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Linking Old Librarianship To New: Aligning 5-Steps Of The Innovator's Dna In Creating Thematic Discovery Systems For The Everglades, L. Bryan Cooper, Margarita Perez Martinez 2015 Florida International University

Linking Old Librarianship To New: Aligning 5-Steps Of The Innovator's Dna In Creating Thematic Discovery Systems For The Everglades, L. Bryan Cooper, Margarita Perez Martinez

Works of the FIU Libraries

This poster presentation from the May 2015 Florida Library Association Conference, along with the Everglades Explorer discovery portal at http://ee.fiu.edu, demonstrates how traditional bibliographic and curatorial principles can be applied to: 1) selection, cross-walking and aggregation of metadata linking end-users to wide-spread digital resources from multiple silos; 2) harvesting of select PDFs, HTML and media for web archiving and access; 3) selection of CMS domains, sub-domains and folders for targeted searching using an API.

Choosing content for this discovery portal is comparable to past scholarly practice of creating and publishing subject bibliographies, except metadata and data are ...


Pathological Effects Of Repeated Concussive Tbi In Mouse Models: Periventricular Damage And Ventriculomegaly, Richard H. Wolferz Jr. 2015 University of Connecticut - Storrs

Pathological Effects Of Repeated Concussive Tbi In Mouse Models: Periventricular Damage And Ventriculomegaly, Richard H. Wolferz Jr.

Honors Scholar Theses

Repeated concussive traumatic brain injury (rcTBI) is the most prominent form of head injury affecting the brain, with an estimated 1.7 million Americans affected each year (Kuhn 2012). Neurologists have been concerned about the danger of repeated head impacts since the 1920’s, but researchers have only begun to understand the long-term effects of rcTBI (McKee 2009). Although symptoms can be as mild as dizziness, current research suggests that multiple concussions can lead to a progressive degenerative brain disease known as chronic traumatic encephalopathy (CTE) (Luo 2008, McKee 2009, Kane 2013). Research on the brain is just beginning to ...


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 ...


The Treat-Nmd Advisory Committee For Therapeutics (Tact): An Innovative De-Risking Model To Foster Orphan Drug Development., Emma Heslop, Cristina Csimma, Volker Straub, John McCall, Kanneboyina Nagaraju, Kathryn R. Wagner, Didier Caizergues, Rudolf Korinthenberg, Kevin M. Flanigan, Petra Kaufmann, Elizabeth McNeil, Jerry Mendell, Sharon Hesterlee, Dominic J. Wells, Kate Bushby 2015 George Washington University

The Treat-Nmd Advisory Committee For Therapeutics (Tact): An Innovative De-Risking Model To Foster Orphan Drug Development., Emma Heslop, Cristina Csimma, Volker Straub, John Mccall, Kanneboyina Nagaraju, Kathryn R. Wagner, Didier Caizergues, Rudolf Korinthenberg, Kevin M. Flanigan, Petra Kaufmann, Elizabeth Mcneil, Jerry Mendell, Sharon Hesterlee, Dominic J. Wells, Kate Bushby

Integrative Systems Biology Faculty Publications

Despite multiple publications on potential therapies for neuromuscular diseases (NMD) in cell and animal models only a handful reach clinical trials. The ability to prioritise drug development according to objective criteria is particularly critical in rare diseases with large unmet needs and a limited numbers of patients who can be enrolled into clinical trials. TREAT-NMD Advisory Committee for Therapeutics (TACT) was established to provide independent and objective guidance on the preclinical and development pathway of potential therapies (whether novel or repurposed) for NMD.We present our experience in the establishment and operation of the TACT. TACT provides a unique resource ...


Genetic Modifiers Of Ambulation In The Cinrg Duchenne Natural History Study., Luca Bello, Akanchha Kesari, Heather A. Gordish-Dressman, Avital Cnaan, Lauren P Morgenroth, Jaya Punetha, Tina Duong, Erik Henricson, Elena Pegoraro, Craig M. McDonald, Eric P. Hoffman 2015 George Washington University

Genetic Modifiers Of Ambulation In The Cinrg Duchenne Natural History Study., Luca Bello, Akanchha Kesari, Heather A. Gordish-Dressman, Avital Cnaan, Lauren P Morgenroth, Jaya Punetha, Tina Duong, Erik Henricson, Elena Pegoraro, Craig M. Mcdonald, Eric P. Hoffman

Integrative Systems Biology Faculty Publications

No abstract provided.


