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2014

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Full-Text Articles in Life Sciences

Ua1c11/55 Gordon Wilson Photo Collection, Wku Archives Dec 2014

Ua1c11/55 Gordon Wilson Photo Collection, Wku Archives

WKU Archives Collection Inventories

Photographs taken by and of Gordon Wilson.


Meeting Calendar Dec 2014

Meeting Calendar

Journal of Medicinally Active Plants

No abstract provided.


Fish Sound Production In The Presence Of Harmful Algal Blooms In The Eastern Gulf Of Mexico, Carrie C. Wall, Chad Lembke, Chuanmin Hu, David A. Mann Dec 2014

Fish Sound Production In The Presence Of Harmful Algal Blooms In The Eastern Gulf Of Mexico, Carrie C. Wall, Chad Lembke, Chuanmin Hu, David A. Mann

Marine Science Faculty Publications

This paper presents the first known research to examine sound production by fishes during harmful algal blooms (HABs). Most fish sound production is species-specific and repetitive, enabling passive acoustic monitoring to identify the distribution and behavior of soniferous species. Autonomous gliders that collect passive acoustic data and environmental data concurrently can be used to establish the oceanographic conditions surrounding sound-producing organisms. Three passive acoustic glider missions were conducted off west-central Florida in October 2011, and September and October 2012. The deployment period for two missions was dictated by the presence of red tide events with the glider path specifically set ...


Rice And Mouse Quantitative Phenotype Prediction In Genome-Wide Association Studies With Support Vector Regression, Abdulrhman Fahad M. Aljouie Dec 2014

Rice And Mouse Quantitative Phenotype Prediction In Genome-Wide Association Studies With Support Vector Regression, Abdulrhman Fahad M. Aljouie

Theses

Quantitative phenotypes prediction from genotype data is significant for pathogenesis, crop yields, and immunity tests. The scientific community conducted many studies to find unobserved quantitative phenotype high predictive ability models. Early genome-wide association studies (GWAS) focused on genetic variants that are associated with disease or phenotype, however, these variants manly covers small portion of the whole genetic variance, and therefore, the effectiveness of predictions obtained using this information may possibly be circumscribed [ 1 ].

Instead, this study shows prediction ability from whole genome single nucleotide polymorphisms (SNPs) data of 1940 genotyped stoke mouse with - 12k SNPs, and 413 genotyped rice inbred ...


Cancer Risk Prediction With Next Generation Sequencing Data Using Machine Learning, Nihir Patel Dec 2014

Cancer Risk Prediction With Next Generation Sequencing Data Using Machine Learning, Nihir Patel

Theses

The use of computational biology for next generation sequencing (NGS) analysis is rapidly increasing in genomics research. However, the effectiveness of NGS data to predict disease abundance is yet unclear. This research investigates the problem in the whole exome NGS data of the chronic lymphocytic leukemia (CLL) available at dbGaP. Initially, raw reads from samples are aligned to the human reference genome using burrows wheeler aligner. From the samples, structural variants, namely, Single Nucleotide Polymorphism (SNP) and Insertion Deletion (INDEL) are identified and are filtered using SAMtools as well as with Genome Analyzer Tool Kit (GATK). Subsequently, the variants are ...


Mechanisms Of Translational Repression Of The Sperm Mitochondria Associated-Cysteine Rich Protein (Smcp) Mrna In Round Spermatids, Danielle L. Cullinane Dec 2014

Mechanisms Of Translational Repression Of The Sperm Mitochondria Associated-Cysteine Rich Protein (Smcp) Mrna In Round Spermatids, Danielle L. Cullinane

Graduate Doctoral Dissertations

The sperm-mitochondria-associated cysteine-rich protein (SMCP) is a male germ cell-specific protein that localizes to the outer membranes of sperm mitochondria and increases sperm motility. The Smcp mRNA is transcribed in early spermatids, and stored in a translationally repressed state for ~7 days before translation is activated in late spermatids. Identifying the cis-elements and trans-factors that repress the Smcp mRNA in early spermatids is important because these factors and elements coordinate the translational activity of hundreds of mRNAs.

A mutation was studied in transgenic mice in which the 16 nucleotides downstream of the first poly(A) signal in the ...


E Pluribus Unum: What Individual Whales Can Tell Us About Enigmatic Species Distribution And Social Organization, Tanya Marie Lubansky Dec 2014

E Pluribus Unum: What Individual Whales Can Tell Us About Enigmatic Species Distribution And Social Organization, Tanya Marie Lubansky

Dissertations

Large whales have historically been difficult to study and many aspects of their ecology remain unknown especially at the long -term population level. The ability to identify individual whales based on natural markings provides the opportunity to track individuals over time and space; this data may offer more insight into the ecology of whales than previously imagined. This study demonstrates use of photo-identification data to model both social structure and habitat selection, minimizing the need for invasive research and greatly increasing the sample size used in such endeavors. A conditional logistic model is written for a 20-year sightings dataset on ...


Identifying Glioblastoma Gene Networks Based On Hypergeometric Test Analysis, Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo Komotar, Jennifer L. Clarke, Ming Zhang, Nagi G. Ayad Dec 2014

Identifying Glioblastoma Gene Networks Based On Hypergeometric Test Analysis, Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo Komotar, Jennifer L. Clarke, Ming Zhang, Nagi G. Ayad

Faculty Publications, Department of Statistics

Patient specific therapy is emerging as an important possibility for many cancer patients. However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques. We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large cohort of patients analyzed by The Cancer Genome Atlas (TCGA). To test this directly, we devised a bioinformatics pipeline to identify differentially expressed genes in ...


No Waste: Nyc, Minda Smiley Dec 2014

No Waste: Nyc, Minda Smiley

Capstones

I produced three video pieces about people who are living zero-waste lifestyles or using zero-waste practices in their businesses. I also wrote a narrative piece about my experience living zero-waste for one week.


Flow Cytometry For Rapid Detection Of Salmonella Spp. In Seed Sprouts, Bledar Bisha, Byron F. Brehm-Stecher Dec 2014

Flow Cytometry For Rapid Detection Of Salmonella Spp. In Seed Sprouts, Bledar Bisha, Byron F. Brehm-Stecher

Food Science and Human Nutrition Publications

Seed sprouts (alfalfa, mung bean, radish, etc.) have been implicated in several recent national and international outbreaks of salmonellosis. Conditions used for sprouting are also conducive to the growth of Salmonella. As a result, this pathogen can quickly grow to very high cell densities during sprouting without any detectable organoleptic impact. Seed sprouts typically also support heavy growth (~108 CFU g−1) of a heterogeneous microbiota consisting of various bacterial, yeast, and mold species, often dominated by non-pathogenic members of the family Enterobacteriaceae. This heavy background may present challenges to the detection of Salmonella, especially if this pathogen is present ...


The Status Of Fishes In The Missouri River, Nebraska: Shoal Chub (Macrhybopsis Hyostoma), Sturgeon Chub (M. Gelida), Sicklefin Chub (M. Meeki), Silver Chub (M. Storeriana), Flathead Chub (Platygobio Gracilis), Plains Minnow (Hybognathus Placitus), Western Silvery Minnow (H. Argyritis), And Brassy Minnow (H. Hankinsoni), Kirk D. Steffensen, Dane A. Shuman, Sam Stukel Dec 2014

The Status Of Fishes In The Missouri River, Nebraska: Shoal Chub (Macrhybopsis Hyostoma), Sturgeon Chub (M. Gelida), Sicklefin Chub (M. Meeki), Silver Chub (M. Storeriana), Flathead Chub (Platygobio Gracilis), Plains Minnow (Hybognathus Placitus), Western Silvery Minnow (H. Argyritis), And Brassy Minnow (H. Hankinsoni), Kirk D. Steffensen, Dane A. Shuman, Sam Stukel

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Throughout the past century, the Missouri River has been highly modified which has negatively affected the native fish community. Previous research quantified the reduction of several native Cyprinidae species and made several recommendations to aid in recovery. However, these recommendations were not implemented. Therefore, the objective of this paper is to assess the current population trends of eight native cyprinid species and develop the current management objectives. Over 335,000 fish were collected from the Missouri River along Nebraska’s eastern border with mini-fyke nets and otter trawls from 2003 to 2012. Target Cyprinidae species consisted of less than five ...


The Status Of Fishes In The Missouri River, Nebraska: Sauger (Sander Canadensis), Kirk D. Steffensen, Sam Stukel, Dane A. Shuman Dec 2014

The Status Of Fishes In The Missouri River, Nebraska: Sauger (Sander Canadensis), Kirk D. Steffensen, Sam Stukel, Dane A. Shuman

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Early fisheries investigation of the Missouri River fish community indicated that Sauger were common throughout Nebraska, including all major Missouri River tributaries. However due to many factors, their current range is restricted to the Missouri River and the lower reaches of a few tributaries. Hesse (1994) recommended listing Sauger as a state endangered species but this recommendation was never implemented. Therefore, the objective of this paper is to reevaluate the current population status of Sauger in the Missouri River along Nebraska’s border. Over 2,100 Sauger have been captured from the Missouri River along Nebraska’s eastern border since ...


When You Can't Watch What You Eat: Examining The Fda’S Recall Process For Food Allergies, Jacob Passy Dec 2014

When You Can't Watch What You Eat: Examining The Fda’S Recall Process For Food Allergies, Jacob Passy

Capstones

Over a third of all recalls for food products in the United States occur due to an undeclared allergen. In these situations, a food product is often mislabeled or contaminated in some way, resulting in the unknown presence of allergen. For food-allergic consumers, a company's mistake can become life-threatening. By investigating data from the Food and Drug Administration, I found that supermarket chains are responsible for about a fifth of all recalls, and that many recalls occur past the product's expiration date. These factors point to the need to improve the FDA's handling of food allergies in ...


The Wild West Of Edible Insects, Kyle Ligman Dec 2014

The Wild West Of Edible Insects, Kyle Ligman

Capstones

After the UN came out with a report in 2013 recommending insects for human consumption, businesses and restaurants in the U.S. have been racing to grow a new industry. This project explores the psychological, regulatory and production challenges they face.


Dietary Variety Is Inversely Associated With Body Adiposity Among Us Adults Using A Novel Food Diversity Index.Pdf, Maya Vadiveloo, L. Beth Dixon, Tod Mijanovich, Brian Elbel, Niyati Parekh Dec 2014

Dietary Variety Is Inversely Associated With Body Adiposity Among Us Adults Using A Novel Food Diversity Index.Pdf, Maya Vadiveloo, L. Beth Dixon, Tod Mijanovich, Brian Elbel, Niyati Parekh

Maya Vadiveloo

Background: Consuming a variety (vs. monotony) of energy-poor, nutrient-dense foods may help individuals adhere to
dietary patterns favorably associated with weight control.
Objective: The objective of this study was to examine whether greater healthful food variety quantified using the US
Healthy Food Diversity (HFD) index favorably influenced body adiposity.
Methods: Men and nonpregnant, nonlactating women aged $20 y with two 24-h recalls from the cross-sectional NHANES
2003–2006 (n = 7470) were included in this study. Dietary recalls were merged with the MyPyramid Equivalent database to
generate the US HFD index, which ranges from 0 to ;1, with higher scores indicative ...


