Digital Commons Network^™

Epigenetic Response To Environmental Change: Dna Methylation Varies With Invasion Status, Aaron W. Schrey, Travis R. Robbins, Jacob Lee, David W. Dukes Jr., Alexandria K. Ragsdale, Christopher J. Thawley

Biology Faculty Publications

Epigenetic mechanisms may be important for a native species’ response to rapid environmental change. Red Imported Fire Ants (Solenopsis invicta Santschi, 1916) were recently introduced to areas occupied by the Eastern Fence Lizard (Sceloporus undulatus Bosc & Daudin, 1801). Behavioral, morphological and physiological phenotypes of the Eastern Fence Lizard have changed following invasion, creating a natural biological system to investigate environmentally induced epigenetic changes.We tested for variation in DNA methylation patterns in Eastern Fence Lizard populations associated with different histories of invasion by Red Imported Fire Ants. At methylation sensitive amplified fragment length polymorphism loci, we detected a higher diversity …

Convergence Of Detrital Stoichiometry Predicts Thresholds Of Nutrient-Stimulated Breakdown In Streams, David W. P. Manning, Amy D. Rosemond, Vladislav Gulis, Jonathan P. Benstead, John S. Kominoski, John C. Maerz

Biology Faculty Publications

Nutrient enrichment of detritus‐based streams increases detrital resource quality for consumers and stimulates breakdown rates of particulate organic carbon (C). The relative importance of dissolved inorganic nitrogen (N) vs. phosphorus (P) for detrital quality and their effects on microbial‐ vs. detritivore‐mediated detrital breakdown are poorly understood. We tested effects of experimental N and P additions on detrital stoichiometry (C:N, C:P) and total and microbial breakdown (i.e., with and without detritivorous shredders, respectively) of five detritus types (four leaf litter species and wood) with different initial C : nutrient content. We enriched five headwater streams continuously for two years at different …

De Novo Assembly And Analysis Of The Chilean Pencil Catfish Trichomycterus Areolatus Transcriptome, Thomas T. Schulze, Jonathan Ali, Maggie Bartlett, Madalyn Mcfarland, Emalie Clement, Harim Won, Austin G. Sanford, Elyssa Monzingo, Matthew C. Martens, Ryan M. Hemsley, Sidharta Kumar, Nicolas Gouin, Alan Kolok, Paul H. Davis

Biology Faculty Publications

Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile’s high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was …

Broad Activation Of Latent Hiv-1 In Vivo, Kirston Barton, Bonnie Hiener, Anni Winckelmann, Thomas Aagaard Rasmussen, Wei Shao, Karen Byth, Robert Lanfear, Ajantha Solomon, James Mcmahon, Sean Harrington, Maria Buzon, Mathias Lichterfeld, Paul W. Denton, Rikke Olesen, Lars Østergaard, Martin Tolstrup, Sharon R. Lewin, Ole Schmeltz Søgaard, Sarah Palmer

Biology Faculty Publications

The ‘shock and kill’ approach to cure human immunodeficiency virus (HIV) includes transcriptional induction of latent HIV-1 proviruses using latency-reversing agents (LRAs) with targeted immunotherapy to purge infected cells. The administration of LRAs (panobinostat or vorinostat) to HIV-1-infected individuals on antiretroviral therapy induces a significant increase in cell-associated unspliced (CA-US) HIV-1 RNA from CD4+ T cells. However, it is important to discern whether the increases in CA-US HIV-1 RNA are due to limited or broad activation of HIV-1 proviruses. Here we use single-genome sequencing to find that the RNA transcripts observed following LRA administration are genetically diverse, indicating activation of …

Using Animal Models To Overcome Temporal, Spatial And Combinatorial Challenges In Hiv Persistence Research, Paul W. Denton, Ole S. Søgaard, Martin Tolstrup

