Electroporation of Alcaligenes eutrophus with (mega) plasmids and genomic DNA fragments.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Electroporation was used as a tool to explore the genetics of the heavy-metal-resistant strain Alcaligenes eutrophus CH34. A 12.9-kb A. eutrophus-Escherichia coli shuttle vector, pMOL850, was constructed to optimize electroporation conditions. This vector is derived from the E. coli plasmid pSUP202 and contains the replication region of the A. eutrophus megaplasmid pMOL28. Electroporation was used to transform A. eutrophus CH34 derivatives with megaplasmids (sizes up to 240 kb), and transform...

Taghavi, S.; Lelie, D.; Mergeay, M.



Resident enhanced repair: novel repair process action on plasmid DNA transformed into Escherichia coli K-12  

International Nuclear Information System (INIS)

The survival of UV-irradiated DNA of plasmid NTP16 was monitored after its transformation into recipient cells containing an essentially homologous undamaged plasmid, pLV9. The presence of pLV9 resulted in a substantial increase in the fraction of damaged NTP16 molecules which survived in the recipient cells. This enhanced survival requires the host uvrA+ and uvrB+ gene products, but not the host recA+ gene product. The requirement for both homologous DNA and the uvrA+ gene products suggests that a novel repair process may act on plasmid DNA. Possible mechanisms for this process are considered


MegaDyne Mega 2000 return electrode. (United States)

The Mega 2000 return electrode, manufactured by MegaDyne Medical Products, is a reusable, capacitively coupled return electrode used in monopolar electrosurgery. It consists of a large--almost two feet by three feet--sheet of flexible conductive fabric that is enclosed in a nonlatex, urethane insulating material. Unlike conductive return electrodes, which are applied adhesively to the patient, the Mega 2000 does not come into direct contact with the patient. Rather, it is placed on an OR table and covered by a protective sheath and, at most, a cover sheet and draw sheet. The patient lies on top of these sheets. The electrode forms a large capacitor with the patient, capacitively coupling the patient into the electrosurgical circuit. Because it is reusable--only the protective sheath is replaced--the Mega 2000 is touted as being a significantly less expensive alternative to traditional conductive return electrodes. And because it is not affixed to the patient, it offers potential advantages for patients having frail skin or extensive skin and tissue damage that would make the use of adhesive return electrodes difficult or impossible. While some healthcare facilities have considered using this return electrode because of its potential clinical and economic benefits, others have questioned its safety because it differs in design from a traditional return electrode. Therefore, we have examined its safety, efficacy, and cost-effectiveness in this Evaluation. We also offer guidance for facilities trying to decide whether to buy the Mega 2000. PMID:11190782



Energy analysis for sustainable mega-cities  

Energy Technology Data Exchange (ETDEWEB)

Cities throughout Asia have experienced unprecedented development over the past decades. In many cases this has contributed to their rapid and uncontrolled growth, which has resulted in a multiplicity of problems, including rapid population increase, enhanced environmental pollution, collapsing traffic systems, dysfunctional waste management, and rapid increases in the consumption of energy, water and other resources. The significant energy use in cities is not very well perceived in Asian countries. Although a number of studies into energy consumption across various sectors have been conducted, most are from the national point of view. Energy demand analysis is not considered important at the level of the city. The thesis is focused on the dynamics of energy utilization in Asian mega-cities, and ultimately aims at providing strategies for maximizing the use of renewable energy in large urban systems. The study aims at providing an in-depth understanding of the complex dynamics of energy utilization in urban mega-centers. An initial general analysis is complemented by a detailed study of the current situation and future outlook for the city of Bangkok, Thailand. An integrated approach applied to the study includes identification of the parameters that affect the utilization of energy in mega-cities and a detailed analysis of energy flows and their various subsystems, including commercial, industrial, residential and that of transportation. The study investigates and evaluates the energy models most commonly used for analyzing and simulating energy utilization. Its purpose is to provide a user-friendly tool suitable for decision-makers in developing an energy model for large cities. In addition, a Multi-Criteria Decision-Making (MCDM) process has been developed to assess whether or not the energy systems meet the sustainability criteria. A metabolic approach has been employed to analyze the energy flow and utilization in selected Asian mega-cities, including Bangkok, Beijing, Shanghai, and Tokyo. The approach is applied to measure the majority of indirect energy flows or the energy embodied in the flows of goods and services involving the residents of those cities. Since the function of cities is to serve the lives of the residents, indirect energy consumption could be regarded as being of equal importance as that of direct energy use. The essence of embodied energy is that an indirect reflection upon behavior following direct energy consumption. It can illustrate how a city relies on the outside, for example other cities, countries, etc. and provides some interesting information that cannot be easily drawn from the direct energy demand. The study reveals that the indirect energy demand is more significant than the direct energy demand in Bangkok, Shanghai, and Tokyo, while direct energy demand is greater than the indirect energy demand in Beijing. This can be explained by the fact that Bangkok, Shanghai, and Tokyo have a greater reliance upon the outside in terms of energy demand. The Long-range Energy Alternative Planning (LEAP) system has been selected to perform Bangkok energy modeling. In a Bangkok case study a range of policy interventions are selected and how these would change the energy development in Bangkok by the year 2025 is examined. Different policies can be grouped by the sectors analyzed. The only supply-side policy considered meets an existing target of having 10% of electricity generated from renewable sources. The study period for the model started in 2005 and ends in 2025, with the year 2000 taken as the base year. The proposed scenarios were evaluated using the MCDM approach to rate their sustainability. Team members found that this method provided a methodology to help decision-makers to systematically identify management objectives and priorities.

Phdungsilp, Aumnad



FACT, Mega-ROSA, SOLAROSA (United States)

The Flexible Array Concentrator Technology (FACT) is a lightweight, high-performance reflective concentrator blanket assembly that can be used on flexible solar array blankets. The FACT concentrator replaces every other row of solar cells on a solar array blanket, significantly reducing the cost of the array. The modular design is highly scalable for the array system designer, and exhibits compact stowage, good off-pointing acceptance, and mass/cost savings. The assembly s relatively low concentration ratio, accompanied by a large radiative area, provides for a low cell operating temperature, and eliminates many of the thermal problems inherent in high-concentration-ratio designs. Unlike other reflector technologies, the FACT concentrator modules function on both z-fold and rolled flexible solar array blankets, as well as rigid array systems. Mega-ROSA (Mega Roll-Out Solar Array) is a new, highly modularized and extremely scalable version of ROSA that provides immense power level range capability from 100 kW to several MW in size. Mega-ROSA will enable extremely high-power spacecraft and SEP-powered missions, including space-tug and largescale planetary science and lunar/asteroid exploration missions. Mega-ROSA's inherent broad power scalability is achieved while retaining ROSA s solar array performance metrics and missionenabling features for lightweight, compact stowage volume and affordability. This innovation will enable future ultra-high-power missions through lowcost (25 to 50% cost savings, depending on PV and blanket technology), lightweight, high specific power (greater than 200 to 400 Watts per kilogram BOL (beginning-of-life) at the wing level depending on PV and blanket technology), compact stowage volume (greater than 50 kilowatts per cubic meter for very large arrays), high reliability, platform simplicity (low failure modes), high deployed strength/stiffness when scaled to huge sizes, and high-voltage operation capability. Mega-ROSA is adaptable to all photovoltaic and concentrator flexible blanket technologies, and can readily accommodate standard multijunction and emerging ultra-lightweight IMM (inverted metamorphic) photovoltaic flexible blanket assemblies, as well as ENTECHs Stretched Lens Array (SLA) and DSSs (Deployable Space Systems) FACT, which allows for cost reduction at the array level.

Spence, Brian; White, Steve; Schmid, Kevin; Douglas Mark



MEGA and it's photon detector system  

International Nuclear Information System (INIS)

MEGA is a basic research project in the United States. The goal of the project is to look for the rare decay of the muon to an electron and a gamma ray. The experimental design, the recent situation and the initial results of the MEGA project are briefly recounted, and the multi-wire proportional chamber for photon detecting is especially illustrated


Evaluating success levels of mega-projects (United States)

Today's mega-projects transcend the traditional trajectories traced within national and technological limitations. Powers unleashed by internationalization of initiatives, in for example space exploration and environmental protection, are arguably only temporarily suppressed by narrower national, economic, and professional disagreements as to how best they should be harnessed. While the world gets its act together there is time to develop the technologies of such supra-mega-project management that will synergize truly diverse resources and smoothly mesh their interfaces. Such mega-projects and their management need to be realistically evaluated, when implementing such improvements. This paper examines current approaches to evaluating mega-projects and questions the validity of extrapolations to the supra-mega-projects of the future. Alternatives to improve such evaluations are proposed and described.

Kumaraswamy, Mohan M.



Manic Episode Associated with Mega Cisterna Magna  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Mega cisterna magna is a part of "Dandy-Walker Complex" and it is characterized by the enlargement of the cisterna magna, morphologically intact vermis and cerebellar hemispheres. We report a case of manic attack in a 23-year-old man with mega cisterna magna. The patient was treated with quetiapine 1,000 mg/day and sodium valproate 1,500 mg/day and the symptoms were ameliorated within 2.5 months. In this case, mega cisterna magna and manic symptoms may be found together coincidentally or any ...

Turan, Tayfun; Bes?irli, Asl?; Asdemir, Akif; O?zsoy, Saliha; Es?el, Ertug?rul



Structuring a mega-project  

Energy Technology Data Exchange (ETDEWEB)

This paper presented an overview of mega-project management. Issues concerning scope, cost and schedule were discussed, with reference to the idea that a choice must be made from the outset as to which of the 3 is a main priority. The importance of preparation and the development of a fully resourced plan was emphasized. The use of the parametric 4-D model was discussed. Lessons that the construction industry may learn from manufacturers were presented along with issues of contract development and the role and importance of the project manager. Issues concerning performance measurement were reviewed, including lagging indicators. Project division factors were also discussed, with reference to data lags, naturally concurrent processes and over the fence units. A case study of Walmart was presented. Project design packages and long lead time items were discussed, as were issues concerning human resources. Functional units were examined in relation to zones of influence and unit integration. Various combinations of zones of influence were presented. Issues concerning span of control and varying relationships within a project were discussed. It was emphasized that great deeds can be accomplished by attracting the best people. tabs., figs.

Kutryk, T. [Husky Oil Operations Ltd., Calgary, AB (Canada)



Characterization of Propionibacterium plasmids.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Plasmid DNAs from 15 Propionibacterium strains were characterized by using restriction endonuclease analyses, DNA-DNA hybridizations, and curing experiments. Restriction endonuclease analysis identified seven distinct plasmids (pRGO1 through pRGO7). Detailed restriction maps were constructed for four of these plasmids. DNA-DNA hybridization analysis revealed that plasmids pRGO1 and pRGO2 had extensive sequence homology and that both were homologous to pRGO7 and to similar sequences of pRGO5. ...

Rehberger, T. G.; Glatz, B. A.



Mobility of Plasmids (United States)

Summary: Plasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts. PMID:20805406

Smillie, Chris; Garcillan-Barcia, M. Pilar; Francia, M. Victoria; Rocha, Eduardo P. C.; de la Cruz, Fernando



Innovative European Solutions in Managing the Mega-Crisis (United States)


Steinhäusler, Friedrich



MegaSquirt : Asennus, säätäminen ja ohjelmointi  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Tässä työssä esitellään jälkiasennettavan moottorinohjausyksikön, MegaSquirtin asennus Boschin L-Jetronic-yksikön tilalle, sen säätäminen käyttökuntoon sekä oman ohjelmiston tekeminen ohjausyksikön tietojen lukemiseen. Kohdeautona toimii Opel Ascona B vuosimallia 1979, 20E-moottorilla. Asennuksen tarkoituksena on saavuttaa parempi toimivuus tulevaisuudessa, kun moottoria tullaan virittämään enemmän. Laitteisto saatiin asennettua onnistuneesti ja toimimaan kohtalais...

Kitinma?ki, Manne



Plasmids encoding therapeutic agents (United States)

Plasmids encoding anti-HIV and anti-anthrax therapeutic agents are disclosed. Plasmid pWKK-500 encodes a fusion protein containing DP178 as a targeting moiety, the ricin A chain, an HIV protease cleavable linker, and a truncated ricin B chain. N-terminal extensions of the fusion protein include the maltose binding protein and a Factor Xa protease site. C-terminal extensions include a hydrophobic linker, an L domain motif peptide, a KDEL ER retention signal, another Factor Xa protease site, an out-of-frame buforin II coding sequence, the lacZ.alpha. peptide, and a polyhistidine tag. More than twenty derivatives of plasmid pWKK-500 are described. Plasmids pWKK-700 and pWKK-800 are similar to pWKK-500 wherein the DP178-encoding sequence is substituted by RANTES- and SDF-1-encoding sequences, respectively. Plasmid pWKK-900 is similar to pWKK-500 wherein the HIV protease cleavable linker is substituted by a lethal factor (LF) peptide-cleavable linker.

Keener, William K. (Idaho Falls, ID)



Plasmid-chromosome recombination of irradiated shuttle vector DNA in African Green Monkey kidney cells  

International Nuclear Information System (INIS)

An autonomously replicating shuttle vector was used to investigate the enhancement of plasmid-chromosome recombination in mammalian host cells by ultraviolet light and gamma radiation. Sequences homologous to the shuttle vector were stably inserted into the genome of African Green Monkey kidney cells to act as the target substrate for these recombination events. The SV40- and pBR322-derived plasmid DNA was irradiated with various doses of radiation before transfection into the transformed mammalian host cells. Ultraviolet light (UV) was found not to induce homologous plasmid-chromosome recombination, while gamma radiation increased the frequency of recombinant plasmids detected. The introduction of specific double-strand breaks in the plasmid or prolonging the time of plasmid residence in the mammalian host cells also enhanced plasmid-chromosome recombination. In contrast, plasmid mutagenesis was found to be increased by plasmid UV irradiation, but not to change with time. Plasmid survival, recombination, and mutagenesis were not affected by treating the mammalian host cells with UV light prior to plasmid transfection. The amp/sup r/ recombinant plasmid molecules analyzed were found to be mostly the result of nonconservative exchanges which appeared to involve both homologous and possibly nonhomologous interactions with the host chromosome


MEGA: A search for the decay ??e?  

International Nuclear Information System (INIS)

The MEGA experiment is designed to search for the rare decay ??e? with a branching ratio sensitivity of ?5x10-13. Production data have been taken during 1992 and 1993, and the detector is working as expected. Following a complete analysis, the present data set should represent an improvement of 12--15 in sensitivity over the previous limit of ??e?. copyright 1995 American Institute of Physics


Vishal Mega-Mart- An Overview  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In the background of high consumerism and income of the urban consumers, in recent year, a number of companies have expressed their interest towards retail sector outlets. As a result, numbers of shopping malls have started their operations in metro and urban areas. Pantaloon, big bazaar, Vishal Mega Mart, Reliance Fresh are the best known examples of retail sector outlets in India.Retailing is the interface between the producer and the individual consumer buying for personal consumptio...

Shikha Gupta; Preeti Khatri; Kapil Gulati; Santosh Chauhan



Pavement technology for mega transportation projects  

Energy Technology Data Exchange (ETDEWEB)

This paper described the use of asphalt and concrete pavement technology for mega projects such as the Duarte Highway in the Dominican Republic, the Colombia Bogota El Dorado International Airport, Highway 407 Express Toll Route north of Toronto, the Cobequid Pass Highway in Nova Scotia and the Fredericton-Moncton Highway in New Brunswick. A mega transportation project is considered to involve more than $100 million in construction costs and use an alternative delivery method such as design-build. It must also include life cycle costing for technology evaluation, fast track construction and total quality management. This paper showed that the durability, flexibility and structural capacity of hot-mix asphalt and PCC concrete make it possible to provide economic, smooth, safe pavements for highways, airports and for heavy traffic conditions under both normal and severe operating environments. In particular, the paper focused on the practical concepts of the pavement technology and the role of contractors in meeting the fast-track technical quality requirements for mega paving projects. The paper emphasized the fact that it is possible to develop sustainable paving projects that integrate transportation infrastructure development with communities and the environment while maintaining safety and performance. 8 refs., 4 tabs., 8 figs.

Emery, J. [John Emery Geotechnical Engineering Ltd., Toronto, ON (Canada)



Air pollution in mega cities in China (United States)

Due to its rapidly expanding economic and industrial developments, China is currently considered to be the engine of the world's economic growth. China's economic growth has been accompanied by an expansion of the urban area population and the emergence of a number of mega cities since the 1990. This expansion has resulted in tremendous increases in energy consumption, emissions of air pollutants and the number of poor air quality days in mega cities and their immediate vicinities. Air pollution has become one of the top environmental concerns in China. Currently, Beijing, Shanghai, and the Pearl River Delta region including Guangzhou, Shenzhen and Hong Kong, and their immediate vicinities are the most economically vibrant regions in China. They accounted for about 20% of the total GDP in China in 2005. These are also areas where many air pollution studies have been conducted, especially over the last 6 years. Based on these previous studies, this review presents the current state of understanding of the air pollution problems in China's mega cities and identifies the immediate challenges to understanding and controlling air pollution in these densely populated areas.

Chan, Chak K.; Yao, Xiaohong


Phytoplasma plasmid DNA extraction. (United States)

Phytoplasma plasmids have generally been detected from DNA extracted from plants and insects using methods designed for the purification of total phytoplasma DNA. Methods include extraction from tissues that are high in phytoplasma titre, such as the phloem of plants, with the use of CsCl-bisbenzimide gradients that exploit the low G+C content of phytoplasma DNA. Many of the methods employed for phytoplasma purification have been described elsewhere in this book. Here we describe in detail two methods that are specifically aimed at isolating plasmid DNA. PMID:22987431

Andersen, Mark T; Liefting, Lia W



Toxin Plasmids of Clostridium perfringens (United States)

SUMMARY In both humans and animals, Clostridium perfringens is an important cause of histotoxic infections and diseases originating in the intestines, such as enteritis and enterotoxemia. The virulence of this Gram-positive, anaerobic bacterium is heavily dependent upon its prolific toxin-producing ability. Many of the ?16 toxins produced by C. perfringens are encoded by large plasmids that range in size from ?45 kb to ?140 kb. These plasmid-encoded toxins are often closely associated with mobile elements. A C. perfringens strain can carry up to three different toxin plasmids, with a single plasmid carrying up to three distinct toxin genes. Molecular Koch's postulate analyses have established the importance of several plasmid-encoded toxins when C. perfringens disease strains cause enteritis or enterotoxemias. Many toxin plasmids are closely related, suggesting a common evolutionary origin. In particular, most toxin plasmids and some antibiotic resistance plasmids of C. perfringens share an ?35-kb region containing a Tn916-related conjugation locus named tcp (transfer of clostridial plasmids). This tcp locus can mediate highly efficient conjugative transfer of these toxin or resistance plasmids. For example, conjugative transfer of a toxin plasmid from an infecting strain to C. perfringens normal intestinal flora strains may help to amplify and prolong an infection. Therefore, the presence of toxin genes on conjugative plasmids, particularly in association with insertion sequences that may mobilize these toxin genes, likely provides C. perfringens with considerable virulence plasticity and adaptability when it causes diseases originating in the gastrointestinal tract. PMID:23699255

Li, Jihong; Adams, Vicki; Bannam, Trudi L.; Miyamoto, Kazuaki; Garcia, Jorge P.; Uzal, Francisco A.; Rood, Julian I.



Plasmid Mediated Degradation of Phenol by Two Bacterial Strains Pseudomonas sp. and Staphylococcus sp.  

Directory of Open Access Journals (Sweden)

Full Text Available Two microorganisms, which utilize phenol as a sole source of carbon and energy, were isolated from an enrichment culture. The microorganisms were identified as Pseudomonas sp. and Staphylococcus sp. The bacterial strains were found to harbor three endogenous plasmids. Two of the plasmids were lost when the microorganisms were treated with ethidium bromide. Loss of the plasmids in the organisms were correlated with the loss of the ability to metabolize phenol. Phenotypic testing of the wild type and cured strains revealed that the gene(s responsible for phenol degradation may reside upon the plasmids.

Asif H. Chowdhuryi



O'Mega An Optimizing Matrix Element Generator  

CERN Document Server

We sketch the architecture of O'Mega, a new optimizing compiler for tree amplitudes in quantum field theory, and briefly describe its usage. O'Mega generates the most efficient code currently available for scattering amplitudes for many polarized particles in the Standard Model and its extensions.

Moretti, M; Reuter, J; Moretti, Mauro; Ohl, Thorsten; Reuter, Juergen



O'Mega An Optimizing Matrix Element Generator  

CERN Document Server

I sketch the architecture of O'Mega, a new optimizing compiler for tree amplitudes in quantum field theory. O'Mega generates the most efficient code currently available for scattering amplitudes for many polarized particles in the standard model. A complete infrastructure for physics beyond the standard model is provided.

Ohl, T



Vishal Mega-Mart- An Overview  

Directory of Open Access Journals (Sweden)

Full Text Available In the background of high consumerism and income of the urban consumers, in recent year, a number of companies have expressed their interest towards retail sector outlets. As a result, numbers of shopping malls have started their operations in metro and urban areas. Pantaloon, big bazaar, Vishal Mega Mart, Reliance Fresh are the best known examples of retail sector outlets in India.Retailing is the interface between the producer and the individual consumer buying for personal consumption. This excludes direct interface between the manufacturer and institutional buyers such as the government and other bulk customers. A retailer is one who stocks the producer’s goods and is involved in the act of selling it to the individual consumer, at a margin of profit. As such, retailing is the last link that connects the individual consumer with the manufacturing and distribution chain. Some of the key features of retailing include: -Selling directly to customers without having any intermediaries-Selling in smaller units / quantities, breaking the bulk-Present in neighborhood or in the location which is quite convenient to the customers.-Very high in numbers-Recognized by their service levels-Fitting any size and or locationThe objective of this article is to study the Marketing Mix and Shareholding pattern of Vishal Mega-Mart, a renowned name in Retail Industry of India.

Shikha Gupta



In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing  

DEFF Research Database (Denmark)

In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of Salmonella enterica serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49 S. Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens.

Zankari, Ea; Larsen, Mette Voldby



In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing (United States)

In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of Salmonella enterica serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49 S. Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens. PMID:24777092

Carattoli, Alessandra; Zankari, Ea; Garcia-Fernandez, Aurora; Voldby Larsen, Mette; Lund, Ole; Villa, Laura; M?ller Aarestrup, Frank



An improved method for including upper size range plasmids in metamobilomes  

DEFF Research Database (Denmark)

Two recently developed isolation methods have shown promise when recovering pure community plasmid DNA (metamobilomes/plasmidomes), which is useful in conducting culture-independent investigations into plasmid ecology. However, both methods employ multiple displacement amplification (MDA) to ensure suitable quantities of plasmid DNA for high-throughput sequencing. This study demonstrates that MDA greatly favors smaller circular DNA elements (10 Kbp). Throughout the study, we used two model plasmids, a 4.4 Kbp cloning vector (pBR322), and a 56 Kbp conjugative plasmid (pKJK10), to represent lower- and upper plasmid size ranges, respectively. Subjecting a mixture of these plasmids to the overall isolation protocol revealed a 34-fold over-amplification of pBR322 after MDA. To address this bias, we propose the addition of an electroelution step that separates different plasmid size ranges prior to MDA in order to reduce size-dependent competition during incubation. Subsequent analyses of metamobilome data from wastewater spiked with the model plasmids showed in silica recovery of pKJK10 to be very poor with the established method and a 1,300-fold overrepresentation of pBR322. Conversely, complete recovery of pKJK10 was enabled with the new modified protocol although considerable care must be taken during electroelution to minimize cross-contamination between samples. For further validation, non-spiked wastewater metamobilomes were mapped to more than 2,500 known plasmid genomes. This displayed an overall recovery of plasmids well into the upper size range (median size: 30 kilobases) with the modified protocol. Analysis of de novo assembled metamobilome data also suggested distinctly better recovery of larger plasmids, as gene functions associated with these plasmids, such as conjugation, was exclusively encoded in the data output generated through the modified protocol. Thus, with the suggested modification, access to a large uncharacterized pool of accessory elements that reside on medium-to-large plasmids has been improved. © 2014 Norman et al.

Norman, Anders; Riber, Leise



Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. (United States)

Plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. To understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the 'evolutionary history' of these plasmids, i.e. the range of hosts in which they have evolved. Since extensive data support the proposal that foreign DNA acquires the host's nucleotide composition during long-term residence, comparison of nucleotide composition of plasmids and chromosomes could shed light on a plasmid's evolutionary history. The average absolute dinucleotide relative abundance difference, termed delta-distance, has been commonly used to measure differences in dinucleotide composition, or 'genomic signature', between bacterial chromosomes and plasmids. Here, we introduce the Mahalanobis distance, which takes into account the variance-covariance structure of the chromosome signatures. We demonstrate that the Mahalanobis distance is better than the delta-distance at measuring genomic signature differences between plasmids and chromosomes of potential hosts. We illustrate the usefulness of this metric for proposing candidate long-term hosts for plasmids, focusing on the virulence plasmids pXO1 from Bacillus anthracis, and pO157 from Escherichia coli O157:H7, as well as the broad host range multi-drug resistance plasmid pB10 from an unknown host. PMID:18953039

Suzuki, Haruo; Sota, Masahiro; Brown, Celeste J; Top, Eva M



Likelihood Analysis for Mega Pixel Maps (United States)

The derivation of cosmological parameters from astrophysical data sets routinely involves operations counts which scale as O(N(exp 3) where N is the number of data points. Currently planned missions, including MAP and Planck, will generate sky maps with N(sub d) = 10(exp 6) or more pixels. Simple "brute force" analysis, applied to such mega-pixel data, would require years of computing even on the fastest computers. We describe an algorithm which allows estimation of the likelihood function in the direct pixel basis. The algorithm uses a conjugate gradient approach to evaluate X2 and a geometric approximation to evaluate the determinant. Monte Carlo simulations provide a correction to the determinant, yielding an unbiased estimate of the likelihood surface in an arbitrary region surrounding the likelihood peak. The algorithm requires O(N(sub d)(exp 3/2) operations and O(Nd) storage for each likelihood evaluation, and allows for significant parallel computation.

Kogut, Alan J.



Likelihood Analysis for Mega-Pixel Maps  

CERN Document Server

The derivation of cosmological parameters from astrophysical data sets routinely involves operations counts which scale as O(N^3) where N is the number of data points. Currently planned missions, including MAP and Planck, will generate sky maps with N = 10^6 or more pixels. Simple ``brute force'' analysis, applied to such mega-pixel data, would require years of computing even on the fastest computers. We describe an algorithm which allows estimation of the likelihood function in the minimum-variance pixel basis. The algorithm uses a conjugate gradient approach to evaluate chi-squared and a geometric approximation to evaluate the determinant. Monte Carlo simulations provide an exact correction to the determinant, yielding an unbiased estimate of the likelihood surface in an arbitrary region surrounding the likelihood peak. The algorithm requires O(N^{3/2}) operations and O(N) storage for each likelihood evaluation, and allows for significant parallel computation.

Kogut, A J



Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids. (United States)

Plasmids play an important role in shaping bacterial evolution and adaptation to heterogeneous environments. As modular genetic elements that are often conjugative, the selective pressures that act on plasmid-borne genes are distinct from those that act on the chromosome. Many bacteria are co-infected by multiple plasmids that impart niche-specific phenotypes. Thus, in addition to host-plasmid dynamics, interactions between co-infecting plasmids are likely to be important drivers of plasmid population dynamics, evolution and ecology. Agrobacterium tumefaciens is a facultative plant pathogen that commonly harbours two distinct megaplasmids. Virulence depends on the presence of the tumour-inducing (Ti) plasmid, with benefits that are primarily restricted to the disease environment. Here, we demonstrate that a second megaplasmid, the At plasmid, confers a competitive advantage in the rhizosphere. To assess the individual and interactive costs of these plasmids, we generated four isogenic derivatives: plasmidless, pAt only, pTi only and pAtpTi, and performed pairwise competitions under carbon-limiting conditions. These studies reveal a low cost to the virulence plasmid when outside of the disease environment, and a strikingly high cost to the At plasmid. In addition, the costs of pAt and pTi in the same host were significantly lower than predicted based on single plasmid costs, signifying the first demonstration of non-additivity between naturally occurring co-resident plasmids. Based on these empirically demonstrated costs and benefits, we developed a resource-consumer model to generate predictions about the frequencies of these genotypes in relevant environments, showing that non-additivity between co-residing plasmids allows for their stable coexistence across environments. PMID:24500159

Morton, Elise R; Platt, Thomas G; Fuqua, Clay; Bever, James D



Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual?based modelling study  

DEFF Research Database (Denmark)

Plasmid invasion in biofilms is often surprisingly limited in spite of the close contact of cells in a biofilm. We hypothesized that this poor plasmid spread into deeper biofilm layers is caused by a dependence of conjugation on the growth rate (relative to the maximum growth rate) of the donor. By extending an individual?based model of microbial growth and interactions to include the dynamics of plasmid carriage and transfer by individual cells, we were able to conduct in silico tests of this and other hypotheses on the dynamics of conjugal plasmid transfer in biofilms. For a generic model plasmid, we find that invasion of a resident biofilm is indeed limited when plasmid transfer depends on growth, but not so in the absence of growth dependence. Using sensitivity analysis we also find that parameters related to timing (i.e. a lag before the transconjugant can transfer, transfer proficiency and scan speed) and spatial reach (EPS yield, conjugal pilus length) are more important for successful plasmid invasionthan the recipients' growth rate or the probability of segregational loss. While this study identifies one factor that can limit plasmid invasion in biofilms, the new individual?based framework introduced in this work is a powerful tool that enables one to test additional hypotheses on the spread and role of plasmids in microbial biofilms.

Merkey, Brian; Lardon, Laurent



Global Analysis and Structural Performance of the Tubed Mega Frame  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The Tubed Mega Frame is a new structure concept for high-rise buildings which is developed by Tyréns. In order to study the structural performance as well as the efficiency of this new concept, a global analysis of the Tubed Mega Frame structure is performed using finite element analysis software ETABS. Besides, the lateral loads that should be applied on the structure according to different codes are also studied. From the design code study for wind loads and seismic design response spectru...

Zhang, Han



Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. (United States)

Plasmid metagenome nucleotide sequence data were recently obtained from wastewater treatment plant (WWTP) bacteria with reduced susceptibility to selected antimicrobial drugs by applying the ultrafast 454-sequencing technology. The sequence dataset comprising 36,071,493 bases (346,427 reads with an average read length of 104 bases) was analysed for genetic diversity and composition by using a newly developed bioinformatic pipeline based on assignment of environmental gene tags (EGTs) to protein families stored in the Pfam database. Short amino acid sequences deduced from the plasmid metagenome sequence reads were compared to profile hidden Markov models underlying Pfam. Obtained matches evidenced that many reads represent genes having predicted functions in plasmid replication, stability and plasmid mobility which indicates that WWTP bacteria harbour genetically stabilised and mobile plasmids. Moreover, the data confirm a high diversity of plasmids residing in WWTP bacteria. The mobile organic peroxide resistance plasmid pMAC from Acinetobacter baumannii was identified as reference plasmid for the most abundant replication module type in the sequenced sample. Accessory plasmid modules encode different transposons, insertion sequences, integrons, resistance and virulence determinants. Most of the matches to Transposase protein families were identified for transposases similar to the one of the chromate resistance transposon Tn5719. Noticeable are hits to beta-lactamase protein families which suggests that plasmids from WWTP bacteria encode different enzymes possessing beta-lactam-hydrolysing activity. Some of the sequence reads correspond to antibiotic resistance genes that were only recently identified in clinical isolates of human pathogens. EGT analysis thus proofed to be a very valuable method to explore genetic diversity and composition of the present plasmid metagenome dataset. PMID:18603322

Schlüter, Andreas; Krause, Lutz; Szczepanowski, Rafael; Goesmann, Alexander; Pühler, Alfred



Trypanosoma mega (Kinetoplastida) from Bufo viridis in Siwah Oasis, Egypt. (United States)

A large pleomorphic trypanosome, identified as Trypanosoma mega, is described from the toad Bufo viridis collected from Siwah Oasis at the Western Desert of Egypt. The prevalence of the trypanosome is 83.3%. Three trypanosome forms are described, small, intermediate and large stumpy form. Observations were also made on the lysed (diffused) trypanosomes. This is the first record of T. mega from B. viridis in Egypt which represents a new host and new geographical location. The measurements of the present trypanosome are given and compared with related forms previously described from Egypt. PMID:9097527

Ashour, A A; Gaafar, N A



Mega-city pollution over East Asia: Satellite Perspective (United States)

East Asian pollution is now one of the top growing environmental concerns with far-reaching impacts on the global tropospheric air quality and climate change. Satellite observations of tropospheric composition provide a unique opportunity to characterize mega-city pollution. Here we focuse on the air quality over major East Asian mega-cities: Beijing, Shanghai, Hongkong, Seoul and Tokyo in 2006. We analyzed time series of tropospheric O3, CO, and NO2 over those cites from TES, SCIAMACHY, and OMI. Results from GEOS-Chem global 3-D CTM simulations and corresponding meteorological variables including temperature and precipitation are used to understand and interpret the seasonal variations of those pollutants and controlling factors such as transport. Beijing is the most polluted among the five cities where ~200 ppbv of O3 and ~400 ppbv of CO in the lower troposphere were frequent. Those mega-cities' air quality is mostly affected by industrial/urban emissions and domestic biofuel burning from China, while the contribution from natural pollution (biomass burning and terrestrial biosphere) are fairly small. The difference in seasonal trends and photochemical O3 productivity among the cities partly reflects the different photochemical environment in the different latitudes. The strong summer monsoon over Asia causes seasonal mitigation of pollutions over those mega-cities.

Shim, C.; Li, Q.; Eldering, A.



Computer tomographic diagnosis of a mega-dolicho basilar artery  

International Nuclear Information System (INIS)

Four mega-dolicho basilar arteries are described, which were found by computer tomography and confirmed by angiography. Two patients showed additional abnormalities or anomalies of other vessels. The computer tomographic features are described. The elongated vessels can produce so-called normal pressure hydrocephalus by impressing the floor of the third ventricle, although the hydrocephalus cannot be confirmed by computer tomographic cisternography. (orig.)


Strategies simulation model for the gas business chain MEGAS  

International Nuclear Information System (INIS)

MEGAS is a simulation model representing fundamental parameters of Corpoven's natural gas and NGL production, handling, processing, transportation and distribution systems in the Venezuelan mid-east, as well as its financial implications. Various strategies regarding development, prices, costs, new business opportunities, production scenarios, demand and energy policies can be evaluated through this model in order to determine, after analyzing the economics results, a set of strategies to follow in the mid and long term. MEGAS could be also used to make risk analysis studies, considering that probabilistic parameters and variables like gas quality, production, demand, plant shutdowns and others are to be represented by their distinctive function. It is possible to set up a probabilistic function for each economic indicator or operating variables with an appropriate experiment design. MEGAS is based on a dynamic simulation language, which facilitates both the real system components representation and the main variables statistical data accumulation. It also allows graphical representation of results and the simulation animation. Demand and price forecasts, new projects, costs and capabilities of the systems are some of the model input data. MEGAS should be considered as a tool that eases the strategic planning of the business, making it possible for the Corporation to foresee changes, both in the domestic and international market, to predict how these changes could affet, to predict how these changes could affect its business affairs and to visualize different return scenarios


Characterization of plasmids in bacterial fish pathogen.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Plasmid profiles of representative fish pathogens, Aeromonas salmonicida, Aeromonas hydrophila, Vibrio anguillarum, Pasteurella piscicida, Yersinia ruckeri, Edwardsiella tarda, and Renibacterium salmoninarum, were determined by agarose gel electrophoresis with four different plasmid detection methods. A combination of two methods was required to detect the plasmids present in these strains and to calculate precisely the molecular weights of the plasmids. Of 38 strains, 28 harbored one or more...

Toranzo, A. E.; Barja, J. L.; Colwell, R. R.; Hetrick, F. M.



Plasmid required for virulence of Agrobacterium tumefaciens  

Energy Technology Data Exchange (ETDEWEB)

The irreversible loss of crown gall-inducing ability of Agrobacterium tumefaciens strain C-58 during growth at 37/sup 0/C is shown to be due to loss of a large plasmid (1.2 x 10/sup 8/ daltons). The gene responsible for this high rate of plasmid loss at elevated temperatures seems to be located on the plasmid. In addition, another spontaneous avirulent variant, A. tumefaciens strain IIBNV6, is shown to lack the virulence plasmid which its virulent sibling strain, IIBV7, possesses. Deoxyribonucleic acid reassociation measurements prove that the plasmid is eliminated, not integrated into the chromosome, in both of the avirulent derivatives. Transfer of virulence from donor strain C-58 to avirulent recipient strain A136 results from the transfer of a plasmid, which appears identical to the donor plasmid by deoxyribonucleic acid reassociation measurements. The transfer of virulence in another cross, K27 x A136, was also shown to result from the transfer of a large plasmid. These findings establish unequivocally that the large plasmid determines virulence. Two additional genetic determinants have been located on the virulence plasmid of A. tumefaciens strain C-58: the ability to utilize nopaline and sensitivity to a bacteriocin produced by strain 84. The latter trait can be exploited for selection of avirulent plasmid-free derivatives of strain C-58. The trait of nopaline utilization appears to be on the virulence plasmid also in strains IIBV7 and K27.

Watson, B.; Currier, T.C.; Gordon, M.P.; Chilton, M.D.; Nester, E.W.



Microcapitalism and the mega-corporation. (United States)

More than 100 miles from Bangalore, India, there's a rural area called Kuppam where one in three citizens is illiterate, more than half of the households have no electricity, and there's a high rate of AIDS. It's exactly this challenging atmosphere that prompted Hewlett-Packard to choose Kuppam as one of its first "i-communities" initiatives. Through the program, HP creates public-private partnerships to accelerate economic development through the application of technology while simultaneously opening new markets and developing new products and services. HP brings to these initiatives the management disciplines of a successful technology business. For example, it unearths customer needs using an iterative cycle that involves prototyping products and services and then closely observing residents' experiences with them. It fields a diversely talented team that brings many skills to the initiative, including deep technical ability, management acumen, and market knowledge. It takes a systems approach, simultaneously examining all the elements that must come together to create a working solution to a given problem. It establishes a "leading platform" on which other players--comapnies, nonprofits, and government agencies--can build technologies and applications. Practices like these help ensure that HP's investment yields real, sustainable results for the community in question. But HP also sees returns to its own business. In Kuppam, the company is discovering the need for (and developing) new products like a solar-powered digital camera, with printer, that fits in a backpack. By engaging the community and its leaders and working with them to design valuable new tools and capabilities, HP is gaining the knowledge it needs to be a stronger competitor in other developing regions. PMID:12884667

Dunn, Debra; Yamashita, Keith



Rare case of dystrophia myotonica with mega cisterna magna  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Myotonic dystrophy is also known as dystrophia myotonica (DM). The condition is composed of at least two clinical disorders with overlapping phenotypes and distinct molecular genetic defects: myotonic dystrophy type 1, the classic disease originally described by Steinert, and myotonic dystrophy type 2, also called proximal myotonic myopathy (PROMM). Mega cisterna magna is thought to be an anatomic variant with no clinical significance. We report a rare case of type 1 dystrophia myotonica in c...

Hetal Pandya; Jitendra Lakhani; Jigar Mehta; Jimmy Dodhania



A study of the decay ? ? e? by the MEGA experiment  

International Nuclear Information System (INIS)

The MEGA experiment is designed to search for the lepton-flavor number non-conserving rare decay ? ? e?. Data- taking is complete, with 450 million events on tape taken over approximately 107 seconds. A small portion of the data sample has been processed through the complete event reconstruction codes to search for the ? ? e? process. No evidence for the ? ? e? decay is observed at a sensitivity of ?7 x 10-11 (90% confidence)



Directory of Open Access Journals (Sweden)

Full Text Available This paper describes the state of the art of a simplified model for integration of services in mega events. The project context, which was financed by the National Research Council – CNPq, is divided into six major areas or functional groups: Urban Mobility, Tourism, Airports, Security, Energy and Telecommunications. The proposal is described in layers, as an infrastructure model of integration and services evaluation, describing its main layers and interaction processes. The proposal described in this paper is restricted to the telecommunication subproject, however, in the modeling of the scenario for the study case, it was necessary to considerate requirements and variables that are common to all subprojects. In the specification process of these requirements, we noticed important processes that interact with some sectors in the city of São Paulo, however, in the mean time, we noticed some failures regarding the integration and collaboration performed by administrators elements of stadiums as main focus in the mega event and part of our case study. Currently, the proposal is in its first version as open software for the evaluation of the services quality and the mega event infrastructure through the use of performance indicators.

Jorge R. B. Garay



Dissolution of mega-voids in resin transfer molding (United States)

Resin transfer molding (RTM) is a common composite manufacturing process. Voids are a common defect encountered in RTM components. A new type of void, the 'Mega-Void', has been identified and addressed by this research. To produce acceptable RTM components requires that the mega-void be eliminated either through prevention or through dissolution. The latter is the topic of this research. Three process parameters affecting mega-void dissolution are researched; (1) Preform/mold vacuum, (2) Resin degas, and (3) Resin curing pressure. To address preform/mold vacuum, analytical and empirical investigations were carried out. Results show that the preform can take-up and retain water. Additional analytical investigations show that gas flow within the preform is molecular in nature. The consequence of this finding is that the removal of moisture and gases from the preform is difficult. Confirming experiments were carried out showing a significant difference between gas pressures within the mold and the gas pressure external to the mold. The resin degas and resin curing pressure parameters were studied by researching the solubility of air in epoxy. An experimental apparatus was designed and fabricated wherein a sample of resin could be subjected to a specified level of vacuum for degassing. Subsequently, a measured amount of air was introduced into the resin sample and the combination pressurized to a controlled pressure. The resin and air were then monitored over time to observe the shrinkage of the air pocket as the air was absorbed by the resin. The experimental results show the pressure of residual air and the resin dissolution pressure both significantly affect the absorption of the air pocket. Higher levels of resin degassing are shown to provide a small benefit to gas dissolution. As a final research effort, composite panels were fabricated using a blind injection setup where a single mold port is used for evacuation and resin injection. In this way, the starting size of the mega-void is fixed and equal to the mold free volume. The three processing parameters were varied in order to show the dissolution of mega-voids when the appropriate parameters are used.

Clark, Paul Nordstrom


Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations. (United States)

Plasmids have a key role in the horizontal transfer of genes among bacteria. Although plasmids are catalysts for bacterial evolution, it is challenging to understand how they can persist in bacterial populations over the long term because of the burden they impose on their hosts (the 'plasmid paradox'). This paradox is especially perplexing in the case of 'small' plasmids, which are unable to self-transfer by conjugation. Here, for the first time, we investigate how interactions between co-infecting plasmids influence plasmid persistence. Using an experimental model system based on interactions between a diverse assemblage of 'large' plasmids and a single small plasmid, pNI105, in the pathogenic bacterium Pseudomonas aeruginosa, we demonstrate that positive epistasis minimizes the cost associated with carrying multiple plasmids over the short term and increases the stability of the small plasmid over a longer time scale. In support of these experimental data, bioinformatic analysis showed that associations between small and large plasmids are more common than would be expected owing to chance alone across a range of families of bacteria; more generally, we find that co-infection with multiple plasmids is more common than would be expected owing to chance across a wide range of bacterial phyla. Collectively, these results suggest that positive epistasis promotes plasmid stability in bacterial populations. These findings pave the way for future mechanistic studies aimed at elucidating the molecular mechanisms of plasmid-plasmid interaction, and evolutionary studies aimed at understanding how the coevolution of plasmids drives the spread of plasmid-encoded traits. PMID:24152711

San Millan, Alvaro; Heilbron, Karl; MacLean, R Craig



The repAC replication system of the Rhizobium leguminosarum pRL7 plasmid is functional: implications regarding the origin and evolution of repABC plasmids. (United States)

The repABC replication/partitioning systems are commonly found in alpha-proteobacteria plasmids and in secondary chromosomes. All of the elements required for their replication and stable maintenance are encoded within a single transcription unit: the repABC operon. The repC gene encodes an initiator protein, while RepA, RepB and centromere-like sequence (parS) direct plasmid segregation. Strains containing two or more repABC plasmids are a common feature in some alpha proteobacteria groups, indicating that the repABC plasmid family embraces several incompatibility groups. Genes encoded within repABC operons are highly dynamic: each one possess its own distinctive phylogeny and homologous recombination events are common within these operons. Additionally, alpha-proteobacterial genomes contain repAB genes not associated with the ctRNA or with repC as well as plasmids whose replication depends on a ctRNA-repC module without the participation of repAB genes. Some alphaproteobacteria have repC genes clustered with other genes that are not involved in replication/partitioning functions. These atypical associations of genes could have an important role in the origin and diversification of new plasmids. Here we evaluated the functionality and possible evolutionary consequences of one of these atypical gene associations: the repAC genes present in the Rhizobium leguminosarum plasmid pRL7. The repAC genes are organized in an operon and they are capable of sustaining replication but in an unstable manner. RepC was essential for replication, and the origin of replication resides within its coding region. In contrast, RepA plays a minor role in the negative regulation of its own transcription. PMID:22975386

Pérez-Segura, Gabriela; Pérez-Oseguera, Angeles; Cevallos, Miguel A



Facilitators and Inhibitors of Bidding and Hosting Mega Sporting Events in Iran  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Legacies of hosting mega sporting events have been attempting idea for both the developed and the developing nations to participate in "bidding" competitions. Through mega sporting events bid process, despite all defined essentials infrastructures, the viewpoint of local organizing committee play a significant role to propose a winning bid and delivery of successful games. This research aims to identify the facilitators and inhibitors of bidding and hosting mega sporting events in Iran from t...

Mohammad Koosha; Bahram Yousefi; Hossein Eydi



Optimizing alkaline lysis for DNA plasmid recovery. (United States)

Optimization of the alkaline lysis (P2) and neutralization (N3) steps in the recovery of DNA plasmids was pursued. Experiments were conducted at the test-tube and 5-litre scales with 3 kb (pUC18) and 20 kb (pQR150) plasmids. The scale and degree of mixing/shear did not affect the optimum yield of supercoiled plasmid during the P2 step, but did effect the time required for the optimum to be achieved. This optimum time for P2 at the large scale was longer (8-9 min), especially when a low-shear impeller was used. Also, when the yield of supercoiled plasmid reached a maximum during the P2 step, the purity (percentage of plasmids in the supercoiled form) simultaneously reached a minimum. As the duration of the N3 step increased from 1 to 6 min, the yield of the supercoiled plasmids remained fairly constant, provided that a lowshear impeller was used. The neutralized (post-N3) plasmid solution was shear-sensitive; however, mixing with a Rushton turbine in a tank (maximum energy dissipation rate in the mixing tank, epsilon (max), 12 m(2)/s(3); mixing-tank power consumption/volume of mixing tank, 2.0 W/m(3)) for 5-10 min resulted in a slight decrease in supercoiled plasmid and a notable increase in genomic DNA concentrations. The loss of the larger 20 kb plasmid (20%) was more than for the 3 kb plasmid. Finally, preparing the cells for alkaline lysis with lysozyme or low-pressure homogenization did not increase the plasmid yield. Furthermore, the homogenizer broke up the genomic DNA into fragments that followed through the entire Qiagen prep with the plasmids as impurities. PMID:12611593

Clemson, Michael; Kelly, William J



Plasmids in several strains of deinococcus radiodurans  

International Nuclear Information System (INIS)

Deinococcus radiodurans is known as a radioresistant bacterium. For the construction of the shuttle vector, plasmids of this bacterium were isolated and investigated. At least two plasmids in the cells of D. radiodurans MR1, KR1 and Sark were found in this experiment. However, a common plasmid among MR1, KR1 and Sark strains could not be found. These plasmids would be useful for the construction of the shuttle vector for cloning radioresistant genes of this bacterium. 13 refs., 2 figs., 1 tab


Plasmid profiles and transfer of plasmid-encoded antibiotic resistance in Lactobacillus plantarum.  

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Plasmids were visualized in strains of Lactobacillus plantarum by use of a rapid method. Plasmids pIP501 and pAM beta 1 were transferred by conjugation from Streptococcus strains to Lactobacillus plantarum, and recipient strains were shown to act as donors in crosses to S. lactis. Attempts to transfer these plasmids between strains of L. plantarum were not successful.

West, C. A.; Warner, P. J.



How to make mega-cities energy efficient?  

Energy Technology Data Exchange (ETDEWEB)

Tokyo is a Megalopolis with 40 million+ population. It has an energy efficient profile due to its uniqueness as extensive mass rail transit networks, high density and compact urban formation, compact space oriented life style. The other feature is extensive use of electric heat pumps (EHP), which entails low carbon city profile. Further possibility is prepared with water thermal energy utilization, which is widely available also through EHP particularly in Tokyo central districts, which could make Tokyo one of the lowest carbon cities in the world. Emerging mega-cities are expected to learn from Tokyo's success and not from western conventional models.

Aoki, Hitoshi; Aoki, Yoshitaka



Stimulating revolutionary science with mega-cash prizes. (United States)

We argue that the most ambitious science is intrinsically riskier science, more likely to fail. It is almost always a safer career strategy for the best scientists to seek to extend knowledge more modestly and to build incrementally on existing ideas and methods. Therefore, higher rewards for success are a necessary incentive to encourage top scientists to work on the most important scientific problems, ones where the solution has potentially revolutionary implications. We suggest that mega-cash prizes (measured in tens of millions of dollars) are a suitable reward for those individuals (or institutions) whose work has triggered radically new directions in science. PMID:18289798

Charlton, Bruce G; Andras, Peter



The Uruguayan Per mic mega flora. A synthesis  

International Nuclear Information System (INIS)

The Permian mega floras of Uruguay. A synthesis. An analysis of the impression and fossil wood floras from the Permian of Uruguay is given through a series of Tables. These show : (1) the list of taxa, (2) anatomical characters of the woods, (3) data on the micro floral associations, (4) paleoenvironmental information and (5) comparisons with contemporaneous Gondwana floras. The evolutionary degree of the woods is briefly analyzed where they correspond to the so-called transition xilotaphofloras as they present typical Paleozoic anatomical characters but with secondary xylem of more advanced characteristics. (author)


Enhancement of plasmid-mediated gene therapy for muscular dystrophy by directed plasmid integration (United States)

Plasmid-mediated gene therapy can restore dystrophin expression in skeletal muscle in the mdx mouse, a model of Duchenne muscular dystrophy. However, sufficient long-term expression and distribution of dystrophin remain a hurdle for translating this technology into a viable treatment for Duchenne muscular dystrophy. To improve plasmid-mediated gene therapy for muscle diseases, we studied the effects of targeted plasmid integration using a phage integrase (?C31) that can mediate the integration of suitably modified plasmids into the mammalian genome. Using a luciferase expression plasmid, we monitored plasmid gene expression noninvasively in living mice by bioluminescence imaging. Coinjection of an integrase plasmid resulted in 5- to 10-fold higher levels of sustained luciferase expression. Likewise, plasmid-mediated dystrophin expression in mdx muscle was enhanced by integration. Using a combination of dystrophin and luciferase plasmids, we analyzed the functional benefit of dystrophin expression in the dystrophic muscle. The expression of dystrophin slowed the loss of luciferase expression associated with muscle degeneration, and that protection was enhanced by targeted integration of the dystrophin plasmid. In the presence of integrase, dystrophin expression was distributed along a much greater length of individual fibers, and this was associated with increased protection against degenerative changes. These data demonstrate the importance of both the level and distribution of dystrophin expression to achieve therapeutic efficacy, and that the efficacy can be enhanced by targeted plasmid integration. PMID:16387861

Bertoni, Carmen; Jarrahian, Sohail; Wheeler, Thurman M.; Li, Yining; Olivares, Eric C.; Calos, Michele P.; Rando, Thomas A.



