. I focus on two endemic montane small mammal species complexes, Hylomyscus mice and Sylvisorex shrews, co-distributed across the Albertine Rift (AR) and Kenya Highlands ...


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