Fauna Census Of Intertidal Cliffs, Mangapwani, Zanzibar, Emily Jankowski 2015 SIT Study Abroad

Fauna Census Of Intertidal Cliffs, Mangapwani, Zanzibar, Emily Jankowski

Independent Study Project (ISP) Collection

Due to their extreme variations in condition over the course of a day, intertidal zones are challenging environments. Organisms that live there must be prepared to cope with both exposure and submersion, not to mention the temperature variations that accompany these conditions. The differing tolerances and adaptations of various organisms to these conditions generally cause patterns of vertical zonation to occur in the intertidal zone, especially when the shore is steep and rocky. Understanding the ecology of shore environments is important to future conservation and management efforts. This study was conducted on a beach in Mangapwani, Zanzibar at at 6 ...


Tyrosine 705 Phosphorylation Of Stat3 Is Associated With Phenotype Severity In Tgfβ1 Transgenic Mice, Eleonora Guadagnin, Jigna Narola, Carsten G. Bonnemann, Yi-Wen Chen 2015 George Washington University

Tyrosine 705 Phosphorylation Of Stat3 Is Associated With Phenotype Severity In Tgfβ1 Transgenic Mice, Eleonora Guadagnin, Jigna Narola, Carsten G. Bonnemann, Yi-Wen Chen

Integrative Systems Biology Faculty Publications

Transforming growth factor beta 1 (TGFβ1) is a key player in skeletal muscle degenerative and regenerative processes. We previously showed that conditionally overexpressing TGFβ1 in skeletal muscles caused myofiber atrophy and endomysial fibrosis in mice. However, the disease severity varied significantly among individual mice. While 40% of mice developed severe muscle pathology and lost body weight within 2 weeks of TGFβ1 transgene induction in muscles, the rest showed milder or no phenotype. This study aims at determining whether signal transducer and activator of transcription 3 (STAT3) plays a role in the phenotypic difference and whether it can be activated by ...


Mir-10b-5p Expression In Huntington's Disease Brain Relates To Age Of Onset And The Extent Of Striatal Involvement, Andrew G. Hoss, Adam Labadorf, Jeanne C. Latourelle, Vinay K. Kartha, Tiffany C. Hadzi, James F. Gusella, Marcy E. MacDonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel, Richard H. Myers 2015 Boston University

Mir-10b-5p Expression In Huntington's Disease Brain Relates To Age Of Onset And The Extent Of Striatal Involvement, Andrew G. Hoss, Adam Labadorf, Jeanne C. Latourelle, Vinay K. Kartha, Tiffany C. Hadzi, James F. Gusella, Marcy E. Macdonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel, Richard H. Myers

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that recognize sites of complementarity of target messenger RNAs, resulting in transcriptional regulation and translational repression of target genes. In Huntington's disease (HD), a neurodegenerative disease caused by a trinucleotide repeat expansion, miRNA dyregulation has been reported, which may impact gene expression and modify the progression and severity of HD.

METHODS: We performed next-generation miRNA sequence analysis in prefrontal cortex (Brodmann Area 9) from 26 HD, 2 HD gene positive, and 36 control brains. Neuropathological information was available for all HD brains, including age at disease onset, CAG-repeat size, Vonsattel grade, and ...


Pipipes: A Set Of Pipelines For Pirna And Transposon Analysis Via Small Rna-Seq, Rna-Seq, Degradome- And Cage-Seq, Chip-Seq And Genomic Dna Sequencing, Bo W. Han, Wei Wang, Phillip D. Zamore, Zhiping Weng 2015 University of Massachusetts Medical School

Pipipes: A Set Of Pipelines For Pirna And Transposon Analysis Via Small Rna-Seq, Rna-Seq, Degradome- And Cage-Seq, Chip-Seq And Genomic Dna Sequencing, Bo W. Han, Wei Wang, Phillip D. Zamore, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

MOTIVATION: PIWI-interacting RNAs (piRNAs), 23-36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile. To address these issues, we developed a coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine ...


Theoretical Investigation Of Intra- And Inter-Cellular Spatiotemporal Calcium Patterns In Microcirculation, Jaimit B. Parikh 2015 Florida International University

Theoretical Investigation Of Intra- And Inter-Cellular Spatiotemporal Calcium Patterns In Microcirculation, Jaimit B. Parikh

FIU Electronic Theses and Dissertations

Microcirculatory vessels are lined by endothelial cells (ECs) which are surrounded by a single or multiple layer of smooth muscle cells (SMCs). Spontaneous and agonist induced spatiotemporal calcium (Ca2+) events are generated in ECs and SMCs, and regulated by complex bi-directional signaling between the two layers which ultimately determines the vessel tone. The contractile state of microcirculatory vessels is an important factor in the determination of vascular resistance, blood flow and blood pressure. This dissertation presents theoretical insights into some of the important and currently unresolved phenomena in microvascular tone regulation. Compartmental and continuum models of isolated EC and ...