Diversity and epidemiology of plasmids from Enterobacteriaceae from human and non-human reservoirs  

DEFF Research Database (Denmark)

The family of Enterobacteriaceae is comprised of Gram negative bacteria found in a variety of natural environments as well as in the gastrointestinal (GI) tracts of humans and many animals including diverse mammals, birds and reptiles. Three species of the enteric bacteria are largely responsible for causing infections both in humans and animals worldwide; these are Escherichia coli, Salmonella enterica and Klebsiella pneumoniae; ß-lactams are antimicrobials commonly prescribed to treat uncomplicated as well as severe infections caused by these Enterobacteriaceae and other Gram negative and also Gram positive bacteria. In particular, aminopenicillins, cephalosporins and carbapenems found broad application in treatment of infections caused by the aforementioned enteric species. Recently however, increasing levels of resistance to ß-lactams is observed in these key infectious agents as well as in many other previously susceptible species. This phenomenon has become a major public concern. Antimicrobials including ß-lactams have been often used in heavy amounts in farming, not only to treat the diagnosed infections in individual animals but also as prophylaxis, metaphylaxis and growth promotion. It is believed that these practices lead to the generation of reservoirs of antimicrobial resistance genes in the GI tracts of intensively reared food - production animals like pigs, poultry and cattle. Moreover, it has been previously shown that the bla genes (e.g. genes encoding resistance to ß-lactams) could be transmitted between different bacteria on mobile genetic elements (MGEs) like plasmids and variety of transposons. Evidences were also published indicating that zoonotic bacteria like E. coli or S. enterica resistant to diverse antimicrobials and harbouring plasmids might have been transmitted from farm animals to humans (farm workers, animal caretakers etc.). It has been therefore speculated whether the plasmids with the bla genes found in Enterobacteriaceae in humans could actually originate from the animal sources. The overall aim of this thesis was to verify if indeed related resistance plasmids can circulate between enteric bacteria from humans and food production animals; and if so, then which of these plasmid species are specifically associated with the epidemic types of blaTEM genes in Enterobacteriaceae. Furthermore, the association of the plasmid encoded blaTEM genes with transposable elements is also studied in order to get a broader perspective of which MGEs are involved in mobilization and spread of these bla genes in the diverse reservoirs. Finally, an attempt is made to encompass ecological aspects of plasmid driven transmission of resistance among the enteric bacteria. In the first study the relationship between plasmids harbouring blaTEM-52 genes isolated from humans, poultry and also meat products was examined. Twenty- two plasmids from a collection of E. coli and different serovars of S. enterica were characterized. The study delivered molecular evidences that epidemiologically related plasmids circulated in the diverse species of enteric bacteria and between humans and animals, and the possible transmission route could have been contaminated food products like meat. Two types of epidemic plasmids were detected in isolates of E. coli and S. enterica; namely undistinguishable IncI1 blaTEM-52 plasmids were found in human and poultry isolates of E. coli and S. enterica; also undistinguishable IncX1 plasmids were isolated from E. coli and S. enterica from human infections, poultry and meat products (from poultry, broiler and beef). The strains harbouring these plasmids were confirmed not to be clonally related, hence indicating the transmission of the plasmids between the different bacteria from humans and animals rather than isolation of the same bacterial clones from the different reservoirs. With relation to the study I, a range of other observations was made. On majority of the examined plasmids, the blaTEM-52 genes resided on the Tn3-related transposons. Further analysis of the genetic environment o

Bielak, Eliza Maria



[A high sensitivity search for MU Gamma: The Mega experiment at LAMPF  

International Nuclear Information System (INIS)

This report describes the work done at Valparaiso University on LAMPF experiment E764, to conclude the neutrino flux calculations, and work done at Valparaiso University and at LANL on LAMPF E969, the MEGA experiment, specifically on the positron arm of the MEGA spectrometer


MegaPipe astrometry for the New Horizons spacecraft  

CERN Document Server

The New Horizons spacecraft, launched by NASA in 2006, will arrive in the Pluto-Charon system on July 14, 2015. There, it will spend a few hours imaging Pluto and its moons. It will then have a small amount of reserve propellant which will be used to direct the probe on to a second, yet to be discovered object in the Kuiper Belt. Data from the MegaPrime camera on CFHT was used to build a precise, high density astrometric reference frame for both the final approach into the Pluto system and the search for the secondary target. Pluto currently lies in the galactic plane. This is a hindrance in that there are potential problems with confusion. However, it is also a benefit, since it allows the use of the UCAC4 astrometric reference catalog, which is normally too sparse for use with MegaCam images. The astrometric accuracy of the final catalogs, as measured by the residuals, is 0.02 arcseconds.

Gwyn, Stephen D J



Performance studies of MicroMegas for the ATLAS experiment (United States)

The performance of MicroMegas (MM) has been extensively studied during several test beam campaigns with high energy particle beams at CERN up to the year 2012, and more recently (June 2013) with electron beams at DESY. Main objectives of the tests were to demonstrate that the requirements could be achieved for the upgrade of the ATLAS Muon Spectrometer, where the MicroMegas will be mounted (along with small-strip Thin Gap Chambers — sTGC) on the New Small Wheel for forward muon detection. The MM layout and operating settings have then been chosen to satisfy the ATLAS upgrade requirements and trigger timing constraints. Results for efficiencies, time resolution and spatial resolution for perpendicular and inclined tracks are presented. Moreover, in ATLAS the MM will operate in a non-uniform magnetic field up to 0.3 T. Dedicated test beam measurements have been carried out in a variable magnetic field between 0 and 1 T. The performance of MM in magnetic fields is also reported along with a comparison to simulations.

Iodice, M.



Plasmid Mediated Salt Tolerance in Root Associated Bacteria from Erigerone linifolious  

Directory of Open Access Journals (Sweden)

Full Text Available Bacterial strains (which could tolerate 2-3M NaCl in the growth medium were isolated from the roots of Erigerone linifolious. They were El-1, El-2, El-3 (from histoplane of roots and REl-1, REl-2, REl-3, REl-4, REl-5 (from the rhizoplane. All bacterial strains were motile rods (except El-2 which were cocci, exhibiting either Gram-negative (El-1, El-2, El-3, REl-1 or Gram-variable (REl-2, REl-3, REl-4, REl-5 staining. These strains were affiliated with genus Delya (El-1, Vibrio (El-3, REl-1, while four Gram-variable strains shaired characters with Bacillus pumilus. They have wide temperature and pH ranges with different optima. These strains also exhibit multiple salts/osmolytes/heavy metals/antibiotics resistance. Curing of plasmids from four of these strains revealed that salt tolerance and most of the other resistances were plasmid encoded. Plasmids residing in these halo-tolerant strains were conjugative (except pSH1413. Hybridization experiments revealed that one of these plasmids (pSH1414 belonged to IncN group of plasmids.

Azra Yasmin



Conservation of plasmid DNA sequences in coronatine-producing pathovars of Pseudomonas syringae  

International Nuclear Information System (INIS)

In Pseudomonas syringae pv. tomato PT23.2, plasmid pPT23A (101 kb) is involved in synthesis of the phytotoxin coronatine. The physical characterization of mutations that abolished coronatine production indicated that at least 30 kb of pPT23A DNA are required for toxin synthesis. In the present study, 32P-labeled DNA fragments from the 30-kb region of pPT23A hybridized to plasmid DNAs from several coronatine-producing pathovars of P. syringae under conditions of high stringency. These experiments indicated that this region of pPT23A was strongly conserved in large plasmids (90 to 105 kb) that reside in P. syringae pv. atropurpurea, glycinea, and morsprunorum. The functional significance of the observed homology was demonstrated in marker-exchange experiments in which Tn5-inactivated sequences from the 30-kb region of pPT23A were used to mutate coronatine synthesis genes in the three heterologous pathovars. Physical characterization of the Tn5 insertions generated by marker exchange indicated that genes controlling coronatine synthesis in P. syringae pv. atropurpurea 1304, glycinea 4180, and morsprunorum 567 and 3714 were located on the large indigenous plasmids where homology was originally detected. Therefore, coronatine biosynthesis genes are strongly conserved in the plasmid DNAs of four producing pathovars, despite their disparate origins (California, Japan, New Zealand, Great Britain, and Italy)


Adaptive plasmid evolution results in host-range expansion of a broad-host-range plasmid. (United States)

Little is known about the range of hosts in which broad-host-range (BHR) plasmids can persist in the absence of selection for plasmid-encoded traits, and whether this "long-term host range" can evolve over time. Previously, the BHR multidrug resistance plasmid pB10 was shown to be highly unstable in Stenotrophomonas maltophilia P21 and Pseudomonas putida H2. To investigate whether this plasmid can adapt to such unfavorable hosts, we performed evolution experiments wherein pB10 was maintained in strain P21, strain H2, and alternatingly in P21 and H2. Plasmids that evolved in P21 and in both hosts showed increased stability and decreased cost in ancestral host P21. However, the latter group showed higher variability in stability patterns, suggesting that regular switching between distinct hosts hampered adaptive plasmid evolution. The plasmids evolved in P21 were also equally or more stable in other hosts compared to pB10, which suggested true host-range expansion. The complete genome sequences of four evolved plasmids with improved stability showed only one or two genetic changes. The stability of plasmids evolved in H2 improved only in their coevolved hosts, not in the ancestral host. Thus a BHR plasmid can adapt to an unfavorable host and thereby expand its long-term host range. PMID:18430943

De Gelder, Leen; Williams, Julia J; Ponciano, José M; Sota, Masahiro; Top, Eva M



A Positive Study on the Residents' Tourism Expectation of Shanghai EXPO  

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Full Text Available The attitude, cognition and expectation of residents in certain eventholding destination play a significant role to the success of this mega-event. This research analyzed the expectation of Shangehai residents, as well as the interdependent relationship between residents' expectation and 2010 Shanghai EXPO focusing on 2010 Shanghai EXPO. This study revealed that factor analysis selected 5 tourism expectation factors (infrastructural& environmentalfactor;positive attitude;social phenomenal;economic and price & real estate.Among Shanghai residents' demographic characteristics, except gender, the otherdemographic variables like age,educationallevel, marital level and profession all have obvious differences with the 5expectation factors.multi-regression analysis also revealed that Shanghai residents' expectation has apositive correlation with the active participating attitudes.Inthe end the insufficiency of this study is put forwardand recommendations on the futurestudyare alsogiven.

ZHANG Yun-yao



Design and Constructing pBGGT Plasmid: a Carrier Plasmid for Betathalassaemia Gene Targeting  

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Full Text Available Background: Most of molecular biology studies depend on making gene constructs. Although commercial plasmids are widely used for this purpose, sometimes due to the nature of the restriction sites or need of multiple subcloning, usual restriction sites available in original multiple cloning sites (MCS of the plasmids could not be easily used, if not impossible at all. Here, we report an easy and fast method to construct suitable plasmid with a new MCS for constructing a 16kb gene targeting plasmid. Methods: Firstly, the suitable MCS was designed by studying the sequence of desired gene fragments in Gene runner software. Two partial complementary 74 base long oligonucleotides were designed and constructed to make this MCS. The original pUC19 MCS was replaced with the new one by enzymatic digestion of the plasmid and removal of the MCS, followed by adding the two complementary oligonucleotides and ligating the construct and transforming it into Ecoli TOP10 F.The new plasmid was then purified and sequenced by M13 forward and reverse primers. Findings: Synthesis of two 74 base polynuclotides was successful, and these polynucleotides formed a double stranded fragment which was successfully inserted between HindIII-EcoRI sites of pUC19. Analysis of intermediate step results showed successful progress of cloning reaction. Final analysis of the plasmid by restriction analysis and sequencing the MCS confirmed authenticity of the new plasmid. Conclusions: The method described here is a fast and easy way to make suitable plasmid out of commercially available plasmids. This process can considerably decrease the time and cost of plasmid construction. Availability of suitable restriction sites in proper order makes it possible to directionally clone the desired gene fragments which is more efficient and excludes screening steps for the right direction of the fragments. The plasmid reported herein is specifically tailored to insert different fragments of a beta-globin gene targeting construct.

F Maryami



Subduction mega-thrust beneath Mt. Fuji, central Japan (United States)

The Philippine Sea plate (PHS) is being subducted beneath Honshu, associated with the buoyant subduction of the Izu-Bonin arc. Many scientists estimated the plate boundary along the northwestern part of the Izu collision zone, however, covered by volcanic products from Mt. Fuji and Hakone volcanoes, no active fault system is recognized. To reveal the location of plate boundary mega-trust and to evaluate the seismic hazards produced by these active faults, we performed deep and shallow high -resolution seismic reflection profiling across the flank of Mt. Fuji and Hakone volcanoes. Deep seismic data were acquired for 34-km-long seismic line, using four vibroseis trucks and explosives (IVI) and a 200 channels recording system. On the deep seismic section, westward dipping reflectors are dominant beneath the Hakone volcano on the PHS and extend to the west at the depth of 7 km beneath sub-horizontal reflectors. The top surface of the west dipping reflectors is interpreted as a plate boundary mega-thrust. The velocity profile obtained by refraction tomography suggests that the high velocity zone on the hanging wall and low velocity westward dipping layer in the footwall, which corresponds the volcanic products of Hakone volcano. The hanging-wall unit consists of the accreted arc crust from the Izu-Bonin arc, Quaternary coarse trough fill and Quaternary volcanic products. On the seismic section, the vertical offset of the top of Vp 5.4 km/sec zone is 2.5 km. Probable Quaternary coarse trough fill, deposited in the trough between the Izu-Bonin arc and Honshu arc, distributed on the mega-thrust forming wedge-shaped geometry. The high-resolution seismic section suggests that the plate boundary fault zone consists of several branching faults. The frontal thrust controlled the thickness of the deposits, probably younger than 300 ka, for 1-km-vertical offset, suggesting that the net slip rate of the major thrust is about 10 mm/y. Based on morphotectonic observation and high-resolution shallow seismic sections, it is highly probable that the thrust displaced the Gotemba debris avalanche deposits dated 2.9 ka (Miyachi et al., 2004). From the seismic hazard point of view, such large slip rate of this thrust indicates that the estimated magnitude of earthquake reaches to be M8-. As the seismogenic source fault is located beneath Mt. Fuji, strong ground motions produced by the movement of this fault, may cause the debris avalanche of the flank of Mt. Fuji and it has potential to produce devastative damage to the cities distributed on the flank of Mt. Fuji. Further research will be needed to obtain more precise estimate the seismic hazards produced by this mega-thrust.

Sato, H.; Ishiyama, T.; Iwasaki, T.; Abe, S.; Kato, N.; Imaizumi, T.; Hirata, N.



Holocene Lake Mega-Chad palaeoshorelines from space (United States)

During the Holocene a giant lake, known as Lake Mega-Chad (LMC), extended over more than 350,000 km 2 in southern Sahara. Morphodynamic features of sedimentary systems outlining the LMC palaeoshorelines have been identified by the joint analyses of new topographic images (Digital Elevation Model) acquired by radar interferometry and Landsat Thematic Mapper images. Here, we characterize for the first time at the scale of the Chad Basin a wave-dominated sedimentary system including river deltas, longshore sandridges, beach ridges, spits and a wave-ravinement surface. They provide new evidence of the environmental impact of Quaternary climate changes in the sahelo-saharan area. Continental trade winds controlled the longshore drift in the northern part of the palaeolake. Two distinct LMC episodes dated as lower and middle Holocene are clearly identified, contemporaneous with the two phases of wetter conditions usually recognized in central and northern Africa.

Schuster, Mathieu; Roquin, Claude; Duringer, Philippe; Brunet, Michel; Caugy, Matthieu; Fontugne, Michel; Taïsso Mackaye, Hassan; Vignaud, Patrick; Ghienne, Jean-François



Producing mega-pixel CMB maps from differential radiometer data  

CERN Document Server

A major goal of cosmology is to obtain sensitive, high resolution maps of the Cosmic Microwave Background (CMB) anisotropy. Such maps, as would be produced by the recently proposed Microwave Anisotropy Probe (MAP), will contain a wealth of primary information about conditions in the early universe. To mitigate systematic effects when observing the microwave background, it is desirable for the raw data to be collected in differential form: as a set of temperature differences between points in the sky. However, the production of large (mega-pixel) maps from a set of temperature differences is a potentially severe computational challenge. We present a new technique for producing maps from differential radiometer data that has a computational cost that grows in the slowest possible way with increasing angular resolution and number of map pixels. The required central processor (CPU) time is proportional to the number of differential data points and the required random access memory (RAM) is proportional to the num...

Wright, E L; Bennett, C L; Wright, Edward L; Hinshaw, Gary; Bennett, Charles L



The Kalimantan Border Oil Palm Mega-project  

International Nuclear Information System (INIS)

d doubt how the 1.8 million hectare oil palm project would trash the primary forests of three National Parks, cut through rugged slopes and mountains utterly unsuitable for oil palm cultivation and annihilate the customary rights land of the indigenous Dayak communities in the border area. This report describes what has come of the Kalimantan border oil palm mega-plan since it was announced, who is involved and what research, lobby and campaigning has led to so far. In particular, this study aims to inform civil society organizations, palm oil buyers, investors and government bodies outside Indonesia about the undiminished threats to the tropical rainforests and indigenous peoples related to Indonesia's oil palm expansion plans and the government's overall development agenda for Kalimantan


HST imaging of MEGA Microlensing Candidates in M31  

Energy Technology Data Exchange (ETDEWEB)

We investigate HST/ACS and WFPC2 images at the positions of five candidate microlensing events from a large survey of variability in M31 (MEGA). Three closely match unresolved sources, and two produce only flux upper limits. All are confined to regions of the color-magnitude diagram where stellar variability is unlikely to be easily confused with microlensing. Red variable stars cannot explain these events (although background supernova are possible for two). If these lenses arise in M31's halo, they are due to masses 0.08 < m/M{sub {circle_dot}} < 0.85 (95% certainty, for a {delta}-function mass distribution), brown dwarfs for disk/disk, and stellar masses for disk/bulge ''self-lensing''.

Cseresnjes, Patrick; Crotts, Arlin P.S.; de Jong, Jelte T.A.; Bergier, Alex; Baltz, Edward A.; Gyuk, Geza; Kuijken, Konrad; Widrow, Lawrence M.; /Columbia U., Astron.; s U., Kingston



Does the Earth show up an impending mega-earthquake?  

CERN Document Server

In line of the intermediate-term monitoring of seismic activity aimed at prediction of the world largest earthquakes the seismic dynamics of the Earth's lithosphere is analysed as a single whole, which is the ultimate scale of the complex hierarchical non-linear system. The present study demonstrates that the lithosphere does behave, at least in intermediate-term scale, as non-linear dynamic system that reveals classical symptoms of instability at the approach of catastrophe, i.e., mega-earthquake. These are: (i) transformation of magnitude distribution, (ii) spatial redistribution of seismic activity, (iii) rise and acceleration of activity, (iv) change of dependencies across magnitudes of different types, and other patterns of collective behaviour. The observed global scale seismic behaviour implies the state of criticality of the Earth lithosphere in the last decade.

Romashkova, L L; Kossobokov, Vladimir G.; Romashkova, Leontina L.



SiO and CH3OH mega-masers in NGC 1068. (United States)

Maser is an acronym for microwave amplification by stimulated emission of radiation; in astronomy mega-masers are masers in galaxies that are ?10(6) times more luminous than typical galactic maser sources. Observational studies of mega-masers can help us to understand their origins and characteristics. More importantly, mega-masers can be used as diagnostic tracers to probe the physical properties of their parent galaxies. Since the late 1970s, only three types of molecules have been found to form mega-masers: H2O, OH and H2CO. Here we report the detection of both SiO and CH3OH mega-masers near the centre of Seyfert 2 galaxy NGC 1068 at millimetre wavelengths, obtained using the IRAM 30-m telescope. We argue that the SiO mega-maser originated from the nuclear disk and the CH3OH mega-maser originated from shock fronts. High-resolution observations in the future will enable us to investigate AGN feedback and determine the masses of central supermassive black holes in such galaxies. PMID:25386834

Wang, Junzhi; Zhang, Jiangshui; Gao, Yu; Zhang, Zhi-Yu; Li, Di; Fang, Min; Shi, Yong



SiO and CH3OH mega-masers in NGC 1068 (United States)

Maser is an acronym for microwave amplification by stimulated emission of radiation; in astronomy mega-masers are masers in galaxies that are ?106 times more luminous than typical galactic maser sources. Observational studies of mega-masers can help us to understand their origins and characteristics. More importantly, mega-masers can be used as diagnostic tracers to probe the physical properties of their parent galaxies. Since the late 1970s, only three types of molecules have been found to form mega-masers: H2O, OH and H2CO. Here we report the detection of both SiO and CH3OH mega-masers near the centre of Seyfert 2 galaxy NGC 1068 at millimetre wavelengths, obtained using the IRAM 30-m telescope. We argue that the SiO mega-maser originated from the nuclear disk and the CH3OH mega-maser originated from shock fronts. High-resolution observations in the future will enable us to investigate AGN feedback and determine the masses of central supermassive black holes in such galaxies.

Wang, Junzhi; Zhang, Jiangshui; Gao, Yu; Zhang, Zhi-Yu; Li, Di; Fang, Min; Shi, Yong



Protein Diversity Confers Specificity in Plasmid Segregation (United States)

The ParG segregation protein (8.6 kDa) of multidrug resistance plasmid TP228 is a homodimeric DNA-binding factor. The ParG dimer consists of intertwined C-terminal domains that adopt a ribbon-helix-helix architecture and a pair of flexible, unstructured N-terminal tails. A variety of plasmids possess partition loci with similar organizations to that of TP228, but instead of ParG homologs, these plasmids specify a diversity of unrelated, but similarly sized, partition proteins. These include the proteobacterial pTAR, pVT745, and pB171 plasmids. The ParG analogs of these plasmids were characterized in parallel with the ParG homolog encoded by the pseudomonal plasmid pVS1. Like ParG, the four proteins are dimeric. No heterodimerization was detectable in vivo among the proteins nor with the prototypical ParG protein, suggesting that monomer-monomer interactions are specific among the five proteins. Nevertheless, as with ParG, the ParG analogs all possess significant amounts of unordered amino acid residues, potentially highlighting a common structural link among the proteins. Furthermore, the ParG analogs bind specifically to the DNA regions located upstream of their homologous parF-like genes. These nucleoprotein interactions are largely restricted to cognate protein-DNA pairs. The results reveal that the partition complexes of these and related plasmids have recruited disparate DNA-binding factors that provide a layer of specificity to the macromolecular interactions that mediate plasmid segregation. PMID:15805511

Fothergill, Timothy J. G.; Barilla, Daniela; Hayes, Finbarr



Investigating fusion plasma instabilities in the Mega Amp Spherical Tokamak using mega electron volt proton emissions (invited)a) (United States)

The proton detector (PD) measures 3 MeV proton yield distributions from deuterium-deuterium fusion reactions within the Mega Amp Spherical Tokamak (MAST). The PD's compact four-channel system of collimated and individually oriented silicon detectors probes different regions of the plasma, detecting protons (with gyro radii large enough to be unconfined) leaving the plasma on curved trajectories during neutral beam injection. From first PD data obtained during plasma operation in 2013, proton production rates (up to several hundred kHz and 1 ms time resolution) during sawtooth events were compared to the corresponding MAST neutron camera data. Fitted proton emission profiles in the poloidal plane demonstrate the capabilities of this new system.

Perez, R. V.; Boeglin, W. U.; Darrow, D. S.; Cecconello, M.; Klimek, I.; Allan, S. Y.; Akers, R. J.; Keeling, D. L.; McClements, K. G.; Scannell, R.; Turnyanskiy, M.; Angulo, A.; Avila, P.; Leon, O.; Lopez, C.; Jones, O. M.; Conway, N. J.; Michael, C. A.



pB264, a small, mobilizable, temperature sensitive plasmid from Rhodococcus  

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Full Text Available Abstract Background Gram-positive bacteria of the genus Rhodococcus have shown an extraordinary capacity for metabolizing recalcitrant organic compounds. One hindrance to the full exploitation of Rhodococcus is the dearth of genetic tools available for strain manipulation. To address this issue, we sought to develop a plasmid-based system for genetic manipulation of a variety of Rhodococcus strains. Results We isolated and sequenced pB264, a 4,970 bp cryptic plasmid from Rhodococcus sp. B264-1 with features of a theta-type replication mechanism. pB264 was nearly identical to pKA22, a previously sequenced but uncharacterized cryptic plasmid. Derivatives of pB264 replicate in a diverse range of Rhodococcus species, showing that this plasmid does not bear the same host range restrictions that have been exhibited by other theta replicating plasmids. Replication or maintenance of pB264 is inhibited at 37°C, making pB264 useful as a suicide vector for genetic manipulation of Rhodococcus. A series of deletions revealed that ca. 1.3 kb from pB264 was sufficient to support replication and stable inheritance of the plasmid. This region includes two open reading frames that encode functions (RepAB that can support replication of pB264 derivatives in trans. Rhodococcus sp. B264-1 will mobilize pB264 into other Rhodococcus species via conjugation, making it possible to genetically modify bacterial strains that are otherwise difficult to transform. The cis-acting element (oriT required for conjugal transfer of pB264 resides within a ca. 0.7 kb region that is distinct from the regions responsible for replication. Conclusion Shuttle vectors derived from pB264 will be useful for genetic studies and strain improvement in Rhodococcus, and will also be useful for studying the processes of theta replication and conjugal transfer among actinomycetes.

Currie Devin H



Residency training program: Perceptions of residents  

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Full Text Available Background: There is a phobia among doctors for the residency training program, since the establishment of the program over 30 years ago. The reason for establishing the program was mainly to provide the much-needed specialists in medicine. Objectives: To ascertain the perception of the residency training program among residents. Materials and Methods: Structured questionnaires were administered to residents at 3 training institutions in Nigeria. Results: One hundred nineteen (85.5% questionnaires were returned out of 140. The ages of respondents ranged from 27 to 42 years, the median age being 30 years. There were 110 males and 9 females. One hundred six (89.1% were junior residents. Ninety (75.6% were sponsored by the training institutions. Seventy-four (62.25% felt their consultants were contributing just 50% or less to their training. Sixty-two (52.2% of the respondents had attended a revision course, conference or seminar within the last 6 months. Majority of the residents would want better remuneration, up-front payment of examination and revision fees, more teaching by the consultants and less emphasis on the provision of services as ways of improving the program. Conclusion: Majority of the residents are sponsored by the training institutions.

Yusufu L. M. D



Proceedings of the Canadian Institute conference on EPC mega-project management  

Energy Technology Data Exchange (ETDEWEB)

The presentations at this conference focused on planning, management and risk mitigation strategies for large scale engineering, procurement and construction projects. Various successful mega-projects in Alberta were reviewed. Issues concerning lump sum contracts, construction, and project workforce planning effects were discussed. Mixed labour agreements were evaluated with reference to mega-project optimization. Various suggestions and improvements for mega-projects were outlined, and issues concerning financing, procurement and construction site management were discussed. Best practices for developing and managing mega-project contracts were evaluated. Various techniques for improving workforce planning were suggested. The conference featured 16 presentations, of which 2 have been catalogued separately for inclusion in this database. tabs., figs.




Proceedings of the Canadian Institute conference on best practices for EPC mega-project management  

Energy Technology Data Exchange (ETDEWEB)

Approaches to effective mega-project management were the focus of this conference. Issues concerning cost-overruns, industry initiatives to improve bottom line forecasting and management of costs were examined. In addition, the reduction of delivery risks was discussed. Management of mega-projects and the creation of smaller components were reviewed. Issues concerning contracts, teams and success in mega-projects were also examined along with techniques to improve scheduling and resource management for mega-projects. Various techniques for improving workforce planning were reviewed, in addition to issues concerning increasing supply and improving productivity of trades people and project managers. Issues concerning unions, project contracts and lump sum payments were discussed as well as partnership approaches. In addition, the advantages of, and challenges to modularization were reviewed. The conference featured 9 presentations, of which 6 have been catalogued separately for inclusion in this database. tabs., figs.




MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data sets from files or web-based repositories, and it ...

Kumar, Sudhir; Nei, Masatoshi; Dudley, Joel; Tamura, Koichiro



Plasmid and chromosome partitioning: surprises from phylogeny  

DEFF Research Database (Denmark)

Plasmids encode partitioning genes (par) that are required for faithful plasmid segregation at cell division. Initially, par loci were identified on plasmids, but more recently they were also found on bacterial chromosomes. We present here a phylogenetic analysis of par loci from plasmids and chromosomes from prokaryotic organisms. All known plasmid-encoded par loci specify three components: a cis-acting centromere-like site and two trans-acting proteins that form a nucleoprotein complex at the centromere (i.e. the partition complex). The proteins are encoded by two genes in an operon that is autoregulated by the par-encoded proteins. In all cases, the upstream gene encodes an ATPase that is essential for partitioning. Recent cytological analyses indicate that the ATPases function as adaptors between a host-encoded component and the partition complex and thereby tether plasmids and chromosomal origin regions to specific subcellular sites (i.e. the poles or quarter-cell positions). Two types of partitioning ATPases are known: the Walker-type ATPases encoded by the par/sop gene family (type I partitioning loci) and the actin-like ATPase encoded by the par locus of plasmid R1 (type II partitioning locus). A phylogenetic analysis of the large family of Walker type of partitioning ATPases yielded a surprising pattern: most of the plasmid-encoded ATPases clustered into distinct subgroups. Surprisingly, however, the par loci encoding these distinct subgroups have different genetic organizations and thus divide the type I loci into types Ia and Ib. A second surprise was that almost all chromosome-encoded ATPases, including members from both Gram-negative and Gram-positive Bacteria and Archaea, clustered into one distinct subgroup. The phylogenetic tree is consistent with lateral gene transfer between Bacteria and Archaea. Using database mining with the ParM ATPase of plasmid R1, we identified a new par gene family from enteric bacteria. These type II loci, which encode ATPases of the actin type, have a genetic organization similar to that of type Ib loci. Udgivelsesdato: Aug

Gerdes, Kenn; MØller-Jensen, Jakob



The Kalimantan Border Oil Palm Mega-project  

Energy Technology Data Exchange (ETDEWEB)

A few years ago, the Indonesian government and sections of the palm oil industry united in the Indonesian Palm Oil Commission (IPOC) to undertake efforts to restore the atrocious public image that the palm oil industry had earned abroad for its role in the demise of Indonesia's tropical rainforests, the massive forest fires and haze in 1997-1998, and for the widespread conflicts between plantation companies and local communities. If IPOC succeeded in restoring the palm oil industry's image abroad, it was shattered again after June 2005 when the Indonesian Minister of Agriculture revealed details of a government plan to develop the world's largest oil palm plantation in a 5-10 kilometer band along the border of Kalimantan and Malaysia. To finance the USD 567 million plantation project, the Indonesian President and Chamber of Commerce and Industry (KADIN) had already met up with the Chinese government and private sector several times, resulting in Memoranda of Understanding between (among other) the Artha Graha and Sinar Mas groups from Indonesia and the Chinese CITIC group and Chinese Development Bank (CDB). The oil palm mega-project, launched in Indonesia under the banner of 'bringing prosperity, security and environmental protection to the Kalimantan border area', turned sour when a business plan developed by the Indonesian State Plantation Corporation (PTPN) began to circulate. This document contained a map that showed beyond doubt how the 1.8 million hectare oil palm project would trash the primary forests of three National Parks, cut through rugged slopes and mountains utterly unsuitable for oil palm cultivation and annihilate the customary rights land of the indigenous Dayak communities in the border area. This report describes what has come of the Kalimantan border oil palm mega-plan since it was announced, who is involved and what research, lobby and campaigning has led to so far. In particular, this study aims to inform civil society organizations, palm oil buyers, investors and government bodies outside Indonesia about the undiminished threats to the tropical rainforests and indigenous peoples related to Indonesia's oil palm expansion plans and the government's overall development agenda for Kalimantan.

Wakker, E. [AIDEnvironment, Amsterdam (Netherlands)



BioShuttle-mediated Plasmid Transfer  

Directory of Open Access Journals (Sweden)

Full Text Available An efficient gene transfer into target tissues and cells is needed for safe and effective treatment of genetic diseases like cancer. In this paper, we describe the development of a transport system and show its ability for transporting plasmids. This non-viral peptide-based BioShuttle-mediated transfer system consists of a nuclear localization address sequence realizing the delivery of the plasmid phNIS-IRES-EGFP coding for two independent reporter genes into nuclei of HeLa cells. The quantification of the transfer efficiency was achieved by measurements of the sodium iodide symporter activity. EGFP gene expression was measured with Confocal Laser Scanning Microscopy and quantified with biostatistical methods by analysis of the frequency of the amplitude distribution in the CLSM images. The results demonstrate that the “BioShuttle”-Technology is an appropriate tool for an effective transfer of genetic material carried by a plasmid.

Klaus Braun, Leonie von Brasch, Ruediger Pipkorn, Volker Ehemann, Juergen Jenne, Herbert Spring, Juergen Debus, Bernd Didinger, Werner Rittgen, Waldemar Waldeck



System modelling and identification of Mega-Amp Spherical Tokamak  

International Nuclear Information System (INIS)

A dynamic system response model for plasma in Mega-Amp Spherical Tokamak (MAST) has been developed using RZIP. This is a linearized tokamak model. It assumes a constant plasma current distribution and axisymmetry. The plasma and conducting structures are approximated by discrete toroidal current filaments. RZIP generates a state-space model of the system behaviour, with PF coil voltages as inputs and various predicted diagnostic measurements as outputs. A separate SIMULINK model has been developed to represent the MAST plant, power supplies and analogue feedback controller. The RZIP and SIMULINK models were combined to produce a complete system model. This combined model was used to simulate test shots under both vacuum and plasma conditions. The two sets of traces cohere reasonably well, with some difference in attenuation levels. System identification experiments were carried out on the PF coils, with particular attention paid to the vertical field coils, under vacuum conditions. The frequency response behaviour was found using an excitation signal comprising a number of sinusoids. The RZIP model was verified by comparing its predicted response with experimental data


System modelling and identification of Mega-Amp Spherical Tokamak  

Energy Technology Data Exchange (ETDEWEB)

A dynamic system response model for plasma in Mega-Amp Spherical Tokamak (MAST) has been developed using RZIP. This is a linearized tokamak model. It assumes a constant plasma current distribution and axisymmetry. The plasma and conducting structures are approximated by discrete toroidal current filaments. RZIP generates a state-space model of the system behaviour, with PF coil voltages as inputs and various predicted diagnostic measurements as outputs. A separate SIMULINK model has been developed to represent the MAST plant, power supplies and analogue feedback controller. The RZIP and SIMULINK models were combined to produce a complete system model. This combined model was used to simulate test shots under both vacuum and plasma conditions. The two sets of traces cohere reasonably well, with some difference in attenuation levels. System identification experiments were carried out on the PF coils, with particular attention paid to the vertical field coils, under vacuum conditions. The frequency response behaviour was found using an excitation signal comprising a number of sinusoids. The RZIP model was verified by comparing its predicted response with experimental data.

Qin, J. E-mail:; Limebeer, D.; McArdle, G.J.; Wainwright, J



The CFHT/MegaCam Stripe-82 Survey (United States)

The CFTH/MegaCam Stripe-82 Survey (CS82) is a joint Canada-France-Brazil project covering ˜ 170 sq. deg. in the SDSS Stripe-82 area down to magnitude 24.1 in the optical i-band with a mean 0.6" seeing (PIs: J.-P. Kneib, A. Leauthaud, M. Makler, L. Van Waerbeke). Its main focus is the study of weak and strong gravitational lensing, with additional applications in other fields such as galaxy evolution and galaxy cluster science. Furthermore, the multitude of existing and future projects in Stripe-82, covering from the radio to the UV and including a large set of spectroscopic data, offers the possibility of exploring applications in many fields of astronomy, thereby enhancing the scientific value of the survey. In this Short Talk, we will give an overview of the main published and ongoing CS82 scientific projects. They include the measurement of the largest contiguous lensing convergence map to date and its peak statistics, providing direct information on the large scale dark matter distribution; the first CMB-lensing × shear cross-correlation measurement, probing the dark matter distribution at redshifts of order 1; galaxy-galaxy lensing measurements around SDSS-III/BOSS galaxies, constraining halo occupation distribution (HOD) models and obtaining complementary mass measurements in combination with BOSS spectroscopic data; the discovery of several new gravitational arc systems and more.

Moraes, B.; Kneib, J.-P.; Leauthaud, A.; Makler, M.; Van Waerbeke, L.; Bundy, K.; Erben, T.; Heymans, C.; Hildebrandt, H.; Miller, L.; Shan, H. Y.; Woods, D.; Charbonnier, A.; Pereira, M. E.



Stress responses and replication of plasmids in bacterial cells  

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Full Text Available Abstract Plasmids, DNA (or rarely RNA molecules which replicate in cells autonomously (independently of chromosomes as non-essential genetic elements, play important roles for microbes grown under specific environmental conditions as well as in scientific laboratories and in biotechnology. For example, bacterial plasmids are excellent models in studies on regulation of DNA replication, and their derivatives are the most commonly used vectors in genetic engineering. Detailed mechanisms of replication initiation, which is the crucial process for efficient maintenance of plasmids in cells, have been elucidated for several plasmids. However, to understand plasmid biology, it is necessary to understand regulation of plasmid DNA replication in response to different environmental conditions in which host cells exist. Knowledge of such regulatory processes is also very important for those who use plasmids as expression vectors to produce large amounts of recombinant proteins. Variable conditions in large-scale fermentations must influence replication of plasmid DNA in cells, thus affecting the efficiency of recombinant gene expression significantly. Contrary to extensively investigated biochemistry of plasmid replication, molecular mechanisms of regulation of plasmid DNA replication in response to various environmental stress conditions are relatively poorly understood. There are, however, recently published studies that add significant data to our knowledge on relations between cellular stress responses and control of plasmid DNA replication. In this review we focus on plasmids derived from bacteriophage ? that are among the best investigated replicons. Nevertheless, recent results of studies on other plasmids are also discussed shortly.

Wegrzyn Alicja



Short-lived tectonic switch mechanism for long-term pulses of volcanic activity after mega-thrust earthquakes  

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Eruptive rates in volcanic arcs increase significantly after mega-thrust earthquakes in subduction zones. Over short to intermediate time periods the link between mega-thrust earthquakes and arc response can be attributed to dynamic triggering processes or static stress changes, but a fundamental mechanism that controls long-term pulses of volcanic activity after mega-thrust earthquakes has not been proposed yet. Using geomechanical, geological, and geophysical arguments, we pro...

Lupi, M.; Miller, S. A.



Characterization of the nodulation plasmid encoded chemoreceptor gene mcpG from Rhizobium leguminosarum  

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Full Text Available Abstract Background In general, chemotaxis in Rhizobium has not been well characterized. Methyl accepting chemotaxis proteins are sensory proteins important in chemotaxis of numerous bacteria, but their involvement in Rhizobium chemotaxis is unclear and merits further investigation. Results A putative methyl accepting chemotaxis protein gene (mcpG of Rhizobium leguminosarum VF39SM was isolated and characterized. The gene was found to reside on the nodulation plasmid, pRleVF39d. The predicted mcpG ORF displayed motifs common to known methyl-accepting chemotaxis proteins, such as two transmembrane domains and high homology to the conserved methylation and signaling domains of well-characterized MCPs. Phenotypic analysis of mcpG mutants using swarm plates did not identify ligands for this putative receptor. Additionally, gene knockouts of mcpG did not affect a mutant strain's ability to compete for nodulation with the wild type. Notably, mcpG was found to be plasmid-encoded in all strains of R. leguminosarum and R. etli examined, though it was found on the nodulation plasmid only in a minority of strains. Conclusions Based on sequence homology R. leguminosarum mcpG gene codes for a methyl accepting chemotaxis protein. The gene is plasmid localized in numerous Rhizobium spp. Although localized to the sym plasmid of VF39SM mcpG does not appear to participate in early nodulation events. A ligand for McpG remains to be found. Apparent McpG orthologs appear in a diverse range of proteobacteria. Identification and characterization of mcpG adds to the family of mcp genes already identified in this organism.

Del Bel Kate L



Simple method for extracting plasmid DNA from lactic acid bacteria. (United States)

Rapid screening and large-scale plasmid DNA isolation procedures are described for lactic acid bacteria, using glass beads to break cells. The rapid screening procedure allows one to obtain plasmid DNA pellets in less than 1 h. This method has been successfully tested on various bacteria from the genera Lactococcus, Leuconostoc, Lactobacillus, Pediococcus, Streptococcus, Enterococcus and Propionibacterium. This procedure yields plasmid DNA with minor chromosomal and plasmid DNA-degraded form contaminations. PMID:7764702

Frère, J



Enhancer Activation Requires trans-Recruitment of a Mega Transcription Factor Complex. (United States)

Enhancers provide critical information directing cell-type-specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here, we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2 MDa complex of diverse DNA-binding transcription factors by ER? at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. PMID:25303530

Liu, Zhijie; Merkurjev, Daria; Yang, Feng; Li, Wenbo; Oh, Soohwan; Friedman, Meyer J; Song, Xiaoyuan; Zhang, Feng; Ma, Qi; Ohgi, Kenneth A; Krones, Anna; Rosenfeld, Michael G



A Resident Engineer. (United States)

This paper examines the work of resident engineers in a university setting. The need for engineers with industrial experience is established, and the benefits of using resident engineers in training programs are cited. Attributes and problems associated with the practice are studied from the viewpoints of industry, government, universities, and…

Chapman, Gary T.


Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. (United States)

The self-transmissible, broad-host-range (BHR) plasmid pMOL98 was previously isolated from polluted soil using a triparental plasmid capture approach and shown to possess a replicon similar to that of the BHR plasmids pSB102 and pIPO2. Here, complete sequence analysis and comparative genomics reveal that the 55.5 kb nucleotide sequence of pMOL98 shows extensive sequence similarity and synteny with the BHR plasmid family that now includes pIPO2, pSB102, pTER331, and pMRAD02. They share a plasmid backbone comprising replication, partitioning and conjugative transfer functions. Comparison of the variable accessory regions of these plasmids shows that the majority of natural transposons, as well as the mini-transposon used to mark the plasmids, are inserted in the parA locus. The transposon unique to pMOL98 appears to have inserted from the chromosome of the recipient strain used in the plasmid capture procedure. This demonstrates the necessity for careful screening of plasmids and host chromosomes to avoid mis-interpretation of plasmid genome content. The presence of very similar BHR plasmids with different accessory genes in geographically distinct locations suggests an important role in horizontal gene exchange and bacterial adaptation for this recently defined plasmid group, which we propose to name "PromA". PMID:19259779

Van der Auwera, Géraldine A; Król, Jaroslaw E; Suzuki, Haruo; Foster, Brian; Van Houdt, Rob; Brown, Celeste J; Mergeay, Max; Top, Eva M



Using a custom mega prosthesis to treat hydatidosis of bone: a report of 3 cases.  

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Full Text Available Three cases of hydatidosis of bone with pathological fracture were treated by wide resection, custom mega prosthesis replacement, and chemotherapy. Two patients were females and one was male, with a mean age of 47 years (range, 38-55 years. Two of them had a pathological fracture of the proximal femur, and one had a pathological fracture of the distal femur. All patients were treated postoperatively with albendazole 400 mg, twice daily, for 12 weeks. During the mean follow-up period of 4.5 years, no recurrence of Echinococcal infection was noticed. The use of the custom mega prosthesis technique has not been reported elsewhere, and hydatid disease of the bone can now be considered an extended indication for custom mega prosthesis in addition to its application in surgery for tumours and massive trauma.

Natarajan MV



Pooling fMRI data: meta-analysis, mega-analysis and multi-center studies  

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Full Text Available The quantitative analysis of pooled data from related fMRI experiments has the potential to significantly accelerate progress in brain mapping. Such data-pooling can be achieved through meta-analysis (the pooled analysis of published results, mega-analysis (the pooled analysis of raw data or multi-site studies which can be seen as designed mega-analyses. Current limitations in function-location brain mapping and how data-pooling can be used to remediate them are reviewed, with particular attention to power aggregation and mitigation of false positive results. Some recently developed analysis tools for meta- and mega-analysis are also presented, and recommendations for the conduct of valid fMRI data pooling are formulated.




Metal resistance and plasmid DNA in Thiobacillus ferrooxidans. (United States)

The minimal inhibitory concentrations of copper and nickel were determined for each of fifteen isolates of T. ferrooxidans native to a Cu/Ni tailings environment. Ten isolates were inhibited by 160 mM Cu2+ or less, and ten were inhibited by 160 mM Ni2+ or less. The isolates were screened for plasmid DNA using an alkaline lysis method and CCC plasmid forms were confirmed using the Hintermann technique. Two isolates were found to be devoid of plasmid DNA, and only one isolate contained more than two plasmids. Variability existed in plasmid size, although the majority were larger than the standard pBR322 (4.3 kbp). One plasmid was selected for further analysis using restriction endonucleases. EcoRI, HindIII and KpnI all cleaved the plasmid in two locations, and PstI cleaved the plasmid in six locations. PstI-digested fragments of the plasmid were ligated into pBR322, and the recombinant plasmids were transformed into Escherichia coli ATCC 8739. Four genetically-different transformants resulted, and each was grown in media containing 2.0 mM Cu2+ and compared to the growth of a control under similar conditions. There was no conferred copper resistance in E. coli, although one recombinant plasmid appeared to decrease the tolerance for E. coli ATCC 8739 to Cu2+. PMID:9801769

Chisholm, I A; Leduc, L G; Ferroni, G D



Location of plasmid-mediated citrate utilization determinant in R27 and incidence in other H incompatibility group plasmids.  

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Citrate utilization (Cit+) is encoded by a specific subgroup of incompatibility HI plasmids, viz., IncHI1 plasmids. Only one IncHI1 plasmid, pRG1271, which originated in a Mexican typhoid outbreak in 1972, did not specify Cit+. All other Cit+ plasmids hybridized to a Cit+ probe, a 2-kilobase BglII fragment derived from the Cit+ transposon Tn3411. The position of the Cit+ determinant was mapped to a 13.5-kilobase ApaI fragment within the prototype IncHI1 plasmid R27. No other functions have be...

Taylor, D. E.; Brose, E. C.



Mega sporting events: A poisoned chalice or a new dawn for low- and middle-income  

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Full Text Available Mega sporting events in South Africa, which has the largest number of HIV-positive people in the world, and India, with 1.8 million deaths of children under 5 each year and 52 million stunted children, raise questions about the effective and, as importantly, the moral imperative of spending billions of dollars to host a sporting event. From a health perspective, selling alcohol and debt tarnishes further the notion of any intangible benefits of mega events to low- and middle-income countries.

Mark Tomlinson



New Research Project For The Next Nankai Trough Mega Thrust Earthquakes -Towards To Understanding The Next Mega Thrust Earthquakes. And Mitigation Damages- (United States)

In the Nankai trough, mega thrust earthquakes are occurring with an interval of 100-200 years. So, many researches are focusing on the Nankai trough to elucidate the recurrence system of mega thrust earthquakes. The recent result of recurrence cycle simulation indicates the difference patterns and intervals of mega- thrust earthquake recurrences in each cycle. However, these results are not satisfied for the evaluation and estimation of next mega thrust earthquakes, so, we have to improve the structure model and the recurrence cycle simulation model with higher reliabilities. Especially, the estimation of recurrence cycle between the Tonankai and Nankai earthquake is very important for disaster preventions. Furthermore, the estimation of in coupled mega thrust earthquake around the Nankai trough such as Sumatra earthquake 2004 will be analyzed. To understand and estimate the next mega thrust earthquakes with detail structures and improved simulation model. We will propose research plan as follows, 1) Construct the detailed crustal medium around the Nankai trough using controlled sources and seismic tomography using dense seismic lines and OBS network arrays. 2) Observations of crustal activities around the Nankai trough and north eastern Japan. 3) Construct the database of long term plate coupling dynamics. And study the diversity of recurrence pattern and scale of next mega thrust earthquakes. 4) Develop the advanced simulation methods. 5) Improve the large scale recurrence cycle simulation model based on theoretical and experimental analyses. 6) Evaluate the precise strong motions and tsunamis for the disaster prevention. 7) Develop the reliable risk management system for next mega thrust earthquake. 8) Develop and contract the real time monitoring system around Kii peninsula. 9) Apply scientific results of Nankai seismogenic zone drilling to recurrence cycle simulation. The simulation research consists of the following five research groups. 1) Construction of database for spatiotemporal evolution of slip on the plate interface in the last 120 years. 2) Construction of database for diversity in the historical Nankai trough great earthquake sequences during several thousand years. 3) Development of advanced simulation methods. 4) Simulation research on factors controlling rupture mode of fault segments. 5) Construction of improved physical simulation model reproducing and predicting large diversity in long-term earthquake cycles. In order to understand the strong ground motions and tsunami expecting for future Nankai trough earthquake in detail for mitigation of possible disasters, we need study ground motions and tsunami from the former events occurred in 1944 and 1946 in detail. We will therefore conduct a computer simulation of strong ground motion and tsunami from the 1944 and 1946 events to reproduce strong ground motion and tsunami from the earthquake. We will modify structural model of elastic properties especially for the shear wave speed (Vs) and quality parameters (Q) that are rather difficult to investigate from geophysical explorations. The results of computer simulation for future Nankai trough earthquake are then used for 1) developing a realistic tsunami hazard map, 2) detail understanding of the damage of tall buildings and other important facilities, and 3) the planning of evacuation and recovery from the strong motion and tsunami disasters.

Kaneda, Y.; Hirahara, K.; Furumura, T.



High-throughput yeast plasmid overexpression screen. (United States)

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, including those with direct relevance to human disease. Because of its short generation time and well-characterized genome, a major experimental advantage of the yeast model system is the ability to perform genetic screens to identify genes and pathways that are involved in a given process. Over the last thirty years such genetic screens have been used to elucidate the cell cycle, secretory pathway, and many more highly conserved aspects of eukaryotic cell biology (1-5). In the last few years, several genomewide libraries of yeast strains and plasmids have been generated (6-10). These collections now allow for the systematic interrogation of gene function using gain- and loss-of-function approaches (11-16). Here we provide a detailed protocol for the use of a high-throughput yeast transformation protocol with a liquid handling robot to perform a plasmid overexpression screen, using an arrayed library of 5,500 yeast plasmids. We have been using these screens to identify genetic modifiers of toxicity associated with the accumulation of aggregation-prone human neurodegenerative disease proteins. The methods presented here are readily adaptable to the study of other cellular phenotypes of interest. PMID:21841759

Fleming, Michael S; Gitler, Aaron D



Transfer of conjugative plasmids among bacteria under environmentally relevant conditions  

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Mobile genetiske elementer (f.eks. plasmider), der ofte bærer ekstra funktioner såsom antibiotikaresistens, eller kataboliske- og xenobiotiske nedbrydnings gener, antages at have en meget vigtigt evolutionær rolle for bakterier. I denne PhD afhandling undersøgte jeg størrelsen af plasmid overførsel under de miljørelevante substrat-begrænsede forhold, den del og diversitet af bakteriel samfund der er involveret i overførslen, og effekten af plasmid donor cellens fysiologiske status og de miljørelevante faktorer (selektive tryk) på plasmid spredning. En ny metode til at kvantificere den fraktion af det oprindelige bakteriesamfund der tager andel i plasmid overførsel blev udviklet. Dyrknings-minimal metode i kombination med reporter gen teknologi og moderne mikroskopi viste en meget høj forekomst af RP4:gfp plasmid overførsel til oprindelige jord bakterier af et bredt værtskab. Der blev også vist at spredningskapacitet af en konjugerbare plasmid, der koder for kviksølv resistens via merA genet, finder sted undersubstrat begrænsede forhold til syntetisk bakterielt samfund. Plasmid overførsel var meget forhøjet ved kontinuert udsættelse af mikrokosms for en høj koncentration af kviksølv. De forskellige vækstrater havde meget lidt effekt på kinetiske overførselsrater af et TOL plasmid fra P. putida KT2442. Til gengæld, kun en lille fraktion af donor celler var i stand til at overføre plasmidet. I konklusion. studierne præsenteret i denne PhD afhandling har bidraget til en bedre forståelse af konjugerbare plasmid udveksling mellem bakterier i naturen.

Musovic, Sanin



The evolution of plasmid-carried antibiotic resistance  

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Full Text Available Abstract Background Antibiotic resistance represents a significant public health problem. When resistance genes are mobile, being carried on plasmids or phages, their spread can be greatly accelerated. Plasmids in particular have been implicated in the spread of antibiotic resistance genes. However, the selective pressures which favour plasmid-carried resistance genes have not been fully established. Here we address this issue with mathematical models of plasmid dynamics in response to different antibiotic treatment regimes. Results We show that transmission of plasmids is a key factor influencing plasmid-borne antibiotic resistance, but the dosage and interval between treatments is also important. Our results also hold when plasmids carrying the resistance gene are in competition with other plasmids that do not carry the resistance gene. By altering the interval between antibiotic treatments, and the dosage of antibiotic, we show that different treatment regimes can select for either plasmid-carried, or chromosome-carried, resistance. Conclusions Our research addresses the effect of environmental variation on the evolution of plasmid-carried antibiotic resistance.

Rankin Daniel J



Plasmid transfer between bacteria in soil microcosms and the field  

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Full Text Available In ibis review factors influencing conjugal plasmid transfer between bacteria and the possible role of naturally occurring selftransmissible plasmide for the dissemination of recombinant DNA in soil will be discussed. In microcosm studies, plasmid transfer between various species of introduced bacteria has been detected. Moreover, plamid transfer to indigenous soil micoorganisms was observed. Soil is an oligotrophic environment and plasmid transfer occurred mainly under conditions which were nutritionally favourable for bacteria, such as in the plant rhizosphere and in the presence of clay minerais or added nutrients. Mobilizable plasmids, lacking the ability to transfer themselves, have been reported to be transferred in the presence of selftransmissible plasmids. A study comparing conjugal transfer in microcosme with those in the field revealed that the transfer rates found in microcosme and in the field were similar. Transfer of chromosomal DNA by plasmid RP4 could only be shown on filters and was not observed in soil. Transfer of plasmids carrying biodegradative genes appeared to be favoured in the presence of the compound that can be degraded. Evidence was found for the presence of naturally-occurring selftransmissible plasmids in bacteria in the rhizosphere which could mobilize recombinant plasmids.

