Interactions of insertion sequences targetting integron associated recombination sites

Bacteria of genus Pseudomonas are known for crossing ecological barriers and establishing in clinical settings. Their ability to withstand antibiotic selection in the clinical environment is largely due to interactions between different mobile genetic elements (MGEs) and the presence of multidrug resistance integrons (MRIs). It is difficult to predict resistance gene maintenance within a bacterial population, as the source of these genes is unknown, and the biological processes governing their flow is difficult to quantify in vivo. This study explores the IS1111-attC subgroup of insertion sequences as a model for this process in Pseudomonads. In this study, IS1111-attC elements were found to be overrepresented within non-clinical Pseudomonas isolates relative to clinical Pseudomonads, as well as an enteric outgroup. The observed IS1111-attC distribution suggests that all instances of IS1111-attC elements in class 1 integrons represent recent invasions of attC sites occurring when class 1 integrons were present in the same cells as chromosomal integrons. Target site preferences and transposition mechanisms of the IS1111-attC elements distribution patterns were investigated using in vitro and in vivo models. These elements were shown to specifically recognize the attC recombination sites of integrons in binding assays and to specifically target the attC in mobility assays. Factors affecting the rate of movement between environmental and clinical Pseudomonads were also examined. Significantly, the IS1111-attC transposase binds preferentially to the single strand forms of the top strand of the attC site, rather than the bottom strand attC site which is the target of the integron integrase. This is the first evidence for IS1111-attC mobility in Pseudomonas cells occurring via a similar mechanism to integron gene mobilization, illustrating a way for these elements both to move between chromosomal and plasmid borne integrons, and to facilitate interactions between them

RNA, the Epicenter of Genetic Information

The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers

Genomic diversity of Lactobacillus salivarius

Lactobacillus salivarius is unusual among the lactobacilli due to its multireplicon genome architecture. The circular megaplasmids harboured by L. salivarius strains encode strain-specific traits for intestinal survival and probiotic activity. L. salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. In terms of probiotic strain selection, it is important to have an understanding of the level of genomic diversity present in this species. Comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) were employed to assess the level of genomic diversity in L. salivarius. The wellcharacterised probiotic strains L. salivarius UCC118 was employed as a genetic reference strain. The group of test strains were chosen to reflect the range of habitats from which L. salivarius strains are frequently recovered, including human, animal, and environmental sources. Strains of L. salivarius were found to be genetically diverse when compared to the UCC118 genome. The most conserved strains were human GIT isolates, while the greatest level of divergence were identified in animal associated isolates. MLST produced a better separation of the test strains according to their isolation origins, than that produced by CGHbased strain clustering. The exopolysaccharide (EPS) associated genes of L. salivarius strains were found to be highly divergent. The EPS-producing phenotype was found to be carbonsource dependent and inversely related to a strain's ability to produce a biofilm. The genome of the porcine isolate L. salivarius JCM1046 was shown by sequencing to harbour four extrachromosomal replicons, a circular megaplasmid (pMP1046A), a putative chromid (pMP1046B), a linear megaplasmid (pLMP1046) and a smaller circular plasmid (pCTN1046) which contains an integrated Tn916-like element (Tn6224), which carries the tetracycline resistance gene tetM. pLMP1046 represents the first sequence of a linear plasmid in a Lactobacillus species. Dissemination of antibiotic resistance genes among species with food or probiotic-association is undesirable, and the identification of Tn6224-like elements in this species has implications for strain selection for probiotic applications. In summary, this thesis used a comparative genomics approach to examine the level of genotypic diversity in L. salivarius, a species which contains probiotic strains. The genome sequence of strain JCM1046 provides additional insight into the spectrum of extrachromosomal replicons present in this species