Greater Healthful Food Variety As Measured By The Us Healthy Food Diversity Index Is Associated With Lower Odds Of Metabolic Syndrome And Its Components In Us Adults.Pdf, Maya Vadiveloo, Niyati Parekh, Josiemer Mattei Dec 2014

Greater Healthful Food Variety As Measured By The Us Healthy Food Diversity Index Is Associated With Lower Odds Of Metabolic Syndrome And Its Components In Us Adults.Pdf, Maya Vadiveloo, Niyati Parekh, Josiemer Mattei

Maya Vadiveloo

Background: Consuming a wider variety of nutrient-dense foods may promote adherence to healthful dietary patterns, leading to improved dietary quality and enhanced metabolic health.
Objective: We used the US Healthy Food Diversity (HFD) index to simultaneously measure dietary variety, quality, and proportionality, hypothesizing a priori that race/ethnicity may moderate associations between diet and health.
Methods: A representative sample of adults (n = 7470) aged 20+ y with two 24-h recalls and complete outcome data from the cross-sectional NHANES 2003–2006 were selected. US HFD values were generated using a previously validated equation with a theoretical range from 0 to nearly ...


American Society Of Parasitologists Newsletter, V. 36, Nos. 3-4, Fall-Winter 2014, Scott Lyell Gardner Dec 2014

American Society Of Parasitologists Newsletter, V. 36, Nos. 3-4, Fall-Winter 2014, Scott Lyell Gardner

Newsletter of the American Society of Parasitologists

No abstract provided.


U.S. Drought Monitor, December 30, 2014, Brad Rippey Dec 2014

U.S. Drought Monitor, December 30, 2014, Brad Rippey

US Ag in Drought Archive

Drought map of U.S. for December 30, 2014 (12/30/14) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.


Evolutionary Genomics And Adaptive Evolution Of The Hedgehog Gene Family (Shh, Ihh And Dhh) In Vertebrates, Joana Pereira, Warren E. Johnson, Stephen J. O'Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vitor Vasconcelos, Agostinho Antunes Dec 2014

Evolutionary Genomics And Adaptive Evolution Of The Hedgehog Gene Family (Shh, Ihh And Dhh) In Vertebrates, Joana Pereira, Warren E. Johnson, Stephen J. O'Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vitor Vasconcelos, Agostinho Antunes

Biology Faculty Articles

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to ...


Modelling Non-Euclideanmovement And Landscape Connectivity In Highly Structured Ecological Networks, Chris Sutherland, Angela Fuller, J. Royle Dec 2014

Modelling Non-Euclideanmovement And Landscape Connectivity In Highly Structured Ecological Networks, Chris Sutherland, Angela Fuller, J. Royle

Environmental Conservation Faculty Publication Series

1. Movement is influenced by landscape structure, configuration and geometry, but measuring distance as perceived by animals poses technical and logistical challenges. Instead, movement is typically measured using Euclidean distance, irrespective of location or landscape structure, or is based on arbitrary cost surfaces. Arecently proposed extension of spatial capture-recapture (SCR)models resolves this issue using spatial encounterhistories of individuals to calculate least-cost paths (ecological distance: Ecology, 94, 2013, 287) thereby relaxingthe Euclidean assumption. We evaluate the consequences of not accounting for movement heterogeneity whenestimating abundance in highly structured landscapes, and demonstrate the value of this approach for estimatingbiologically realistic space-use ...


Modelling Non-Euclideanmovement And Landscape Connectivity In Highly Structured Ecological Networks, Chris Sutherland, Angela Fuller, J. Royle Dec 2014

Modelling Non-Euclideanmovement And Landscape Connectivity In Highly Structured Ecological Networks, Chris Sutherland, Angela Fuller, J. Royle

Chris Sutherland

1. Movement is influenced by landscape structure, configuration and geometry, but measuring distance as perceived by animals poses technical and logistical challenges. Instead, movement is typically measured using Euclidean distance, irrespective of location or landscape structure, or is based on arbitrary cost surfaces. A
recently proposed extension of spatial capture-recapture (SCR)models resolves this issue using spatial encounter
histories of individuals to calculate least-cost paths (ecological distance: Ecology, 94, 2013, 287) thereby relaxing
the Euclidean assumption. We evaluate the consequences of not accounting for movement heterogeneity when
estimating abundance in highly structured landscapes, and demonstrate the value of this approach ...