Eric Smit



Synapsis-Mediated Fusion of Free DNA Ends Forms Inverted Dimer Plasmids in Yeast  

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When yeast (Saccharomyces cerevisiae) is transformed with linearized plasmid DNA and the ends of the plasmid do not share homology with the yeast genome, circular inverted (head-to-head) dimer plasmids are the principal product of repair. By measurements of the DNA concentration dependence of transformation with a linearized plasmid, and by transformation with mixtures of genetically marked plasmids, we show that two plasmid molecules are required to form an inverted dimer plasmid. Several ob...

Kunes, S.; Botstein, D.; Fox, M. S.



A comparison of the modern seismogenic Nankai mega-splay fault and the exhumed ancient mega-splay fault, the Nobeoka thrust (United States)

Mega-splay fault branched from plate boundary megathrust in subduction zone is located around the border between outer and inner wedges and is considered to cause great earthquake and tsunami such as 1960 Alaska earthquake, 1944 and 1946 Nankai-Tonankai earthquakes, and 2004 Sumatra earthquakes. Therefore, understanding the fault mechanics of the mega-splay fault is essential toward assessing their role in the plate boundary processes and seismo-tsunamigenesis. Seismic reflection studies for the mega-splay fault in 2D and 3D in the Nankai forearc present the reflector with negative or positive polarities with various amplitudes and suggest complicated petrophysical properties and condition of the fault and its surroundings. The Nankai mega-splay fault at a depth of ~5km is going to be drilled and cored by Integrated Ocean Drilling Program, NantroSEIZE experiments and is expected for great progress of understanding of the fault mechanics. Deep portion of the megasplay fault and its connection to the plate boundary megathrust is, however, impossible to be accessed by direct drilling. Far and near field geophysical observation is therefore only way to access the modern and active megasplay fault. On-land exhumed and fossilized mega-splay faults, on the other hand, give a clue for the fault mechanics when they were active in depth although the exhumation and fossilization process modifies their primary properties due to physico-chemical weathering and crack opening by unloading. Our previous studies from the Nobeoka thrust in Kyushu, southwest Japan present well-preservation of primary faulting processes and clear contrast of physical property between the hanging wall and footwall. We have conducted the seismic, drilling, coring and logging investigation into the Nobeoka thrust to the depth of ~250 m including ~40m hanging wall and ~210 m footwall. The coring was ~99% recovery and full logging was successful. The result of the logging together with triangular S-wave vibro-seismic array investigation presents a clear contrast between the hanging wall and footwall. The results indicate how the fossilized megasplay fault is useful to investigate the primary properties in depth,excluding the secondary effects associated with exhumation and surface weathering.

Kimura, G.; Hamahashi, M.; Yamaguchi, A.; Saito, S.; Fukuchi, R.; Kameda, J.; Hamada, Y.; Fujimoto, K.; Hashimoto, Y.; Hina, S.; Eida, M.; Kitamura, Y.



Testing of MicroMegas for ATLAS Muon Small wheel Detection Panels  

CERN Document Server

This document consists of a brief summary of all the research that I have done here as a summer student working together with the MicroMegas group. It mainly focuses on several testing techniques that have been carried out on an L2 panel to verify sseveral criteria such as flatness and flexibility.

Borg, Miryea Nicole



Measurement of the 237Np(n,f) Cross Section with the MicroMegas Detector (United States)

The measurement of the 237Np(n,f) cross section with reference to the standard 238U(n,f) reaction was performed with a MicroMegas detector at the neutron facility of the 5.5 MV Tandem accelerator laboratory at NCSR “Demokritos”. The performance of the detector as far as the gain and resolution function are concerned will be presented.

Diakaki, M.; Kokkoris, M.; Kyrtsos, A.; Nicolis, N. G.; Skordis, E.; Vlastou, R.; Andriamonje, S.; Berthoumieux, E.; Lagoyannis, A.



Determination of plasmid-encoded functions in Rhizobium leguminosarum biovar trifolii using proteome analysis of plasmid-cured derivatives. (United States)

We have used proteome analysis of derivatives of R. leguminosarum biovar trifolii strain ANU843, cured of indigenous plasmids by a direct selection system, to investigate plasmid-encoded functions. Under the conditions used, the plasmid-encoded gene products contributed to only a small proportion of the 2000 proteins visualised in the two-dimensional (2-D) protein map of strain ANU843. The level of synthesis of thirty-nine proteins was affected after curing of either plasmid a, c or e. The differences observed upon plasmid curing included: protein loss, up/down-regulation of specific proteins and novel synthesis of some proteins. This suggests that a complex interplay between the cured plasmid and the remaining replicons is occurring. Twenty-two proteins appeared to be absent in the cured strains and these presumably are encoded by plasmid genes. Of these, a small heat shock protein, a cold shock protein, a hypothetical YTFG-29.7 kDa protein, and the alpha and beta subunits of the electron transfer flavoprotein were identified by N-terminal microsequencing and predicted to be encoded by plasmid e. Four of the sequenced proteins putatively encoded on plasmid e and two encoded on plasmid c were novel. In addition, curing of plasmid e and c consistently decreased the levels of 3-isopropylmalate dehydratase and malate dehydrogenase, respectively, suggesting that levels of these proteins may be influenced by plasmid-encoded functions. A protein with homology to 4-oxalocrotonate tautomerase, which is involved in the biodegradation of phenolic compounds, was found to be newly synthesised in the strain cured of plasmid e. Proteome analysis provides a sensitive tool to examine the functional organisation of the Rhizobium genome and the global gene interactions which occur between the different replicons. PMID:9740057

Guerreiro, N; Stepkowski, T; Rolfe, B G; Djordjevic, M A



3-D geometry and physical property of the Mega-Splay Fault in Nankai trough (United States)

The Nankai trough is a subduction zone, where the Philippine Sea plate is being subducted beneath southwest Japan at a rate of ~4-6.5 cm/y at an azimuth of ~300°-315°. A lot of operations have been done in Nankai, such as three-dimensional seismic reflection surveys and Deep Sea Drilling Project (DSDP), Ocean Drilling Program (ODP), Integrated Ocean Drilling Program (IODP). They revealed that there is a large splay fault, referred to as 'Mega-Splay'. The Mega-Splay Fault has caused a series of catastrophic earthquakes and submarine landslides, which may have led to TSUNAMI. Since fault development history may have affected the geometry of the Mega-Splay Fault and physical property within the fault zone, they need to be examined in detail. In this research, we used 3-D pre-stack depth migration (PSDM), 3-D pre-stack time migration (PSTM) and P-wave velocity in C0004B well (Logging data), in order to interpret 3-D structure of Mega-Splay Fault. The analysis in this research is basically divided into two parts. One is structural interpretation of Splay Fault, based on the high amplitude reflection surface on seismic profiles. The other part is acoustic impedance inversion (AI inversion), in which we inverted seismic waveform into physical property (in this study, acoustic impedance), with the P-wave velocity data at C0004B near Mega-Splay Fault. The 3-D PSDM (or PSTM) clearly images details of Splay Fault, with good continuity of reflections along the fault. It is possible on each seismic profile to trace the high amplitude lines, where rock-properties significantly change. Since Mega-Splay Fault has 45-59m width along the wells, we interpreted the upper limit and the lower limit of the Mega-Splay Fault, based on the high amplitude surfaces along 3-D PSDM. Our interpretation shows that the width of Mega-Splay Fault has variation along the fault, and the plan geometry of the fault toe has a salient at the middle of the 3D box area, suggesting the fault could be divided into two segments: the eastern part and western part. In AI inversion, the 3-D PSTM and P-wave velocity at C0004B were used to build a physical property model around Mega-Splay Fault. AI Inversion is a methodology to invert seismic waveforms with physical property data, into acoustic impedance. Acoustic Impedance governs the ability of a rock to allow the passage of an acoustic wave. In this analysis, we used Hampson-Russell STRATA to perform post-stack seismic inversion. Our results show that there is a low acoustic impedance layer in the upper zone of Splay Fault. 3-D distribution of the low acoustic impedance layer in the fault zone has a variation in the width, similar to the 3-D interpretation of the geometry. This suggests that there are a relationship between structural geometry and physical property along the Mega-Splay Fault.

Masui, R.; Tsuji, T.; Yamada, Y.; Environmental Resource; System Engineering laboratory



Isolation of Clinical Strains of Pseudomonas aeruginosa Harboring Different Plasmids  

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Full Text Available Aim of this study was to investigate the presence of plasmids among the strains of P. aeruginosa isolated from clinically diagnosed cases in Tehran in 2006. A total of 38 strains of P. aeruginosa were isolated. With the exception of one isolate, all P. aeruginosa strains harbored at least one plasmid band. The electrophoretic analysis of plasmid DNAs showed different number of plasmid bands among the strains tested. The DNA band of 1.4 kbp was evident in 84.2% of the strains. Approximately 71 and 21% of the isolates harbored concomitantly two and three plasmids, respectively. Isolation of strains with diverse types of plasmids suggests the different cluster of P. aeruginosa might be disseminated during the current study period.

R. Ranjbar




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Full Text Available Plasmid profile analysis (PP is a method of determining a number and size of plasmids in bacterial isolates. When using plasmid profile analysis in determining epidemical strain for evaluation of this method, it is necessary to compare epidemiological strains with non-epidemiological ones isolated in the same period of time. Plasmid profile determination is performed by lyses of bacterial cell, chromosomal denaturation, sedimentation of cells fragments by centrifugation, and precipitation of DNA with ethanol. DNA is separated by gel electrophoresis based on its molecule mass. Plasmids could be also analyzed by restriction enzymes, as well as by direct techniques, such as hybridization and electronomicroscopically. Using of plasmid profile analysis enables resolving numerous outbreaks caused by Enterobacteriaceae, especially Salmonella. This method could be performed alone for Salmonella enterica serotype Enteritidis, but also as a complementary method to phage typing (phagotypization, and other molecular genetic based techniques.

Predrag Stojanovic



Phage t: a group T plasmid-dependent bacteriophage. (United States)

Phage t was isolated from sewage from Pretoria. It formed plaques only on Escherichia coli and Salmonella typhimurium strains that carried plasmids belonging to incompatibility group T. Five of six group T plasmids permitted visible lysis of R+ host strains. There was no visible lysis of E. coli J53-2 or S. typhimurium LT2trpA8 carrying the T plasmid Rts1 although the strains supported phage growth as indicated by at least a 10-fold increase in phage titre. The latter strains transferred the plasmid at high frequency to E. coli strain CSH2 and the resulting transconjugants plated the phage. Proteus mirabilis strain PM5006(R402) failed to support phage growth although it transferred the plasmid and concomitant phage sensitivity to E. coli J53-2. The phage was hexagonal in outline, RNA-containing, resistant to chloroform and adsorbed to the shafts of pili determined by T plasmids. PMID:6121840

Bradley, D E; Coetzee, J N; Bothma, T; Hedges, R W



MegaMIR: The Megapixel Mid-Infrared Instrument for the Large Binocular Telescope Interferometer (United States)

The Megapixel Mid-infrared Instrument (MegaMIR) is a proposed Fizeau-mode camera for the Large Binocular Telescope operating at wavelengths between 5 and 28 micrometers. The camera will be used in conjunction with the Large Binocular Telescope Interferometer (LBTI), a cryogenic optical system that combines the beams from twin 8.4-m telescopes in a phase coherent manner. Unlike other interferometric systems, the co-mounted telescopes on the LBT satisfy the sine condition, providing diffraction-limited resolution over the 40" field of view of the camera. With a 22.8-m baseline, MegaMIR will yield 0.1" angular resolution, making it the highest resolution wide field imager in the thermal infrared for at least the next decade. MegaMIR will utilize a newly developed 1024 x 1024 pixel Si:As detector array that has been optimized for use at high backgrounds. This new detector is a derivative of the Wide-field Infrared Survey Explorer (WISE) low-background detector. The combination of high angular resolution and wide field imaging will be a unique scientific capability for astronomy. Key benefits will be realized in planetary science, galactic, and extra-galactic astronomy. High angular resolution is essential to disentangle highly complex sources, particularly in star formation regions and external galaxies, and MegaMIR provides this performance over a full field of view. Because of the great impact being made by space observatories like the Spitzer Space Telescope, the number of available targets for study has greatly increased in recent years, and MegaMIR will allow efficient follow up science.

Mainzer, Amanda K.; Young, Erick; Hong, John; Werner, Mike; Hinz, Phil; Gorjan, Varoujan; Ressler, Michael E.



Pathogenomics of the Virulence Plasmids of Escherichia coli  

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Summary: Bacterial plasmids are self-replicating, extrachromosomal elements that are key agents of change in microbial populations. They promote the dissemination of a variety of traits, including virulence, enhanced fitness, resistance to antimicrobial agents, and metabolism of rare substances. Escherichia coli, perhaps the most studied of microorganisms, has been found to possess a variety of plasmid types. Included among these are plasmids associated with virulence. Several types of E. col...

Johnson, Timothy J.; Nolan, Lisa K.



Processes for the production of pharmaceutical grade plasmid DNA  

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Plasmid DNA is currently used in gene therapy and genetic vaccination as a vector system for the delivery of therapeutic genes. Clinical trials as well as future therapeutics demand large amounts of high quality plasmid DNA that fulfils the specifications set by regulatory authorities. This thesis describes the development, analysis, and evaluation of pharmaceutical plasmid DNA production processes comprising cultivation, product isolation, and purification as well as stability assessment dur...

Voß, Carsten



Establishment of a Replicating Plasmid in Rickettsia prowazekii  

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Rickettsia prowazekii, the causative agent of epidemic typhus, grows only within the cytosol of eukaryotic host cells. This obligate intracellular lifestyle has restricted the genetic analysis of this pathogen and critical tools, such as replicating plasmid vectors, have not been developed for this species. Although replicating plasmids have not been reported in R. prowazekii, the existence of well-characterized plasmids in several less pathogenic rickettsial species provides an opportunity t...

Wood, David O.; Hines, Andria; Tucker, Aimee M.; Woodard, Andrew; Driskell, Lonnie O.; Burkhardt, Nicole Y.; Kurtti, Timothy J.; Baldridge, Gerald D.; Munderloh, Ulrike G.



Identification of plasmid partition function in coryneform bacteria  

Energy Technology Data Exchange (ETDEWEB)

The authors have identified and characterized a partition function that is required for stable maintenance of plasmids in the coryneform bacteria Brevibacterium flavum MJ233 and Corynebacterium glutamicum ATCC 31831. This function is localized to a HindIII-NspV fragment (673 bp) adjacent to the replication region of the plasmid, named pBY503, from Brevibacterium stationis IFO 12144. The function was independent of copy number control and was not associated directly with plasmid replication functions. This fragment was able to stabilize the unstable plasmids in cis but not in trans.

Kurusu, Yasurou; Satoh, Yukie; Inui, Masayuki; Kohama, Keiko; Kobayashi, Miki; Terasawa, Masato; Yukawa, Hideaki (Mitsubishi Petrochemical Co., Ltd., Ibaraki (Japan))



Enhanced transgene expression from chromatinized plasmid DNA in mouse liver. (United States)

Plasmid DNA was chromatinized with core histones (H2A, H2B, H3, and H4) in vitro and was delivered into mouse liver by hydrodynamics-based administration. Transgene expression from the chromatinized plasmid DNA was more efficient than that from plasmid DNA delivered in the naked form. The use of acetylation-enriched histones isolated from cells treated with a histone deacetylase inhibitor (trichostatin A) seemed to be more effective. These results indicated that chromatinized plasmid DNA is useful for efficient transgene expression in vivo. PMID:23247018

Kamiya, Hiroyuki; Miyamoto, Shiho; Goto, Hitomi; Kanda, Genki N; Kobayashi, Miwako; Matsuoka, Ichiro; Harashima, Hideyoshi



Construction of a eukaryotic expression plasmid of Humanin*  

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Objective: To construct a eukaryotic expression plasmid pcDNA3.1(-)-Humanin. Methods: The recombinant plasmid pGEMEX-1-Humanin was digested with restriction endonucleases BamH I and Hind III and the Humanin gene fragments, about 100 bp length, were obtained. Then the Humanin gene fragments were inserted into eukaryotic expression vector pcDNA3.1(-) and the recombinant plasmids pcDNA3.1(-)-Humanin were identified by sequencing. Results: Recombinant plasmid DNA successfully produced a band whic...

Luo, Ben-yan; Chen, Xiang-ming; Tang, Min; Chen, Feng; Chen, Zhi



Plasmids foster diversification and adaptation of bacterial populations in soil. (United States)

It is increasingly being recognized that the transfer of conjugative plasmids across species boundaries plays a vital role in the adaptability of bacterial populations in soil. There are specific driving forces and constraints of plasmid transfer within bacterial communities in soils. Plasmid-mediated genetic variation allows bacteria to respond rapidly with adaptive responses to challenges such as irregular antibiotic or metal concentrations, or opportunities such as the utilization of xenobiotic compounds. Cultivation-independent detection and capture of plasmids from soil bacteria, and complete sequencing have provided new insights into the role and ecology of plasmids. Broad host range plasmids such as those belonging to IncP-1 transfer a wealth of accessory functions which are carried by similar plasmid backbones. Plasmids with a narrower host range can be more specifically adapted to particular species and often transfer genes which complement chromosomally encoded functions. Plasmids seem to be an ancient and successful strategy to ensure survival of a soil population in spatial and temporal heterogeneous conditions with various environmental stresses or opportunities that occur irregularly or as a novel challenge in soil. PMID:22393901

Heuer, Holger; Smalla, Kornelia



Ornamental fish as a source of plasmid-mediated quinolone resistance genes and antibiotic resistance plasmids. (United States)

Growing ornamental fish industry is associated with public health concerns including extensive antibiotic use accompanied by increasing antibiotic resistance. The aim of this study was to analyze Aeromonas isolates from imported tropical ornamental fish and coldwater koi carps bred in the Czech Republic to assess the potential risk of ornamental fish as a source of plasmid-mediated quinolone resistance genes (PMQR) and antibiotic resistance plasmids. A collection of Aeromonas spp. with reduced susceptibility to ciprofloxacin (MIC ? 0.05 mg/L) was selected for the detection of PMQR genes. Isolates harbouring PMQR genes were further analyzed for the additional antibiotic resistance, integron content, clonality, biofilm production and transferability of PMQR genes by conjugation and transformation. Comparative analysis of plasmids carrying PMQR genes was performed. Fifteen (19%, n=80) isolates from koi carps and 18 (24%, n=76) isolates from imported ornamental fish were positive for qnrS2, aac(6')-Ib-cr or qnrB17 genes. PMQR-positive isolates from imported ornamental fish showed higher MIC levels to quinolones, multiresistance and diverse content of antibiotic resistance genes and integrons compared to the isolates from the carps. Related IncU plasmids harbouring qnrS2 and aac(6')-Ib-cr genes were found in Aeromonas spp. from imported ornamental fish and koi carps from various geographical areas. Ornamental fish may represent a potential source of multiresistant bacteria and mobile genetic elements for the environment and for humans. PMID:24629900

Dobiasova, Hana; Kutilova, Iva; Piackova, Veronika; Vesely, Tomas; Cizek, Alois; Dolejska, Monika



Integrated bariatric surgery residency  

Directory of Open Access Journals (Sweden)

Full Text Available Adam EM Eltorai Warren Alpert Medical School of Brown University, RI, USA Abstract: Obesity is a major public health concern. Given its lasting efficacy for improving obesity and obesity-related diseases, bariatric surgery is an increasingly common treatment option. As the implementation of the Affordable Care Act progresses, the impending physician shortage will become more severe. Thus there will be an even greater need for doctors specialized in the management and treatment of obese patients. The development of integrated bariatric surgery residency programs could be considered and is discussed herein. Keywords: obesity, bariatric surgery, integrated residency, surgery education

Eltorai AE



Degradative Plasmid and Heavy Metal Resistance Plasmid Naturally Coexist in Phenol and Cyanide Assimilating Bacteria  

Directory of Open Access Journals (Sweden)

Full Text Available Problem statement: Heavy metals are known to be powerful inhibitors of xenobiotics biodegradation activities. Alleviation the inhibitory effect of these metals on the phenol biodegradation activities in presence of heavy metals resistant plasmid was investigated. Approach: Combination of genetic systems of degradation of xenobiotic compound and heavy metal resistance was one of the approaches to the creation of polyfunctional strains for bioremediation of soil after co-contamination with organic pollutants and heavy metals. Results: A bacterial strain Pseudomonas putida PhCN (pPhCN1, pPhCN2 had been obtained. This bacterium contained two plasmids, a 120 Kb catabolic plasmid that encode for breakdown of phenol (pPhCN1 and pPhCN2 plasmid (100 Kb that code for cadmium and copper resistant. Cyanide assimilation by this bacterium was encoded by chromosomal genes. The inhibitory effect of cadmium (Cd2+ or copper (Cu2+ on the degradation of phenol and cyanide by P. putida strains PhCN and PhCN1 (contained pPhCN1 were investigated. The resistant strain PhCN showed high ability to degrade phenol and cyanide in presence of Cd2+ or Cu2+ comparing with the sensitive strain PhCN1. In addition, Cd2+ or Cu2+ was also found to exert a strong inhibitory effect on the C23O dioxygenase enzyme activity in the presence of cyanide as a nitrogen source. Conclusion: The presence of heavy metal resistance plasmid alleviated the inhibitory effect of metals on the phenol and cyanide assimilation by resistant strain.

Bahig E.  Deeb



Implementing Resident Work Hour Limitations (United States)

Objective To determine the impact of work hour limitations imposed by the 405 (Bell) Regulations as perceived by general surgery residents in New York State. Summary Background Data New Accreditation Council for Graduate Medical Education (ACGME) requirements on resident duty hours are scheduled to undergo nationwide implementation in July 2003. State regulations stipulating similar resident work hour limitations have already been enacted in New York. Methods A statewide survey of residents enrolled in general surgery residencies in New York was administered. Results Most respondents reported general compliance with 405 Regulations in their residency programs, a finding corroborated by reported work hours and call schedules. Whereas a majority of residents reported improved quality of life as a result of the work hour limitations, a substantial portion reported negative impacts on surgical training and quality and continuity of patient care. Negative perceptions of the impact of duty hour restrictions were more prevalent among senior residents and residents at academic medical centers than among junior residents and residents at community hospitals. Conclusions Implementation of resident work hour limitations in general surgery residencies may have negative consequences for patient care and resident education. As surgical residency programs develop strategies for complying with ACGME requirements, these negative consequences must be addressed. PMID:12677136

Whang, Edward E.; Mello, Michelle M.; Ashley, Stanley W.; Zinner, Michael J.



Residence Time Distribution. (United States)

Slurry phase residence time in the SRC-II dissolver is a major process variable affecting the extent of conversion to distillate products. Kinetic studies have shown that overall conversion of vacuum bottoms to lighter hydrocarbons is a zero order process...



Evolving seismogenic plate boundary megathrust and mega-splay faults in subduction zone (Invited) (United States)

Understanding the fault mechanism and its relationship to the sesimo-tsunamigenesis is a key of the scientific targets of subduction zone and therefore NantroSEIZE project of IODP and future new drilling project of International Ocean Discovery Program keeps focusing on that. Mega-splay fault branched from plate boundary megathrust in subduction zone is located around the border between outer and inner wedges and is considered to cause great earthquake and tsunami such as 1960 Alaska earthquake, 1944 and 1946 Nankai-Tonankai earthquakes, and 2004 Sumatra earthquakes. Seismic reflection studies for the mega-splay fault in 2D and 3D in the Nankai forearc present the reflector with negative or positive polarities with various amplitudes and suggest complicated petrophysical properties and condition of the fault and its surroundings. The Nankai mega-splay fault at a depth of ~5km is going to be drilled and cored by NantroSEIZE experiments and is expected for great progress of understanding of the fault mechanics. Before drilling the really targeted seismogenic fault, we are conducting many exercises of geophysical and geological observations. The core-log-seismic integrated exercise for the exhumed mega-splay fault by drilling was operated for the Nobeoka thrust in the Shimanto Belt, Kyushu, Japan. The Nobeoka thrust was once buried in the depth >~10km and suffered maximum temperature >~300 dgree C. As the core recovery is ~99%, perfect correlation between the core and logging data is possible. Thickness of the fault zone is >200 m with a ~50 cm thick central fault core dividing the phyllitic hanging wall and the footwall of broken-melange like cataclasite. A-few-meter-thick discrete damage zones with fault cores are recognized by difference in physical properties and visual deformation textures at several horizons in the fault zone. Host rocks for those damaged zones are completely lithified cataclasites with abundant mineral veins, which record the older and deeper deformation in the maximum depth >10km. Temperature difference between the hanging wall and footwall suggests the displacement along the Nobeoka thrust is >10km, which is almost similar to the mega-splay fault in the Nankai Trough. Geological and physical properties of the Nobeoka thrust suggest an evolving process of the seismogenic mega-splay fault associated with seismogenic up-thrust of the inner wedge of the accretionary prism.

Kimura, G.; Hamahashi, M.; Fukuchi, R.; Yamaguchi, A.; Kameda, J.; Kitamura, Y.; Hashimoto, Y.; Hamada, Y.; Saito, S.; Kawasaki, R.



A mega-splay fault system and tsunami hazard in the southern Ryukyu subduction zone (United States)

In April 1771, a subduction earthquake generated a great tsunami that struck the south Ryukyu islands and killed ˜12,000 people, whereas its mechanism is still enigmatic (Nakata and Kawana, 1995; Nakamura, 2006; Matsumoto et al., 2009). In this paper, we show its probable source on a mega-splay fault system existing along the southern Ryukyu forearc. Analyses of deep multi-channel seismic reflection profiles indicate that the mega-splay fault system is rising from the summit of a ˜1 km high ridge situated at a ˜5° landward dipping plate interface. An outer ridge marks the seafloor outcrop of the splay fault system and separates the landward inner wedge and the oceanward outer wedge. The inner wedge is uplifting and exhibits widespread normal faulting while the outer wedge shows folded structures. The mega-splay fault system is parallel to the Ryukyu Trench east of 125.5°E and is estimated to be ˜450 km long. The origin of this south Ryukyu mega-splay fault system is ascribed to a resistant subduction of the elevated transverse ridges associated with the subducting portion of the trench-parallel Luzon-Okinawa Fracture Zone. In contrast, no similar splay fault is found west of 125.5°E where the oblique subduction has produced large shear zones along the south Ryukyu forearc. We infer that a thrust earthquake linked to the mega-splay fault system is responsible for the south Ryukyu tsunami. However, another possible scenario of generating a large tsunami affecting the south Ryukyu islands is that the subducted ridge in the western end of the mega-splay fault system nucleated a large earthquake and simultaneously triggered the ˜100 km long E-W trending strike-slip fault west of 125.5°E and induced a southward-dipping tsunami-genic subsidence. In any case, after a quiescence of ˜241 yr, a large earthquake and tsunami is anticipated in the south Ryukyu forearc in the near future.

Hsu, Shu-Kun; Yeh, Yi-Ching; Sibuet, Jean-Claude; Doo, Wen-Bin; Tsai, Ching-Hui



Linear plasmids in plant mitochondria: peaceful coexistences or malicious invasions? (United States)

Plant mitochondria contain small extrachromosomal DNAs in addition to a large and complex main mitochondrial genome. These molecules can be regarded as extrachromosomal replicons or plasmids, of which there are two forms, circular and linear. Linear mitochondrial plasmids are present in many fungi and in some plants, but they seem to be absent from most animal cells. They usually have a common structural feature, called an invertron, that is characterized by the presence of terminal inverted repeats and proteins covalently attached to their 5 termini. Linear mitochondrial plasmids possess one to six ORFs that can encode unknown proteins but often code for the DNA and RNA polymerases. Although the functions of most linear plasmids in plant mitochondria are unknown, some plasmids may be associated with mitochondrial genome rearrangements and may have phenotypic effects due to their integration into mitochondrial genome. The Brassica 11.6-kb plasmid, one of the linear mitochondrial plasmids in plants, shows a non-maternal inheritance, in contrast to mitochondrial genomes. The origin of these plasmids is still a mystery, but indirect evidence indicates the possibility of horizontal transfer from fungal mitochondria. In this review, the main features of these unique DNAs present in plant mitochondria are described. PMID:18326073

Handa, Hirokazu



Competition favours reduced cost of plasmids to host bacteria. (United States)

Conjugative plasmids of Gram-negative bacteria have both vertical and horizontal modes of transmission: they are segregated to daughter cells during division, and transferred between hosts by plasmid-encoded conjugative machinery. Despite maintaining horizontal mobility, many plasmids carry fertility inhibition (fin) systems that repress their own conjugative transfer. To assess the ecological basis of self-transfer repression, we compared the invasion of bacterial populations by fin(+) and fin(-) variants of the plasmid R1 using a computational model and co-culture competitions. We observed that the fin(+) variant had a modest cost to the host (measured by reduction in growth rate), while the fin(-) variant incurred a larger cost. In simulations and empirical competitions the fin(-) plasmid invaded cultures quickly, but was subsequently displaced by the fin(+) plasmid. This indicated a competitive advantage to reducing horizontal transmission and allowing increased host replication. Computational simulations predicted that the advantage associated with reduced cost to the host would be maintained over a wide range of environmental conditions and plasmid costs. We infer that vertical transmission in concert with competitive exclusion favour decreased horizontal mobility of plasmids. Similar dynamics may exert evolutionary pressure on parasites, such as temperate bacteriophages and vertically transmitted animal viruses, to limit their rates of horizontal transfer. PMID:19340086

Haft, Rembrandt J F; Mittler, John E; Traxler, Beth




A series of thirty marine and estuarine bacterial isolates was examined for the ability to naturally transform with plasmid DNA. One isolate from Tampa Bay, Florida, identified as Vibrio parahaemolyticus, successfully incorporated and maintained the broad host range plasmid pKT23...


Plasmid-mediated UV-protection in Myxococcus xanthus  

International Nuclear Information System (INIS)

Plasmid R 46 was successfully transferred from Escherichia coli K-12 into Myxococcus xanthus strain MD-1 but not into M. xanthus strain XK. Plasmid R 68.45 was transferred from E. coli K-12 into both strains of M. xanthus. The effects of these plasmids on survival of M. xanthus after ultraviolet (UV) - 254 nm irradiation, the ability of M. xanthus to reactivate irradiated myxophages, and Weigle reactivation of UV-irradiated myxophages by M. xanthus were studied. Plasmid R 46 had no effect on UV survival of M. xanthus, but increased the host's ability to reactivate irradiated myxophages. Plasmid R 68.45 protected M. xanthus strains MD-1 and XK against the lethal effects of UV irradiation and also increased the host's ability to reactivate irradiated myxophages. (orig.)


Study of the performance of the MicroMegas chambers for the ATLAS muon spectrometer upgrade.  

CERN Document Server

MicroMegas (Micro MEsh Gaseous Structures) chambers and sTGC (small Thin Gap Chambers) have been chosen for the upgrade of the forward muon detectors of the ATLAS experiment to provide precision tracking and trigger capabilities. The MicroMegas chambers have been designed to allow operation in a high rate environment, to guarantee a resolution below 100 micron per point on a large area and to provide a fast trigger signal. In the last months several tests have been done on small area prototypes in order to verify that the requirements on resolution and rate capabilities are well matched. The results of the performance studies done on beams at CERN and of the ageing studies done at Saclay, are presented.

Bini, C; The ATLAS collaboration



The CFHT MegaCam filter, shutter and roll pitch mechanisms. (United States)

MegaCam is an imaging CCD camera with a 1 square degree field of view for the new MegaPrime prime focus of the 3.6 meter Canada-France-Hawaii Telescope. This CCD camera is fixed on an aluminum structure, called Camembert for its shape, housing a shutter, a filter system and a roll pitch system to tune the CCD mosaic plane. The shutter is made with 1 meter diameter honeycomb half disks that rotates to covers or exposes the CCD mosaic. On this shutter a calibration source is fixed to monitor the CCD and its electronics. The filter system is made of a jukebox with a capacity of eight 30 cm square filters and of a loading arm to place them under the field of view. The instrument was delivered to the CFHT observatory on June 10, 2002 and first light is scheduled in October 2002.

Aune, Stephan; Boulade, Olivier; Charlot, Xavier; Abbon, P.; Borgeaud, Pierre; Carton, Pierre-Henri; Carty, M.; Da Costa, J.; Desforge, D.; Deschamps, H.; Eppellé, Dominique; Gallais, Pascal; Gosset, L.; Granelli, Remy; Gros, Michel; de Kat, Jean; Loiseau, Denis; Ritou, J. L.; Roussé, Jean Y.; Starzynski, Pierre; Vignal, Nicolas; Vigroux, Laurent G.



Multilocus sequence typing of IncN plasmids  

DEFF Research Database (Denmark)

OBJECTIVES: Incompatibility group N (IncN) plasmids have been associated with the dissemination of antimicrobial resistance and are a major vehicle for the spread of blaVIM-1 in humans and blaCTX-M-1 in animals. A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids. METHODS: Twelve fully sequenced IncN plasmids available at GenBank were analysed in silico for selecting the loci for the IncN-specific pMLST. A total of 58 plasmids originating from different reservoirs (human, pig, poultry, cattle and horses) and geographic regions (Italy, Greece, Denmark, UK and The Netherlands) were classified by DNA sequencing of the amplicons obtained for the repA, traJ and korA loci. RESULTS: Eleven sequence types (STs) were defined on the basis of allele sequences of the three selected loci. Most plasmids carrying blaCTX-M-1 (24/27) isolated in different countries from both animals and humans belonged to ST1, suggesting dissemination of an epidemic plasmid through the food chain. Fifteen of 17 plasmids carrying blaVIM-1 from Klebsiella pneumoniae and Escherichia coli, isolated during a 5year period in Greece were assigned to ST10, suggesting that spread and persistence of this particular IncN-carrying blaVIM-1 lineage in Greece. CONCLUSIONS: This study proposes the use of pMLST as a suitable and rapid method for identification of IncN epidemic plasmid lineages. The recent spread of blaCTX-M-1 among humans and animals seems to be associated with the dissemination of an epidemic IncN plasmid lineage.

García-Fernández, Aurora; Villa, Laura



A Case with Mega Cisterna Magna Renal and Ear Anomalies: Is This a New Syndrome?  

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Background. Extrarenal pathologies may be associated with renal position and fusion anomalies. According to the literature, our patient is the first horseshoe kidney case that had mega cisterna magna, arachnodactyly, and mild mental retardation. Case Report. A 9-year-old boy admitted because of the myoclonic jerks. He had a dysmorphic face, low-set and cup-shaped ears, arachnodactyly, and mild mental retardation. The patient's laboratory findings were normal except for a mild leucocytosis and...

Çapan Konca; Bahar Caliskan; Mehmet Ali Tas




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This study aims at carrying out validity and reliability studies and the adaption of Turkish version of the scale titled “Mega Event Impact Scale” and developed by Jie ve Yan (2010). The scale, which consists of five-point Likert scale 42 items, was administered to the local audience following 2011 Erzurum 25. Winter Universiade. The subjects of the study were 412 people (55 % male and 45 % female), who were chosen through random sampling method. Explanatory factor analysis, applied to de...

Kerem Y?ld?r?m ?im?ek



Management of juxta articular giant cell tumors around the knee by custom mega prosthetic arthroplasty  

Directory of Open Access Journals (Sweden)

Full Text Available Background: Juxtaarticular giant cell tumors around the knee are common and pose a special problem of reconstruction after tumor excision. This article analyzes the functional outcome after resection of juxtaarticular giant cell tumors around the knee and replacement by custom mega prosthetic arthroplasty. Materials and Methods: One hundred and forty-three patients with juxtaarticular giant cell tumors around the knee with mean age of 30.8 years (range 15 to 64 years underwent resection and replacement by custom mega prosthetic arthroplasty during the period 1994 to 2005. Eighty-one patients were males and 62 were females. Fourteen patients were in Enneking Stage 2 while 129 patients were in Stage 3. Distal femur was involved in 87 patients and proximal tibia in 56 patients. Forty patients presented with pathological fracture at the time of diagnosis. The technique of sleeve resection of the quadriceps musculature was followed to achieve local clearance in distal femoral tumors, and for proximal tibial lesions resection of the tumor-bearing part and a medial gastronemius rotation flap was used routinely. The prosthesis used was a rotating hinge custom mega prosthesis manufactured locally. Results: The mean follow-up was 5.4 years (1.5 years to 11 years. Functional results were analyzed using Enneking criteria. Excellent results were obtained in 90 patients (62% and 39 patients had good (27% results. Periprosthetic fracture (8.3% and infection (6.9% were the most common complications followed by aseptic loosening (4.2%. Recurrence of lesion was found in only one patient (0.69% who was managed with wide local excision. Conclusion: Custom mega prosthetic arthroplasty is effective in achieving the desired goals of reconstruction with good functional results and least complications in selected patients.

Natarajan Mayil



Mini-MegaTORTORA — multichannel system for wide-field optical monitoring with high temporal resolution (United States)

We report on a multi-objective and transforming 9-channel monitoring system, the Mini-MegaTORTORA (MMT-9). This system combines a wide field of view with a subsecond temporal resolution in the monitoring regime, and is able to reconfigure itself, in fractions of a second, to a follow-up mode which has better sensitivity and provides us with multi-color and polarimetric information on detected transients simultaneously.

Sasyuk, V.; Beskin, G.; Karpov, S.; Bondar, S.; Perkov, A.; Ivanov, E.; Katkova, E.; Shearer, A.



[A review of the firefighting techniques used on the tanker 'Mega Borg' explosion  

International Nuclear Information System (INIS)

This paper reviews the events leading up to the explosion and fire of the Mega Borg, a Norwegian tanker which exploded in the Gulf of Mexico in June of 1990. It briefly discusses the fire fighting strategy used to cool the ship prior to foam application and the types of equipment used. It also briefly discusses the lightering operation and the cargo recovery and dewatering operations which took place after the fire was extinguished


Integrated bariatric surgery residency (United States)

Obesity is a major public health concern. Given its lasting efficacy for improving obesity and obesity-related diseases, bariatric surgery is an increasingly common treatment option. As the implementation of the Affordable Care Act progresses, the impending physician shortage will become more severe. Thus there will be an even greater need for doctors specialized in the management and treatment of obese patients. The development of integrated bariatric surgery residency programs could be considered and is discussed herein.

Eltorai, Adam EM



The MEGA BORG: The value of cooperative damage assessment to trustees, PRPs, and the environment  

International Nuclear Information System (INIS)

The Natural Resource Damage Assessment (NRDA) process provides natural resource trustees with a method for restoring publicly owned or managed natural resources and their services that are injured as a result of an oil or chemical release. The NRDA process is simple in concept, but provides significant challenges for natural resource trustees. Although the impacts of marine pollution have been studied for many years, the quantification, economic evaluation, and restoration of these impacts brings up controversial scientific, legal, and economic issues. The 1990 MEGA BORG spill in the Gulf of Mexico is an example of a cooperative assessment. Within a few days of the spill, the Texas Water Commission and the National Oceanic and Atmospheric Administration (NOAA) reached and agreement with the owners of the MEGA BORG under which the owners would fund a preliminary assessment of the environmental impact of the spill. Five projects were funded to determine whether there was sufficient injury to justify the completion of a natural resource damage assessment. The MEGA BORG provides an example of a cooperative and scientifically balanced approach to the initiation of damage assessment activities and illustrates the benefits of a cooperative assessment


Ultra Mega Power Projects: Additional Re-Structural Capacity to Existing Indian Grid System  

Directory of Open Access Journals (Sweden)

Full Text Available The demand for power in India is ever increasing, as industrial sector is one of the largest consumers of electrical energy in India. More and more efforts are made by the Government every year to overcome this problem. Ultra Mega Power projects (UMPP are a series of ambitious power projects planned by the Government of India. With India being a country of chronic power deficit, the Government of India has planned to provide 'power for all' by the end of the eleventh plan. This would entail a creation of an additional capacity of at least 100,000 MW. The Ultra Mega Power projects, each with a capacity of 4000 megawatts or above, are being developed with an aim to bridge this gap. The UMPPs are seen as an expansion of the MPP (Mega Power Projects projects that the Government of India undertook in the nineties but met with limited success. The Ministry of Power in association with Central Electricity Authority and Power Finance Corporation Ltd. has launched an initiative for development of coal-based UMPP's in India. These projects will be awarded to developers on the basis of competitive bidding.




Phage type conversion in Salmonella enterica serotype Enteritidis caused by the introduction of a resistance plasmid of incompatibility group X (IncX)  

DEFF Research Database (Denmark)

The plasmid pOG670, a 54 kb, conjugative plasmid that specifies resistance to ampicillin and kanamycin and belonging to the incompatibility group X (IncX), was transferred into 10 isolates of Salmonella enterica serotype Enteritidis belonging to 10 different phage types (PT1, 2, 3, 4, 8, 9, 9b, 10, 11 and 13). Acquisition of the plasmid by these strains did not result in the loss of any resident plasmids but resulted in phage type conversion in 8 of the 10 strains (PT1, 2, 4, 8, 9, 9b, 10 and 11). The observed changes in phage type were found to result from the loss of sensitivity to 3 of the 10 typing phages used (phages 3, 5 and 7). Where the conversion resulted in a change to a defined phage type, both the new and original PTs belonged to the same, previously described, evolutionary lines. Enteritidis PTs 1, 4 and 8, commonly associated with poultry world-wide, were converted to PTs 21, 6 and 13a respectively. The results indicate a different route for phage type conversion Enteritidis from others reportedin the literature and, although IncX plasmids are not normally present in PT8 or PT13a, may suggest a possible mechanism/link connecting these phage types.

Baggesen, Dorte Lau



Expected residence time model  

International Nuclear Information System (INIS)

The Transportation Technology Department of Sandia National Laboratories develops analytical and computational tools for the US Department of Energy to assess the radiological consequences and risks from the transportation of radioactive materials by all modes. When large quantities of materials are to be transported movements may occur over an extended period of time in what is collectively referred as a ''shipping campaign''. Since the routes over which the shipments occur often remain the same, cumulative exposure to individuals inhabiting the population zones adjacent to the transport links must be estimated. However, individuals do not remain in the same residences throughout their lifetimes and, in fact, move quite often. To appropriately allocate exposures among populations over extended periods of time, perhaps years, requires a model that accounts for three population categories; (1) the original populations residing in the areas adjacent to the transport links, (2) individuals moving out and (3) individuals moving into residences in the designated areas. The model described here accounts for these conditions and will be incorporated as a user option in the RADTRAN computer code for transportation consequence and risk analysis (Reference 1). RADTRAN is a computer code for estimating the consequences and risks associated with the transport of radioactive materials


Identificación de mega?ambientes para potenciar el uso de genotipos superiores de arroz en Panamá / Identifying mega?environments to enhance the use of superior rice genotypes in Panama  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Spanish Abstract in spanish El objetivo de este trabajo fue evaluar tres métodos para identificar mega?ambientes, para optimizar el uso del potencial genético de los cultivares de arroz, durante el proceso de selección, y para hacer recomendaciones sobre siembras comerciales en Panamá. Los datos experimentales fueron obtenidos [...] de los ensayos de productividad de cultivares precoces realizados entre 2006 y 2008. Para lograr la estratificación de los ambientes y definir los mega?ambientes, se utilizaron los métodos del genotipo vencedor mediante el modelo AMMI1, el modelo biplot GGE y el de conglomerado por el método de Ward, complementado con el biplot GGE. Los tres métodos utilizados identificaron dos mega?ambientes, donde los cultivares sobresalientes fueron Fedearroz 473 e Idiap 145?05. Hubo una coincidencia de 100% en el agrupamiento del conglomerado x el biplot GGE, mientras que entre conglomerado x AMMI1 y biplot GGE x AMMI1 fue de 95,2%. El genotipo más estable, en ambos mega?ambientes, fue el cultivar Idiap 145?05, lo que indica capacidad de adaptación amplia y específica. La capacidad adaptativa de los genotipos superiores y no las condiciones agroclimáticas de las localidades evaluadas fue responsable de la definición de los mega?ambientes. Abstract in english The objective of this work was to evaluate three methods to identify mega?environments, in order to optimize the use of the genetic potential of rice cultivars during the selection process and to make recommendations for commercial plantations in Panama. Experimental data were obtained from the test [...] performance, between 2006 and 2008, for early maturing cultivars. To achieve the stratification of environments and define mega?environments, the winner genotype method by the AMMI1 model, GGE biplot model and cluster by Ward's method supplemented by GGE biplot were used. The three methods used identified two mega?environments, where the outstanding cultivars were Fedearroz 473 e Idiap 145?05. There was 100% coincidence in the grouping of the cluster x the GGE biplot, with 95.2% coincidence between the AMMI1 x cluster and GGE biplot x AMMI1. The most stable genotype, in both mega?environments, was the Idiap?145?05 cultivar, which indicates its broad and specific adaptive capacity. The adaptive capacity of the superior genotypes and not the agroclimatic conditions of the assessed localities was responsible for defining the mega?environments.

Ismael, Camargo& #8209; Buitrago; Evelyn, Quirós& #8209; Mc Intire; Román, Gordón& #8209; Mendoza.



Challenges to publishing pharmacy resident research projects from the perspectives of residency program directors and residents (United States)

Objective To identify barriers to completing and publishing pharmacy residency research projects from the perspective of program directors and former residents. Methods This was a cross-sectional survey of pharmacy residency program directors and former post-graduate year one and two residents. Directors of pharmacy residency programs whose residents present their projects at the Western States Conference (n=216) were invited to complete an online survey and asked to forward the survey to former residents of their program in 2009, 2010, or 2011. The survey focused on four broad areas: 1) demographic characteristics of the residency programs, directors, and residents; 2) perceived value of the research project; 3) perceived barriers with various stages of research; and 4) self-identified barriers to successful research project completion and publication. Results A total of 32 program directors and 98 residents completed the survey. The minority of programs offered formal residency research training. Both groups reported value in the research project as part of residency training. Significantly more directors reported obtaining institutional review board approval and working through the publication process as barriers to the research project (46.7% vs. 22.6% and 73.3% vs. 43.0%, respectively p<0.05) while residents were more likely to report collecting and analyzing the data as barriers (34.4% vs. 13.3% and 39.8% vs. 20.0%, respectively, p<0.05). Both groups self-identified time constraints and limitations in study design or quality of the study as barriers. However, while program directors also indicated lack of resident motivation (65.5%), residents reported lack of mentorship or program structural issues (43.3%). Conclusions Overall, while both groups found value in the residency research projects, there were barriers identified by both groups. The results of this study may provide areas of opportunity for improving the quality and publication rates of resident research projects. PMID:24223082

Irwin, Adriane N.; Olson, Kari L.; Joline, Brigitte R.; Witt, Daniel M.; Patel, Rachana J.


Challenges to publishing pharmacy resident research projects from the perspectives of residency program directors and residents  

Directory of Open Access Journals (Sweden)

Full Text Available Objective: To identify barriers to completing and publishing pharmacy residency research projects from the perspective of program directors and former residents.Methods: This was a cross-sectional survey of pharmacy residency program directors and former post-graduate year one and two residents. Directors of pharmacy residency programs whose residents present their projects at the Western States Conference (n=216 were invited to complete an online survey and asked to forward the survey to former residents of their program in 2009, 2010, or 2011. The survey focused on four broad areas: 1 demographic characteristics of the residency programs, directors, and residents; 2 perceived value of the research project; 3 perceived barriers with various stages of research; and 4 self-identified barriers to successful research project completion and publication.Results: A total of 32 program directors and 98 residents completed the survey. The minority of programs offered formal residency research training. Both groups reported value in the research project as part of residency training. Significantly more directors reported obtaining institutional review board approval and working through the publication process as barriers to the research project (46.7% vs. 22.6% and 73.3% vs. 43.0%, respectively p<0.05 while residents were more likely to report collecting and analyzing the data as barriers (34.4% vs. 13.3% and 39.8% vs. 20.0%, respectively, p<0.05. Both groups self-identified time constraints and limitations in study design or quality of the study as barriers. However, while program directors also indicated lack of resident motivation (65.5%, residents reported lack of mentorship or program structural issues (43.3%. Conclusion: Overall, while both groups found value in the residency research projects, there were barriers identified by both groups. The results of this study may provide areas of opportunity for improving the quality and publication rates of resident research projects.

Olson KL



The Salmonella typhimurium virulence plasmid encodes a positive regulator of a plasmid-encoded virulence gene. (United States)

The 90-kb virulence plasmid of Salmonella typhimurium is necessary for invasion beyond the Peyer's patches to the mesenteric lymph nodes and spleens of orally inoculated mice. Two Tn5 insertions located on the left side of a previously identified 14-kb virulence region (P. A. Gulig and R. Curtiss III, Infect. Immun. 58:3262-3271, 1988) and mapping 272 bp from each other exhibited opposite effects on splenic infection of mice after oral inoculation. spvR23::Tn5 decreased splenic infection by 1,000-fold, whereas a spv-14::Tn5 mutant outcompeted wild-type S. typhimurium for splenic infection by 27-fold in mice fed mixtures of mutated and wild-type S. typhimurium. spvR23::Tn5 was complemented by a virulence plasmid subclone with an insert sequence encoding only an 891-bp open reading frame specifying a 33,000-molecular-weight protein. The amino acid sequence of this open reading frame had significant homology to members of the LysR family of positive regulatory proteins; thus, the gene was named spvR (salmonella plasmid virulence). To examine the possible regulatory effects of spvR on other virulence genes, we constructed a lacZ operon fusion in a downstream virulence gene, spvB. When spvR subcloned behind the lac promoter was provided on a separate plasmid in trans to the spvB-lacZ operon fusion, transcription of spvB increased 15-fold. spv-14::Tn5, which conferred a competitive advantage to S. typhimurium, increased the expression of a spvR-lacZ operon fusion in cis. spvR is therefore a positive regulator of spvB and an essential virulence gene of S. typhimurium. As opposed to having spvR subcloned behind the lac promoter, the wild-type spvR gene present on the virulence plasmid did not function to positively regulate spvB-lacZ in trans when salmonellae were grown to the log phase in L broth, suggesting that this regulatory system is activated in vivo during infection. PMID:1657882

Caldwell, A L; Gulig, P A



MegaNatural((R)) Gold Grapeseed Extract: In Vitro Antioxidant and In Vivo Human Supplementation Studies. (United States)

Epidemiological studies have produced solid evidence that consumption of fruits results in a reduction of cancer and cardiovascular disease. Red wine has been hypothesized to reduce the risk of heart disease as a result of its antioxidant, endothelial relaxation, and antiplatelet aggregation mechanisms. We investigated a commercial California wine grapeseed extract, MegaNatural((R)) Gold, and compared it to grapes, grape juice, red wine, other grapeseed extracts, and commercial extracts with respect to antioxidant activity, using an oxidation-reduction colorimetric assay. The quality of the antioxidants was determined with the use of an in vitro model of heart disease, a dose-response inhibition of low-density lipoprotein oxidation. MegaNatural((R)) Gold had a superior quantity/quality antioxidant index compared with all other samples tested. In nine subjects given 600 mg of MegaNatural((R)) Gold, the plasma antioxidant activity as measured by the RANDOX assay was significantly increased by 12% after both 1 and 2 hours. This was equivalent to drinking 300 ml of red wine or consuming 1,250 mg of vitamin C, as found in a previous study. We then determined the dose-response human plasma bioavailability of one of the polyphenols in MegaNatural((R)) Gold (epicatechin) in nine human subjects after giving 200 and 300 mg of the product. The in vivo antioxidant activity was also measured. The higher dose was much more effective. A long-term human supplementation study with 2 x 300 mg/day of MegaNatural((R)) Gold was then done on 17 (9 normal and 8 hypercholesterolemic) subjects. Plasma cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol concentrations were significantly decreased in the subjects with high cholesterol. Triglycerides were significantly increased in the high-cholesterol subjects but were still in the normal range after supplementation. Plasma antioxidant capacity was significantly improved in the high-cholesterol subjects. There was no change in plasma lipids or antioxidant capacity in the normal subjects. PMID:12639284

Vinson, Joe A.; Proch, John; Bose, Pratima



A socio-ecological adaptive approach to contaminated mega-site management: from 'control and correct' to 'coping with change'. (United States)

Mega-sites have a notable impact on surrounding ecological systems. At such sites there are substantial risks associated with complex socio-ecological interactions that are hard to characterize, let alone model and predict. While the urge to control and clean-up mega-sites (control and correct) is understandable, rather than setting a goal of cleaning up such sites, we suggest a more realistic response strategy is to address these massive and persistent sources of contamination by acknowledging their position as new features of the socio-ecological landscapes within which they are located. As it seems nearly impossible to clean up such sites, we argue for consideration of a 'coping with change' rather than a 'control and correct' approach. This strategy recognizes that the current management option for a mega-site, in light of its physical complexities and due to changing societal preferences, geochemical transformations, hydrogeology knowledge and remedial technology options may not remain optimal in future, and therefore needs to be continuously adapted, as community, ecology, technology and understanding change over time. This approach creates an opportunity to consider the relationship between a mega-site and its human and ecological environments in a different and more dynamic way. Our proposed approach relies on iterative adaptive management to incorporate mega-site management into the overall socio-ecological systems of the site's context. This approach effectively embeds mega-site management planning in a triple bottom line and environmental sustainability structure, rather than simply using single measures of success, such as contaminant-based guidelines. Recognizing that there is probably no best solution for managing a mega-site, we present a starting point for engaging constructively with this seemingly intractable issue. Therefore, we aim to initiate discussion about a new approach to mega-site management, in which the complexity of the problems posed by mega-sites is reflected upon in its entirety. These complexities are associated with uncertainties and unknowns that have to be addressed, as they have an impact on the strategies being developed and applied. We contend that the best that can be hoped for in mega-site management is an acceptable solution for the current state of affairs, with good flexibility to modify strategies as new site conditions, remediation possibilities, community preferences and management objectives develop over time. PMID:21890232

Schirmer, Mario; Lyon, Ken; Armstrong, James E; Farrell, Katharine N



A socio-ecological adaptive approach to contaminated mega-site management: From 'control and correct' to 'coping with change' (United States)

Mega-sites have a notable impact on surrounding ecological systems. At such sites there are substantial risks associated with complex socio-ecological interactions that are hard to characterize, let alone model and predict. While the urge to control and clean-up mega-sites (control and correct) is understandable, rather than setting a goal of cleaning up such sites, we suggest a more realistic response strategy is to address these massive and persistent sources of contamination by acknowledging their position as new features of the socio-ecological landscapes within which they are located. As it seems nearly impossible to clean up such sites, we argue for consideration of a 'coping with change' rather than a 'control and correct' approach. This strategy recognizes that the current management option for a mega-site, in light of its physical complexities and due to changing societal preferences, geochemical transformations, hydrogeology knowledge and remedial technology options may not remain optimal in future, and therefore needs to be continuously adapted, as community, ecology, technology and understanding change over time. This approach creates an opportunity to consider the relationship between a mega-site and its human and ecological environments in a different and more dynamic way. Our proposed approach relies on iterative adaptive management to incorporate mega-site management into the overall socio-ecological systems of the site's context. This approach effectively embeds mega-site management planning in a triple bottom line and environmental sustainability structure, rather than simply using single measures of success, such as contaminant-based guidelines. Recognizing that there is probably no best solution for managing a mega-site, we present a starting point for engaging constructively with this seemingly intractable issue. Therefore, we aim to initiate discussion about a new approach to mega-site management, in which the complexity of the problems posed by mega-sites is reflected upon in its entirety. These complexities are associated with uncertainties and unknowns that have to be addressed, as they have an impact on the strategies being developed and applied. We contend that the best that can be hoped for in mega-site management is an acceptable solution for the current state of affairs, with good flexibility to modify strategies as new site conditions, remediation possibilities, community preferences and management objectives develop over time.

Schirmer, Mario; Lyon, Ken; Armstrong, James E.; Farrell, Katharine N.



Plasmid-associated sensitivity of Bacillus thuringiensis to UV light  

International Nuclear Information System (INIS)

Spores and vegetative cells of Bacillus thuringiensis were more sensitive to UV light than were spores or cells of plasmid-cured B. thuringiensis strains or of the closely related Bacillus cereus. Introduction of B. thuringiensis plasmids into B. cereus by cell mating increased the UV sensitivity of the cells and spores. Protoxins encoded by one or more B. thuringiensis plasmids were not involved in spore sensitivity, since a B. thuringiensis strain conditional for protoxin accumulation was equally sensitive at the permissive and nonpermissive temperatures. In addition, introduction of either a cloned protoxin gene, the cloning vector, or another plasmid not containing a protoxin gene into a plasmid-cured strain of B. thuringiensis all increased the UV sensitivity of the spores. Although the variety of small, acid-soluble proteins was the same in the spores of all strains examined, the quantity of dipicolinic acid was about twice as high in the plasmid-containing strains, and this may account for the differences in UV sensitivity of the spores. The cells of some strains harboring only B. thuringiensis plasmids were much more sensitive than cells of any of the other strains, and the differences were much greater than observed with spores


Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum. (United States)

Lateral transfer of bacterial plasmids is thought to play an important role in microbial evolution and population dynamics. However, this assumption is based primarily on investigations of medically or agriculturally important bacterial species. To explore the role of lateral transfer in the evolution of bacterial systems not under intensive, human-mediated selection, we examined the association of genotypes at plasmid-encoded and chromosomal loci of native Rhizobium, the nitrogen-fixing symbiont of legumes. To this end, Rhizobium leguminosarum strains nodulating sympatric species of native Trifolium were characterized genetically at plasmid-encoded symbiotic (sym) regions (nodulation AB and nodulation CIJT loci) and a repeated chromosomal locus not involved in the symbiosis with legumes. Restriction fragment length polymorphism analysis was used to distinguish genetic groups at plasmid and chromosomal loci. The correlation between major sym and chromosomal genotypes and the distribution of genotypes across host plant species and sampling location were determined using chi2 analysis. In contrast to findings of previous studies, a strict association existed between major sym plasmid and chromosomal genetic groups, suggesting a lack of successful sym plasmid transfer between major Rhizobium chromosomal types. These data indicate that previous observations of sym plasmid transfer in agricultural settings may seriously overestimate the rates of successful conjugation in systems not impacted by human activities. In addition, a nonrandom distribution of Rhizobium genotypes across host plant species and sampling site demonstrates the importance of both factors in shaping Rhizobium population dynamics. PMID:9144264

Wernegreen, J J; Harding, E E; Riley, M A



Antibiotic resistance plasmids of Staphylococcus aureus and their clinical importance  

International Nuclear Information System (INIS)

A variety of plasmids were isolated physically, and most antibiotic resistance is thought to be plasmid mediated. A number of characters (e.g., resistance to erythromycin or methicillin, and production of pigment) are determined by genes that do not give clear indications of either plasmid or chromosomal location. Although the formation of a particular plasmid is probably, even in bacterial terms, a very rare event, once formed such an element can spread rapidly among the bacterial population. The spectacular increase in the incidence of penicillinase-producing hospital strains in the late 1940's could have been due in part to this process. Evidence is stronger, however, for the intercell transfer of recently isolated plasmids coding for resistance to fusidic acid (and penicillinase production), or for neomycin, or for tetracycline resistance. Study of bacterial plasmids can resolve fundamental biochemical problems, and give some insight into the life of the cell at the molecular level. But the immediate application of the study of staphylococcal plasmids may be directed towards improving the effectiveness of antibiotic therapy. The most important aspect of future anti-staphylococcal chemotherapy should thus be the limitation of the use of antibiotics, particularly for application to the skin and nose. (U.S.)


Establishment of a replicating plasmid in Rickettsia prowazekii. (United States)

Rickettsia prowazekii, the causative agent of epidemic typhus, grows only within the cytosol of eukaryotic host cells. This obligate intracellular lifestyle has restricted the genetic analysis of this pathogen and critical tools, such as replicating plasmid vectors, have not been developed for this species. Although replicating plasmids have not been reported in R. prowazekii, the existence of well-characterized plasmids in several less pathogenic rickettsial species provides an opportunity to expand the genetic systems available for the study of this human pathogen. Competent R. prowazekii were transformed with pRAM18dRGA, a 10.3 kb vector derived from pRAM18 of R. amblyommii. A plasmid-containing population of R. prowazekii was obtained following growth under antibiotic selection, and the rickettsial plasmid was maintained extrachromosomally throughout multiple passages. The transformant population exhibited a generation time comparable to that of the wild type strain with a copy number of approximately 1 plasmid per rickettsia. These results demonstrate for the first time that a plasmid can be maintained in R. prowazekii, providing an important genetic tool for the study of this obligate intracellular pathogen. PMID:22529927

Wood, David O; Hines, Andria; Tucker, Aimee M; Woodard, Andrew; Driskell, Lonnie O; Burkhardt, Nicole Y; Kurtti, Timothy J; Baldridge, Gerald D; Munderloh, Ulrike G



Molecular characterization of Chlamydia trachomatis and Chlamydia psittaci plasmids. (United States)

Plasmids from Chlamydia trachomatis LGV-434 (serotype L2) and Chlamydia psittaci meningopneumonitis strain Cal-10 were cloned into the BamHI and EcoRI sites of pBR322, respectively. The recombinant plasmids pCTL2 and pCPMn, each containing an entire respective chlamydial plasmid, were transformed into Escherichia coli. The sizes of the plasmids of C. trachomatis and C. psittaci were 7.3 and 6.2 kilobases, respectively. The two plasmids were found to be distinct by restriction endonuclease analysis, DNA-DNA hybridization, and electron microscopic heteroduplex analysis. However, partial homology was observed between restriction fragments of pCTL2 and pCPMn by Southern blot analysis. Polypeptide products encoded by these plasmids were synthesized in vitro by an E. coli-directed transcription-translation system and in vivo in E. coli maxicells and minicells. None of these polypeptides was immunoreactive with anti-chlamydial sera by immunoblotting or immunoprecipitation. Based on the comparative analysis data, the C. trachomatis and C. psittaci plasmids were found to share little genetic relatedness. Images PMID:3943908

Joseph, T; Nano, F E; Garon, C F; Caldwell, H D



Regulation of replication and maintenance functions of broad host-range plasmid RK2. (United States)

Replication of broad host-range plasmid RK2 depends on a cisacting vegatative replication origin oriVRK2 and the polypeptide product(s) of the trans-acting gene trfA as well as on host-specified products. The trfA gene is the second cistron in a polycistronic unit whose first cistron may be kilD, one of 4 known RK2-specified kil loci (kilA, B, C, and D) which are inhibitory for bacterial host or plasmid vector in the absence of kor functions which suppress in trans the effect of their respective kil genes. Transcription of the operon containing trfA is negatively regulated by the products of both the trfB locus (alias korD and korA) and korB. The loci, trfB and korB, are expressed from a single transcriptional unit which we propose to be negatively autoregulated by the products of both loci, although an additional, weaker and unregulated transcript may also express korB. While deletions in the oriVRK2 region have indicated the presence of copy number control elements adjacent to and possibly overlapping with the minimal oriVRK2 segment, the overriding control of copy number seems to reside in the trfB and korB loci which in conjunction appear to reduce expression of the trfA gene to levels limiting for replication. Coregulation of trfA with kil genes may indicate that kil genes play a role in plasmid maintenance other than replication. PMID:2990413

Thomas, C M; Smith, C A; Shingler, V; Cross, M A; Hussain, A A; Pinkney, M



Structural Organization of Virulence-Associated Plasmids of Yersinia pestis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The complete nucleotide sequence and gene organization of the three virulence plasmids from Yersinia pestis KIM5 were determined. Plasmid pPCP1 (9,610 bp) has a GC content of 45.3% and encodes two previously known virulence factors, an associated protein, and a single copy of IS100. Plasmid pCD1 (70,504 bp) has a GC content of 44.8%. It is known to encode a number of essential virulence determinants, regulatory functions, and a multiprotein secretory system comprising the low-calcium response...

Hu, Ping; Elliott, Jeffrey; Mccready, Paula; Skowronski, Evan; Garnes, Jeffrey; Kobayashi, Arthur; Brubaker, Robert R.; Garcia, Emilio



Isolation and characterization of two plasmids from Bifidobacterium longum. (United States)

In order to develop a cloning vector system which can be used in Bifidobacterium sp., we screened about 100 bifidobacteria from the faeces of adults and children. Among them, only one strain, identified as B. longum KJ, was shown to contain extrachromosomal DNAs. Bifidobacterium longum KJ showed multiple plasmid DNA bands which were resolved to be multimers of two plasmids designated pKJ36 and pKJ50. These plasmids were cloned into the Escherichia coli vector pUC19 as pMS36 and pMS50, respectively, and restriction-mapped. PMID:9248072

Park, M S; Lee, K H; Ji, G E



Plasmid genes required for microcin B17 production.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The production of the antibiotic substance microcin B17 (Mcc) is determined by a 3.5-kilobase DNA fragment from plasmid pMccB17. Several Mcc- mutations on plasmid pMccB17 were obtained by both transposon insertion and nitrosoguanidine mutagenesis. Plasmids carrying these mutations were tested for their ability to complement Mcc- insertion or deletion mutations on pMM102 (pMM102 is a pBR322 derivative carrying the region encoding microcin B17). Results from these experiments indicate that at l...

San Milla?n, J. L.; Kolter, R.; Moreno, F.



Control of the ccd operon in plasmid F.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The F sex factor plasmid of Escherichia coli contains a pair of genes, ccdA and ccdB, whose protein gene products are involved in an unusual feature of plasmid maintenance. The CcdB protein is a cytotoxin that becomes activated when the F plasmid is lost, thereby killing the F- segregant cells. In F+ cells, the CcdA protein protects against the lethal effects of CcdB. In the present study we show that ccdA and ccdB expressions are negatively autoregulated at the level of transcription. Geneti...

Tam, J. E.; Kline, B. C.



Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids. (United States)

Conjugative plasmids are typically locked in intergenomic and sexual conflicts with co-resident rivals, whose translocation they block using fertility inhibition factors (FINs). We describe here the first crystal structure of an enigmatic FIN Osa deployed by the proteobacterial plasmid pSa. Osa contains a catalytically active version of the ParB/Sulfiredoxin fold with both ATPase and DNase activity, the latter being regulated by an ATP-dependent switch. Using the Agrobacterium tumefaciens VirB/D4 type IV secretion system (T4SS), a relative of the conjugative T4SS, we demonstrate that catalytically active Osa blocks T-DNA transfer into plants. With a partially reconstituted T4SS in vitro, we show that Osa degrades T-DNA in the T-DNA-VirD2 complex before its translocation. Further, we present evidence for conservation and interplay between ATPase and DNase activities throughout the ParB/Sulfiredoxin fold, using other members of the family, namely P1 ParB and RK2 KorB, which have general functional implications across diverse biological contexts. PMID:25358815

Maindola, Priyank; Raina, Rahul; Goyal, Parveen; Atmakuri, Krishnamohan; Ojha, Abhishek; Gupta, Sourabh; Christie, Peter J; Iyer, Lakshminarayan M; Aravind, L; Arockiasamy, Arulandu



Resident Peritoneal NK cells  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Here we describe a new population of NK cells that reside in the normal, un-inflamed peritoneal cavity. Phenotypically, they share some similarities with the small population of CD49b negative, CD27 positive immature splenic NK cells, and liver NK cells but differ in their expression of CD62L, TRAIL and EOMES. Functionally, the peritoneal NK cells resemble the immature splenic NK cells in their production of IFN-?, GM-CSF and TNF-? and in the killing of YAC-1 target cells. We also found tha...

Gonzaga, Rosemary; Matzinger, Polly; Perez-diez, Ainhoa



Bacterial Mitosis: ParM of Plasmid R1 Moves Plasmid DNA by an Actin-like Insertional Polymerization Mechanism  

DEFF Research Database (Denmark)

Bacterial DNA segregation takes place in an active and ordered fashion. In the case of Escherichia coli plasmid R1, the partitioning system (par) separates paired plasmid copies and moves them to opposite cell poles. Here we address the mechanism by which the three components of the R1 par system act together to generate the force required for plasmid movement during segregation. ParR protein binds cooperatively to the centromeric parC DNA region, thereby forming a complex that interacts with the filament-forming actin-like ParM protein in an ATP-dependent manner, suggesting that plasmid movement is powered by insertional polymerization of ParM. Consistently, we find that segregating plasmids are positioned at the ends of extending ParM filaments. Thus, the process of R1 plasmid segregation in E. coli appears to be mechanistically analogous to the actin-based motility operating in eukaryotic cells. In addition, we find evidence suggesting that plasmid pairing is required for ParM polymerization. Udgivelsesdato: Dec 2003

MØller-Jensen, Jakob; Borch, Jonas



Location of plasmid-mediated citrate utilization determinant in R27 and incidence in other H incompatibility group plasmids. (United States)

Citrate utilization (Cit+) is encoded by a specific subgroup of incompatibility HI plasmids, viz., IncHI1 plasmids. Only one IncHI1 plasmid, pRG1271, which originated in a Mexican typhoid outbreak in 1972, did not specify Cit+. All other Cit+ plasmids hybridized to a Cit+ probe, a 2-kilobase BglII fragment derived from the Cit+ transposon Tn3411. The position of the Cit+ determinant was mapped to a 13.5-kilobase ApaI fragment within the prototype IncHI1 plasmid R27. No other functions have been mapped within this region. Citrate utilization mediated by IncHI1 was observed only after a prolonged lag period of approximately 150 h, and certain Escherichia coli strains, e.g., E. coli K-12 J53-1, were not able to utilize citrate specified by the H plasmids. Most E. coli strains harboring the multicopy Cit+ plasmid pOH2, a derivative of pBR322, required only 18 to 24 h to express the Cit+ phenotype, but E. coli J53-1 (pOH2) required at least 72 h for expression. PMID:3024564

Taylor, D E; Brose, E C



Resident and faculty perceptions of a surgical residency program merger. (United States)

To evaluate resident and faculty perceptions of a residency merger process.Survey of faculty and residents of a recently merged general surgical residency. Nineteen separate program characteristics were evaluated via a numerical scoring system, and additional written commentary regarding dominant perceived benefits and detriments of the merger was solicited. Statistical significance was evaluated on numerically scored items by applying the Mann-Whitney U test to median values expressed with interquartile ranges, comparing resident and faculty responses.Scoring system responses from faculty and residents were generally similar. The merger was seen as neutral to positive in its impact on academic issues, but it had more negative effects on issues related to overall program atmosphere and morale. Statistically significant differences between resident and faculty responses were noted in 2 areas: teaching conference timing and overall program effectiveness in preparing for practice. Both of these areas were more favorably impacted by the merger from the residents' perspective, and more negatively as judged by the faculty (p < 0.05). Written commentary by both groups similarly emphasized areas of academic strengthening as a positive effect of the merger, and relationship and morale issues as being more negatively impacted.As reflected by resident and faculty perceptions, program mergers may provide opportunities to strengthen and enhance the academic and clinical foundation of residency. This may, however, occur at the expense of morale and relational issues, which may be negatively impacted by program administrative and geographic expansion. PMID:11275250

Mellinger, J; Bonnell, B; Passinault, W; Wilcox, R; Vanderkolk, W; Baker, R; Davis, A; Brasser, B



Genetic and molecular characterization of pR351 plasmid from enteropathogenic Escherichia coli strain. (United States)

A pR351 plasmid (Tc Ap Cb) conferring drug resistance of naturally occurring E. coli strain was examined. Conjugation and transduction experiments have indicated that this plasmid is R plasmid aggregate consisting of three independent plasmids: a) conjugative plasmid pR351 A (SuTc) fi- (F) belonging to incompatibility group L, b) conjugative plasmid pR351 B (SuApCb) fi- (F) belonging to incompatibility O, and c) non-conjugative plasmid pR351 C (ApCb). The existance of these plasmids in pR351 plasmid aggregate was confirmed by the agarose gel analysis of plasmid DNA isolated from the lysates of E. coli J53 transconjugants carrying pR351 A or pR351 B plasmids and from E. coli K12 C600 transductant carrying pR351 C plasmid. Molecular mass of these plasmids was found to be 55.60 and 3 Mdal respectively. The non-conjugative pR351 C plasmid could be mobilized by Col B and F factors. Our findings have indicated that two fi- (F) R plasmids can stably coexist in R plasmid aggregate. PMID:2695005

Czarny, A; Lagowska-Z?otorzycka, M; Mulczyk, M



Natural plasmid transformation in a high-frequency-of transformation marine Vibrio strain  

International Nuclear Information System (INIS)

-9 was the result of uptake and expression of plasmid DNA by a competent mutant (HfT strain). Additionally, it was found that a strain of Vibrio parahaemolyticus, USFS 3420, could be naturally transformed with plasmid DNA. Natural plasmid transformation by high-transforming mutants may be a means of plasmid acquisition by natural aquatic bacterial populations


A circular plasmid from the yeast Torulaspora delbrueckii. (United States)

A new member of the 2-micron family of plasmids, named pTD1, was found in the yeast Torulaspora delbrueckii, a widespread yeast associated with food. Nucleotide sequences revealed the presence of a pair of inverted repeats and three open reading frames, one of which is a homologue of the FLP recombinase gene of 2-micron plasmid. An ARS region was identified, by replication in Saccharomyces cerevisiae and T. delbrueckii, near one of the inverted repeats. By the use of pTD1 derivatives and auxotrophic mutant hosts an efficient host-vector system was established for T. delbrueckii. So far, the 2-micron family of plasmids is restricted to four closely related genera (Q6 group): Saccharomyces, Zygosaccharomyces, Kluyveromyces, and Torulaspora. After a survey of 2500 strains belonging to about 500 species (80 genera) of yeast, no circular plasmids were found in other genera. PMID:9435022

Blaisonneau, J; Sor, F; Cheret, G; Yarrow, D; Fukuhara, H



Effect of detergents on pathogenicity plasmids of escherichias. (United States)

The study dealth with effects of cationic detergents miramistin (alkylamidopropyldimethylbenzylammonium chloride), catamine AB (alkyldimethylbenzylammonium chloride) and the anionic compound sodium dodecyl sulphate (SDS) on the elimination from E. coli cells of plasmids determining the Hly, Ent and, indirectly, Col, F, and R markers of pathogenicity as well as their transfer upon conjugation. At subbacteriostatic concentrations, miramistin and catamine AB were found to suppress the transfer of Hly, Ent, F, and R plasmids during conjugation when applied to the donor, recipient or added to the conjugation medium without, however, eliminating plasmids. This is due to the disruption by detergents of F, J pili and other surface cell structures resulting in diminished ability to conjugate. Anionic SDS eliminated F and R plasmids without affecting Hly, Ent and Col. PMID:3058793

Krivoshein YuS; Achkasova YuN; Bryzgunova, N I; Sarachan, T A; Myshak, V I; Miloserdova, N A



Modelling the spatial dynamics of plasmid transfer and persistence. (United States)

Bacterial plasmids are extra-chromosomal genetic elements that code for a wide variety of phenotypes in their bacterial hosts and are maintained in bacterial communities through both vertical and horizontal transfer. Current mathematical models of plasmid-bacteria dynamics, based almost exclusively on mass-action differential equations that describe these interactions in completely mixed environments, fail to adequately explain phenomena such as the long-term persistence of plasmids in natural and clinical bacterial communities. This failure is, at least in part, due to the absence of any spatial structure in these models, whereas most bacterial populations are spatially structured in microcolonies and biofilms. To help bridge the gap between theoretical predictions and observed patterns of plasmid spread and persistence, an individual-based lattice model (interacting particle system) that provides a predictive framework for understanding the dynamics of plasmid-bacteria interactions in spatially structured populations is presented here. To assess the accuracy and flexibility of the model, a series of experiments that monitored plasmid loss and horizontal transfer of the IncP-1beta plasmid pB10 : : rfp in Escherichia coli K12 and other bacterial populations grown on agar surfaces were performed. The model-based visual patterns of plasmid loss and spread, as well as quantitative predictions of the effects of different initial parental strain densities and incubation time on densities of transconjugants formed on a 2D grid, were in agreement with this and previously published empirical data. These results include features of spatially structured populations that are not predicted by mass-action differential equation models. PMID:17660444

Krone, Stephen M; Lu, Ruinan; Fox, Randal; Suzuki, Haruo; Top, Eva M



Pyrosequencing of the Vir plasmid of necrotoxigenic Escherichia coli. (United States)

Necrotoxigenic Escherichia coli, or NTEC, are defined as E. coli producing the toxin known as cytotoxic necrotizing factor, or CNF. NTEC are responsible for various diseases of humans and animals, including urinary tract infection, septicemia, and diarrhea. A subgroup of NTEC known as NTEC-2 produce a variant of CNF (CNF-2) whose gene is located on a plasmid known as Vir. Because of its involvement in NTEC-2 pathogenesis and its broad distribution among production animals, a Vir plasmid from a bovine NTEC-2 strain was sequenced and analyzed. This plasmid was found to belong to the RepFIB and RepFIIA replicon types, and it totaled 138,682 base pairs in size. Within this plasmid was an approximately 60-kb pathogenicity island, defined by its possession of multiple virulence factors within distinct genetic regions of lower G+C content bounded by inverted repeats. Within this PAI were a variety of putative virulence factors, including F17b fimbrial genes, genes of a novel fimbrial operon, tibAC, hemolysins, and the cnf2 and cdt toxin-encoding genes. The occurrence of this plasmid's virulence- and replication-associated genes was sought among a collection of 96 CNF-2-positive isolates. The most prevalent genes among this collection included repA (RepFIB), cnf2, an ompP homolog, and the tib-AC genes encoding for aggregation and biofilm formation. The Vir plasmid has evolved from an IncFIB ancestral backbone, with the RepFIB locus apparently driving the acquisition of its accessory virulence-associated elements via site-specific recombination. Overall, the completed sequence of a Vir plasmid increases our understanding of NTEC-2 pathogenomics and IncFIB plasmid evolution. PMID:20060660

Johnson, Timothy J; DebRoy, Chitrita; Belton, Shayla; Williams, Michele L; Lawrence, Mark; Nolan, Lisa K; Thorsness, Jessica L



Plasmid Accumulation Reduces Life Span in Saccharomyces cerevisiae*  

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Aging in the yeast Saccharomyces cerevisiae is under the control of multiple pathways. The production and accumulation of extrachromosomal rDNA circles (ERCs) is one pathway that has been proposed to bring about aging in yeast. To test this proposal, we have developed a plasmid-based model system to study the role of DNA episomes in reduction of yeast life span. Recombinant plasmids containing different replication origins, cis-acting partitioning elements, and selectable marker genes were co...

Falco?n, Alaric A.; Aris, John P.



Isolation and properties of plasmids from Deinococcus radiodurans Sark  

International Nuclear Information System (INIS)

Radioresistant bacterium, Deinococcus radiodurans, can repair completely almost all of DNA damages including double strand breaks induced by gamma-rays up to about 5 kGy. In order to reveal the repair mechanism, it is necessary to develop a cloning vector available for the genetic analysis. We tried to isolate plasmids from D.radiodurans Sark strain. In the present paper the isolation and properties of plasmids were described. (author)


Sport mega-events: can legacies and development be equitable and sustainable? / Mega-eventos esportivos: podem desenvolvimento e legado ser equalitários e sustentáveis? / Sport mega-eventos: pueden ser legados y el desarrollo equitativo y sostenible?  

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Full Text Available SciELO Brazil | Language: English Abstract in portuguese Os mega-eventos esportivos (MEE) envolvem lutas para se determinar a definição de legado e as prioridades que guiam os processos de planejamento, financiamento e processos de implementação de resultados. A história mostra que os legados refletem os interesses do capital, e os benefícios são usufruid [...] os principalmente, se não exclusivamente, por interesses empresariais poderosos, por alguns líderes políticos e por organizações que governam o esporte de alto rendimento. Este artigo aborda os desafios enfrentados pelas cidades e países que hospedam MEE e demonstra que legados justos e equalitários e resultados em termos de desenvolvimento são alcançados somente quando as vozes e os interesses da população em geral são ouvidos e considerados como prioridade durante o processo de planejamento, financiamento e implementação. Ele também demonstra que a representação plena no processo de definição e prossecução de legados e a consecução de resultados em termos de desenvolvimento podem ser prejudicados por crenças populares sobre o poder do esporte. Abstract in spanish Los mega-eventos deportivos (DME) implican luchas para determinar la definición del legado y las prioridades que guían los procesos de planificación, financiación financiamiento y ejecución de los resultados. La historia muestra que los legados reflejan los intereses del capital y que los beneficios [...] son disfrutados principalmente, si no exclusivamente por los intereses empresariales poderosos, por algunos líderes políticos y por las organizaciones que dirigen los deportes de alto rendimiento. Este artículo aborda los desafíos que enfrentan las ciudades y los países anfitriones de los DME, y demuestra que legados justos y equitativos y resultados en sentido de desarrollo se logran solamente cuando se considera y se da prioridad a las voces e intereses de la población en general durante el proceso de planificación, financiamiento e implementación. Él también demuestra que la representación plena en el proceso de definición y consecución de los legados y los resultados en sentido de desarrollo pueden ser socavadas por las creencias populares sobre el poder del deporte. Abstract in english Sport mega-events (SMEs) involve struggles to determine the definition of legacy and the outcome priorities that guide legacy planning, funding, and implementation processes. History shows that legacies reflect the interests of capital, and legacy benefits are enjoyed primarily, if not exclusively, [...] by powerful business interests, a few political leaders, and organizations that govern high performance sports. This paper addresses challenges faced by cities and countries that host SMEs, and shows that fair and equitable legacies and developmental outcomes are achieved only when the voices and interests of the general population are taken into account and given priority during the process of planning, funding and implementation. It also explains how full representation in the process of defining and achieving legacies and developmental outcomes may be undermined by populist beliefs about the power of sport.

Jay, Coakley; Doralice Lange, Souza.



The characteristics of micrococcus (deinococcus) radiodurans sark plasmids  

International Nuclear Information System (INIS)

The characterization of micrococcus (deinococcus) radiodurans sark plasmids. This bacterium has been classified as a new genus deinococcus radiodurans which is resistant to gamma-rays. It can repair itself completely almost all of DNA damages including double strand breaks induced by gamma-rays up to about 5 KGy. To reveal the repair mechanism, several investigations had been done to develop a cloning vector available for the genetic analysis. For this purpose D. radiodurans Sark are to be prepared as a vector by studying the characteristics of its plasmid. Plasmids were isolated by electrophoresis using 0.6% low-melting-temperature agarose in TAE and run for 5.5 hours, followed by the identification. An antibiotic marker was also carried out in this experiment to identify its location in the genetic materials of the cell, beside making a restriction map of the plasmid. Results have shown that D. radiodurans Sark has 4 plasmids (P1, P2, P3, and P4) and the refampicin resistant genes were not found in the plasmid. (authors). 14 refs; 4 figs


Plasmid vector with temperature-controlled gene expression  

International Nuclear Information System (INIS)

In plasmid pBR327, a fragment 169 b.p. long including promotor p3 of the bla gene has been deleted. The deletional derivative so obtained (pSP2) has been used to construct a recombinant plasmid bearing a fragment of phage ? DNA with the p/sub R/ promotor and the gene of the temperature-sensitive repressor cI. It has been shown that the plasmid vector so constructed (pCE119) with promotor cR performs repressor-cI-controlled transcription of the bla gene, as a result of which induction for an hour at 420C leads to an almost 100-fold increase in the amount of product of the bla gene as compared with that at 320C. The possibility of the use of plasmid cPE119 for the expression of other genes has been demonstrated for the case of the semisynthetic ?-galactosidase gene of E. coli. In this case, on induction of the cells with recombinant plasmid pCEZ12 for 3 hours at 420C, a 300-fold increase in the amount of active ?-galactosidase, as compared with that at 320C, was observed. It is important to point out that under these conditions (at 420C), at least 99% of the cells containing the plasmid retain the phenotype lacZ+, which indicates the stability of the proposed vector system


Plasmid Stability in PHA-Producing Recombinant Escherichia coli Strains  

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Full Text Available Polyhydroxyalcanoates (PHAs are biodegradable polyesters synthesized by numerous prokaryotic organisms from renewable carbon sources. In this study, the stability of three plasmids (pBHR68, pBHR71 and pBHR77, containing the PHA biosynthesis genes from Ralstonia eutropha and Pseudomonas aeruginosa, was investigated in recombinant E. coli JM101 and DH10B cultures performed at 37°C for 96 h. After 72 h of cultivation, cell growth was resumed due to ampicillin depletion, which allowed the recovery of plasmid-free cells. All plasmids showed almost 100% stability for the first 24 h and up to 30-35 generations. The most stable culture, E. coli strain JM101 harboring the plasmid pBHR68, achieved 50% after 110 generations of growth, while, a similar reduction was observed in the other cultures within 60-80 generations. The best performance of the JM101 strain cultures concerning plasmid stability can be attributed to its best adaptability to the environmental conditions and stability of plasmid-host system.

Gustavo Graciano Fonseca



The role of mega dams in reducing sediment fluxes: A case study of large Asian rivers (United States)

SummaryIn order to sustain the ever growing population and to meet water and energy requirements of the rapidly growing economies, most of the large rivers draining through East, Southern and Southeast (ESSE) Asian region have been regulated all along their courses, over the past few decades. For instance, ESSE Asian countries (China, Taiwan, Vietnam, Myanmar, Thailand, India, Pakistan and Bangladesh) host about 250 mega dams and several tens of thousands of large and small reservoirs. The present study provides a revised estimate on annual suspended sediment fluxes of the large rivers draining through ESSE region, including the latest data of the Indian peninsula rivers. In the last 50 years, the combined annual sediment flux of the large Chinese rivers has been reduced from 1800 million tons (Mt) to about 370 Mt. We estimate that at present the Indian peninsular rivers collectively transport about 83 Mt of sediment annually. The Ganga-Brahmaputra and the Indus, contribute 850 and 13 Mt of sediments, respectively to the oceans. Our revised estimates suggest that at present the large rivers of ESSE region, collectively delivering ?2150 Mt of sediment annually to the oceans. We show that at decadal scale, decline in sediment fluxes of the large Asian rivers are proportional to the number of mega dams present in the respective catchments. We also demonstrate that storage of sediment-laden water of major flood events (major-event), led to huge sediment trapping behind mega dams. Thus, ongoing and planned dam constructions activities across ESSE Asia may further reduce the annual sediment fluxes.

Gupta, Harish; Kao, Shuh-Ji; Dai, Minhan



Census 2000 Resident Population (United States)

On December 28, 2000, the US Census Bureau released its preliminary results for the 2000 Census. According to the Bureau, "the nation's resident population on Census Day, April 1, 2000 was 281,421,906, a 13.2 percent rise over the 248,709,873 counted in the 1990 census" -- an increase that exceeded the Bureau's projections. Visitors to the site can examine tables and maps showing population data for states, congressional districts, and US overseas population as well as state population rankings and percentage change since the 1990 Census. The site also provides a press release summarizing the data and background information on congressional apportionment -- the constitutional cause of the census -- as well as a link to educational materials for studying the census in schools (see the January 11, 2000 Scout Report for the Social Sciences).



Detection and Characterization of Conjugative Degradative Plasmids in Xenobiotic-Degrading Sphingomonas Strains  

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A systematic survey for the presence of plasmids in 17 different xenobiotic-degrading Sphingomonas strains was performed. In almost all analyzed strains, two to five plasmids with sizes of about 50 to 500 kb were detected by using pulsed-field gel electrophoresis. A comparison of plasmid preparations untreated or treated with S1 nuclease suggested that, in general, Sphingomonas plasmids are circular. Hybridization experiments with labeled gene probes suggested that large plasmids are involved...

Basta, Tamara; Keck, Andreas; Klein, Joachim; Stolz, Andreas



Exposing Plasmids as the Achilles’ Heel of Drug-Resistant Bacteria  

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Many multi-drug resistant bacterial pathogens harbor large plasmids that encode proteins conferring resistance to antibiotics. While the acquisition of these plasmids often enables bacteria to survive in the presence of antibiotics, it is possible that plasmids also represent a vulnerability that can be exploited in tailored antibacterial therapy. This review highlights three recently described strategies designed to specifically combat bacteria harboring such plasmids: Inhibition of plasmid ...

Williams, Julia J.; Hergenrother, Paul J.



Novel Plasmid Transformation Method Mediated by Chrysotile, Sliding Friction, and Elastic Body Exposure  

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Escherichia coli as a plasmid recipient cell was dispersed in a chrysotile colloidal solution, containing chrysotile adsorbed to plasmid DNA (chrysotile-plasmid cell mixture). Following this, the chrysotile-plasmid cell mixture was dropped onto the surface of an elastic body, such as agarose, and treated physically by sliding a polystyrene streak bar over the elastic body to create friction. Plasmid DNA was easily incorporated into E. coli, and antibiotic resistance was conferred by transform...

Naoto Yoshida; Toshiaki Nakajima-Kambe; Kaori Matsuki; Toshiya Shigeno



Hofmeister series salts enhance purification of plasmid DNA by non-ionic detergents  

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Ion-exchange chromatography is the standard technique used for plasmid DNA purification, an essential molecular biology procedure. Non-ionic detergents (NIDs) have been used for plasmid DNA purification, but it is unclear whether Hofmeister series salts (HSS) change the solubility and phase separation properties of specific NIDs, enhancing plasmid DNA purification. After scaling-up NID-mediated plasmid DNA isolation, we established that NIDs in HSS solutions minimize plasmid DNA contamination...

Lezin, George; Kuehn, Michael R.; Brunelli, Luca



An Olympic city in the making: Rio de Janeiro mega-event strategy 1993-2016  

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In October 2009, the city of Rio de Janeiro was announced the host of the XXXI Olympic Games. The news came as surprise to many commentators which have previously placed the city as the underdog amidst more high-profile bids, but for those involved with the Brazilian bid the award was the culmination of a project initiated sixteen years earlier. During this period Rio de Janeiro's mega-event strategy evolved through failed Olympic bids, the hosting of the Pan American Games and the mobilisati...

Silvestre, Gabriel



Development of a hardened imaging system for the Laser MegaJoule  

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Full Text Available The Laser MegaJoule (LMJ facility will host inertial confinement fusion experiments in order to achieve ignition by imploding a Deuterium-Tritium microballoon. In this context an X-ray imager is necessary to diagnose the core size and shape of the DT-target in the 10–100?keV band in complement of neutron imaging system. Such a diagnostic will be composed of two parts: an X-ray optical system and a detection assembly. Each element will be affected by the harsh environment created by fusion reactions.

Rousseau A.



New horizons for extreme light physics with mega-science project XCELS  

International Nuclear Information System (INIS)

A short review of the Russian mega-science project XCELS and scientific problems to be solved are presented. We discuss the origin of multi-beam design to attain the highest field magnitude at optimal focusing. Then, we formulate particular physical problems of fundamental interest that can be solved within this project. They include new regimes of single particle motions mostly due to the radiation reaction force (RR) effects when efficient gamma ray generation occurs, new regimes of non-linear electrodynamics, as well as QED resulting in highly efficient plasma converter for gamma rays, and probing non-perturbative QED with dipole or superluminal atto-second pulses


Tunable Mega-Ampere Electron Current Propagation in Solids by Dynamic Control of Lattice Melt (United States)

The influence of lattice-melt-induced resistivity gradients on the transport of mega-ampere currents of fast electrons in solids is investigated numerically and experimentally using laser-accelerated protons to induce isochoric heating. Tailoring the heating profile enables the resistive magnetic fields which strongly influence the current propagation to be manipulated. This tunable laser-driven process enables important fast electron beam properties, including the beam divergence, profile, and symmetry to be actively tailored, and without recourse to complex target manufacture.

MacLellan, D. A.; Carroll, D. C.; Gray, R. J.; Booth, N.; Burza, M.; Desjarlais, M. P.; Du, F.; Neely, D.; Powell, H. W.; Robinson, A. P. L.; Scott, G. G.; Yuan, X. H.; Wahlström, C.-G.; McKenna, P.



Rupture process of the 2013 Okhotsk deep mega earthquake from iterative backprojection and compress sensing methods (United States)

On May 24th 2013 a Mw 8.3 normal faulting earthquake occurred at a depth of approximately 600 km beneath the sea of Okhotsk, Russia. It is a rare mega earthquake that ever occurred at such a great depth. We use the time-domain iterative backprojection (IBP) method [1] and also the frequency-domain compressive sensing (CS) technique[2] to investigate the rupture process and energy radiation of this mega earthquake. We currently use the teleseismic P-wave data from about 350 stations of USArray. IBP is an improved method of the traditional backprojection method, which more accurately locates subevents (energy burst) during earthquake rupture and determines the rupture speeds. The total rupture duration of this earthquake is about 35 s with a nearly N-S rupture direction. We find that the rupture is bilateral in the beginning 15 seconds with slow rupture speeds: about 2.5km/s for the northward rupture and about 2 km/s for the southward rupture. After that, the northward rupture stopped while the rupture towards south continued. The average southward rupture speed between 20-35 s is approximately 5 km/s, lower than the shear wave speed (about 5.5 km/s) at the hypocenter depth. The total rupture length is about 140km, in a nearly N-S direction, with a southward rupture length about 100 km and a northward rupture length about 40 km. We also use the CS method, a sparse source inversion technique, to study the frequency-dependent seismic radiation of this mega earthquake. We observe clear along-strike frequency dependence of the spatial and temporal distribution of seismic radiation and rupture process. The results from both methods are generally similar. In the next step, we'll use data from dense arrays in southwest China and also global stations for further analysis in order to more comprehensively study the rupture process of this deep mega earthquake. Reference [1] Yao H, Shearer P M, Gerstoft P. Subevent location and rupture imaging using iterative backprojection for the 2011 Tohoku Mw 9.0 earthquake. Geophysical Journal International, 2012, 190(2): 1152-1168. [2]Yao H, Gerstoft P, Shearer P M, et al. Compressive sensing of the Tohoku-Oki Mw 9.0 earthquake: Frequency-dependent rupture modes. Geophysical Research Letters, 2011, 38(20).

Qin, W.; Yin, J.; Yao, H.



Incorporating resident research into the dermatology residency program  

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Full Text Available Richard F Wagner Jr, Sharon S Raimer, Brent C Kelly Department of Dermatology, The University of Texas Medical Branch, Galveston, Texas, USA Abstract: Programmatic changes for the dermatology residency program at The University of Texas Medical Branch were first introduced in 2005, with the faculty goal incorporating formal dermatology research projects into the 3-year postgraduate training period. This curriculum initially developed as a recommendation for voluntary scholarly project activity by residents, but it evolved into a program requirement for all residents in 2009. Departmental support for this activity includes assignment of a faculty mentor with similar interest about the research topic, financial support from the department for needed supplies, materials, and statistical consultation with the Office of Biostatistics for study design and data analysis, a 2-week elective that provides protected time from clinical activities for the purpose of preparing research for publication and submission to a peer-reviewed medical journal, and a departmental award in recognition for the best resident scholarly project each year. Since the inception of this program, five classes have graduated a total of 16 residents. Ten residents submitted their research studies for peer review and published their scholarly projects in seven dermatology journals through the current academic year. These articles included three prospective investigations, three surveys, one article related to dermatology education, one retrospective chart review, one case series, and one article about dermatopathology. An additional article from a 2012 graduate about dermatology education has also been submitted to a journal. This new program for residents was adapted from our historically successful Dermatology Honors Research Program for medical students at The University of Texas Medical Branch. Our experience with this academic initiative to promote dermatology research by residents is outlined. It is recommended that additional residency programs should consider adopting similar research programs to enrich resident education. Keywords: dermatology, resident, research, education, accreditation

Wagner RF Jr



Status and Perspectives of the Mini-MegaTORTORA Wide-field Monitoring System with High Temporal Resolution  

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Full Text Available Here we briefly summarize our long-term experience of constructing and operating wide-field monitoring cameras with sub-second temporal resolution to look for optical components of GRBs, fast-moving satellites and meteors. The general hardware requirements for these systems are discussed, along with algorithms for real-time detection and classification of various kinds of short optical transients. We also give a status report on the next generation, the MegaTORTORA multi-objective and transforming monitoring system, whose 6-channel (Mini-MegaTORTORA-Spain and 9-channel prototypes (Mini-MegaTORTORA-Kazan we have been building at SAO RAS. This system combines a wide field of view with subsecond temporal resolution in monitoring regime, and is able, within fractions of a second, to reconfigure itself to follow-up mode, which has better sensitivity and simultaneously provides multi-color and polarimetric information on detected transients.

Sergey Karpov



Measurement of residence times and residence-time distributions  

International Nuclear Information System (INIS)

In this chapter the use of radioisotopes for the measurement of residence-times with particular reference to vessel failure in the chemical industry is discussed. Ideal and non-ideal flow models and the more important parameters of models are discussed. Examples are given of the effect of process malfunction on residence times. (U.K.)


Resident training in pathology: From resident's point of view  

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Full Text Available In many recent studies in the literature have described and commented on “competency based resident training” in pathology. According to this model, competencies are subclassified in 6 main categories: Patient care, medical knowledge, practice based learning and improvement, interpersonal and communication skills, professionalism, and systems based practice. Assessment of competency forms the main component of this model.Under the framework of Ankara Society of Pathology, a working group, composed of 11 residents, 6 of which representing the Training and Research Hospitals of Ministry of Health and the rest representing the university hospitals in Ankara, was established in order to participate in the think-tank about resident training in pathology. A questionnaire, composed of 12 questions, was prepared. According to this questionnaire, the number of trainers in the university hospitals is much higher than in the commercial hospitals. While the total number of cases and cases per resident do not differ between the university and commercial hospitals, microscopes used for the educational purposes are significantly less in the commercial hospitals, that is due to less number of binocular microscopes. The amount of resident training program, which consists of intra and intersectional meetings, are similar in the university and commercial hospitals, however, theoretic lectures are given only in 3 departments. Residents working in the university hospitals have obviously heavier burden than in the commercial hospitals. Lastly, residents generally exclaimed that the time dedicated to the macroscopy training is less sufficient than time used for the microscopy training.The factors affecting the training of resident in pathology are divided into two main groups: 1 Factors directly affecting training (quality of trainer, time dedicated for education, feed back, eg. and 2 Conditions which waste residents' time. For instant, workload which does need qualified staff and increases the burden on residents may be reassigned to medical secretary or pathology assistants; therefore energy of residents can be saved for educational activities. Optimization of physical working conditions, assortment of training programs, rotation in lacking subjects and consultations will enhance the quality of the education of the resident. Feedback assessment of trainer and trainee is an essential part of a training program.In conclusion, an ideal resident from the resident's point of view is the person who is endowed with medical and pathological knowledge, orderly interrelates with staff, professionally communicates with clinicians, manages a laboratory and is trained hard to achieve all the above mentioned competencies.





The transduction of Pseudomonas aeruginosa plasmid Rms149 by the generalized transducing phage DS1 was shown to occur during a nine day incubation of environmental test chambers in a freshwater reservoir. Plasmid DNA was transferred from a nonlysogenic plasmid donor to a DS1 lyso...


Photon detector for MEGA. Final report, July 16, 1992--May 31, 1993  

International Nuclear Information System (INIS)

During the past year, we have continued our work on the photon detector for the MEGA experiment at Los Alamos. The MEGA photon detector is designed to observe the 52.83 MeV photon produced in a ? ? e? decay with an energy resolution of 1.25 MeV, a position resolution of 2 x 5 mm2, a directional resolution of 10 degree, a time resolution of 500 ps, and an efficiency of about 5.4%. (All quoted resolutions are FWHM.) It consists of three independent concentric cylindrical pair spectrometers mounted within a 1.5 T magnetic field produced by a superconducting solenoid magnet. Each pair spectrometer includes two thin (0.045 radiation lengths each) Pb foils to convert photons into e+e- pairs. The two smaller pair spectrometers have three drift chamber layers to track the e+e- pairs and thereby determine both their locations and their vector momenta. The third pair spectrometer has four layers of drift chamber, together with a larger turning region, to provide better tracking information for high energy photons such as those from the ?0 ? 2? decay


Computer Analysis of Residency Training. (United States)

A computerized patient record-keeping system in a pediatric residency program revealed limitations in residents' patient experiences and imbalances in their workload and curriculum and has been used by the faculty to correct them. The system uses eight interactive programs in the BASIC language. (MSE)

Simon, Frank A.



Residence Hall Seating That Works. (United States)

Describes the seating chosen for residence halls at the Massachusetts Institute of Technology and the University of New England. The seating required depends on ergonomics, aesthetics, durability, cost, and code requirements. In addition, residence halls must have a range of seating types to accommodate various uses. (SLD)

Wiens, Janet



Research on Trypanosoma cruzi and Analysis of Inflammatory Infiltrate in Esophagus and Colon from Chronic Chagasic Patients with and without Mega (United States)

To compare parasitism and inflammatory process in esophagus and colon from chronic chagasic patients, immunohistochemistry was carried out to research for T. cruzi and to evaluate the inflammatory infiltrate in the muscular and myenteric plexus in 39 esophagi (20 with and 19 without megaesophagus) and 50 colons (25 with and 25 without megacolon). The frequency of T. cruzi in megaesophagus was 20%, and in megacolon it was 4%. No amastigotes were found in organs without mega; considering the total of esophagi (with and without mega), the frequency of T. cruzi would be 10% and 2% in the colon. Myositis and ganglionitis were more frequent and intense in organs with mega compared to those without mega, and in esophagus compared to colon. Qualitatively, inflammatory infiltration in esophagus and colon, with or without mega, was similar, consisting predominantly of T lymphocytes (CD3+), scarce macrophages (CD68+), and rare B lymphocytes (CD20+). PMID:22131997

Côbo, Eliângela de Castro; Silveira, Thales Parenti; Micheletti, Adilha Misson; Crema, Eduardo; Adad, Sheila Jorge



Gas and Dust Phenomena of Mega-earthquakes and the Cause (United States)

A mega-earthquake suddenly releases a large to extremely large amount of kinetic energy within a few tens to two hundreds seconds and over ten to hundreds kilometer distances in the Earth's crust and on ground surface. It also generates seismic waves that can be received globally and co-seismic ground damages such co-seismic ruptures and landslides. However, such vast, dramatic and devastating kinetic actions in the Earth's crustal rocks and on the ground soils cannot be known or predicted by people at few weeks, days, hours, or minutes before they are happening. Although seismologists can develop and use seismometers to report the locations and magnitudes of earthquakes within minutes of their occurrence, they cannot predict earthquakes at present. Therefore, damage earthquakes have caused and would continue to cause huge disasters, fatalities and injuries to our human beings. This problem may indicate that it is necessary to re-examine the cause of mega-earthquakes in addition to the conventional cause of active fault elastic rebounding. In the last ten years, many mega-earthquakes occurred in China and around the Pacific Ocean and caused many casualties to human beings and devastating disasters to environments. The author will give a brief review on the impacts of the mega-earthquakes happened in recent years. He will then present many gas and dust related phenomena associated with the sudden occurrences of these mega earthquakes. They include the 2001 Kunlunshan Earthquake M8.1, 2008 Wenchuan Earthquake M8.0 and the 2010 Yushu Earthquake M7.1 in China, the 2010 Haiti Earthquake M7.0, the 2010 Mexicali Earthquake M7.2, the 2010 Chile Earthquake M8.8, the 2011 Christchurch earthquake M6.3 and the 2011 Japan Earthquake M9.0 around the Pacific Ocean. He will discuss the cause of these gas and dust related phenomena. He will use these phenomena and their common cause to show that the earthquakes were caused the rapid migration and expansion of highly compressed and dense natural (methane) gas suddenly escaped from deep crust traps along deep fault zones. References Yue, ZQ, 2009. The source of energy power directly causing the May 12 Wenchuan Earthquake: Huge extremely pressurized natural gases trapped in deep Longmen Shan faults. News Journal of China Society of Rock Mechanics and Engineering, 86 (2009 (2)), 45-50. Yue, ZQ, 2010. Features and mechanism of coseismic surface ruptures by Wenchuan Earthquake. in Rock Stress and Earthquake, edited by Furen Xie, Taylor & Francis Group, London, ISBN 978-0-415-60165-8, 761-768. Yue, ZQ, 2013a. Natural gas eruption mechanism for earthquake landslides: illustrated with comparison between Donghekou and Papandayan Rockslide-debris flows. in Earthquake-induced Landslides, K. Ugai et al. (eds.), Springer-Verlage Berlin, Chapter 51: pp. 485-494 Yue ZQ, 2013b. On incorrectness in elastic rebound theory for cause of earthquakes. Paper No. S20-003 of Session S20, Proceedings of the 13th International Conference on Fracture, June 16-21, Beijing. Yue ZQ, 2013c. On nature of earthquakes with cause of compressed methane gas expansion and migration in crustal rocks, in Proceedings of Fifth Biot Conference on Poromechanics in Memory of Karl von Terzaghi (1883-1963), July 10-12, Vienna, edited by C. Hellmich et al, @ASCE, pp. 507-516.

Yue, Z.



The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. (United States)

The nucleotide sequence of the biphenyl catabolic transposon Tn4371 has been completed and analyzed. It confirmed that the element has a mosaic structure made of several building blocks. In addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of Achromobacter georgiopolitanum KKS102, Tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, plasmid functions. One gene cluster contains most of the genes required to express a type IV secretion-mating pair formation apparatus coupled with a TraG ATPase, all of which are related to those found on IncP and Ti plasmids. Orthologues of all Tn4371 plasmid-related genes and of the tyrosine recombinase gene were found, with a very similar organization, in the chromosome of Ralstonia solanacearum and on the yet-to-be-determined genomic sequences of Erwinia chrysanthemi and Azotobacter vinelandii. In each of these chromosomal segments, conserved segments were separated by different groups of genes, which also differed from the Tn4371 bph genes. The conserved blocks of genes were also identified, in at least two copies, in the chromosome of Ralstonia metallidurans CH34. Tn4371 thus appears to represent a new family of potentially mobile genomic islands with a broad host range since they reside in a wide range of soil proteobacteria, including plant pathogens. PMID:12902278

Toussaint, Ariane; Merlin, Christophe; Monchy, Sébastien; Benotmane, M Abderrafi; Leplae, Raphaël; Mergeay, Max; Springael, Dirk



Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum  

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BACKGROUND: Industrial production of biofuels and other products by cellulolytic microorganisms is of interest but hindered by the nascent state of genetic tools. Although a genetic system for Clostridium thermocellum DSM1313 has recently been developed, available methods achieve relatively low efficiency and similar plasmids can transform C. thermocellum at dramatically different efficiencies. RESULTS: We report an increase in transformation efficiency of C. thermocellum for a variety of plasmids by using DNA that has been methylated by Escherichia coli Dam but not Dcm methylases. When isolated from a dam+ dcm+ E. coli strain, pAMG206 transforms C. thermocellum 100-fold better than the similar plasmid pAMG205, which contains an additional Dcm methylation site in the pyrF gene. Upon removal of Dcm methylation, transformation with pAMG206 showed a four- to seven-fold increase in efficiency; however, transformation efficiency of pAMG205 increased 500-fold. Removal of the Dcm methylation site from the pAM205 pyrF gene via silent mutation resulted in increased transformation efficiencies equivalent to that of pAMG206. Upon proper methylation, transformation efficiency of plasmids bearing the pMK3 and pB6A origins of replication increased ca. three orders of magnitude. CONCLUSION: E. coli Dcm methylation decreases transformation efficiency in C. thermocellum DSM1313. The use of properly methylated plasmid DNA should facilitate genetic manipulation of this industrially relevant bacterium.

Guss, Adam M [ORNL; Olson, Daniel G. [Thayer School of Engineering at Dartmouth; Caiazza, Nicky [Mascoma Corporation; Lynd, Lee R [Thayer School of Engineering at Dartmouth



Efficient transposition of IS204-derived plasmids in Streptomyces coelicolor. (United States)

In order to study functional gene expression in Streptomyces coelicolor, a mini-transposon encoding the apramycin resistance gene aac(3)IV within its inverted repeat (IR) boundaries was constructed based on IS204, which was previously identified in the genome of Nocardia asteroides YP21. The mini-transposon and IS204 transposase gene were then put on a kanamycin-resistant conjugative plasmid pDZY101 that can only replicate in Escherichia coli. After mating with S. coelicolor A3(2) M145, resistant colonies arose efficiently on both apramycin and kanamycin plates. Plasmid rescue indicated that entire plasmids were inserted into the M145 genome with cleavage at an inverted repeat junction formed by the right inverted repeat (IRR) and the last 18bp of the transposase gene, while the left inverted repeat (IRL) was untouched. Southern blot analysis of the mutants using an aac(3)IV gene probe showed that transposition of plasmid pDZY101 was genetically stable, with a single-copy insertion within the S. coelicolor M145 genome. Several mutagenesis libraries of S. coelicolor M145 were constructed using plasmid pDZY101 derivatives and the transposon insertion site was determined. The correlation between novel mutant phenotypes and previously uncharacterized genes was established and these transposon locations were widely scattered around the genome. PMID:22079690

Zhang, Xincheng; Bao, Yun; Shi, Xunlong; Ou, Xijun; Zhou, Pei; Ding, Xiaoming



Plasmid rearrangements in the photosynthetic bacterium Rhodopseudomonas sphaeroides. (United States)

Mu d1(Ap lac) was introduced into the photosynthetic bacterium Rhodopseudomonas sphaeroides 2.4.1. via the R-plasmid R751 in an attempt to isolate fusion derivatives involving photosynthetic operons. The selection system is potentially very powerful since R. sphaeroides is normally Lac negative. Among the exconjugants, photosynthesis-deficient mutants were recovered, some of which had elevated beta-galactosidase levels. Among the mutants examined, beta-galactosidase expression was linked exclusively to R751 . Many of the photosynthesis-deficient mutants were found to have alterations in their indigenous plasmids which apparently involved the exchange of DNA from one plasmid to another. Southern blot analysis revealed that there are extensive DNA sequences which are shared by the two plasmids that are involved in the rearrangements and that no exogenous DNA sequences appear to be involved. It was further discovered that plasmid rearrangement is a general phenomenon which can occur spontaneously in R. sphaeroides 2.4.1 and shows a high correlation with a photosynthesis minus phenotype. Images PMID:6327628

Nano, F E; Kaplan, S



Predicting polycyclic aromatic hydrocarbon concentrations in resident aquatic organisms using passive samplers and partial least-squares calibration. (United States)

The current work sought to develop predictive models between time-weighted average polycyclic aromatic hydrocarbon (PAH) concentrations in the freely dissolved phase and those present in resident aquatic organisms. We deployed semipermeable membrane passive sampling devices (SPMDs) and collected resident crayfish (Pacifastacus leniusculus) at nine locations within and outside of the Portland Harbor Superfund Mega-site in Portland, OR. Study results show that crayfish and aqueous phase samples collected within the Mega-site had PAH profiles enriched in high molecular weight PAHs and that freely dissolved PAH profiles tended to be more populated by low molecular weight PAHs compared to crayfish tissues. Results also show that of several modeling approaches, a two-factor partial least-squares (PLS) calibration model using detection limit substitution provided the best predictive power for estimating PAH concentrations in crayfish, where the model explained ?72% of the variation in the data set and provided predictions within ?3× of measured values. Importantly, PLS calibration provided a means to estimate PAH concentrations in tissues when concentrations were below detection in the freely dissolved phase. The impact of measurements below detection limits is discussed. PMID:24800862

Forsberg, Norman D; Smith, Brian W; Sower, Greg J; Anderson, Kim A



Cloning and expression of a plasmid-linked pediocin determinant trait of Pediococcus acidilactici F. (United States)

Plasmid DNA from Pediococcus acidilactici F was prepared by lysozyme-mutanolysin method and purified by cesium chloride-ethidium bromide (CsCl-EtBr) density gradient ultracentrifugation. Agarose gel electrophoresis of plasmid DNA and plasmid-curing experiments suggested that bacteriocin activity was harboured on a small plasmid of approximately 9.1 kb (kilobasepair) in Pediococcus acidilactici F. Plasmid encoding bacteriocin production in P. acidilactici F was examined for restriction enzyme cleavage patterns and its map has been constructed. An Escherichia coli strain transformed with the recombinant plasmid, pQE322, produced and, most probably, secreted pediocin F. PMID:10746198

Osmana?ao?lu, O; Beyatli, Y; Gündüz, U



Cryptic Streptococcus mutans 5.6-kb plasmids encode a toxin–antitoxin system for plasmid stabilization  

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Full Text Available Background: In all Streptococcus mutans strains, 5–13% carry a 5.6-kb plasmid. Despite its frequency, little is known about its mediated functions with most of the information coming from a single study focussing on plasmid pUA140. Objective: Here, we describe the sequence and genetic organization of two S. mutans 5.6-kb plasmids, pDC09 and pNC101. Results: Based on PicoGreen dsDNA quantification and Real-Time quantitative PCR (RTQ-PCR, the plasmid copy number was found to range between 10 and 74, depending on the strain tested. In contrast to literature, we identified six instead of five open reading frames (ORFs. While the putative gene products of ORF1 (as a Rep-protein and ORF2 (as a Mob-protein could be confirmed as being identical to those from pUA140, the functions of ORF3 (unknown and ORF 4 (possibly AtpE homologue could not be further revealed. However, the product of ORF5 showed a fairly high identity (38–50% and structural similarity (58–74% to RelE of Streptococcus pneumoniae, Streptococcus equi, and Streptococcus downei. In addition, we identified a functionally corresponding ORF6 encoding a protein with 61–68% identity (81–86% similarity to the S. equi and S. downei antitoxin of the RelB family. RelE and RelB together form a plasmid-encoded toxin-antitoxin (TA system, RelBEplas. Despite its rather limited sequence similarity with chromosomal TA systems in S. mutans (RelBEchro, MazEF, HicBA, we found similar tertiary structures applying I-Tasser protein prediction analysis. Conclusion: Type II-toxins, as the plasmid-encoded RelE, are RNA endonucleases. Depending on their mRNA cleavage activity, they might 1 kill every plasmid-free progeny, thereby stabilizing plasmid transfer at the expense of the host and/or 2 help S. mutans enter a dormant state and survive unfavourable environmental conditions. Whilst a function in plasmid stabilization has been confirmed, a function in persistence under nutritional stress, tested here by inducing amino acid starvation, could not be demonstrated so far.

Anke Rheinberg



Plasmid-mediated streptomycin resistance of listeria monocytogenes. (United States)

A strain of streptomycin-resistant Listeria monocytogenes LM35 isolated from imported frozen beef was examined in this study. In conjugation studies, the L. monocytogenes LM35 strain harbouring two plasmids of 54, 3.0, 2.8 and 2.7 kilobase was used as the donor and streptomycin-sensitive and plasmidless L. monocytogenes LM65 and LM100 strains as the recipients. Streptomycin resistance was transferred to L. monocytogenes LM65 and LM100 strains at frequencies of 3.3 × 10(-8) and 1.2 × 10(-9) per input donor cells, respectively. In both occasions, we also observed the concomitant transfer of the donor's 54 kilobase plasmid. These results suggest that streptomycin resistance in L. monocytogenes LM35 was mediated by the 54 kilobase plasmid. PMID:22973158

Purwati, E; Radu, S; Hassan, Z; Ling, O W; Rahim, R A



Aeromonas aquariorum clinical isolates: antimicrobial profiles, plasmids and genetic determinants. (United States)

The objective of this study was to investigate the antimicrobial resistance patterns of 47 clinical isolates of Aeromonas aquariorum and to identify the presence of plasmids and the relevant antibiotic resistance genes (ARGs). Antibiotic susceptibilities were determined by the standard disc diffusion method. The presence of plasmids and ARGs was detected by gel electrophoresis and monoplex PCR. Resistance to amoxicillin/clavulanic acid (98%), amoxicillin (91%), gentamicin (13%), trimethoprim/sulfamethoxazole (11%) and kanamycin (6%) was observed, whilst no ciprofloxacin- or amikacin-resistant strains were detected. All isolates harboured plasmids with sizes ranging from ca. 2 kb to 10 kb. PCR revealed that A. aquariorum carried three ?-lactam resistance genes (bla(TEM), bla(MOX) and bla(PSE)) and two sulphonamide resistance genes (sul1 and sul2). This study provides further understanding of the phenotypic and genotypic characteristics of multiresistant A. aquariorum clinical isolates. PMID:23312608

Puah, Suat-Moi; Puthucheary, S D; Liew, Fong-Yin; Chua, Kek-Heng



42 CFR 483.10 - Resident rights. (United States)

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Genetic characterization of plasmid pRJ5 of Staphylococcus aureus compared to plasmid pE194  

International Nuclear Information System (INIS)

The pRJ5, a naturally occurring constitutive macrolide, lincosamide and streptogramin B (MLS) resistance plasmid of Staphylococcus aureus, was compared to pE194, a plasmid that confers the inducible phenotype. pRJ5 was stable in all strains of S. aureus tested, even under growth at 43O C, which distinguished it from pE194 which was shown to be thermo-sensitive for replication. pRJ5, like pE194, was highly unstable in Bacillus subtilis when the cells were grown in nonselective conditions. Multimeric forms of pRJ5 DNA were detected in the few cells of B. subtilis that retained this plasmid. pE194 was transduced by phages ? 11 and ? 443 at frequencies 400 and 20-fold higher, respectively, than pRJ5. Both plasmids were co-transduced with the plasmid pRJ4. pRJ5 was shown to be compatible with pE194. Therefore they belong to distinct Inc groups. Hybridization studies revealed that pRJ5 shares a 1.35 kb region of homology to pE194, which is limited to the erm gene, conferring MLS resistance. (author)


Construction and Characterization of a Highly Efficient Francisella Shuttle Plasmid (United States)

Francisella tularensis is a facultative intracellular pathogen that infects a wide variety of mammals and causes tularemia in humans. It is recognized as a potential agent of bioterrorism due to its low infectious dose and multiple routes of transmission. To date, genetic manipulation in Francisella spp. has been limited due to the inefficiency of DNA transformation, the relative lack of useful selective markers, and the lack of stably replicating plasmids. Therefore, the goal of this study was to develop an enhanced shuttle plasmid that could be utilized for a variety of genetic procedures in both Francisella and Escherichia coli. A hybrid plasmid, pFNLTP1, was isolated that was transformed by electroporation at frequencies of >1 × 107 CFU ?g of DNA?1 in F. tularensis LVS, Francisella novicida U112, and E. coli DH5?. Furthermore, this plasmid was stably maintained in F. tularensis LVS after passage in the absence of antibiotic selection in vitro and after 3 days of growth in J774A.1 macrophages. Importantly, F. tularensis LVS derivatives carrying pFNLTP1 were unaltered in their growth characteristics in laboratory medium and macrophages compared to wild-type LVS. We also constructed derivatives of pFNLTP1 containing expanded multiple cloning sites or temperature-sensitive mutations that failed to allow plasmid replication in F. tularensis LVS at the nonpermissive temperature. In addition, the utility of pFNLTP1 as a vehicle for gene expression, as well as complementation, was demonstrated. In summary, we describe construction of a Francisella shuttle plasmid that is transformed at high efficiency, is stably maintained, and does not alter the growth of Francisella in macrophages. This new tool should significantly enhance genetic manipulation and characterization of F. tularensis and other Francisella biotypes. PMID:15574954

Maier, Tamara M.; Havig, Andrea; Casey, Monika; Nano, Francis E.; Frank, Dara W.; Zahrt, Thomas C.



The Aftershock Analyses of 27 February 2010 Chile M=8.8 Mega Earthquake (United States)

In 1960, the biggest earthquake (M=9.5), the human ever recorded event, occurred in south Chile. Subsequently several mega earthquake (M >8) occurred, including the M=8.8 earthquake in 2010. This reflects that an incomplete release of tectonic energy exists in the Chile subduction system. The west coast of Chile is a long convergence plate boundary between the Nazca and the South American plate. The Nazca Plate subducts beneath the South American Plate toward the northeast with a convergence rate of about 6.5 cm/year, accumulating the stress in the lower part of the subducted plate to some extent resulting in destructive ruptures. On 27 February 2010, the Maule mega earthquake (M=8.8) occurred offshore central Chile. The epicenter (35.9° S, 72.73° W) is located at 115 km, NE of Concepción, the second biggest city in Chile. The main shock was a thrust-type subduction earthquake where the Nazca Plate subducted into the South America Plate (the Chile subduction system). The focal depth of main shock is 35 km which caused more than 500-km long rupture in the accretionary prism and produced a destructive tsunami of more than 20 m. It killed several hundreds of people and damaged countless buildings. Even up to today, aftershocks and volcanic activities continue to occur in this region. During May-August of last year, we shipped 20 OBSs to Chile and conducted two aftershock surveys in the tsunami-affected area. The OBSs recorded more than 4,000 aftershock events, magnitude from M=6.0 to 1.0. Results show that the aftershock data were concentrated into two masses: the landward side of the paleo-accretionary prism and the seaward side of the subducting plate, leaving a "white zone" in the frontal accretionary prisms. Both data sets consistently indicate the same result. The angle between the paleo-accretionary prism and the subduction plate seems to be greater than that of the frontal-accretionary prism. We suggest that the greater of the splay fault angle the higher the risk for the occurrence of a destructive tsunami. Even though our study covered only a short period of aftershocks it appears to show shows important basic characteristics of the 2010 Maule mega event.

Lee, C.-S.; Klingelhoefer, F.; Gutscher, M.; Miller, M.; Gallardo, V.



Association of lupin mitochondrial plasmid DNA with mitochondrial protein  

International Nuclear Information System (INIS)

Lupinus albus mitochondrial plasmids and Lupinus mitochondrial and total proteins have been used for studying the formation of complexes by gel retardation and UV crosslinking assays. All the results suggest formation of a specific complex between mitochondrial plasmids and proteins. Lupinus albus mitochondrial proteins recovered from the complex and resolved by two-dimensional gel electrophoresis (2-D SDS-PAGE) displayed a pI of about 5.6 and 5.8 and a molecular weight of 30 and 31 kDa. (author)


Restriction Fragment Length Polymorphisms of Virulence Plasmids in Rhodococcus equi  

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Virulent Rhodococcus equi, which is a well-known cause of pyogranulomatous pneumonia in foals, possesses a large plasmid encoding virulence-associated 15- to 17-kDa antigens. Foal and soil isolates from five countries—Argentina, Australia, Canada, France, and Japan—were investigated for the presence of 15- to 17-kDa antigens by colony blotting, using the monoclonal antibody 10G5, and the gene coding for 15- to 17-kDa antigens by PCR. Plasmid DNAs extracted from positive isolates were dige...

Takai, Shinji; Shoda, Masato; Sasaki, Yukako; Tsubaki, Shiro; Fortier, Guillaume; Pronost, Stephane; Rahal, Karim; Becu, Teotimo; Begg, Angela; Browning, Glenn; Nicholson, Vivian M.; Prescott, John F.



Currents, Water Budget and Turn-Over Time Within A Man-Made Coastal Mega-Structure: Palm Jumeirah, Southern Arabian Gulf, United Arab Emirates (United States)

Large-scale land reclamation projects along the coastline of Dubai, United Arab Emirates (UAE), are set to expand from 45 km of natural shoreline to more than 1,500 km by 2010. The increasing scale of coastal development in Dubai has large-scale effects on water movement throughout the project area. Palm Jumeirah is the oldest, most well-developed of several man-made coastal mega-constructions in Dubai. This construction project started 6 years ago, has an overall surface area of 7.9 km2 and a footprint of 23 km2, and is connected to the coast via a 5-km long spine from the mainland to the crescent tip. We made time series observations of hydrographic properties and currents within the Palm Jumeirah Lagoon (PJL) during 29 days in April/May 2008 to examine the current flows, water budget, salt transport, and turn-over time. The currents and water flow within the PJL were quite variable, with stronger currents, greater material transports, lower water temperatures, and slightly lower salinities in areas close to the entrances where flushing is ample. Due to the shallow water depths, we found only weak vertical stratification during a tidal cycle. The lagoon system is comprised of 18 blind channels surrounded by a semi-circular open channel, which in turn is linked to the coastal waters by 4 gaps (one each on the East and West sides and two at the base of the development) in the rocky breakwater that surrounds the development. We found substantial differences in water discharge between the east and west gaps, with high discharge on average exiting the east gap and extremely low water discharge exiting the west gap. Our results indicate that the PJL is flushed unequally between the east and west sides with residence times of 1.2 and 42 days for the east and west sides of the development, respectively. Previous studies of water residence time using the DELFT3D hydrodynamics simulation modeling software did not capture this difference accurately, estimating residence times for the two sides of PJL to be 14 and 28 days, respectively. Stratification remains absent during the spring-neap tidal cycle with well mixed conditions throughout the lagoon system. PJL tides are mixed mainly semidiurnal, with the spring and neap tidal ranges measuring 116 and 56 cm, respectively, with no measureable change in either amplitude or phase within the man-made lagoon.

Cavalcante, G.; Kjerfve, B.



Evidence for the involvement of the incC locus of broad host range plasmid RK2 in plasmid maintenance. (United States)

Plasmid pRK2501 is a deletion derivative of broad host range plasmid RK2 and encodes two trfB-regulated operons: the trfA operon which codes for both kilD, which interferes with plasmid maintenance if unregulated, and trfA whose protein product(s) is essential for replication from oriVRK2; and part of the trfB operon, containing both trfB/korA/korD, whose product negatively regulates transcription of both trfA and trfB operons, and incC, the product of which interferes in trans with inheritance of RK2 and certain of its derivatives. Plasmid pRK2501ts3 is a derivative with a point mutation in trfB, rendering plasmid maintenance temperature sensitive. Transcriptional fusions of the trfB operon and the galK gene demonstrate that this mutation derepresses trfB operon transcription at both 30 and 42 degrees C. The trfA operon is also derepressed by this mutation. Since the trfB gene product appears to be defective at both permissive and non-permissive temperatures the temperature sensitivity of pRK2501ts3 must be due to a secondary effect. In fact, it appears to arise from the inhibitory behavior of derepressed incC at the non-permissive temperature since a major class of "revertant" of pRK2501ts3 contains deletions inactivating incC and a reconstruction experiment demonstrates that such a deletion is sufficient for "reversion." Maxicell experiments show that at the non-permissive temperature the trfA operon polypeptide products are produced at much lower levels, an effect partly reversed by a deletion affecting incC. It is proposed that incC normally plays a role in maintenance of IncP plasmids by modulation of trfA operon expression. PMID:3016778

Thomas, C M



Mega Borg oil spill of the Texas coast: An open-water bioremediation test  

International Nuclear Information System (INIS)

Nature has developed hydrocarbons as a part of life. Since the origin of life, more than 60,000 organic molecules have evolved that make up protoplasm; a given percentage of these molecules are hydrocarbons. Commercial hydrocarbon deposits are a by-product of this natural process and a continual source of oil in the aquatic environment through seeps. As a result, nature has also evolved a recycling system for the hydrocarbons. This cycle is the basis for a program of bioremediation using microorganisms. Effort has been made to develop mixed cultures capable of a wide range of hydrocarbon metabolism and co-metabolism. The cultures are economically produced in high concentrations as a dry powder with a shelf life of one year. The result is an economical process for the application of bacteria to hydrocarbon pollutants on water and soils. The process of bioremediation to the recent Mega Borg accident will be discussed


Overview of the ARGOS X-ray framing camera for Laser MegaJoulea) (United States)

Commissariat à l'Énergie Atomique et aux Énergies Alternatives has developed the ARGOS X-ray framing camera to perform two-dimensional, high-timing resolution imaging of an imploding target on the French high-power laser facility Laser MegaJoule. The main features of this camera are: a microchannel plate gated X-ray detector, a spring-loaded CCD camera that maintains proximity focus in any orientation, and electronics packages that provide remotely-selectable high-voltages to modify the exposure-time of the camera. These components are integrated into an "air-box" that protects them from the harsh environmental conditions. A miniaturized X-ray generator is also part of the device for in situ self-testing purposes.

Trosseille, C.; Aubert, D.; Auger, L.; Bazzoli, S.; Beck, T.; Brunel, P.; Burillo, M.; Chollet, C.; Gazave, J.; Jasmin, S.; Maruenda, P.; Moreau, I.; Oudot, G.; Raimbourg, J.; Soullié, G.; Stemmler, P.; Zuber, C.



Finding ultracool brown dwarfs with MegaCam on CFHT: method and first results (United States)

Aims: We present the first results of a wide field survey for cool brown dwarfs with the MegaCam camera on the CFHT telescope, the Canada-France Brown Dwarf Survey, hereafter CFBDS. Our objectives are to find ultracool brown dwarfs and to constrain the field-brown dwarf mass function thanks to a larger sample of L and T dwarfs. Methods: We identify candidates in CFHT/MegaCam i' and z' images using optimised psf-fitting within Source Extractor, and follow them up with pointed near-infrared imaging on several telescopes. Results: We have so far analysed over 350 square degrees and found 770 brown dwarf candidates brighter than z'_AB=22.5. We currently have J-band photometry for 220 of these candidates, which confirms 37% as potential L or T dwarfs. Some are among the reddest and farthest brown dwarfs currently known, including an independent identification of the recently published ULAS J003402.77-005206.7 and the discovery of a second brown dwarf later than T8, CFBDS J005910.83-011401.3. Infrared spectra of three T dwarf candidates confirm their nature, and validate the selection process. Conclusions: The completed survey will discover ~100 T dwarfs and ~500 L dwarfs or M dwarfs later than M8, approximately doubling the number of currently known brown dwarfs. The resulting sample will have a very well-defined selection function, and will therefore produce a very clean luminosity function. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA, at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at TERAPIX and the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on observations made with the ESO New Technology Telescope at the La Silla Observatory under programme ID 76.C-0540(A), 77.C-0594, 77.A-0707, 78.A-0651, 78.C-0629 and 79.A-0663. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Science and Technology Facilities Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), CNPq (Brazil) and CONICET (Argentina). Based on observations with the Kitt Peak National Observatory, National Optical Astronomy Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc. (AURA) under cooperative agreement with the National Science Foundation. Based on observations made with the Nordic Optical Telescope, operated on the island of La Palma jointly by Denmark, Finland, Iceland, Norway, and Sweden, in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. This paper includes data taken at The McDonald Observatory of The University of Texas at Austin.

Delorme, P.; Willott, C. J.; Forveille, T.; Delfosse, X.; Reylé, C.; Bertin, E.; Albert, L.; Artigau, E.; Robin, A. C.; Allard, F.; Doyon, R.; Hill, G. J.



Mega-ampere ion currents and nuclear reactions in the focal laser spot  

International Nuclear Information System (INIS)

The plasma response to a picosecond multiterawatt laser-pulse is characterized by several distinctly different time scales. In the present paper we consider the plasma evolution on the slow time scale typical for excitations of the ionic component. A relativistically strong laser pulse (1018-1019 W/cm2) is shown to drive, under proper conditions, mega-ampere ion currents with typical ion energies of 50-150 keV. This feature of the ultra-intense laser-plasma interaction may be of interest for nuclear fusion since the ion energy involved is close to the resonance peak of the cross-section for the D-T reaction


The first light of Mini-MegaTORTORA wide-field monitoring system  

CERN Document Server

Here we describe the first light of the novel 9-channel wide-field optical monitoring system with sub-second temporal resolution, Mini-MegaTORTORA, which is being tested now at Special Astrophysical Observatory on Russian Caucasus. The system is able to observe the sky simultaneously in either wide (~900 square degrees) or narrow (~100 square degrees) fields of view, either in clear light or with any combination of color (Johnson B, V or R) polarimetric filters installed, with exposure times ranging from 100 ms to 100 s. The primary goal of the system is the detection of rapid -- with sub-second characteristic time-scales -- optical transients, but it may be also used for studying the variability of the sky objects on longer time scales.

Biryukov, A; Karpov, S; Bondar, S; Ivanov, E; Katkova, E; Perkov, A; Sasyuk, V



megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. (United States)

Rare-cleaving endonucleases have emerged as important tools for making targeted genome modifications. While multiple platforms are now available to generate reagents for research applications, each existing platform has significant limitations in one or more of three key properties necessary for therapeutic application: efficiency of cleavage at the desired target site, specificity of cleavage (i.e. rate of cleavage at 'off-target' sites), and efficient/facile means for delivery to desired target cells. Here, we describe the development of a single-chain rare-cleaving nuclease architecture, which we designate 'megaTAL', in which the DNA binding region of a transcription activator-like (TAL) effector is used to 'address' a site-specific meganuclease adjacent to a single desired genomic target site. This architecture allows the generation of extremely active and hyper-specific compact nucleases that are compatible with all current viral and nonviral cell delivery methods. PMID:24285304

Boissel, Sandrine; Jarjour, Jordan; Astrakhan, Alexander; Adey, Andrew; Gouble, Agnès; Duchateau, Philippe; Shendure, Jay; Stoddard, Barry L; Certo, Michael T; Baker, David; Scharenberg, Andrew M



High-power optical coatings for a mega-joule class ICF laser  

International Nuclear Information System (INIS)

As a consequence of advancements in Inertial Confinement Fusion research, LLNL is developing plans for a new 1.5 to 2 mega-joule solid-state Nd:glass laser designed to achieve fusion ignition. The new design is possible in part due to advances in optical coatings suitable for high power laser systems. High damage threshold mirrors and polarizers are comprised of electron beam deposited dielectric multilayers. Subthreshold illumination, or laser conditioning, of the multilayer coatings results in an increase in the damage thresholds by factors of 2 to 3 at 1.06?m, thus meeting the fluence requirements of the advanced architecture. For anti-reflective coatings, protective organic coatings for non-linear crystals and phase plates for beam smoothing, sol-gel films provide high damage thresholds coatings at low cost


Narrow linewidth picosecond pulsed laser with mega-watt peak power at UV wavelength  

Energy Technology Data Exchange (ETDEWEB)

We demonstrate a master oscillator power amplifier (MOPA) burst mode laser system to generate 66 ps/402.5 MHz pulses with mega-watt peak power at 355 nm. The seed laser is based on a direct electro-optic modulation of a fiber laser output. A very high extinction ratio (45 dB) has been achieved by using an adaptive bias control. The multi-stage Nd:YAG amplifier system allows a uniformly temporal shaping of macropulses with tunable pulse duration. The light output form the amplifier is converted to 355 nm and over 1 MW UV peak power is obtained when the laser is operating in a 5- s/10-Hz macropulse mode. The laser output has a transform limited spectrum bandwidth with a very narrow linewidth of individual laser mode. The immediate application of the laser system is the laser assisted hydrogen ion beam stripping for the Spallation Neutron Source (SNS).

Liu, Yun [ORNL; Huang, Chunning [ORNL; Deibele, Craig Edmond [ORNL



Conjugal transfer of group B streptococcal plasmids and comobilization of Escherichia coli-Streptococcus shuttle plasmids to Lactobacillus plantarum.  

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The antibiotic resistance group B streptococcal plasmids, pIP501 and pVA797, were conjugally transferred from Streptococcus faecalis to Lactobacillus plantarum. The Escherichia coli-Streptococcus shuttle plasmids, pVA838 and pSA3, were mobilized from S. sanguis to L. plantarum by pVA797 via cointegrate formation. pVA838 readily resolved from pVA797 and was present in L. plantarum as deletion derivatives. The pVA797::pSA3 cointegrate failed to resolve in L. plantarum.

Shrago, A. W.; Dobrogosz, W. J.



Aerosol chemical characteristics of a mega-city in Southeast Asia (Dhaka-Bangladesh) (United States)

Elemental carbon (EC), organic carbon (OC), organic acids, major inorganic ions and trace elements were determined in aerosol samples collected under pre-monsoon conditions (March-April 2001) in Dhaka (Bangladesh). Using the Fe content of the aerosol to reconstruct the aerosol mass from soil-type mineralic material, a mass balance of the Dhaka aerosol was achieved. From this follows that on the average around 76% of the aerosol is from soil-type material, around 18% of carbonaceous material, and around 6% soluble ions and trace elements (without iron) Dhaka aerosol, while As appears to be of geogenic origin. Organic acids contributed only 0.72% C to OC and were much less abundant relative to OC than at European sites. The trace elements levels in Dhaka were much lower than at comparable Southeast Asian mega-cities (e.g. Lahore, Pakistan), but considerably higher than reported for European and US cities under present day conditions. The correlation between EC and OC was quite high ( R2=0.81) indicating a potential joint source of emission for carbonaceous aerosols. The EC/total carbon (TC) and K/EC ratios indicated that biomass combustion was not a main contributor to EC in Dhaka, which implicates that fossil fuel combustion is the major contributor to EC levels in the Dhaka aerosol. The differences in the EC/TC and K/EC ratios in the three mega-cities in Southeast Asia (data available from Dhaka, Bangladesh; Lahore, Pakistan; and Mumbai, India) indicate that the aerosol source mix in Southeast Asian cities varies considerably at a national or even regional scale.

Salam, Abdus; Bauer, Heidi; Kassin, Karin; Mohammad Ullah, Shah; Puxbaum, Hans


Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches  

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Full Text Available Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Results Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae with 13,533 species and 1,401 sites. Conclusion By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations underscore the importance of using large phylogenies to uncover important evolutionary patterns and we present a fast and simple method for constructing these phylogenies.

Beaulieu Jeremy M



The application of water soluble, mega-Stokes-shifted BODIPY fluorophores to cell and tissue imaging. (United States)

BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) fluorophores are widely used in bioimaging to label proteins, lipids and nucleotides, but in spite of their attractive optical properties they tend to be prone to self-quenching because of their notably small Stokes shift. Herein, we compare two BODIPY compounds from a recently developed family of naphthyridine substituted BODIPY derivatives, one a visible emitting derivative (BODIPY-VIS) and one a near-infrared emitting fluorophore with a Stokes shift of approximately 165 nm as contrast reagents for live mammalian cells and murine brain tissue. The compounds were rendered water soluble by their conjugation to polyethylene glycol (PEG). Both PEGylated compounds exhibited good cell uptake compared with their parent compounds and confocal fluorescence microscopy revealed all dyes explored to be nuclear excluding, localizing predominantly within the lipophilic organelles; the endoplasmic reticulum and mitochondria. Cytotoxicity studies revealed that these BODIPY derivatives are modestly cytotoxic at concentrations exceeding 10 ?M where they induce apoptosis and necrosis. Although the quantum yield of emission of the visible emitting fluorophore was over an order of magnitude greater than the Mega-Stokes shifted probe, the latter showed considerably reduced tendency to self quench and less interference from autofluorescence. The near-infrared probe also showed good penetrability and staining in live tissue samples. In the latter case similar tendency to exclude the nucleus and to localize in the mitochondria and endoplasmic reticulum was observed as in live cells. This to our knowledge is the first demonstration of such a Mega-Stokes BODIPY probe applied to cell and tissue imaging. PMID:24467513

Moriarty, R D; Martin, A; Adamson, K; O'Reilly, E; Mollard, P; Forster, R J; Keyes, T E



Description of a 2,683-Base-Pair Plasmid Containing qnrD in Two Providencia rettgeri Isolates (United States)

qnr genes are plasmid-mediated quinolone resistance genes mainly harbored on large conjugative multiresistant plasmids. The qnrD gene was recently observed in Salmonella enterica on a small nonconjugative plasmid (p2007057). We describe two strains of Providencia rettgeri harboring qnrD on nonconjugative plasmids. The plasmids were 99% identical, with 2,683 bp and four open reading frames, including qnrD, but exhibited only 53% identity with the plasmid found in S. enterica. PMID:21986831

Cambau, Emmanuelle; Neuwirth, Catherine; Nenninger, Thomas; Mbadi, Aurore; Brasme, Lucien; Vernet-Garnier, Veronique; Bajolet, Odile; de Champs, Christophe




Plasmid pSI30 was constructed to increase the sensitivity of detection of a genetically engineered microorganism (GEM) and its recombinant DNA in environmental samples. his broad host-range, mobilizable plasmid contained chlorocatechol (clc) degradative genes, antibiotic resistan...


Selection criteria of residents for residency programs in Kuwait  

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Full Text Available Abstract Background In Kuwait, 21 residency training programs were offered in the year 2011; however, no data is available regarding the criteria of selecting residents for these programs. This study aims to provide information about the importance of these criteria. Methods A self-administered questionnaire was used to collect data from members (e.g. chairmen, directors, assistants …etc. of residency programs in Kuwait. A total of 108 members were invited to participate. They were asked to rate the importance level (scale from 1 to 5 of criteria that may affect the acceptance of an applicant to their residency programs. Average scores were calculated for each criterion. Results Of the 108 members invited to participate, only 12 (11.1% declined to participate. Interview performance was ranked as the most important criteria for selecting residents (average score: 4.63/5.00, followed by grade point average (average score: 3.78/5.00 and honors during medical school (average score: 3.67/5.00. On the other hand, receiving disciplinary action during medical school and failure in a required clerkship were considered as the most concerning among other criteria used to reject applicants (average scores: 3.83/5.00 and 3.54/5.00 respectively. Minor differences regarding the importance level of each criterion were noted across different programs. Conclusions This study provided general information about the criteria that are used to accept/reject applicants to residency programs in Kuwait. Future studies should be conducted to investigate each criterion individually, and to assess if these criteria are related to residents' success during their training.

Marwan Yousef



The resolution and regeneration of a cointegrate plasmid reveals a model for plasmid evolution mediated by conjugation and oriT site-specific recombination. (United States)

Cointegrate plasmids are useful models for the study of plasmid evolution if their evolutionary processes can be replicated under laboratory conditions. pBMB0228, a 17?706?bp native plasmid originally isolated from Bacillus thuringiensis strain YBT-1518, carries two nematicidal crystal protein genes, cry6Aa and cry55Aa. In this study, we show that pBMB0228 is in fact a cointegrate of two plasmids and contains two functional replication regions and two functional mobilization regions. Upon introduction into B.?thuringiensis strain BMB171, pBMB0228 spontaneously resolves into two constituent plasmids via recombination at its oriT1 and oriT2 sites. The resolution does not require conjugation but can be promoted by conjugation. We further confirm that the resolution is mediated by oriT site-specific recombination requiring Mob02281 or Mob02282. Additionally, the two constituent plasmids of pBMB0228 are mobilizable, and can fuse back via oriT site-specific integration after entering into the same cell by conjugation. Our study confirms that native plasmid can reversibly interconvert between a cointegrate structure and its constituent plasmids. This study provides insight into the evolution of cointegrate plasmids, linking plasmid evolution with conjugation and the oriT site-specific recombination function of relaxase. PMID:23826996

Wang, Pengxia; Zhang, Chunyi; Zhu, Yiguang; Deng, Yun; Guo, Suxia; Peng, Donghai; Ruan, Lifang; Sun, Ming



Virulence genes promote conjugative transfer of the Ti plasmid between Agrobacterium strains.  

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Certain virulence region operons of the Agrobacterium tumefaciens Ti plasmid promoted conjugative Ti plasmid transfer. Mutations in the vir region of pTiC58 inhibited conjugative plasmid transfer between A. tumefaciens strains. Mutations in virA, virG, 5' virB, and virE had the greatest effect on plasmid transfer, and mutations in virC had no effect. Transfer inhibition in vir mutants occurred in the presence or absence of acetosyringone.

Steck, T. R.; Kado, C. I.



Plasmid Heterogeneity in Spanish Isolates of Agrobacterium tumefaciens from Thirteen Different Hosts  

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Plasmid DNA was isolated from 80 Spanish isolates of Agrobacterium tumefaciens from 13 hosts of several geographical and temporal origins. One to five plasmids occurred in all of the isolates studied. Plasmid sizes varied between 5 and greater than 1,000 MDa. Generally, there was no correlation between plasmid number or size and geographical origin, host, biovar, sensitivity to agrocin 84, or opine-catabolizing ability of the different isolates.

Albiach, Maria R.; Lopez, Maria M.



Plasmid marker rescue transformation proceeds by breakage-reunion in Bacillus subtilis.  

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Bacillus subtilis carrying a plasmid which replicates with a copy number of about 1 was transformed with linearized homologous plasmid DNA labeled with the heavy isotopes 2H and 15N, in the presence of 32Pi and 6-(p-hydroxyphenylazo)-uracil to inhibit DNA replication. Plasmid DNA was isolated from the transformed culture and fractionated in cesium chloride density gradients. The distribution of total and donor plasmid DNA was examined, using specific hybridization probes. The synthesis of new...

Weinrauch, Y.; Dubnau, D.



Characterization of a circular plasmid from Borrelia burgdorferi, etiologic agent of Lyme disease.  

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Borrelia burgdorferi, the etiologic agent of Lyme disease, was recently shown to contain plasmid DNA. Two plasmid species have been described in strain CT1, a Wisconsin tick isolate: a 9.2-kilobase entity; and a larger, 70-kilobase entity. Characterization of the 9.2-kilobase entity by using DNase I and restriction endonucleases demonstrated that the plasmid is supercoiled and exists as a stable dimer in this strain. The role played by the plasmid in B. burgdorferi is unknown.

Hyde, F. W.; Johnson, R. C.



Plasmid DNA damage caused by stibine and trimethylstibine  

International Nuclear Information System (INIS)

equipotent with trimethylarsine using this plasmid DNA-nicking assay. Reaction of trimethylantimony dichloride with either glutathione or L-cysteine to produce DNA-damaging trimethylstibine was observed with a trimethylantimony dichloride concentration as low as 50 ?M and L-cysteine or glutathione concentrations as low as 500 and 200 ?M, respectively, for a 24 h incubation


Recombinogenic engineering of conjugative plasmids with fluorescent marker cassettes  

DEFF Research Database (Denmark)

An efficient approach for the insertion of fluorescent marker genes with sequence specificity into conjugative plasmids in Escherichia coli is described. For this purpose, homologous recombination of linear double-stranded targeting DNA was mediated by the bacteriophage lambda recombination functions using very short regions of homology. Initial manipulation of the IncFII target plasmids R1 and R1drd19 indicated that the linear targeting DNA should be devoid of all extraneous homologies to. the target molecule for optimal insertion specificity. Indeed, a simple recombination assay proved that in the presence of additional homologous regions in the targeting DNA, strand exchanges occurred exclusively within the longest regions of homology. A versatile panel of vectors was created to facilitate convenient PCR amplification of targeting DNAs containing various combinations of different antibiotic resistance genes and fluorescent markers. The choice of 5' non-homologous extensions in primer pairs used for amplifying the marker cassettes determines the site specificity of the targeting DNA. This methodology is applicable to the modification of all plasmids that replicate in E coli and is not restricted by plasmid size.

Molin, SØren



Geminiviruses: a tale of a plasmid becoming a virus  

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Full Text Available Abstract Background Geminiviruses (family Geminiviridae are small single-stranded (ss DNA viruses infecting plants. Their virion morphology is unique in the known viral world – two incomplete T = 1 icosahedra are joined together to form twinned particles. Geminiviruses utilize a rolling-circle mode to replicate their genomes. A limited sequence similarity between the three conserved motifs of the rolling-circle replication initiation proteins (RCR Reps of geminiviruses and plasmids of Gram-positive bacteria allowed Koonin and Ilyina to propose that geminiviruses descend from bacterial replicons. Results Phylogenetic and clustering analyses of various RCR Reps suggest that Rep proteins of geminiviruses share a most recent common ancestor with Reps encoded on plasmids of phytoplasmas, parasitic wall-less bacteria replicating both in plant and insect cells and therefore occupying a common ecological niche with geminiviruses. Capsid protein of Satellite tobacco necrosis virus was found to be the best template for homology-based structural modeling of the geminiviral capsid protein. Good stereochemical quality of the generated models indicates that the geminiviral capsid protein shares the same structural fold, the viral jelly-roll, with the vast majority of icosahedral plant-infecting ssRNA viruses. Conclusion We propose a plasmid-to-virus transition scenario, where a phytoplasmal plasmid acquired a capsid-coding gene from a plant RNA virus to give rise to the ancestor of geminiviruses.

Krupovic Mart



[Chromatographic separation of plasmid DNA by anion-exchange cryogel]. (United States)

Plasmid DNA (pDNA) is used as an important vector for gene therapy, and its wide application is restricted by the purity and yield. To obtain high-purity pDNA, a chromatographic method based on anion-exchange supermacroporous cryogel was explored. The anion-exchange cryogel was prepared by grafting diethylaminoethyl-dextran to the epoxide groups of polyacrylamide-based matrix and pUC19 plasmid was used as a target to test the method. The plasmid was transferred into Escherichia coli DH5alpha, cultivated, harvested and lysed. The obtained culture was centrifuged and the supernatant was used as the plasmid feedstock, which was loaded into the anion-exchange cryogel bed for chromatographic separation. By optimizing the pH of running buffer and the elution conditions, high-purity pDNA was obtained by elution with 0.5 mol/L sodium chloride solution at pH 6.6. Compared to the traditional methods for purification of pDNA, animal source enzymes and toxic reagents were not involved in the present separation process, ensuring the safety of both the purification operations and the obtained pDNA. PMID:23185899

Guo, Yantao; Shen, Shaochuan; Yun, Junxian; Yao, Kejian



Cloning vectors for Streptococcus thermophilus derived from a native plasmid. (United States)

A 3.5-kb native plasmid (pND103) was identified in Streptococcus thermophilus ST2-1. Preliminary sequence analysis indicated that pND103 belongs to group I S. thermophilus plasmids. A region of approximately 2 kb appears to contain three components: a plus origin of replication (ori) typical of plasmids that replicate via rolling circle replication; a gene encoding a replication protein (rep); and a gene encoding a small heat shock protein (hsp). pND103 was then used to construct S. thermophilus/Escherichia coli hybrid cloning vectors by ligating different portions of pND103 to an origin-probe vector (pND330) composed of pUC19 and a Gram-positive erythromycin resistance gene. The shuttle vectors (pND913, pND914 and pND915) were successfully introduced back into plasmid-free S. thermophilus ST3-1 as well as to Lactococcus lactis LM0230 and E. coli JM109. Segregational and structural stability study indicated that these vectors can be maintained in these hosts. The results indicated that pND913, pND914 and pND915 are potential shuttle cloning vectors for S. thermophilus. PMID:12423750

Su, Ping; Jury, Karen; Allison, Gwen E; Wong, Wing Yee; Kim, Woojin S; Liu, Chun-Qiang; Vancov, Tony; Dunn, Noel W



Tragedy of the commons among antibiotic resistance plasmids. (United States)

As social interactions are increasingly recognized as important determinants of microbial fitness, sociobiology is being enlisted to better understand the evolution of clinically relevant microbes and, potentially, to influence their evolution to aid human health. Of special interest are situations in which there exists a "tragedy of the commons," where natural selection leads to a net reduction in fitness for all members of a population. Here, I demonstrate the existence of a tragedy of the commons among antibiotic resistance plasmids of bacteria. In serial transfer culture, plasmids evolved a greater ability to superinfect already-infected bacteria, increasing plasmid fitness when evolved genotypes were rare. Evolved plasmids, however, fell victim to their own success, reducing the density of their bacterial hosts when they became common and suffering reduced fitness through vertical transmission. Social interactions can thus be an important determinant of evolution for the molecular endosymbionts of bacteria. These results also identify an avenue of evolution that reduces proliferation of both antibiotic resistance genes and their bacterial hosts. PMID:22486703

Smith, Jeff




The concentration of plasmid pBR322 DNA in nonculturable Escherichia coli JM83 was measured to determine whether the plasmid concentration changed during survival of E. coli in marine and estuarine water. . coli JM83 containing the plasmid pBR322 was placed in both sterile seawat...


Complete Genome Sequences of IncI1 Plasmids Carrying Extended-Spectrum ?-Lactamase Genes (United States)

Extended spectrum beta-lactamases (ESBLs) confer resistance to clinically relevant antibiotics. Often, the resistance genes are carried by conjugative plasmids which are responsible for dissemination. Five IncI1 plasmids carrying ESBLs from commensal and clinical Escherichia coli isolates were completely sequenced and annotated along with a non-ESBL carrying IncI1 plasmid. PMID:25169863

Bossers, Alex; Harders, Frank; van Essen-Zandbergen, Alieda; Mevius, Dik J.



Complete Genome Sequences of IncI1 Plasmids Carrying Extended-Spectrum ?-Lactamase Genes. (United States)

Extended spectrum beta-lactamases (ESBLs) confer resistance to clinically relevant antibiotics. Often, the resistance genes are carried by conjugative plasmids which are responsible for dissemination. Five IncI1 plasmids carrying ESBLs from commensal and clinical Escherichia coli isolates were completely sequenced and annotated along with a non-ESBL carrying IncI1 plasmid. PMID:25169863

Brouwer, Michael S M; Bossers, Alex; Harders, Frank; van Essen-Zandbergen, Alieda; Mevius, Dik J; Smith, Hilde E



NIC, a conjugative nicotine-nicotinate degradative plasmid in Pseudomonas convexa. (United States)

The plasmid nature of genes specifying degradation of nicotine and nicotinate in Pseudomas convexa strain 1 (Pc1) is indicated by mitomycin curing and conjugational transfer to other strains. The NIC plasmid appears to be compatible with other metabolic plasmids in Pseudomonas putida. PMID:670150

Thacker, R; Rørvig, O; Kahlon, P; Gunsalus, I C



The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated  

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Full Text Available Abstract Background Staphylococcus aureus is major human and animal pathogen. Plasmids often carry resistance genes and virulence genes that can disseminate through S. aureus populations by horizontal gene transfer (HGT mechanisms. Sequences of S. aureus plasmids in the public domain and data from multi-strain microarrays were analysed to investigate (i the distribution of resistance genes and virulence genes on S. aureus plasmids, and (ii the distribution of plasmids between S. aureus lineages. Results A total of 21 plasmid rep gene families, of which 13 were novel to this study, were characterised using a previously proposed classification system. 243 sequenced plasmids were assigned to 39 plasmid groups that each possessed a unique combination of rep genes. We show some resistance genes (including ermC and cat and virulence genes (including entA, entG, entJ, entP were associated with specific plasmid groups suggesting there are genetic pressures preventing recombination of these genes into novel plasmid groups. Whole genome microarray analysis revealed that plasmid rep, resistance and virulence genes were associated with S. aureus lineages, suggesting restriction-modification (RM barriers to HGT of plasmids between strains exist. Conjugation transfer (tra complex genes were rare. Conclusion This study argues that genetic pressures are restraining the spread of resistance and virulence genes amongst S. aureus plasmids, and amongst S. aureus populations, delaying the emergence of fully virulent and resistant strains.

McCarthy Alex J



Mix and match of KPC-2 encoding plasmids in Enterobacteriaceae-comparative genomics. (United States)

We performed comparative sequence analysis of 3 blaKPC-2 encoding plasmids to examine evolution of these plasmids and their dissemination. We found that all of them have an IncN replicon with a newly determined IncN plasmid sequence type (ST), ST15. The 2 Klebsiella pneumoniae (KPN) plasmids also harbor an IncF2A1-B1- replicon. The blaKPC-2 is located in the Tn4401c transposon with a newly discovered mutation in the P2 promoter. Screening of the 27 additional blaKPC-2 carrying plasmids from Enterobacter cloacae, Escherichia coli (EC), and K. pneumoniae showed that: all KPN and EC plasmids are IncN plasmids belonging to ST15; 4/7 KPN and 1/6 EC plasmids contain an additional IncF2A1-B1- replicon; all Enterobacter plasmids belong to neither IncN nor IncF2A1-B1- replicon plasmids; 6/7 KPN and 2/5 EC plasmids carry the mutated P2 promoter. Study of the blaKPC-2 environment, transposon, pMLST, and Inc group suggests transposon and plasmid inter- and intra-species dissemination and evolution. PMID:24743043

Chmelnitsky, Inna; Shklyar, Maya; Leavitt, Azita; Sadovsky, Evgeniya; Navon-Venezia, Shiri; Ben Dalak, Maayan; Edgar, Rotem; Carmeli, Yehuda



Plasmid transformation of competent Bacillus subtilis by lysed protoplast DNA. (United States)

Transformation of competent Bacillus subtilis with DNA obtained from lysed protoplasts (LP transformation) was analyzed using several different plasmid vectors: pC194, pUB110, pCB1 (consisting of pC194 and pBluescript II SK+), and pAC32R2 (consisting of pUB110 derivative and pUC19). LP transformation of B. subtilis QB936 with pCB1 was 6500-fold higher than that achieved using conventional transformation with purified DNA. Greater transformation efficiencies were also obtained using pAC32R2. However, transformation frequencies using both protoplast-derived and purified pC194 were very low (1.4-2.0×10(2) transformants per ?g DNA). Hence, the efficiency of transformation depends on the nucleotide sequence of the donor plasmid. The LP transformation frequency using pC194 obtained from an add5 mutant was remarkably enhanced (1.6×10(8) transformants per ?g DNA), indicating that this unique form of high molecular weight DNA is likely responsible for part of the stimulatory effect. Chromosomal DNA inhibited plasmid transformation using pC194 and pUB110, but had little effect on pCB1 transformation. Conversely, pCB1 DNA did not inhibit transformation with protoplast-derived chromosomal DNA. Competence proteins under the control of transcription factor ComK were likely required for LP plasmid transformation. The DNA concentration-dependence of plasmid transformation was first order and the slope value was one. PMID:22564792

Akamatsu, Takashi; Taguchi, Hisataka



Plasmid copy number underlies adaptive mutability in bacteria. (United States)

The origin of mutations under selection has been intensively studied using the Cairns-Foster system, in which cells of an Escherichia coli lac mutant are plated on lactose and give rise to 100 Lac(+) revertants over several days. These revertants have been attributed variously to stress-induced mutagenesis of nongrowing cells or to selective improvement of preexisting weakly Lac(+) cells with no mutagenesis. Most revertant colonies (90%) contain stably Lac(+) cells, while others (10%) contain cells with an unstable amplification of the leaky mutant lac allele. Evidence is presented that both stable and unstable Lac(+) revertant colonies are initiated by preexisting cells with multiple copies of the F'lac plasmid, which carries the mutant lac allele. The tetracycline analog anhydrotetracycline (AnTc) inhibits growth of cells with multiple copies of the tetA gene. Populations with tetA on their F'lac plasmid include rare cells with an elevated plasmid copy number and multiple copies of both the tetA and lac genes. Pregrowth of such populations with AnTc reduces the number of cells with multiple F'lac copies and consequently the number of Lac(+) colonies appearing under selection. Revertant yield is restored rapidly by a few generations of growth without AnTc. We suggest that preexisting cells with multiple F'lac copies divide very little under selection but have enough energy to replicate their F'lac plasmids repeatedly until reversion initiates a stable Lac(+) colony. Preexisting cells whose high-copy plasmid includes an internal lac duplication grow under selection and produce an unstable Lac(+) colony. In this model, all revertant colonies are initiated by preexisting cells and cannot be stress induced. PMID:25173846

Sano, Emiko; Maisnier-Patin, Sophie; Aboubechara, John Paul; Quiñones-Soto, Semarhy; Roth, John R



Short-lived tectonic switch mechanism for long-term pulses of volcanic activity after mega-thrust earthquakes  

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Full Text Available Eruptive rates in volcanic arcs increase significantly after mega-thrust earthquakes in subduction zones. Over short to intermediate time periods the link between mega-thrust earthquakes and arc response can be attributed to dynamic triggering processes or static stress changes, but a fundamental mechanism that controls long-term pulses of volcanic activity after mega-thrust earthquakes has not been proposed yet. Using geomechanical, geological, and geophysical arguments, we propose that increased eruption rates over longer timescales are due to the relaxation of the compressional regime that accompanies mega-thrust subduction zone earthquakes. More specifically, the reduction of the horizontal stress ?h promotes the occurrence of short-lived strike-slip kinematics rather than reverse faulting in the volcanic arc. The relaxation of the pre-earthquake compressional regime facilitates magma mobilization by providing a short-circuit pathway to shallow depths by significantly increasing the hydraulic properties of the system. The timescale for the onset of strike-slip faulting depends on the degree of shear stress accumulated in the arc during inter-seismic periods, which in turn is connected to the degree of strain-partitioning at convergent margins. We performed Coulomb stress transfer analysis to determine the order of magnitude of the stress perturbations in present-day volcanic arcs in response to five actual mega-thrust earthquakes; the 2005 M8.6, 2007 M8.5, and 2007 M7.9 Sumatra earthquakes; the 2010 M8.8 Maule, Chile earthquake; and the 2011 M9.0 Tohoku, Japan earthquake. We find that all, but one, the shallow earthquakes that occurred in the arcs of Sumatra, Chile and Japan show a marked lateral component. Our hypothesis suggests that the long-term response of volcanic arcs to subduction zone mega-thrust earthquakes will be manifested as predominantly strike-slip seismic events, and that these future earthquakes will be followed closely by seismic swarms, inflation, and other indications of a rising magma source.

M. Lupi



Gene delivery of bone morphogenetic protein-2 plasmid DNA promotes bone formation in a large animal model. (United States)

In the field of bone regeneration, BMP-2 is considered one of the most important growth factors because of its strong osteogenic activity, and is therefore extensively used in clinical practice. However, the short half-life of BMP-2 protein necessitates the use of supraphysiological doses, leading to severe side-effects. This study investigated the efficiency of bone formation at ectopic and orthotopic sites as a result of a low-cost, prolonged presence of BMP-2 in a large animal model. Constructs consisting of alginate hydrogel and BMP-2 cDNA, together acting as a non-viral gene-activated matrix, were combined with goat multipotent stromal cells (gMSCs) and implanted in spinal cassettes or, together with ceramic granules, intramuscularly in goats, both for 16 weeks. Bone formation occurred in all cell-seeded ectopic constructs, but the constructs containing both gMSCs and BMP-2 plasmid DNA showed higher collagen I and bone levels, indicating an osteogenic effect of the BMP-2 plasmid DNA. This was not seen in unseeded constructs, even though transfected, BMP-2-producing cells were detected in all constructs containing plasmid DNA. Orthotopic constructs showed mainly bone formation in the unseeded groups. Besides bone, calcified alginate was present in these groups, acting as a surface for new bone formation. In conclusion, transfection of seeded or resident cells from this DNA delivery system led to stable expression of BMP-2 during 16 weeks, and promoted osteogenic differentiation and subsequent bone formation in cell-seeded constructs at an ectopic location and in cell-free constructs at an orthotopic location in a large animal model. Copyright © 2012 John Wiley & Sons, Ltd. PMID:22888035

Wegman, Fiona; Geuze, Ruth E; van der Helm, Yvonne J; Cumhur Öner, F; Dhert, Wouter J A; Alblas, Jacqueline



42 CFR 483.10 - Resident rights. (United States)

...implements at the resident's own expense. (j) Access and visitation rights. (1) The resident... The resident has the right to have reasonable access...calls can be made without being overheard. (l) Personal... The resident has the right to retain and use...



38 CFR 51.70 - Resident rights. (United States)

...implements at the resident's own expense. (j) Access and visitation rights. (1) The resident... The resident has the right to reasonable access to...calls can be made without being overheard. (l) Personal... The resident has the right to retain and use...



DNA Sequence of a ColV Plasmid and Prevalence of Selected Plasmid-Encoded Virulence Genes among Avian Escherichia coli Strains  

Digital Repository Infrastructure Vision for European Research (DRIVER)

ColV plasmids have long been associated with the virulence of Escherichia coli, despite the fact that their namesake trait, ColV production, does not appear to contribute to virulence. Such plasmids or their associated sequences appear to be quite common among avian pathogenic E. coli (APEC) and are strongly linked to the virulence of these organisms. In the present study, a 180-kb ColV plasmid was sequenced and analyzed. This plasmid, pAPEC-O2-ColV, possesses a 93-kb region containing severa...

Johnson, Timothy J.; Siek, Kylie E.; Johnson, Sara J.; Nolan, Lisa K.



Long- term manure exposure increases soil bacterial community potential for plasmid uptake  

DEFF Research Database (Denmark)

Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent and was dominated by ?- and ?-Proteobacteria.

Musovic, Sanin; Klümper, Uli



Conservation of Plasmid-Encoded Traits among Bean-Nodulating Rhizobium Species (United States)

Rhizobium etli type strain CFN42 contains six plasmids. We analyzed the distribution of genetic markers from some of these plasmids in bean-nodulating strains belonging to different species (Rhizobium etli, Rhizobium gallicum, Rhizobium giardinii, Rhizobium leguminosarum, and Sinorhizobium fredii). Our results indicate that independent of geographic origin, R. etli strains usually share not only the pSym plasmid but also other plasmids containing symbiosis-related genes, with a similar organization. In contrast, strains belonging to other bean-nodulating species seem to have acquired only the pSym plasmid from R. etli. PMID:11976134

Brom, Susana; Girard, Lourdes; Garcia-de los Santos, Alejandro; Sanjuan-Pinilla, Julio M.; Olivares, Jose; Sanjuan, Juan



Mega jardines infantiles: heterotopías para el gobierno de la población infantil en Medellín / Mega-kindergartens: heterotopias for governing the infant population in Medellin / Mega jardins de infância: heterotopias para o governo da população infantil em Medellin  

Scientific Electronic Library Online (English)

Full Text Available SciELO Colombia | Language: Spanish Abstract in portuguese No marco de uma política integral de atenção para a infância, durante as últimas administrações a cidade de Medellín realizou um grande investimento em infraestrutura, especificamente para a construção, em lugares estratégicos da cidade, de grandes jardins de infância. Este texto tem como propósito [...] pensar em chave foucaultiana esses espaços como heterotopias, isto é, como espaços para o governo (governamentalidade) da população infantil. No texto se considera que a reestruturação e ressignificação do espaço educativo escolar e das práticas desenvolvidas na sua interioridade não obedecem, principalmente, a uma preocupação pedagógica ou filantrópica que poderia ser interpretada de maneira independente de um contexto histórico e social, nas margens de determinados interesses e relações de poder. Numa primeira parte, seguindo Foucault, se revisa o conceito de heterotopia e se propõe que esses espaços educativos outros -além da sua função educativa e formativa- cumprem um papel governamental em quanto permitem o governo da população infantil ao constituírem-se em lugares estratégicos para a implantação de tecnologias sociais como a prevenção. Abstract in spanish En el marco de una nueva política de atención integral a la infancia, durante las últimas administraciones la ciudad de Medellín ha venido realizando una considerable inversión en infraestructura urbana, específicamente con la creación, en lugares estratégicos de la ciudad, de grandes jardines infan [...] tiles. Este escrito tiene como propósito pensar en clave foucaultiana esos espacios como heterotopías, es decir, como espacios otros para el gobierno (gubernamentalidad) de la población infantil. Partimos así, del presupuesto según el cual la reestructuración y resignificación del espacio educativo escolar y de las prácticas en su interior no obedece a una suerte de preocupación pedagógica y filantrópica que sin más se pueda considerar desligada de un contexto histórico y social y al margen de ciertos intereses y de ciertas relaciones de poder. Para ello, y de la mano de Foucault, en una primera parte se le pasa revista al concepto de heterotopía y a sus particularidades; en la segunda parte, se profundiza en la caracterización de los mega jardines infantiles como heterotopías y se plantea que estos espacios educativos otros -además de su función educativa y formativa- cumplen con un papel gubernamental en el sentido que permiten el gobierno de la población infantil gracias a que se convierten en lugares estratégicos para la implementación de tecnologías sociales como la prevención. Abstract in english Under a new policy of comprehensive child care during the past administrations Medellin has been making a considerable investment in urban infrastructure, specifically the creation in strategic locations in the city, large kindergartens. This paper aims to reflect upon these spaces as key Foucauldia [...] n heterotopias, ie, as other spaces for the government (governmentality) of children. So, we start from the estimation that restructuring and redefining educational space and practices therein are not due to a kind of educational and philanthropic concern that no more can be considered detached from a historical and social context and outside certain interests and certain power relations.

Andrés Klaus, Runge Peña; Sara Carolina, Carrillo David.



Novel DC ring topology and protection system - a comprehensive solution for mega city power grids (United States)

The development of mega cities leads to increased load concentration and brings additional challenges to managing the electrical grid while keeping power available for critical loads. Techniques using FACTS devices are being applied to alleviate power management difficulties and to confine faults in their originating areas in order to limit the risk of cascading failures in the grid. The addition of many FACTS devices often results in control and protection coordination difficulties, power oscillations between connected networks, subsynchronous resonance problems, and torsional interactions with nearby generator units. The most effective solution is obtained when the individual AC subsystems representing sources and loads are decoupled so a fault in a given subsystem is not propagated to another subsystem. This solution can be achieved by the deployment of a DC system where power sources and loads are connected to the DC bus through voltage source converters. For a mega city, this would be conceived as a DC ring feeding multiple loads and connected to remote and local power sources. Unfortunately, the lack of fast DC circuit breakers has been one of the key issues affecting extensive applications of DC systems with common DC buses; a DC fault would discharge all the capacitors of the DC bus and cause delays in system recovery and possibly a wide system collapse. In this research, I provide a comprehensive solution to mega city power grid problems by proposing a DC system topology that enables grid expansions without affecting existing protection settings or changing existing AC breaker ratings. I also propose the means for protecting the DC system by designing a fast DC breaker and developing a control algorithm capable of isolating DC faults without blocking converter stations or depleting DC bus capacitors. My contribution is three folds: (1) I modeled and simulated Shanghai power grid and performed a study to identify short circuit and voltage stability problems using data provided by ABB corporate research located in China. I built on the work that had been performed in ABB China by considering different contingencies and I applied solutions using individual FACTS devices such as FCL, SVC-LightRTM, and HVDC-LightRTM. I analyzed the results from each solution in order to assess its merits and limitations in dealing with fault current and voltage stability problems. Then I presented a novel DC ring topology that provides redundancy, better protection against cascading faults, and does not increase short circuit levels. With this topology, adding loads or power sources does not impact system protection or performance. (2) I proposed two novel designs for a DC circuit breaker that is of critical importance to DC applications using multiple converter stations. The proposed designs solve the problem of DC fault clearing without causing significant voltage drops, current oscillations, or shutting down of any converter station connected to the DC bus. The DC breaker rated at a voltage of 320 kV and a current of 3000 A can interrupt DC currents as high as 70 kA within 800 mus. (3) I proposed a novel placement of the DC circuit breakers within the DC ring topology combined with an intelligent protection algorithm that optimizes fault detection and isolation without affecting the rest of the DC system. The protection scheme uses local measurements and special coordination techniques for clearing solid faults and uses differential measurements to identify and isolate high impedance faults.

Haj-Maharsi, Mohamed Yassine


Tracking aeolian transport patterns across a mega-nourishment using video imagery (United States)

Coastal dune areas protect the hinterland from flooding. In order to maintain the safety level provided by the dunes, it may be necessary to artificially supply the beach-dune system with sand. How to best design these shore nourishments, amongst others with respect to optimal dune growth on the long-term (decadal scale), is not yet clear. One reason for this is that current models for aeolian transport on beaches appear to have limited predictive capabilities regarding annual onshore sediment supply. These limited capabilities may be attributed to the lack of appropriate input data, for instance on moisture content of the beach surface, or shortcomings in process understanding. However, it may also be argued that for the long-term prediction of onshore aeolian sand supply from the beach to the dunes, we may need to develop some aggregated-scale transport equations, because the detailed input data required for the application of process-scale transport equations may never be available in reality. A first step towards the development of such new concepts for aggregated-scale transport equations is to increase phenomenological insight into the characteristics and number of aeolian transport events that account for the annual volume changes of the foredunes. This requires high-frequency, long-term data sets to capture the only intermittently occurring aeolian transport events. Automated video image collection seems a promising way to collect such data. In the present study we describe the movement (direction and speed) of sand patches and aeolian bed forms across a nourished site, using video imagery, to characterize aeolian transport pathways and their variability in time. The study site is a mega-nourishment (21 Mm3 of sand) that was recently constructed at the Dutch coast. This mega-nourishment, also referred to as the Sand Motor, is a pilot project that may potentially replace current practice of more frequently applying small scale nourishments. The mega-nourishment site has been, and still is, monitored intensively since its construction in 2011. The monitoring program includes an Argus video system consisting of 8 cameras, mounted on a 40 meter high tower in the middle of the Sand Motor, which collects snap shots and time-exposure images every half an hour. Also two Pan-Tilt-Zoom cameras can be used to zoom in at specific locations. In addition to the remote sensing by Argus, also bathymetric and topographic surveys are conducted every two months, LIDAR flights cover the beach and dune area every six months, and in the near future dune topography will be measured using Terrestrial laser scanning. A weather station mounted at the tower also collects wind data. These additional data sources will be used later on to explain observed aeolian transport pathways and assess their effect on dune evolution.

Wijnberg, Kathelijne; van der Weerd, Lianne; Hulscher, Suzanne



Transmission rates and phenotypic effects of mitochondrial plasmids and cytotypes in Silene vulgaris. (United States)

We investigated the transmission properties and the phenotypic effects of two mitochondrial plasmids in a population of the bladder campion, Silene vulgaris. In reciprocal crosses between plasmid-free and plasmid-carrying plants, no cases of paternal transmission or loss during maternal transmission were recorded. Neither was any transmission via pollen observed when plasmid-carrying plants of S. vulgaris were used to pollinate plasmid-free plants of the closely related species Silene uniflora. The phenotypic effects of the plasmids were investigated by comparing germination rate, early growth properties, and the gender of plants grown from seeds with and without plasmids. A significant association between plasmid status, on the one hand, and germination propensity and offspring gender, on the other, was found. However, because all plants carrying plasmids in the experiment shared the same cytoplasmic background, the exact contribution of the plasmid to the phenotypic variation could not be determined. Taken together, our experiments show that in S. vulgaris the mt-plasmids are not currently involved in any strong genetic conflict, but that they evolve in close association with their mitochondrial host. PMID:12353751

Andersson-Ceplitis, Helene; Bengtsson, Bengt O



Partition-associated incompatibility caused by random assortment of pure plasmid clusters  

DEFF Research Database (Denmark)

Summary Bacterial plasmids and chromosomes encode centromere-like partition loci that actively segregate DNA before cell division. The molecular mechanism behind DNA segregation in bacteria is largely unknown. Here we analyse the mechanism of partition-associated incompatibility for plasmid pB171, a phenotype associated with all known plasmid-encoded centromere loci. An R1 plasmid carrying par2 from plasmid pB171 was destabilized by the presence of an F plasmid carrying parC1, parC2 or the entire par2 locus of pB171. Strikingly, cytological double-labelling experiments revealed no evidence of long-lived pairing of plasmids. Instead, pure R1 and F foci were positioned along the length of the cell, and in a random order. Thus, our results raise the possibility that partition-mediated plasmid incompatibility is not caused by pairing of heterologous plasmids but instead by random positioning of pure plasmid clusters along the long axis of the cell. The strength of the incompatibility was correlated with the capability of the plasmids to compete for the mid-cell position.

Ebersbach, Gitte; Sherratt, David J



Major families of multiresistant plasmids from geographically and epidemiologically diverse staphylococci. (United States)

Staphylococci are increasingly aggressive human pathogens suggesting that active evolution is spreading novel virulence and resistance phenotypes. Large staphylococcal plasmids commonly carry antibiotic resistances and virulence loci, but relatively few have been completely sequenced. We determined the plasmid content of 280 staphylococci isolated in diverse geographical regions from the 1940s to the 2000s and found that 79% of strains carried at least one large plasmid >20 kb and that 75% of these large plasmids were 20-30 kb. Using restriction fragment length polymorphism (RFLP) analysis, we grouped 43% of all large plasmids into three major families, showing remarkably conserved intercontinental spread of multiresistant staphylococcal plasmids over seven decades. In total, we sequenced 93 complete and 57 partial staphylococcal plasmids ranging in size from 1.3 kb to 64.9 kb, tripling the number of complete sequences for staphylococcal plasmids >20 kb in the NCBI RefSeq database. These plasmids typically carried multiple antimicrobial and metal resistances and virulence genes, transposases and recombinases. Remarkably, plasmids within each of the three main families were >98% identical, apart from insertions and deletions, despite being isolated from strains decades apart and on different continents. This suggests enormous selective pressure has optimized the content of certain plasmids despite their large size and complex organization. PMID:22384369

Shearer, Julia E S; Wireman, Joy; Hostetler, Jessica; Forberger, Heather; Borman, Jon; Gill, John; Sanchez, Susan; Mankin, Alexander; Lamarre, Jacqueline; Lindsay, Jodi A; Bayles, Kenneth; Nicholson, Ainsley; O'Brien, Frances; Jensen, Slade O; Firth, Neville; Skurray, Ronald A; Summers, Anne O



The Emotional Intelligence of Resident Physicians  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Since academic literature indicates that emotional intelligence (EI) is tied to work performance, there is increasing interest in understanding physician EI. We studied the EI of resident physicians in surgery, pediatric, and pathology residency programs at three academic centers to describe the EI profiles of residents in different specialties and determine whether gender differences in resident physician EI profiles mirror those in the general population. 325 residents were electronically...

Mckinley, Sophia Kim



Evolutionary dynamics of mitochondrial plasmids in natural populations of Silene vulgaris. (United States)

Although plasmid-like mitochondrial DNA molecules have been investigated in a number of cultivated plant species, knowledge about their occurrence and behavior in natural plant populations is scarce. In the bladder campion, Silene vulgaris, a common weed of northern Europe, mt-plasmids of three different sizes were detected in a survey of S. vulgaris populations in southern Sweden. Two of the three plasmids usually occurred together within individual plants and showed large variation in frequency between populations. From F(ST)-estimates of plasmids, mitochondrial markers, and nuclear markers it was concluded that the plasmids are predominantly maternally inherited in their natural habitat, as observed in greenhouse experiments. The association between mt-plasmids and mitochondrial haplotype was strong, but not complete, in the natural material. These results indicate that the mt-plasmids of S. vulgaris have evolved toward almost strict maternal inheritance. PMID:12353752

Andersson-Ceplitis, Helene



Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome. (United States)

Using a computational pipeline based on similarity networks reconstruction we analysed the 1133 genes of the Burkholderia vietnamiensis (Bv) G4 five plasmids, showing that gene and operon duplication played an important role in shaping the plasmid architecture. Several single/multiple duplications occurring at intra- and/or interplasmids level involving 253 paralogous genes (stand-alone, clustered or operons) were detected. An extensive gene/operon exchange between plasmids and chromosomes was also disclosed. The larger the plasmid, the higher the number and size of paralogous fragments. Many paralogs encoded mobile genetic elements and duplicated very recently, suggesting that the rearrangement of the Bv plastic genome is ongoing. Concerning the "molecular habitat" and the "taxonomical status" (the Preferential Organismal Sharing) of Bv plasmid genes, most of them have been exchanged with other plasmids of bacteria belonging (or phylogenetically very close) to Burkholderia, suggesting that taxonomical proximity of bacterial strains is a crucial issue in plasmid-mediated gene exchange. PMID:24576463

Maida, Isabel; Fondi, Marco; Orlandini, Valerio; Emiliani, Giovanni; Papaleo, Maria Cristiana; Perrin, Elena; Fani, Renato



Biological behavior of plasmid in Rhizobium sp. strain S25 from Tephrosia candida. (United States)

Rhizobium sp. strain S25 was isolated from the nodule on Tephrosia candida in Hainan Province, China. The strain showed high stress tolerance. The plasmid profile of strain S25, examined by the Eckhardt procedure, indicated that the strain harbors only one plasmid with an estimated size of 150 kb. The plasmid was shown to carry nod and nif genes by hybridization with probes of nodABC and nifHDK genes. Plasmid curing was carried out using the Bacillus subtilis sacB to generate derivatives of strain S25. In comparison with the parent strain S25, the cured derivative lost its ability to nodulate the host plant. Loss of the plasmid reduced significantly the strain's tolerance to acid, nitrous, and multiple antibiotics. The properties of the cured strain also indicated that the plasmid was involved in carbon and nitrogen metabolism. Reintroduction of the plasmid from S25 in the cured derivative restored its original biological phenotypes. PMID:9735317

Zou, X; Feng, X L; Chen, W X; Li, F D



Study on the effect of humidity and dust on leakage current of bulk micro-MEGAS detector  

CERN Document Server

In this paper, the effect of humidity and dust trapped in avalanche region on leakage current of bulk micro-MEGAS detector is studied. Pyralux PC1025 layers of DuPont are introduced in bulk technique and micro-MEGAS detector with pillars of 300{\\mu}m in diameter is fabricated. Leakage current is tested in air with different humidity. Silicon carbide powder and PMMA (polymethyl methacrylate) powder are added as dust to avalanche region. Leakage current with and without powder is tested in air and results are depicted in the same figure. Test results indicate that leakage current increases with both storage humidity and test humidity, and also increases when powder is introduced in avalanche region.

Wang, Bo; Qi, Hui-Rong; Liu, Jing; Zhang, Xin-Shuai; Zhang, Tian-Chong; Yi, Fu-Ting; Ou-Yang, Qun; Chen, Yuan-Bo



Studies on the drift properties and spatial resolution using a microMEGAS-equipped time projection chamber  

International Nuclear Information System (INIS)

R and D studies on the performance as well as on the gas properties of the microMEGAS-based time projection chamber with standard readout were carried out in June 2005 using 4 GeV/c pion beam in a magnetic field from 0 to 1 T at the proton synchrotron beam line at KEK, Japan. Analysis of the electron drift velocity, diffusion constant and point resolution of padrow measurement for MicroMEGAS TPC filled with 95% argon and 5% isobutane gas are presented. The underlying physical mechanism which determines the optimal TPC performance are briefly discussed. Preliminary measurements of gas properties and spatial resolution in close agreement with the analytical calculation and MAGBOLTZ simulation are summarized and presented in this paper. (author)


On the Strength of the Carbon Nanotube-Based Space Elevator Cable: From Nano- to Mega-Mechanics  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this paper different deterministic and statistical models, based on new quantized theories proposed by the author, are presented to estimate the strength of a real, thus defective, space elevator cable. The cable, of ~100 megameters in length, is composed by carbon nanotubes, ~100 nanometers long: thus, its design involves from the nano- to the mega-mechanics. The predicted strengths are extensively compared with the experiments and the atomistic simulations on carbon nan...

Pugno, Nicola M.



The in vivo J-difference editing MEGA-PRESS technique for the detection of n-3 fatty acids. (United States)

In this study, we present a method for the detection of n-3 fatty acid (n-3 FA) signals using MRS in adipose tissue in vivo. This method (called oMEGA-PRESS) is based on the selective detection of the CH3 signal of n-3 FA using the MEGA-PRESS (MEshcher-GArwood Point-RESolved Spectroscopy) J-difference editing technique. We optimized the envelope shape and frequency of spectral editing pulses to minimize the spurious co-editing and incomplete subtraction of the CH3 signal of other FAs, which normally obscure the n-3 FA CH3 signal in MR spectra acquired using standard PRESS techniques. The post-processing of the individual data scans with the phase and frequency correction before data subtraction and averaging was implemented to further improve the quality of in vivo spectra. The technique was optimized in vitro on lipid phantoms using various concentrations of n-3 FA and examined in vivo at 3 T on 15 healthy volunteers. The proportion of n-3 FA estimated by the oMEGA-PRESS method in phantoms showed a highly significant linear correlation with the n-3 FA content determined by gas chromatography. The signal attributed to n-3 FA was observed in all subjects. Comparisons with the standard PRESS technique revealed an enhanced identification of the n-3 FA signal using oMEGA-PRESS. The presented method may be useful for the non-invasive quantification of n-3 FA in adipose tissue, and could aid in obtaining a better understanding of various aspects of n-3 FA metabolism. Copyright © 2014 John Wiley & Sons, Ltd. PMID:25199506

Skoch, Antonín; Tošner, Zden?k; Hájek, Milan



Measuring the regional economic impact of mega-events: what are the benefits of the 2014 Olympics for Sochi?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The economic benefits of mega-events such as the Olympic Games are much touted but little quantified. This paper first presents a systematisation of the money streams associated with hosting the Olympic Games and then introduces basic concepts from regional economics. On this basis it outlines a general model that could be employed to estimate the regional economic impact of tourism associated with the Olympic Winter Games in Sochi in 2014.

Mu?ller, Martin



Clinical and radiological mid- to longterm results after transfer of the posterior femoral condyle (PCT) and MegaOATS  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Seit 1996 wird bei jungen und aktiven Patienten mit großen osteochondralen Defekten in der femoralen Belastungszone ein autologer Transfer der posterioren Femurkondyle (MegaOATS) durchgeführt. Ziel der Studie war die Evaluierung mittel- bis langfristiger Ergebnisse. Dazu wurden die ersten 33 Patienten nachuntersucht, Röntgenaufnahmen und von 16 Patienten MRTs angefertigt. Der mediane Lysholm Score stieg nach durchschnittlich 66,4 Monaten hochsignifikant (p<0,001) von praeoperativ 49,...

Minzlaff, Philipp



Urban entrepreneurialism and mega-events in transitional urban China : a case study of Expo 2010 in Shanghai  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Fordism-Keynesianism gradually transited to neoliberalism during 1970s economic recession in capitalist society, shifting urban governance from managerialism to entrepreneurialism. At the same time, China’s 1978 political-economic reform has led to a rapid development and a profound urban transformation characterized by globalization, neo-liberal decentralization and marketization over the past thirty years. To sustain the development and further promote the transformation, mega-events as o...

Li, Lingyue; ???



Navigating mega projects through complexity and uncertainty: strategic and adaptive capacity in planning and decision-making  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Over the last few decades, there has been an increasing interest in mega projects from both policy makers and academics. Of particular concern to both has been the seemingly structural time and cost overruns associated with these projects. In response a tendency, especially of policy makers, has been to look for ways of simplifying the decision and planning process. In academia the focus has been more on how to increase transparency and accountability in an attempt to prevent issues such as s...

Giezen, M.



Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. (United States)

Broad-host-range (BHR) IncP-1 plasmids have the ability to transfer between and replicate in nearly all species of the Alpha-, Beta- and Gammaproteobacteria, but surprisingly few data are available on the stability of these plasmids in strains within their host range. Moreover, even though molecular interactions between the bacterial host and its plasmid(s) exist, no systematic study to date has compared the stability of the same plasmid among different hosts. The goal of this study was to examine whether the stability characteristics of an IncP-1 plasmid can be variable between strains within the host range of the plasmid. Therefore, 19 strains within the Alpha-, Beta- or Gammaproteobacteria carrying the IncP-1beta plasmid pB10 were serially propagated in non-selective medium and the fraction of segregants was monitored through replica-picking. Remarkably, a large variation in the stability of pB10 in different strains was found, even between strains within the same genus or species. Ten strains showed no detectable plasmid loss over about 200 generations, and in two strains plasmid-free clones were only sporadically observed. In contrast, three strains, Pseudomonas koreensis R28, Pseudomonas putida H2 and Stenotrophomonas maltophilia P21, exhibited rapid plasmid loss within 80 generations. Parameter estimation after mathematical modelling of these stability data suggested high frequencies of segregation (about 0.04 per generation) or high plasmid cost (i.e. a relative fitness decrease in plasmid-bearing cells of about 15 and 40 %), which was confirmed experimentally. The models also suggested that plasmid reuptake by conjugation only played a significant role in plasmid stability in one of the three strains. Four of the 19 strains lost the plasmid very slowly over about 600 generations. The erratic decrease of the plasmid-containing fraction and simulation of the data with a new mathematical model suggested that plasmid cost was variable over time due to compensatory mutations. The findings of this study demonstrate that the ability of a so-called 'BHR' plasmid to persist in a bacterial population is influenced by strain-specific traits, and therefore observations made for one strain should not be generalized for the entire species or genus. PMID:17259616

De Gelder, Leen; Ponciano, José M; Joyce, Paul; Top, Eva M



Spheroplast formation and plasmid isolation from Rhodococcus spp. (United States)

The genus Rhodococcus comprises aerobic gram-positive actinomycetes that show considerable morphological and metabolic diversity and are known to be involved in the development of plant diseases and degradation of environmental pollutants. We describe a method for cell lysis and large plasmid DNA isolation from Rhodococcus by creating lysozyme susceptible cells by predigestion with the enzyme mutanolysin. Mutanolysin action resulted in the liberation of reducing sugars and free amino acids from the peptidoglycan layers of the cell wall. A 1-h predigestion with mutanolysin followed by a 0.5-h incubation with lysozyme resulted in spheroplast formation. Complete lysis of cells and efficient isolation of intact large plasmid DNA (108 kb) from wild-type Rhodococcus strains was confirmed. PMID:8292332

Assaf, N A; Dick, W A



Residence time vs influence time (United States)

The concepts of age, residence time, exposure time and influence time provide space and time dependent quantitative measures of the rate at which water masses and pollutants enter and/or leave a control domain. To help avoid confusion between these concepts, this paper provides clear definitions of the residence time and the influence time. The similarities and differences between them are illustrated using both a simplified 1D advection-diffusion model and a realistic two-dimensional model of the Scheldt Estuary (Belgium and the Netherlands). The residence time of a water parcel in a control domain is the time taken by this parcel to leave the control domain for the first time. The influence time is the time required to replace the water in the domain of interest by renewing water. For steady flows, the influence time is numerically identical to the age of the renewing water, but the two timescales differ for unsteady flows. The residence time measures the influence of a hypothetical point discharge on a control domain. In environmental studies, it provides a measure of the effectiveness of hydrodynamic processes at helping a semi-enclosed basin to recover from a local pollution event. The influence time quantifies the local influence of a tracer that would be uniformly distributed in the control domain at the initial time. It is therefore a relevant diagnostic tool in impact studies focusing on the local persistence of a pollution problem initially affecting a large domain.

Delhez, Éric J. M.; de Brye, Benjamin; de Brauwere, Anouk; Deleersnijder, Éric



The Virulence Plasmid of Yersinia, an Antihost Genome  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The 70-kb virulence plasmid enables Yersinia spp. (Yersinia pestis, Y. pseudotuberculosis, and Y. enterocolitica) to survive and multiply in the lymphoid tissues of their host. It encodes the Yop virulon, an integrated system allowing extracellular bacteria to disarm the cells involved in the immune response, to disrupt their communications, or even to induce their apoptosis by the injection of bacterial effector proteins. This system consists of the Yop proteins and their dedicated type III ...

Cornelis, G. R.; Boland, A.; Boyd, A. P.; Geuijen, C.; Iriarte, M.; Neyt, C.; Sory, M. P.; Stainier, I.



Improvement of bacterial transformation efficiency using plasmid artificial modification  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have developed a method to improve the transformation efficiency in genome-sequenced bacteria, using ‘Plasmid Artificial Modification’ (PAM), using the host's own restriction system. In this method, a shuttle vector was pre-methylated in Escherichia coli cells, which carry all the putative genes encoding the DNA modification enzymes of the target microorganism, before electroporation was performed. In the case of Bifidobacterium adolescentis ATCC15703 and pKKT427 (3.9 kb E. coli-Bifido...

Yasui, Kazumasa; Kano, Yasunobu; Tanaka, Kaori; Watanabe, Kunitomo; Shimizu-kadota, Mariko; Yoshikawa, Hirofumi; Suzuki, Tohru



Mercury and organomercurial resistance determined by plasmids in Staphylococcus aureus  

Energy Technology Data Exchange (ETDEWEB)

Four independently isolated plasmids of S. aureus contain genes conferring resistance to ionic mercury (Hg/sup 2 +/) and the organomercurials phenylmercury acetate (PMA), p-hydroxymeribenzoate (pHMB), and florescein mercuric acetate (FMA), but not merbromin, thiomerosal, methyl- or ethyl-mercury to which broad-range plasmids from other species confer resistance. The mechanism of resistance to PMA involves enzymatic hydrolysis (hydrolase) to benzene plus Hg/sup 2 +/ which is reduced (reductase) to Hg/sup 0/ and lost from the system by volatilization. The organomercurials, FMA, and pHMB are not degraded and resistance involves some other mechanism. Resistance to mercury and all organomercurials is inducible. The range of inducers includes mercury, PMA, and several organomercurials including merbromin which is not a substrate. Mercury-sensitive mutants have been isolated from plasmids pII147 and pI258 and they fall into three classes: (i) strains devoid of both hydrolase and reductase activities; (ii) strains with normal hydrolase activity, and no reductase; and (iii) strains with normal hydrolase activity and low and variable levels of reductase. The mutants were sensitive to all organomercurials as well as mercury.

Weiss, A.A.; Murphy, S.D.; Silver, S.D.



Cloning-independent plasmid construction for genetic studies in streptococci. (United States)

Shuttle plasmids are among the few routinely utilized tools in the Streptococcus mutans genetic system that still require the use of classical cloning methodologies and intermediate hosts for genetic manipulation. Accordingly, it typically requires considerably less time and effort to introduce mutations onto the S. mutans chromosome than it does to construct shuttle vectors for expressing genes in trans. Occasionally, shuttle vector constructs also exhibit toxicity in Escherichia coli, which prevents their proper assembly. To circumvent these limitations, we modified a prolonged overlap extension PCR (POE-PCR) protocol to facilitate direct plasmid assembly in S. mutans. Using solely PCR, we created the reporter vector pZX7, which contains a single minimal streptococcal replication origin and harbors a spectinomycin resistance cassette and the gusA gene encoding ?-glucuronidase. We compared the efficiency of pZX7 assembly using multiple strains of S. mutans and were able to obtain from 5 × 10³ to 2 × 10? CFU/?g PCR product. Likewise, we used pZX7 to further demonstrate that Streptococcus sanguinis and Streptococcus gordonii are also excellent hosts for cloning-independent plasmid assembly, which suggests that this system is likely to function in numerous other streptococci. Consequently, it should be possible to completely forgo the use of E. coli-Streptococcus shuttle vectors in many streptococcal species, thereby decreasing the time and effort required to assemble constructs and eliminating any toxicity issues associated with intermediate hosts. PMID:23673081

Xie, Zhoujie; Qi, Fengxia; Merritt, Justin



Control of the ccd operon in plasmid F. (United States)

The F sex factor plasmid of Escherichia coli contains a pair of genes, ccdA and ccdB, whose protein gene products are involved in an unusual feature of plasmid maintenance. The CcdB protein is a cytotoxin that becomes activated when the F plasmid is lost, thereby killing the F- segregant cells. In F+ cells, the CcdA protein protects against the lethal effects of CcdB. In the present study we show that ccdA and ccdB expressions are negatively autoregulated at the level of transcription. Genetic studies showed that repression required at least ccdB; ccdA alone was without effect, and ccdB alone was not examined because it is lethal. Ccd-operator complexes were purified and contained a mixture of both CcdA and CcdB proteins; however, we could not conclude from our results whether CcdA was necessary for DNA binding or autorepression. By using restriction fragments of the promoter-operator region, we obtained results indicating that at least two DNA-binding sites existed for the Ccd protein(s). Subsequent footprinting of the binding sites showed protection over about a 113-base-pair region encompassing the putative promoter-operator and the beginning of the ccdA gene. PMID:2651399

Tam, J E; Kline, B C



High-level gentamicin-resistant Enterococcus faecium strains isolated from bone marrow transplant patients: accumulation of antibiotic resistance genes, large plasmids and clonal strain dissemination. (United States)

Twenty-six high-level gentamicin-resistant (HLGR) Enterococcus faecium strains colonising neutropenic bone marrow transplant patients were studied. Polymerase chain reaction analysis showed that high-level gentamicin resistance was mediated by the aac(6')-Ia-aph(2'')-Ie gene; the aph(2'')-Id gene responsible for gentamicin resistance was also detected in 16 strains. Multiple antibiotic resistance was related to the presence of aph(3')-IIIa, ant(6)-Ia, erm(B), erm (A) and tet(M) genes. Strains clustered into 18 groups according to their plasmid content as well as 16 pulsed-field gel electrophoresis (PFGE) patterns. Although the majority of PFGE patterns were single isolates, three microclones were identified. Hybridisation showed that in the majority of the strains the aac(6')-aph(2'') gene resided on a large plasmid of ca. 96kb detected only on PFGE gels. Based on these findings, colonisation by HLGR E. faecium strains was a result of either possibly related plasmid spread or strain dissemination. PMID:17360161

Abbassi, Mohamed Salah; Achour, Wafa; Hassen, Assia Ben



Assessment of injury from the MEGA BORG oil spill: A case of cooperative damage assessment  

International Nuclear Information System (INIS)

The tanker MEGA BORG exploded while lightering about 60 miles offshore of Galveston, Texas on 8 June 1990. The explosion was followed by a spectacular fire and major release of Angolan crude. Up to 5.1 million gallons of the 41 million gallon cargo was lost to the sea or burning over a period of seven days. Vessel interests took responsibility for the spill and employed skimming and dispersive cleanup techniques. It is estimated that approximately 126 gallons ultimately reached shore in western Louisiana. Within a day of the explosion, the Norwegian vessel owner, French cargo owner and the Norwegian vessel insurer entered into discussion with the Texas Water Commission and the National Oceanic and Atmospheric Administration regarding damage assessment options. Within the next two days the owners agreed to fund and participate in a cooperative preliminary assessment of environmental injury. Five projects were funded to determine whether there was sufficient injury to justify the completion of a full natural resource damage assessment: (1) Fate of spilled oil; (2) Effects on shrimp fishery; (3) Effects on marine mammals and turtles; (4) Effects of beach oiling and (5) Effects on recreation. Funds were also provided for report preparation and project management. Several issues of major concern were considered by vessel interests prior to agreement. Many of these issues are common to consideration of cooperative assessments and may be critical importance to future incidents particularly if the damage assessment regulations developed pursuant to the Oil Pollution Act encourage cooperative responses


MegaZ-LRG: A photometric redshift catalogue of one million SDSS Luminous Red Galaxies  

CERN Document Server

We describe the construction of MegaZ-LRG, a photometric redshift catalogue of over one million luminous red galaxies (LRGs) in the redshift range 0.4 < z < 0.7 with limiting magnitude i < 20. The catalogue is selected from the imaging data of the Sloan Digital Sky Survey Data Release 4. The 2dF-SDSS LRG and Quasar (2SLAQ) spectroscopic redshift catalogue of 13,000 intermediate-redshift LRGs provides a photometric redshift training set, allowing use of ANNz, a neural network-based photometric-redshift estimator. The rms photometric redshift accuracy obtained for an evaluation set selected from the 2SLAQ sample is sigma_z = 0.049 averaged over all galaxies, and sigma_z = 0.040 for a brighter subsample (i < 19.0). The catalogue is expected to contain ~5 per cent stellar contamination. The ANNz code is used to compute a refined star/galaxy probability based on a range of photometric parameters; this allows the contamination fraction to be reduced to 2 per cent with negligible loss of genuine galaxies...

Collister, A A; Blake, C; Cannon, R; Croom, S; Drinkwater, M; Edge, A; Eisenstein, D; Loveday, J; Nichol, R; Pimbblet, K; De Propris, R; Roseboom, I; Ross, N; Schneider, D P; Shanks, T; Wake, D; Collister, Adrian; Lahav, Ofer; Blake, Chris; Cannon, Russell; Croom, Scott; Drinkwater, Michael; Edge, Alastair; Eisenstein, Daniel; Loveday, Jon; Nichol, Robert; Pimbblet, Kevin; Propris, Roberto De; Roseboom, Isaac; Ross, Nic; Schneider, Donald P.; Shanks, Tom; Wake, David



Scandinavian Links: Mega Bridges/Tunnels Linking the Scandinavian Peninsula to the European Continent  

DEFF Research Database (Denmark)

The European Round Table of Industrialists identified in the 1980ies 14 missing links in the transportation network of the continent. Three of them were found around the Danish island of Zealand. One link is within the nation, the other two are between nations. One link connects heavy economic centres, one joins more thinly populated regions, and the last one links peripheral areas. Two of them (The Great Belt Link and the Oresund Link) have been constructed and are in full operation. The third (the Fehmarnbelt Link) has been decided 2008 on bilateral government level. The three links are impressive mega structures spanning international waterways. These waterways between the Baltic Sea and the North Sea have played major roles in history. The length of each of the crossings are around 20 km. The fixed links closes gaps between the Scandinavian and European motorway and rail networks. They concentrate traffic flows and create strong transport corridors. They are the basis of new regional development regimes.“Ferries connect systems, fixed links unite systems”.

Matthiessen, Christian Wichmann; Knowles, Richard D.



Dense transient plasmas driven by a mega-ampere device in the Chilean Nuclear Energy Commission  

International Nuclear Information System (INIS)

Recently, the pulse power generator SPEED 2, a medium energy and large current device (187kJ, 4MA, 300kV, 400ns, dI/dt ? 1013 A/s), has been transfered from the Duesseldorf University to the Plasma Physics Group of the Comision Chilena de Energia Nuclear (CCHEN). The SPEED 2 arrived at CCHEN in May 2001 and was in operation in January 2002, being the most powerful device for dense transient plasma in the Southern Hemisphere. Experiments in different Z-pinch configurations using the SPEED 2 generator will be carried out at CCHEN in the future. Possible objectives using the SPEED 2 devices are discussed in this work: a) Neutron flux characteristics from plasma focus discharges operating in D2 (with temporal and spatial resolution) correlated to discharge parameters, plasma dynamics and instabilities. Particular investigation of the effect of insulator surface preparation and conditioning on pinch behavior and neutron yield, b) High brightness and soft X- ray radiation from transient electrical discharges, especially in wire arrays, and c) Magnetic confinement in a quasistatic z-pinch at mega ampere peak current. Plasma dynamics and stability in an original quasi-static z-pinch configuration (a gas embedded compressional Z-pinch) and in a combination scheme that use gas puff and plasma focus will be studied at high current using the SPEED 2 generator. Results about SPEED 2 performance, obtained in Chile, are presented


Properties of GPS noise at Japan islands before and after Tohoku mega-earthquake. (United States)

The field of 3-components GPS signals is analyzed for the network of 1203 stations at the Japanese islands from January 30 up to March 26, 2011. This time interval includes just over 40 days of observation before the Tohoku mega-earthquake on March 11, 2011 (M?=?9.0) and nearly 16 days of observation following this event. The signals from each station are three-component time series with time step 30 minutes. We study the statistical properties of the random fluctuations of GPS signals before and after the seismic catastrophe after transition to increments. The values of wavelet-based spectral index for GPS noise components for each station were estimated separately for pieces of records before and after seismic event. The maps of the noise spectral index are constructed as the values for grid size of 50?×?50 nodes covering the region under study, based on information from 10 stations closest to each node. These maps clearly extract the region of future seismic catastrophe by relatively high noise spectral index. The using of principal components method distinguished this spatial anomaly more explicitly. These results support the hypothesis that statistical properties of random fluctuations of geophysical fields carry important information about earthquake preparation. PMID:25077067

Lyubushin, Alexey; Yakovlev, Pavel



Dolicomegarterias ilíacas.: Presentación de un caso. Iliac mega-dolicho arteries: Presentation of a case  

Directory of Open Access Journals (Sweden)

Full Text Available Las anomalías del árbol vascular son comunes. Los aneurismas aislados de las arterias ilíacas son de observación bastante rara. Representan un porcentaje escaso de las distintas estadísticas y a menudo se resalta su aislamiento, precisamente para recordar su rareza. Reportamos un caso masculino, de 74 años de edad, que asistió a consulta por presentar síntomas urinarios. Se le realizó un ultrasonido de abdomen, observándose hidronefrosis renal bilateral moderada, además masas complejas una en cada fosa ilíaca. Se le indicó Tomografía Axial Computarizada de abdomen, donde se confirmó la hidronefrosis renal bilateral y aneurismas de ambas arterias ilíacas. Se completó el estudio con un Angiotac, y se demostró que ambas ilíacas estaban tortuosas y dilatadas (DOLICOMEGARTERIAS.Vascular tree anomalies are common. Iliac arteries isolated aneurisms are very unusual. They represent an scarce percent of the different statistics and their isolation is frequently highlighted, precisely to recollect their rareness.We report the case of a male, 74-years-old patient, assisting the consultation with urinary symptoms. An abdominal ultrasound was made, showing moderated bilateral renal hydronephrosis and also complex masses in each iliac fosse. An abdomen computed axial tomography was indicated, confirming the bilateral renal hydronephrosis and aneurisms in both iliac arteries. The study was completed with an Angiotac and it was demonstrated that both iliac arteries were tortuous and dilated ( Mega-dolicho arteries .

Yariana Martínez Sánchez



Dolicomegarterias ilíacas.: Presentación de un caso. / Iliac mega-dolicho arteries: Presentation of a case  

Scientific Electronic Library Online (English)

Full Text Available SciELO Cuba | Language: Spanish Abstract in spanish Las anomalías del árbol vascular son comunes. Los aneurismas aislados de las arterias ilíacas son de observación bastante rara. Representan un porcentaje escaso de las distintas estadísticas y a menudo se resalta su aislamiento, precisamente para recordar su rareza. Reportamos un caso masculino, de [...] 74 años de edad, que asistió a consulta por presentar síntomas urinarios. Se le realizó un ultrasonido de abdomen, observándose hidronefrosis renal bilateral moderada, además masas complejas una en cada fosa ilíaca. Se le indicó Tomografía Axial Computarizada de abdomen, donde se confirmó la hidronefrosis renal bilateral y aneurismas de ambas arterias ilíacas. Se completó el estudio con un Angiotac, y se demostró que ambas ilíacas estaban tortuosas y dilatadas (DOLICOMEGARTERIAS). Abstract in english Vascular tree anomalies are common. Iliac arteries isolated aneurisms are very unusual. They represent an scarce percent of the different statistics and their isolation is frequently highlighted, precisely to recollect their rareness.We report the case of a male, 74-years-old patient, assisting the [...] consultation with urinary symptoms. An abdominal ultrasound was made, showing moderated bilateral renal hydronephrosis and also complex masses in each iliac fosse. An abdomen computed axial tomography was indicated, confirming the bilateral renal hydronephrosis and aneurisms in both iliac arteries. The study was completed with an Angiotac and it was demonstrated that both iliac arteries were tortuous and dilated ( Mega-dolicho arteries ).

Yariana, Martínez Sánchez; Enélida, Matos Abrahantes; Juliana M, Tarajano Márquez; Jacqueline, Ramos Serpa; José Antonio, Rodríguez González.


Sustainable urban transport indicators: tool for evaluating transport sustainability in the mega cities of Pakistan  

International Nuclear Information System (INIS)

Urban Transport is an important sector to accomplish the goal of sustainable development in Pakistan. This is important because of the high growth of the transport sector's energy consumption, road crashes and greenhouse gas emissions. This becomes significant in the Pakistani cities where motor vehicle fleet is growing at two to three times the rate of population. Transport Policies has resulted high growth of urban road traffic, increasing air and noise pollution throughout the country. This situation raised the question how to achieve sustainable urban transport in the mega cities of Pakistan? Development of sustainable urban transport indicators will provide an opportunity to analyze current transport policies to assess Pakistan progress towards or away from sustainability. Medium Term Development Framework (2005-10) has selected to analyze against establish sustainable urban transport indicators for Pakistan. On the basis of analysis, it has found that MWF has tried to address transport problem in a piecemeal manner, rather than adopting a holistic approach. Implementing MTDF policies on transport is not fully matched with a long term commitment to achieving sustainable development in Pakistan. (author)


Integrated predictive modeling simulations of the Mega-Amp Spherical Tokamak  

International Nuclear Information System (INIS)

Integrated predictive modeling simulations are carried out using the BALDUR transport code [Singer et al., Comput. Phys. Commun. 49, 275 (1982)] for high confinement mode (H-mode) and low confinement mode (L-mode) discharges in the Mega-Amp Spherical Tokamak (MAST) [Sykes et al., Phys. Plasmas 8, 2101 (2001)]. Simulation results, obtained using either the Multi-Mode transport model (MMM95) or, alternatively, the mixed-Bohm/gyro-Bohm transport model, are compared with experimental data. In addition to the anomalous transport, neoclassical transport is included in the simulations and the ion thermal diffusivity in the inner third of the plasma is found to be predominantly neoclassical. The sawtooth oscillations in the simulations radially spread the neutral beam injection heating profiles across a broad sawtooth mixing region. The broad sawtooth oscillations also flatten the central temperature and electron density profiles. Simulation results for the electron temperature and density profiles are compared with experimental data to test the applicability of these models and the BALDUR integrated modeling code in the limit of low aspect ratio toroidal plasmas


Observational study of aerosol hygroscopic growth factors over rural area near Beijing mega-city  

Directory of Open Access Journals (Sweden)

Full Text Available We investigated aerosol hygroscopic growth property and its influence on scattering coefficient using M9003 nephelometers in coupling with a relative humidity controlled inlet system at a rural site near Beijing mega-city (Jingjintang from 24th April to15th May 2006. Inlet relative humidity was controlled in an increasing range of 40%–90% while the aerosol hygroscopic growth factor, f(RH=80%, varied in a range of 1.07–2.35 during the measurement. Estimated periodic mean values of aerosol hygroscopic growth factors are 1.27–1.34, 1.17–1.23, 1.55–1.59 and 2.33–2.48 for clean, dust, urban pollution and mixed pollution periods respectively. An examination of chemical composition of daily filter samples highlighted that aerosol hygroscopicity was generally enhanced with the increasing ratio of ammonium sulfate (AS to organic matter (OMC. Furthermore, strong hygroscopic organic aerosols were observed on 11th (f(RH=80%=2.23 and 15th (f(RH=80%=2.21 of May with organic carbon proportions of PM2.1 reaching 42.3% and 43.0% respectively. Back-trajectory analysis indicated that solar radiation and vertical convective movement along the air mass pathway might strongly influence the hygroscopic properties of organic matter.

X. L. Pan



Electron spin resonance dating of mega-fauna from Lagoa dos Porcos, Piaui (Brazil))  

International Nuclear Information System (INIS)

Excavations performed at Lagoa dos Porcos site revealed a vast amount of extinct mammal fossil remains, becoming one of the richest palaeontological occurrences in the Serra da Capivara National Park region, a UNESCO World Heritage. Although anatomic and taxonomic aspects of extinct Quaternary mammals are relatively well known, chronologic information for deposits is rare. In this context, electron spin resonance (ESR) dating of mega-fauna samples provides important information for establishing a chronological background. This work presents the ESR dating of two teeth, one of Gomphotheriidae and other of Toxodontinae. Dose-response curves of each sample were constructed using spectra acquired with a JEOL FA-200 X-Band spectrometer resulting in equivalent dose (De) of 220±40 Gy and 39±2 Gy for Toxodontinae and Gomphotheriidae tooth, respectively. The conversion of De in age was made using ROSY ESR dating software resulting in 26±4 and 22±3 ka. These results place Lagoa dos Porcos fossil assemblage within the Late Pleistocene. These dates overlap with a period of abrupt increase in rainfall in northeast Brazil, and it is possible that this environmental change is related to the formation of this deposit. (authors)


Defining temporal spatial patterns of mega city Istanbul to see the impacts of increasing population. (United States)

Rapid land use change has taken place over the last few decades in Istanbul. As most of the metropolitan areas, Istanbul faces increasing problems connected to increasing population and urbanisation. In this study, temporal changes of Istanbul's land use/cover were defined using remotely sensed data and post classification change detection method. For the aim of the study, relevant information was derived from different dated Landsat Thematic Mapper (TM) satellite data by using Unsupervised Iterative Self-Organizing Data Analysis Technique (ISODATA) and results were examined with matrix analysis method. Ground truth data were used for the classification and accuracy assessment of the classification. Temporal changes of land use/cover classes of the mega city Istanbul between the years of 1992, 1997 and 2005 were examined for the management and decision making process. Landsat TM images were classified into six land use/cover types: forest-green area, bare land, water surface, road, urban area, and mining area. The results show that urban areas and road categories are increased greatly by 13,630 and 5,018ha, respectively, but forest-green areas decreased by 77,722ha over 13years between 1992 and 2005. The reason for the decrease in green areas is mainly because of development of unplanned urbanization and unavoidable migration. PMID:18157736

Sanli, Fusun Balik; Balcik, Filiz Bektas; Goksel, Cigdem



Regional flood dynamics in a bifurcating mega delta simulated in a global river model (United States)

this paper we show the importance of bifurcation channels for flow in river mega deltas through the use of a new computational scheme implemented in the global hydrodynamic model, CaMa-Flood (Catchment-based Macro-scale Floodplain model). First, we developed a new river network map based on SRTM3 DEM (Shuttle Radar Topography Mission 3 arc-second Digital Elevation Model) and HydroSHEDS (hydrological data and maps based on shuttle elevation derivatives at multiple scales) which includes bifurcation channels. Next, we implemented a new bifurcation scheme in CaMa-Flood capable of routing flow along this network and used the model to simulate the Mekong River. We show that in the Mekong delta such channels route about 50% of total flow and that their representation is essential for realistic hydrodynamic simulations. A simulation without bifurcation channels was obviously unrealistic because no flow occurred between the mainstem and adjacent channels even when their water level difference was >6 m. The bifurcation channels are extracted from globally available data sets; thus, it is straightforward to expand the proposed scheme to global-scale studies.

