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Hear After: Matters Of Life And Death In David Tudor’S Electronic Music, You Nakai 2014 University of Massachusetts - Amherst

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 University of Massachusetts - Amherst

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 ...


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 Himmelfarb Health Sciences Library, The George Washington University

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 ...


Aquaponics And Basil Plant Density, Danika L. MacMaster, Brook Murphy, Dudley Burton 2014 California Polytechnic State University

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

STEM Teacher and Researcher (STAR) 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 ...


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 ...


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 ...


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 Himmelfarb Health Sciences Library, The George Washington 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 ...


High-Throughput Genome Scaffolding From In Vivo Dna Interaction Frequency, Noam Kaplan, Job Dekker 2014 University of Massachusetts Medical School

High-Throughput Genome Scaffolding From In Vivo Dna Interaction Frequency, Noam Kaplan, Job Dekker

Clinical and Translational Science Research Retreat

Despite the advancement of DNA-sequencing technology, assembly of complex genomes remains a major challenge. Surprisingly, the quality of published assemblies of complex genomes has in fact decreased, due to the discrepancy between the rate of advancement of short read sequencing and that of scaffolding technology. Short read sequencing typically yields accurate, but disconnected, contigs. However, high-throughput scaffolding of contigs into chromosomes, based on long-insert paired-end read libraries, is a difficult task and yields highly fragmented genomes. Further scaffolding, which is required to improve the degree of completion of genome sequences, typically relies on laborious or low-throughput methods. We have developed ...


Optimal Experimental Design For Parameter Identification And Model Selection, René Schenkendorf 2014 SelectedWorks

Optimal Experimental Design For Parameter Identification And Model Selection, René Schenkendorf

René Schenkendorf

No abstract provided.


Multiple Transcription Factors Directly Regulate Hox Gene Lin-39 Expression In Ventral Hypodermal Cells Of The C. Elegans Embryo And Larva, Including The Hypodermal Fate Regulators Lin-26 And Elt-6, Wan-Ju Liu, John S. Reece-Hoyes, Albertha J. M. Walhout, David M. Eisenmann 2014 University of Massachusetts Medical School

Multiple Transcription Factors Directly Regulate Hox Gene Lin-39 Expression In Ventral Hypodermal Cells Of The C. Elegans Embryo And Larva, Including The Hypodermal Fate Regulators Lin-26 And Elt-6, Wan-Ju Liu, John S. Reece-Hoyes, Albertha J. M. Walhout, David M. Eisenmann

Program in Systems Biology Publications and Presentations

BACKGROUND: Hox genes encode master regulators of regional fate specification during early metazoan development. Much is known about the initiation and regulation of Hox gene expression in Drosophila and vertebrates, but less is known in the non-arthropod invertebrate model system, C. elegans. The C. elegans Hox gene lin-39 is required for correct fate specification in the midbody region, including the Vulval Precursor Cells (VPCs). To better understand lin-39 regulation and function, we aimed to identify transcription factors necessary for lin-39 expression in the VPCs, and in particular sought factors that initiate lin-39 expression in the embryo.

RESULTS: We used the ...


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 ...


Clinical And Physiological Analysis Of Very Long Apneas In Premature Infants, Anne Mennen 2014 College of William and Mary

Clinical And Physiological Analysis Of Very Long Apneas In Premature Infants, Anne Mennen

Honors Theses

Apnea is common in premature infants, and in severe cases it may impair development. Data recorded during apnea events by hospital monitors at the University of Virginia Neonatal Intensive Care Unit (NICU) include EKG, chest impedance, and pulse oximetry signals. In previous work, an apnea detection algorithm was developed that filtered the cardiac artifact from the chest impedance signal to improve detection of apneas [1]. An unexpected result was the discovery that Very Long Apneas (VLAs) lasting more than 60 seconds are not rare. We use this findings in our research to provide new information about these apneas and to ...


Defining Functional Dna Elements In The Human Genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, ENCODE Project Consortium 2014 University of Massachusetts Medical School

Defining Functional Dna Elements In The Human Genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, Encode Project Consortium

Program in Systems Biology Publications and Presentations

With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily ...


Inheritance Of An Extended Diapause Trait In The Northern Corn Rootworm, Diabrotica Barberi (Coleoptera: Chrysomelidae), B. W. French, Brad S. Coates, Thomas W. Sappington 2014 Iowa State University

Inheritance Of An Extended Diapause Trait In The Northern Corn Rootworm, Diabrotica Barberi (Coleoptera: Chrysomelidae), B. W. French, Brad S. Coates, Thomas W. Sappington

Entomology Publications and Papers

Diapause is an adaptive trait that delays development or reproduction under unfavourable circumstances. The northern corn rootworm,Diabrotica barberi Smith & Lawrence, an important maize, Zea mays L., pest in the Diabroticite species complex, overwinters in diapause during the egg stage. Some NCR populations are adapted to crop rotation by expressing an extended diapause (ED) trait that delays embryonic development for 2 years. This ED trait has increased in frequency and geographic distribution since first reported in Illinois in 1932. Reciprocal single pair crosses among beetles from a laboratory colony with the ancestral 1-year diapause trait and field collected beetles with ...


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 ...


Effects Of Entomopathogens On Mortality Of Western Corn Rootworm (Coleoptera: Chrysomelidae) And Fitness Costs Of Resistance To Cry3bb1 Maize, Amanda Hoffmann, B. Wade French, Stefan T. Jaronski, Aaron J. Gassmann 2014 Iowa State University

Effects Of Entomopathogens On Mortality Of Western Corn Rootworm (Coleoptera: Chrysomelidae) And Fitness Costs Of Resistance To Cry3bb1 Maize, Amanda Hoffmann, B. Wade French, Stefan T. Jaronski, Aaron J. Gassmann

Entomology Publications and Papers

Fitness costs can delay pest resistance to crops that produce insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt), and past research has found that entomopathogens impose fitness costs of Bt resistance. In addition, entomopathogens can be used for integrated pest management by providing biological control of pests. The western corn rootworm,Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is a major pest of maize and is currently managed by planting of Bt maize. We tested whether entomopathogenic nematodes and fungi increased mortality of western corn rootworm and whether these entomopathogens increased fitness costs of resistance to Cry3Bb1 maize. We exposed ...


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 ...


Dysferlin Regulates Cell Membrane Repair By Facilitating Injury-Triggered Acid Sphingomyelinase Secretion, Aurelia Defour, Jack H. Van der Meulen, Rujuta R. Bhatt, Anne Bigot, R. Bashir, Kanneboyina Nagaraju, Jyoti K. Jaiswal 2014 Himmelfarb Health Sciences Library, The George Washington University

Dysferlin Regulates Cell Membrane Repair By Facilitating Injury-Triggered Acid Sphingomyelinase Secretion, Aurelia Defour, Jack H. Van Der Meulen, Rujuta R. Bhatt, Anne Bigot, R. Bashir, Kanneboyina Nagaraju, Jyoti K. Jaiswal

Integrative Systems Biology Faculty Publications

Dysferlin deficiency compromises the repair of injured muscle, but the underlying cellular mechanism remains elusive. To study this phenomenon, we have developed mouse and human myoblast models for dysferlinopathy. These dysferlinopathic myoblasts undergo normal differentiation but have a deficit in their ability to repair focal injury to their cell membrane. Imaging cells undergoing repair showed that dysferlin-deficit decreased the number of lysosomes present at the cell membrane, resulting in a delay and reduction in injury-triggered lysosomal exocytosis. We find repair of injured cells does not involve formation of intracellular membrane patch through lysosome–lysosome fusion; instead, individual lysosomes fuse with ...


Phylogenetics And Evolution Of The Paleotropical Woody Bamboos (Poaceae: Bambusoideae: Bambuseae), Hathairat Chokthaweepanich 2014 Iowa State University

Phylogenetics And Evolution Of The Paleotropical Woody Bamboos (Poaceae: Bambusoideae: Bambuseae), Hathairat Chokthaweepanich

Graduate Theses and Dissertations

The paleotropical woody bamboos (PWB) are members of Bambuseae (tropical woody bamboos) in subfamily Bambusoideae of the grass family (Poaceae). Although the PWB are important in ecological and economic functions, the phylogenetic relationships of the PWB remain equivocal. All four currently recognized subtribes of the PWB have never been completely examined for their evolutionary relationships and no morphological synapomorphy of the PWB has ever been revealed in previously published work. Six chloroplast sequences with coding (ndhF3' and matK) and non-coding (rpl16 intron, rps16 intron, trnD-trnT spacer, and trnT-trnL spacer) regions and three low-copy nuclear sequences (GPA1, Pabp1, and PvCel1) are ...


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