Biology Faculty Publications

Research challenges associated with understanding HIV persistence during antiretroviral therapy can be categorized as temporal, spatial and combinatorial. Temporal research challenges relate to the timing of events during establishment and maintenance of HIV persistence. Spatial research challenges regard the anatomical locations and cell subsets that harbor persistent HIV. Combinatorial research challenges pertain to the order of administration, timing of administration and specific combinations of compounds to be administered during HIV eradication therapy. Overcoming these challenges will improve our understanding of HIV persistence and move the field closer to achieving eradication of persistent HIV. Given that humanized mice and non-human primate …

Construction Of High Resolution Genetic Linkage Maps To Improve The Soybean Genome Sequence Assembly Glyma1.01, Qijian Song, Jerry Jenkins, Gaofeng Jia, David L. Hyten, Vince Pantalone, Scott A. Jackson, Jeremy Schmutz, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Background: A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, …

Genome-Wide Discriminatory Information Patterns Of Cytosine Dna Methylation, Robersy Sanchez, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Cytosine DNA methylation (CDM) is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurements were used: (1) the amount of information gained/lost with the CDM changes I_R and (2) the uncertainty of not observing a SNP LC_R. We hypothesize that epigenetic marks are chromosomal footprints accounting for different ontogenetic and phylogenetic histories of individual populations. A machine learning approach is proposed to …

Expression Of Apoplast-Targeted Plant Defensin Mtdef4.2 Confers Resistance To Leaf Rust Pathogen Puccinia Triticina But Does Not Affect Mycorrhizal Symbiosis In Transgenic Wheat, Jagdeep Kaur, John Fellers, Alok Adholeya, Siva L.S. Velivelli, Kaoutar El-Mounadi, Natalya Nersesian, Thomas Clemente, Dilip Shah

Department of Agronomy and Horticulture: Faculty Publications

Rust fungi of the order Pucciniales are destructive pathogens of wheat worldwide. Leaf rust caused by the obligate, biotrophic basidiomycete fungus Puccinia triticina (Pt) is an economically important disease capable of causing up to 50 % yield losses. Historically, resistant wheat cultivars have been used to control leaf rust, but genetic resistance is ephemeral and breaks down with the emergence of new virulent Pt races. There is a need to develop alternative measures for control of leaf rust in wheat. Development of transgenic wheat expressing an antifungal defensin offers a promising approach to complement the endogenous resistance genes …

Lack Of Host Specialization On Winter Annual Grasses In The Fungal Seed Bank Pathogen Pyrenophora Semeniperda, Julie Beckstead, Susan E. Meyer, Tony S. Ishizuka, Kelsey M. Mcevoy, Craig E. Coleman

Biology Faculty Scholarship

Generalist plant pathogens may have wide host ranges, but many exhibit varying degrees of host specialization, with multiple pathogen races that have narrower host ranges. These races are often genetically distinct, with each race causing highest disease incidence on its host of origin. We examined host specialization in the seed pathogen Pyrenophora semeniperda by reciprocally inoculating pathogen strains from Bromus tectorum and from four other winter annual grass weeds (Bromus diandrus, Bromus rubens, Bromus arvensis and Taeniatherum caput-medusae) onto dormant seeds of B. tectorum and each alternate host. We found that host species varied in …

Tripartite Motif Containing 28 (Trim28) Promotes Breast Cancer Metastasis By Stabilizing Twist1 Protein., Dianzheng Zhang, Boxv Zhou, Li Zhu, Md Asaduzzaman Khan, Tao He, Sufang Zhou, Jian He, Xiaoling Lu, Hanchun Chen, Yongxiang Zhao, Junjiang Fu

PCOM Scholarly Works

TRIM28 regulates its target genes at both transcriptional and posttranscriptional levels. Here we report that a TRIM28-TWIST1-EMT axis exists in breast cancer cells and TRIM28 promotes breast cancer metastasis by stabilizing TWIST1 and subsequently enhancing EMT. We find that TRIM28 is highly expressed in both cancer cell lines and advanced breast cancer tissues, and the levels of TRIM28 and TWIST1 are positively correlated with the aggressiveness of breast carcinomas. Overexpression and depletion of TRIM28 up- and down-regulates the protein, but not the mRNA levels of TWIST1, respectively, suggesting that TRIM28 upregulates TWIST1 post-transcriptionally. Overexpression of TRIM28 in breast cancer cell …

A Dramaturgical Analysis Of The Miracle Worker, Abby Butzer

All Graduate Theses, Dissertations, and Other Capstone Projects

This document is a thesis submitted in partial fulfillment of the Master of Arts degree in theatre. It is a dramaturgical analysis for William Gibson's play The Miracle Worker, providing a reference for directors and actors. The thesis explores the play's medical and pedagogical history in six chapters: the physiology and psychology of language acquisition as it pertains to sight and/or hearing impaired children, a pedagogical comparison of Samuel G. Howe and Annie Sullivan, a modern diagnosis of the fever that destroyed Helen Keller's vision and hearing, the 19th century pathology and treatment options for the disease of the eye …

Biogeographic Divergences In The Iberian Flora. A Morpho-Anatomic,Issr-Based, And Environmental Study Of Iberian Buxus Sempervirens L., Márcia Carvalho, João Rocha, Valdemar Carnide, Sandra Martins, Maurici Mus, Francisco Amich, Rubim Almeida, Claúdia Machado, Berta Gonçalves, Eunice Bacelar, Antonio Crespi

Turkish Journal of Botany

Iberian Buxus spp. Are represented by B. Sempervirens, restricted to the Cantabrian, eastern Iberian Peninsula, and northeastern mountain systems, emerging scarcely in Portugal, and by B. Balearica that occurs in the Betic deep river valleys and in the Balearic islands. The genetic affinity existent between fifteen populations of B. Sempervirens was evaluated by seven ISSRs primers. Moreover, leaf morpho-anatomical measurements indicative of leaf performance (such as leaf area, leaf mass per unit area, width, length, shape factor, tissues thickness, stomatal density, and quantification of epi- and intracuticular waxes) and environmental characterization were conducted to get insight into the functional ecology …

Cladonia Trapezuntica (Cladoniaceae, Lichenized Ascomycota): A Robust Morphotype Of Pycnothelia Papillaria, A Taxonomic Study With Conservational Survey, Ayhan Şenkardeşler, Demet Cansaran Duman, Laszlo Lökös, Teuvo Ahti

Turkish Journal of Botany

The long-neglected lichen described as Cladonia trapezuntica was rediscovered at its type locality in Turkey thanks to historical maps available at the Natural History Museum in Vienna. Molecular, morphological, and chemical analyses were applied to determine whether C. Trapezuntica is a distinct species or rather falls within the phenotypic variation of Pycnothelia papillaria. Although most of the podetia appear to be unusual for P. Papillaria, the molecular evidence indicates that C. Trapezuntica should be considered as a synonym of P. Papillaria, and the cushion-like growth form, taller podetia with irregular to dichotomously or trichotomously branching pattern, and scarce primary thallus …

A New Species Of Lepiota, Lepiota Lahorensis, From Lahore, Pakistan, Tayyaba Qasim, Abdul Khalid, Else Vellinga

Turkish Journal of Botany

Lepiota lahorensis sp. nov. is described from Lahore, Pakistan. Its characterizing features are pinkish brown pileus with dark brown furfuraceous scales, oblong to ellipsoid spores, clavate cheilocystidia, and pileus covering made up of trichodermal elements without shorter elements at their base. The phylogenetic analysis based on nuclear ribosomal internal transcribed spacer sequence shows its unique position in sect. Ovisporae.