Yamazaki, Dai; Sato, Tomoko; Kanae, Shinjiro; Hirabayashi, Yukiko; Bates, Paul D.



Liquid Metal Angiography for Mega Contrast X-ray Visualization of Vascular Network  

CERN Document Server

Visualizing the anatomical vessel networks plays a vital role in physiological or pathological investigations. However, identifying the fine structures of the smallest capillary vessels via conventional imaging ways remains a big challenge. Here, the room temperature liquid metal angiography was proposed for the first time to produce mega contrast X-ray images for multi-scale vasculature mapping. Gallium was used as the room temperature liquid metal contrast agent and perfused into the vessels of in vitro pig hearts and kidneys. We scanned the samples under X-ray and compared the angiograms with those obtained via conventional contrast agent--the iohexol. As quantitatively proved by the gray scale histograms, the contrast of the vessels to the surrounding tissues in the liquid metal angiograms is orders higher than that of the iohexol enhanced images. And the resolution of the angiograms has reached 100{\\mu}m, which means the capillaries can be clearly distinguished in the liquid metal enhanced images. With t...

Wang, Qian; Pan, Keqin; Liu, Jing



Toroidal ripple transport of beam ions in the mega-ampere spherical tokamak  

Energy Technology Data Exchange (ETDEWEB)

The transport of injected beam ions due to toroidal magnetic field ripple in the mega-ampere spherical tokamak (MAST) is quantified using a full orbit particle tracking code, with collisional slowing-down and pitch-angle scattering by electrons and bulk ions taken into account. It is shown that the level of ripple losses is generally rather low, although it depends sensitively on the major radius of the outer midplane plasma edge; for typical values of this parameter in MAST plasmas, the reduction in beam heating power due specifically to ripple transport is less than 1%, and the ripple contribution to beam ion diffusivity is of the order of 0.1 m{sup 2} s{sup -1} or less. It is concluded that ripple effects make only a small contribution to anomalous transport rates that have been invoked to account for measured neutron rates and plasma stored energies in some MAST discharges. Delayed (non-prompt) losses are shown to occur close to the outer midplane, suggesting that banana-drift diffusion is the most likely cause of the ripple-induced losses.

McClements, K. G. [EURATOM/CCFE Fusion Association, Culham Science Centre, Abingdon, Oxfordshire OX14 3DB (United Kingdom); Hole, M. J. [Plasma Research Laboratory, Research School of Physical Science and Engineering, Australian National University, Canberra, ACT 0200 (Australia)



A high resolution Mirnov array for the Mega Ampere Spherical Tokamak. (United States)

Over the past two decades, the increase in neutral-beam heating and alpha particle production in magnetically confined fusion plasmas has led to an increase in energetic particle driven mode activity, much of which has an electromagnetic signature which can be detected by the use of external Mirnov coils. Typically, the frequency and spatial wave number band of such oscillations increase with increasing injection energy, offering new challenges for diagnostic design. In particular, as the frequency approaches the megahertz range, care must be taken to model the stray capacitance of the coil, which limits the resonant frequency of the probe; model transmission line effects in the system, which if unchecked can produce system resonances; and minimize coil conductive shielding, so as to minimize skin currents which limit the frequency response of the coil. As well as optimizing the frequency response, the coils should also be positioned to confidently identify oscillations over a wide wave number band. This work, which draws on new techniques in stray capacitance modeling and coil positioning, is a case study of the outboard Mirnov array for high-frequency acquisition in the Mega Ampere Spherical Tokamak, and is intended as a roadmap for the design of high frequency, weak field strength magnetic diagnostics. PMID:20059144

Hole, M J; Appel, L C; Martin, R



Widespread Mega-Pockmarks Imaged Along the Western Edge of the Cocos Ridge (United States)

A large field (245km2) of 31 seabed mega-pockmarks was imaged between the Cocos ridge and the Quepos plateau on ~16.5 Ma oceanic crust generated at the Cocos-Nazca spreading center. The imaged pockmarks represent only a fraction of the much larger pockmark field evident in 100 m grid cell bathymetry data secured from MGDS. The pockmarks are clustered around 1800-2100 mbsl and were mapped using EM122 multibeam sonar, a 3.5 kHz sub-bottom profiler, and 3D Multi-Channel Seismic (MCS) aboard R/V Marcus G. Langseth during the CRISP seismic survey (2011). Using a constrained swath width of 1.4 km, the increased sounding density facilitated bathymetry/backscatter to be gridded at 10m and 8m respectively. The diameter of the pockmarks varies from ~1 km to ~2 km with a relief range of ~30-80 m, and average slopes of 15°. The MCS data also reveal older buried pockmarks in trench adjacent sediments. Small high-backscatter mounds occur within a subset of the pockmarks, which may indicate bioherms or carbonate banks above focused fluid flow conduits. Based on drilling results of DSDP Site 158 and ODP Site 1381, the pockmarks appear to be the result of paleo-differential advancement of a silica diagenetic front (opal-A to opal-CT). Although, the pockmarks may be erosional features sourced at depth from dewatering of sediments inter-bedded with igneous layers.

Gibson, J. C.; Kluesner, J. W.; Silver, E. A.; Bangs, N. L.; McIntosh, K. D.



Numerical analysis of the direct drive illumination uniformity for the Laser MegaJoule facility  

Energy Technology Data Exchange (ETDEWEB)

The illumination uniformity provided during the initial imprinting phase of the laser foot pulse in a direct drive scenario at the Laser MegaJoule facility has been analyzed. This study analyzes the quality of the illumination of a spherical capsule and concerns the uniformity of the first shock generate in the absorber of an Inertial Confinement Fusion capsule. Four configurations making use of all or some of the 80 laser beams organized in the 20 quads of the cones at 49° and 131° with respect to the polar axis have been considered in order to assemble the foot pulse. Elliptical and circular super-gaussian laser intensity profiles taking into account beam-to-beam power imbalance (10%), pointing error (50??m), and target positioning (20??m) have been considered. It has been found that the use of the Polar Direct Drive technique can in some cases reduce the irradiation non-uniformity by a factor as high as 50%. In all cases, elliptical profile provides better results in comparison with the circular one and it is shown that the minimum of the non-uniformity is also a function of the capsule radius.

Temporal, M., E-mail: [Centre de Mathématiques et de Leurs Applications, ENS Cachan and CNRS, 61 Av. du President Wilson, F-94235 Cachan Cedex (France); Canaud, B. [CEA, DIF, F-91297 Arpajon Cedex (France); Garbett, W. J. [AWE plc, Aldermaston, Reading, Berkshire RG7 4PR (United Kingdom); Ramis, R. [ETSI Aeronáuticos, Universidad Politécnica de Madrid, 28040 Madrid (Spain)



How soon would the next mega-earthquake occur in Japan?  

Directory of Open Access Journals (Sweden)

Full Text Available The problem of seismic danger estimate in Japan after Tohoku mega-earthquake 11 March of 2011 is considered. The estimates are based on processing low-frequency seismic noise wave-forms from broadband network F-net. A new method of dynamic estimate of seismic danger is used for this problem. The method is based on calculating multi-fractal properties and minimum entropy of squared orthogonal wavelet coefficients for seismic noise. The analysis of the data using notion of “spots of seismic danger” shows that the seismic danger in Japan remains at high level after 2011. 03. 11 within north-east part of Philippine plate—at the region of Nankai Though which traditionally is regarded as the place of strongest earthquakes. It is well known that estimate of time moment of future shock is the most difficult problem in earthquake prediction. In this paper we try to find some peculiarities of the seismic noise data which could extract future danger time interval by analogy with the behavior before Tohoku earthquake. Two possible precursors of this type were found. They are the results of estimates within 1-year moving time window: based on correlation between 2 mean multi-fractal parameters of the noise and based on cluster analysis of annual clouds of 4 mean noise parameters. Both peculiarities of the noise data extract time interval 2013-2014 as the danger.

Alexey Lyubushin



Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community. (United States)

Horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. Even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. In this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced by the donor strain and that various mating conditions and isolation strategies increased the diversity of transconjugants detected. To detect transconjugants, the plasmid pB10 was marked with lacp-rfp, while rfp expression was repressed in the donors by chromosomal lacI(q). The phylogeny of 306 transconjugants obtained was determined by analysis of partial 16S rRNA gene sequences. The transconjugants belonged to 15 genera of the alpha- and gamma-Proteobacteria. The phylogenetic diversity of transconjugants obtained in separate matings with donors Pseudomonas putida SM1443, Ralstonia eutropha JMP228, and Sinorhizobium meliloti RM1021 was significantly different. For example, the transconjugants obtained after matings in sludge with S. meliloti RM1021 included eight genera that were not represented among the transconjugants obtained with the other two donors. Our results indicate that the spectrum of hosts to which a promiscuous plasmid transfers in a microbial community can be strongly influenced by the donor from which it transfers. PMID:16151119

De Gelder, Leen; Vandecasteele, Frederik P J; Brown, Celeste J; Forney, Larry J; Top, Eva M



Estimaton of the Mean Repeat Time of Mega Earthquakes Occurring in the Hellenic Arc and Trench, East Mediterranean Sea (United States)

Along the boundary of the Eurasian and African lithospheric plates the Hellenic Arc and Trench (HAT), Greece, is a highly active seismotectonic system producing historical earthquakes up to magnitude M~8. The best known examples are the possibly interplate tsunamigenic earthquakes of AD 21 July 365 and 8 August 1303. The 365 earthquake ruptured the western segment (WHAT) while the 1303 earthquake ruptured the eastern segment (EHAT). However, no other similar events are known to have taken place in the past implying that those earthquakes are of very long return period. The future repeat of such mega earthquake-tsunami events constitutes a major threat not only for Greek settlements but also for remote communities in several places of the East Mediterranean Sea. Therefore, it is of profound scientific interest and of societal urgency to assess the mean repeat time (mrt) of mega earthquakes along HAT. The earthquake cycle in HAT is very poorly understood due to the very small number of the known HAT mega earthquakes. Because of this difficulty our methodology is based on the statistics of the earthquake catalogue. The data contained in existing earthquake catalogues are usually based on seismic recordings from spatially, temporally, and often also instrumentally heterogeneous seismological networks. However, the mrt assessment necessitates catalogues that are complete both with respect to the relative frequency of occurrence of events in a wide range of magnitudes and over as long as possible a time span. Based on the several inhomogeneous earthquake catalogues for HAT covering the time period from the antiquity up to the present, we compile a new homogeneous earthquake catalogue and calculate the maximum earthquake magnitude, Mmax, for both the WHAT and EHAT from a maximum likelihood scheme. Adopting that the G-R relation is valid over a wide magnitude spectrum and for long time segments the mrt is also calculated by applying several statistical techniques on G-R (e.g. least-squares, extreme values, maximum likelihood). We repeat calculations for several time periods (e.g. early historical, late historical, early instrumental, late instrumental). Results are compared and evaluated in view of the observation that WHAT and EHAT did not ruptured by mega earthquakes in the last centuries, which may indicate that the plate interface is strongly coupled, and that mega earthquakes are under preparation along HAT.

Daskalaki, E.; Papadopoulos, G. A.



Bacillus anthracis Virulent Plasmid pX02 Genes Found in Large Plasmids of Two Other Bacillus Species  

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In order to cause the disease anthrax, Bacillus anthracis requires two plasmids, pX01 and pX02, which carry toxin and capsule genes, respectively, that are used as genetic targets in the laboratory detection of the bacterium. Clinical, forensic, and environmental samples that test positive by PCR protocols established by the Centers for Disease Control and Prevention for B. anthracis are considered to be potentially B. anthracis until confirmed by culture and a secondary battery of tests. We ...

Luna, Vicki A.; King, Debra S.; Peak, K. Kealy; Reeves, Frank; Heberlein-larson, Lea; Veguilla, William; Heller, L.; Duncan, Kathleen E.; Cannons, Andrew C.; Amuso, Philip; Cattani, Jacqueline



The FLP protein of the yeast 2-microns plasmid: expression of a eukaryotic genetic recombination system in Escherichia coli.  

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The FLP gene of the yeast 2-microns plasmid is involved in a site-specific recombination event that results in the inversion of a set of sequences within the plasmid. This gene has been cloned and expressed in Escherichia coli. Expression of the FLP gene results in efficient recombination within the bacterial cell, which is specific for plasmids containing at least one 2-microns plasmid recombination site. This work demonstrates that (i) FLP protein is actively involved in 2-microns plasmid r...

Cox, M. M.



42 CFR 488.335 - Action on complaints of resident neglect and abuse, and misappropriation of resident property. (United States)

...false Action on complaints of resident neglect and abuse, and misappropriation of resident...335 Action on complaints of resident neglect and abuse, and misappropriation of resident...must review all allegations of resident neglect and abuse, and misappropriation of...



RK2 plasmid dynamics in Caulobacter crescentus cells--two modes of DNA replication initiation. (United States)

Undisturbed plasmid dynamics is required for the stable maintenance of plasmid DNA in bacterial cells. In this work, we analysed subcellular localization, DNA synthesis and nucleoprotein complex formation of plasmid RK2 during the cell cycle of Caulobacter crescentus. Our microscopic observations showed asymmetrical distribution of plasmid RK2 foci between the two compartments of Caulobacter predivisional cells, resulting in asymmetrical allocation of plasmids to progeny cells. Moreover, using a quantitative PCR (qPCR) method, we estimated that multiple plasmid particles form a single fluorescent focus and that the number of plasmids per focus is approximately equal in both swarmer and predivisional Caulobacter cells. Analysis of the dynamics of TrfA-oriV complex formation during the Caulobacter cell cycle revealed that TrfA binds oriV primarily during the G1 phase, however, plasmid DNA synthesis occurs during the S and G2 phases of the Caulobacter cell cycle. Both in vitro and in vivo analysis of RK2 replication initiation in C. crescentus cells demonstrated that it is independent of the Caulobacter DnaA protein in the presence of the longer version of TrfA protein, TrfA-44. However, in vivo stability tests of plasmid RK2 derivatives suggested that a DnaA-dependent mode of plasmid replication initiation is also possible. PMID:23538715

Wegrzyn, Katarzyna; Witosinska, Monika; Schweiger, Pawel; Bury, Katarzyna; Jenal, Urs; Konieczny, Igor



Comparison of antibiotic susceptibility tests, plasmid profiles and restriction enzyme analysis of plasmid DNA of methicillin susceptible and resistant-Staphylococcus aureus strains isolated from intensive care units.  

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In respect to epidemiological survey, plasmids profiles and REAP seems to discriminate more respect to antibiotic sensitivity tests but at the same time neither of them were 100% accurately differential. According to the plasmid profile of the 3rd MSSA (Turkey group, a multi-drug resistance by antibiotic susceptibility tests were noticed and showed the same plasmid profile in MRSA first subgroup of the 3rd group, but the same groups were different in REAP tests. In order to distinguish the discriminatory power of the strains, where REAP is better than plasmid profile and antibiotic sensitivity tests, we may formulate the statement into the following; REAP > plasmid profile > antibiotic sensitivity tests. For typing and gathering of epidemiological data, it is suggested that all 3 methods should be employed in clinical laboratories as they are cheap, practical and easily interpreted.

Mohammed A. Tayfour



Investigation of diversity of plasmids carrying the blaTEM-52 gene  

DEFF Research Database (Denmark)

OBJECTIVES: To investigate the diversity of plasmids that carry blaTEM-52 genes among Escherichia coli and Salmonella enterica originating from animals, meat products and humans. METHODS: A collection of 22 blaTEM-52-encoding plasmids was characterized by restriction fragment length polymorphism (RFLP), replicon typing (by PCR or replicon sequencing), susceptibility testing, assessment of plasmid ability to self-transfer by conjugation and typing of the genetic environment of the blaTEM-52 gene. Detected IncI1 plasmids underwent further plasmid multilocus sequence typing. RESULTS: RFLP profiles demonstrated dissemination of blaTEM-52 in Denmark (imported meat from Germany), France, Belgium and the Netherlands from 2000 to 2006 by mainly two different plasmids, one encoding blaTEM-52b (IncX1A, 45 kb) and the other blaTEM-52c (IncI1, 80 kb). In addition, blaTEM-52b was also found to be located on various other plasmids belonging to IncA/C and IncL/M, while blaTEM-52c was found on IncN-like as well as on IncR plasmids. In the majority of cases (n = 21) the blaTEM-52 gene was located on a Tn3 transposon. Seven out of 10 blaTEM-52 plasmids tested in conjugation experiments were shown to be capable of self-transfer to a plasmid-free E. coli recipient. CONCLUSIONS: The blaTEM-52 gene found in humans could have been transmitted on transferable plasmids originating from animal sources. Some of the blaTEM-52 plasmids carry replicons that differ from the classical ones. Two novel replicons were detected, IncX1A and IncN-like. Unlike its predecessor blaTEM-1, the blaTEM-52 gene was not detected on F-type replicons suggesting that this gene evolved on other types of plasmid scaffolds.

Bielak, Eliza Maria; JØrgensen, Mikael Skaanning



42 CFR 483.20 - Resident assessment. (United States)

...months. (c) Quarterly review assessment. A facility...resident using the quarterly review instrument specified by the State...assessments to develop, review, and revise the resident's...professional standards of quality; and (ii) Be...



38 CFR 51.110 - Resident assessment. (United States)

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38 CFR 51.70 - Resident rights. (United States)

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42 CFR 483.20 - Resident assessment. (United States) status, and requires interdisciplinary review or revision of the... (ii) Prepared by an interdisciplinary team, that includes the...resident to adjust to his or her new living environment. ...after January 1, 1989, any new resident with—...



Enhanced nuclear import and transfection efficiency of plasmid DNA using streptavidin-fused importin-beta. (United States)

In order to enhance the nuclear import of exogenous genes, novel plasmid DNA/importin-beta conjugates, which consist of a biotinylated plasmid DNA and a recombinant streptavidin-fused importin-beta, were prepared. The spacer length between plasmid DNA and biotin and the number of introduced biotin were adjusted. The microinjection of plasmid DNA/importin-beta conjugates into the cytoplasm of NIH3T3 cells resulted in the nuclear localization of conjugates and the higher expression efficiency, compared to intact plasmid DNA alone. These results indicate that plasmid DNA/importin-beta conjugates would be an important tool to enhance the nuclear localization of exogenous DNA in non-viral gene delivery system. PMID:15710511

Nagasaki, Takeshi; Kawazu, Takeshi; Tachibana, Taro; Tamagaki, Seizo; Shinkai, Seiji



Detection of Conjugative Plasmid Encoded Ampicillin and Tetracycline Resistant in Klebsiella pneumonia  

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Full Text Available Klebsiella pneumonia were isolated and identified on the basis of morphology, growth, and biochemical characteristics. All the isolates offered different resistance patterns against antibiotics including Ampicillin, Cefotaxime, Erythromycin, tetracycline and Chloramphenicol. Transformation and conjugation techniques were used for plasmid transfer studies. The conjugation experiment showed that ? 51kbp conjugative plasmid conferring resistance to tetracycline and ampicillins were successfully transferred to the recipient cells E. coli MM294. The rest of the plasmid borne markers was non-conjugative/nontransferable. Conjugative plasmids carry a tremendous potential to disseminate resistance markers to distant recipient cells. The protocol is reliable enough to be used for large-scale visualization of native plasmids and we have used it to visualize and isolate DNA from hundreds of multidrug resistance plasmids.

Dogan Ozdemir



Cloning of plasmid genes encoding resistance to cadmium, zinc, and cobalt in Alcaligenes eutrophus CH34  

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A 238-kilobase-pair plasmid, pMOL30, confers resistance to cadmium, zinc, and cobalt salts in Alcaligenes eutrophus CH34. After Tn5 mutagenesis, restriction nuclease analysis, and Southern DNA-DNA hybridization, a 9.1-kilobase-pair EcoRI fragment was found to harbor all of these resistance properties and was cloned into the broad-host-range hybrid plasmid pRK290. When transferred to a plasmid-free derivative of CH34, the hybrid plasmid conferred the same degree of resistance as the parent plasmid pMOL30. In two other Alcaligenes strains, the hybrid plasmid was expressed, but to a lower degree than in CH34 derivatives.

Nies, D.; Mergeay, M.; Friedrich, B.; Schlegel, H.G.



Role of Plasmid of Pseudomonas putida S3A in Nylon 6 Degradation  

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Full Text Available Pseudomonas putida S3A was isolated in previous study and selected for its good ability to degrade nylon 6, nylon 66 and nylon 6 film as a sole source of carbon and nitrogen. Thus, plasmid profile of this bacterium was studied. Results showed that this isolate harbored small plasmid DNA bands. In order to study the role of its plasmid in degradation of nylon 6 film, curing experiment was performed using Sodium Dodecyl Sulfate (SDS and showed that two colonies had lost their ability to degrade nylon 6 film as a sole source of carbon and nitrogen. Plasmid DNA extraction from one of these colonies indicated the loss of plasmid DNA bands and this referred that the plasmid DNA bands could be responsible for degrading of nylon 6 film in P. putida S3A.

Riyam B. Al-Baldawi



[Incompatibility group P-7 plasmids responsible for biodegradation of naphthalene and salicylate in fluorescent pseudomonads]. (United States)

Analysis of seven plasmids (77 to 135 kbp in size) of the P-7 incompatibility group that are responsible for the biodegradation of naphthalene and salicylate has shown that the main natural host of IncP-7 plasmids is the species Pseudomonas fluorescens. The IncP-7 plasmids are structurally diverse and do not form groups, as is evident from their cluster analysis. The naphthalene catabolism genes of six of the IncP-7 plasmids are conservative and homologous to the catabolic genes of NAH7 and pDTG1 plasmids. The pAK5 plasmid contains the classical nahA gene, which codes for naphthalene dioxygenase, and the salicylate 5-hydroxylase gene (nagG) sequence, which makes the conversion of salicylate to gentisate possible. PMID:16119847

Izmalkova, T Iu; Sazonova, O I; Sokolov, S L; Kosheleva, I A; Boronin, A M



Underwater Dendrochronology of the Sierra Nevada: Testing the Medieval Mega-Drought Hypothesis (United States)

As stated in the NAS STR Report, "regional and large-scale reconstructions of changes in other climatic variables, such as precipitation, over the last 2,000 years would provide a valuable complement to those made for temperature." In this context, we focus on the 'Medieval Mega-drought Hypothesis', which is based on radiocarbon dating of dead trees and stumps found underwater in Sierra Nevada lakes and streambeds, and states that century-long dry periods caused lakes to retreat and streams to dry up, with the most recent mega-droughts happening during medieval times. While several paleoclimatic records support this hypothesis, some do not, and the possibility exists that geomorphic processes, such as landslides caused by seismic events, were responsible for the presence of trees and stumps under current bodies of water. Given the relevance of this hypothesis, not only for sustainable water management but also for social stability and security, it is necessary to test it beyond reasonable doubt. One way to do so is by measuring the location, orientation, and time of origin of underwater trees, to determine if they were transported or grew in situ. For example, during 2005 wood samples were retrieved from submerged trees at Fallen Leaf Lake, California. The trees had been previously located and documented using an ROV that can obtain high resolution color video, and collect small surface samples using a gripper, down to a water depth of about 150 m. For tree-ring dating, a reference chronology from AD 543 to 2003 was developed using live and dead western juniper trees located near the lake. One underwater sample, i.e. a branch cross section that included 69 rings, was then dated to AD 1085-1153. This shows that it is feasible to obtain calendar dates and continuous ring-width series from underwater trees in the Sierra Nevada. Submerged trees in Fallen Leaf Lake were mapped in summer 2006 using an EdgeTech 4200 side-scan system capable of decimeter resolution. The 5 km2 side-scan survey required about two days of survey time, providing rapid identification of the underwater targets. Side-scan sonar imagery was complemented with sub-bottom seismic CHIRP profiling to assess fault movement and landslide formation. Initial evaluation of these data does not suggest a landslide origin for submerged trees in Fallen Leaf Lake. However, sub-bottom mapping of the West Tahoe fault underlying the southernmost end of Fallen Leaf Lake, combined with evidence that these trees are at a depth equivalent to the modern level of Lake Tahoe, may suggest a linkage between Fallen Leaf Lake levels and earthquake-generated permeability along the West Tahoe fault. These preliminary results indicate that the question of climatic vs. non-climatic origin of submerged trees is best answered by mapping and dating them in more than one lake. As tree-ring samples are collected and entered into a master chronology, they could also yield a continuous, annually resolved record over several millennia, because some submerged trees have already been radiocarbon dated to the mid-Holocene. It is by collating a myriad of wood samples buried in streambeds and lakes that the longest tree-ring chronologies, now going back 12,460 years, have been developed in central Europe.

Biondi, F.; Kleppe, J. A.; Brothers, D.; Kent, G.



Lituya Bay Landslide Impact Generated Mega-Tsunami 50th Anniversary (United States)

On July 10, 1958, an earthquake Mw 8.3 along the Fairweather fault triggered a major subaerial landslide into Gilbert Inlet at the head of Lituya Bay on the southern coast of Alaska. The landslide impacted the water at high speed generating a giant tsunami and the highest wave runup in recorded history. The mega-tsunami runup to an elevation of 524 m caused total forest destruction and erosion down to bedrock on a spur ridge in direct prolongation of the slide axis. A cross section of Gilbert Inlet was rebuilt at 1:675 scale in a two-dimensional physical laboratory model based on the generalized Froude similarity. A pneumatic landslide tsunami generator was used to generate a high-speed granular slide with controlled impact characteristics. State-of-the-art laser measurement techniques such as particle image velocimetry (PIV) and laser distance sensors (LDS) were applied to the decisive initial phase with landslide impact and wave generation as well as the runup on the headland. PIV provided instantaneous velocity vector fields in a large area of interest and gave insight into kinematics of wave generation and runup. The entire process of a high-speed granular landslide impact may be subdivided into two main stages: (a) Landslide impact and penetration with flow separation, cavity formation and wave generation, and (b) air cavity collapse with landslide run-out and debris detrainment causing massive phase mixing. Formation of a large air cavity — similar to an asteroid impact — in the back of the landslide is highlighted. A three-dimenional pneumatic landslide tsunami generator was designed, constructed and successfully deployed in the tsunami wave basin at OSU. The Lituya Bay landslide was reproduced in a three-dimensional physical model at 1:400 scale. The landslide surface velocities distribution was measured with PIV. The measured tsunami amplitude and runup heights serve as benchmark for analytical and numerical models.

Fritz, Hermann M.; Mohammed, Fahad; Yoo, Jeseon



Two-fluid simulations of driven reconnection in the mega-ampere spherical tokamak (United States)

In the merging-compression method of plasma start-up, two flux-ropes with parallel toroidal current are formed around in-vessel poloidal field coils, before merging to form a spherical tokamak plasma. This start-up method, used in the Mega-Ampere Spherical Tokamak (MAST), is studied as a high Lundquist number and low plasma-beta magnetic reconnection experiment. In this paper, 2D fluid simulations are presented of this merging process in order to understand the underlying physics, and better interpret the experimental data. These simulations examine the individual and combined effects of tight-aspect ratio geometry and two-fluid physics on the merging. The ideal self-driven flux-rope dynamics are coupled to the diffusion layer physics, resulting in a large range of phenomena. For resistive MHD simulations, the flux-ropes enter the sloshing regime for normalised resistivity ? ?10-5. In Hall-MHD, three regimes are found for the qualitative behaviour of the current sheet, depending on the ratio of the current sheet width to the ion-sound radius. These are a stable collisional regime, an open X-point regime, and an intermediate regime that is highly unstable to tearing-type instabilities. In toroidal axisymmetric geometry, the final state after merging is a MAST-like spherical tokamak with nested flux-surfaces. It is also shown that the evolution of simulated 1D radial density profiles closely resembles the Thomson scattering electron density measurements in MAST. An intuitive explanation for the origin of the measured density structures is proposed, based upon the results of the toroidal Hall-MHD simulations.

Stanier, A.; Browning, P.; Gordovskyy, M.; McClements, K. G.; Gryaznevich, M. P.; Lukin, V. S.



Chemical characteristics of PM10 during the summer in the mega-city Guangzhou, China (United States)

With rapid economic development and the acceleration of urbanization, air pollution has become a serious problem in the mega-city Guangzhou, China. A field campaign to sample and analyze particulate matter (PM) chemical components was performed from July 6, 2006 to July 26, 2006, in Guangzhou. During the campaign, the average mass concentration of PM10 was 89.0 ± 46.6 ?g m- 3 (the error represents one standard deviation). The PM10, sulfate, nitrate, ammonium, organic carbon (OC), and elemental carbon (EC) mass frequency distributions were analyzed. The [NO3-]/[SO42 -] mass ratio varied from 0.1 to 0.3, with an average of 0.2. A Pearson correlation analysis between [SO42 -] and [NH4+] and between [NO3-] and [Na+] showed that SO42 - existed as (NH4)2SO4 and NO3- existed as NH4NO3 and NaNO3. Sulfate, nitrate, ammonium, EC and POM (particulate organic matter) accounted for 24.4%, 4.9%, 5.7%, 5.7% and 21.0%, respectively, of the PM10 mass concentration during clean days and 25.7%, 3.9%, 7.9%, 5.4% and 20.8%, respectively, on hazy days. Among these species, SNA (sulfate, nitrate, and ammonium) were the most abundant, accounting for 35.0% and 37.5% of the PM10 during clean and hazy days, respectively. The sum of POM and EC accounted for 26.7% and 26.2% of PM10 in Guangzhou during clean and hazy days, respectively. There was no apparent difference in the chemical composition of PM10 between clean and haze days.

Han, Tingting; Liu, Xingang; Zhang, Yuanhang; Gu, Jianwei; Tian, Hezhong; Zeng, Limin; Chang, Shih-Yu; Cheng, Yafang; Lu, Keding; Hu, Min



The Coxiella burnetii Cryptic Plasmid Is Enriched in Genes Encoding Type IV Secretion System Substrates? †  

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The intracellular bacterial pathogen Coxiella burnetii directs biogenesis of a phagolysosome-like parasitophorous vacuole (PV), in which it replicates. The organism encodes a Dot/Icm type IV secretion system (T4SS) predicted to deliver to the host cytosol effector proteins that mediate PV formation and other cellular events. All C. burnetii isolates carry a large, autonomously replicating plasmid or have chromosomally integrated plasmid-like sequences (IPS), suggesting that plasmid and IPS ge...

Voth, Daniel E.; Beare, Paul A.; Howe, Dale; Sharma, Uma M.; Samoilis, Georgios; Cockrell, Diane C.; Omsland, Anders; Heinzen, Robert A.



appR gene product activates transcription of microcin C7 plasmid genes.  

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Microcin C7 (MccC7) is encoded by Escherichia coli plasmid pMccC7. However, some strains of E. coli K-12 carrying this plasmid do not produce this antibiotic. Here we show that these strains differ in the gene locus appR. This chromosomal gene product controls MccC7 production by activating the transcription of some, but not all, MccC7 plasmid genes.

Di?az-guerra, L.; Moreno, F.; San Milla?n, J. L.



Plasmid profiles and antibiotic susceptibility patterns of Staphylococcus aureus isolates from Nigeria. (United States)

In an investigation into the problems of infections due to Staphylococcus aureus in Nigeria, 100 strains were isolated from various hospitals in Lagos. The strains were screened for the presence of plasmids and for susceptibility to antimicrobial agents. Plasmids were extracted by modification of the method of Takahashi and Nagono[1]. The plasmids were diverse in nature. The strains were found to be highly resistant to commonly prescribed antibiotics. PMID:8669391

Olukoya, D K; Asielue, J O; Olasupo, N A; Ikea, J K



Characterization of the plasmidic beta-lactamase CMY-2, which is responsible for cephamycin resistance.  

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The phenotype of Klebsiella pneumoniae HEL-1 indicates a plasmidic cephamycinase gene (blaCMY-2). Its sequence shows one open reading frame coding for a protein of 381 amino acids. CMY-2 is classified as class C beta-lactamase that is closely related to the plasmidic enzymes BIL-1 and LAT-1 and the chromosomal AmpC of Citrobacter freundii. The blaCMY-2 gene possibly was translocated onto a plasmid of C. freundii which spread to K. pneumoniae.

Bauernfeind, A.; Stemplinger, I.; Jungwirth, R.; Giamarellou, H.



Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community  

DEFF Research Database (Denmark)

Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.The ISME Journal advance online publication, 21 October 2014; doi:10.1038/ismej.2014.191.

Klümper, Uli; Riber, Leise



appR gene product activates transcription of microcin C7 plasmid genes. (United States)

Microcin C7 (MccC7) is encoded by Escherichia coli plasmid pMccC7. However, some strains of E. coli K-12 carrying this plasmid do not produce this antibiotic. Here we show that these strains differ in the gene locus appR. This chromosomal gene product controls MccC7 production by activating the transcription of some, but not all, MccC7 plasmid genes. PMID:2651423

Díaz-Guerra, L; Moreno, F; San Millán, J L



Within-host competition selects for plasmid-encoded toxin–antitoxin systems  

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Toxin–antitoxin (TA) systems are commonly found on bacterial plasmids. The antitoxin inhibits toxin activity unless the system is lost from the cell. Then the shorter lived antitoxin degrades and the cell becomes susceptible to the toxin. Selection for plasmid-encoded TA systems was initially thought to result from their reducing the number of plasmid-free cells arising during growth in monoculture. However, modelling and experiments have shown that this mechanism can only explain the succe...

Cooper, Tim F.; Paixa?o, Tiago; Heinemann, Jack A.



Fast, non-toxic, and inexpensive n-butanol preparation of recombinant plasmids  

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Full Text Available Various commercial and non-commercial plasmid preparation protocols are currently available. However, the kits are expensive and many of the protocols contain toxic chemicals. Here we present a novel, optimized and, therefore, very advantageous plasmid preparation protocol using n-butanol. The preparation can be performed quickly and no toxic chemicals are used, at overall costs of about one cent per plasmid preparation.

Brieger Jürgen



Cloning in Streptococcus lactis of plasmid-mediated UV resistance and effect on prophage stability  

International Nuclear Information System (INIS)

Plasmid pIL7 (33 kilobases) from Streptococcus lactis enhances UV resistance and prophage stability. A 5.4-kilobase pIL7 fragment carrying genes coding for both characters was cloned into S. lactis, using plasmid pHV1301 as the cloning vector. The recombinant plasmid was subsequently transferred to three other S. lactis strains by transformation or protoplast fusion. Cloned genes were expressed in all tested strains


The Chief Resident Role in Emergency Medicine Residency Programs  

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Full Text Available Study Objectives: Although other specialties have examined the role of the chief resident (CR, the role and training of the emergency medicine (EM CR has largely been undefined.Methods: A survey was mailed to all EM CRs and their respective program directors (PD in 124 EM residency programs. The survey consisted of questions defining demographics, duties of the typical CR, and opinions regarding the level of support and training received. Multiple choice, Likert scale (1 strong agreement, 5 strong disagreement and short-answer responses were used. We analyzed associations between CR and PD responses using Chi-square, Student’s T and Mann-Whitney U tests.Results: Seventy-six percent of CRs and 65% of PDs responded and were similar except for age (31 vs. 42 years; p<0.001. CR respondents were most often male, in year 3 of training and held the position for 12 months. CRs and PDs agreed that the assigned level of responsibility is appropriate (2.63 vs. 2.73, p=0.15; but CRs underestimate their influence in the residency program (1.94 vs. 2.34, p=0.002 and the emergency department (2.61 vs. 3.03, p=0.002. The majority of CRs (70% and PDs (77% report participating in an extramural training program, and those CRs who participated in training felt more prepared for their job duties (2.26 vs. 2.73; p=0.03.Conclusion: EM CRs feel they have appropriate job responsibility but believe they are less influential in program and department administration than PD respondents. Extramural training programs for incoming CRs are widely used and felt to be helpful. [West J Emerg Med. 2010; 11(2:120-125.

Hafner, John W. Jr., MD, MPH



Reversible entrapment of plasmid deoxyribonucleic acid on different chromatographic supports. (United States)

HPLC based analytical assay is a powerful technique that can be used to efficiently monitor plasmid DNA (pDNA) purity and quantity throughout the entire purification process. Anion exchange monolithic and non-porous particle based stationary phases were used to study the recovery of the different pDNA isoforms from the analytical column. Three differently sized pDNA molecules of 3.0kbp, 5.2kbp and 14.0kbp were used. Plasmid DNA was injected onto columns under the binding conditions and the separation of the isoforms took place by increasing the ionic strength of the elution buffer. While there was no substantial decrease of the recovered supercoiled and linear isoforms of the pDNA with the increase of the plasmid size and with the increase of the flow rate (recoveries in all cases larger than 75%), a pronounced decrease of the oc isoform recovery was observed. The entrapment of the oc pDNA isoform occurred under non-binding conditions as well. The partial oc isoform elution from the column could be achieved by decreasing the flow rate of the elution mobile phase. The results suggested a reversible entrapment of the oc isoform in the restrictions within the pores of the monolithic material as well as within the intra-particle space of the non-porous particles. This phenomenon was observed on both types of the stationary phase morphologies and could only be connected to the size of a void space through which the pDNA needs to migrate. A prediction of reversible pDNA entrapment was successfully estimated with the calculation of Peclet numbers, Pe, which defines the ratio between a convective and diffusive mass transport. PMID:24021834

Gabor, Boštjan; ?ernigoj, Urh; Barut, Miloš; Štrancar, Aleš



Plasmid marker rescue transformation proceeds by breakage-reunion in Bacillus subtilis  

International Nuclear Information System (INIS)

Bacillus subtilis carrying a plasmid which replicates with a copy number of about 1 was transformed with linearized homologous plasmid DNA labeled with the heavy isotopes 2H and 15N, in the presence of 32Pi and 6-(p-hydroxyphenylazo)-uracil to inhibit DNA replication. Plasmid DNA was isolated from the transformed culture and fractionated in cesium chloride density gradients. The distribution of total and donor plasmid DNA was examined, using specific hybridization probes. The synthesis of new DNA, associated with the integration of donor moiety, was also monitored. Donor-specific sequences were present at a density intermediate between that of light and hybrid DNA. This recombinant DNA represented 1.4% of total plasmid DNA. The latter value corresponded well with the transforming activity (1.7%) obtained for the donor marker. Newly synthesized material associated with plasmid DNA at the recombinant density amounted to a minor portion of the recombinant plasmid DNA. These data suggest that, like chromosomal transformation, plasmid marker rescue transformation does not require replication for the integration of donor markers and, also like chromosomal transformation, proceeds by a breakage-reunion mechanism. The extent of donor DNA replacement of recipient DNA per plasmid molecule of 54 kilobases (27 kilobase pairs) was estimated as 16 kilobases


Prevalence of Pseudomonas aeruginosa FP plasmids which enhance spontaneous and UV-induced mutagenesis  

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From work reported here and from previous studies 16 out of 53 (30%) FP plasmids (i.e. those plasmids that promote host chromosome transfer) of Pseudomonas aeruginosa are found to protect host cells against UV irradiation. 13 of these UV-protecting FP plasmids were tested to determine their mode of DNA repair and were found to contribute to error-prone repair because of their enhancement of UV-induced mutagenesis and in most instances spontaneous mutagenesis as well. Some of these plasmids were tested for their behaviour in a DNA polymerase I deficient (Pol-) mutant of P. aeruginosa; the remainder could not be tested due to plasmid instability in the Pol- mutant. 11 of these FP plasmids provided wild type level of UV protection to the mutant. 4 of the plasmids tested (FP18, FP103, FP109 and FP111) were able to enhance the mutant's ability to host cell reactivate UV irradiated phage, though not to the level of the Pol+ parent. The presence of FP18 or FP111 in the Pol- mutant did not increase polymerase I-like enzymatic activity. It is concluded that the plasmids do not confer a polymerase activity functionally equivalent to host DNA polymerase I. The implications of the prevalence of FP plasmids in P. aeruginosa which enhance multagenesis are discussed. (Auth.)


Repair of UV-irradiated plasmid DNA in excision repair deficient mutants of Saccharomyces cerevisiae  

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The repair of UV-irradiated DNA of plasmid YEp13 was studied in the incision defective strains by measurement of cell transformation frequency. In Saccharomyces cerevisiae, rad1,2,3 and 4 mutants could repair UV-damaged plasmid DNA. In Escherichia coli, uvrA mutant was unable to repair UV-damaged plasmid DNA; however, pretreatment of the plasmid with Micrococcus luteus endonuclease increased repair. It was concluded that all the mutations of yeast were probably limited only to the nuclear DNA. (author)


New and Redesigned pRS Plasmid Shuttle Vectors for Genetic Manipulation of Saccharomyces cerevisiae  

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We have constructed a set of 42 plasmid shuttle vectors based on the widely used pRS series for use in the budding yeast Saccharomyces cerevisiae and the bacterium Escherichia coli. This set of pRSII plasmids includes new shuttle vectors that can be used with histidine and adenine auxotrophic laboratory yeast strains carrying mutations in the genes HIS2 and ADE1, respectively. Our pRSII plasmids also include updated versions of commonly used pRS plasmids from which common restriction sites th...

Chee, Mark K.; Haase, Steven B.



Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles  

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Full Text Available Abstract Background Temperature-sensitive (Ts plasmids are useful tools for genetic engineering, but there are currently none compatible with the gram positive, thermophilic, obligate anaerobe, Clostridium thermocellum. Traditional mutagenesis techniques yield Ts mutants at a low frequency, and therefore requires the development of high-throughput screening protocols, which are also not available for this organism. Recently there has been progress in the development of computer algorithms which can predict Ts mutations. Most plasmids currently used for genetic modification of C. thermocellum are based on the replicon of plasmid pNW33N, which replicates using the RepB replication protein. To address this problem, we set out to create a Ts plasmid by mutating the gene coding for the RepB replication protein using an algorithm designed by Varadarajan et al. (1996 for predicting Ts mutants based on the amino-acid sequence of the protein. Results A library of 34 mutant plasmids was designed, synthesized and screened, resulting in 6 mutants which exhibited a Ts phenotype. Of these 6, the one with the most temperature-sensitive phenotype (M166A was compared with the original plasmid. It exhibited lower stability at 48°C and was completely unable to replicate at 55°C. Conclusions The plasmid described in this work could be useful in future efforts to genetically engineer C. thermocellum, and the method used to generate this plasmid may be useful for others trying to make Ts plasmids.

Olson Daniel G



Plasmids which make their host bacteria mutable as well as resistant to ultraviolet irradiation  

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Some of the naturally occurring I?, I zeta, M, N, O and T group plasmids increase both the mutability and UV resistance of their host bacteria, while group H and S plasmids only increase mutability. This suggests that these two plasmid-mediated repair functions are separable. The two functions have no direct relation to their restriction-modification systems and nitrofuran resistant functions. In addition, the close linking between the restriction-modification genes and these repair function genes was suggested in group N plasmids. (author)


Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. (United States)

Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (approximately 12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication. PMID:20403814

Soler, Nicolas; Marguet, Evelyne; Cortez, Diego; Desnoues, Nicole; Keller, Jenny; van Tilbeurgh, Herman; Sezonov, Guennadi; Forterre, Patrick



Cloning of plasmid genes encoding resistance to cadmium, zinc, and cobalt in Alcaligenes eutrophus CH34.  

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A 238-kilobase-pair plasmid, pMOL30, confers resistance to cadmium, zinc, and cobalt salts in Alcaligenes eutrophus CH34. After Tn5 mutagenesis, restriction nuclease analysis, and Southern DNA-DNA hybridization, a 9.1-kilobase-pair EcoRI fragment was found to harbor all of these resistance properties and was cloned into the broad-host-range hybrid plasmid pRK290. When transferred to a plasmid-free derivative of CH34, the hybrid plasmid conferred the same degree of resistance as the parent pla...

Nies, D.; Mergeay, M.; Friedrich, B.; Schlegel, H. G.



Manure Enhances Plasmid Mobilization and Survival of Pseudomonas putida Introduced into Field Soil  

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We report a field study on plasmid mobilization in an agricultural soil. The influence of pig manure on the mobilization of the IncQ plasmid pIE723 by indigenous plasmids or by the IncP(alpha) plasmid pGP527 into the recipient Pseudomonas putida UWC1 (Rif(supr) Nal(supr)) was studied in field soil. Six plots were prepared in duplicate, three of which were treated with manure prior to inoculation of the donor and recipient strains. As a donor strain, either Escherichia coli J53(pIE723) or E. c...

Gotz, A.; Smalla, K.



Bacterium containing plasmids with foreign DNA, still imageSite: DNA Interactive ( (United States)

Illustration of bacterium containing plasmids with foreign DNA. By the end of the 1960s, DNA could be cut and pasted. But scientists needed a mechanism to copy it in order to maintain a large enough sample to work with. That breakthrough came in 1971, when scientists found an efficient way to introduce tiny loops of DNA called plasmids into E. coli. These loops of plasmid DNA can carry a package of foreign DNA into the host cell, and confer a benefit such as drug resistance. Scientists can import plasmids containing a selected piece of DNA into a bacterium. Normal bacterial reproduction produces huge quantities of the desired DNA.



Magnetic Nanoparticles for Plasmid DNA Adsorption via Hydrophobic Interaction  

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Full Text Available This study aims the preparation of magnetic poly(2-hydroxyethylmethacrylate-N-methacryloyl-L-phenylalanine, [poly(HEMA-MAPA] nanoparticles for plasmid DNA separation on the basis of hydrophobic interactions. Magnetic nanoparticles will be produced emulsion polymerization of 2-hydroxyethylmethacrylate (HEMA and N-methacryloyl-L-phenylalanine (MAPA monomers. Nanosized particles including hydrophobic groups stemmed from polymerizable derivative of phenylalanine aminoacid were evaluated to offer surface area that is enough for the higher capacity DNA purification than commercial micronsized sorbents for DNA purification.

Gungunes H.



El erizo de mar Diadema antillarum Phillipi, 1845 influye sobre la diversidad y composición de la comunidad de mega-invertebrados vágiles en fondos rocosos del Archipiélago Canario / The sea urchin Diadema antillarum Phillipi, 1845 influences the diversity and composition of the mobile mega-invertebrate community on rocky bottoms off the Canary Archipelago  

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: Spanish Abstract in spanish Se describe el efecto de la densidad del erizo Diadema antillarum sobre la diversidad y composición de la comunidad de mega-invertebrados vágiles (> 2 cm) que habita fondos rocosos del Archipiélago Canario (Atlántico oriental). Específicamente, se predijo que (1) las altas densidades de D. antillaru [...] m producen una baja diversidad de la comunidad de mega-invertebrados vágiles, y (2) la composición de las comunidades de mega-invertebrados varía entre fondos con diferentes densidades de D. antillarum. La presencia de especies mega-invertebradas, y la densidad de individuos de D. antillarum, se registraron visualmente en cuadrados de 2 x 2 m (n = 16 réplicas) en un total de 24 localidades (tres localidades en cada una de las ocho islas principales del archipiélago), visitadas en cuatro ocasiones entre febrero-2003 y octubre-2004. Se observaron 33 taxones de mega-invertebrados vágiles. Se registró una relación inversa entre la riqueza específica y la densidad de D. antillarum (r s = -0,20; P 8 ind. m-2), la riqueza de especies fue siempre baja ( Abstract in english The effect of the sea urchin Diadema antillarum density over the diversity and composition of the mobile mega-invertebrate community (> 2 cm) inhabiting shallow rocky reefs off the Canary Archipelago (eastern Atlantic) is described. Specifically, it was predicted that (1) high densities of D. antill [...] arum produce a low diversity of the mobile mega-invertebrate community, and (2) the composition of this community changes between rocky bottoms (= reefs) under different densities of D. antillarum. The presence of mega-invertebrate taxa, and the density of D. antillarum individuals were recorded visually using 2 x 2 m quadrats (n = 16 replicates) in each of 24 locations (three locations in each of the eight main islands of the archipelago), which were visited in four occasions between February-2003 and October-2004. Thrity-three taxa of mobile mega-invertebrates were observed. We registered a decline in the richness of such assemblages with increasing densities of D. antillarum (r s = -0.20; P 8 ind. m-2). A CAP ordination analysis showed significant differences in the composition of the mega-invertebrate community between rocky bottoms under different densities of D. antillarum, and we registered a negative correlation between the presence of some taxa and the densities of sea urchin. Consequently, the sea urchin D. antillarum influences the diversity and composition of the mobile mega-invertebrate community on rocky bottoms off the Canary Archipelago.

Leonor, Ortega; Fernando, Tuya; Ricardo J, Haroun.



The internal structure of the Mega-dunes in the Badainjaran desert revealed by ground penetrating radar and its implications to arid hydrology (United States)

Badainjaran desert in northwestern China has the world's highest stationary sand dunes, which are up to 500 m tall. Despite the prevailing dry and windy weather conditions the mega dunes were relatively moist underneath a dry surface layer of about 20 cm. It is very common to see a lake directly at the foot of the leeward side of a mega dune. Using 50- and 100-MHz antenna we conducted ground penetrating radar (GPR) surveys on both the windward and leeward of three mega dunes in southeastern Badainjaran desert. The GPR surveys clearly revealed the existence of numerous, almost evenly spaced calcareous cement and travertine features at shallow depth on the windward side of the mega dunes. The leeward tilted orientation of these calcareous cement and travertine features will be likely inducing more infiltration toward the leeward thus getting more recharge to the lake than the windward side. This trend may be one key factors to keep the lake exist in a very arid environment with high evaporation rate. The GPR profile also clearly depicted the shape of the water table beneath the mega dunes. The water table is gradually elevated outward from the lake, implies that the lake is possibly recharged by both precipitation from the vadose zone and the free water recharge from beneath the water table. A preliminary precipitation-evaporation-yield analysis based on our observation indicates that the lakes we studied may be survival if no further reduction of precipitation in this desert area.

Qian, R.; Li, J.; Liu, L.



Evaluation of Intern, Resident and Patient’s KnowledgeOf their Right Charter in Ahvaz Jundishapur University Educational Hospitals  

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Full Text Available Background and Objective: Provisions of law and medical ethics is one of the principles of patient satisfaction. The hospitals are inseparable units of social medicine which provide services for all the people in the community. In addition, educational hospitals are centers for education and the students acquire experience their. Obeying the laws of community medicine and patients' right charter are unavoidable to provide high quality services, health care and treatment. As follow-up regulatory bodies scattered in the annual evaluation of health service providers, this study was necessary.Subjects and Methods: This cross-sectional study has been done in order to assess patient & interns & resident’s awareness in 2010. The data collection instrument was a questionnaire based on patients' rights provisions. Sampling has been done randomly based on maximum amount of 433 people.Results: Among 433 people, there were 261 visitors, 103 residents, 69 interns, 181 males (% 48.8. The result show that in average %25.5 of visitors and %14.45 of physicians knew nothing about patients right contents, meanwhile %29.8 of visitors and %61.7 of physicians completely knew it.Conclusion: Considering, Ahvaz Jundishapur educational medical university is one of the first rate universities and Ahvaz is one of the developing mega cities; results could be clear lack of good transferring of information or some other reasons which could be suggestible for other studies.

Ahmad Ghorbani



Functional division and reconstruction of a plasmid replication origin: molecular dissection of the oriV of the broad-host-range plasmid RSF1010.  

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Two single-stranded DNA initiation signals (designated ssi) present in the origin of vegetative DNA replication (oriV) of the broad-host-range plasmid RSF1010 are essential for the priming of replication of each complementary DNA strand of this plasmid in Escherichia coli. Each of the RSF1010 ssi signals, ssiA and ssiB, could be replaced by a primosome assembly site from plasmid pACY184 or from bacteriophage phi X174. In these chimeric origins, replication of the strand complementary to that ...

Honda, Y.; Sakai, H.; Hiasa, H.; Tanaka, K.; Komano, T.; Bagdasarian, M.



2003 survey of Canadian radiation oncology residents  

International Nuclear Information System (INIS)

Purpose: Radiation oncology's popularity as a career in Canada has surged in the past 5 years. Consequently, resident numbers in Canadian radiation oncology residencies are at all-time highs. This study aimed to survey Canadian radiation oncology residents about their opinions of their specialty and training experiences. Methods and Materials: Residents of Canadian radiation oncology residencies that enroll trainees through the Canadian Resident Matching Service were identified from a national database. Residents were mailed an anonymous survey. Results: Eight of 101 (7.9%) potential respondents were foreign funded. Fifty-two of 101 (51.5%) residents responded. A strong record of graduating its residents was the most important factor residents considered when choosing programs. Satisfaction with their program was expressed by 92.3% of respondents, and 94.3% expressed satisfaction with their specialty. Respondents planning to practice in Canada totaled 80.8%, and 76.9% plan to have academic careers. Respondents identified job availability and receiving adequate teaching from preceptors during residency as their most important concerns. Conclusions: Though most respondents are satisfied with their programs and specialty, job availability and adequate teaching are concerns. In the future, limited time and resources and the continued popularity of radiation oncology as a career will magnify the challenge of training competent radiation oncologists in Canada


Neurocritical Care Training for the Neurosurgery Resident  

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Full Text Available Introduction: Recent data has associated favorable outcomes in patients who were treated in a “semi-closed” intensive care unit and attended to by a devoted team of neurointensivists as opposed to the neurosurgeons. This has led many to question the need for dedicated critical care education in the neurosurgical residency training program. Our aim was to determine what current neurosurgery residents and program directors/chairman thoughts were on NCC education in neurosurgical resident training, and to discuss possible methods to allow for collaboration between the NCC team and the neurosurgeons. Methods: Surveys were sent out electronically to all residency programs. Thirty-nine responses from junior residents, 36 responses from senior/chief residents, and eight responses from program directors/chairman were obtained. Results: No statistical difference between the majority responses of the different level residents, and between program directors/chairman and combined resident responses. Conclusions: Clearly, neurosurgery residents of all levels and program directors/chairman value NCC education and see a valuable role for this knowledge in their future. Most residents however do not want to spend an additional year of fellowship training to become certified neurointensivists. We discuss the role of NCC education in residency training and possible solutions to allow collaboration between the NCC team and the neurosurgical team.

Paul EKaloostian



Rapid and inexpensive method for isolating plasmid DNA  

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A small-scale and economical method for isolating plasmid DNA from bacteria is described. The method provides DNA of suitable quality for most DNA manipulation techniques. This DNA can be used for restriction endonuclease digestion, southern blot hybridization, nick translation and end labeling of DNA probes, Polymerase Chain Reaction (PCR) -based techniques, transformation, DNA cycle-sequencing, and Chain-termination method for DNA sequencing. The entire procedure is adapted to 1.5 ml microfuge tubes and takes approximately 30 mins. The DNA isolated by this method has the same purity produced by CTAB and cesium chloride precipitation and purification procedures respectively. The two previous methods require many hours to obtain the final product and require the use of very expensive equipment as ultracentrifuge. This method is well suited for the isolation of plasmid DNA from a large number of bacterial samples and in a very short time and low cost in laboratories where chemicals, expensive equipment and finance are limited factors in conducting molecular research. (authors). 11refs. 11refs


Introducing "optimal challenges" in resident training  

DEFF Research Database (Denmark)

Background: Residents are often caught between two interests: the resident’s desire to participate in challenging learning situations and the department’s work planning. However, these interests may clash if they are not coordinated by the senior doctors, and challenging learning situations risk being subject to work planning. Summary of work: Inspired by Csikszentmihalyi’s concept of optimal challenges, an intervention study aimed at introducing a more suitable planning of resident’s learning in terms of optimal allocation of educational patient contacts. The objective was to coordinating residents’ individual competences and learning needs with patient characteristics in order to match each resident with a case (an outpatient or a patient) that meets the learning needs of the resident and thus pose an optimal challenge to the resident. Summary of results: The preliminary results show that the residents benefit from the intervention because they experienced more optimal challenges than before the intervention. However, the matching of resident and case seems to work against the established culture in the department: the daily work has for many years been organized so that senior doctors have their “own” patients and they do not “share” patients with residents. Thus the patients were accustomed to have their “own” specialist doctor. Conclusion: The intervention generated optimal challenges, but revealed the need for more team-based organization of senior doctors and residents’ working relationships in order to meet the health system’s and the patients’ call for continuity in the treatment. Take-home message: The matching of resident and case stimulates optimal learning situations, but cultural and organizational values concerning the doctor-patient continuity are challenged.

SØrensen, Anette Bagger; Christensen, Mette Krogh


Phenotypic and molecular characterization of conjugative antibiotic resistance plasmids isolated from bacterial communities of activated sludge. (United States)

In order to isolate antibiotic resistance plasmids from bacterial communities found in activated sludge, derivatives of the 3-chlorobenzoate-degrading strain Pseudomonas sp. B13, tagged with the green fluorescent protein as an identification marker, were used as recipients in filter crosses. Transconjugants were selected on agar plates containing 3-chlorobenzoate as the sole carbon source and the antibiotic tetracycline, streptomycin or spectinomycin, and were recovered at frequencies in the range of 10(-5) to 10(-8) per recipient. A total of 12 distinct plasmids, designated pB1-pB12, was identified. Their sizes ranged between 41 to 69 kb and they conferred various patterns of antibiotic resistance on their hosts. Two of the plasmids, pB10 and pB11, also mediated resistance to inorganic mercury. Seven of the 12 plasmids were identified as broad-host-range plasmids, displaying extremely high transfer frequencies in filter crosses, ranging from 10(-1) to 10(-2) per recipient cell. Ten of the 12 plasmids belonged to the IncP incompatibility group, based on replicon typing using IncP group-specific PCR primers. DNA sequencing of PCR amplification products further revealed that eight of the 12 plasmids belonged to the IncPbeta subgroup, whereas two plasmids were identified as IncPalpha plasmids. Analysis of the IncP-specific PCR products revealed considerable differences among the IncPbeta plasmids at the DNA sequence level. In order to characterize the gene "load" of the IncP plasmids, restriction fragments were cloned and their DNA sequences established. A remarkable diversity of putative proteins encoded by these fragments was identified. Besides transposases and proteins involved in antibiotic resistance, two putative DNA invertases belonging to the Din family, a methyltransferase of a type I restriction/modification system, a superoxide dismutase, parts of a putative efflux system belonging to the RND family, and proteins of unknown function were identified. PMID:10821181

Dröge, M; Pühler, A; Selbitschka, W



Characterization and comparative analysis of antibiotic resistance plasmids isolated from a wastewater treatment plant (United States)

A wastewater treatment plant (WWTP) is an environment high in nutrient concentration with diverse bacterial populations and can provide an ideal environment for the proliferation of mobile elements such as plasmids. WWTPs have also been identified as reservoirs for antibiotic resistance genes that are associated with human pathogens. The objectives of this study were to isolate and characterize self-transmissible or mobilizable resistance plasmids associated with effluent from WWTP. An enrichment culture approach designed to capture plasmids conferring resistance to high concentrations of erythromycin was used to capture plasmids from an urban WWTP servicing a population of ca. 210,000. DNA sequencing of the plasmids revealed diversity of plasmids represented by incompatibility groups IncU, col-E, IncFII and IncP-1?. Genes coding resistance to clinically relevant antibiotics (macrolide, tetracycline, beta-lactam, trimethoprim, chloramphenicol, sulphonamide), quaternary ammonium compounds and heavy metals were co-located on these plasmids, often within transposable and integrative mobile elements. Several of the plasmids were self-transmissible or mobilizable and could be maintained in the absence of antibiotic selection. The IncFII plasmid pEFC36a showed the highest degree of sequence identity to plasmid R1 which has been isolated in England more than 50 years ago from a patient suffering from a Salmonella infection. Functional conservation of key regulatory features of this F-like conjugation module were demonstrated by the finding that the conjugation frequency of pEFC36a could be stimulated by the positive regulator of plasmid R1 DNA transfer genes, TraJ.

Rahube, Teddie O.; Viana, Laia S.; Koraimann, Gunther; Yost, Christopher K.



Aerosol optical properties and radiative forcing over mega-city Karachi (United States)

Aerosol optical properties have been analyzed through the ground-based Aerosol Robotic Network (AERONET) over the mega city Karachi during August 2006-July 2007. The aerosol optical depth (AOD) is strongly dependent on wavelength; for shorter wavelengths AOD values are higher than at longer wavelengths. The results reveal that the monthly average AOD at 500 nm ranges from 0.31 to 0.92 with an annual mean of 0.48 ± 0.18 and monthly averaged angstrom exponent (Alpha) ranges from 0.17 to 1.05 with an annual mean of 0.49 ± 0.31. The maximum monthly average AOD value of 0.92 ± 0.28 with the corresponding Alpha value of 0.21 ± 0.11 is found for July 2007, while the minimum monthly average AOD value of 0.31 ± 0.11 with the corresponding Alpha value of 0.53 ± 0.13 is recorded for March 2007. The volume size distribution in the coarse mode is higher in summer and lower in winter, whereas in the accumulation mode the volume size distribution is higher in winter than in other seasons due to the hygroscopic growth of aerosol particles. The single scattering albedo (SSA) during spring, autumn and summer seasons shows a slight increase with the wavelength and ranges from 0.88 ± 0.02 to 0.97 ± 0.01. The asymmetry parameter (ASY) is also wavelength dependent and varies from 0.61 ± 0.03 to 0.74 ± 0.02 during the year. The aerosol radiative forcing (ARF) for the whole observation period at the top of the atmosphere (TOA) is in the range of - 7 to - 35 Wm -2 (average - 22 ± 6 Wm -2), at the surface from - 56 to - 96 Wm -2 (average - 73 ± 12 Wm -2), increasing the atmospheric forcing from + 38 to + 61 Wm -2(average + 51 ± 13 Wm -2). The SBDART-AERONET radiative forcing at the surface and TOA agree with correlation of 0.92 and 0.82, respectively.

Alam, Khan; Trautmann, Thomas; Blaschke, Thomas



Southeast Asian Mega-Droughts of the Past 5 Centuries from Tree Rings and Historical Records (United States)

The need for understanding the natural range of climate variability in the monsoon regions of Asia - among the worldês most heavily populated and most dependent on agriculture - is critical for making sound planning decisions in the face of expected hydrological changes associated with global climate change. As part of a US National Science Foundation-funded project (Tree Ring Reconstructions of Asian Monsoon Climate Variability) we have produced climate-responsive tree-ring records from tropical Asia that span the past five centuries. We find compelling evidence for 18th century decadal-scale summer monsoon droughts that span from India to Vietnam. Historical records corroborate that periods of severe drought occurred across much of the region during this time, while speleothem and coral records suggest multiple decadal-scale droughts for much of the Little Ice Age period in India, and elevated Sea Surface Temperature (SST) during the 18th century for much of the tropical Pacific, respectively. Tropical Pacific SST anomalies are seen as one key component to monsoon variability over the study region, with El Ni?o and La Ni?a like conditions resulting in rainfall reductions and increases, respectively, with corresponding opposite-sign anomalies across much of western North America. Persistent anomaly trends in the SST fields can result in the kinds of decadal-scale variability our studies suggest, although this is not the entire story. We explore the role of the Interdecadal Pacific Oscillation (IPO), first defined in 1999 as a Pacific-wide measure of variability that is physically distinct from both the Pacific Decadal Oscillation (PDO) and the El Ni?o Southern Oscillation (ENSO), in contributing to protracted -mega-droughts" in the region related to weakening monsoon strength, as suggested by recent research. Interestingly, near-millennium-aged conifers from Vietnam and Laos have been located and much longer records are now being constructed. Of great interest is the period of the late 14th and early 15th centuries when a very week monsoon is thought to have occurred, possibly contributing to the demise of the Angkor Wat civilization in Cambodia.

Buckley, B. M.



Seismogenic Mega-splay Fault in Subduction Zone-Modern and Ancient Examples from Southwest Japan (United States)

In the Nankai Trough, SW Japan, 1944 Tonankai earthquake took place along a mega splay fault branching from the plate boundary between the upper Eurasian and lower Phillipine Sea Plate (Park et al., 2002). The splay fault is recognized as a strong reflector showing partly negative polarity with a wavelength of ca. 200 m (Park et al., 2002). The fault appears to make a boundary between the underthrusted sediments in the deep portion (> 6km), cut the Nankai accretionary prism in a shallow part, and appears a cold seep spot on the sea bottom surface (Ashi, person. Com.). A major out-of-sequence thrust (the Nobeoka Thrust) cutting the ancient accretionary prism of the Shimanto Belt into two subbelts is observed in the Kyushu Island, SW Japan (Murata, 1986; Kondo et al., in press). The fault was located under the thermal condition ca. 250¡OC in terms of vitrinite reflectance and fluid inclusion geo-thermo-barometry, that is enough within the seismogenic zone by thermal model (Hyndman et al., 1997) and is a good analog for the modern splay fault in the Nankai Trough mentioned above. Structural analysis of the thrust shows that the damage zone around the thrust is a few hundred meters thick (Kondo, et al., in press) and is characterized by strong brittle deformation with ubiquitous development of crack-seal and shear-parallel veins. Hanging-wall side of the Nobeoka Thrust is composed of shale/sandstone dominated phyllites, of which deformation is characterized primarily by plastic flow and pressure solution overprinted by brittle cataclastic shear and cracking. Several thin cataclasitc shear zones represent extremely fine fragmental components or re-crystalized clays. Their chemical aspect indicates preferential Fe and Mg concentration, which is suggestive of preferential melting of micaceous and chrolite of host rocks due to frictional heating. Asymmetric development of cracks surrounding the thin shear zones is also characteristic. The asymmetric cracks are quite resemble to that developed in the process zone of fault (Vermilye and Sholz, 1998), that indicates upward propagation of rupture. The footwall side of the Nobeoka Thrust is completely brittle, and crack seal or shear zone filling quartz or calcite veins are developed. Geometric relationship of these veins with the fault is quite systematic, therefore indicates quite active fluid deposite and flow in the damage zone. Fluid inclusion analysis indicates that fluid passing through strongly deformed part of damage zone was hotter than that in less deformed part. Such a passage may be possible only during dynamic dilatant rupture associated with seismic event.

Kimura, G.; Okamoto, S.



Large aftershocks of the Maule 2010 mega earthquake in Central Chile (United States)

The very large Mw 8.8 Maule earthquake of 27 February 2010 has been studied in great detail using seismic, geodetic tsunami and geologic data. This event was followed by a long series of aftershocks that have been relocated by several authors. One of the curious characteristics of this mega earthquake is that for the first few months it had very few large aftershocks and that many were not located on the main fault plane of the event. After three years, although there were many small aftershocks, only 22 larger than Mw 6 are listed in the CMT catalogue; the two largest aftershock having a magnitude of 7.1. According to Bath's rule at least one aftershock should have had a magnitude larger than 7.5. These larger aftershocks form a very tenuous network of events that do not cover entire fault surface as is the case of many other large earthquakes. A likely interpretation of our results is that the aftershock series will continue over a long period of time with large aftershocks in the future. The largest aftershocks of 2010 were a large outer rise event at 08 UT, two hours after the main shock of 27 February 2010 and located in the outer rise off the Arauco peninsula; and two large shallow crustal events of Mw 7.1 and 6.8 on 11 March 2010 near the city of Pichilemu. In the last couple of years the aftershock activity has continued and several larger aftershocks have occurred on the main fault of the Maule event. Here we study these aftershocks using relocation techniques and finite source modelling of the far field seismic radiation. Among the aftershocks that we study, three are particularly interesting: these are the events of Mw 7.1 on 2 January 2011 near the southern end of the 2010 rupture, that of Mw 6.8 on 11 February 2011 in the neighbourhood of the hypocenter of the Maule event and that of Mw 7.1 of 25 March 2012 in the northern patch of the main event. These aftershocks were located at different places of the 2010 rupture, on the plate interface close the bottom of the 2010 rupture zone. We compare this series of aftershocks with that of other large Chilean earthquakes of the last 40 years concluding that earthquakes of Mw < 8 tend to occur near the bottom of the plate interface. Ruptures extend towards the trench only for very large events that break the entire plate interface.

Buforn, Elisa; Pro, Carmen; Fuenzalida, Amaya; Ruiz, Sergio; Madariaga, Raul



Mega fire emissions in Siberia: potential supply of soluble iron from forests to the ocean (United States)

Significant amounts of carbon and nutrients are released to the atmosphere due to large fires in forests. Characterization of the spatial distribution and temporal variation of the intense fire emissions is crucial for assessing the atmospheric loadings of aerosols and trace gases. This paper discusses issues of the representation of forest fires in the estimation of emissions and the application to an atmospheric chemistry transport model (CTM). The potential contribution of forest fires to the deposition of soluble iron (Fe) into the ocean is highlighted, with a focus on mega fires in eastern Siberia. Satellite products of burned area, active fire, and land cover are used to estimate biomass burning emissions in conjunction with a biogeochemical model. Satellite-derived plume height from MISR is used for the injection height of boreal forest fire emissions. This methodology is applied to quantify fire emission rates in each three-dimensional grid location in the high latitude Northern Hemisphere (> 30° N latitude) over a 5-year period from 2001 to 2005. There is large interannual variation in forest burned area during 2001-2005 (13-51 × 103 km2 yr-1) which results in a corresponding variation in the annual emissions of carbon monoxide (CO) (12-78 Tg CO yr-1). Satellite observations of CO from MOPITT are used to evaluate the model performance in simulating the spatial distribution and temporal variation of the fire emissions. During the major Siberian fire seasons in the summer of 2002 and in the spring of 2003, the model results for CO enhancements due to intense fires are in good agreement with MOPITT observations. These fire emission rates are applied to the aerosol chemistry transport model to examine the relative importance of biomass burning sources of soluble iron compared to those from dust sources. Compared to the dust sources without the atmospheric processing by acidic species, extreme fire events contribute to a significant deposition of soluble iron (10-60%) to downwind regions over the western North Pacific Ocean. It may imply that the supply of nutrients from large forest fires plays a role as a negative biosphere-climate feedback with regards to the ocean fertilization.

Ito, A.



Mega fire emissions in Siberia: potential supply of soluble iron from forests to the ocean  

Directory of Open Access Journals (Sweden)

Full Text Available Significant amounts of carbon and nutrients are released to the atmosphere due to large fires in forests. Characterization of the spatial distribution and temporal variation of the intense fire emissions is crucial for assessing the atmospheric loadings of aerosols and trace gases. This paper discusses issues of the representation of forest fires in the estimation of emissions and the application to an atmospheric chemistry transport model (CTM. The potential contribution of forest fires to the deposition of soluble iron (Fe into the ocean is highlighted, with a focus on mega fires in eastern Siberia. Satellite products of burned area, active fire, and land cover are used to estimate biomass burning emissions in conjunction with a biogeochemical model. Satellite-derived plume height from MISR is used for the injection height of boreal forest fire emissions. This methodology is applied to quantify fire emission rates in each three-dimensional grid location in the high latitude Northern Hemisphere (> 30° N latitude over a 5-year period from 2001 to 2005. There is large interannual variation in forest burned area during 2001–2005 (13–51 × 103 km2 yr?1 which results in a corresponding variation in the annual emissions of carbon monoxide (CO (12–78 Tg CO yr?1. Satellite observations of CO from MOPITT are used to evaluate the model performance in simulating the spatial distribution and temporal variation of the fire emissions. During the major Siberian fire seasons in the summer of 2002 and in the spring of 2003, the model results for CO enhancements due to intense fires are in good agreement with MOPITT observations. These fire emission rates are applied to the aerosol chemistry transport model to examine the relative importance of biomass burning sources of soluble iron compared to those from dust sources. Compared to the dust sources without the atmospheric processing by acidic species, extreme fire events contribute to a significant deposition of soluble iron (10–60% to downwind regions over the western North Pacific Ocean. It may imply that the supply of nutrients from large forest fires plays a role as a negative biosphere-climate feedback with regards to the ocean fertilization.

A. Ito



Evaluation of an ion-exchange membrane for the purification of plasmid DNA. (United States)

Separation and purification of large quantities of plasmid DNA (pDNA) is a particularly difficult manufacturing issue because of the relatively low capacity, flow rate and purity observed using traditional bead-based chromatography. The objective of the present study was to evaluate the performance of anion-exchange membranes for the purification of pDNA from Escherichia coli lysate solution. The fate of host-cell protein and endotoxin relative to pDNA was measured and used to calculate recoveries, mass balances, dynamic capacities and purification factors as a function of the flow rate and loading volume of the lysate solution. Breakthrough curves were not sigmoidal and symmetric in shape. They rose sharply at first, and then slowly towards, but never reaching, saturation. Conversely, elution curves were independent of flow rate. pDNA bound tightly to the membranes, whereas protein and endotoxin did not. Dynamic binding capacity for pDNA was 20-25 times greater, and the flow rate was 55-550 times greater, than values observed for beads. However, some pDNA bound irreversibly to the membrane surface and was not removed completely during elution. The intrinsic rate of pDNA adsorption to the membrane was found to be rate-limiting, whereas effects of liquid-phase mass transfer and flow non-idealities were negligible. These results were interpreted using models of adsorption that included steric effects using the 'car-parking-problem' model, and surface residence time effects using the spreading model. This work demonstrated the advantages of ion-exchange membranes compared with beads for the purification of large biomolecules such as pDNA. PMID:12689337

Endres, Heather N; Johnson, Julie A C; Ross, Carl A; Welp, John K; Etzel, Mark R



Unique needs of women pharmacy residents. (United States)

The needs of women residents in hospital pharmacy programs are discussed with respect to the responsibilities of preceptors to help residents prepare for a successful career. Women were a small minority within the profession of pharmacy until recently. More than half of the current hospital pharmacy residents are women, while over 95% of the preceptors of residency training programs are men. Hospital pharmacy preceptors can help meet the unique needs of women residents, so that women pharmacists can achieve the career successes of which they are capable. Preceptors can help women residents make career decisions and develop career goals and strategies. Preceptors should ensure that women residents develop the broad base of knowledge and skills necessary for advancement. Women residents should be encouraged to get involved in pharmacy organizations, and the importance of networking should be stressed. It is important that women residents develop a business style so that they are perceived as confident and competent. Preceptors must recognize that most women will have conflicts in their roles of career woman, wife, and mother. Preceptors can also help women residents by making managerial changes (e.g., offering part-time positions and flexible scheduling) that will facilitate integration of the professional and personal responsibilities of women. PMID:7180857

Johnson, M W



Neurocritical care education during neurology residency (United States)

Objective: Limited information is available regarding the current state of neurocritical care education for neurology residents. The goal of our survey was to assess the need and current state of neurocritical care training for neurology residents. Methods: A survey instrument was developed and, with the support of the American Academy of Neurology, distributed to residency program directors of 132 accredited neurology programs in the United States in 2011. Results: A response rate of 74% (98 of 132) was achieved. A dedicated neuroscience intensive care unit (neuro-ICU) existed in 64%. Fifty-six percent of residency programs offer a dedicated rotation in the neuro-ICU, lasting 4 weeks on average. Where available, the neuro-ICU rotation was required in the vast majority (91%) of programs. Neurology residents' exposure to the fundamental principles of neurocritical care was obtained through a variety of mechanisms. Of program directors, 37% indicated that residents would be interested in performing away rotations in a neuro-ICU. From 2005 to 2010, the number of programs sending at least one resident into a neuro-ICU fellowship increased from 14% to 35%. Conclusions: Despite the expansion of neurocritical care, large proportions of US neurology residents have limited exposure to a neuro-ICU and neurointensivists. Formal training in the principles of neurocritical care may be highly variable. The results of this survey suggest a charge to address the variability of resident education and to develop standardized curricula in neurocritical care for neurology residents. PMID:22573636

Drogan, O.; Manno, E.; Geocadin, R.G.; Ziai, W.




The authors use a mathematical model to analyze the dynamics of loss of nonconjugative pACYC184 from populations of Escherichia coli B in glucose-limited continuous culture. The model incorporates both plasmid segregation and selection against plasmid carriage. It is concluded th...


Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. (United States)

Public health officials have raised concerns that plasmid transfer between Enterobacteriaceae species may spread resistance to carbapenems, an antibiotic class of last resort, thereby rendering common health care-associated infections nearly impossible to treat. To determine the diversity of carbapenemase-encoding plasmids and assess their mobility among bacterial species, we performed comprehensive surveillance and genomic sequencing of carbapenem-resistant Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center patient population and hospital environment. We isolated a repertoire of carbapenemase-encoding Enterobacteriaceae, including multiple strains of Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing with full end-to-end assembly revealed that these organisms carry the carbapenem resistance genes on a wide array of plasmids. K. pneumoniae and E. cloacae isolated simultaneously from a single patient harbored two different carbapenemase-encoding plasmids, indicating that plasmid transfer between organisms was unlikely within this patient. We did, however, find evidence of horizontal transfer of carbapenemase-encoding plasmids between K. pneumoniae, E. cloacae, and C. freundii in the hospital environment. Our data, including full plasmid identification, challenge assumptions about horizontal gene transfer events within patients and identify possible connections between patients and the hospital environment. In addition, we identified a new carbapenemase-encoding plasmid of potentially high clinical impact carried by K. pneumoniae, E. coli, E. cloacae, and Pantoea species, in unrelated patients and in the hospital environment. PMID:25232178

Conlan, Sean; Thomas, Pamela J; Deming, Clayton; Park, Morgan; Lau, Anna F; Dekker, John P; Snitkin, Evan S; Clark, Tyson A; Luong, Khai; Song, Yi; Tsai, Yu-Chih; Boitano, Matthew; Dayal, Jyoti; Brooks, Shelise Y; Schmidt, Brian; Young, Alice C; Thomas, James W; Bouffard, Gerard G; Blakesley, Robert W; Mullikin, James C; Korlach, Jonas; Henderson, David K; Frank, Karen M; Palmore, Tara N; Segre, Julia A



[IncP-7 plasmids' classification based on structural diversity of their basic replicons]. (United States)

The structural diversity of basic replicons and repB gene of the IncP-7 plasmids' collection was firstly assessed on the basis of PCR, restriction analysis and partial sequencing. It has been revealed that DNA fragment containing gene for UvrD-like helicase RepB is a part of all known P-7 replicons, but often serves as hot place for diverse IS-elements invasion. The first system of P-7 plasmids' classification has been worked out on the basis of determined repA-oriV-par WABC nucleotide divergency. Most degradation plasmids established to be belonging to large beta-subgroup, streptomycin resistance plasmid Rms148 (IncP-7 archetype)--to alpha-subgroup, carbazole degradation plasmid pCAR1 and NAH/SAL-plasmids from pY-line (Yamal oil deposits)--to gamma-subgroup and CAP-plasmid pBS270 with potentially reduced P-7 replicon--to delta-subgroup. It has been observed that the type of IncP-7 basic replicon molecular organization does not correlate with fixed phenotypic character in most cases, that is plasmids encoding different phenotypic markers could be members of the same P-7 subgroup. PMID:23808156

Volkova, O V; Panov, A V; Kosheleva, I A; Boronin, A M



Complete Nucleotide Sequence of a Citrobacter freundii Plasmid Carrying KPC-2 in a Unique Genetic Environment. (United States)

The complete and annotated nucleotide sequence of a 54,036-bp plasmid harboring a blaKPC-2 gene that is clonally present in Citrobacter isolates from different species is presented. The plasmid belongs to incompatibility group N (IncN) and harbors the class A carbapenemase KPC-2 in a unique genetic environment. PMID:25395635

Yao, Yancheng; Imirzalioglu, Can; Hain, Torsten; Kaase, Martin; Gatermann, Soeren; Exner, Martin; Mielke, Martin; Hauri, Anja; Dragneva, Yolanta; Bill, Rita; Wendt, Constanze; Wirtz, Angela; Domann, Eugen; Chakraborty, Trinad



Design and application of a new cryptic-plasmid-based shuttle vector for Magnetospirillum magneticum. (United States)

A 3.7-kb cryptic plasmid designated pMGT was found in Magnetospirillum magneticum MGT-1. It was characterized and used for the development of an improved expression system in strain AMB-1 through the construction of a shuttle vector, pUMG. An electroporation method for magnetic bacteria that uses the cryptic plasmid was also developed. PMID:12839813

Okamura, Yoshiko; Takeyama, Haruko; Sekine, Takumi; Sakaguchi, Toshifumi; Wahyudi, Aris Tri; Sato, Rika; Kamiya, Shinji; Matsunaga, Tadashi



Conjugal plasmid transfer (pAM beta 1) in Lactobacillus plantarum.  

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The streptococcal plasmid pAM beta 1 (erythromycin resistance) was transferred via conjugation from Streptococcus faecalis to Lactobacillus plantarum and was transferred among L. plantarum strains. Streptococcus sanguis Challis was transformed with pAM beta 1 isolated from these transconjugants, and transformants harboring intact pAM beta 1 could conjugate the plasmid back to L. plantarum.

Shrago, A. W.; Chassy, B. M.



Transfer of Carbapenem-Resistant Plasmid from Klebsiella pneumoniae ST258 to Escherichia coli in Patient  

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Klebsiella pneumoniae carbapenemase (KPC) 3–producing Escherichia coli was isolated from a carrier of KPC-3–producing K. pneumoniae. The KPC-3 plasmid was identical in isolates of both species. The patient's gut flora contained a carbapenem-susceptible E. coli strain isogenic with the KPC-3–producing isolate, which suggests horizontal interspecies plasmid transfer.

Goren, Moran G.; Carmeli, Yehuda; Schwaber, Mitchell J.; Chmelnitsky, Inna; Schechner, Vered; Navon-venezia, Shiri



Comparative studies of Danish Flavobacterium psychrophilum isolates: ribotypes, plasmid profiles, serotypes and virulence  

DEFF Research Database (Denmark)

Ribotyping and plasmid profiling were carried out on 299 Danish Flavobacterium psychrophilum isolates from farmed rainbow trout, Oncorhynchus mykiss (Walbaum). The isolates had been characterized biochemically and serologically in another study. The isolates were very homogeneous, 254 isolates had the same ribotype A (restriction enzyme EcoRI) and 284 isolates harboured one 3.3 kb plasmid. Seventy-five per cent of the F. psychrophilum isolates had ribotype A, one 3.3 kb plasmid and belonged to either serotype Th or Fd. Virulence studies with representatives of the dominant groups classified such isolates as virulent, and an extra small or large plasmid did not change the virulence level. A relationship between the serotypes Fd and Th, certain ribotypes, and virulence was found. The isolates belonging to serotype Fp(T) and to ribotype B were less virulent. Only a few isolates with other ribotypes were found and these were also less virulent. Isolates that did not have the 3.3 kb plasmid were also less virulent. The virulent isolates all harboured the 3.3 kb plasmid; however, there was no clear correlation between virulence and plasmid content as a 3.3 kb plasmid was also found in less virulent isolates.

Madsen, Lone; Dalsgaard, Inger



Analysis of the physiological control of replication of ColE1-type plasmids. (United States)

The physiology of ColE1-type plasmid replication in a growing host has been examined both theoretically, using computer simulation, and experimentally, by observing replication of the plasmid pBR322 after a nutritional shift-up from glycerol minimal medium (doubling time 71 min) to LB medium (doubling time 24 min). The theory was based on a negative control model and uses three rate equations: for the accumulation of cell mass, for the accumulation of the replication inhibitor, and for the rate of plasmid synthesis. The implications of the theory were explored by simulating the effects of changes in the expression of replication control genes. The nutritional shift-up experiment showed that plasmid replication was blocked immediately after the shift for about half a mass doubling time; after that time, replication rapidly increased until plasmid numbers per unit volume of culture parallelled the increase in culture mass. After the establishment of steady-state growth in the post-shift medium, the plasmid concentration (plasmids per cell mass) was reduced in comparison to pre-shift growth in the same proportion as the culture doubling time. The results showed that plasmid replication factors are under metabolic control and that the changes in the control of these factors compensate one another during steady-state growth, but not immediately after the medium shift. PMID:2443764

Bremer, H; Lin-Chao, S



Characterization of plasmids that encode streptomycin-resistance in bacterial epiphytes of apple. (United States)

Streptomycin resistance in strains of Pseudomonas syringae pv. papulans, Pantoea agglomerans and a yellow-pigmented, non-fluorescent Pseudomonas sp. (Py), isolated from apple orchards in New York and Washington states, is predominantly associated with strA-strB genes carried on conjugal plasmids (R plasmids). None of 128 resistant Erwinia amylovora strains from the eastern and western USA hybridized with a strA-strB probe, SMP3. Resistant Py strains transfered R plasmids to Ps. syringae pv. papulans and to Py in vitro at frequencies of 10(-1)-10(-2) per recipient cell whereas Ps. syringae pv. papulans transferred its plasmids at frequencies of 10(-2) to below detectable levels. Transfer of R plasmids to P. agglomerans was not detected and resistant P. agglomerans did not transfer their R plasmids to any recipients. R plasmids were found to be highly diverse as measured by DNA fingerprint analysis. Transfer-deficient transposon mutants of R plasmid pCPP519 were generated, and 3.9 kb EcoRI and 3.0 kb SmaI fragments that hybridized with a Tn5 probe were cloned and sequenced. The deduced amino acid sequences of the 3.9 kb fragment were similar to proteins involved in replication, nicking at oriT, and piliation in other bacteria. PMID:10347868

Huang, T C; Burr, T J



Cloning, sequencing, and sequence analysis of two novel plasmids from the thermophilic anaerobic bacterium Anaerocellum thermophilum  

DEFF Research Database (Denmark)

The nucleotide sequence of two novel plasmids isolated from the extreme thermophilic anaerobic bacterium Anaerocellum thermophilum DSM6725 (A. thermophilum), growing optimally at 70degreesC, has been determined. pBAS2 was found to be a 3653 bp plasmid with a GC content of 43%, and the sequence revealed 10 open reading frames (ORFs). The two largest of these, namely Orf21 and Orf41, showed similarity to a Bacillus plasmid recombinase and a Pseudoalteromonas plasmid replication protein, respectively. A sequence with homology to double stranded replication origins from rolling circle plasmids was found, but no single stranded intermediates, characteristic of rolling circle replication, were found on Southern blots. The larger plasmid, pBAL, was found to be a 8294 bp plasmid with a GC content of 39%. It revealed 17 ORFs, of which three showed similarity at the amino acid (aa) level to known proteins. Orf22 showed the strongest similarity (33% aa) to replication proteins from large multiresistance Staphylococcal and Lactococcal plasmids, all of which are believed to replicate via a theta-like replication mechanism. Orf32 showed similarity to both DNA repair proteins and DNA polymerases with highest similarity to DNA repair protein from Campylobacter jejuni (25% aa). Orf34 showed similarity to sigma factors with highest similarity (28% aa) to the sporulation specific Sigma factor, Sigma 28(K) from Bacillus thuringiensis.

Clausen, Anders; Mikkelsen, Marie Just



Efficient transformation of Amycolatopsis orientalis (Nocardia orientalis) protoplasts by Streptomyces plasmids.  

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Conditions for efficient transformation of Amycolatopsis orientalis (Nocardia orientalis) protoplasts by Streptomyces plasmid cloning vectors were identified. Three streptomycete plasmid origins of replication function in A. orientalis, as do the apramycin resistance gene from Escherichia coli, the thiostrepton resistance gene from Streptomyces azureus, and the tyrosinase gene from Streptomyces antibioticus. A. orientalis appears to express some restriction and modification, because highest t...

Matsushima, P.; Mchenney, M. A.; Baltz, R. H.



Characterization of a plasmid-encoded urease gene cluster found in members of the family Enterobacteriaceae. (United States)

Plasmid-encoded urease gene clusters found in uropathogenic isolates of Escherichia coli, Providencia stuartii, and Salmonella cubana demonstrated DNA homology, similar positions of restriction endonuclease cleavage sites, and manners of urease expression and therefore represent the same locus. DNA sequence analysis indicated that the plasmid-encoded urease genes are closely related to the Proteus mirabilis urease genes. PMID:8449894

D'Orazio, S E; Collins, C M



Design and Application of a New Cryptic-Plasmid-Based Shuttle Vector for Magnetospirillum magneticum  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A 3.7-kb cryptic plasmid designated pMGT was found in Magnetospirillum magneticum MGT-1. It was characterized and used for the development of an improved expression system in strain AMB-1 through the construction of a shuttle vector, pUMG. An electroporation method for magnetic bacteria that uses the cryptic plasmid was also developed.

Okamura, Yoshiko; Takeyama, Haruko; Sekine, Takumi; Sakaguchi, Toshifumi; Wahyudi, Aris Tri; Sato, Rika; Kamiya, Shinji; Matsunaga, Tadashi



Elucidating the Kinetics of Expression and Immune Cell Infiltration Resulting from Plasmid Gene Delivery Enhanced by Surface Dermal Electroporation  

Directory of Open Access Journals (Sweden)

Full Text Available The skin is an attractive tissue for vaccination in a clinical setting due to the accessibility of the target, the ease of monitoring and most importantly the immune competent nature of the dermal tissue. While skin electroporation offers an exciting and novel future methodology for the delivery of DNA vaccines in the clinic, little is known about the actual mechanism of the approach and the elucidation of the resulting immune responses. To further understand the mechanism of this platform, the expression kinetics and localization of a reporter plasmid delivered via a surface dermal electroporation (SEP device as well as the effect that this treatment would have on the resident immune cells in that tissue was investigated. Initially a time course (day 0 to day 21 of enhanced gene delivery with electroporation (EP was performed to observe the localization of green fluorescent protein (GFP expression and the kinetics of its appearance as well as clearance. Using gross imaging, GFP expression was not detected on the surface of the skin until 8 h post treatment. However, histological analysis by fluorescent microscopy revealed GFP positive cells as early as 1 h after plasmid delivery and electroporation. Peak GFP expression was observed at 24 h and the expression was maintained in skin for up to seven days. Using an antibody specific for a keratinocyte cell surface marker, reporter gene positive keratinocytes in the epidermis were identified. H&E staining of treated skin sections demonstrated an influx of monocytes and granulocytes at the EP site starting at 4 h and persisting up to day 14 post treatment. Immunological staining revealed a significant migration of lymphocytic cells to the EP site, congregating around cells expressing the delivered antigen. In conclusion, this study provides insights into the expression kinetics following EP enhanced DNA delivery targeting the dermal space. These findings may have implications in the future to design efficient DNA vaccination strategies for the clinic.

Kate E. Broderick



Mega-events, Local Economies, and Global Status: What Happened before the 2008 Olympics in Beijing and the 2010 World Expo in Shanghai  

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Mega-events such as the World Cup and the Olympics have been used for economic development, urban transformation and global status enhancement. Beijing and Shanghai embraced these purposes when they won the bids for the 2008 Olympics and the 2010 World Expo respectively. This article examines the pre-event economic changes in Beijing and Shanghai that are associated with their pursuit of mega-events. Changes in a group of economic indicators are tracked from 1997 to 2006. It was found that af...

Jian Sun; Lin Ye



Regular cellular distribution of plasmids by oscillating and filament-forming ParA ATPase of plasmid pB171  

DEFF Research Database (Denmark)

Centromere-like loci from bacteria segregate plasmids to progeny cells before cell division. The ParA ATPase (a MinD homologue) of the par2 locus from plasmid pB171 forms oscillating helical structures over the nucleoid. Here we show that par2 distributes plasmid foci regularly along the length of the cell even in cells with many plasmids. In vitro, ParA binds ATP and ADP and has a cooperative ATPase activity. Moreover, ParA forms ATP-dependent filaments and cables, suggesting that ParA can provide the mechanical force for the observed regular distribution of plasmids. ParA and ParB interact with each other in a bacterial two-hybrid assay but do not interact with FtsZ, eight other essential cell division proteins or MreB actin. Based on these observations, we propose a simple model for how oscillating ParA filaments can mediate regular cellular distribution of plasmids. The model functions without the involvement of partition-specific host cell receptors and is thus consistent with the striking observation that partition loci can function in heterologous host organisms.

Ebersbach, Gitte; Ringgaard, Simon



Genetic organization and conjugal plasmid DNA transfer of pHP69, a plasmid from a Korean isolate of Helicobacter pylori. (United States)

We isolated pHP69, a 9,153 bp plasmid from Helicobacter pylori with a 33.98% (G+C) content. We identified 11 open reading frames (ORFs), including replication initiation protein A (repA), fic (cAMP-induced filamentation protein), mccC, mccB, mobA, mobD, mobB, and mobC, as well as four 22 bp tandem repeat sequences. The nucleic acid and predicted amino acid sequences of these ORFs exhibited significant homology to those of other H. pylori plasmids. pHP69 repA encodes a replication initiation protein and its amino acid sequence is similar to those of replicase proteins from theta-type plasmids. pHP69 contains two types of repeat sequences (R1 and R2), a MOBHEN family mobilization region comprising mobC, mobA, mobB, and mobD, and genes encoding microcin B and C. Among the 36 H. pylori strains containing plasmids, mobA or mccBC are present in 12 or 6, respectively and 3 contain both genes. To examine intrinsic capability of H. pylori for conjugative plasmid transfer, a shuttle vector pBHP69KH containing pHP69 and replication origin of pBR322 was constructed. It was shown that this vector could stably replicate and be mobilized among clinical H. pylori strains and demonstrated to gene transfer by natural plasmid. PMID:23274982

Joo, Jung-Soo; Song, Jae-Young; Baik, Seung-Chul; Lee, Woo-Kon; Cho, Myung-Je; Lee, Kon-Ho; Cho, YoungAh; Youn, Hee-Shang; Seo, Ji-Hyun; Rhee, Kwang-Ho; Kang, Hyung-Lyun



Design of deepwater HP/HT pipe-in-pipe flowlines crossing mega-furrows in the Gulf of Mexico  

Energy Technology Data Exchange (ETDEWEB)

Two 12-mile long pipe-in-pipe (PIP) with HT/HP flow lines were recently designed for the Chinook offshore oil field in the Gulf of Mexico. The routes of the flow line of the Chinook crosses continuous mega-furrows at the water depth ranging from 8200 ft to 8800 ft. The design of the temperature and pressure of the flow lines were 250 deg F and 12,684 psi, respectively. The detailed finite element analysis was performed to predict flow line in-place behavior. The strain-based criterion of API RP 1111 was used where stresses were greater than allowable limits of the ASME B31.8 and found to be satisfactory. The fatigue analysis of the spans pipe subjected to Vortex Induced Vibration (VIV) showed the need for VIV mitigation measures. It was decided that the entire length of the flow lines crossing the mega-furrows should be stake. The analysis of the stake fatigue life of the flow lines resulted greater than the required 25 years service life. Further analysis was performed on the PIP system to optimize the centralizer spacing to sufficiently limit the buckling of inner pipe under operation conditions and prevent crushing of the insulation in the annulus. J-lay analysis of the installation determining the amount of the inner pipe pre-tensioning that was required to eliminate locked-in stresses in the inner and outer pipes. (author)

Tang, Tianxi Andy; Chacko, Jacob; Zhou, Mengjuan Jane; Omonoji, Gabriel O. [TECHNIP USA, Houston, TX (United States); Eigbe, Uwa [INTECSEA, Houston, TX (United States)



Effects of Land Use Change on Tropical Coastal Systems are Exacerbated by the Decline of Marine Mega-Herbivores (United States)

Land use changes in tropical regions such as deforestation, mining activities, and shrimp farming, not only affect freshwater and terrestrial ecosystems, but also have a strong impact on coastal marine ecosystems. The increased influx of sediments and nutrients affects these ecosystems in multiple ways. Seagrass meadows that line coastal marine ecosystems provide important ecosystem services, e.g. sediment trapping, coastal protection and fisheries. Based on studies in East Kalimantan (Indonesia) we have shown that seagrass meadow parameters may provide more reliable indicators of land use change than the sampling of either marine sediments or water quality chemical parameters. Observations of changes in ecosystem functioning are particularly valuable for those areas where flux values are lacking and rapid surveys are needed. Time series of estuarine seagrass transects can show not only the intensity, but also the radius of action of land use change on coastal marine systems. Marine mega-herbivores pose a strong top-down control in seagrass ecosystems. We will provide a conceptual model, based on experimental evidence, to show that the global decline of marine mega-herbivore populations (as a result of large-scale poaching) may decrease the resilience of seagrass systems to increased anthropogenic forcing including land use changes. These outcomes not only urge the need for better regulation of land use change, but also for the establishment of marine protected areas (MPA's) in tropical coastal regions.

Lamers, L. P.; Christianen, M. J.; Govers, L. L.; Kiswara, W.; Bouma, T.; Roelofs, J. G.; Van Katwijk, M. M.



Optimized MEGA-SPECIAL for in vivo glutamine detection in the rat brain at 14.1?T. (United States)

Glutamine has multiple roles in brain metabolism and its concentration can be altered in various pathological conditions. An accurate knowledge of its concentration is therefore highly desirable to monitor and study several brain disorders in vivo. However, in recent years, several MRS studies have reported conflicting glutamine concentrations in the human brain. A recent hypothesis for explaining these discrepancies is that a short T2 component of the glutamine signal may impact on its quantification at long echo times. The present study therefore aimed to investigate the impact of acquisition parameters on the quantified glutamine concentration using two different acquisition techniques, SPECIAL at ultra-short echo time and MEGA-SPECIAL at moderate echo time. For this purpose, MEGA-SPECIAL was optimized for the first time for glutamine detection. Based on the very good agreement of the glutamine concentration obtained between the two measurements, it was concluded that no impact of a short T2 component of the glutamine signal was detected. Copyright © 2014 John Wiley & Sons, Ltd. PMID:25070114

Craveiro, Mélanie; Cudalbu, Cristina; Mlynárik, Vladimir; Gruetter, Rolf



Frequency and diversity of small cryptic plasmids in the genus Rahnella  

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Full Text Available Abstract Background Rahnella is a widely distributed genus belonging to the Enterobacteriaceae and frequently present on vegetables. Although Rahnella has interesting agro-economical and industrial properties and several strains possess antibiotic resistances and toxin genes which might spread within microbial communities, little is known about plasmids of this genus. Thus, we isolated a number of Rahnella strains and investigated their complements of small plasmids. Results In total 53 strains were investigated and 11 plasmids observed. Seven belonged to the ColE1 family; one was ColE2-like and three shared homology to rolling circle plasmids. One of them belonged to the pC194/pUB110 family and two showed similarity to poorly characterised plasmid groups. The G+C content of two rolling circle plasmids deviated considerably from that of Rahnella, indicating that their usual hosts might belong to other genera. Most ColE1-like plasmids formed a subgroup within the ColE1 family that seems to be fairly specific for Rahnella. Intriguingly, the multimer resolution sites of all ColE1-like plasmids had the same orientation with respect to the origin of replication. This arrangement might be necessary to prevent inappropriate synthesis of a small regulatory RNA that regulates cell division. Although the ColE1-like plasmids did not possess any mobilisation system, they shared large parts with high sequence identity in coding and non-coding regions. In addition, highly homologous regions of plasmids isolated from Rahnella and the chromosomes of Erwinia tasmaniensis and Photorhabdus luminescens could be identified. Conclusions For the genus Rahnella we observed plasmid-containing isolates at a frequency of 19%, which is in the average range for Enterobacteriaceae. These plasmids belonged to diffent groups with members of the ColE1-family most frequently found. Regions of striking sequence homology of plasmids and bacterial chromosomes highlight the importance of plasmids for lateral gene transfer (including chromosomal sequences to distinct genera.

Summers David K



Housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in Rhizobium etli and Rhizobium leguminosarum  

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Full Text Available Abstract Background A traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. Exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. The genome sequence of R. etli CFN42 predicts the presence of panC and panB genes clustered together on the 642 kb plasmid p42f and a second copy of panB on plasmid p42e. They encode putative pantothenate biosynthesis enzymes (pantoate-?-alanine ligase and 3-methyl-2-oxobutanoate hydroxymethyltransferase, respectively. Due to their ubiquitous distribution and relevance in the central metabolism of the cell, these genes are considered part of the core genome; thus, their occurrence in a plasmid is noteworthy. In this study we investigate the contribution of these genes to pantothenate biosynthesis, examine whether their presence in plasmids is a prevalent characteristic of the Rhizobiales with multipartite genomes, and assess the possibility that the panCB genes may have reached plasmids by horizontal gene transfer. Results Analysis of mutants confirmed that the panC and panB genes located on plasmid p42f are indispensable for the synthesis of pantothenate. A screening of the location of panCB genes among members of the Rhizobiales showed that only R. etli and R. leguminosarum strains carry panCB genes in plasmids. The panCB phylogeny attested a common origin for chromosomal and plasmid-borne panCB sequences, suggesting that the R. etli and R. leguminosarum panCB genes are orthologs rather than xenologs. The panCB genes could not totally restore the ability of a strain cured of plasmid p42f to grow in minimal medium. Conclusions This study shows experimental evidence that core panCB genes located in plasmids of R. etli and R. leguminosarum are indispensable for the synthesis of pantothenate. The unusual presence of panCB genes in plasmids of Rhizobiales may be due to an intragenomic transfer from chromosome to plasmid. Plasmid p42f encodes other functions required for growth in minimal medium. Our results support the hypothesis of cooperation among different replicons for basic cellular functions in multipartite rhizobia genomes.

los Santos Alejandro



Effect of the atmospheric pressure nonequilibrium plasmas on the conformational changes of plasmid DNA  

International Nuclear Information System (INIS)

The cold atmospheric pressure plasma, which has been widely used for biomedical applications, may potentially affect the conformation of DNA. In this letter, an atmospheric pressure plasma plume is used to investigate its effects on the conformational changes of DNA of plasmid pAHC25. It is found that the plasma plume could cause plasmid DNA topology alteration, resulting in the percentage of the supercoiled plasmid DNA form decreased while that of the open circular and linearized form of plasmid DNA increased as detected by agrose gel electrophoresis. On the other hand, further investigation by using polymerase chain reaction method shows that the atmospheric pressure plasma jet treatments under proper conditions does not affect the genes of the plasmid DNA, which may have potential application in increasing the transformation frequency by genetic engineering.


Tn5-induced pBS286 plasmid mutations blocking early stages of napthalene oxidation  

International Nuclear Information System (INIS)

The authors present data on the further analysis of the structural and functional organization of the nah region of plasmid pBS286 controlling the constitutive oxidation of naphthalene by Pseudomonas putida cells. They have studied Tn5-induced mutations blocking early stages of naphthalene oxidation. They present and discuss data providing evidence that, in contrast to plasmid NAH7, the mechanism of regulation of the nahl operon of plasmid NPL-1, the parent plasmid of plasmid pBS286, with inducible synthesis of naphthalene dioxygenase can include elements of a negative control with participation of the regulatory locus R, located proximal to the structural nah genes and closely linked to or overlapped by the inverted control DNA segment (4.2 kb). They also present data on the possibility of regulation of the activity of the catechol-splitting meta-pathway genes with the participation of products of early stages of naphthalene oxidation


Biochemical properties, enterohaemolysin production and plasmid carriage of Shiga toxin-producing Escherichia coli strains  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Thirty-eight strains of Shiga toxin-producing Escherichia coli (STEC) were characterised in terms of biochemical properties, enterohaemolysin production and plasmid carriage. A wide variation in the biochemical properties was observed among the STEC, with 14 distinct biotypes identified. Biotype 1 w [...] as the most common, found in 29% of the strains. Enterohaemolysin production was detected in 29% of the strains. Most of the bacterial strains (95%) carried one or more plasmids and considerable heterogeneity in size and combinations was observed. Seven distinct plasmid profiles were identified. The most common profile, characterised by the presence of a single plasmid of ~90 kb, was found in 50% of these strains. These data indicate extensive diversity among STEC strains. No correlation was found among biotype, serotype, enterohaemolysin production and plasmid profile.

Mario RSM, Souza; Giseli, Klassen; Fabiana De, Toni; Liu U, Rigo; Caroline, Henkes; Caroline P, Pigatto; Cibelle de Borba, Dalagassa; Cyntia MT, Fadel-Picheth.



A Bipolar Spindle of Antiparallel ParM Filaments Drives Bacterial Plasmid Segregation  

DEFF Research Database (Denmark)

To ensure their stable inheritance by daughter cells during cell division, bacterial low copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between sister plasmids. In the ParMRC system of Escherichia coli R1 plasmid, ParM, an actin-like protein, forms the spindle between ParRC complexes on sister plasmids. Using a combination of structural work and total internal reflection fluorescence microscopy, we show that ParRC bound and could accelerate growth at only one end of polar ParM filaments, mechanistically resembling eukaryotic formins. The architecture of ParM filaments enabled two ParRC-bound filaments to associate in an antiparallel orientation, forming a bipolar spindle. The spindle elongated as a bundle of at least two antiparallel filaments, thereby pushing two plasmid clusters toward the poles.

Gayathri, P; Fujii, T



Effect of chromosomal homology on plasmid transfer and transformation in Streptococcus pneumoniae  

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The obvious rarity of simultanaeous uptake of two recombinant plasmids bearing the same chromosomal segment militated against the likelihood of cloning such segments by the conventional approach. However, it was possible to clone chromosomal genes in S. pneumoniae, and clones of two well-studied pneumococcal genes, malM, which