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 ...


Culture Conditions Affect Expression Of Dux4 In Fshd Myoblasts, Sachchida Nand Pandey, Hunain Khawaja, Yi-Wen Chen 2015 George Washington University

Culture Conditions Affect Expression Of Dux4 In Fshd Myoblasts, Sachchida Nand Pandey, Hunain Khawaja, Yi-Wen Chen

Integrative Systems Biology Faculty Publications

Facioscapulohumeral muscular dystrophy (FSHD) is believed to be caused by aberrant expression of double homeobox 4 (DUX4) due to epigenetic changes of the D4Z4 region at chromosome 4q35. Detecting DUX4 is challenging due to its stochastic expression pattern and low transcription level. In this study, we examined different cDNA synthesis strategies and the sensitivity for DUX4 detection. In addition, we investigated the effects of dexamethasone and knockout serum replacement (KOSR) on DUX4 expression in culture. Our data showed that DUX4 was consistently detected in cDNA samples synthesized using Superscript III. The sensitivity of DUX4 detection was higher in the samples ...


Muscular Dystrophy In The Mdx Mouse Is A Severe Myopathy Compounded By Hypotrophy, Hypertrophy And Hyperplasia., William Duddy, Stephanie Duguez, Helen Johnston, Tatiana V. Cohen, Aditi Phadke, Heather Gordish-Dressman, Kanneboyina Nagaraju, Viola Gnocchi, SiewHui Low, Terence Partridge 2015 George Washington University

Muscular Dystrophy In The Mdx Mouse Is A Severe Myopathy Compounded By Hypotrophy, Hypertrophy And Hyperplasia., William Duddy, Stephanie Duguez, Helen Johnston, Tatiana V. Cohen, Aditi Phadke, Heather Gordish-Dressman, Kanneboyina Nagaraju, Viola Gnocchi, Siewhui Low, Terence Partridge

Integrative Systems Biology Faculty Publications

Background

Preclinical testing of potential therapies for Duchenne muscular dystrophy (DMD) is conducted predominantly of the mdx mouse. But lack of a detailed quantitative description of the pathology of this animal limits our ability to evaluate the effectiveness of putative therapies or their relevance to DMD.

Methods

Accordingly, we have measured the main cellular components of muscle growth and regeneration over the period of postnatal growth and early pathology in mdx and wild-type (WT) mice; phalloidin binding is used as a measure of fibre size, myonuclear counts and BrdU labelling as records of myogenic activity.

Results

We confirm a two-phase ...


The N-Acetylglutamate Synthase Family: Structures, Function And Mechanisms, Dashuang Shi, Norma M. Allewell, Mendel Tuchman 2015 George Washington University

The N-Acetylglutamate Synthase Family: Structures, Function And Mechanisms, Dashuang Shi, Norma M. Allewell, Mendel Tuchman

Integrative Systems Biology Faculty Publications

N-acetylglutamate synthase (NAGS) catalyzes the production of N-acetylglutamate (NAG) from acetyl-CoA and L-glutamate. In microorganisms and plants, the enzyme functions in the arginine biosynthetic pathway, while in mammals, its major role is to produce the essential co-factor of carbamoyl phosphate synthetase 1 (CPS1) in the urea cycle. Recent work has shown that several different genes encode enzymes that can catalyze NAG formation. A bifunctional enzyme was identified in certain bacteria, which catalyzes both NAGS and N-acetylglutamate kinase (NAGK) activities, the first two steps of the arginine biosynthetic pathway. Interestingly, these bifunctional enzymes have higher sequence similarity to vertebrate NAGS than ...


The Actn3 R577x Polymorphism Is Associated With Cardiometabolic Fitness In Healthy Young Adults., Chelsea L Deschamps, Kimberly E Connors, Matthias S Klein, Virginia L Johnsen, Jane Shearer, Hans J Vogel, Joseph M. Devaney, Heather Gordish-Dressman, Gina M Many, Whitney Barfield, Eric P. Hoffman, William E Kraus, Dustin S Hittel 2015 George Washington University

The Actn3 R577x Polymorphism Is Associated With Cardiometabolic Fitness In Healthy Young Adults., Chelsea L Deschamps, Kimberly E Connors, Matthias S Klein, Virginia L Johnsen, Jane Shearer, Hans J Vogel, Joseph M. Devaney, Heather Gordish-Dressman, Gina M Many, Whitney Barfield, Eric P. Hoffman, William E Kraus, Dustin S Hittel