Labellum Micromorphology Of Some Orchid Genera (Orchidaceae) Distributed In The Black Sea Region In Turkey, Şenay Süngü Şeker, Mustafa Kemal Akbulut, Gülcan Şenel

Turkish Journal of Botany

A detailed micromorphological analysis of the labellum was carried out using both light and scanning electron microscopy on 14 genera (Anacamptis, Cephalanthera, Coeloglossum, Dactylorhiza, Gymnadenia, Himantoglossum, Limodorum, Neottia, Orchis, Ophrys, Platanthera, Serapias, Spiranthes, and Steveniella) of Orchidaceae in Turkey. In the samples, various epidermal features were identified in the spur that developmentally are invaginations of the labellum and the adaxial surface of the labellum. Typical secretory cells and inclusions such as starch or calcium oxalate crystals of different sizes and shapes were found within the structure of individuals. In many genera, characteristically shaped secretory trichomes and papillae were concentrated at …

Induction And Development Of Anther-Derived Gametic Embryos In Cucumber (Cucumis Sativus L.) By Optimizing The Macronutrient And Agar Concentrations In Culture Medium, Mohammad Reza Abdollahi, Samereh Najafi, Hasan Sarikhani, Sayyed Saeed Moosavi

Turkish Journal of Biology

Anther culture response of a cucumber cultivar (Beta Alpha) and three Iranian landraces of cucumber (Basmenj, Isfahani, and Korki) on MS culture media with an altered macronutrient strength (half, full, 1.5-fold, and double-strength) or various concentrations of agar (0, 3.5, 7, and 14 g L-1) was evaluated in two separate experiments. The effect of different concentrations of agar on the development of callus-derived embryos was also assessed. The androgenic potentials of various cucumbers were significantly (P < 0.01) influenced by the different macronutrient strengths and agar concentrations, although anther culture responses could vary according to the cucumber type. A doubled strength of macronutrients in culture medium resulted in the highest percentage of callogenesis (100%) in Isfahani cucumber, while use of full strength of macronutrients produced the highest percentage of embryogenic calli (83.33%) in the mentioned landrace compared to other tested forms. The maximum number of gametic embryos (1.26 and 1.23 embryos/anther) differentiated from Isfahani anther cultures on full- and half-strength MS medium, respectively. In the second experiment, the highest percentages of callogenesis were obtained in MS culture media solidified with 14 g L-1 and 7 g L-1 agar for Basmenj, with 3.5 g L-1 agar or liquid medium for Isfahani, with 7 g L-1 agar for Beta Alpha, and with 14 g L-1 agar for Korki. Culture media solidified with 7 g L-1 agar produced the highest percentage of embryogenic calli compared to other treatments. Anther culture of Korki cucumber on culture medium with 14 g L-1 agar produced the maximum number of embryos per anther compared to other cucumbers. Improved production of mature somatic embryos (torpedo and cotyledonary embryos) was achieved with higher agar concentrations (7 and 14 g L-1) for the cucumber cultivar and all landraces.

Androgenic Responses Of 64 Ornamental Pepper (Capsicum Annuum L.)Genotypes To Shed-Microspore Culture In The Autumn Season, Esi̇n Ari, Hi̇lal Bedi̇r, Selcen Yildirim, Tolga Yildirim

Turkish Journal of Biology

The recent gradual increase in interest and demand for multipurpose ornamental peppers has encouraged intensive breeding studies, especially for use in landscape. However, information in the literature about haploidy is limited. Thus, first, we intend to identify proper morphological markers for quick selection of suitable flower buds containing convenient microspores in two sample ornamental pepper genotypes with and without anthocyanin in external appearance. Secondly, the androgenic responses of 64 genotypes are determined in the autumn season through shed-microspore culture. Based on DAPI-assisted results, the calyx/bud ratio can be used as an effective morphological marker for proper bud selection in both …

Civil Rights—From Negative Restriction To Affirmative Obligation: A Call For Massachusetts To Recognize A Right To Rehabilitation Beginning With Juvenile Offenders, Jennifer L. Weekley

Western New England Law Review

In Diatchenko v. District Attorney for Suffolk District, 1 N.E.3d 270 (Mass. 2013) the Massachusetts Supreme Judicial Court sparked significant juvenile sentencing reform in the state. Previously an outlier for its harsh treatment of juveniles, the Commonwealth now prohibits the imposition of life imprisonment without the possibility of parole for juvenile offenders. This crucial step forward in juvenile justice is dually rooted in neuroscience advancements and society’s ever-evolving standards of decency. The premise is simply that children are different. Children are categorically impulsive, more susceptible to negative environmental influences, and their malleable character is less persuasive evidence of irretrievable depravity …

The Health Exception, Monica E. Eppinger

All Faculty Scholarship

The abortion doctrine laid out in Roe v. Wade permits a procedure necessary to preserve the life or the health of the pregnant woman, setting out what has come to be called the “life exception” and the “health exception.” This Article investigates the background and antecedents of the health exception, identifying three periods of formation and change up to the drafting of the Model Penal Code in 1959. It argues that theories of health lie at the heart of legal doctrine, shaping common-law treatment of abortion and persisting in nineteenth- and twentieth-century statutes. This account reveals origins of a health …

The Journey Of Transitioning: Being A Trans-Athlete In College Sport, Alexandra Klein

Master of Education in Applied Human Development Graduate Projects

The NCAA’s stance on transgender athletes is such that universities should adopt new policies and practices to best provide equal opportunities for all transgender students wishing to compete on a collegiate athletic team. However, there is very little research about transgender athletes in college sport. This case study serves as the voice of one collegiate-athlete who is transitioning from female to male while continuing to be a Division I athlete. The limited research on transgender athletes provides some insight into their experiences before, during and after the athlete came out as transgender (e.g., Lucas-Carr & Krane, 2012; Semerjian & Cohen, …

Textual Analysis: Hard Knocks, Eric Vendemia

Master of Education in Applied Human Development Graduate Projects

This study uses textual analysis to examine how masculinity is conveyed through HBO’s docu-series Hard Knocks. NFL players featured on HBO’s docu-series Hard Knocks are examined to see examples of masculine behavior in the NFL. NFL football is characterized by competitiveness, strength, violence and aggression and Hard Knocks showcases it in a raw form. This study observes the framework and context of the gender order, masculinity, hegemonic masculinity, war-football comparisons, men’s relationship with sport, the physical body in the NFL, and NFL’s current issues. The specific scenes give rare glimpses of training camp in the NFL. The scenes showcase relationships …

Dying Fast: Suicide In Individuals With Gambling Disorder, Stacey A. Tovino

Faculty Articles

These published remarks carefully document the history of health insurance coverage of gambling disorder. They begin by providing examples of gambling disorder insurance benefit disparities in the contexts of public health care programs and private health plans. They proceed by reviewing the effect of three pieces of legislation, including the Mental Health Parity Act of 1996, the Paul Wellstone and Pete Domenici Mental Health Parity and Addiction Equity Act of 2008, and the Affordable Care Act of 2010, on public and private insurance coverage of gambling disorder. They highlight the partial victory that will occur in some states beginning in …

Studying School Improvement Teams To Analyze Multiple Stakeholder Engagement In Decision-Making In Public Education, Julie A. Dibari

Open Access Dissertations

Since the Industrial Revolution, when schools became larger and the missions broader, there has been an attempt by a wide range of stakeholders to have a voice in public education. More recently, through No Child Left Behind and Race to the Top, the federal government began to increase requirements for multiple stakeholder engagement in decision-making for schools requesting Title I funds. As the need for a more educated workforce has grown, businesses have also sought to have a voice in improving education. Additionally, experts in the field of parent, school and community engagement, have called for the inclusion of parents, …

