Bacteriophage Mu DNA replication in vitro

Journal ArticleAn in vitro system for bacteriophage Mu DNA replication using lysates on cellophane discs is described. Mu replication was monitored by DNA hybridization. Using a thermoinducible Mu Iysogen, 30-50% of all DNA synthesis in vitro was Mu-specific

DNA-topoisomerase modification

Journal ArticleThe first reports of topoisomerase modification were published in 1982 and 1983 (Mills et al. 1982; Durban et al. 1983; Ferro et al. 1983; Jongstra-Bilen et al. 1983). Although a wide variety of posttranslational modifications of DNA topoisomerases may occur, this chapter focuses only on phosphorylation and poly(ADP-ribosylation), which have been observed both in vitro and in vivo. The experimental data suggest a regulatory role, but the precise cellular functions of these DNA topoisomerase modifications remain undefined at the present time

Senior Theses: Department of Physical Sciences

1992 Senior Theses from the Department of Physical Science at Morehead State University. The Abundance, Diversity, and Stratigraphy of the Upper Crab Orchard Formation, Lewis County, Kentucky by Patrick M. Higgins. The Modification of Flemion for Use in a Solid Electrolyte Battery by Timothy Howard. Simple Analog Computers by Leah Carol Ross

Organic bioelectronics: using highly conjugated polymers to interface with biomolecules, cells and tissues in the human body

Conjugated polymers exhibit interesting material and optoelectronic properties that make them well-suited to the development of biointerfaces. Their biologically relevant mechanical characteristics, ability to be chemically modified, and mixed electronic and ionic charge transport are captured within the diverse field of organic bioelectronics. Conjugated polymers have been used in wide range of device architectures, and cell and tissue scaffolds. These devices enable biosensing of many biomolecules, such as metabolites, nucleic acids and more. Devices can be used to both stimulate and sense the behavior of cells and tissues. Similarly, tissue interfaces permit interaction with complex organs, aiding both fundamental biological understanding and providing new opportunities for stimulating regenerative behaviors and bioelectronic based therapeutics. Applications of these materials are broad, and much continues to be uncovered about their fundamental properties. This report covers the current understanding of the fundamentals of conjugated polymer biointerfaces and their interactions with biomolecules, cells and tissues in the human body. An overview of current materials and devices is presented, along with highlighted major in vivo and in vitro applications. Finally, open research questions and opportunities are discussed

Identification of Listeria monocytogenes Determinants Required for Biofilm Formation

Listeria monocytogenes is a Gram-positive, food-borne pathogen of humans and animals. L. monocytogenes is considered to be a potential public health risk by the U.S. Food and Drug Administration (FDA), as this bacterium can easily contaminate ready-to-eat (RTE) foods and cause an invasive, life-threatening disease (listeriosis). Bacteria can adhere and grow on multiple surfaces and persist within biofilms in food processing plants, providing resistance to sanitizers and other antimicrobial agents. While whole genome sequencing has led to the identification of biofilm synthesis gene clusters in many bacterial species, bioinformatics has not identified the biofilm synthesis genes within the L. monocytogenes genome. To identify genes necessary for L. monocytogenes biofilm formation, we performed a transposon mutagenesis library screen using a recently constructed Himar1 mariner transposon. Approximately 10,000 transposon mutants within L. monocytogenes strain 10403S were screened for biofilm formation in 96-well polyvinyl chloride (PVC) microtiter plates with 70 Himar1 insertion mutants identified that produced significantly less biofilms. DNA sequencing of the transposon insertion sites within the isolated mutants revealed transposon insertions within 38 distinct genetic loci. The identification of mutants bearing insertions within several flagellar motility genes previously known to be required for the initial stages of biofilm formation validated the ability of the mutagenesis screen to identify L. monocytogenes biofilm-defective mutants. Two newly identified genetic loci, dltABCD and phoPR, were selected for deletion analysis and both ΔdltABCD and ΔphoPR bacterial strains displayed biofilm formation defects in the PVC microtiter plate assay, confirming these loci contribute to biofilm formation by L. monocytogenes

A pp-adic RanSaC algorithm for stereo vision using Hensel lifting

A $p$-adic variation of the Ran(dom) Sa(mple) C(onsensus) method for solving the relative pose problem in stereo vision is developped. From two 2-adically encoded images a random sample of five pairs of corresponding points is taken, and the equations for the essential matrix are solved by lifting solutions modulo 2 to the 2-adic integers. A recently devised $p$-adic hierarchical classification algorithm imitating the known LBG quantisation method classifies the solutions for all the samples after having determined the number of clusters using the known intra-inter validity of clusterings. In the successful case, a cluster ranking will determine the cluster containing a 2-adic approximation to the "true" solution of the problem.Comment: 15 pages; typos removed, abstract changed, computation error remove

GWIPS-viz: development of a ribo-seq genome browser

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing

Protocol for a realist review of workplace learning in postgraduate medical education and training

Postgraduate medical education and training (PGMET) is a complex social process which happens predominantly during the delivery of patient care. The clinical learning environment (CLE), the context for PGMET, shapes the development of the doctors who learn and work within it, ultimately impacting the quality and safety of patient care. Clinical workplaces are complex, dynamic systems in which learning emerges from non-linear interactions within a network of related factors and activities. Those tasked with the design and delivery of postgraduate medical education and training need to understand the relationship between the processes of medical workplace learning and these contextual elements in order to optimise conditions for learning. We propose to conduct a realist synthesis of the literature to address the overarching questions; how, why and in what circumstances do doctors learn in clinical environments? This review is part of a funded projected with the overall aim of producing guidelines and recommendations for the design of high quality clinical learning environments for postgraduate medical education and training

Electrical protection design for integrated motor drives with carbon fibre composite casings for aircraft

Replacing traditionally aluminum non-electrically active components of integrated motor drives (IMD) (e.g. casings) with lighter-weight carbon fibre reinforced polymer (CFRP) for offers a route to the key weight savings, desirable in future aircraft electric applications. However, CFRP casing designs must accommodate electrical interactions with encased equipment. Approaches to fault management and electrical protection must ensure that both electrical power system (EPS) and CFRP casing are protected against electrical faults. Knowledge of the electrical and thermal response of the CFRP casing underpins fault resilient casing design. The proposed CFRP casing is a wound filament (WF) CFRP tube for an integrated motor drive. This paper presents the first experimentally validated methodology to capture macro-scale electrical and thermal response of a WF CFRP tube to low frequency current. This knowledge is subsequently combined with wider EPS design considerations, including electrical grounding and bonding, to control fault response, enabling implementation of appropriate protection solutions. The results indicate that tuning casing resistance is not a viable, immediate option to control fault response, and that wider electrical system design options (grounding topologies) must be considered. Hence incorporation of CFRP for non-electrically active components to improve power density, has significant impact on wider electrical power system design

Global MYCN Transcription Factor Binding Analysis in Neuroblastoma Reveals Association with Distinct E-Box Motifs and Regions of DNA Hypermethylation

BACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p\u3c0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the activity of individual genes, and that of a mediator of global chromatin structure