En El Do De La Unión Europea: Registro De Denominaciones De Origen Protegidas, Indicaciones Geográficas Protegidas, Etc., Luis González Vaqué, Cristina Vidreras Pérez Dec 2014

En El Do De La Unión Europea: Registro De Denominaciones De Origen Protegidas, Indicaciones Geográficas Protegidas, Etc., Luis González Vaqué, Cristina Vidreras Pérez

Luis González Vaqué

No abstract provided.


Integration Of Developmental And Environmental Signals Via A Polyadenylation Factor In Arabidopsis, Man Liu, Ruqiang Xu, Carrie Merrill, Liwei Hong, Carol Von Lanken, Arthur G. Hunt, Qingshun Q. Li Dec 2014

Integration Of Developmental And Environmental Signals Via A Polyadenylation Factor In Arabidopsis, Man Liu, Ruqiang Xu, Carrie Merrill, Liwei Hong, Carol Von Lanken, Arthur G. Hunt, Qingshun Q. Li

Plant and Soil Sciences Faculty Publications

The ability to integrate environmental and developmental signals with physiological responses is critical for plant survival. How this integration is done, particularly through posttranscriptional control of gene expression, is poorly understood. Previously, it was found that the 30 kD subunit of Arabidopsis cleavage and polyadenylation specificity factor (AtCPSF30) is a calmodulin-regulated RNA-binding protein. Here we demonstrated that mutant plants (oxt6) deficient in AtCPSF30 possess a novel range of phenotypes--reduced fertility, reduced lateral root formation, and altered sensitivities to oxidative stress and a number of plant hormones (auxin, cytokinin, gibberellic acid, and ACC). While the wild-type AtCPSF30 (C30G) was able to ...


The Effect Of Disturbance Regime On Darwinia Glaucophylla (Myrtaceae) And Its Habitat, Carmen Booyens, Anita Chalmers, Douglas Beckers Dec 2014

The Effect Of Disturbance Regime On Darwinia Glaucophylla (Myrtaceae) And Its Habitat, Carmen Booyens, Anita Chalmers, Douglas Beckers

Science and Mathematics Papers and Journal Articles

The effect of disturbance regime (time since last fire or slashing) on the vulnerable plant species, Darwinia glaucophylla, was assessed on the Central Coast of New South Wales (NSW), Australia. The abundance, growth and flowering of D. glaucophylla adults and abundance and growth of seedlings was measured within sites that had either been recently burnt (≤ 5 years), long unburnt (≥ 14 years) or regularly slashed (30 cm above ground) along a utility easement. Our results showed that Darwinia glaucophylla was most abundant at slashed sites, followed by recently burnt sites; it was present but not abundant at unslashed sites that were ...


Baseline Survey For Street Dogs In Guam, John D. Boone Dec 2014

Baseline Survey For Street Dogs In Guam, John D. Boone

Stray and Feral Animal Populations Collection

As is the case for many inhabited islands in Pacific region, dogs are common, including freeroaming street dogs that may be owned or unowned. Reproduction among dogs is largely unchecked, and many owned dogs do not receive adequate levels of basic care in the home or veterinary care when needed. For all of these reasons, Humane Society International (HSI) is exploring options for improving the management of street dog populations and promoting better treatment and care of all dogs on Guam and on the nearby islands of Rota and Saipan. One of the initial steps in this process was to ...


Winter Activity Of Bats In Southeastern Nebraska: An Acoustic Study, Jeremy A. White, Brett R. Andersen, Hans W. Otto, Cliff A. Lemen, Patricia W. Freeman Dec 2014

Winter Activity Of Bats In Southeastern Nebraska: An Acoustic Study, Jeremy A. White, Brett R. Andersen, Hans W. Otto, Cliff A. Lemen, Patricia W. Freeman

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Many North American bats are active outside hibernacula in winter, but no information on winter activity has been reported for Nebraska. We recorded activity of bats during two winters (December-February 2012-2013 and 2013-2014) at one location in southeastern Nebraska with an acoustic detector. Bats were active throughout both winters and temperature at sunset was a good predictor of bat activity. Red bats (Lasiurus borealis) were active at our site in early December but were not recorded later in winter. We suspect these individuals were late migrants to more southern wintering sites. Big brown bats (Eptesicus fuscus) were recorded in each ...


A Single Vertebrate Dna Virus Protein Disarms Invertebrate Immunity To Rna Virus Infection, Don B. Gammon, Sophie Duraffour, Daniel K. Rozelle, Heidi Hehnly, Rita Sharma, Michael E. Sparks, Cara C. West, Ying Chen, James J. Moresco, Graciela Andrei, John H. Connor, Darryl Conte Jr., Dawn E. Gundersen-Rindal, William L. Marshall, John R. Yates, Neal S. Silverman, Craig C. Mello Dec 2014

A Single Vertebrate Dna Virus Protein Disarms Invertebrate Immunity To Rna Virus Infection, Don B. Gammon, Sophie Duraffour, Daniel K. Rozelle, Heidi Hehnly, Rita Sharma, Michael E. Sparks, Cara C. West, Ying Chen, James J. Moresco, Graciela Andrei, John H. Connor, Darryl Conte Jr., Dawn E. Gundersen-Rindal, William L. Marshall, John R. Yates, Neal S. Silverman, Craig C. Mello

Neal Silverman

Virus-host interactions drive a remarkable diversity of immune responses and countermeasures. We found that two RNA viruses with broad host ranges, vesicular stomatitis virus (VSV) and Sindbis virus (SINV), are completely restricted in their replication after entry into Lepidopteran cells. This restriction is overcome when cells are co-infected with vaccinia virus (VACV), a vertebrate DNA virus. Using RNAi screening, we show that Lepidopteran RNAi, Nuclear Factor-kappaB, and ubiquitin-proteasome pathways restrict RNA virus infection. Surprisingly, a highly conserved, uncharacterized VACV protein, A51R, can partially overcome this virus restriction. We show that A51R is also critical for VACV replication in vertebrate cells ...


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 Dec 2014

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

Genomics and Precision Medicine 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 ...


Dna-Guided Establishment Of Canonical Nucleosome Patterns In A Eukaryotic Genome, Leslie Y. Beh, Noam Kaplan, Manuel M. Muller, Tom W. Muir, Laura F. Landweber Dec 2014

Dna-Guided Establishment Of Canonical Nucleosome Patterns In A Eukaryotic Genome, Leslie Y. Beh, Noam Kaplan, Manuel M. Muller, Tom W. Muir, Laura F. Landweber

University of Massachusetts Medical School Faculty Publications

A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array ...


Real-Time Kinetic Studies Of Bacillus Subtilis Oxalate Decarboxylase And Ceriporiopsis Subvermispora Oxalate Oxidase Using Luminescent Oxygen Sensor, Laura Molina, Thomas Goodall, Umar Twahir, Ellen W. Moomaw Dec 2014

Real-Time Kinetic Studies Of Bacillus Subtilis Oxalate Decarboxylase And Ceriporiopsis Subvermispora Oxalate Oxidase Using Luminescent Oxygen Sensor, Laura Molina, Thomas Goodall, Umar Twahir, Ellen W. Moomaw

Faculty Publications

Oxalate decarboxylase (OxDC), an enzyme of the bicupin superfamily, catalyzes the decomposition of oxalate into carbon dioxide and formate at an optimal pH of 4.3 in the presence of oxygen. However, about 0.2% of all reactions occur through an oxidase mechanism that consumes oxygen while producing two equivalents of carbon dioxide and one equivalent of hydrogen peroxide. The kinetics of oxidase activity were studied by measuring the consumption of dissolved oxygen over time using a luminescent oxygen sensor. We describe the implementation of and improvements to the oxygen consumption assay. The oxidase activity of wild type OxDC was ...