Integrative Systems Biology Faculty Publications

Homozygosity for a premature stop codon (X) in the ACTN3 “sprinter” gene is common in humans despite the fact that it reduces muscle size, strength and power. Because of the close relationship between skeletal muscle function and cardiometabolic health we examined the influence of ACTN3 R577X polymorphism over cardiovascular and metabolic characteristics of young adults (n = 98 males, n = 102 females; 23 ± 4.2 years) from our Assessing Inherent Markers for Metabolic syndrome in the Young (AIMMY) study. Both males and females with the RR vs XX genotype achieved higher mean VO2 peak scores (47.8 ± 1.5 vs 43 ...


The Sensitivity Of Soil Respiration To Soil Temperature, Moisture, And Carbon Supply At The Global Scale, Andrew Hursh 2015 University of Montana - Missoula

The Sensitivity Of Soil Respiration To Soil Temperature, Moisture, And Carbon Supply At The Global Scale, Andrew Hursh

Theses, Dissertations, Professional Papers

Soil respiration is one of the most important terms in the global carbon budget, yet we know very little about how important environmental factors control this process at the global scale. Soils contain more carbon than terrestrial biomass and the atmosphere combined and contribute ten times more carbon dioxide to the atmosphere each year than the burning of fossil fuels. This study provides new insight on the factors driving soil respiration at the global scale by assimilating satellite observations of soil moisture, temperature, and net primary productivity with the Global Soil Respiration Database (SRDB).While temperature, moisture, carbon supply and ...


He Use Of Urinary And Kidney Silam Proteomics To Monitor Kidney Response To High Dose Morpholino Oligonucleotides In The Mdx Mouse, Aiping Zhang, Kitipong Uaesoontrachoon, Conner Shaughnessy, Jharna R. Das, Sree Rayavarapu, Kristy J. Brown, Patricio E. Ray, Kanneboyina Nagaraju, John N. van den Anker, Eric P. Hoffman, Yetrib Hathout 2015 George Washington University

He Use Of Urinary And Kidney Silam Proteomics To Monitor Kidney Response To High Dose Morpholino Oligonucleotides In The Mdx Mouse, Aiping Zhang, Kitipong Uaesoontrachoon, Conner Shaughnessy, Jharna R. Das, Sree Rayavarapu, Kristy J. Brown, Patricio E. Ray, Kanneboyina Nagaraju, John N. Van Den Anker, Eric P. Hoffman, Yetrib Hathout

Integrative Systems Biology Faculty Publications

Phosphorodiamidate morpholino oligonucleotides (PMO) are used as a promising exon-skipping gene therapy for Duchenne muscular dystrophy (DMD). One potential complication of high dose PMO therapy is its transient accumulation in the kidneys. Therefore new urinary biomarkers are needed to monitor this treatment. Here, we carried out a pilot proteomic profiling study using stable isotope labeling in mammals (SILAM) strategy to identify new biomarkers to monitor the effect of PMO on the kidneys of the dystrophin deficient mouse model for DMD (mdx-23). We first assessed the baseline renal status of the mdx-23 mouse compared to the wild type (C57BL10) mouse, and ...


Comparative Functional Characterization Of The Csr-1 22g-Rna Pathway In Caenorhabditis Nematodes, Shikui Tu, Monica Z. Wu, Jie Wang, Asher D. Cutter, Zhiping Weng, Julie M. Claycomb 2015 University of Massachusetts Medical School

Comparative Functional Characterization Of The Csr-1 22g-Rna Pathway In Caenorhabditis Nematodes, Shikui Tu, Monica Z. Wu, Jie Wang, Asher D. Cutter, Zhiping Weng, Julie M. Claycomb

Program in Bioinformatics and Integrative Biology Publications and Presentations

As a champion of small RNA research for two decades, Caenorhabditis elegans has revealed the essential Argonaute CSR-1 to play key nuclear roles in modulating chromatin, chromosome segregation and germline gene expression via 22G-small RNAs. Despite CSR-1 being preserved among diverse nematodes, the conservation and divergence in function of the targets of small RNA pathways remains poorly resolved. Here we apply comparative functional genomic analysis between C. elegans and Caenorhabditis briggsae to characterize the CSR-1 pathway, its targets and their evolution. C. briggsae CSR-1-associated small RNAs that we identified by immunoprecipitation-small RNA sequencing overlap with 22G-RNAs depleted in cbr-csr-1 RNAi-treated ...


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 ...


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