How Does A Personal Trainer’S Appearance Impact How Potential Clients Perceive Them?, Kali Morgenstern

Master of Education in Applied Human Development Graduate Projects

Personal trainer’ duties are to assist clients with proper form, motivate, provide a sense of accountability, create individualized work out plans, and help clients achieve an overall healthy lifestyle. Oftentimes, personal trainers are judged base on physical appearance rather than certifications, education, and level of experience. The purpose of this study was to better understand how potential clients view personal trainers based on appearance. In an effort to assist and enhance the careers of personal trainers in the future, this study provides guidance regarding perceptions and opinions of potential clients. An Exploratory Design was used to lay the groundwork for …

Cluster Enhanced Nanopore Spectrometry, Amy Chavis

Theses and Dissertations

Nanopore sensing is a label-free method used to characterize water-soluble molecules. Recent work describes how Au₂₅(SG)₁₈ clusters improve the single molecule nanopore spectrometry (SMNS) technique when analyzing polyethylene glycol (PEG). This thesis will further study and optimize the enhancement effect resulting from a cluster’s presence. Additionally, a model describing the interaction between a cluster and PEG is developed to assist in understanding this mechanism of enhancement. This thesis will also discuss expanding the SMNS method to detect peptides, using Au₂₅(SG)₁₈ for enhancement, and adjusting solution conditions to improve the sensitivity of the SMNS system …

Holistic Products: Designing With Time, Gifts, And Ritual, Jeremy P. Zietz

Theses and Dissertations

The notion of “you are what you buy” is an updated adage from “you are what you eat”. It makes a connection between our everyday objects and their effect on our lived experience. Looking at our relationships with our things as a type of contract, we must be intentional to shape these object contracts for our own good and health. Instead of our society’s design talents being put toward a consumerist agenda, designers must direct research and development which addresses the effects of our products holistically.

Various concepts have emerged in my creative practice which demand a deeper research and …

Acute And Chronic Effects Of Inhalants In Intracranial Self-Stimulation, Matthew Tracy

Theses and Dissertations

Inhalants are a loosely defined diverse group of volatile substances which people abuse. Despite widespread misuse of inhalants, there are limited preclinical methods available to study the reinforcement-like properties of inhalants. One procedure which has demonstrated substantial promise as a tool to investigate inhalant pharmacology is the intracranial self-stimulation (ICSS) procedure. ICSS utilizes pulses of electrical stimulation to the mesolimbic reward pathway to serve as a temporally defined and controlled operant reinforcer with a highly adjustable efficacy. The first aim of the project was to characterize the effects of commonly abused inhalants: including toluene, trichloroethane, nitrous oxide, isoflurane and R134a …

Behind The Nylon Curtain: Social Cohesion, Law, And The Disaggregation Of American Culture, Rebecca Roiphe, Doni Gewirtzman

Articles & Chapters

No abstract provided.

Collaboration Between Schools And Child Welfare Agencies In Florida To Address The Educational Needs Of Children In Foster Care, Kele Stewart, Vanessa Thorrington

Articles

No abstract provided.

Leech Host Specificity And Its Effect On Rates Of Parasitism In Two Pond Turtle Species, Sternotherus Odoratus And Chrysemys Picta, Linda Valentina Araya

Theses, Dissertations and Culminating Projects

Appropriate host selection by parasites is critical for ensuring offspring survival, optimal feeding location, and protection from predators. Leeches (Placobdella spp.) are known to parasitize bottom-dwelling turtle species more frequently than basking turtle species, but it is not known whether this bias is evolutionarily advantageous. I tested two potential factors that could influence host selection by leeches: differential chance of encounter due to habitat usage, and chemosensory bias of leeches toward bottom-dwelling species. I first confirmed that Chrysemys picta (Eastern painted turtle, a basking species) and Sternotherus odoratus (common musk turtle, a bottom-dwelling species) in Lake Wapalanne in Sussex County, …