Guidelines for conducting birth defects surveillance

"In January of 1999, the National Birth Defects Prevention Network (NBDPN) established a Surveillance Guidelines and Standards Committee (SGSC) in order to develop and promote the use of standards and guidelines for birth defects surveillance programs in the United States. This set of guidelines is designed to serve as an important first step in the documentation of this process and as the vehicle for dissemination of the committee's findings. The Guidelines for Conducting Birth Defects Surveillance (henceforth referred to as The Surveillance Guidelines) were developed with three major long-term objectives in mind: To improve the quality of state birth defects surveillance data, including accuracy, comparability, completeness, and timeliness; To enhance the utility of state birth defects surveillance data for research on the distribution and etiology of birth defects; To encourage and promote the use of state birth defects surveillance data for the purposes of linking affected children with services and evaluation of those services. The technical guidelines that make up this document provide a way of improving the quality of birth defects surveillance data, which in turn enhances their use in support of the latter two objectives. Fundamental to quality is ensuring that procedures for all aspects of data definition, collection, management, and analysis are established and followed. Because state-based surveillance systems operate with different objectives and data needs, it is clear that, with respect to procedures and standards, 'one size does not fit all.' It is also clear, however, that common guidelines can provide a basis for the development of system-specific operating procedures and supporting manuals." - p. iIntroduction -- -- Chapter 1. The Whys and Hows of Birth Defects Surveillance - Using Data -- -- Chapter 2. Legislation -- Appendix 2.1. Sample State Legislation -- Appendix 2.2. Table of Birth Defects Legislation -- Appendix 2.3. Definitions Used to Determine Covered Entity Status Under the Privacy Rule -- Appendix 2.4. Office of Civil Rights (OCR) HIPAA Privacy Regulation Text -- -- Chapter 3.Case Definition -- Appendix 3.1. Birth Defects Included in the Case Definition of the National Birth Defects Prevention Network -- Appendix 3.2. NBDPN Abstractor's Instructions -- Appendix 3.3. Examples of Conditions Considered to Be Minor Anomalies -- Appendix 3.4. Conditions Related to Prematurity in Infants Born at Less Than 36 Weeks Gestation -- -- Chapter 4. Data Variables -- Appendix 4.1. Descriptions of Minimum (Core) Data Variables -- Appendix 4.2. Descriptions of Recommended Data Variables -- -- Chapter 5. Classification and Coding -- Appendix 5.1. Texas Disease Index -- Appendix 5.2. 6-Digit CDC Codes (updated 8/2007) -- -- Chapter 6. Case Ascertainment Methods -- Appendix 6.1. Data Source Described in Detail - Vital Records -- Appendix 6.2. Data Source Described in Detail - Hospital Data Sets -- Appendix 6.3. Data Source Described in Detail - Hospital and Patient Services Logs -- Appendix 6.4. Data Source Described in Detail - Genetic Services -- -- Chapter 7. Data Quality Management -- Appendix 7.1. Data Sources Descriptive Assessment Tool -- -- Chapter 8. Statistical Methods -- -- Chapter 9. Data Management and Security -- -- Chapter 10. Data Collaboration and Dissemination through the NBDPN -- -- Chapter 11. Data Presentation -- Appendix 11.1. Data Suppression -- Appendix 11.2. Use of Geographic Information Systems (GIS) to Map Data -- Appendix 11.3. Data Users Matrix -- Appendix 11.4. What Type of Chart or Graph Should I Use?edited by Lowell E. Sever."June 2004."Support for development, production, and distribution of these guidelines was provided by the Birth Defects State Research Partnerships Team, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention.Title from title caption (viewed on Jan. 6, 2012).Mode of access: Internet from the CDC web site as an Acrobat .pdf file ((7.6 MB, 627 p.).System requirements: Adobe Acrobat Reader.Includes bibliographical references.Text in PDF format.National Birth Defects Prevention Network (NBDPN). Guidelines for Conducting Birth Defects Surveillance. Sever, LE, ed. Atlanta, GA: National Birth Defects Prevention Network, Inc., June 2004

Music in Evolution and Evolution in Music

Music in Evolution and Evolution in Music by Steven Jan is a comprehensive account of the relationships between evolutionary theory and music. Examining the ‘evolutionary algorithm’ that drives biological and musical-cultural evolution, the book provides a distinctive commentary on how musicality and music can shed light on our understanding of Darwin’s famous theory, and vice-versa. Comprised of seven chapters, with several musical examples, figures and definitions of terms, this original and accessible book is a valuable resource for anyone interested in the relationships between music and evolutionary thought. Jan guides the reader through key evolutionary ideas and the development of human musicality, before exploring cultural evolution, evolutionary ideas in musical scholarship, animal vocalisations, music generated through technology, and the nature of consciousness as an evolutionary phenomenon. A unique examination of how evolutionary thought intersects with music, Music in Evolution and Evolution in Music is essential to our understanding of how and why music arose in our species and why it is such a significant presence in our lives

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp